diff --git a/doc/Manual.html b/doc/Manual.html
index a8a9bcd529d77db473184fec656c06f97e4f19f3..5a7436319ef31c321248e5ed0f602aadc153a00d 100644
--- a/doc/Manual.html
+++ b/doc/Manual.html
@@ -32,8 +32,7 @@
- <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
- <link rel="next" title="1. Introduction" href="Section_intro.html"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -72,22 +71,16 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
+</ul>
+</div>
</div>
@@ -172,192 +165,13 @@ 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’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 & 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 & 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 & 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></li>
-<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
+<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>
</ul>
</BODY></div>
@@ -366,13 +180,6 @@ 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 a8c7da001afbd836bcbc50dd9106a5c2537e5ccc..22a4831671181e9d5ea68b7fb2fcbba5cc07c160 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>5. Accelerating LAMMPS performance — LAMMPS 15 May 2015 version documentation</title>
+ <title>Accelerating LAMMPS performance — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <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"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,31 +71,20 @@
- <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>
+ <!-- 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>
</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 & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.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>
@@ -120,7 +107,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>5. Accelerating LAMMPS performance</li>
+ <li>Accelerating LAMMPS performance</li>
<li class="wy-breadcrumbs-aside">
@@ -135,7 +122,7 @@
<div itemprop="articleBody">
<div class="section" id="accelerating-lammps-performance">
-<h1>5. Accelerating LAMMPS performance<a class="headerlink" href="#accelerating-lammps-performance" title="Permalink to this headline">¶</a></h1>
+<h1>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>
@@ -163,7 +150,7 @@ 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>5.1. Measuring performance<a class="headerlink" href="#measuring-performance" title="Permalink to this headline">¶</a></h2>
+<span id="acc-1"></span><h2>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
@@ -204,7 +191,7 @@ LAMMPS, to obtain synchronized timings.</p>
<hr class="docutils" />
</div>
<div class="section" id="general-strategies">
-<span id="acc-2"></span><h2>5.2. General strategies<a class="headerlink" href="#general-strategies" title="Permalink to this headline">¶</a></h2>
+<span id="acc-2"></span><h2>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>
@@ -257,7 +244,7 @@ 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>5.3. 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>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
@@ -449,7 +436,7 @@ CPU.</li>
<hr class="docutils" />
</div>
<div class="section" id="comparison-of-various-accelerator-packages">
-<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>
+<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>
<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
@@ -520,7 +507,7 @@ is generally not a problem since typical runs are computation-limited
rather than memory-limited.</li>
</ul>
<div class="section" id="examples">
-<h3>5.4.1. Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h3>
+<h3>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">
@@ -538,15 +525,6 @@ 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 77c9c68bf557d2b914eab8acb65ebd0caf4d65dc..224017192dbea7b24b3823e841197fc1dce2e642 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>3. Commands — LAMMPS 15 May 2015 version documentation</title>
+ <title>Commands — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <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"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,37 +71,26 @@
- <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>
+ <!-- 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>
</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.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>
@@ -126,7 +113,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>3. Commands</li>
+ <li>Commands</li>
<li class="wy-breadcrumbs-aside">
@@ -141,7 +128,7 @@
<div itemprop="articleBody">
<div class="section" id="commands">
-<h1>3. Commands<a class="headerlink" href="#commands" title="Permalink to this headline">¶</a></h1>
+<h1>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">
@@ -153,7 +140,7 @@ 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>3.1. LAMMPS input script<a class="headerlink" href="#lammps-input-script" title="Permalink to this headline">¶</a></h2>
+<span id="cmd-1"></span><h2>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
@@ -200,7 +187,7 @@ 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>3.2. Parsing rules<a class="headerlink" href="#parsing-rules" title="Permalink to this headline">¶</a></h2>
+<span id="cmd-2"></span><h2>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
@@ -304,7 +291,7 @@ 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>3.3. Input script structure<a class="headerlink" href="#input-script-structure" title="Permalink to this headline">¶</a></h2>
+<span id="cmd-3"></span><h2>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 “examples” directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
@@ -383,7 +370,7 @@ 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>3.4. 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>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
@@ -442,7 +429,7 @@ in the command’s documentation.</p>
<hr class="docutils" />
</div>
<div class="section" id="individual-commands">
-<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>
+<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>
<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
@@ -588,7 +575,7 @@ in the command’s documentation.</p>
</div>
<hr class="docutils" />
<div class="section" id="fix-styles">
-<h2>3.6. Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -810,7 +797,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
</div>
<hr class="docutils" />
<div class="section" id="compute-styles">
-<h2>3.7. Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -944,7 +931,7 @@ 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>3.8. Pair_style potentials<a class="headerlink" href="#pair-style-potentials" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -1156,7 +1143,7 @@ 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>3.9. Bond_style potentials<a class="headerlink" href="#bond-style-potentials" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -1204,7 +1191,7 @@ 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>3.10. Angle_style potentials<a class="headerlink" href="#angle-style-potentials" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -1261,7 +1248,7 @@ 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>3.11. Dihedral_style potentials<a class="headerlink" href="#dihedral-style-potentials" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -1313,7 +1300,7 @@ 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>3.12. Improper_style potentials<a class="headerlink" href="#improper-style-potentials" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -1358,7 +1345,7 @@ 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>3.13. Kspace solvers<a class="headerlink" href="#kspace-solvers" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -1398,15 +1385,6 @@ 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 037ce3b8195fabe65b6278a8f6ba7ce477f03328..b8565e9977d1877e97a35d46a9bec915db8dd024 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>12. Errors — LAMMPS 15 May 2015 version documentation</title>
+ <title>Errors — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <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"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,29 +71,18 @@
- <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 & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></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 & 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>
+ <!-- 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 & 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>
</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
-
+</div>
</div>
@@ -118,7 +105,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>12. Errors</li>
+ <li>Errors</li>
<li class="wy-breadcrumbs-aside">
@@ -133,7 +120,7 @@
<div itemprop="articleBody">
<div class="section" id="errors">
-<h1>12. Errors<a class="headerlink" href="#errors" title="Permalink to this headline">¶</a></h1>
+<h1>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">
@@ -143,7 +130,7 @@ 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>12.1. Common problems<a class="headerlink" href="#common-problems" title="Permalink to this headline">¶</a></h2>
+<span id="err-1"></span><h2>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
@@ -232,7 +219,7 @@ 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>12.2. Reporting bugs<a class="headerlink" href="#reporting-bugs" title="Permalink to this headline">¶</a></h2>
+<span id="err-2"></span><h2>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
@@ -254,7 +241,7 @@ causing the problem.</p>
<hr class="docutils" />
</div>
<div class="section" id="error-warning-messages">
-<span id="err-3"></span><h2>12.3. Error & warning messages<a class="headerlink" href="#error-warning-messages" title="Permalink to this headline">¶</a></h2>
+<span id="err-3"></span><h2>Error & 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
@@ -269,7 +256,7 @@ error occurs and is not self-explanatory, you’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>12.4. Errors:<a class="headerlink" href="#error" title="Permalink to this headline">¶</a></h2>
+<span id="id2"></span><h2>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
@@ -5788,7 +5775,7 @@ read_restart, or create_box command.</dd>
</dl>
</div>
<div class="section" id="warnings">
-<span id="warn"></span><h2>12.5. Warnings:<a class="headerlink" href="#warnings" title="Permalink to this headline">¶</a></h2>
+<span id="warn"></span><h2>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
@@ -6299,15 +6286,6 @@ 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 d24ca83dedc712b943c9d6681a543ec7b13d9597..2866e57570b8033aa2c98ceb1d1a19010e02ccaf 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>7. Example problems — LAMMPS 15 May 2015 version documentation</title>
+ <title>Example problems — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
- <link rel="next" title="8. Performance & scalability" href="Section_perf.html"/>
- <link rel="prev" title="6. How-to discussions" href="Section_howto.html"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,22 +71,11 @@
- <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 & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- Local TOC -->
+ <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">Example problems</a></li>
</ul>
-
+</div>
</div>
@@ -111,7 +98,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>7. Example problems</li>
+ <li>Example problems</li>
<li class="wy-breadcrumbs-aside">
@@ -126,7 +113,7 @@
<div itemprop="articleBody">
<div class="section" id="example-problems">
-<h1>7. Example problems<a class="headerlink" href="#example-problems" title="Permalink to this headline">¶</a></h1>
+<h1>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
@@ -318,15 +305,6 @@ 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 & 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 3d3e00aacc44ac49f277e92260a4786b98f78722..b409943b1425c557095d52023a95bb6e714c51cb 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>13. Future and history — LAMMPS 15 May 2015 version documentation</title>
+ <title>Future and history — LAMMPS 15 May 2015 version documentation</title>
@@ -32,8 +32,7 @@
- <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
- <link rel="prev" title="12. Errors" href="Section_errors.html"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -72,26 +71,15 @@
- <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 & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface 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>
+ <!-- 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>
</li>
</ul>
-
+</div>
</div>
@@ -114,7 +102,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>13. Future and history</li>
+ <li>Future and history</li>
<li class="wy-breadcrumbs-aside">
@@ -129,7 +117,7 @@
<div itemprop="articleBody">
<div class="section" id="future-and-history">
-<h1>13. Future and history<a class="headerlink" href="#future-and-history" title="Permalink to this headline">¶</a></h1>
+<h1>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>
@@ -139,7 +127,7 @@ 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>13.1. Coming attractions<a class="headerlink" href="#coming-attractions" title="Permalink to this headline">¶</a></h2>
+<span id="hist-1"></span><h2>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
@@ -150,7 +138,7 @@ your wish to the list.</p>
<hr class="docutils" />
</div>
<div class="section" id="past-versions">
-<span id="hist-2"></span><h2>13.2. Past versions<a class="headerlink" href="#past-versions" title="Permalink to this headline">¶</a></h2>
+<span id="hist-2"></span><h2>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
& development agreement (CRADA) between two DOE labs (Sandia and LLNL)
and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was
@@ -238,13 +226,6 @@ 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 a9777f52a18e53ff806452e822bffc6be64839e3..752f10f1d7d6b4a7d4cb1797d747ef4a6940a6c5 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>6. How-to discussions — LAMMPS 15 May 2015 version documentation</title>
+ <title>How-to discussions — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <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"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,77 +71,66 @@
- <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>
+ <!-- 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>
</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>
+<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>
</ul>
</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>
+<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>
</ul>
</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>
+<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>
</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 & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.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>
@@ -166,7 +153,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>6. How-to discussions</li>
+ <li>How-to discussions</li>
<li class="wy-breadcrumbs-aside">
@@ -181,7 +168,7 @@
<div itemprop="articleBody">
<div class="section" id="how-to-discussions">
-<h1>6. How-to discussions<a class="headerlink" href="#how-to-discussions" title="Permalink to this headline">¶</a></h1>
+<h1>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>
@@ -217,7 +204,7 @@
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>6.1. Restarting a simulation<a class="headerlink" href="#restarting-a-simulation" title="Permalink to this headline">¶</a></h2>
+<span id="howto-1"></span><h2>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
@@ -310,7 +297,7 @@ but not in data files.</p>
<hr class="docutils" />
</div>
<div class="section" id="d-simulations">
-<span id="howto-2"></span><h2>6.2. 2d simulations<a class="headerlink" href="#d-simulations" title="Permalink to this headline">¶</a></h2>
+<span id="howto-2"></span><h2>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>
@@ -342,7 +329,7 @@ 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>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>
+<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>
<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
@@ -404,7 +391,7 @@ 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>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>
+<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>
<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 “multiple simulations” means continue a previous simulation for
@@ -487,7 +474,7 @@ 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>6.5. Multi-replica simulations<a class="headerlink" href="#multi-replica-simulations" title="Permalink to this headline">¶</a></h2>
+<span id="howto-5"></span><h2>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
@@ -534,7 +521,7 @@ physical processors.</p>
<hr class="docutils" />
</div>
<div class="section" id="granular-models">
-<span id="howto-6"></span><h2>6.6. Granular models<a class="headerlink" href="#granular-models" title="Permalink to this headline">¶</a></h2>
+<span id="howto-6"></span><h2>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>
@@ -575,7 +562,7 @@ 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>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline">¶</a></h2>
+<span id="howto-7"></span><h2>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.
@@ -627,7 +614,7 @@ details:</p>
<hr class="docutils" />
</div>
<div class="section" id="tip4p-water-model">
-<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>
+<span id="howto-8"></span><h2>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.
@@ -723,7 +710,7 @@ 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>6.9. SPC water model<a class="headerlink" href="#spc-water-model" title="Permalink to this headline">¶</a></h2>
+<span id="howto-9"></span><h2>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
@@ -762,7 +749,7 @@ 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>6.10. 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>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
@@ -843,7 +830,7 @@ 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>6.11. Visualizing LAMMPS snapshots<a class="headerlink" href="#visualizing-lammps-snapshots" title="Permalink to this headline">¶</a></h2>
+<span id="howto-11"></span><h2>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
@@ -886,7 +873,7 @@ 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>6.12. 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>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
@@ -1064,7 +1051,7 @@ on non-equilibrium MD (NEMD) simulations.</p>
<hr class="docutils" />
</div>
<div class="section" id="nemd-simulations">
-<span id="howto-13"></span><h2>6.13. NEMD simulations<a class="headerlink" href="#nemd-simulations" title="Permalink to this headline">¶</a></h2>
+<span id="howto-13"></span><h2>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’s rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
@@ -1094,7 +1081,7 @@ 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>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>
+<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>
<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
@@ -1114,7 +1101,7 @@ 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>6.14.1. Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -1184,7 +1171,7 @@ 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>6.14.2. Pair potentials<a class="headerlink" href="#pair-potentials" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -1211,7 +1198,7 @@ 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>6.14.3. Time integration<a class="headerlink" href="#time-integration" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -1246,7 +1233,7 @@ 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>6.14.4. Computes, thermodynamics, and dump output<a class="headerlink" href="#computes-thermodynamics-and-dump-output" title="Permalink to this headline">¶</a></h3>
+<h3>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">
@@ -1277,7 +1264,7 @@ 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>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>
+<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>
<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
@@ -1306,7 +1293,7 @@ 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>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>
+<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>
<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
@@ -1343,7 +1330,7 @@ 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>6.15.1. 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>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
@@ -1353,7 +1340,7 @@ 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>6.15.2. Scalar/vector/array data<a class="headerlink" href="#scalar-vector-array-data" title="Permalink to this headline">¶</a></h3>
+<span id="scalar"></span><h3>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 “compute” or “fix” or “variable” that generates data
@@ -1387,7 +1374,7 @@ 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>6.15.3. Thermodynamic output<a class="headerlink" href="#thermodynamic-output" title="Permalink to this headline">¶</a></h3>
+<span id="thermo"></span><h3>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
@@ -1411,7 +1398,7 @@ 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>6.15.4. Dump file output<a class="headerlink" href="#dump-file-output" title="Permalink to this headline">¶</a></h3>
+<span id="dump"></span><h3>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>
@@ -1432,7 +1419,7 @@ 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>6.15.5. 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>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>
@@ -1478,7 +1465,7 @@ 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>6.15.6. 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>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 “reduce” them (sum, min, max,
ave) to scalar quantities. These are produced as output values which
@@ -1499,7 +1486,7 @@ 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>6.15.7. 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>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>
@@ -1519,7 +1506,7 @@ 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>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>
+<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>
<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
@@ -1529,7 +1516,7 @@ values have the word “atom” or “local” in their style na
without the word “atom” or “local” produce global values.</p>
</div>
<div class="section" id="fixes-that-generate-values-to-output">
-<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>
+<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>
<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
@@ -1538,7 +1525,7 @@ 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>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>
+<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>
<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-
@@ -1548,7 +1535,7 @@ 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>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>
+<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>
<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
@@ -1680,7 +1667,7 @@ 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>6.16. 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>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
@@ -1816,7 +1803,7 @@ thermodynamic output.</p>
<hr class="docutils" />
</div>
<div class="section" id="walls">
-<span id="howto-17"></span><h2>6.17. Walls<a class="headerlink" href="#walls" title="Permalink to this headline">¶</a></h2>
+<span id="howto-17"></span><h2>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
@@ -1880,7 +1867,7 @@ frictional walls, as well as triangulated surfaces.</p>
<hr class="docutils" />
</div>
<div class="section" id="elastic-constants">
-<span id="howto-18"></span><h2>6.18. Elastic constants<a class="headerlink" href="#elastic-constants" title="Permalink to this headline">¶</a></h2>
+<span id="howto-18"></span><h2>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.
@@ -1912,7 +1899,7 @@ 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>6.19. 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>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
@@ -1987,7 +1974,7 @@ LAMMPS.</p>
<hr class="docutils" />
</div>
<div class="section" id="calculating-thermal-conductivity">
-<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>
+<span id="howto-20"></span><h2>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
@@ -2041,7 +2028,7 @@ formalism.</p>
<hr class="docutils" />
</div>
<div class="section" id="calculating-viscosity">
-<span id="howto-21"></span><h2>6.21. Calculating viscosity<a class="headerlink" href="#calculating-viscosity" title="Permalink to this headline">¶</a></h2>
+<span id="howto-21"></span><h2>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
@@ -2162,7 +2149,7 @@ print "average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3"
<hr class="docutils" />
</div>
<div class="section" id="calculating-a-diffusion-coefficient">
-<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>
+<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>
<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
@@ -2184,7 +2171,7 @@ 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>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>
+<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>
<p>In LAMMS, “chunks” 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
@@ -2201,7 +2188,7 @@ 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>6.23.1. Compute chunk/atom command:<a class="headerlink" href="#compute-chunk-atom-command" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -2259,7 +2246,7 @@ 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>6.23.2. Fix ave/chunk command:<a class="headerlink" href="#fix-ave-chunk-command" title="Permalink to this headline">¶</a></h3>
+<h3>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
@@ -2273,7 +2260,7 @@ fix produces a global array as output with one row of values per
chunk.</p>
</div>
<div class="section" id="compute-chunk-commands">
-<h3>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>
+<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>
<p>Currently the following computes operate on chunks of atoms to produce
per-chunk values.</p>
<ul class="simple">
@@ -2310,7 +2297,7 @@ largest cluster or fastest diffusing molecule.</li>
</ul>
</div>
<div class="section" id="example-calculations-with-chunks">
-<h3>6.23.4. Example calculations with chunks<a class="headerlink" href="#example-calculations-with-chunks" title="Permalink to this headline">¶</a></h3>
+<h3>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">
@@ -2359,7 +2346,7 @@ 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>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>
+<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>
<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
@@ -2452,7 +2439,7 @@ to specify this command explicitly.</p>
<hr class="docutils" />
</div>
<div class="section" id="polarizable-models">
-<span id="howto-25"></span><h2>6.25. Polarizable models<a class="headerlink" href="#polarizable-models" title="Permalink to this headline">¶</a></h2>
+<span id="howto-25"></span><h2>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>
@@ -2522,7 +2509,7 @@ well.</p>
<hr class="docutils" />
</div>
<div class="section" id="adiabatic-core-shell-model">
-<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>
+<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>
<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
@@ -2700,7 +2687,7 @@ 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>6.27. Drude induced dipoles<a class="headerlink" href="#drude-induced-dipoles" title="Permalink to this headline">¶</a></h2>
+<span id="howto-27"></span><h2>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
@@ -2777,15 +2764,6 @@ Phys, 79, 926 (1983).</p>
</div>
<footer>
- <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
-
- <a href="Section_example.html" class="btn btn-neutral float-right" title="7. Example problems" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
-
-
- <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 98a0006744f2d97925714ef439eb29109d23cfc0..6ed9b5105a3301547ccf3ab8e3c3a2216a4bfa86 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>1. Introduction — LAMMPS 15 May 2015 version documentation</title>
+ <title>Introduction — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <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"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,42 +71,31 @@
- <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>
+ <!-- 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>
</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>
+<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>
</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 & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.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 +118,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>1. Introduction</li>
+ <li>Introduction</li>
<li class="wy-breadcrumbs-aside">
@@ -146,7 +133,7 @@
<div itemprop="articleBody">
<div class="section" id="introduction">
-<h1>1. Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h1>
+<h1>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’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
@@ -160,7 +147,7 @@ over the years.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="what-is-lammps">
-<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>
+<span id="intro-1"></span><h2>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
@@ -211,14 +198,14 @@ 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>1.2. LAMMPS features<a class="headerlink" href="#lammps-features" title="Permalink to this headline">¶</a></h2>
+<span id="intro-2"></span><h2>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’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>1.2.1. General features<a class="headerlink" href="#general-features" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -237,7 +224,7 @@ it to LAMMPS.</p>
</ul>
</div>
<div class="section" id="particle-and-model-types">
-<h3>1.2.2. Particle and model types<a class="headerlink" href="#particle-and-model-types" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -255,7 +242,7 @@ it to LAMMPS.</p>
</ul>
</div>
<div class="section" id="force-fields">
-<h3>1.2.3. Force fields<a class="headerlink" href="#force-fields" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -284,7 +271,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="atom-creation">
-<h3>1.2.4. Atom creation<a class="headerlink" href="#atom-creation" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -297,7 +284,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="ensembles-constraints-and-boundary-conditions">
-<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>
+<h3>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>
@@ -317,7 +304,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="integrators">
-<h3>1.2.6. Integrators<a class="headerlink" href="#integrators" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -329,13 +316,13 @@ commands)</p>
</ul>
</div>
<div class="section" id="diagnostics">
-<h3>1.2.7. Diagnostics<a class="headerlink" href="#diagnostics" title="Permalink to this headline">¶</a></h3>
+<h3>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>1.2.8. Output<a class="headerlink" href="#output" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -350,14 +337,14 @@ commands)</p>
</ul>
</div>
<div class="section" id="multi-replica-models">
-<h3>1.2.9. Multi-replica models<a class="headerlink" href="#multi-replica-models" title="Permalink to this headline">¶</a></h3>
+<h3>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>1.2.10. Pre- and post-processing<a class="headerlink" href="#pre-and-post-processing" title="Permalink to this headline">¶</a></h3>
+<h3>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>
@@ -368,7 +355,7 @@ written in <a class="reference external" href="http://www.python.org">Python</a>
</ul>
</div>
<div class="section" id="specialized-features">
-<h3>1.2.11. Specialized features<a class="headerlink" href="#specialized-features" title="Permalink to this headline">¶</a></h3>
+<h3>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">
@@ -392,7 +379,7 @@ molecular dynamics options:</p>
</div>
</div>
<div class="section" id="lammps-non-features">
-<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>
+<span id="intro-3"></span><h2>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’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
@@ -485,7 +472,7 @@ spatial-decomposition version exist.</p>
<hr class="docutils" />
</div>
<div class="section" id="open-source-distribution">
-<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>
+<span id="intro-4"></span><h2>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
@@ -547,7 +534,7 @@ encouraged.</li>
<hr class="docutils" />
</div>
<div class="section" id="acknowledgments-and-citations">
-<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>
+<span id="intro-5"></span><h2>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
@@ -616,15 +603,6 @@ 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 60948b933a6cc38e386d74e525efdb5f7f7e302b..eeeb2c581f891b5c097775aedd81235f9e0e13fc 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>10. Modifying & extending LAMMPS — LAMMPS 15 May 2015 version documentation</title>
+ <title>Modifying & extending LAMMPS — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <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"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,39 +71,28 @@
- <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 & 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 & 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>
+ <!-- Local TOC -->
+ <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">Modifying & 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>
</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.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>
@@ -128,7 +115,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>10. Modifying & extending LAMMPS</li>
+ <li>Modifying & extending LAMMPS</li>
<li class="wy-breadcrumbs-aside">
@@ -143,7 +130,7 @@
<div itemprop="articleBody">
<div class="section" id="modifying-extending-lammps">
-<h1>10. Modifying & extending LAMMPS<a class="headerlink" href="#modifying-extending-lammps" title="Permalink to this headline">¶</a></h1>
+<h1>Modifying & 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">
@@ -253,7 +240,7 @@ 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>10.1. Atom styles<a class="headerlink" href="#atom-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-1"></span><h2>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
@@ -400,7 +387,7 @@ 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>10.2. 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>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>
@@ -451,7 +438,7 @@ for details and specific additional methods.</p>
<hr class="docutils" />
</div>
<div class="section" id="compute-styles">
-<span id="mod-3"></span><h2>10.3. Compute styles<a class="headerlink" href="#compute-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-3"></span><h2>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
@@ -518,10 +505,10 @@ class. See compute.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="dump-styles">
-<span id="mod-4"></span><h2>10.4. Dump styles<a class="headerlink" href="#dump-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-4"></span><h2>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>10.5. 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>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
@@ -560,7 +547,7 @@ 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>10.6. Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-6"></span><h2>Fix styles<a class="headerlink" href="#fix-styles" title="Permalink to this headline">¶</a></h2>
<p>In LAMMPS, a “fix” 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,
@@ -768,7 +755,7 @@ 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>10.7. Input script commands<a class="headerlink" href="#input-script-commands" title="Permalink to this headline">¶</a></h2>
+<span id="mod-7"></span><h2>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 “command” method. For example, the create_atoms,
read_data, velocity, and run commands are all implemented in this
@@ -794,7 +781,7 @@ needed.</p>
<hr class="docutils" />
</div>
<div class="section" id="kspace-computations">
-<span id="mod-8"></span><h2>10.8. Kspace computations<a class="headerlink" href="#kspace-computations" title="Permalink to this headline">¶</a></h2>
+<span id="mod-8"></span><h2>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>
@@ -824,7 +811,7 @@ class. See kspace.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="minimization-styles">
-<span id="mod-9"></span><h2>10.9. Minimization styles<a class="headerlink" href="#minimization-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-9"></span><h2>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>
@@ -851,7 +838,7 @@ class. See min.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="pairwise-potentials">
-<span id="mod-10"></span><h2>10.10. Pairwise potentials<a class="headerlink" href="#pairwise-potentials" title="Permalink to this headline">¶</a></h2>
+<span id="mod-10"></span><h2>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
@@ -899,7 +886,7 @@ 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>10.11. Region styles<a class="headerlink" href="#region-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-11"></span><h2>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
@@ -921,7 +908,7 @@ class. See region.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="body-styles">
-<span id="mod-12"></span><h2>10.12. Body styles<a class="headerlink" href="#body-styles" title="Permalink to this headline">¶</a></h2>
+<span id="mod-12"></span><h2>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,
@@ -969,7 +956,7 @@ class. See body.h for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="thermodynamic-output-options">
-<span id="mod-13"></span><h2>10.13. Thermodynamic output options<a class="headerlink" href="#thermodynamic-output-options" title="Permalink to this headline">¶</a></h2>
+<span id="mod-13"></span><h2>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: “one” and “multi”. There
@@ -993,7 +980,7 @@ 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>10.14. Variable options<a class="headerlink" href="#variable-options" title="Permalink to this headline">¶</a></h2>
+<span id="mod-14"></span><h2>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
@@ -1027,7 +1014,7 @@ 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>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>
+<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>
<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
@@ -1165,15 +1152,6 @@ 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 e87a45ca539eeacebdcd771e21114da5d8211702..6d903eb0b32be7e56f8c054fe3ce9628e285d0d0 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>4. Packages — LAMMPS 15 May 2015 version documentation</title>
+ <title>Packages — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <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"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,45 +71,34 @@
- <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>
+ <!-- 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>
</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.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>
@@ -134,7 +121,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>4. Packages</li>
+ <li>Packages</li>
<li class="wy-breadcrumbs-aside">
@@ -149,7 +136,7 @@
<div itemprop="articleBody">
<div class="section" id="packages">
-<h1>4. Packages<a class="headerlink" href="#packages" title="Permalink to this headline">¶</a></h1>
+<h1>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">
@@ -170,7 +157,7 @@ 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>4.1. Standard packages<a class="headerlink" href="#standard-packages" title="Permalink to this headline">¶</a></h2>
+<span id="pkg-1"></span><h2>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>
@@ -552,7 +539,7 @@ 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>4.2. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
+<span id="pkg-2"></span><h2>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>
@@ -876,7 +863,7 @@ below.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-atc-package">
-<h2>4.3. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h2>
+<h2>USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements a “fix atc” 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
@@ -896,7 +883,7 @@ you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-awpmd-package">
-<h2>4.4. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h2>
+<h2>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>
@@ -911,7 +898,7 @@ have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-cg-cmm-package">
-<h2>4.5. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h2>
+<h2>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">
@@ -946,7 +933,7 @@ simulation systems.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-colvars-package">
-<h2>4.6. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h2>
+<h2>USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h2>
<p>This package implements the “fix colvars” command which can be
used in a LAMMPS input script.</p>
<p>This fix allows to use “collective variables” to implement
@@ -975,7 +962,7 @@ beta quality.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-cuda-package">
-<h2>4.7. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h2>
+<h2>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>
@@ -993,7 +980,7 @@ tu-ilmenau.de). Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-diffraction-package">
-<h2>4.8. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h2>
+<h2>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>
@@ -1009,7 +996,7 @@ Arkansas. Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-drude-package">
-<h2>4.9. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h2>
+<h2>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>
@@ -1029,7 +1016,7 @@ Agilio Padua.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-eff-package">
-<h2>4.10. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h2>
+<h2>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,
@@ -1063,7 +1050,7 @@ have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-fep-package">
-<h2>4.11. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h2>
+<h2>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>
@@ -1078,7 +1065,7 @@ Contact him directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-intel-package">
-<h2>4.12. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -1090,7 +1077,7 @@ Intel(R) Xeon Phi(TM) coprocessor.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-lb-package">
-<h2>4.13. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h2>
+<h2>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>
@@ -1102,7 +1089,7 @@ Western Ontario. Contact them directly if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-misc-package">
-<h2>4.14. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h2>
+<h2>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>
@@ -1119,7 +1106,7 @@ about the feature or its coding.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-molfile-package">
-<h2>4.15. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -1138,7 +1125,7 @@ application itself.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-omp-package">
-<h2>4.16. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h2>
+<h2>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>
@@ -1149,7 +1136,7 @@ styles, and fix styles.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-phonon-package">
-<h2>4.17. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h2>
+<h2>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>
@@ -1161,7 +1148,7 @@ if you have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-qmmm-package">
-<h2>4.18. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h2>
+<h2>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>
@@ -1178,7 +1165,7 @@ without changes to LAMMPS itself.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-qtb-package">
-<h2>4.19. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -1200,7 +1187,7 @@ have questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-reaxc-package">
-<h2>4.20. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h2>
+<h2>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
@@ -1228,7 +1215,7 @@ questions.</p>
</div>
<hr class="docutils" />
<div class="section" id="user-sph-package">
-<h2>4.21. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h2>
+<h2>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">
@@ -1255,15 +1242,6 @@ 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 7ca825c2d882631c000cafdd0d1e5e8ee3a2a646..e656585da649530184cd21b63841577caa0557ab 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>8. Performance & scalability — LAMMPS 15 May 2015 version documentation</title>
+ <title>Performance & scalability — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <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"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,22 +71,11 @@
- <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 & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- Local TOC -->
+ <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">Performance & scalability</a></li>
</ul>
-
+</div>
</div>
@@ -111,7 +98,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>8. Performance & scalability</li>
+ <li>Performance & scalability</li>
<li class="wy-breadcrumbs-aside">
@@ -126,7 +113,7 @@
<div itemprop="articleBody">
<div class="section" id="performance-scalability">
-<h1>8. Performance & scalability<a class="headerlink" href="#performance-scalability" title="Permalink to this headline">¶</a></h1>
+<h1>Performance & 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
@@ -225,15 +212,6 @@ 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 afbc823f103b5b4378f616268bc961cf7c021f3a..ed550b556514f092f0ba58a9e19074af93f77f63 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>11. Python interface to LAMMPS — LAMMPS 15 May 2015 version documentation</title>
+ <title>Python interface to LAMMPS — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <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 & extending LAMMPS" href="Section_modify.html"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,37 +71,26 @@
- <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 & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & 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>
+ <!-- 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>
</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>
+<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>
</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>
@@ -126,7 +113,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>11. Python interface to LAMMPS</li>
+ <li>Python interface to LAMMPS</li>
<li class="wy-breadcrumbs-aside">
@@ -141,7 +128,7 @@
<div itemprop="articleBody">
<div class="section" id="python-interface-to-lammps">
-<h1>11. Python interface to LAMMPS<a class="headerlink" href="#python-interface-to-lammps" title="Permalink to this headline">¶</a></h1>
+<h1>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
@@ -187,7 +174,7 @@ 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>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>
+<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>
<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
@@ -227,7 +214,7 @@ 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>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>
+<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>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is not currently possible to use the
@@ -288,7 +275,7 @@ 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>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>
+<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>
<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
@@ -310,7 +297,7 @@ system.</p>
<hr class="docutils" />
</div>
<div class="section" id="installing-the-python-wrapper-into-python">
-<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>
+<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>
<p>For Python to invoke LAMMPS, there are 2 files it needs to know about:</p>
<ul class="simple">
<li>python/lammps.py</li>
@@ -372,7 +359,7 @@ 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>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>
+<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>
<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>
@@ -458,7 +445,7 @@ the right one.</p>
<hr class="docutils" />
</div>
<div class="section" id="testing-the-python-lammps-interface">
-<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>
+<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>
<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">>>> </span><span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span>
@@ -485,7 +472,7 @@ 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>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>
+<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>
<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">>>> </span><span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span>
@@ -505,7 +492,7 @@ typed something like:</p>
</div>
</div>
<div class="section" id="test-lammps-and-python-in-parallel">
-<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>
+<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>
<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>
@@ -539,7 +526,7 @@ script should be pypar.finalize(), to insure MPI is shut down
correctly.</p>
</div>
<div class="section" id="running-python-scripts">
-<h3>11.6.3. <strong>Running Python scripts:</strong><a class="headerlink" href="#running-python-scripts" title="Permalink to this headline">¶</a></h3>
+<h3><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
@@ -566,7 +553,7 @@ 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>11.7. 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>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 “lammps” module, the source code for which is in
python/lammps.py, which creates a “lammps” object, with a set of
@@ -783,7 +770,7 @@ Python script. Isn’t ctypes amazing?</li>
</ul>
</div>
<div class="section" id="example-python-scripts-that-use-lammps">
-<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>
+<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>
<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
@@ -850,7 +837,7 @@ 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-f968d92e-84e6-426c-9743-2b912364e267"
+<a data-lightbox="group-18a49424-552b-4e40-84e6-3c68f302c35c"
href="_images/screenshot_gl.jpg"
class=""
title=""
@@ -860,7 +847,7 @@ different visualization package options. Click to see larger images:</p>
width="25%"
height="auto"
alt=""/>
- </a><a data-lightbox="group-35a178b2-c4be-409d-9395-728435f7f9a6"
+ </a><a data-lightbox="group-2b79ab21-07b7-47a3-81c3-94a3021a26e0"
href="_images/screenshot_atomeye.jpg"
class=""
title=""
@@ -870,7 +857,7 @@ different visualization package options. Click to see larger images:</p>
width="25%"
height="auto"
alt=""/>
- </a><a data-lightbox="group-5aa3c8f0-688f-42ab-9152-4b74f5a93c60"
+ </a><a data-lightbox="group-f4ded497-3be9-4ca3-99ca-0b3b2731bb5b"
href="_images/screenshot_pymol.jpg"
class=""
title=""
@@ -880,7 +867,7 @@ different visualization package options. Click to see larger images:</p>
width="25%"
height="auto"
alt=""/>
- </a><a data-lightbox="group-88f5e60c-df83-4a41-a12f-072e05d8edd0"
+ </a><a data-lightbox="group-0c7ab672-9c97-4a40-b3ac-1a55870e2905"
href="_images/screenshot_vmd.jpg"
class=""
title=""
@@ -898,15 +885,6 @@ 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 & 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 165165f7df8f23ebe7c8f0cf513dd5b9e568cc79..a369d55cec0e6df6c9819e28167eafaee3ef2798 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>2. Getting Started — LAMMPS 15 May 2015 version documentation</title>
+ <title>Getting Started — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <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"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,39 +71,28 @@
- <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’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>
+ <!-- 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’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>
</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>
+<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>
</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 & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.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>
@@ -128,7 +115,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>2. Getting Started</li>
+ <li>Getting Started</li>
<li class="wy-breadcrumbs-aside">
@@ -143,7 +130,7 @@
<div itemprop="articleBody">
<div class="section" id="getting-started">
-<h1>2. Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
+<h1>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">
@@ -159,7 +146,7 @@ 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>2.1. What’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>What’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>
@@ -217,7 +204,7 @@ 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>2.2. Making LAMMPS<a class="headerlink" href="#making-lammps" title="Permalink to this headline">¶</a></h2>
+<span id="start-2"></span><h2>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>
@@ -680,7 +667,7 @@ 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>2.3. 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>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>
@@ -944,7 +931,7 @@ 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>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>
+<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>
<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
@@ -1075,14 +1062,14 @@ and MPI options to use, via the “-cc” and “-mpi” switche
<hr class="docutils" />
</div>
<div class="section" id="building-lammps-as-a-library">
-<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>
+<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>
<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>2.5.1. <strong>Static library:</strong><a class="headerlink" href="#static-library" title="Permalink to this headline">¶</a></h3>
+<h3><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>
@@ -1096,7 +1083,7 @@ 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>2.5.2. <strong>Shared library:</strong><a class="headerlink" href="#shared-library" title="Permalink to this headline">¶</a></h3>
+<h3><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
@@ -1149,7 +1136,7 @@ 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>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>
+<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>
<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
@@ -1164,7 +1151,7 @@ that use it.</p>
</div>
</div>
<div class="section" id="calling-the-lammps-library">
-<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>
+<h3><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
@@ -1187,7 +1174,7 @@ interface and how to extend it for your needs.</p>
</div>
</div>
<div class="section" id="running-lammps">
-<span id="start-6"></span><h2>2.6. Running LAMMPS<a class="headerlink" href="#running-lammps" title="Permalink to this headline">¶</a></h2>
+<span id="start-6"></span><h2>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>
@@ -1289,7 +1276,7 @@ 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>2.7. Command-line options<a class="headerlink" href="#command-line-options" title="Permalink to this headline">¶</a></h2>
+<span id="start-7"></span><h2>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>
@@ -1701,7 +1688,7 @@ 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>2.8. LAMMPS screen output<a class="headerlink" href="#lammps-screen-output" title="Permalink to this headline">¶</a></h2>
+<span id="start-8"></span><h2>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
@@ -1797,7 +1784,7 @@ 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>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>
+<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>
<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
@@ -1834,15 +1821,6 @@ 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>
-
<hr/>
diff --git a/doc/Section_tools.html b/doc/Section_tools.html
index 8a28d0bf4857ecefff5e83a4ddc780b97b1eaa2f..ced60ae7357d9ea3e1755a2d9f0ab6bfa5733b8d 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>9. Additional tools — LAMMPS 15 May 2015 version documentation</title>
+ <title>Additional tools — LAMMPS 15 May 2015 version documentation</title>
@@ -32,9 +32,7 @@
- <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
- <link rel="next" title="10. Modifying & extending LAMMPS" href="Section_modify.html"/>
- <link rel="prev" title="8. Performance & scalability" href="Section_perf.html"/>
+ <link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -73,55 +71,44 @@
- <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 & 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>
+ <!-- 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>
</li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.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>
@@ -144,7 +131,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> »</li>
- <li>9. Additional tools</li>
+ <li>Additional tools</li>
<li class="wy-breadcrumbs-aside">
@@ -159,7 +146,7 @@
<div itemprop="articleBody">
<div class="section" id="additional-tools">
-<h1>9. Additional tools<a class="headerlink" href="#additional-tools" title="Permalink to this headline">¶</a></h1>
+<h1>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
@@ -216,7 +203,7 @@ own sub-directories with their own Makefiles.</p>
</ul>
<hr class="docutils" />
<div class="section" id="amber2lmp-tool">
-<span id="amber"></span><h2>9.1. amber2lmp tool<a class="headerlink" href="#amber2lmp-tool" title="Permalink to this headline">¶</a></h2>
+<span id="amber"></span><h2>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>
@@ -229,7 +216,7 @@ necessary modifications yourself.</p>
<hr class="docutils" />
</div>
<div class="section" id="binary2txt-tool">
-<span id="binary"></span><h2>9.2. binary2txt tool<a class="headerlink" href="#binary2txt-tool" title="Permalink to this headline">¶</a></h2>
+<span id="binary"></span><h2>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 ...
@@ -241,7 +228,7 @@ 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>9.3. ch2lmp tool<a class="headerlink" href="#ch2lmp-tool" title="Permalink to this headline">¶</a></h2>
+<span id="charmm"></span><h2>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
@@ -254,7 +241,7 @@ 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>9.4. chain tool<a class="headerlink" href="#chain-tool" title="Permalink to this headline">¶</a></h2>
+<span id="chain"></span><h2>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
@@ -270,7 +257,7 @@ 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>9.5. colvars tools<a class="headerlink" href="#colvars-tools" title="Permalink to this headline">¶</a></h2>
+<span id="colvars"></span><h2>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 “make”.</p>
@@ -288,7 +275,7 @@ gmail.com) at ICTP, Italy.</p>
<hr class="docutils" />
</div>
<div class="section" id="createatoms-tool">
-<span id="create"></span><h2>9.6. createatoms tool<a class="headerlink" href="#createatoms-tool" title="Permalink to this headline">¶</a></h2>
+<span id="create"></span><h2>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
@@ -298,7 +285,7 @@ coordinates in LAMMPS or other formats.</p>
<hr class="docutils" />
</div>
<div class="section" id="data2xmovie-tool">
-<span id="data"></span><h2>9.7. data2xmovie tool<a class="headerlink" href="#data2xmovie-tool" title="Permalink to this headline">¶</a></h2>
+<span id="data"></span><h2>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
@@ -310,7 +297,7 @@ running the tool is</p>
<hr class="docutils" />
</div>
<div class="section" id="eam-database-tool">
-<span id="eamdb"></span><h2>9.8. eam database tool<a class="headerlink" href="#eam-database-tool" title="Permalink to this headline">¶</a></h2>
+<span id="eamdb"></span><h2>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,
@@ -322,7 +309,7 @@ and is based on his paper:</p>
<hr class="docutils" />
</div>
<div class="section" id="eam-generate-tool">
-<span id="eamgn"></span><h2>9.9. eam generate tool<a class="headerlink" href="#eam-generate-tool" title="Permalink to this headline">¶</a></h2>
+<span id="eamgn"></span><h2>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
@@ -332,7 +319,7 @@ 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>9.10. eff tool<a class="headerlink" href="#eff-tool" title="Permalink to this headline">¶</a></h2>
+<span id="eff"></span><h2>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>
@@ -341,7 +328,7 @@ electron force field (eFF).</p>
<hr class="docutils" />
</div>
<div class="section" id="emacs-tool">
-<span id="emacs"></span><h2>9.11. emacs tool<a class="headerlink" href="#emacs-tool" title="Permalink to this headline">¶</a></h2>
+<span id="emacs"></span><h2>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>
@@ -350,7 +337,7 @@ with various highlighting options setup.</p>
<hr class="docutils" />
</div>
<div class="section" id="fep-tool">
-<span id="fep"></span><h2>9.12. fep tool<a class="headerlink" href="#fep-tool" title="Permalink to this headline">¶</a></h2>
+<span id="fep"></span><h2>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>
@@ -360,7 +347,7 @@ 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>9.13. i-pi tool<a class="headerlink" href="#i-pi-tool" title="Permalink to this headline">¶</a></h2>
+<span id="ipi"></span><h2>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
@@ -374,7 +361,7 @@ calculations with LAMMPS.</p>
<hr class="docutils" />
</div>
<div class="section" id="ipp-tool">
-<span id="ipp"></span><h2>9.14. ipp tool<a class="headerlink" href="#ipp-tool" title="Permalink to this headline">¶</a></h2>
+<span id="ipp"></span><h2>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>
@@ -385,7 +372,7 @@ tools/createatoms tool’s input file.</p>
<hr class="docutils" />
</div>
<div class="section" id="kate-tool">
-<span id="kate"></span><h2>9.15. kate tool<a class="headerlink" href="#kate-tool" title="Permalink to this headline">¶</a></h2>
+<span id="kate"></span><h2>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>
@@ -394,7 +381,7 @@ scripts. See the README.txt file for details.</p>
<hr class="docutils" />
</div>
<div class="section" id="lmp2arc-tool">
-<span id="arc"></span><h2>9.16. lmp2arc tool<a class="headerlink" href="#lmp2arc-tool" title="Permalink to this headline">¶</a></h2>
+<span id="arc"></span><h2>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’ Insight MD code (formerly
MSI/Biosym and its Discover MD code). See the README file for more
@@ -407,7 +394,7 @@ Greathouse at Sandia (jagreat at sandia.gov).</p>
<hr class="docutils" />
</div>
<div class="section" id="lmp2cfg-tool">
-<span id="cfg"></span><h2>9.17. lmp2cfg tool<a class="headerlink" href="#lmp2cfg-tool" title="Permalink to this headline">¶</a></h2>
+<span id="cfg"></span><h2>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
@@ -416,7 +403,7 @@ the README file for more information.</p>
<hr class="docutils" />
</div>
<div class="section" id="lmp2vmd-tool">
-<span id="vmd"></span><h2>9.18. lmp2vmd tool<a class="headerlink" href="#lmp2vmd-tool" title="Permalink to this headline">¶</a></h2>
+<span id="vmd"></span><h2>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>
@@ -425,7 +412,7 @@ 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>9.19. matlab tool<a class="headerlink" href="#matlab-tool" title="Permalink to this headline">¶</a></h2>
+<span id="matlab"></span><h2>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
@@ -438,7 +425,7 @@ visualizer.</p>
<hr class="docutils" />
</div>
<div class="section" id="micelle2d-tool">
-<span id="micelle"></span><h2>9.20. micelle2d tool<a class="headerlink" href="#micelle2d-tool" title="Permalink to this headline">¶</a></h2>
+<span id="micelle"></span><h2>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
@@ -454,7 +441,7 @@ 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>9.21. moltemplate tool<a class="headerlink" href="#moltemplate-tool" title="Permalink to this headline">¶</a></h2>
+<span id="moltemplate"></span><h2>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
@@ -466,7 +453,7 @@ supports it. It has its own WWW page at
<hr class="docutils" />
</div>
<div class="section" id="msi2lmp-tool">
-<span id="msi"></span><h2>9.22. msi2lmp tool<a class="headerlink" href="#msi2lmp-tool" title="Permalink to this headline">¶</a></h2>
+<span id="msi"></span><h2>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’ Insight MD code (formerly MSI/Biosym and
its Discover MD code). See the README file for more information.</p>
@@ -479,7 +466,7 @@ experiment with it yourself.</p>
<hr class="docutils" />
</div>
<div class="section" id="phonon-tool">
-<span id="phonon"></span><h2>9.23. phonon tool<a class="headerlink" href="#phonon-tool" title="Permalink to this headline">¶</a></h2>
+<span id="phonon"></span><h2>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>
@@ -491,7 +478,7 @@ University.</p>
<hr class="docutils" />
</div>
<div class="section" id="polymer-bonding-tool">
-<span id="polybond"></span><h2>9.24. polymer bonding tool<a class="headerlink" href="#polymer-bonding-tool" title="Permalink to this headline">¶</a></h2>
+<span id="polybond"></span><h2>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 “programmable polymer bonding”. The Python file
lmpsdata.py provides a “Lmpsdata” class with various methods which can
@@ -502,7 +489,7 @@ complex bonding topologies.</p>
<hr class="docutils" />
</div>
<div class="section" id="pymol-asphere-tool">
-<span id="pymol"></span><h2>9.25. pymol_asphere tool<a class="headerlink" href="#pymol-asphere-tool" title="Permalink to this headline">¶</a></h2>
+<span id="pymol"></span><h2>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>
@@ -513,7 +500,7 @@ examples directory within pymol_asphere for more information.</p>
<hr class="docutils" />
</div>
<div class="section" id="python-tool">
-<span id="pythontools"></span><h2>9.26. python tool<a class="headerlink" href="#python-tool" title="Permalink to this headline">¶</a></h2>
+<span id="pythontools"></span><h2>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">
@@ -528,7 +515,7 @@ 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>9.27. reax tool<a class="headerlink" href="#reax-tool" title="Permalink to this headline">¶</a></h2>
+<span id="reax"></span><h2>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
@@ -537,7 +524,7 @@ the README.txt file for more info.</p>
<hr class="docutils" />
</div>
<div class="section" id="restart2data-tool">
-<span id="restart"></span><h2>9.28. restart2data tool<a class="headerlink" href="#restart2data-tool" title="Permalink to this headline">¶</a></h2>
+<span id="restart"></span><h2>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
@@ -576,7 +563,7 @@ 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>9.29. vim tool<a class="headerlink" href="#vim-tool" title="Permalink to this headline">¶</a></h2>
+<span id="vim"></span><h2>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>
@@ -585,7 +572,7 @@ ziegenhain.com)</p>
<hr class="docutils" />
</div>
<div class="section" id="xmgrace-tool">
-<span id="xmgrace"></span><h2>9.30. xmgrace tool<a class="headerlink" href="#xmgrace-tool" title="Permalink to this headline">¶</a></h2>
+<span id="xmgrace"></span><h2>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
@@ -597,7 +584,7 @@ simulation.</p>
<hr class="docutils" />
</div>
<div class="section" id="xmovie-tool">
-<span id="xmovie"></span><h2>9.31. xmovie tool<a class="headerlink" href="#xmovie-tool" title="Permalink to this headline">¶</a></h2>
+<span id="xmovie"></span><h2>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
@@ -628,15 +615,6 @@ 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 & 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 & 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 2020b2c494f7f83e43e5e81cc0d5483e3fe8897a..46d881b3c390aed38d0d8490cf1a418f645af2a6 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:
+ :numbered: // comment
Section_intro
Section_start
@@ -91,8 +91,8 @@ it gives quick access to documentation for all LAMMPS commands.
Indices and tables
==================
-* :ref:`genindex`
-* :ref:`search`
+* :ref:`genindex` // comment
+* :ref:`search` // comment
.. raw:: html
diff --git a/doc/_sources/fix.txt b/doc/_sources/fix.txt
index c0f1630eef0a1cfeaa2b236346456919a3ce685d..bf6fa2bb7b3b27297a5b24655807ed3988a16770 100644
--- a/doc/_sources/fix.txt
+++ b/doc/_sources/fix.txt
@@ -177,7 +177,7 @@ in the fix section of :ref:`this page <cmd_5>`.
* :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
* :doc:`ave/atom <fix_ave_atom>` - compute per-atom time-averaged quantities
-* :doc:`ave/correlate <fix_correlate_atom>` - compute/output time correlations
+* :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
* :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
* :doc:`ave/spatial <fix_ave_spatial>` - compute/output time-averaged per-atom quantities by layer
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
diff --git a/doc/_sources/pair_hybrid.txt b/doc/_sources/pair_hybrid.txt
index e31248fe22d2910fe03796eadde964d40a61a481..f770227ace89acf016e706d5383c3987ac0287f5 100644
--- a/doc/_sources/pair_hybrid.txt
+++ b/doc/_sources/pair_hybrid.txt
@@ -214,14 +214,13 @@ potentials.
Different force fields (e.g. CHARMM vs AMBER) may have different rules
-for applying these factors to modulate the strength of pairwise
+for applying weightings that change the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
-neighbors in the molecular bond topology. Specific
-:doc:`special_bonds <special_bonds>` settings can be assigned to
-different pair hybrid sub-styles via the :doc:`pair_modify special <pair_modify>` special command, using its *pair* keyword
-and optional *special* argument. This allows multiple force fields to
-be used to a model a hybrid system. See the
-:doc:`special_bonds <special_bonds>` doc page for details.
+neighbors in the molecular bond topology, as normally set by the
+:doc:`special_bonds <special_bonds>` command. Different weights can be
+assigned to different pair hybrid sub-styles via the :doc:`pair_modify special <pair_modify>` command. This allows multiple force fields
+to be used in a model of a hybrid system. See the
+:doc:`pair_modify <pair_modify>` doc page for details.
The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the :doc:`compute pair <compute_pair>` command.
diff --git a/doc/_sources/pair_modify.txt b/doc/_sources/pair_modify.txt
index 22328a88640f400e89a1c2a7338cf56dfea025a7..93bcdb503d2f5f9ad06315786f1ea3703cc067a6 100644
--- a/doc/_sources/pair_modify.txt
+++ b/doc/_sources/pair_modify.txt
@@ -11,14 +11,14 @@ Syntax
pair_modify keyword values ...
* one or more keyword/value pairs may be listed
-* keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner* or *tabinner/disp* or *tail* or *compute*
+* keyword = *pair* or *special* or *shift* or *mix* or *table* or *table/disp* or *tabinner* or *tabinner/disp* or *tail* or *compute*
.. parsed-literal::
*pair* values = sub-style N special which w1 wt2 wt3
sub-style = sub-style of :doc:`pair hybrid <pair_hybrid>`
N = which instance of sub-style (only if sub-style is used multiple times)
- special = optional if want to override :doc:`special_bonds <special_bonds>` settings for sub-style
- which = *lj/coul* or *lj* or *coul*
+ *special* values = flavor w1 w2 w3
+ flavor = *lj/coul* or *lj* or *coul*
w1,w2,w3 = weights from 0.0 to 1.0 inclusive
*mix* value = *geometric* or *arithmetic* or *sixthpower*
*shift* value = *yes* or *no*
@@ -50,15 +50,24 @@ Description
Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.
-If used, the *pair* keyword and its optional *special* arguments must
-appear first in the list of keywords. It can only be used with the
-:doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles and when used
-it means that all the following parameters will only be modified for
-the specified sub-style. If the *pair* keyword is not used, and the
-pair style is *hybrid* or *hybrid/overlay*, all the following
-parameters keywords will be applied to all sub-styles. A more detailed
-explanation of the *pair* keyword syntax, including its optional
-*special* argument are given below.
+If used, the *pair* keyword must appear first in the list of keywords.
+It can only be used with the :doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles. It means that all the
+following parameters will only be modified for the specified
+sub-style. If the sub-style is defined multiple times, then an
+additional numeric argument *N* must also be specified, which is a
+number from 1 to M where M is the number of times the sub-style was
+listed in the :doc:`pair_style hybrid <pair_hybrid>` command. The extra
+number indicates which instance of the sub-style the remaining
+keywords will be applied to. Note that if the *pair* keyword is not
+used, and the pair style is *hybrid* or *hybrid/overlay*, then all the
+specified keywords will be applied to all sub-styles.
+
+If used, the *special* keyword must appear second in the list of
+keywords, and must follow the *pair* keyword. Like the *pair*
+keyword, it also can only be used with the :doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles. Its parameters are
+similar to the :doc:`special_bonds <special_bonds>` command, and it
+overrides the special_bond settings for the specified sub-style. More
+details are given below.
The *mix* keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
@@ -208,50 +217,28 @@ pair style be defined.
----------
-Use of the pair keyword
------------------------
-
-If used, the *pair* keyword and its optional *special* arguments must
-appear first in the list of keywords. It can only be used with the
-:doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles and when used
-it means that all the following parameters will only be modified for
-the specified sub-style. If the *pair* keyword is not used, and the
-pair style is *hybrid* or *hybrid/overlay*, all the following
-parameters keywords will be applied to all sub-styles. A more detailed
-explanation of the *pair* keyword syntax, including its optional
-*special* argument are given below.
-
-As mentioned above, the *pair* keyword can only be used with the
-:doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles, and must
-come first in the list of keywords. If used, the subsequent keywords
-will only be applied to the specified sub-style. If the sub-style is
-defined multiple times, then an additional numeric argument *N* must
-also be specified, which is a number from 1 to M where M is the number
-of times the sub-style was listed in the :doc:`pair_style hybrid <pair_hybrid>` command. The extra number indicates which
-instance of the sub-style the pair_modify keywords will be applied to.
-
-If the optional *special* argument is used, then the settings of the
-:doc:`special_bonds <special_bonds>` command are overridden for the
-specified sub-style. The *special* argument requires 4 additional
-arguments: *which* and w1,w2,w3. These are analogous to arguments in
-the :doc:`special_bonds <special_bonds>` command. The *which* argument
-can be *lj* to change the Lennard-Jones settings, *coul* to change the
-Coulombic settings, or *lj/coul* to change both to the same values.
-The w1,w2,w3 arguments are numeric weights from 0.0 to 1.0 inclusive,
-for the 1-2, 1-3, and 1-4 bond topology neighbors. For example, these
-commands
+Use of *special* keyword
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+The *special* keyword requires 4 values similar to those specified
+with the :doc:`special_bonds <special_bonds>` command, *flavor* and
+w1,w2,w3. The *flavor* argument can be *lj* to change the
+Lennard-Jones settings, *coul* to change the Coulombic settings, or
+*lj/coul* to change both to the same set of 3 values. The w1,w2,w3
+values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
+1-3, and 1-4 bond topology neighbors. For example, these commands
.. parsed-literal::
special_bonds lj/coul 0.0 0.0 0.1
- pair_hybrid lj/charmm/coul/charmm 8.0 10.0 lj/cut/coul/cut 10.0
- pair_modify pair lj/charmm/coul/charmm special lj/coul 0.0 0.0 0.0
- pair_modify pair lj/cut/coul/cut special lj 0.0 0.0 0.5
- pair_modify pair lj/cut/coul/cut special coul 0.0 0.0 0.8333
+ pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+ pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+ pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
+ pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.8333
show how to use both the CHARMM and AMBER force fields in a single
simulation. The first pair modify command sets the special bonds to
-CHARMM values (all 0.0). The latter 2 pair modify commands set the
+CHARMM values (all 0.0). The last 2 pair modify commands set the
standard AMBER values for LJ and Coulombic weights.
.. warning::
@@ -260,13 +247,13 @@ standard AMBER values for LJ and Coulombic weights.
:doc:`special_bonds <special_bonds>` command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
exclude those pairs from the neighbor list entirely. Weights of 1.0
- store the neighbor with no weight flag applied. Neither of these
- neighbor effects can be changed by setting a sub-style weight to a
+ store the neighbor with no weighting applied. The format of the
+ neighbor list cannot be changed by setting a sub-style weight to a
non-zero or non-one value. Thus an error is generated if the new
- sub-style value is not 0.0 (or 1.0) and the global setting is 0.0 (or
+ sub-style value is not 0.0 (or 1.0) when the global setting is 0.0 (or
1.0). Note that as in the example above, the global factor can simply
be set a value other than 0.0 or 1.0, then overridden by any of the
- sub-styles to a value that is 0.0 or 1.0.
+ sub-styles with a value that is 0.0 or 1.0.
----------
diff --git a/doc/accelerate_cuda.html b/doc/accelerate_cuda.html
index 9d72bb76f55e27a9901eb1b71ca9eed13afd9f8b..c07d20d5123e3be9822a3fd9a98653612f649349 100644
--- a/doc/accelerate_cuda.html
+++ b/doc/accelerate_cuda.html
@@ -71,22 +71,14 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/accelerate_gpu.html b/doc/accelerate_gpu.html
index e10f0da364a608b7bcb8c2e337e595a79e3fd566..17c71584a360b8ebf76516845b62e44930774b11 100644
--- a/doc/accelerate_gpu.html
+++ b/doc/accelerate_gpu.html
@@ -71,22 +71,14 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/accelerate_intel.html b/doc/accelerate_intel.html
index 79a19f26dab7aac89f5a64e030c0f2b9b196f8ca..9409a80b45290eea0c1ba6e3c427e264851e87db 100644
--- a/doc/accelerate_intel.html
+++ b/doc/accelerate_intel.html
@@ -71,22 +71,14 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/accelerate_kokkos.html b/doc/accelerate_kokkos.html
index d3581579121375e45c94f5131b2368d434425b3b..b5dbc00d351ddccd6952ae1edc1f0fff1bedcb74 100644
--- a/doc/accelerate_kokkos.html
+++ b/doc/accelerate_kokkos.html
@@ -71,22 +71,14 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/accelerate_omp.html b/doc/accelerate_omp.html
index ff6c8702a0406c062770e0098765a076668d516c..5655e310654423bd26e353207dd5950fc199ca8b 100644
--- a/doc/accelerate_omp.html
+++ b/doc/accelerate_omp.html
@@ -71,22 +71,14 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/accelerate_opt.html b/doc/accelerate_opt.html
index d79d441d62bf3b74207e7bcd1fbd563293a2cfd0..d85dd2f50b699991e10cbbfa869a98c7c4234b71 100644
--- a/doc/accelerate_opt.html
+++ b/doc/accelerate_opt.html
@@ -71,22 +71,14 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_charmm.html b/doc/angle_charmm.html
index f7291a37ca69218abff41f3d7c787f4adbb771d6..fcfb5789500024cb154f472a2db2a89214c5304f 100644
--- a/doc/angle_charmm.html
+++ b/doc/angle_charmm.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_class2.html b/doc/angle_class2.html
index b8d6d3c871c6e7b10c13b2b3093b4718b7e719bf..65318403615533de5527f8cf3cbad98c3c283625 100644
--- a/doc/angle_class2.html
+++ b/doc/angle_class2.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_coeff.html b/doc/angle_coeff.html
index b0e5ca7147c3ca1a60b762fd24a7f69963828d54..858c047547d4b028dc06d9b161055ca3dc929c71 100644
--- a/doc/angle_coeff.html
+++ b/doc/angle_coeff.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_cosine.html b/doc/angle_cosine.html
index ea68ca3d78fbdb72e4f3f9169d4da6eddc5bfdec..33fcd0d788c2a5ff7abefa9df75ff54110262daf 100644
--- a/doc/angle_cosine.html
+++ b/doc/angle_cosine.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_cosine_delta.html b/doc/angle_cosine_delta.html
index 7920c8ab9abd6bdaf703e0d87259a083483650b2..ca4a9d8ac02016436400079136355d0ec6570a82 100644
--- a/doc/angle_cosine_delta.html
+++ b/doc/angle_cosine_delta.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_cosine_periodic.html b/doc/angle_cosine_periodic.html
index 945db4de6f7b36c6d425bf71b6701c90730d9ce6..4e5138bbff102a6928ee7df82ccf5afec0e2dad2 100644
--- a/doc/angle_cosine_periodic.html
+++ b/doc/angle_cosine_periodic.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_cosine_shift.html b/doc/angle_cosine_shift.html
index dc387120696c9704affe90858a3083a29034d0f4..a50e43105b1dfdadcebb5623bb4360c81ae3ca6a 100644
--- a/doc/angle_cosine_shift.html
+++ b/doc/angle_cosine_shift.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_cosine_shift_exp.html b/doc/angle_cosine_shift_exp.html
index ff3b1cb40c606bbd3dafa54f3da8257f1125e253..2a7d3b6065c971b8e416bb24dd8991441f232537 100644
--- a/doc/angle_cosine_shift_exp.html
+++ b/doc/angle_cosine_shift_exp.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_cosine_squared.html b/doc/angle_cosine_squared.html
index 18e8651503c977219bb1b928939a53fa773531d9..c626e36f00f6d0b968d6835bb5019c0bb39b6bbc 100644
--- a/doc/angle_cosine_squared.html
+++ b/doc/angle_cosine_squared.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_dipole.html b/doc/angle_dipole.html
index eec7ff223413144352b0d345a4433061b52ae91e..d6a163227414ca93fb0efde72eb98ff2f9bda431 100644
--- a/doc/angle_dipole.html
+++ b/doc/angle_dipole.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_fourier.html b/doc/angle_fourier.html
index 80cfb68c06a19c51810875f08c5f3b0d47d6c83d..e16f48c73a8e6a5ab4f40d15f1cd95a7033e2285 100644
--- a/doc/angle_fourier.html
+++ b/doc/angle_fourier.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_fourier_simple.html b/doc/angle_fourier_simple.html
index ef9392db3d3eabd76a1f90ad40e80cb5e4431fac..04075def301968e74cdef37ff30cb10e8d45583f 100644
--- a/doc/angle_fourier_simple.html
+++ b/doc/angle_fourier_simple.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_harmonic.html b/doc/angle_harmonic.html
index 49d9fe4d9add2d2f302204423c591eeb27beadaf..211adab4fa751b5faf35ef926a98f48e004eee5b 100644
--- a/doc/angle_harmonic.html
+++ b/doc/angle_harmonic.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_hybrid.html b/doc/angle_hybrid.html
index ebe07c66dc6368d947e371435b3eea8c3b20248f..f857bd46620aa0623763642cbe911c1fe4e18bc5 100644
--- a/doc/angle_hybrid.html
+++ b/doc/angle_hybrid.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_none.html b/doc/angle_none.html
index 323e9009838d23317975acf5de9cf7b8a96d405a..95bd494d242c45f0972a66dd4e4b5ca85ea92378 100644
--- a/doc/angle_none.html
+++ b/doc/angle_none.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_quartic.html b/doc/angle_quartic.html
index e6031bd2502b3c081c976ebc3cceabf96d46a354..418829561da2714715572d4014f1ea47d50e455e 100644
--- a/doc/angle_quartic.html
+++ b/doc/angle_quartic.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_sdk.html b/doc/angle_sdk.html
index ef6f739f51e6685b607de4c05013d56ba8fed77f..5b3ae13a2be0e98f730e27e16c22899196f9bd7e 100644
--- a/doc/angle_sdk.html
+++ b/doc/angle_sdk.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_style.html b/doc/angle_style.html
index 5fa54ae6bad80e9d3c2ff541e8be07e5167c9f57..a03fb3042bc8f1a1b8b4c22a8eab703cd0f4dc43 100644
--- a/doc/angle_style.html
+++ b/doc/angle_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/angle_table.html b/doc/angle_table.html
index 06a5947c77a340bc280a67c01a5aa77a12a04498..433b9e34592ea7c5825e43a6cd0b08f17ec8ebda 100644
--- a/doc/angle_table.html
+++ b/doc/angle_table.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/atom_modify.html b/doc/atom_modify.html
index f22a02dc8b1e24878ff4714ecceb5a5c9548844e..328f6f15bdd8214b2ac217309c5d6772a00219ad 100644
--- a/doc/atom_modify.html
+++ b/doc/atom_modify.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/atom_style.html b/doc/atom_style.html
index 833e034cdfa391574b6a30f9c2a37aeb3acc6563..a3372600c2fec8e428e0754f537a00a252bfd909 100644
--- a/doc/atom_style.html
+++ b/doc/atom_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/balance.html b/doc/balance.html
index 4c6c21eeccace57b4b70f63eb9e06b05244c10ad..96ff0e44962b696df123f9f547ca5e6947d07d15 100644
--- a/doc/balance.html
+++ b/doc/balance.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
@@ -264,7 +260,7 @@ 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 “grid” method
has been applied.</p>
-<a data-lightbox="group-33581b25-ff7a-4993-af10-3eb635606c51"
+<a data-lightbox="group-022505f1-dc20-4757-8079-1c46a98561c1"
href="_images/balance_uniform.jpg"
class=""
title=""
@@ -274,7 +270,7 @@ has been applied.</p>
width="25%"
height="auto"
alt=""/>
- </a><a data-lightbox="group-0707698a-5184-4a24-a0b3-55e008c10da2"
+ </a><a data-lightbox="group-33c706ca-ec21-410d-8dea-549388d6ccd9"
href="_images/balance_nonuniform.jpg"
class=""
title=""
@@ -284,7 +280,7 @@ has been applied.</p>
width="25%"
height="auto"
alt=""/>
- </a><a data-lightbox="group-153ac620-167c-4887-8859-4d5f616526fe"
+ </a><a data-lightbox="group-eb041c99-4215-4b9b-8dbd-437cfbda53dd"
href="_images/balance_rcb.jpg"
class=""
title=""
diff --git a/doc/body.html b/doc/body.html
index 395f9c2b57ac5e1c95f07c9c92b039c591c22b0c..269c59c903d3b1c3f1a2c5f5ad2c5075e9358e33 100644
--- a/doc/body.html
+++ b/doc/body.html
@@ -71,22 +71,11 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- Local TOC -->
+ <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">Body particles</a></li>
</ul>
-
+</div>
</div>
diff --git a/doc/bond_class2.html b/doc/bond_class2.html
index 5a38be9089b0f759539a30af46da1bcceed98660..51660727fd3b3061225ad6fecb88a02630e6374b 100644
--- a/doc/bond_class2.html
+++ b/doc/bond_class2.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_coeff.html b/doc/bond_coeff.html
index 62049c831ca3ed2c99f0343f13a9583069d6673f..03f8ce3cea14af5fd59f237861f0b32902d6f19f 100644
--- a/doc/bond_coeff.html
+++ b/doc/bond_coeff.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_fene.html b/doc/bond_fene.html
index b3f5b7dae2f84c5bc6d6efc7e7c0e075883fb44d..181a7b095f5c7ddeda60a87ce0595e3e5c6f69cd 100644
--- a/doc/bond_fene.html
+++ b/doc/bond_fene.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_fene_expand.html b/doc/bond_fene_expand.html
index 1c6ef1391a8d2ad52e0b8def2bdb8ee2c49f579b..4eaded2c23c509d93a69ce0769dfe8fdf24a189d 100644
--- a/doc/bond_fene_expand.html
+++ b/doc/bond_fene_expand.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_harmonic.html b/doc/bond_harmonic.html
index 5a7945443c22b70d06afc28f11df7089590e945e..432cbdabbfc1dd378a58526d754f8060067ff363 100644
--- a/doc/bond_harmonic.html
+++ b/doc/bond_harmonic.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_harmonic_shift.html b/doc/bond_harmonic_shift.html
index 71dbec85df237e4525298e69405251840a199a1d..b02b2aefcdaea3beb1eb1b8279ff99954fa324ca 100644
--- a/doc/bond_harmonic_shift.html
+++ b/doc/bond_harmonic_shift.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_harmonic_shift_cut.html b/doc/bond_harmonic_shift_cut.html
index c5fdac49a0e5ac8d61060cbc38c63c53baa5e323..9429d4b58d3fd4d0729726c8b0669c75b8ef4443 100644
--- a/doc/bond_harmonic_shift_cut.html
+++ b/doc/bond_harmonic_shift_cut.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_hybrid.html b/doc/bond_hybrid.html
index facb59d7cd67c02af6585d335238fa8c11048102..700465ebb59a6db388cccd31cdf0786456284ea0 100644
--- a/doc/bond_hybrid.html
+++ b/doc/bond_hybrid.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_morse.html b/doc/bond_morse.html
index c61d28fe84573798e27ee3dc9074f4a261247ab7..1f2b6a5544ad9f81c0e6367b6bfc38b9ac889a8e 100644
--- a/doc/bond_morse.html
+++ b/doc/bond_morse.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_none.html b/doc/bond_none.html
index 99cf94369b33bbc8011788409ccbd97d726112fa..27331d64b8f914240ee92f8fee62ac6df2828acb 100644
--- a/doc/bond_none.html
+++ b/doc/bond_none.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_nonlinear.html b/doc/bond_nonlinear.html
index 511a7a7a89ab1c0d510fb48f6a0401d814f7d11d..d9b922e4836f0e87b6f281666a4fa4938b26978d 100644
--- a/doc/bond_nonlinear.html
+++ b/doc/bond_nonlinear.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_quartic.html b/doc/bond_quartic.html
index 85007981318cdcf20514b8bdd7c9d0740e49507b..3176b87c56966142e74654cb3de15a72e95c0aa4 100644
--- a/doc/bond_quartic.html
+++ b/doc/bond_quartic.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_style.html b/doc/bond_style.html
index 58589a58e5e7bfbd5139bd9dcbc4ddda3a40f9bd..992bd282a9eb86b87e1c1fd74fa3becf7b56efb1 100644
--- a/doc/bond_style.html
+++ b/doc/bond_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/bond_table.html b/doc/bond_table.html
index c82d39abd06ae4f09688356cb3a562de1362f381..ed22cb937583db636dec51999396bd83f4ee0fe7 100644
--- a/doc/bond_table.html
+++ b/doc/bond_table.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/boundary.html b/doc/boundary.html
index d30e58f10d2c9fbac9f92bf2b48fb7299c85c0a6..12e642395d5772256b0b444707434e1ee24f23d2 100644
--- a/doc/boundary.html
+++ b/doc/boundary.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/box.html b/doc/box.html
index 5d3ff9a4bf90d458fb1bcd3ef60042550e72cbf0..716dad40de166f444c1e56cfe5a61c5578b91856 100644
--- a/doc/box.html
+++ b/doc/box.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/change_box.html b/doc/change_box.html
index 84f5fe73ecd9ba3e3b0eebbfb8c7783da5383573..c4c00f7ac755d4e13360ebea94533ef870030093 100644
--- a/doc/change_box.html
+++ b/doc/change_box.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/clear.html b/doc/clear.html
index c5f62772b3012849185fd7e58da1af77a8e62bed..2c0591142159bdb275f3e918e1b0b22c5e9b6a17 100644
--- a/doc/clear.html
+++ b/doc/clear.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/comm_modify.html b/doc/comm_modify.html
index 90da72d542b1f2b146908f468dd22a5a50eb224e..fad4c8f635b1867ec631347f5b9ea4be5c1c6aaa 100644
--- a/doc/comm_modify.html
+++ b/doc/comm_modify.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/comm_style.html b/doc/comm_style.html
index 5994c404fb22ba33839ebaa93c42e32f72085def..5c2e09621182fa8cec96bc8083e636c0510f53d1 100644
--- a/doc/comm_style.html
+++ b/doc/comm_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute.html b/doc/compute.html
index 430b76aaa79f16ef00b87961ba556a5d94bf3704..7bc5bf2f4141003afd3bd3c51e6c3e135b2b9cc6 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_ackland_atom.html b/doc/compute_ackland_atom.html
index 6eced7e3da421c3720fe51a17b54200857799b04..1587e210249842add7be90d7b74f165a730845ca 100644
--- a/doc/compute_ackland_atom.html
+++ b/doc/compute_ackland_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_angle_local.html b/doc/compute_angle_local.html
index 2ef282ffd7197939e87c8b580b71f21d9b80e77a..9b04c55089fd3ec188d8838e06a90228c041e8cf 100644
--- a/doc/compute_angle_local.html
+++ b/doc/compute_angle_local.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_angmom_chunk.html b/doc/compute_angmom_chunk.html
index c47e774cf309f4dff94b951bdf6d56d7b080e3fb..cfb9e6f2f582a86367dab90c5e0b2169012fea9b 100644
--- a/doc/compute_angmom_chunk.html
+++ b/doc/compute_angmom_chunk.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_basal_atom.html b/doc/compute_basal_atom.html
index ede5677efae4f3ab012fb87ac817a381cf18a11c..1f10e810e96e276a2ad7ee5385a87915b7c9f31c 100644
--- a/doc/compute_basal_atom.html
+++ b/doc/compute_basal_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_body_local.html b/doc/compute_body_local.html
index d2c467e515b1a84149d97cf1a0c1551dac9948dc..c57240c1364a8a492c8589ade1d70ce50f343593 100644
--- a/doc/compute_body_local.html
+++ b/doc/compute_body_local.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_bond_local.html b/doc/compute_bond_local.html
index 84dd7084a327999450419ff3b67fc1009cc99e52..14af46f93de00f8e7f1756bcd4c697e8ed479144 100644
--- a/doc/compute_bond_local.html
+++ b/doc/compute_bond_local.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_centro_atom.html b/doc/compute_centro_atom.html
index 4e1c3340cd2eba5cd65c6c798ecec8c70f4f27ee..e31bb9de0fd5ce560f32550552c0e77a78172c13 100644
--- a/doc/compute_centro_atom.html
+++ b/doc/compute_centro_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_chunk_atom.html b/doc/compute_chunk_atom.html
index 306d9d769f4d1d5cc8212fd851c636eb8c00963a..ba3f6447b1f62d3f5f7d3ca40c0bb9f2d8f3bb72 100644
--- a/doc/compute_chunk_atom.html
+++ b/doc/compute_chunk_atom.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_cluster_atom.html b/doc/compute_cluster_atom.html
index fbaa84dc51a2d75957a4cbedaa8aca4894e4aa35..e7e238483e616a6a04bda8f2f393210981117dc4 100644
--- a/doc/compute_cluster_atom.html
+++ b/doc/compute_cluster_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_cna_atom.html b/doc/compute_cna_atom.html
index c4e638d90194d776953189797c19b71facf8f73e..994420238257416b3d0d945dd446e2f811227688 100644
--- a/doc/compute_cna_atom.html
+++ b/doc/compute_cna_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_com.html b/doc/compute_com.html
index fcc0e2e1dea09e82cbb8da496ff1cc322af09418..ad41c7659a8b78b2ecbc9df89b6a36d7bf92ccd9 100644
--- a/doc/compute_com.html
+++ b/doc/compute_com.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_com_chunk.html b/doc/compute_com_chunk.html
index 198884804c495d1f63b620cc02b0a0ea2933c334..b1c5c7b543f9f9d6dde0cbee83c456add3393609 100644
--- a/doc/compute_com_chunk.html
+++ b/doc/compute_com_chunk.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_contact_atom.html b/doc/compute_contact_atom.html
index 73acc85d9c90dbd44d42a0125cd3f35b92f9b8ad..0ce40913bb1f7aebf7054590108d26a476d2757b 100644
--- a/doc/compute_contact_atom.html
+++ b/doc/compute_contact_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_coord_atom.html b/doc/compute_coord_atom.html
index ead3130fecc69efc7182187c6a4628fe94f9d15a..44bcb8f80a88ff05d94bb96e749c8e30659ad88c 100644
--- a/doc/compute_coord_atom.html
+++ b/doc/compute_coord_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_damage_atom.html b/doc/compute_damage_atom.html
index 3e3603d5e829b1eaf72508fd051e7ae74082c330..03f8033590e4cdefbdc96d499243acef3b71ec2b 100644
--- a/doc/compute_damage_atom.html
+++ b/doc/compute_damage_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_dihedral_local.html b/doc/compute_dihedral_local.html
index ec76231f1b1238e000d8953f5f64200a8bfb90f7..1b571cb89223a62711aa970f594379765a86a09c 100644
--- a/doc/compute_dihedral_local.html
+++ b/doc/compute_dihedral_local.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_dilatation_atom.html b/doc/compute_dilatation_atom.html
index 879ca93ad927bc2606784b49d7d3516121b2cb6c..960cd4a5629f607f5083285f2dcb7da86f968385 100644
--- a/doc/compute_dilatation_atom.html
+++ b/doc/compute_dilatation_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html
index ba9ab618d72afeb20776a4b5f1b4eb6403f6bd12..6584752de6d52e1e7399e229667dc4926e52dbae 100644
--- a/doc/compute_displace_atom.html
+++ b/doc/compute_displace_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_erotate_asphere.html b/doc/compute_erotate_asphere.html
index 189819cd22cc7b9406a1bb651dfc861fc0858266..5438b97004be3a6bc03a0e07c44fe2d9161553a2 100644
--- a/doc/compute_erotate_asphere.html
+++ b/doc/compute_erotate_asphere.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_erotate_rigid.html b/doc/compute_erotate_rigid.html
index fe9eb3d09d2be578ab3269006132ae7d092b5552..f3a4ae3b5157485ca6c6c76dcc5a4a04a83d6ce9 100644
--- a/doc/compute_erotate_rigid.html
+++ b/doc/compute_erotate_rigid.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_erotate_sphere.html b/doc/compute_erotate_sphere.html
index 71f70a6a5162f25dc8cae31c1ca178bfd6daec17..0c6c9abf5223bf84bdb75db2486ac69db64e13d2 100644
--- a/doc/compute_erotate_sphere.html
+++ b/doc/compute_erotate_sphere.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_erotate_sphere_atom.html b/doc/compute_erotate_sphere_atom.html
index ba93f416d368015feecfc6a00678b74e56c86281..86bf51bf4f1631d8b2751eed8830313ce1df21fd 100644
--- a/doc/compute_erotate_sphere_atom.html
+++ b/doc/compute_erotate_sphere_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_event_displace.html b/doc/compute_event_displace.html
index 87e4d4a52f3dd37389060f18c9a14f7c761b853f..db6245b63fd0043d6c42c828045cee8b5834f62d 100644
--- a/doc/compute_event_displace.html
+++ b/doc/compute_event_displace.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_fep.html b/doc/compute_fep.html
index acf5cf2520eb17de60d15afdad2a011a746784a0..a79535300ae2ca74699c56161f09ab4a534bc1f1 100644
--- a/doc/compute_fep.html
+++ b/doc/compute_fep.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_group_group.html b/doc/compute_group_group.html
index c1cb90f7925cf5652114582e465f7aa1ad626162..ef3558486489fb278075f561c0fbfacf3a53260f 100644
--- a/doc/compute_group_group.html
+++ b/doc/compute_group_group.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_gyration.html b/doc/compute_gyration.html
index 9a7e19aac8d2a7cb65ae723e906beea53f74a976..8856f90e883e7b2c445dd0cc0596d6db600f3a98 100644
--- a/doc/compute_gyration.html
+++ b/doc/compute_gyration.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_gyration_chunk.html b/doc/compute_gyration_chunk.html
index d1bbdabf5e1dfb0bd09961a8ddbca4de7d7805ac..6b015885c4c3ce5883cc633f29b27b76fec9a27c 100644
--- a/doc/compute_gyration_chunk.html
+++ b/doc/compute_gyration_chunk.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_heat_flux.html b/doc/compute_heat_flux.html
index a6c3acdec0d2c3ae5ab2b5de63035097e7b4acdc..76c0c746d3f2218ba6ffd05313f2263a486ea1c9 100644
--- a/doc/compute_heat_flux.html
+++ b/doc/compute_heat_flux.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_improper_local.html b/doc/compute_improper_local.html
index e4ffac2c177ad6d207ed37d5bd043485313ef695..e020e1b2970258c383392f78696762daa6724afe 100644
--- a/doc/compute_improper_local.html
+++ b/doc/compute_improper_local.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_inertia_chunk.html b/doc/compute_inertia_chunk.html
index c63b67ae66101464fb94e63034e14aeda476ff43..077e68b64b6082416a6c6e658433256f20ca726a 100644
--- a/doc/compute_inertia_chunk.html
+++ b/doc/compute_inertia_chunk.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_ke.html b/doc/compute_ke.html
index 9323b997e39353ba210044678bcba4f53f032dff..832a5ab7a80908c4d1618484349cba53950debe2 100644
--- a/doc/compute_ke.html
+++ b/doc/compute_ke.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_ke_atom.html b/doc/compute_ke_atom.html
index 96efdf209c8881c04b279057cf1e0b8e29504a08..1cbf62db7312177b485b5ccfe864800af15a768e 100644
--- a/doc/compute_ke_atom.html
+++ b/doc/compute_ke_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_ke_atom_eff.html b/doc/compute_ke_atom_eff.html
index 7e6f39a0278f2ab0e37b03f62b5f86cecc987b46..601b5d973661c9df09a0a1ec3f8bc4291e0baa3c 100644
--- a/doc/compute_ke_atom_eff.html
+++ b/doc/compute_ke_atom_eff.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_ke_eff.html b/doc/compute_ke_eff.html
index 573492f1c7504c9e8dad47fd542735d503bcd62d..6fd3b7680d8b85171da67bb298e39090adc6f23e 100644
--- a/doc/compute_ke_eff.html
+++ b/doc/compute_ke_eff.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_ke_rigid.html b/doc/compute_ke_rigid.html
index c4bb398c360360e4ce73ab831843102fa6f62c5f..0894bae607b32f40f9fa4c5cee10593a04beec76 100644
--- a/doc/compute_ke_rigid.html
+++ b/doc/compute_ke_rigid.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_meso_e_atom.html b/doc/compute_meso_e_atom.html
index 42799e289f65f74af389873848e676cfd260e338..f9f625139ee587ea1bfa09859da4663244ea643d 100644
--- a/doc/compute_meso_e_atom.html
+++ b/doc/compute_meso_e_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_meso_rho_atom.html b/doc/compute_meso_rho_atom.html
index 1fae15b8e140fcc3ad593c7b389aaf0864855fe4..f0363e50bece3a79e39ab46f59a15cf4814773f9 100644
--- a/doc/compute_meso_rho_atom.html
+++ b/doc/compute_meso_rho_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_meso_t_atom.html b/doc/compute_meso_t_atom.html
index 307cc822ec6064eb407c370154631f1d74ba52b6..baf808673bba9c7978349f383d1c2c5b9cf7ed5a 100644
--- a/doc/compute_meso_t_atom.html
+++ b/doc/compute_meso_t_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_modify.html b/doc/compute_modify.html
index 5cf714eb0b4652247b6e34210a91563dfaf3c3e8..895445b575004cfdcc6a13e2d6470ee0b41243e2 100644
--- a/doc/compute_modify.html
+++ b/doc/compute_modify.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_msd.html b/doc/compute_msd.html
index 2a02e6d65acc6ecabf04babb099bcd38a6d35313..b71ab21a12eca9f5b86a09dec6ee73be1ecc11a3 100644
--- a/doc/compute_msd.html
+++ b/doc/compute_msd.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_msd_chunk.html b/doc/compute_msd_chunk.html
index 9bf4c15773038d608ad7d2cf97878b72d9ea6f92..08a9004740a9815bdf1379b1631518839a453b58 100644
--- a/doc/compute_msd_chunk.html
+++ b/doc/compute_msd_chunk.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_msd_nongauss.html b/doc/compute_msd_nongauss.html
index 904989ad8674e23581ec21e5031a002ea264858b..7a5274cf58a9e79b9d37748a75566625945e5a8e 100644
--- a/doc/compute_msd_nongauss.html
+++ b/doc/compute_msd_nongauss.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_omega_chunk.html b/doc/compute_omega_chunk.html
index a5fcd48ac533fa5fd02f4e9e43843332346ecf75..a81984fc93bc5d7b01f35b18da4b284bd8b6bbc0 100644
--- a/doc/compute_omega_chunk.html
+++ b/doc/compute_omega_chunk.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_pair.html b/doc/compute_pair.html
index 4ea8a47ad6d6fe9c040f1c1d9655c0c97e78bcbb..b9947db5108290352be3f521cd0f15ffd9e24f93 100644
--- a/doc/compute_pair.html
+++ b/doc/compute_pair.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_pair_local.html b/doc/compute_pair_local.html
index cde85f05c2a82dd9b6eebc679e326363f934a077..a6779f209ef68170cfb84f0d9a8b66cf7eafd379 100644
--- a/doc/compute_pair_local.html
+++ b/doc/compute_pair_local.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_pe.html b/doc/compute_pe.html
index 5dfc8fae63fdb4749d5b03c126eb56a966db61b6..5ab475a436fd1acbcaa5eaaa1a5be276d3a3b64f 100644
--- a/doc/compute_pe.html
+++ b/doc/compute_pe.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html
index 0863dbd97aafa1118d760cd07bbfe512708a2de9..99c6e1fe49317b40485ef9b8da44ecc887914c6d 100644
--- a/doc/compute_pe_atom.html
+++ b/doc/compute_pe_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_plasticity_atom.html b/doc/compute_plasticity_atom.html
index 10179425448ffe02486bbe9c2164e0f3acc1239b..f8aec584d46b07e184a3718923f8650d21fdd65e 100644
--- a/doc/compute_plasticity_atom.html
+++ b/doc/compute_plasticity_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_pressure.html b/doc/compute_pressure.html
index 62808529641831dc3ce075554a0a6432299c0d5f..3c3b3ea4bd5ffc76264df04dea2448e52254bd51 100644
--- a/doc/compute_pressure.html
+++ b/doc/compute_pressure.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_property_atom.html b/doc/compute_property_atom.html
index 8bbe9473d7cd9eeff4c8658561dc4be338871441..7daf52a51f35bfaef51f2abce88eb773eede77ef 100644
--- a/doc/compute_property_atom.html
+++ b/doc/compute_property_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_property_chunk.html b/doc/compute_property_chunk.html
index 24bef3366fe73f4206f3e17c95c9433f0c66acc2..726bb05328e9854100053feccb14f4a674f4924b 100644
--- a/doc/compute_property_chunk.html
+++ b/doc/compute_property_chunk.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_property_local.html b/doc/compute_property_local.html
index e0b55f073ae4dec50ed20503056c5f3b9d168dbe..391b82e376f94456318a3bb8497e0780da8c99cf 100644
--- a/doc/compute_property_local.html
+++ b/doc/compute_property_local.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_rdf.html b/doc/compute_rdf.html
index 3ff1eeb00367968e82ce92e176fb16d98e1f0149..df69c9d25e86955c28535a68019d42bd00c5c2e6 100644
--- a/doc/compute_rdf.html
+++ b/doc/compute_rdf.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_reduce.html b/doc/compute_reduce.html
index 32bf5be8f64a844da5c0296cb599d46796410f7e..3fa16b7b691d0fe1a2ac5af20862e1b587b2a0fd 100644
--- a/doc/compute_reduce.html
+++ b/doc/compute_reduce.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_saed.html b/doc/compute_saed.html
index ad8f5afd3752f1bee63a8b4674b9804c55ff0567..42026964541dc1f71bf9fec07e1859577c0ca730 100644
--- a/doc/compute_saed.html
+++ b/doc/compute_saed.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
@@ -181,7 +178,7 @@ 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-4d85a0d4-231c-430d-8dc3-0b8dbabd8286"
+<a data-lightbox="group-e8932333-9eca-4cdc-8b3f-74fb5ad39868"
href="_images/saed_mesh.jpg"
class=""
title=""
@@ -218,7 +215,7 @@ 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-10fe2ddf-b034-43ff-90c4-823988063225"
+<a data-lightbox="group-0164466b-c5e5-48d4-ba75-5dfe407cce93"
href="_images/saed_ewald_intersect.jpg"
class=""
title=""
diff --git a/doc/compute_slice.html b/doc/compute_slice.html
index c964ae82313ea660356b0b9ac492a3ec6422e241..a6dee96c55a518f0fec9766d401e9f24e995eb2a 100644
--- a/doc/compute_slice.html
+++ b/doc/compute_slice.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_sna_atom.html b/doc/compute_sna_atom.html
index d4a721a5d05fb9445d405bc1cad72cc22ddb0d21..4650a20cfcd6c4c2d521f1f3259a540f0007582e 100644
--- a/doc/compute_sna_atom.html
+++ b/doc/compute_sna_atom.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_stress_atom.html b/doc/compute_stress_atom.html
index 8b1e101e9c84f2580581a62a6b6cfc6ff436d176..ca9484156cbed04d4381cb39d854726dd38c8439 100644
--- a/doc/compute_stress_atom.html
+++ b/doc/compute_stress_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp.html b/doc/compute_temp.html
index 2199ee2a1005d914cda2d531f2f3564a0083753a..dc25b06f0f467bb639958d024a53caefaf11ec89 100644
--- a/doc/compute_temp.html
+++ b/doc/compute_temp.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_asphere.html b/doc/compute_temp_asphere.html
index a3ed191f2e36603d141ece531da298aed9daca56..994c552bea8cf7ceab6fae42adac06c82b31ea05 100644
--- a/doc/compute_temp_asphere.html
+++ b/doc/compute_temp_asphere.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_chunk.html b/doc/compute_temp_chunk.html
index 519a3f66b5e8d3e6bfb9ca60d28c6f9801df7ee7..96030b5cd64853d5e1ecf3e625e44cceefa57726 100644
--- a/doc/compute_temp_chunk.html
+++ b/doc/compute_temp_chunk.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_com.html b/doc/compute_temp_com.html
index 16268a6ff765570d2eb4d42b121920ffd1672441..1c03b323da2842991938e0e53199d5e59ca22c2d 100644
--- a/doc/compute_temp_com.html
+++ b/doc/compute_temp_com.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_cs.html b/doc/compute_temp_cs.html
index b06cb449bace99689debb063a1b111de17283c77..0e6a03a54f03636148df0f596ca396f2fea2def3 100644
--- a/doc/compute_temp_cs.html
+++ b/doc/compute_temp_cs.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_deform.html b/doc/compute_temp_deform.html
index 6b1a5cb33a0ef8b8cd2cd34ce7ff7264acd401f5..eb9e456de90f42c668dbf4dc0a68508d4fd2822e 100644
--- a/doc/compute_temp_deform.html
+++ b/doc/compute_temp_deform.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_deform_eff.html b/doc/compute_temp_deform_eff.html
index 293ee7fea2c1a40e44322ac3a91d1af64764f56a..a89f2e010526bd7187a64847550466e27c430140 100644
--- a/doc/compute_temp_deform_eff.html
+++ b/doc/compute_temp_deform_eff.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_drude.html b/doc/compute_temp_drude.html
index 35b8702094402c4958e091c6fba71ffbdfb36458..0cfff19d6051a1a4006defe53e988b6a83a16076 100644
--- a/doc/compute_temp_drude.html
+++ b/doc/compute_temp_drude.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_eff.html b/doc/compute_temp_eff.html
index 126d0efc5010d5d11ca83452600b48515f6c9f7f..6e12a248e9fc6c50bf449af81fc97ec39d071ed4 100644
--- a/doc/compute_temp_eff.html
+++ b/doc/compute_temp_eff.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_partial.html b/doc/compute_temp_partial.html
index 5cefaf325bd6fbd94d8a91c34630ed19e20b85d9..f368d76c6a850951423dc31dd1d1be93ded1de24 100644
--- a/doc/compute_temp_partial.html
+++ b/doc/compute_temp_partial.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_profile.html b/doc/compute_temp_profile.html
index 2a980d335ba42e2ace29001bd175e96ce5545e3b..b6fa80df268749c48c3abd3d900b091ed6c54c5b 100644
--- a/doc/compute_temp_profile.html
+++ b/doc/compute_temp_profile.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_ramp.html b/doc/compute_temp_ramp.html
index bbed00c8dee3eb2f4527fb84f9087b44292120d1..b6cf5454bf019ce32bc4ab9811c5423f951b7349 100644
--- a/doc/compute_temp_ramp.html
+++ b/doc/compute_temp_ramp.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_region.html b/doc/compute_temp_region.html
index f5509e1c535c4b2ed1c2be949972e21d02a04dd6..892b1ad4b72709303d00db09c5a1758b38d8b05a 100644
--- a/doc/compute_temp_region.html
+++ b/doc/compute_temp_region.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_region_eff.html b/doc/compute_temp_region_eff.html
index 74882a365726ad8ea109f39bc67ad72597220863..0dfca69f1940cb59b89dc949488492d84d7646ec 100644
--- a/doc/compute_temp_region_eff.html
+++ b/doc/compute_temp_region_eff.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_rotate.html b/doc/compute_temp_rotate.html
index 7be51832f682ac0f93fb9ef404ba005b00e56862..b8b7887f03dda0768e3326be558783b8ec02e279 100644
--- a/doc/compute_temp_rotate.html
+++ b/doc/compute_temp_rotate.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_temp_sphere.html b/doc/compute_temp_sphere.html
index e83c04d618ef2515c8e4e9ec1267bdd0248d64fe..6a14e3f490874cbd4f5d13d28b6f89ca89f11f42 100644
--- a/doc/compute_temp_sphere.html
+++ b/doc/compute_temp_sphere.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_ti.html b/doc/compute_ti.html
index 4fba0a348a5429b92b86cbbf25a6261b18669d95..b962ca3f8d68349e1f0bac6b2a86489cb73e203e 100644
--- a/doc/compute_ti.html
+++ b/doc/compute_ti.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_torque_chunk.html b/doc/compute_torque_chunk.html
index b7e9d65336ef1e4f9e23b3f6056a53303839c447..f9e36d365647dbde4b2cad65e0c92f73446ce448 100644
--- a/doc/compute_torque_chunk.html
+++ b/doc/compute_torque_chunk.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_vacf.html b/doc/compute_vacf.html
index b577f73f6dd059555914e15ccad368de894f75b7..ee08d2dbb83c8bb13a24a874cfaaf5fdeb303c71 100644
--- a/doc/compute_vacf.html
+++ b/doc/compute_vacf.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_vcm_chunk.html b/doc/compute_vcm_chunk.html
index ab6e9d93cae6ea8d4cc5691688cf74b591d9b1dc..444c6c3bd7a84deb2f032e24be88be839a293c9b 100644
--- a/doc/compute_vcm_chunk.html
+++ b/doc/compute_vcm_chunk.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_voronoi_atom.html b/doc/compute_voronoi_atom.html
index 11c04d290a7b5680733af910bfd5e52f57a84178..ad4540a6bdd49288715a1db5923f4f64e738b35b 100644
--- a/doc/compute_voronoi_atom.html
+++ b/doc/compute_voronoi_atom.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/compute_xrd.html b/doc/compute_xrd.html
index 3ed7652d7b399cfe77cdbd4db51aaccf4a5d5017..57d3a5c64c6230a7b5c5f74e34e19ff8e432fe2b 100644
--- a/doc/compute_xrd.html
+++ b/doc/compute_xrd.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
@@ -184,7 +181,7 @@ 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-5934c95b-ab98-4e61-ac7b-1d0095757e11"
+<a data-lightbox="group-4cb07d20-1b72-4b88-b799-aadc6e950f2e"
href="_images/xrd_mesh.jpg"
class=""
title=""
diff --git a/doc/create_atoms.html b/doc/create_atoms.html
index 9c27aad0d11127450c9838b97adfc012277e7b8c..f7980c3ea95b651f42f052da735ab8f9723fed42 100644
--- a/doc/create_atoms.html
+++ b/doc/create_atoms.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
@@ -340,7 +337,7 @@ variable v equal "(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-96d1a702-fca6-4b2c-8b5a-97ff5358d30b"
+<a data-lightbox="group-dc1611ed-f44e-47c4-a61a-d8696c9be612"
href="_images/sinusoid.jpg"
class=""
title=""
diff --git a/doc/create_bonds.html b/doc/create_bonds.html
index da36a89501012fc7fd79938cf5a5566fc0328466..c97c753984f7a8cf3798bf9c1c2a384a314f0b29 100644
--- a/doc/create_bonds.html
+++ b/doc/create_bonds.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/create_box.html b/doc/create_box.html
index 6fbb043ede0811bfa9f3c1a79c07abd18a4a0902..979d32ecc76b2be1569040a8cff3260690ee91d3 100644
--- a/doc/create_box.html
+++ b/doc/create_box.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/delete_atoms.html b/doc/delete_atoms.html
index bac8d33e0cb819c35a1eb033c35770af95aa3006..535d25512a84ca18fb95fb576ed496fecf8be46b 100644
--- a/doc/delete_atoms.html
+++ b/doc/delete_atoms.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/delete_bonds.html b/doc/delete_bonds.html
index 4e2246784671f02bfd1c391a46c03d3148ae3942..8ff3d9050aceca2dbf7fd41212f5f6b3f6e6b272 100644
--- a/doc/delete_bonds.html
+++ b/doc/delete_bonds.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dielectric.html b/doc/dielectric.html
index 33c97b563cc3d0ecd8f4de284ceebfdb0fb3e565..cec1a103c033cba9cbd707c65fce9a10e47108ae 100644
--- a/doc/dielectric.html
+++ b/doc/dielectric.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_charmm.html b/doc/dihedral_charmm.html
index bd4dc5878564ed5075b5ffb62fb2857d4876a221..1a977c4f0322bbd583eb28838fb886a8d7d81862 100644
--- a/doc/dihedral_charmm.html
+++ b/doc/dihedral_charmm.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_class2.html b/doc/dihedral_class2.html
index 43fca11ef66a04f10a6134c704bd4c18d225fe0b..83834885ac66f5109ea1a6b3e4136baa6bf4b4b3 100644
--- a/doc/dihedral_class2.html
+++ b/doc/dihedral_class2.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_coeff.html b/doc/dihedral_coeff.html
index 6253f33f06c5f0f9d0f6b28a9372fd8eb2586fe1..7ed367dd2f701469b9db96af22c61f993df1d49a 100644
--- a/doc/dihedral_coeff.html
+++ b/doc/dihedral_coeff.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_cosine_shift_exp.html b/doc/dihedral_cosine_shift_exp.html
index cf8d36d05c09f36aa27bf1d40832a86b15bb7d5d..5e5e8776cf769c30daed241d04b0448ec7d6e317 100644
--- a/doc/dihedral_cosine_shift_exp.html
+++ b/doc/dihedral_cosine_shift_exp.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_fourier.html b/doc/dihedral_fourier.html
index 3c47399ae13ad6de8e8b207dfe9f266534a67ef5..d28cdd8e8808144930de8123b97fbd3f8fb36367 100644
--- a/doc/dihedral_fourier.html
+++ b/doc/dihedral_fourier.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_harmonic.html b/doc/dihedral_harmonic.html
index 1fdeadcd01726f275de89bb64b53d111d531aec1..08d26f8882ddacb42047cfabc9114f837ef6cbbb 100644
--- a/doc/dihedral_harmonic.html
+++ b/doc/dihedral_harmonic.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_helix.html b/doc/dihedral_helix.html
index 36379e2718b0386a5e19ab6f9f0428ab77fe8d07..a732939bb70e6890290867b0bb5dc0708875dc7d 100644
--- a/doc/dihedral_helix.html
+++ b/doc/dihedral_helix.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_hybrid.html b/doc/dihedral_hybrid.html
index d2baa444fcdad7619d54882a0c1e500ad04e4c71..56a0ccb1fb91260b762ce7e77569931bb6763793 100644
--- a/doc/dihedral_hybrid.html
+++ b/doc/dihedral_hybrid.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_multi_harmonic.html b/doc/dihedral_multi_harmonic.html
index 029e8c0f2f521ebef3c3dcbe38ab4ee7de8bba76..06db32302ce6b6f97b87f221ae7d9f82db31fa4e 100644
--- a/doc/dihedral_multi_harmonic.html
+++ b/doc/dihedral_multi_harmonic.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_nharmonic.html b/doc/dihedral_nharmonic.html
index 8ed2f36a04235a665c4f21c1d611494470dd2da8..9d8d03b5774813b6fe83093b88917d46ef7d5636 100644
--- a/doc/dihedral_nharmonic.html
+++ b/doc/dihedral_nharmonic.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_none.html b/doc/dihedral_none.html
index d92ce032766d922c920e2a029bd67935db594069..4121a004c515e1cebc26695f0563a26c9004993e 100644
--- a/doc/dihedral_none.html
+++ b/doc/dihedral_none.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_opls.html b/doc/dihedral_opls.html
index aef5464d1ba40cee7751f7ed976217077436e15c..5b06a43febe4f17636a6835586b65c53ca22838f 100644
--- a/doc/dihedral_opls.html
+++ b/doc/dihedral_opls.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_quadratic.html b/doc/dihedral_quadratic.html
index cf50d5f171e515a2ae7b8e0d8732cc09f98be805..a0aa1983f17cef31b8bd0ed7bf14090f3ce272ac 100644
--- a/doc/dihedral_quadratic.html
+++ b/doc/dihedral_quadratic.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_style.html b/doc/dihedral_style.html
index ecdf7c1b8cb5d9ef8b8d85dd92e67d155d791e1a..ccebd790214cb45bd479d78428604aa9dff1b8f2 100644
--- a/doc/dihedral_style.html
+++ b/doc/dihedral_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dihedral_table.html b/doc/dihedral_table.html
index 28c64e89ccc588d4b0b19c200055350ec84dc129..60b76ce3e6c83d6218134e7ce0162dbd7896c4d6 100644
--- a/doc/dihedral_table.html
+++ b/doc/dihedral_table.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dimension.html b/doc/dimension.html
index f4970856645e94e827149537b1e9671f4d8a6572..d3328a6b115c6eb1137373306af640396ba33ffa 100644
--- a/doc/dimension.html
+++ b/doc/dimension.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/displace_atoms.html b/doc/displace_atoms.html
index c004fe2e7345ae07bef18648fbc338d473399dcc..771ff84f3967c71c310dd52c31aa0348261a78e6 100644
--- a/doc/displace_atoms.html
+++ b/doc/displace_atoms.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dump.html b/doc/dump.html
index 2dc203748783f31f731bb7fd277c42e7b7d9fdcb..c1129a588ddb14962a246d3611f4480a4723da6f 100644
--- a/doc/dump.html
+++ b/doc/dump.html
@@ -71,22 +71,22 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dump_image.html b/doc/dump_image.html
index 18e64ab9b822568f7db344f6ef87158a2ec26ed4..650449bb5e16796c8c4bb9d4a68f9db7ab820e1b 100644
--- a/doc/dump_image.html
+++ b/doc/dump_image.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
@@ -219,7 +217,7 @@ 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-77118bd7-5459-47d2-af9b-88f09a243fa2"
+<DIV ALIGN=center><a data-lightbox="group-e192ca54-87f4-4dc9-beb3-6c451b74e02e"
href="_images/dump1.jpg"
class=""
title=""
@@ -229,7 +227,7 @@ to see the full-size images:</p>
width="25%"
height="auto"
alt=""/>
- </a><a data-lightbox="group-bd38bd84-9e94-4e9c-b0ac-5f9c8b1e28e0"
+ </a><a data-lightbox="group-11e5599d-f653-4fdc-b86a-e4354aea5ceb"
href="_images/dump2.jpg"
class=""
title=""
diff --git a/doc/dump_modify.html b/doc/dump_modify.html
index bcb61e559cb29df48245cba78c5792bc8d0477bf..f54640f0f0a6c36801ca890f1e3e01285e630e8a 100644
--- a/doc/dump_modify.html
+++ b/doc/dump_modify.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/dump_molfile.html b/doc/dump_molfile.html
index c8eb0e1a1f3aa4bf53fe5eb5ec362cb0ca118db2..4d18f8d20873e4f9b11f81adaff875b56e96d7af 100644
--- a/doc/dump_molfile.html
+++ b/doc/dump_molfile.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/echo.html b/doc/echo.html
index 091c391294bdfb3d7a096fc6d0b9f3e75a9046da..2e2d8c0b1c94e3dda275f92aef72f378dc97f2d3 100644
--- a/doc/echo.html
+++ b/doc/echo.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix.html b/doc/fix.html
index 5044f14a25d338eb8302f3829406b7aa8cc7845d..3c2e83b594316b039758dcc40d4ea2e268d2fef8 100644
--- a/doc/fix.html
+++ b/doc/fix.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
@@ -281,7 +277,7 @@ in the fix section of <a class="reference internal" href="Section_commands.html#
<li><a class="reference internal" href="fix_append_atoms.html"><em>append/atoms</em></a> - append atoms to a running simulation</li>
<li><a class="reference internal" href="fix_aveforce.html"><em>aveforce</em></a> - add an averaged force to each atom</li>
<li><a class="reference internal" href="fix_ave_atom.html"><em>ave/atom</em></a> - compute per-atom time-averaged quantities</li>
-<li><code class="xref doc docutils literal"><span class="pre">ave/correlate</span></code> - compute/output time correlations</li>
+<li><a class="reference internal" href="fix_ave_correlate.html"><em>ave/correlate</em></a> - compute/output time correlations</li>
<li><a class="reference internal" href="fix_ave_histo.html"><em>ave/histo</em></a> - compute/output time-averaged histograms</li>
<li><a class="reference internal" href="fix_ave_spatial.html"><em>ave/spatial</em></a> - compute/output time-averaged per-atom quantities by layer</li>
<li><a class="reference internal" href="fix_ave_time.html"><em>ave/time</em></a> - compute/output global time-averaged quantities</li>
diff --git a/doc/fix_adapt.html b/doc/fix_adapt.html
index 455eb8966fe1c92ec735485f0ddc46b05a091ed1..4ae37520dd3aa00270cf55c20e519c03d24fb8b2 100644
--- a/doc/fix_adapt.html
+++ b/doc/fix_adapt.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_adapt_fep.html b/doc/fix_adapt_fep.html
index 94587dba4eb77080bfd113538d2403e847536550..f4abbda5064064563fb453d607f33c523f4a41e1 100644
--- a/doc/fix_adapt_fep.html
+++ b/doc/fix_adapt_fep.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_addforce.html b/doc/fix_addforce.html
index 3f4c2078d5d4f15696531b6ea9653a03677e4367..dbf5fc889956c03a9c810009086af7b67b668248 100644
--- a/doc/fix_addforce.html
+++ b/doc/fix_addforce.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_addtorque.html b/doc/fix_addtorque.html
index 1dc50b17420093da296c2475e80f6e900e9f9f8b..5c1803aea150baf7427e3282964eaff56769cdd6 100644
--- a/doc/fix_addtorque.html
+++ b/doc/fix_addtorque.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_append_atoms.html b/doc/fix_append_atoms.html
index 64aaafa6acdc616d9c482b3c174f8a4954e0208e..badfbfc571bdcdd8af1c51b69076a3745f90309b 100644
--- a/doc/fix_append_atoms.html
+++ b/doc/fix_append_atoms.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_atc.html b/doc/fix_atc.html
index d9df172ce3df9383ba3c50724865be1332013beb..c5085c13efdf9208dad5e4752d13d9acfc3e92f1 100644
--- a/doc/fix_atc.html
+++ b/doc/fix_atc.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_atom_swap.html b/doc/fix_atom_swap.html
index 981bb3ff25b4d71d19f37fceecf49d86025e98ae..0999c92a54b204da48e627fe7028fc92b3b66df0 100644
--- a/doc/fix_atom_swap.html
+++ b/doc/fix_atom_swap.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ave_atom.html b/doc/fix_ave_atom.html
index dc2378438028d6ff801524a4dadeeb2f2309ae71..73f3d55ffdcfae6ba20eec74e6c2c6d307f9470c 100644
--- a/doc/fix_ave_atom.html
+++ b/doc/fix_ave_atom.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ave_chunk.html b/doc/fix_ave_chunk.html
index 5e9cfbaa205906e4fc115dbac7450336a91ef53b..0088d85a89378288090275af95aab0bfa1f46749 100644
--- a/doc/fix_ave_chunk.html
+++ b/doc/fix_ave_chunk.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ave_correlate.html b/doc/fix_ave_correlate.html
index 19cce7b1d6ef36a33969c45b6b581361ba2359cf..50ad652a5eb9acfbb051195f90e495e20323afa1 100644
--- a/doc/fix_ave_correlate.html
+++ b/doc/fix_ave_correlate.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ave_histo.html b/doc/fix_ave_histo.html
index 27b334822d9ceb926271b6e598c4b1457f1f1a9c..73446ec01bff3dc80508f29e86ac07e9e8cea6e8 100644
--- a/doc/fix_ave_histo.html
+++ b/doc/fix_ave_histo.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html
index acabe52d8b4f2fda54ea6a948d3de4261d34843a..23cbd4178fd00d453b5414cfe8265d7e0d48063f 100644
--- a/doc/fix_ave_spatial.html
+++ b/doc/fix_ave_spatial.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ave_spatial_sphere.html b/doc/fix_ave_spatial_sphere.html
index f855aad247a7a118e00cc48365437051f6919345..827005c306dcad254ba01536b046b00f672b39bc 100644
--- a/doc/fix_ave_spatial_sphere.html
+++ b/doc/fix_ave_spatial_sphere.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html
index 4aaea3d3365e280f3b306592ee64cc3aed05ead9..46d6b9d01aafc3c042ddf1b45b5c2b3e74fd2420 100644
--- a/doc/fix_ave_time.html
+++ b/doc/fix_ave_time.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_aveforce.html b/doc/fix_aveforce.html
index e094f9f96c946d836a8bdbc7b90a8fe0637d91fb..a708c226623f696b1fe041fb465cae069e0555f2 100644
--- a/doc/fix_aveforce.html
+++ b/doc/fix_aveforce.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_balance.html b/doc/fix_balance.html
index 83c18fd61220a721e450d9e71c8ab774c1ee89ad..75c7302c894e971e6c5c7967a1df209545a0918d 100644
--- a/doc/fix_balance.html
+++ b/doc/fix_balance.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
@@ -236,7 +233,7 @@ 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 “grid” method has been
applied.</p>
-<a data-lightbox="group-f1f3e3c4-616c-4aff-b122-61d27af7bfdc"
+<a data-lightbox="group-81a0acf3-2704-4e8c-999d-f210ed19b6fb"
href="_images/balance_uniform.jpg"
class=""
title=""
@@ -246,7 +243,7 @@ applied.</p>
width="25%"
height="auto"
alt=""/>
- </a><a data-lightbox="group-9b9c124b-90cb-488e-997c-fcb6507316fe"
+ </a><a data-lightbox="group-179f972b-1283-4638-9dc8-06f905f8ec46"
href="_images/balance_nonuniform.jpg"
class=""
title=""
@@ -256,7 +253,7 @@ applied.</p>
width="25%"
height="auto"
alt=""/>
- </a><a data-lightbox="group-4fa70153-35a0-4141-93dd-dc224b4644d6"
+ </a><a data-lightbox="group-7ab5baf9-d2bb-4e63-91dc-357beed9ae5b"
href="_images/balance_rcb.jpg"
class=""
title=""
diff --git a/doc/fix_bond_break.html b/doc/fix_bond_break.html
index 314eb761ad8b19867081a0084bf0295d7f6e6e23..a48bc3a9a482b376d74881972c0b6d0bed0db280 100644
--- a/doc/fix_bond_break.html
+++ b/doc/fix_bond_break.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_bond_create.html b/doc/fix_bond_create.html
index 786cf08d21a4ac44037309bce9736a30dd40d4ef..0538bf43db740083f7bf274f4b72b4039478e16c 100644
--- a/doc/fix_bond_create.html
+++ b/doc/fix_bond_create.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_bond_swap.html b/doc/fix_bond_swap.html
index 06647f5c77717c74c1ab39d368f7ee61f9e7b2d9..c6e6bd7d7a50f2dc6ab2a161fcecb4b03dee0ac1 100644
--- a/doc/fix_bond_swap.html
+++ b/doc/fix_bond_swap.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_box_relax.html b/doc/fix_box_relax.html
index f710e801480b486cbdcad26000e632d9ed6b3704..30888ac8ce58c4cb57b8045fcfeef51505646e23 100644
--- a/doc/fix_box_relax.html
+++ b/doc/fix_box_relax.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_colvars.html b/doc/fix_colvars.html
index 333d36ccdd0fd773a2e69d35ad18e29b405fa0a9..e04a5788f766818a8605e5fe99b51cda368baf79 100644
--- a/doc/fix_colvars.html
+++ b/doc/fix_colvars.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_deform.html b/doc/fix_deform.html
index 2818c948f5e94f2fb2d4d09f1de4846333841631..5035955d0b613a1b24889c1fa804b70f3589ee06 100644
--- a/doc/fix_deform.html
+++ b/doc/fix_deform.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_deposit.html b/doc/fix_deposit.html
index b8af4f375fbddb88196b66067d58b5638f956cda..08b4f683775524709b0c5c410c987169a9a1a0ea 100644
--- a/doc/fix_deposit.html
+++ b/doc/fix_deposit.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_drag.html b/doc/fix_drag.html
index 57890192f0b8f09aac894279830c32ea2e3900bf..c055bab1d9c334241f1c29032bedac7b457f56cb 100644
--- a/doc/fix_drag.html
+++ b/doc/fix_drag.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_drude.html b/doc/fix_drude.html
index 3abf31119a51e38c6461b7980bda3aaa6481d545..ee7b8527e8601b2b46727f559f577cd95985c430 100644
--- a/doc/fix_drude.html
+++ b/doc/fix_drude.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_drude_transform.html b/doc/fix_drude_transform.html
index 6ada4fbd1dd16ced10c4ee9883dd5a8b63fb165c..139279042a7692f04437a464d9aeff8d23f734d2 100644
--- a/doc/fix_drude_transform.html
+++ b/doc/fix_drude_transform.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_dt_reset.html b/doc/fix_dt_reset.html
index 10201fb1d50c4bf61969ae75d0163e36a40959c4..7af002d0c566167122c594f72af2454eb84f6ff9 100644
--- a/doc/fix_dt_reset.html
+++ b/doc/fix_dt_reset.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_efield.html b/doc/fix_efield.html
index c6ad4d3ece0acef53b9feb6a13b715ac16770234..072d0dcec7653d705d63736225eecc663e89121c 100644
--- a/doc/fix_efield.html
+++ b/doc/fix_efield.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_enforce2d.html b/doc/fix_enforce2d.html
index d9fb418975347ed7a1d287819479a702799b7347..ac8118a8e89ea0e1cd434bf5c2eb604fa9312ef7 100644
--- a/doc/fix_enforce2d.html
+++ b/doc/fix_enforce2d.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_evaporate.html b/doc/fix_evaporate.html
index 766c3a4458fff76d6f1345a76560e54a276debe2..e29b74d215f29c9d6b1a1fd95beae4af4ff49d9f 100644
--- a/doc/fix_evaporate.html
+++ b/doc/fix_evaporate.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_external.html b/doc/fix_external.html
index 6f14b235208b85359b3487d22ded0c06ebca815d..4c978321d885096b992ea38ce4d7694bca7ec6e2 100644
--- a/doc/fix_external.html
+++ b/doc/fix_external.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_freeze.html b/doc/fix_freeze.html
index 9455f6834208b2c0c16984d7192bb9cbaefe4f95..b28e8d4d05efd7497a6e0b1ac37fae24871bbda5 100644
--- a/doc/fix_freeze.html
+++ b/doc/fix_freeze.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_gcmc.html b/doc/fix_gcmc.html
index 90944af00bc11bd8eff8c85892198d286eb39fbe..a1701654498168b1d9b5917acaee125e9f65dd3d 100644
--- a/doc/fix_gcmc.html
+++ b/doc/fix_gcmc.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_gld.html b/doc/fix_gld.html
index 190643368f70739fe55e12eb81d9f287b1a2a411..b8b53209fd3ed2abe49d6155d9973068e5d9f5cf 100644
--- a/doc/fix_gld.html
+++ b/doc/fix_gld.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_gle.html b/doc/fix_gle.html
index 667b3433fe0da6b924b0740f563ee91930ddb2ce..8e2e3e0caa7b5d418e3aa2dd388d0d11dcf21345 100644
--- a/doc/fix_gle.html
+++ b/doc/fix_gle.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_gravity.html b/doc/fix_gravity.html
index 5f3510535723793ac3f0086b2ddc52bcc82b035b..e3e19daa9dce67d1e216f42156c06531561deb38 100644
--- a/doc/fix_gravity.html
+++ b/doc/fix_gravity.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_heat.html b/doc/fix_heat.html
index 33f26a521326eb47c760adae0c62762612962d27..80c07c39f05aa78d17826497c09a5bc9fe5fda2e 100644
--- a/doc/fix_heat.html
+++ b/doc/fix_heat.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_imd.html b/doc/fix_imd.html
index 4e8fd268f9c7394c0041e7f6f067def2b1cc1ad2..a3abc0f02c198f6c94057bbf42d4ee7fb16df2fe 100644
--- a/doc/fix_imd.html
+++ b/doc/fix_imd.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_indent.html b/doc/fix_indent.html
index 8da6806d320dccdea4bd6392356d462187824fa7..c4c9e1ef64a5e5e10594b88a5df5ef1b7e0a7739 100644
--- a/doc/fix_indent.html
+++ b/doc/fix_indent.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ipi.html b/doc/fix_ipi.html
index 5047039156e4a77e253db730f092ce19f324a482..2c03c2bdbf2eca0e403c857fadee74d7ebc2afb7 100644
--- a/doc/fix_ipi.html
+++ b/doc/fix_ipi.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html
index 649bbe7994f99d05fb29617cba6871cfa5c92830..062f755382cd0f8b0780993a2d35728b7dc89a59 100644
--- a/doc/fix_langevin.html
+++ b/doc/fix_langevin.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_langevin_drude.html b/doc/fix_langevin_drude.html
index 104474e7b0ea3f5728a4f03fb3263cc70ab3b49e..723c909894626c57857c746a8313bbb7ec85103e 100644
--- a/doc/fix_langevin_drude.html
+++ b/doc/fix_langevin_drude.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_langevin_eff.html b/doc/fix_langevin_eff.html
index 5cb16c4208ddfece6a8457fc266bf745e4f1eea6..918bfaee80fa8d2cbab58acee02954b7246adafa 100644
--- a/doc/fix_langevin_eff.html
+++ b/doc/fix_langevin_eff.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_lb_fluid.html b/doc/fix_lb_fluid.html
index b6fcbe1ab5a579e723ca7194865305b79949a00b..f21ec76d2283e4a84e18de71c0291fa0b6666a88 100644
--- a/doc/fix_lb_fluid.html
+++ b/doc/fix_lb_fluid.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_lb_momentum.html b/doc/fix_lb_momentum.html
index 699c068b1d30ea12ebef03948ac41c77ae6375a0..e39c69f3dc39d15c62e4d768d0ac30578b4f2df3 100644
--- a/doc/fix_lb_momentum.html
+++ b/doc/fix_lb_momentum.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_lb_pc.html b/doc/fix_lb_pc.html
index e90c0181ff74fd5c15fd9e0a6e2fe967fcfc4365..c4f35267501da144dcb42d236b1269f5d5591700 100644
--- a/doc/fix_lb_pc.html
+++ b/doc/fix_lb_pc.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_lb_rigid_pc_sphere.html b/doc/fix_lb_rigid_pc_sphere.html
index 2cbc0e2b2c2f86b6ec4b490e0f4f9e23b6493db4..0cae51b22bfca1b15f4a412616f768d94f4f406b 100644
--- a/doc/fix_lb_rigid_pc_sphere.html
+++ b/doc/fix_lb_rigid_pc_sphere.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_lb_viscous.html b/doc/fix_lb_viscous.html
index 7d519090b0608dba95ec76bc276128daec7b834b..af33ffedc872b05872de5ade94d5ecdb6648ae64 100644
--- a/doc/fix_lb_viscous.html
+++ b/doc/fix_lb_viscous.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_lineforce.html b/doc/fix_lineforce.html
index 4c539d324344ace67bcd3ba3c57766c0bdb0adf4..a8d043e227fbea6f1f404b56f7d78998eac8209b 100644
--- a/doc/fix_lineforce.html
+++ b/doc/fix_lineforce.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_meso.html b/doc/fix_meso.html
index bd437891f58a7cae907403498ffe40942ddfe290..90c82b8ad59174e1b072638ad4627b392fecd450 100644
--- a/doc/fix_meso.html
+++ b/doc/fix_meso.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_meso_stationary.html b/doc/fix_meso_stationary.html
index 7c3e201a9903d65c15c8c665eae5cb0c258846fb..9e7384ebdf02a06bc8b85b9660e4417c7290bf45 100644
--- a/doc/fix_meso_stationary.html
+++ b/doc/fix_meso_stationary.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_modify.html b/doc/fix_modify.html
index f82a24493be449ba3ee247493afc0401dbd8bedb..adedf9ee4c419147d0e280c07a715eee6f0c484a 100644
--- a/doc/fix_modify.html
+++ b/doc/fix_modify.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_momentum.html b/doc/fix_momentum.html
index da69360c464101383e38f26c4251466ad8e5c691..2f6b853c6da886805754ec94e574e9bd40b44de0 100644
--- a/doc/fix_momentum.html
+++ b/doc/fix_momentum.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_move.html b/doc/fix_move.html
index 773f8cbfa44d6c3e1d15fd092e3e61a663ce3a43..7954158a9a4875ca9fe22432f475c6c87d1aacbf 100644
--- a/doc/fix_move.html
+++ b/doc/fix_move.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_msst.html b/doc/fix_msst.html
index 781c59c57e6dbff31cef668a4f7bc866de384dee..42adfa43823e4746331dd0fc4146c34668623c01 100644
--- a/doc/fix_msst.html
+++ b/doc/fix_msst.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_neb.html b/doc/fix_neb.html
index efdc5e54773615a573aa46c6fbeffa8392b4c54a..f436b56b8fdb053519b70a775b947d9ed39ee400 100644
--- a/doc/fix_neb.html
+++ b/doc/fix_neb.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nh.html b/doc/fix_nh.html
index 34a7b0c506ac281da4abe630d31481310770d1fc..ff7089948188e0c2b4c46fda7c999a955fc403d5 100644
--- a/doc/fix_nh.html
+++ b/doc/fix_nh.html
@@ -71,22 +71,27 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nh_eff.html b/doc/fix_nh_eff.html
index b96f76f36048e53248306c87f24a2410262eee27..7d7fa2a0306c0b9560a0bec21bd5bf984848fd1c 100644
--- a/doc/fix_nh_eff.html
+++ b/doc/fix_nh_eff.html
@@ -71,22 +71,22 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nph_asphere.html b/doc/fix_nph_asphere.html
index b39c1b8ecf9fb23d458acf16a12d0aacfbd9ceca..606de618366864178ccf71c5ebad7c79548041a3 100644
--- a/doc/fix_nph_asphere.html
+++ b/doc/fix_nph_asphere.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nph_sphere.html b/doc/fix_nph_sphere.html
index 0a03a408c53848635ef7d6f2b2fd4fb69faecf35..12ff1372c6f58ade3aab39678b95b399e493370c 100644
--- a/doc/fix_nph_sphere.html
+++ b/doc/fix_nph_sphere.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nphug.html b/doc/fix_nphug.html
index c61bfeba96b5e575026c84b064077ff8b79fc4a1..231824aee2a7f396d7855d429557371990f9700e 100644
--- a/doc/fix_nphug.html
+++ b/doc/fix_nphug.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html
index 43af050032b5a4645a60e921f204e94b232737cb..e263467b6f7d8092d67f6cd30f5fe9a0ebd949b8 100644
--- a/doc/fix_npt_asphere.html
+++ b/doc/fix_npt_asphere.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_npt_sphere.html b/doc/fix_npt_sphere.html
index 6aef8fd8e50a666f3d67f825167795d6ec86c484..cf2758cf6ba2884b012cd696be39fb78b46a6fad 100644
--- a/doc/fix_npt_sphere.html
+++ b/doc/fix_npt_sphere.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nve.html b/doc/fix_nve.html
index bee222996472720eae6cbb25ddf7f6b83534bcf2..aef04fef0cd2043ece9a1a8d4f2d218e3f95bfd5 100644
--- a/doc/fix_nve.html
+++ b/doc/fix_nve.html
@@ -71,22 +71,22 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nve_asphere.html b/doc/fix_nve_asphere.html
index 756ead116e091e0e1ac9e2fbcc30de1c7c13b7b6..d817e0db567a200f1570e37b8d88029be5b16e93 100644
--- a/doc/fix_nve_asphere.html
+++ b/doc/fix_nve_asphere.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nve_asphere_noforce.html b/doc/fix_nve_asphere_noforce.html
index adb934dd163eb576ff033d8e94c4305b70b67f00..fe905ae567f5fe3dccbf945f5edd1c2a706e0d62 100644
--- a/doc/fix_nve_asphere_noforce.html
+++ b/doc/fix_nve_asphere_noforce.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nve_body.html b/doc/fix_nve_body.html
index 00641b9448d832627b3c6b67580bab09aad3fc4e..d6ca4f13dd82098dce70d06e28cd4ce6d7aa6608 100644
--- a/doc/fix_nve_body.html
+++ b/doc/fix_nve_body.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nve_eff.html b/doc/fix_nve_eff.html
index 02b5e7e85c0f7298d9e71c823f693eefbaae747b..5dc8819a529434e68dfd3ab498f557440d1813e1 100644
--- a/doc/fix_nve_eff.html
+++ b/doc/fix_nve_eff.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nve_limit.html b/doc/fix_nve_limit.html
index a3e6a64d84c1f0b2e15c207be639ab0251c5de8a..fcd3ca44a339984a128f0645a9c7b38b56ec09fd 100644
--- a/doc/fix_nve_limit.html
+++ b/doc/fix_nve_limit.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nve_line.html b/doc/fix_nve_line.html
index 870cbfab9c4b7661d501dabe95d3dc69acc4e789..3168d8095b7d915cb396cb8e8b6a1a99692d86d5 100644
--- a/doc/fix_nve_line.html
+++ b/doc/fix_nve_line.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nve_noforce.html b/doc/fix_nve_noforce.html
index b2c89494e620df478d72c17ff175b904453f115c..d1105db138062bf8c3692a6b5fc9c6c2e422260c 100644
--- a/doc/fix_nve_noforce.html
+++ b/doc/fix_nve_noforce.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nve_sphere.html b/doc/fix_nve_sphere.html
index 8683040c84e4ab0781dc558b2ba8d584c1bdf3a3..e18ad03e5610f6833128331b4c5d9f98dda050e1 100644
--- a/doc/fix_nve_sphere.html
+++ b/doc/fix_nve_sphere.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nve_tri.html b/doc/fix_nve_tri.html
index 2d5adc789c2184645cdc352c0a180dfa39f673c9..bc7c44a3972e3952f9e5a0f87908328fe11cef4c 100644
--- a/doc/fix_nve_tri.html
+++ b/doc/fix_nve_tri.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html
index 922d4e85d9f978cc3a3beab0eb2508400bae86da..a1d7a3e675fb1e795f15810a7dbdbc7bc7bafbcf 100644
--- a/doc/fix_nvt_asphere.html
+++ b/doc/fix_nvt_asphere.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html
index 50dd7bfec906056cc43f6fd8b519927aeeca7709..425fee3a869fa994b0c4848123648d4a280f1bfb 100644
--- a/doc/fix_nvt_sllod.html
+++ b/doc/fix_nvt_sllod.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nvt_sllod_eff.html b/doc/fix_nvt_sllod_eff.html
index 84f036f16f8343889648d069598f6421d4e32d8a..fe5e07030ac20c73699505699015d45b72c10221 100644
--- a/doc/fix_nvt_sllod_eff.html
+++ b/doc/fix_nvt_sllod_eff.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_nvt_sphere.html b/doc/fix_nvt_sphere.html
index 9d5fc29112eeeeefbfb199b6552093a30925030b..91962139354d05ceefaa1612ae3eef40172a05c5 100644
--- a/doc/fix_nvt_sphere.html
+++ b/doc/fix_nvt_sphere.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_oneway.html b/doc/fix_oneway.html
index e175849311e291c20e80700d8bcd473511539955..4232bf7c6d6c7498aa248cfeb3948978bfb935cf 100644
--- a/doc/fix_oneway.html
+++ b/doc/fix_oneway.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_orient_fcc.html b/doc/fix_orient_fcc.html
index 514be39ac2a903d5222e05b35d07a47d94253771..a4a8d3db7d755cd264c0ba4f90acdd5a3c43804d 100644
--- a/doc/fix_orient_fcc.html
+++ b/doc/fix_orient_fcc.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_phonon.html b/doc/fix_phonon.html
index 1a03183d5424f790b4dd016f06edd0403f9b01d4..0c58f0b28d0eb6e04d563f8b26d2ac4920f2588a 100644
--- a/doc/fix_phonon.html
+++ b/doc/fix_phonon.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_pimd.html b/doc/fix_pimd.html
index 47d76b5f7dccebcaf838870b091ec733b663d832..7bd63c359859623e6ad0457459dcdadacae0f03b 100644
--- a/doc/fix_pimd.html
+++ b/doc/fix_pimd.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_planeforce.html b/doc/fix_planeforce.html
index d4b8163baaa96aa54636952411ec249638b8e479..21c2d771a142ea51a03344a78a2110e4c0812fc4 100644
--- a/doc/fix_planeforce.html
+++ b/doc/fix_planeforce.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_poems.html b/doc/fix_poems.html
index cd55db7b6295378e5740d64d7c96bd1374fef693..5141e7f72d02039bbaae3c38f34e6b55d15a62aa 100644
--- a/doc/fix_poems.html
+++ b/doc/fix_poems.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_pour.html b/doc/fix_pour.html
index d6871e48f31a061e4c1141ed41747629fcdb8685..48ea78d4030e88ff3bc8c4f6a1bff165c84847ca 100644
--- a/doc/fix_pour.html
+++ b/doc/fix_pour.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_press_berendsen.html b/doc/fix_press_berendsen.html
index 3e8a7db809d95df89f3ea8d1eae1e6609ecb17d3..9c1565bef3ea024b703840da61d6e02a92ae8589 100644
--- a/doc/fix_press_berendsen.html
+++ b/doc/fix_press_berendsen.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_print.html b/doc/fix_print.html
index 252f42dc9d3e98799271b47a5a87afdc5f1b5cd6..35bc9990b5dbd9bb5f25ed235edbfce8510b0a5c 100644
--- a/doc/fix_print.html
+++ b/doc/fix_print.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_property_atom.html b/doc/fix_property_atom.html
index 5d3cd62f7bbc0398f4703b956b419d0d8069df8d..6e372bbd649f78857d413eb4a276e549ce84130c 100644
--- a/doc/fix_property_atom.html
+++ b/doc/fix_property_atom.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_qbmsst.html b/doc/fix_qbmsst.html
index 73ac2ccc12aacc5de3ccaf17501b19e0b8980df3..2c16c028a717e243bdc9161250e568b100b7590b 100644
--- a/doc/fix_qbmsst.html
+++ b/doc/fix_qbmsst.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_qeq.html b/doc/fix_qeq.html
index 1f792863e9eab45d2f1528fc3c2b7c1ecf01637a..582f75075a66be163afed5a8a5d0e137839c6eff 100644
--- a/doc/fix_qeq.html
+++ b/doc/fix_qeq.html
@@ -71,22 +71,22 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_qeq_comb.html b/doc/fix_qeq_comb.html
index ecd61640a2d2eb472e5361a9191cb104bf873f1b..4f425269b504a9fcedecbf61af87b8999f465410 100644
--- a/doc/fix_qeq_comb.html
+++ b/doc/fix_qeq_comb.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_qeq_reax.html b/doc/fix_qeq_reax.html
index ecb5eebb512b3684d3a7622f2e2165cfc6451654..17b17950d2ce5a3f1d20d1c73c2527933f52f344 100644
--- a/doc/fix_qeq_reax.html
+++ b/doc/fix_qeq_reax.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_qmmm.html b/doc/fix_qmmm.html
index 3d09f9e145f78ecc3e2e635a90db15bafd581c45..9bd2e070f327425b3d2ddbfb6267eca475628637 100644
--- a/doc/fix_qmmm.html
+++ b/doc/fix_qmmm.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_qtb.html b/doc/fix_qtb.html
index 28f5312012aa32e94036893b1bf45383edee10e1..45e751e2b0d080a6e7c5c03cd280089d77847704 100644
--- a/doc/fix_qtb.html
+++ b/doc/fix_qtb.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_reax_bonds.html b/doc/fix_reax_bonds.html
index 247de5a64b35523c80440a8395b42da82103ceda..696887119f737bad4ee245d8ebe3e889fa856cfa 100644
--- a/doc/fix_reax_bonds.html
+++ b/doc/fix_reax_bonds.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_reaxc_species.html b/doc/fix_reaxc_species.html
index 12c4b5bcea3e220e0bac74933c1e600adb2a5f60..8441aa98b5dfa9837b39006300f881f164b35855 100644
--- a/doc/fix_reaxc_species.html
+++ b/doc/fix_reaxc_species.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_recenter.html b/doc/fix_recenter.html
index dddacbefb58f4838728494167c232eb5df50f171..755e24148f46d36a0b954dfed5a99aee0ab74c41 100644
--- a/doc/fix_recenter.html
+++ b/doc/fix_recenter.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_restrain.html b/doc/fix_restrain.html
index 98bac49737d59200ba3c7a02d420efb7e757b158..2f00a086632819a7b872c4b95cb542500219cf1f 100644
--- a/doc/fix_restrain.html
+++ b/doc/fix_restrain.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html
index 9976d3ceed8dc4a995a52ae7ef29cb225802fcbc..26e567f43c95f1a5d7ada8ee7569b81cae582f93 100644
--- a/doc/fix_rigid.html
+++ b/doc/fix_rigid.html
@@ -71,22 +71,29 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_saed_vtk.html b/doc/fix_saed_vtk.html
index f9e3cfb3fed21dbe0c324c88c88eec384106c325..6a78fb0be3156e0448056b272fff59c6b1cd73bc 100644
--- a/doc/fix_saed_vtk.html
+++ b/doc/fix_saed_vtk.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_setforce.html b/doc/fix_setforce.html
index 1ef87110683bcf8f48cca42523564ed54196e7be..032b9f3e2563f24bcb867b5cf29bfebf5cc691e0 100644
--- a/doc/fix_setforce.html
+++ b/doc/fix_setforce.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_shake.html b/doc/fix_shake.html
index 026f47cfb3897632fb4b76aba30801d374c378b6..01069fd272412926f43aa2b3afa1435b3c663076 100644
--- a/doc/fix_shake.html
+++ b/doc/fix_shake.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_smd.html b/doc/fix_smd.html
index 57519d8fd69acc522fc4db6b8a4a9a4c4814ffe8..fd4fe5cc0f9562141c7a2752a7a72cee60917f0d 100644
--- a/doc/fix_smd.html
+++ b/doc/fix_smd.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_spring.html b/doc/fix_spring.html
index 20dc15928a45e99e08d16aff89cc0ccb7a961ecf..5100e6c9830d23c1fba47e1d10b91a5892c7b9da 100644
--- a/doc/fix_spring.html
+++ b/doc/fix_spring.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_spring_rg.html b/doc/fix_spring_rg.html
index bad950f2ac2675dba9f0ce11328db2b8ceef44f8..a008ff5baa35d4d1f649d8d5ee35de0bc8410a6b 100644
--- a/doc/fix_spring_rg.html
+++ b/doc/fix_spring_rg.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_spring_self.html b/doc/fix_spring_self.html
index 07eac846455ddc8282fc0439ab85fcf110534ebc..1bd8cb17e97dd9e0d0f26b0f6a5702a62bb8701c 100644
--- a/doc/fix_spring_self.html
+++ b/doc/fix_spring_self.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_srd.html b/doc/fix_srd.html
index 84c53b465b44efb21b254a5027ee7104d3e74283..f9a58197951d5dfa304a236724175aba4ccc7deb 100644
--- a/doc/fix_srd.html
+++ b/doc/fix_srd.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_store_force.html b/doc/fix_store_force.html
index d80f67e8fe2b3749c4ab5d3da5639ef081c4a959..8ed6c890cfd9d141a43b94534ffc309887517897 100644
--- a/doc/fix_store_force.html
+++ b/doc/fix_store_force.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_store_state.html b/doc/fix_store_state.html
index 9f2a78fb80b7d4d550e00e2b603b50fe53d4341d..8c0a3ec96904abeb1b31336b1952fda1bd36dec2 100644
--- a/doc/fix_store_state.html
+++ b/doc/fix_store_state.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_temp_berendsen.html b/doc/fix_temp_berendsen.html
index cdd52561e0fa9a796498912d05d9df795a47eafb..1e06f6c94860db3eab67dcedfcf4f6859732f442 100644
--- a/doc/fix_temp_berendsen.html
+++ b/doc/fix_temp_berendsen.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_temp_csvr.html b/doc/fix_temp_csvr.html
index 2d37d3d7aa17cc4137f41eb1ec0d6ac4d8007225..700b0159f414e416864ff55124e2e17ad9961eaa 100644
--- a/doc/fix_temp_csvr.html
+++ b/doc/fix_temp_csvr.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html
index 259276c30b8fd1a0169d1a160f4da1385572639b..2d1d3d10c96e7eaa3ba160dc170fe24ccc2ecbc6 100644
--- a/doc/fix_temp_rescale.html
+++ b/doc/fix_temp_rescale.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_temp_rescale_eff.html b/doc/fix_temp_rescale_eff.html
index 02815095421cfa8a01779866fa49b5932dc54c50..c230e0b8e8e37adcb9dde10d6b3aac3ace647a21 100644
--- a/doc/fix_temp_rescale_eff.html
+++ b/doc/fix_temp_rescale_eff.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_tfmc.html b/doc/fix_tfmc.html
index 86f223316e8d9133ba1e492d2dde684e9038d710..7eee4def77d92d7f7b8f00b76654c405a646a97b 100644
--- a/doc/fix_tfmc.html
+++ b/doc/fix_tfmc.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_thermal_conductivity.html b/doc/fix_thermal_conductivity.html
index 636bb82b7eba48f3f4596c283d765339d0e3e452..0fcd4c28cc347583ae718e5b73dd9aed4228532a 100644
--- a/doc/fix_thermal_conductivity.html
+++ b/doc/fix_thermal_conductivity.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ti_rs.html b/doc/fix_ti_rs.html
index ae47a6362ef3dae6651e9d9f7dce97551320965b..b409b19369fb96919d25fdb70e8d58ad08d9b27c 100644
--- a/doc/fix_ti_rs.html
+++ b/doc/fix_ti_rs.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ti_spring.html b/doc/fix_ti_spring.html
index 885226889ecec70071968e7f37c64149b215d4c5..5945f56a2a5c97e6ec89688b711fa1e69ddcea92 100644
--- a/doc/fix_ti_spring.html
+++ b/doc/fix_ti_spring.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_tmd.html b/doc/fix_tmd.html
index 935f3d8ab5e5994c2a128b38975f1c7dda6a8120..eb43e52bf739ffc6135616b567293025745b4a9a 100644
--- a/doc/fix_tmd.html
+++ b/doc/fix_tmd.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_ttm.html b/doc/fix_ttm.html
index dd1a33b5913170d94d9beb227b7cb35ac2378155..09d3cf7eb1b83c34e5882c323bddd83f2a59170b 100644
--- a/doc/fix_ttm.html
+++ b/doc/fix_ttm.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_tune_kspace.html b/doc/fix_tune_kspace.html
index 945fd9164a6fcb888c340ec300b67555a82a9917..a26614ffa0c8db78891fe0d27b393b503fdcb288 100644
--- a/doc/fix_tune_kspace.html
+++ b/doc/fix_tune_kspace.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_vector.html b/doc/fix_vector.html
index 32fe399cafc3b1760fa3ebf4ed395493616939d3..e68be69a945d0117e1128275b08f254c030dc840 100644
--- a/doc/fix_vector.html
+++ b/doc/fix_vector.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_viscosity.html b/doc/fix_viscosity.html
index 3abae3157c6372000f5497a80e38ad49bcbab0d5..742e2ef2e08e819f192f8840a898020a0772d96b 100644
--- a/doc/fix_viscosity.html
+++ b/doc/fix_viscosity.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_viscous.html b/doc/fix_viscous.html
index 9c6326cebab598c529a4c8d9780a47f98aef7f0b..7efa77dffc8a2f90f4fa29870a8903455ce04aa9 100644
--- a/doc/fix_viscous.html
+++ b/doc/fix_viscous.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_wall.html b/doc/fix_wall.html
index 16d107b93f167faeec9b52dbfc4a0e4f0cae58d2..5e2aaafba6a7328455dbabdd35ae46b558d989ec 100644
--- a/doc/fix_wall.html
+++ b/doc/fix_wall.html
@@ -71,22 +71,24 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_wall_gran.html b/doc/fix_wall_gran.html
index d140f8fce323959b3348e72547878bfef8fdcd20..2005aa324c999024e12b8dc8d4100f4778de8bd7 100644
--- a/doc/fix_wall_gran.html
+++ b/doc/fix_wall_gran.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_wall_piston.html b/doc/fix_wall_piston.html
index 5e8bba762c8a41311e7748ff5445ab940167017d..92687bc77e4d4d32f0fbb7562d35b64e571b13b6 100644
--- a/doc/fix_wall_piston.html
+++ b/doc/fix_wall_piston.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_wall_reflect.html b/doc/fix_wall_reflect.html
index b8d30e3a1b89e0c23cefddf053fc0eb218a937b9..b0ca51c1b4bcaf3bc896d86c3bc90700458a95c2 100644
--- a/doc/fix_wall_reflect.html
+++ b/doc/fix_wall_reflect.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_wall_region.html b/doc/fix_wall_region.html
index 93d445d60da73055a260a71f305e1df1ff125d8b..d1b3c730944e67ed133886e02e6195105d5a4905 100644
--- a/doc/fix_wall_region.html
+++ b/doc/fix_wall_region.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/fix_wall_srd.html b/doc/fix_wall_srd.html
index 01439852e1879c6c90b977fa87d146e41973536a..15005bd163922031aa0152f815a5970237c139e8 100644
--- a/doc/fix_wall_srd.html
+++ b/doc/fix_wall_srd.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/genindex.html b/doc/genindex.html
index b92abe245ccaf87427bbfcacde9110e68da5bd71..66d31544a93663e23eca4b2be38ae0c7c874a832 100644
--- a/doc/genindex.html
+++ b/doc/genindex.html
@@ -72,22 +72,8 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
-</ul>
-
+ <!-- Local TOC -->
+ <div class="local-toc"></div>
</div>
diff --git a/doc/group.html b/doc/group.html
index 0f8e3a730d69923cedbad7f1c2484623844bdd8a..d11f3501042b4ac321c444883cf5901c5e910ae5 100644
--- a/doc/group.html
+++ b/doc/group.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/group2ndx.html b/doc/group2ndx.html
index c8a69575db4b7fd651df099d73d95b214f27ab2c..95036af6df502b88bdeff616f8d434ece91ab75c 100644
--- a/doc/group2ndx.html
+++ b/doc/group2ndx.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/if.html b/doc/if.html
index 10c5bff65610ea77dcacc1f85b271828effeb3f1..0d8ddeb3e0865b7e9f0f1d71736300f31daecf7d 100644
--- a/doc/if.html
+++ b/doc/if.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_class2.html b/doc/improper_class2.html
index 7dcb39292e6b4f3bfbc90988109f41085b3de9cf..4c56f1d40d89a1006a5add29202bbdefd5c93200 100644
--- a/doc/improper_class2.html
+++ b/doc/improper_class2.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_coeff.html b/doc/improper_coeff.html
index 8cd6103e7bb5c07f1b60c204a854096ed7752971..c195e35b88367d10f1aae8821e06de3db395b801 100644
--- a/doc/improper_coeff.html
+++ b/doc/improper_coeff.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_cossq.html b/doc/improper_cossq.html
index 44fe88923880826626c7ced51905e4bb56d8e39a..8cd3a326e18b547ff759c25b0c27b46d46ca23e2 100644
--- a/doc/improper_cossq.html
+++ b/doc/improper_cossq.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_cvff.html b/doc/improper_cvff.html
index bdf769fbb6a5703771335ab3723a5ac4a4461452..fadcf3dc6fe56410ce6e374f22dc4d50a31c19f6 100644
--- a/doc/improper_cvff.html
+++ b/doc/improper_cvff.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_fourier.html b/doc/improper_fourier.html
index 42d8d3a57a85fae2c19f65fbf5cd4b2af510fb25..8a6f5f72cbad99ff59982c5b9e1841eb0f57638c 100644
--- a/doc/improper_fourier.html
+++ b/doc/improper_fourier.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_harmonic.html b/doc/improper_harmonic.html
index 34f6158b3b9071f88bef524bd41915e5ab9b5f6d..5c22c5115d4e113e9e9c2a9bdb9b17ee04b364ba 100644
--- a/doc/improper_harmonic.html
+++ b/doc/improper_harmonic.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_hybrid.html b/doc/improper_hybrid.html
index 0c82ac2ddac753f980ace66ba81c67a594fe8812..b0d84d8c5ec083248706907e475457a094ddfdbb 100644
--- a/doc/improper_hybrid.html
+++ b/doc/improper_hybrid.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_none.html b/doc/improper_none.html
index f213204ce7e1114876387ea982cf587d09d0de97..8a53edf3115c2a0f3d5e58d8e3051e27e69f91cb 100644
--- a/doc/improper_none.html
+++ b/doc/improper_none.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_ring.html b/doc/improper_ring.html
index 243f2a53579ae8abcdf58c4a1d08e5d892c7f3cd..5f05d7d1e48878bce81b1434f9c273ab8ae8817e 100644
--- a/doc/improper_ring.html
+++ b/doc/improper_ring.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_style.html b/doc/improper_style.html
index dff01c8080f7981ac36d7aba96e1b4b4a1822982..1731bd46f66e5032b0dc627cea6a1ce356852f60 100644
--- a/doc/improper_style.html
+++ b/doc/improper_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/improper_umbrella.html b/doc/improper_umbrella.html
index f13730c84cea3ff5b6e77d5ef299e28c069a1824..84d5549173084f1acbdd76679557b995cd26a100 100644
--- a/doc/improper_umbrella.html
+++ b/doc/improper_umbrella.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/include.html b/doc/include.html
index 756f8b539c9c5eaf791ece3f4024d7397366e9b0..13809a6f32274ae6c8c9ad0b5d8c8fbac937cd72 100644
--- a/doc/include.html
+++ b/doc/include.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/info.html b/doc/info.html
index 85700766f80e53d3d7ae827323ac71701a623439..3ddf5d38cbb4ba2b1d058b925ad6a4f7dcc636d7 100644
--- a/doc/info.html
+++ b/doc/info.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/jump.html b/doc/jump.html
index 7e0e4fe2efb1f9eaa3e470e4c6a378a6bd76cb03..3800d625542c65823a62d2de137cb1d33294dbfa 100644
--- a/doc/jump.html
+++ b/doc/jump.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/kspace_modify.html b/doc/kspace_modify.html
index 4b754da8e207741778afa640aa10b0b2d833720b..48ea59182b1b2bd227218bf5479aa3424183d3d6 100644
--- a/doc/kspace_modify.html
+++ b/doc/kspace_modify.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/kspace_style.html b/doc/kspace_style.html
index 273b2812dbec8bb1b00db7db37c6c5f74eedc48b..7eb9617dcd2606facf03aafb3994593091a8c33b 100644
--- a/doc/kspace_style.html
+++ b/doc/kspace_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/label.html b/doc/label.html
index b1160fe291d074be360ff992fc41d2fa8c108be9..4ef27abcbb9e578b042f0d8e0784d81a58d311a4 100644
--- a/doc/label.html
+++ b/doc/label.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/lattice.html b/doc/lattice.html
index 1a123ad21e95ac9f0068eec3f3757bf39fd4f063..077f51e00a60e109728482c0fa548dfde7d1633a 100644
--- a/doc/lattice.html
+++ b/doc/lattice.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/log.html b/doc/log.html
index 7e016aa5658916d6c2214477a724977f9410338f..074b94723aaf2f990e34f79efd2a986e9e1c7df3 100644
--- a/doc/log.html
+++ b/doc/log.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/mass.html b/doc/mass.html
index 570f7ae2aa7772388659fa9a519fca262b337b21..49ada99059811321a1731dcc8f994bf5497cec50 100644
--- a/doc/mass.html
+++ b/doc/mass.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/min_modify.html b/doc/min_modify.html
index 740389337bfce11bc0360586ce9a39830474fd09..e99379bfa86a0eb8ab357e64789cbba52f759db1 100644
--- a/doc/min_modify.html
+++ b/doc/min_modify.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/min_style.html b/doc/min_style.html
index beb1b978ea53079796af1bff6a125ac2a1f57069..6aed250304cc18bbdc5a0351c0a9e6b46a19bcda 100644
--- a/doc/min_style.html
+++ b/doc/min_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/minimize.html b/doc/minimize.html
index 13d95d3a70d243b330949ffc1bd2f5fd6b68f66e..94704360613ca650321e908fed24fc3405fa079d 100644
--- a/doc/minimize.html
+++ b/doc/minimize.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/molecule.html b/doc/molecule.html
index 0dd45bf085eab443fe87e4b966a0d66ba25cad76..e8f733b9eebcdad9c9f63cc4ad10efaeceb5a697 100644
--- a/doc/molecule.html
+++ b/doc/molecule.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/neb.html b/doc/neb.html
index 21a206a4030c417c8c021573b628a537749daa30..2f2e54f01ba5a9a28d71ce83c1f8cd4194d32e1b 100644
--- a/doc/neb.html
+++ b/doc/neb.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
@@ -478,7 +474,7 @@ 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-c61430f0-d76f-4b5b-a9a4-4e7e7008db81"
+<a data-lightbox="group-6deb607f-8ab1-40f5-b335-d0d60b4fa35e"
href="_images/hop1.jpg"
class=""
title=""
@@ -488,7 +484,7 @@ image.</p>
width="25%"
height="auto"
alt=""/>
- </a><a data-lightbox="group-bf1830e1-0337-4532-a5de-0bb6bc176738"
+ </a><a data-lightbox="group-686d4075-8a0d-469a-a341-c26360cd0b3a"
href="_images/hop2.jpg"
class=""
title=""
diff --git a/doc/neigh_modify.html b/doc/neigh_modify.html
index f141cd370e53472ccfa2433f4e31d1cb5e8b2161..53dd717ad1a8427bbf58b668509fce108df37811 100644
--- a/doc/neigh_modify.html
+++ b/doc/neigh_modify.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/neighbor.html b/doc/neighbor.html
index 40617b49cb71d5e758b0befb4550909d7ab0d800..9c3770268a0cf0f39c47af038b10cb3774b1c724 100644
--- a/doc/neighbor.html
+++ b/doc/neighbor.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/newton.html b/doc/newton.html
index d6ee4e1721f09d519ec7e933b90585f2ec678d45..cad2e8520bd3e74f9eafacb3ab563e9f0b2c9c30 100644
--- a/doc/newton.html
+++ b/doc/newton.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/next.html b/doc/next.html
index ffa07feb2e35eb41eed6171ce173d64701c51ef2..94ebe5936382f6afa4da1e540b03c0e459b70ce0 100644
--- a/doc/next.html
+++ b/doc/next.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/package.html b/doc/package.html
index 9b174968651505e59c47f95ec38e2507cfeddb7a..28396de5f8449c733cc6c5ac0390b7f2f0c8c6b1 100644
--- a/doc/package.html
+++ b/doc/package.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_adp.html b/doc/pair_adp.html
index 2fb4753bbc36b33786524aaa07a2f7ba75227e76..89dd053a33f13fe690f4c3f7bddf7f46f974c577 100644
--- a/doc/pair_adp.html
+++ b/doc/pair_adp.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_airebo.html b/doc/pair_airebo.html
index b5d916ecee59a75bcd05fd922b04d0cb0ce483d0..61db7e7945e30aeb9e282b27969229462f8e6c83 100644
--- a/doc/pair_airebo.html
+++ b/doc/pair_airebo.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_awpmd.html b/doc/pair_awpmd.html
index b8d9a0122329b519a7bdcf513ee081ec98be8c08..45165c798c9b4c54f9f3333b07c8dd8aba3e3ac7 100644
--- a/doc/pair_awpmd.html
+++ b/doc/pair_awpmd.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_beck.html b/doc/pair_beck.html
index 2d9660fdc301c77ec9ad83aefac40e256c91104a..15ea86191941fec80eb4f9d24484ce3552f8a852 100644
--- a/doc/pair_beck.html
+++ b/doc/pair_beck.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_body.html b/doc/pair_body.html
index 7da16a7be5ed59fc2e8ba230467c74a1a74b8814..2fbcd28892f6271ced79b960960df5393eda1c01 100644
--- a/doc/pair_body.html
+++ b/doc/pair_body.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_bop.html b/doc/pair_bop.html
index 97e3db4e7bbb7b9559f3f6ed279e4cfc425c895e..934d7be4cff278496e59e7e8d51e6708d32edb5a 100644
--- a/doc/pair_bop.html
+++ b/doc/pair_bop.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_born.html b/doc/pair_born.html
index 1eff56e6adebcc43b69156cdcab8cee5f51fb2db..83f0214fe580ad7e7297ca62601078865499311e 100644
--- a/doc/pair_born.html
+++ b/doc/pair_born.html
@@ -71,22 +71,30 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_brownian.html b/doc/pair_brownian.html
index 9fde4e0c9558f9a57e999f8787016deb8abf2d5f..748071730fdaa10ba163e91c57bb31167910d520 100644
--- a/doc/pair_brownian.html
+++ b/doc/pair_brownian.html
@@ -71,22 +71,22 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_buck.html b/doc/pair_buck.html
index 760b1a77906aeb214915b6053b3581ffcd592546..013267873565e52256197e5ef86e808cd9813280 100644
--- a/doc/pair_buck.html
+++ b/doc/pair_buck.html
@@ -71,22 +71,35 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_buck_long.html b/doc/pair_buck_long.html
index 1eef4b69c5ef09ddffb3390e8da73755c75047d3..83ee3f3efb884fa78d4687d7bf8a9965ff57ce2c 100644
--- a/doc/pair_buck_long.html
+++ b/doc/pair_buck_long.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_charmm.html b/doc/pair_charmm.html
index 21d43c4e2da1267d18f7d4959be4672de95d2ee1..d99951405bd2f83723ff2c0107b6a400d3072f07 100644
--- a/doc/pair_charmm.html
+++ b/doc/pair_charmm.html
@@ -71,22 +71,31 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_class2.html b/doc/pair_class2.html
index 5651d3dce4993289a0278d827baffe97f9c49bc1..c99769c09b6036e2b54cff349a3225eb6109f5d5 100644
--- a/doc/pair_class2.html
+++ b/doc/pair_class2.html
@@ -71,22 +71,31 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html
index 660fa3859f1382cf767a3ef58e9c1e06c2961be2..a1bc88e6bb5239dcfd4d23cc18a6fc4426a908ec 100644
--- a/doc/pair_coeff.html
+++ b/doc/pair_coeff.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_colloid.html b/doc/pair_colloid.html
index e2b7d4fe039818b1d85b571808459a70445e28d2..52b3345e2bebb4e2fc32dc272070b95175b27493 100644
--- a/doc/pair_colloid.html
+++ b/doc/pair_colloid.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_comb.html b/doc/pair_comb.html
index 327773f672eb09bef80e2f3cc3f292b606595020..5ca071eb4ea3ea472f081f1da07c958b59c670c6 100644
--- a/doc/pair_comb.html
+++ b/doc/pair_comb.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_coul.html b/doc/pair_coul.html
index d84ac4ac20d3353171fa4d28b321f8d9e5c32978..50f38dcc0f709a3c0ba1443d5fcf770833fa3919 100644
--- a/doc/pair_coul.html
+++ b/doc/pair_coul.html
@@ -71,22 +71,44 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_coul_diel.html b/doc/pair_coul_diel.html
index 95ae37441b0125fab5a91cdb16b671aa2ff131a9..1056ce88fbbc6799ddb96d636b3ca5613c93cea1 100644
--- a/doc/pair_coul_diel.html
+++ b/doc/pair_coul_diel.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_cs.html b/doc/pair_cs.html
index f9ab8b530a105a5700d79577b49bccfd5a6c8ccb..2cd161ddccdc41c7236be83eeb46548d5bbf4c39 100644
--- a/doc/pair_cs.html
+++ b/doc/pair_cs.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_dipole.html b/doc/pair_dipole.html
index 81d40aa417d0e88deca179a0a858ad7b11f9ca40..2f267a7fc8f8af147f7f48bb31989d4ba297a174 100644
--- a/doc/pair_dipole.html
+++ b/doc/pair_dipole.html
@@ -71,22 +71,25 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_dpd.html b/doc/pair_dpd.html
index ac9ae019df521b89731c5cd3ebe12f0c1e57a587..2a9784458627d2851c09864978aacc02ac603602 100644
--- a/doc/pair_dpd.html
+++ b/doc/pair_dpd.html
@@ -71,22 +71,23 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_dsmc.html b/doc/pair_dsmc.html
index 054f1c86cadfa49bad169c12c1d3597abfd044b8..943afbc2590fe82cf5e752ca2706377a1b3c84c6 100644
--- a/doc/pair_dsmc.html
+++ b/doc/pair_dsmc.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_eam.html b/doc/pair_eam.html
index 6fe40119705f8d9875f7c8441a47283b4c571486..99be5bc173980e9b1655b3ee2a057d23514b04f6 100644
--- a/doc/pair_eam.html
+++ b/doc/pair_eam.html
@@ -71,22 +71,37 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_edip.html b/doc/pair_edip.html
index 10bec3af9466690694a20a953e44c77f9be98de3..750f878dd714e9e67f063e3a38c6d1f788b4b252 100644
--- a/doc/pair_edip.html
+++ b/doc/pair_edip.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_eff.html b/doc/pair_eff.html
index ef0b423f1b33e3894969e7f7965c819b630955dd..9616fa5cc16e153dab0aab1aec890892ea1d6c2c 100644
--- a/doc/pair_eff.html
+++ b/doc/pair_eff.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_eim.html b/doc/pair_eim.html
index 158e274552a9a15e6323674207799e4a78513907..0527a786aced6a59279e150756b20858c34bf1bf 100644
--- a/doc/pair_eim.html
+++ b/doc/pair_eim.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_gauss.html b/doc/pair_gauss.html
index edca55e39282e98c66a57a2e53f94a2faad95495..132a256ad69c2fa693ed8d8f4413aa8b356b0726 100644
--- a/doc/pair_gauss.html
+++ b/doc/pair_gauss.html
@@ -71,22 +71,22 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_gayberne.html b/doc/pair_gayberne.html
index b96b2cbaba8bd6ff87b7d4f858097416ab6dff92..7c7b6e963d6b8ceb67516bc99913dff4e446c742 100644
--- a/doc/pair_gayberne.html
+++ b/doc/pair_gayberne.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_gran.html b/doc/pair_gran.html
index 35367583abd2e2a22f559461dc5a1eb5056027db..249c5cb4474f450f664a2ad31d5df6e04cff553c 100644
--- a/doc/pair_gran.html
+++ b/doc/pair_gran.html
@@ -71,22 +71,24 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_gromacs.html b/doc/pair_gromacs.html
index cbb11c1e97185b9bd344adcfcee9c983dc83d67d..8fb4eaee588607f28bb4835f32dd0badd891a34b 100644
--- a/doc/pair_gromacs.html
+++ b/doc/pair_gromacs.html
@@ -71,22 +71,24 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_hbond_dreiding.html b/doc/pair_hbond_dreiding.html
index 8f074322f97fa19524d3dd9f26e8ed389f7abb2d..e392e5dd911a48d2bfbc94089a94d7b6c214edab 100644
--- a/doc/pair_hbond_dreiding.html
+++ b/doc/pair_hbond_dreiding.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_hybrid.html b/doc/pair_hybrid.html
index 4ffe8f91b5518ff770b241fd434a69844494448f..b2fe5ad2bd6a097e0fe0f147c37cbe7835da7dd8 100644
--- a/doc/pair_hybrid.html
+++ b/doc/pair_hybrid.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
@@ -305,14 +304,13 @@ attributes from several atom styles, due to using multiple pair
potentials.</p>
<hr class="docutils" />
<p>Different force fields (e.g. CHARMM vs AMBER) may have different rules
-for applying these factors to modulate the strength of pairwise
+for applying weightings that change the strength of pairwise
interactions bewteen pairs of atoms that are also 1-2, 1-3, and 1-4
-neighbors in the molecular bond topology. Specific
-<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> settings can be assigned to
-different pair hybrid sub-styles via the <a class="reference internal" href="pair_modify.html"><em>pair_modify special</em></a> special command, using its <em>pair</em> keyword
-and optional <em>special</em> argument. This allows multiple force fields to
-be used to a model a hybrid system. See the
-<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> doc page for details.</p>
+neighbors in the molecular bond topology, as normally set by the
+<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. Different weights can be
+assigned to different pair hybrid sub-styles via the <a class="reference internal" href="pair_modify.html"><em>pair_modify special</em></a> command. This allows multiple force fields
+to be used in a model of a hybrid system. See the
+<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> doc page for details.</p>
<p>The potential energy contribution to the overall system due to an
individual sub-style can be accessed and output via the <a class="reference internal" href="compute_pair.html"><em>compute pair</em></a> command.</p>
<hr class="docutils" />
diff --git a/doc/pair_kim.html b/doc/pair_kim.html
index febaadd865e614b4229d4a6ec90e31c1f45081af..461a4ce0afc792e8b89fc66824070d81e22aa7a4 100644
--- a/doc/pair_kim.html
+++ b/doc/pair_kim.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lcbop.html b/doc/pair_lcbop.html
index b4877c3866d6f4a1c12fc611299ace9f07ef7c1f..6bdd398d6f7cfa2f6cb94148a7fc73051e8359d2 100644
--- a/doc/pair_lcbop.html
+++ b/doc/pair_lcbop.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_line_lj.html b/doc/pair_line_lj.html
index fce51ba245988b880f77513811952c098fc53242..72ae33255600bd0ec3c7bc5748b6932c2206e4ba 100644
--- a/doc/pair_line_lj.html
+++ b/doc/pair_line_lj.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_list.html b/doc/pair_list.html
index 184b2cb1f5a2b76bbef4acacf5b5867ca6ace083..f0133f7e18f92f5acb97343c71fb6299f2f5d97a 100644
--- a/doc/pair_list.html
+++ b/doc/pair_list.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lj.html b/doc/pair_lj.html
index e9e911dc333cb5cca1aa13e710ba581186ae43b2..8f50bcebf38f8463d673a2a66ad2f1fd03e6e98b 100644
--- a/doc/pair_lj.html
+++ b/doc/pair_lj.html
@@ -71,22 +71,51 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lj96.html b/doc/pair_lj96.html
index 9abb31482f5cd40a9dd5b42aaef1d49b63e243af..74631de3135c9dff234e53ec4ed689410008c146 100644
--- a/doc/pair_lj96.html
+++ b/doc/pair_lj96.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lj_cubic.html b/doc/pair_lj_cubic.html
index 5f85a8114fef12305aebbbd30ecfae70196311d4..3b192b6906b46d208e98102b7bc4ecdfb078227a 100644
--- a/doc/pair_lj_cubic.html
+++ b/doc/pair_lj_cubic.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lj_expand.html b/doc/pair_lj_expand.html
index ce1f8af3bdf6f6a05741396c41b3d2259f7267aa..cc7c27ceb6bd431a599a617b8d6e550cdbaad5c1 100644
--- a/doc/pair_lj_expand.html
+++ b/doc/pair_lj_expand.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lj_long.html b/doc/pair_lj_long.html
index 4b712d2d5cbb91affd3bebd1f9447bce8de1fed9..123a367a63257a131789df233b5263a40f834e5d 100644
--- a/doc/pair_lj_long.html
+++ b/doc/pair_lj_long.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lj_sf.html b/doc/pair_lj_sf.html
index ead29c3165564091c5c9416136919460fb0c442b..d7a8ff42a1724dfa5fa1fef93fc3339a4ce59c7c 100644
--- a/doc/pair_lj_sf.html
+++ b/doc/pair_lj_sf.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lj_smooth.html b/doc/pair_lj_smooth.html
index 4a658275c32bd9be4a8d9aa904f2c96a49fa4eae..c71fb41915989e51d3fad679c5b30ee8dfd04a6b 100644
--- a/doc/pair_lj_smooth.html
+++ b/doc/pair_lj_smooth.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lj_smooth_linear.html b/doc/pair_lj_smooth_linear.html
index 07ec2ddebc97951e33e403333bbbef56b35e66c5..c43ed541273409f7b88fe17c68efcc709fb692b9 100644
--- a/doc/pair_lj_smooth_linear.html
+++ b/doc/pair_lj_smooth_linear.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lj_soft.html b/doc/pair_lj_soft.html
index cdf818c9550742e22d60d2b0347d23af5d05498e..720060469c896e80931c1029a2df7981189d61d2 100644
--- a/doc/pair_lj_soft.html
+++ b/doc/pair_lj_soft.html
@@ -71,22 +71,33 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lubricate.html b/doc/pair_lubricate.html
index ec44958b25bdfbaa11bff4e790b37e82958013d7..630df31f370fe3d5692aa06a4bf6b19243e4c7e0 100644
--- a/doc/pair_lubricate.html
+++ b/doc/pair_lubricate.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_lubricateU.html b/doc/pair_lubricateU.html
index 5638ed174bb6c756477d4b867b8ef6dbc8c40de4..15fe5342635f0674f21a7d4a6f7d2e321b3ade92 100644
--- a/doc/pair_lubricateU.html
+++ b/doc/pair_lubricateU.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_meam.html b/doc/pair_meam.html
index 47938aef132023d0cceb51cbd28c57b5572d78a5..168ac42d0505976f43687415252e4e5b01975035 100644
--- a/doc/pair_meam.html
+++ b/doc/pair_meam.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_meam_spline.html b/doc/pair_meam_spline.html
index a6eeeec9686b004aca77561d2feda056858d01f0..a72f7365e38c06b276cba3f643fe1b9dc65a8d27 100644
--- a/doc/pair_meam_spline.html
+++ b/doc/pair_meam_spline.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_meam_sw_spline.html b/doc/pair_meam_sw_spline.html
index fb28bed911730d96a3fa2e8d781886785e24bf57..d7f756eab2e71e1dd2e122d780ec8ebccfbab82a 100644
--- a/doc/pair_meam_sw_spline.html
+++ b/doc/pair_meam_sw_spline.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_mie.html b/doc/pair_mie.html
index 405c7cfb0cb03c36bda86777fb134487eee70244..f00f3b79515b5f28d3dc3d91bdab6da3b8594095 100644
--- a/doc/pair_mie.html
+++ b/doc/pair_mie.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_modify.html b/doc/pair_modify.html
index 3a6ce798eca64b8e6e4a2117c76fc1f63a20b5a1..bf1f8ac0ce2579c974329141c0eedc2e710ede36 100644
--- a/doc/pair_modify.html
+++ b/doc/pair_modify.html
@@ -71,22 +71,22 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+<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>
@@ -132,14 +132,14 @@
</div>
<ul class="simple">
<li>one or more keyword/value pairs may be listed</li>
-<li>keyword = <em>pair</em> or <em>shift</em> or <em>mix</em> or <em>table</em> or <em>table/disp</em> or <em>tabinner</em> or <em>tabinner/disp</em> or <em>tail</em> or <em>compute</em></li>
+<li>keyword = <em>pair</em> or <em>special</em> or <em>shift</em> or <em>mix</em> or <em>table</em> or <em>table/disp</em> or <em>tabinner</em> or <em>tabinner/disp</em> or <em>tail</em> or <em>compute</em></li>
</ul>
<pre class="literal-block">
<em>pair</em> values = sub-style N special which w1 wt2 wt3
sub-style = sub-style of <a class="reference internal" href="pair_hybrid.html"><em>pair hybrid</em></a>
N = which instance of sub-style (only if sub-style is used multiple times)
- special = optional if want to override <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> settings for sub-style
- which = <em>lj/coul</em> or <em>lj</em> or <em>coul</em>
+ <em>special</em> values = flavor w1 w2 w3
+ flavor = <em>lj/coul</em> or <em>lj</em> or <em>coul</em>
w1,w2,w3 = weights from 0.0 to 1.0 inclusive
<em>mix</em> value = <em>geometric</em> or <em>arithmetic</em> or <em>sixthpower</em>
<em>shift</em> value = <em>yes</em> or <em>no</em>
@@ -167,15 +167,23 @@ pair_modify table 12
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Modify the parameters of the currently defined pair style. Not all
parameters are relevant to all pair styles.</p>
-<p>If used, the <em>pair</em> keyword and its optional <em>special</em> arguments must
-appear first in the list of keywords. It can only be used with the
-<a class="reference internal" href="pair_hybrid.html"><em>hybrid and hybrid/overlay</em></a> pair styles and when used
-it means that all the following parameters will only be modified for
-the specified sub-style. If the <em>pair</em> keyword is not used, and the
-pair style is <em>hybrid</em> or <em>hybrid/overlay</em>, all the following
-parameters keywords will be applied to all sub-styles. A more detailed
-explanation of the <em>pair</em> keyword syntax, including its optional
-<em>special</em> argument are given below.</p>
+<p>If used, the <em>pair</em> keyword must appear first in the list of keywords.
+It can only be used with the <a class="reference internal" href="pair_hybrid.html"><em>hybrid and hybrid/overlay</em></a> pair styles. It means that all the
+following parameters will only be modified for the specified
+sub-style. If the sub-style is defined multiple times, then an
+additional numeric argument <em>N</em> must also be specified, which is a
+number from 1 to M where M is the number of times the sub-style was
+listed in the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> command. The extra
+number indicates which instance of the sub-style the remaining
+keywords will be applied to. Note that if the <em>pair</em> keyword is not
+used, and the pair style is <em>hybrid</em> or <em>hybrid/overlay</em>, then all the
+specified keywords will be applied to all sub-styles.</p>
+<p>If used, the <em>special</em> keyword must appear second in the list of
+keywords, and must follow the <em>pair</em> keyword. Like the <em>pair</em>
+keyword, it also can only be used with the <a class="reference internal" href="pair_hybrid.html"><em>hybrid and hybrid/overlay</em></a> pair styles. Its parameters are
+similar to the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command, and it
+overrides the special_bond settings for the specified sub-style. More
+details are given below.</p>
<p>The <em>mix</em> keyword affects pair coefficients for interactions between
atoms of type I and J, when I != J and the coefficients are not
explicitly set in the input script. Note that coefficients for I = J
@@ -308,45 +316,25 @@ a pair style will not work, because the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command requires a Kspace-compatible
pair style be defined.</p>
<hr class="docutils" />
-<div class="section" id="use-of-the-pair-keyword">
-<h3>Use of the pair keyword<a class="headerlink" href="#use-of-the-pair-keyword" title="Permalink to this headline">¶</a></h3>
-<p>If used, the <em>pair</em> keyword and its optional <em>special</em> arguments must
-appear first in the list of keywords. It can only be used with the
-<a class="reference internal" href="pair_hybrid.html"><em>hybrid and hybrid/overlay</em></a> pair styles and when used
-it means that all the following parameters will only be modified for
-the specified sub-style. If the <em>pair</em> keyword is not used, and the
-pair style is <em>hybrid</em> or <em>hybrid/overlay</em>, all the following
-parameters keywords will be applied to all sub-styles. A more detailed
-explanation of the <em>pair</em> keyword syntax, including its optional
-<em>special</em> argument are given below.</p>
-<p>As mentioned above, the <em>pair</em> keyword can only be used with the
-<a class="reference internal" href="pair_hybrid.html"><em>hybrid and hybrid/overlay</em></a> pair styles, and must
-come first in the list of keywords. If used, the subsequent keywords
-will only be applied to the specified sub-style. If the sub-style is
-defined multiple times, then an additional numeric argument <em>N</em> must
-also be specified, which is a number from 1 to M where M is the number
-of times the sub-style was listed in the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> command. The extra number indicates which
-instance of the sub-style the pair_modify keywords will be applied to.</p>
-<p>If the optional <em>special</em> argument is used, then the settings of the
-<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command are overridden for the
-specified sub-style. The <em>special</em> argument requires 4 additional
-arguments: <em>which</em> and w1,w2,w3. These are analogous to arguments in
-the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. The <em>which</em> argument
-can be <em>lj</em> to change the Lennard-Jones settings, <em>coul</em> to change the
-Coulombic settings, or <em>lj/coul</em> to change both to the same values.
-The w1,w2,w3 arguments are numeric weights from 0.0 to 1.0 inclusive,
-for the 1-2, 1-3, and 1-4 bond topology neighbors. For example, these
-commands</p>
+<div class="section" id="use-of-special-keyword">
+<h3>Use of <em>special</em> keyword<a class="headerlink" href="#use-of-special-keyword" title="Permalink to this headline">¶</a></h3>
+<p>The <em>special</em> keyword requires 4 values similar to those specified
+with the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command, <em>flavor</em> and
+w1,w2,w3. The <em>flavor</em> argument can be <em>lj</em> to change the
+Lennard-Jones settings, <em>coul</em> to change the Coulombic settings, or
+<em>lj/coul</em> to change both to the same set of 3 values. The w1,w2,w3
+values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
+1-3, and 1-4 bond topology neighbors. For example, these commands</p>
<div class="highlight-python"><div class="highlight"><pre>special_bonds lj/coul 0.0 0.0 0.1
-pair_hybrid lj/charmm/coul/charmm 8.0 10.0 lj/cut/coul/cut 10.0
-pair_modify pair lj/charmm/coul/charmm special lj/coul 0.0 0.0 0.0
-pair_modify pair lj/cut/coul/cut special lj 0.0 0.0 0.5
-pair_modify pair lj/cut/coul/cut special coul 0.0 0.0 0.8333
+pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
+pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.8333
</pre></div>
</div>
<p>show how to use both the CHARMM and AMBER force fields in a single
simulation. The first pair modify command sets the special bonds to
-CHARMM values (all 0.0). The latter 2 pair modify commands set the
+CHARMM values (all 0.0). The last 2 pair modify commands set the
standard AMBER values for LJ and Coulombic weights.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
@@ -354,13 +342,13 @@ standard AMBER values for LJ and Coulombic weights.</p>
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command affect the construction of
neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
exclude those pairs from the neighbor list entirely. Weights of 1.0
-store the neighbor with no weight flag applied. Neither of these
-neighbor effects can be changed by setting a sub-style weight to a
+store the neighbor with no weighting applied. The format of the
+neighbor list cannot be changed by setting a sub-style weight to a
non-zero or non-one value. Thus an error is generated if the new
-sub-style value is not 0.0 (or 1.0) and the global setting is 0.0 (or
+sub-style value is not 0.0 (or 1.0) when the global setting is 0.0 (or
1.0). Note that as in the example above, the global factor can simply
be set a value other than 0.0 or 1.0, then overridden by any of the
-sub-styles to a value that is 0.0 or 1.0.</p>
+sub-styles with a value that is 0.0 or 1.0.</p>
</div>
</div>
</div>
diff --git a/doc/pair_morse.html b/doc/pair_morse.html
index 1866f54b98ae884c6ab4d7a016ef60428110825a..110fa42dac52e1f3e44d1fcc94cd4c68350f5722 100644
--- a/doc/pair_morse.html
+++ b/doc/pair_morse.html
@@ -71,22 +71,22 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_nb3b_harmonic.html b/doc/pair_nb3b_harmonic.html
index eb89b4d3917e5d5060d55e6374f9ed60328ebf4f..b856434c942c7fe10c5acc71d700e592b08e38a7 100644
--- a/doc/pair_nb3b_harmonic.html
+++ b/doc/pair_nb3b_harmonic.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_nm.html b/doc/pair_nm.html
index 424edf7fe5dc869d83cad8cf91e6c490cd810f89..22dd832219420e07ba58917660908d5be9e02d21 100644
--- a/doc/pair_nm.html
+++ b/doc/pair_nm.html
@@ -71,22 +71,23 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_none.html b/doc/pair_none.html
index fb921365660a63fb110042e63b920502e11bd62b..b16cdd2dd6f6aaad099682d2ada7c729d5d99c53 100644
--- a/doc/pair_none.html
+++ b/doc/pair_none.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_peri.html b/doc/pair_peri.html
index a6b22224f9defb224f7b8aa9cf2225397c76a5dd..16fac92a601764f9999157f8f47de9b2283ec343 100644
--- a/doc/pair_peri.html
+++ b/doc/pair_peri.html
@@ -71,22 +71,23 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_polymorphic.html b/doc/pair_polymorphic.html
index 57178b236514ad714b11e96f6d0a4c83b9affc8d..4a16f9245c327b30c4ed27a205e5d6510f02b3c8 100644
--- a/doc/pair_polymorphic.html
+++ b/doc/pair_polymorphic.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_quip.html b/doc/pair_quip.html
index 5d2d31bbe86af30f1ce57da7f9f83f2ac381f662..a98091c11f7d8bec9a7feb9133d4a0766883eaa1 100644
--- a/doc/pair_quip.html
+++ b/doc/pair_quip.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_reax.html b/doc/pair_reax.html
index 6779e45695b599ca546f2519f31015be9e023868..558e147c547db8bf35ca64d0b409b2a9516fe5d5 100644
--- a/doc/pair_reax.html
+++ b/doc/pair_reax.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_reax_c.html b/doc/pair_reax_c.html
index 8192eaace6d5ed568e8434077e6a6a88d5626b1b..4d69c2c164916674afb22a39bed4df165aed7422 100644
--- a/doc/pair_reax_c.html
+++ b/doc/pair_reax_c.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_resquared.html b/doc/pair_resquared.html
index 3afc0b89c90ea465aff6dec73706eb081b4d8c8a..bc1132963f16eb4db5d6ab32a0491b626c91b763 100644
--- a/doc/pair_resquared.html
+++ b/doc/pair_resquared.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_sdk.html b/doc/pair_sdk.html
index a548ea27cceab4fa8ce7c646008d0c544f4a5d65..43d49e089e490cf4624c1afb7a69ae053bfbf080 100644
--- a/doc/pair_sdk.html
+++ b/doc/pair_sdk.html
@@ -71,22 +71,24 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_snap.html b/doc/pair_snap.html
index 0c52e49fc39f4e5ecf12e9a7590ad0ccc980a4b7..43bea1e499556c364137c4d4b05a04f1ac247a43 100644
--- a/doc/pair_snap.html
+++ b/doc/pair_snap.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_soft.html b/doc/pair_soft.html
index c404b0a08b336dc374803669243bd7546e6e0df7..74953e89385de0385f2824cb8a039d91cb0d1f4a 100644
--- a/doc/pair_soft.html
+++ b/doc/pair_soft.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_sph_heatconduction.html b/doc/pair_sph_heatconduction.html
index a76aedb23b85cc1398bb6ad66fec68fdf17c43ff..bec49ff69c4bb5030349488810304800c14e142d 100644
--- a/doc/pair_sph_heatconduction.html
+++ b/doc/pair_sph_heatconduction.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_sph_idealgas.html b/doc/pair_sph_idealgas.html
index f93bc5e24e7707357c071e999e6418fa193f1399..d72481f1287356550e3badb467cd2e43b25abefd 100644
--- a/doc/pair_sph_idealgas.html
+++ b/doc/pair_sph_idealgas.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_sph_lj.html b/doc/pair_sph_lj.html
index ea2a9a37fe255a930de2ff85d049e6ac0c24f931..e4a95c4dafe6c087824b3e5a2c68bc69446d56a7 100644
--- a/doc/pair_sph_lj.html
+++ b/doc/pair_sph_lj.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_sph_rhosum.html b/doc/pair_sph_rhosum.html
index 31325d3b534709f4659d6e2cd5dc6a7cf721a198..c1907f280880f6db0e120f2981a732f2c56852e8 100644
--- a/doc/pair_sph_rhosum.html
+++ b/doc/pair_sph_rhosum.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_sph_taitwater.html b/doc/pair_sph_taitwater.html
index f61dc8a2f64f2a55ba67234484a3299854cfef90..c0693b7bd627baaca63dc05cf95b0ac6b89d955a 100644
--- a/doc/pair_sph_taitwater.html
+++ b/doc/pair_sph_taitwater.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_sph_taitwater_morris.html b/doc/pair_sph_taitwater_morris.html
index 5838d769e06e2e91d4afb4861acabdf2dd1235c2..333a36cfde19e10e3c2808db463ed084ee854ed1 100644
--- a/doc/pair_sph_taitwater_morris.html
+++ b/doc/pair_sph_taitwater_morris.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_srp.html b/doc/pair_srp.html
index 5bd6ae4f2368a9bbd7c5b288fd4603041da753a4..dd4e0c8d60421472bb7f3f19cb093f101fdd6500 100644
--- a/doc/pair_srp.html
+++ b/doc/pair_srp.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_style.html b/doc/pair_style.html
index 5c609bb33fafb9db52bf0be33dc03a6ddaf8d347..a76441dd8521774ae9c7b42d3425584d60e08967 100644
--- a/doc/pair_style.html
+++ b/doc/pair_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_sw.html b/doc/pair_sw.html
index 4892074dd3d2e97d093f919723b535d73c24d16f..5d6e3b1302955a6b81c1e69cc7917ac4f2191fdf 100644
--- a/doc/pair_sw.html
+++ b/doc/pair_sw.html
@@ -71,22 +71,23 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_table.html b/doc/pair_table.html
index 7d2c20725e8fcc2f85bee1af3f688a4924f318f4..96a7cdc10cfb84f45a27b460adcbd062c8f6a86c 100644
--- a/doc/pair_table.html
+++ b/doc/pair_table.html
@@ -71,22 +71,21 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_tersoff.html b/doc/pair_tersoff.html
index 0ced9f121b58ce77b637fc74d9f257e7e03abe33..18ed260aacc1ce0e7169c8c022bade047a151a1e 100644
--- a/doc/pair_tersoff.html
+++ b/doc/pair_tersoff.html
@@ -71,22 +71,23 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_tersoff_mod.html b/doc/pair_tersoff_mod.html
index 1ef79de50be62b96e66b2c30f5e2f01a2c2b8d55..e629994211624f668c6db321312866d69417aa0e 100644
--- a/doc/pair_tersoff_mod.html
+++ b/doc/pair_tersoff_mod.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_tersoff_zbl.html b/doc/pair_tersoff_zbl.html
index 72106802af17e329cb31b54da6417ff6c84aefac..c7cd3870c05fac1de15c478e490e3a705e5ff0de 100644
--- a/doc/pair_tersoff_zbl.html
+++ b/doc/pair_tersoff_zbl.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_thole.html b/doc/pair_thole.html
index a9b25e7edd7948ffdbcd7977904139d034b331a9..6c1272f4e91417512e003947d276dbee205be72e 100644
--- a/doc/pair_thole.html
+++ b/doc/pair_thole.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_tri_lj.html b/doc/pair_tri_lj.html
index 780a05d6888b622a03e920802c71e4cd84a49255..e8356942cd4452fc059e320ac843d93757133ba7 100644
--- a/doc/pair_tri_lj.html
+++ b/doc/pair_tri_lj.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_write.html b/doc/pair_write.html
index 7bbe5154bd6236bad5c70334630961534cc332eb..4c323a18824603bfe16b64ce7722ba503075d3f7 100644
--- a/doc/pair_write.html
+++ b/doc/pair_write.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_yukawa.html b/doc/pair_yukawa.html
index 0e757f551df8b01a4548c3ea3967659d47575c93..a71c1122b2dce3d6aaf5527a6df4bbb6dd3ced94 100644
--- a/doc/pair_yukawa.html
+++ b/doc/pair_yukawa.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_yukawa_colloid.html b/doc/pair_yukawa_colloid.html
index 4e3eb36bce2563168894e8a3259531ce359ceae0..351c0f5441fb9a8aa51c5019486f9b30d07e2422 100644
--- a/doc/pair_yukawa_colloid.html
+++ b/doc/pair_yukawa_colloid.html
@@ -71,22 +71,20 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/pair_zbl.html b/doc/pair_zbl.html
index fd96e2129d612abc7487d2175aec7d53b9656a48..c9f17acae023dc602ef753c7c48e682a256666b7 100644
--- a/doc/pair_zbl.html
+++ b/doc/pair_zbl.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/partition.html b/doc/partition.html
index 7dc37d190eb17ebebbd9504444fd1aa6ce6a68d5..2666e58ab8071fc86acd945cfea955ac6d765161 100644
--- a/doc/partition.html
+++ b/doc/partition.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/prd.html b/doc/prd.html
index cffdd530ab6489b61f88b5e6ae6beb4fd389e660..106f479d95e554d316b9b2aff888542ca53aedaa 100644
--- a/doc/prd.html
+++ b/doc/prd.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/print.html b/doc/print.html
index c8a3cc9f7d0c796f1525433f7e3d800ac8792a88..97b495ce3cae0cec5f4eb68e7591e40ce6133af7 100644
--- a/doc/print.html
+++ b/doc/print.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/processors.html b/doc/processors.html
index ce086ef402adf0ef4ca74c432a47cb566de60940..8087e76edfd2013c185ad6de95fc28460af472cb 100644
--- a/doc/processors.html
+++ b/doc/processors.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/python.html b/doc/python.html
index 8459a712e91931fab3328cb6d9ac2c1a53ac5ac4..83cdb3dca1d32faaf4e12e07ea3c80979b0c3d6e 100644
--- a/doc/python.html
+++ b/doc/python.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/quit.html b/doc/quit.html
index 4e3309dea5f4f355bc871f5a2f59f2fe0d0e8cbf..1206f4c1aec3963292590680b533b4e8baef8153 100644
--- a/doc/quit.html
+++ b/doc/quit.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/read_data.html b/doc/read_data.html
index 8f304177e1619f86da389c41914b2b5b51c416bd..8a3377705b042408fd8317c4007af42536425c7b 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/read_dump.html b/doc/read_dump.html
index 0da7d5863b25fcc0d0bf2eac6085f1585cdd6268..d48f2db4061dbfdfb01f6455b73cacde60b8ef83 100644
--- a/doc/read_dump.html
+++ b/doc/read_dump.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/read_restart.html b/doc/read_restart.html
index 2746a69dd6bd8cabdb04a731be425bc7ad76ec9f..341c5cfdab5addc70f65745da7eb048b407f4edf 100644
--- a/doc/read_restart.html
+++ b/doc/read_restart.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/region.html b/doc/region.html
index e6fca45dac3f529a0d1fad55c691e419f80775d5..c1882abe18eb68aeaa8531221978b3ebc21cd587 100644
--- a/doc/region.html
+++ b/doc/region.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/replicate.html b/doc/replicate.html
index 4a0d76e36c964a318e2d460c17f8a531d14ad7ae..cd929eace15567a49086f2f4ee520b86955c2d53 100644
--- a/doc/replicate.html
+++ b/doc/replicate.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/rerun.html b/doc/rerun.html
index fbdab497d646e949b63305ecc0c15513aa51d382..507f109e63b52e16782fc5a9c507f94008cedb82 100644
--- a/doc/rerun.html
+++ b/doc/rerun.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/reset_timestep.html b/doc/reset_timestep.html
index 59cc1680091a7c66ff46d2d1885eff1bde490c63..6784989f86c6af462f22777ac82f61b5fa7cd331 100644
--- a/doc/reset_timestep.html
+++ b/doc/reset_timestep.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/restart.html b/doc/restart.html
index 1b8b86d45076fae51d11df869f8697c794629147..b34eaa1dc39dc37e58f4f546975652447b8e8c3b 100644
--- a/doc/restart.html
+++ b/doc/restart.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/run.html b/doc/run.html
index 41595b4dd6aae322774cd2de039bfb0e7b8c229e..8ae57422f015e107de4e0cbfc2a00ef2a6b98978 100644
--- a/doc/run.html
+++ b/doc/run.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/run_style.html b/doc/run_style.html
index 91dab73e5497926dd42ae0836c445e81ab73197d..71004e4636aea28fb44daa4de83135da059ae5de 100644
--- a/doc/run_style.html
+++ b/doc/run_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/search.html b/doc/search.html
index 31a6e1cfd0ef49321dfa7d9299fa7235b4efafa1..f0c19a98d7f0cef20a911c3d7cd9445bd3fc9b07 100644
--- a/doc/search.html
+++ b/doc/search.html
@@ -71,22 +71,8 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
-</ul>
-
+ <!-- Local TOC -->
+ <div class="local-toc"></div>
</div>
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 147d1f7ae13a1979a28db2b3e56e04e81d2507a8..9902f222da163643b7612f4646e2a20a4174ba62 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
-Search.setIndex({envversion:47,filenames:["Manual","Section_accelerate","Section_commands","Section_errors","Section_example","Section_history","Section_howto","Section_intro","Section_modify","Section_packages","Section_perf","Section_python","Section_start","Section_tools","accelerate_cuda","accelerate_gpu","accelerate_intel","accelerate_kokkos","accelerate_omp","accelerate_opt","angle_charmm","angle_class2","angle_coeff","angle_cosine","angle_cosine_delta","angle_cosine_periodic","angle_cosine_shift","angle_cosine_shift_exp","angle_cosine_squared","angle_dipole","angle_fourier","angle_fourier_simple","angle_harmonic","angle_hybrid","angle_none","angle_quartic","angle_sdk","angle_style","angle_table","atom_modify","atom_style","balance","body","bond_class2","bond_coeff","bond_fene","bond_fene_expand","bond_harmonic","bond_harmonic_shift","bond_harmonic_shift_cut","bond_hybrid","bond_morse","bond_none","bond_nonlinear","bond_quartic","bond_style","bond_table","boundary","box","change_box","clear","comm_modify","comm_style","compute","compute_ackland_atom","compute_angle_local","compute_angmom_chunk","compute_basal_atom","compute_body_local","compute_bond_local","compute_centro_atom","compute_chunk_atom","compute_cluster_atom","compute_cna_atom","compute_com","compute_com_chunk","compute_contact_atom","compute_coord_atom","compute_damage_atom","compute_dihedral_local","compute_dilatation_atom","compute_displace_atom","compute_erotate_asphere","compute_erotate_rigid","compute_erotate_sphere","compute_erotate_sphere_atom","compute_event_displace","compute_fep","compute_group_group","compute_gyration","compute_gyration_chunk","compute_heat_flux","compute_improper_local","compute_inertia_chunk","compute_ke","compute_ke_atom","compute_ke_atom_eff","compute_ke_eff","compute_ke_rigid","compute_meso_e_atom","compute_meso_rho_atom","compute_meso_t_atom","compute_modify","compute_msd","compute_msd_chunk","compute_msd_nongauss","compute_omega_chunk","compute_pair","compute_pair_local","compute_pe","compute_pe_atom","compute_plasticity_atom","compute_pressure","compute_property_atom","compute_property_chunk","compute_property_local","compute_rdf","compute_reduce","compute_saed","compute_slice","compute_sna_atom","compute_stress_atom","compute_temp","compute_temp_asphere","compute_temp_chunk","compute_temp_com","compute_temp_cs","compute_temp_deform","compute_temp_deform_eff","compute_temp_drude","compute_temp_eff","compute_temp_partial","compute_temp_profile","compute_temp_ramp","compute_temp_region","compute_temp_region_eff","compute_temp_rotate","compute_temp_sphere","compute_ti","compute_torque_chunk","compute_vacf","compute_vcm_chunk","compute_voronoi_atom","compute_xrd","create_atoms","create_bonds","create_box","delete_atoms","delete_bonds","dielectric","dihedral_charmm","dihedral_class2","dihedral_coeff","dihedral_cosine_shift_exp","dihedral_fourier","dihedral_harmonic","dihedral_helix","dihedral_hybrid","dihedral_multi_harmonic","dihedral_nharmonic","dihedral_none","dihedral_opls","dihedral_quadratic","dihedral_style","dihedral_table","dimension","displace_atoms","dump","dump_image","dump_modify","dump_molfile","echo","fix","fix_adapt","fix_adapt_fep","fix_addforce","fix_addtorque","fix_append_atoms","fix_atc","fix_atom_swap","fix_ave_atom","fix_ave_chunk","fix_ave_correlate","fix_ave_histo","fix_ave_spatial","fix_ave_spatial_sphere","fix_ave_time","fix_aveforce","fix_balance","fix_bond_break","fix_bond_create","fix_bond_swap","fix_box_relax","fix_colvars","fix_deform","fix_deposit","fix_drag","fix_drude","fix_drude_transform","fix_dt_reset","fix_efield","fix_enforce2d","fix_evaporate","fix_external","fix_freeze","fix_gcmc","fix_gld","fix_gle","fix_gravity","fix_heat","fix_imd","fix_indent","fix_ipi","fix_langevin","fix_langevin_drude","fix_langevin_eff","fix_lb_fluid","fix_lb_momentum","fix_lb_pc","fix_lb_rigid_pc_sphere","fix_lb_viscous","fix_lineforce","fix_meso","fix_meso_stationary","fix_modify","fix_momentum","fix_move","fix_msst","fix_neb","fix_nh","fix_nh_eff","fix_nph_asphere","fix_nph_sphere","fix_nphug","fix_npt_asphere","fix_npt_sphere","fix_nve","fix_nve_asphere","fix_nve_asphere_noforce","fix_nve_body","fix_nve_eff","fix_nve_limit","fix_nve_line","fix_nve_noforce","fix_nve_sphere","fix_nve_tri","fix_nvt_asphere","fix_nvt_sllod","fix_nvt_sllod_eff","fix_nvt_sphere","fix_oneway","fix_orient_fcc","fix_phonon","fix_pimd","fix_planeforce","fix_poems","fix_pour","fix_press_berendsen","fix_print","fix_property_atom","fix_qbmsst","fix_qeq","fix_qeq_comb","fix_qeq_reax","fix_qmmm","fix_qtb","fix_reax_bonds","fix_reaxc_species","fix_recenter","fix_restrain","fix_rigid","fix_saed_vtk","fix_setforce","fix_shake","fix_smd","fix_spring","fix_spring_rg","fix_spring_self","fix_srd","fix_store_force","fix_store_state","fix_temp_berendsen","fix_temp_csvr","fix_temp_rescale","fix_temp_rescale_eff","fix_tfmc","fix_thermal_conductivity","fix_ti_rs","fix_ti_spring","fix_tmd","fix_ttm","fix_tune_kspace","fix_vector","fix_viscosity","fix_viscous","fix_wall","fix_wall_gran","fix_wall_piston","fix_wall_reflect","fix_wall_region","fix_wall_srd","group","group2ndx","if","improper_class2","improper_coeff","improper_cossq","improper_cvff","improper_fourier","improper_harmonic","improper_hybrid","improper_none","improper_ring","improper_style","improper_umbrella","include","info","jump","kspace_modify","kspace_style","label","lattice","log","mass","min_modify","min_style","minimize","molecule","neb","neigh_modify","neighbor","newton","next","package","pair_adp","pair_airebo","pair_awpmd","pair_beck","pair_body","pair_bop","pair_born","pair_brownian","pair_buck","pair_buck_long","pair_charmm","pair_class2","pair_coeff","pair_colloid","pair_comb","pair_coul","pair_coul_diel","pair_cs","pair_dipole","pair_dpd","pair_dsmc","pair_eam","pair_edip","pair_eff","pair_eim","pair_gauss","pair_gayberne","pair_gran","pair_gromacs","pair_hbond_dreiding","pair_hybrid","pair_kim","pair_lcbop","pair_line_lj","pair_list","pair_lj","pair_lj96","pair_lj_cubic","pair_lj_expand","pair_lj_long","pair_lj_sf","pair_lj_smooth","pair_lj_smooth_linear","pair_lj_soft","pair_lubricate","pair_lubricateU","pair_meam","pair_meam_spline","pair_meam_sw_spline","pair_mie","pair_modify","pair_morse","pair_nb3b_harmonic","pair_nm","pair_none","pair_peri","pair_polymorphic","pair_quip","pair_reax","pair_reax_c","pair_resquared","pair_sdk","pair_snap","pair_soft","pair_sph_heatconduction","pair_sph_idealgas","pair_sph_lj","pair_sph_rhosum","pair_sph_taitwater","pair_sph_taitwater_morris","pair_srp","pair_style","pair_sw","pair_table","pair_tersoff","pair_tersoff_mod","pair_tersoff_zbl","pair_thole","pair_tri_lj","pair_write","pair_yukawa","pair_yukawa_colloid","pair_zbl","partition","prd","print","processors","python","quit","read_data","read_dump","read_restart","region","replicate","rerun","reset_timestep","restart","run","run_style","set","shell","special_bonds","suffix","tad","temper","thermo","thermo_modify","thermo_style","timestep","tutorial_drude","uncompute","undump","unfix","units","variable","velocity","write_data","write_dump","write_restart"],objects:{},objnames:{},objtypes:{},terms:{"00a":287,"00b":287,"02214e23":91,"03275e":447,"0b1":11,"0e20":[303,426,448],"0e4":[227,296,361],"0e5":227,"0x98b5e0":168,"100k":1,"1024x1024":168,"10e":351,"10f":3,"10g":448,"10th":[418,424,437],"10x":[3,325,326,328,329,339],"10x10x10":132,"10x20x20":321,"11e":10,"15g":[169,448],"16x":1,"18986e":326,"18e":10,"1_prop":6,"1st":[2,6,8,12,20,22,38,44,56,57,58,60,87,138,150,152,164,173,174,181,182,183,184,185,186,190,194,229,258,268,289,301,305,323,329,334,335,339,346,348,355,357,358,365,366,375,376,380,381,382,386,390,396,406,407,408,409,410,417,423,431,432,435,448],"1x2x2":420,"2000k":168,"20x":339,"23899e":326,"2400k":168,"256k":10,"25x":10,"298k":350,"2k_ss":357,"2nd":[2,3,6,11,12,15,17,38,45,46,56,57,60,71,77,88,133,164,169,181,182,183,184,185,186,190,192,194,229,270,274,275,301,304,310,317,326,327,328,329,333,335,348,357,363,364,380,396,405,406,407,408,409,410,423,430,432,435,448],"2pi":164,"2theta":143,"2x1x2":420,"2x2x1":420,"2x2x2":420,"2x4x10":420,"2x5":357,"300k":[207,270,449],"32k":10,"3419e":227,"3806504e":[6,91],"38e":10,"3n_k":206,"3nk":260,"3nkb":265,"3rd":[15,17,20,38,56,71,105,114,164,181,182,183,184,185,186,190,270,271,301,327,331,333,348,357,363,364,396,406,407,408,409,410,423,430,435,448],"3x3":[91,321],"4857990943e":357,"4_94":11,"4th":[6,38,56,81,103,104,116,140,150,164,169,275,301,319,332,334,335,339,355,358,365,380,386,390,396,406,407,408,410,423,430,435,438,452],"4x10":317,"4x2x10":420,"4x6x10":420,"50k":1,"53xx":18,"54xx":18,"55e":10,"5_1":339,"5kx":[175,200],"5nlog_2":12,"5th":[116,326,440],"6021765e":447,"6863e22":389,"6x6":6,"72360e":227,"7797e":227,"8032044e":447,"8x1":6,"8x2":[6,12],"9e18":[12,39],"9e9":389,"9jan09":[296,361],"9th":328,"__main__":421,"__pthread_key_cr":12,"_j1m1m1":120,"_j2m2m2":120,"_serial":12,"abstract":17,"boolean":[3,301,303],"break":[2,3,7,8,12,54,55,59,148,172],"byte":[3,12,440],"case":[1,2,3,6,8,11,12,13,15,16,17,18,39,40,41,45,46,59,61,63,71,73,104,108,114,116,117,122,123,124,125,127,130,131,132,133,134,136,137,138,142,144,146,147,148,150,167,168,169,175,176,180,181,182,183,184,185,186,187,188,190,192,194,198,200,202,205,208,209,211,212,213,214,216,227,229,230,231,232,233,234,235,246,247,249,251,252,257,259,260,261,262,269,270,272,274,275,278,281,282,283,285,286,290,292,293,295,296,298,299,300,301,303,317,318,319,321,323,325,326,327,328,330,332,333,335,344,347,349,351,355,357,360,361,363,364,365,367,377,378,379,380,384,386,390,393,397,407,408,410,418,421,423,425,426,430,431,433,435,437,439,440,441,443,447,448,449,451,452],"catch":[1,3,421],"char":[6,8],"class":[1,3,5,6,7,8,9,11,12,13,22,37,44,55,152,163,203,259,305,313,345,364,392,393,405,421,423],"default":[1,2,3,6,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36],"export":[168,346],"final":[3,5,6,7,8,11,12,17,41,59,87,121,169,180,181,182,183,184,185,186,188,192,194,205,228,229,233,260,264,270,271,274,287,289,290,297,303,326,328,334,335,339,355,358,365,377,380,386,390,391,406,407,408,410,418,431,437,443,448,450],"float":[3,6,8,12,40,42,71,113,167,169,210,259,271,280,357,421,423,433,440,448],"function":[1,3,6,7,8,9,11,12,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,45,46,47,48,49,51,53,54,56,63,66,71,80,87,91,93,100,106,109,112,116,117,120,122,131,138,139,140,150,151,153,154,155,156,158,159,161,162,164,167,169,173,174,175,176,178,182,187,190,192,193,194,199,200,201,203,204,206,208,209,211,213,214,216,226,228,229,231,232,233,234,235,236,243,244,246,247,249,252,253,257,262,264,265,269,270,272,273,281,282,283,287,288,290,292,294,295,298,300,303,304,306,307,308,309,312,314,318,319,326,334,335,336,337,339,340,341,342,343,344,345,347,348,349,350,352,353,355,356,357,358,359,360,361,362,363,364,367,368,369,370,371,372,373,374,375,376,377,378,380,381,382,383,384,385,386,387,389,390,392,393,394,395,397,398,399,400,401,402,403,406,407,408,409,410,411,412,413,414,415,416,420,421,426,428,430,432,433,439,443],"import":[1,2,3,6,11,17,71,87,105,144,155,172,181,184,192,208,213,214,229,265,270,281,282,283,285,290,300,302,328,364,377,421,423,432,440,443],"int":[3,6,8,11,101,203,205,213,215,265,290,440],"long":[1,2,3,6,7,8,9,10,12,14,15,16,18,36,59,61,87,88,108,109,110,112,121,138,142,145,149,150,156,166,168,172,173,174,178,179,205,229,230,261,263,270,273,275,278,279,285,290,291,303,315,317,318,319,324,326,328,329,330,333,337],"new":[0,3,5,6,7],"null":[3,6,91,112,121,144,172,187,193,196,199,226,259,268,272,274,275,276,296,334,335,348,355,358,361,364,365,366,380,381,382,386,390,392,393,396,406,408,409,410,423,426,431,433,449],"public":[0,7,8,12,203,212,358,391],"return":[2,3,6,8,11,14,15,16,17,18,19,41,71,108,117,142,144,169,181,184,185,194,203,303,315,317,361,420,421,430,433,439,448],"short":[1,3,6,7,13,16,142,229,270,278,291,319,329,330,333,335,339,340,342,343,344,348,349,351,357,364,369,373,377,380,384,387,395,407,411,418,421,431,437,443],"static":[2,3,5,6,7,8],"switch":[1,3,6,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,91,109,112,120,122,131,143,150,151,153,154,155,156,158,159,161,162,164,168,171,175,179,187,201,204,208,212,213,216,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,287,288,294,304,306,307,308,309,312,314,315,317,319,322,328,332,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,417,418,420,423,425,430,432,436,438,448,450,452],"throw":440,"true":[6,12,13,17,108,115,167,188,190,194,229,230,251,252,253,257,270,285,289,301,303,333,357,361,406,421,425,433,448],"try":[1,3,8,12,17,19,181,210,216,286,287,288,293,421,448],"var":[3,11,12,144,301,317,434,448],"void":[4,6,7,8,41,147,188,203,426],"while":[3,9,10,11,12,13,14,18,71,105,120,127,142,155,167,170,185,192,194,198,206,207,212,213,214,216,229,247,260,265,267,291,319,326,333,339,350,355,393,408,410,418,421,432,437,443],a10:303,a123:303,a12:394,a2m:[6,91],a_0:[216,290,339],a_0_real:216,a_1:290,a_2:290,a_3:290,a_4:290,a_c:347,a_cc:347,a_f:410,a_i:411,a_ij:339,a_j:411,a_pi:339,a_sigma:339,a_ss:347,aacut:252,aat:151,aatom1:115,aatom2:115,aatom3:115,ab_23_cd:303,abbrevi:12,abc:[3,12,303,421,448],abf:193,abf_integr:13,abi:170,abil:[3,9,192,229,257,270,357],abl:[3,8,11,12,39,86,167,170,191,200,204,286,293,333,421,448,451],ablat:290,about:[0,1,3,4,6,8,9,10,11,12,13,17,39,41,42,61,63,78,108,115,116,118,138,144,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,198,199,200,201,202,203,204,205,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,228,233,236,237,238,239,240,241,242,243,244,245,250,251,252,254,255,256,257,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,278,279,281,282,283,284,285,286,287,288,289,290,292,293,294,295,297,298,299,300,301,316,319,325,326,328,333,338,344,349,364,389,393,415,421,424,425,430,431,433,438,448,450,452],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,57,63,64,68,70,71,72,73,76,77,86,87,89,90,91,93,94,96,97,112,114,116,118,120,121,122,123,124,125,126,127,130,131,132,133,134,136,137,138,142,143,144,146,147,150,151,152,153,154,155,156,157,158,159,161,162,164,167,168,169,172,173,174,175,176,181,182,183,184,185,186,188,191,192,194,195,200,203,205,209,211,213,214,215,219,228,229,233,253,256,258,263,269,270,274,275,278,281,282,283,284,301,303,304,305,306,307,308,309,310,312,314,319,321,323,327,328,332,333,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,423,424,425,426,427,430,431,432,433,434,437,438,441,443,448,449,451,452],abscissa:407,absenc:176,absent:443,absolut:[3,169,193,194,198,274,280,318,319,326,361,369,424],absorb:290,absoult:319,ac3:143,academ:205,acc:285,acceler:0,accelri:[6,13],accept:[7,87,144,169,179,191,194,205,285,343,373,431,438],acceptor:363,access:[0,3,6,7,8,9,11,12,16,40,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,85,88,89,90,91,92,93,95,96,99,100,101,103,104,105,106,107,108,110,111,112,113,114,115,117,118,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,143,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,213,215,216,217,218,219,220,221,222,223,225,226,227,228,229,233,236,237,238,239,240,241,242,243,244,245,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,292,293,294,295,296,297,298,299,300,318,333,359,361,363,364,380,392,393,397,420,421,424,429,441,448],accidenti:312,accler:16,accommod:177,accomod:229,accompani:8,accomplish:[16,194,217,243],accord:[64,71,168,179,189,190,216,229,252,260,274,287,288,290,295,296,298,299,300,329,333,357,361,372,375,390,397,399,400,402,403,404,432,437,448],accordingli:[11,14,123,137,148,329,378,379],account:[3,6,9,87,118,142,143,152,163,182,183,199,210,211,213,229,234,235,246,247,249,251,255,261,270,271,273,275,276,277,278,281,282,283,286,290,293,308,327,349,361,369,373,378,379,380,420,437,449],accuml:[3,270,286,293],accumul:[1,6,8,15,71,172,182,213,270,274,292,316,333,429,447],accur:[1,3,6,15,17,38,41,56,127,188,227,265,270,273,278,286,293,299,301,319,339,357,360,361,384,394,405,407,408,410,437,448],accuraci:[1,3,6,12,41,167,169,188,207,229,262,273,291,301,318,319,325,357,384,392,393,407,413,432,437,443,448,451],ach:318,achiev:[1,3,6,16,17,18,41,188,207,229,230,252,253,260,318,432],achiv:18,acid:9,ackland1:355,ackland2:355,ackland:2,acknowledg:0,acml:12,aco:448,acolor:[168,169],acoust:252,acquir:[3,6,58,61,62,147,190,192,194,229,388,428,443],across:[1,2,3,6,9,12,13,15,41,57,61,65,68,69,71,79,92,107,108,115,117,132,146,148,181,183,184,185,188,199,209,270,271,286,290,293,299,303,328,333,418,423,426,427,431,440],act:[3,6,108,129,198,208,211,212,213,214,216,219,228,270,285,287,288,290,299,300,301,326,341,352,360,361,363,394,404],acta:[118,143,334],action:[2,6,11,12,71,206,211,288,443],activ:[5,8,11,12,13,14,55,59,87,142,179,193,206,210,213,219,228,250,270,289,316,377,405,417,445,448],actual:[1,3,6,8,12,56,62,127,167,169,173,174,187,189,190,198,213,214,247,251,257,265,274,278,280,281,282,283,285,291,300,301,318,329,360,362,372,378,379,420,421,432,433,441,448],adam:[318,319],adapt:[2,3,9,87,138,172],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,19,40,42,71,87,91,102,114,117,119,142,144,145,167,168,172,173,174,175,176,178,180,181,182,183,184,185,186,190,193,198,200,203,207,208,209,211,213,215,216,220,227,228,229,230,231,232,233,234,235,246,247,248,249,251,259,269,270,272,273,275,277,281,283,284,288,289,290,292,294,295,299,301,319,321,325,327,335,340,342,345,349,357,364,369,380,384,387,393,395,421,423,424,429,431,433,435,443],add_molecul:178,add_speci:178,add_to_nodeset:178,addforc:[2,3,172],addit:[0,1,2,3,4,6,7,8,9,11],addition:[6,8,16,278,300,360,394],address:[7,8,11,168,212],addtorqu:2,adequ:[278,291,318,328,432],adher:29,adhikari:216,adiabat:0,adiam:[168,169],adjac:[39,144,328,384,407,408,437,438],adjiman:383,adjust:[3,6,16,17,41,59,118,123,124,127,128,131,132,137,138,143,148,167,168,181,188,192,194,210,213,217,221,225,226,229,230,233,247,251,254,256,257,260,261,262,263,268,270,278,282,286,291,293,294,295,297,298,300,318,319,326,328,333,335,354,378,379,410,433,449],admiss:233,adof:[124,181],adopt:[269,443],adp:[2,3,7],adri:[9,266,392,393],adust:138,advanc:[3,210,339,418,429],advantag:[1,6,8,11,14,18,39,40,41,188,333,356,432,437],advect:[3,6,278],advertis:8,advis:[328,391],afer:3,affect:[1,6,10,14,15,16,17,40,60,61,71,88,117,121,128,142,148,169,174,181,182,183,184,185,186,189,190,191,192,194,195,203,209,211,213,219,226,230,231,232,234,235,241,246,247,249,270,271,276,290,300,312,318,324,325,326,328,329,330,333,357,378,379,384,420,421,423,426,428,431,433],affin:[16,17,18,194,333,348],afil:207,aforement:18,afresh:[258,431,448],afshar:353,after:[2,3,5,6,8,9,11,12,15,16,21,22,33,39,40,41,44,50,57,58,59,61,63,71,123,124,125,126,127,128,131,132,133,134,136,137,144,145,147,148,151,152,157,166,167,168,169,170,172,173,174,178,179,181,182,188,189,190,191,192,194,198,205,216,217,218,219,220,225,226,227,229,234,235,241,246,247,249,252,256,260,268,270,273,279,281,282,283,285,286,287,288,289,293,295,297,301,304,305,310,317,323,324,326,327,329,331,332,333,334,335,339,346,348,355,356,357,358,364,365,366,377,378,379,380,381,382,386,390,392,393,396,406,408,409,410,418,420,422,423,424,425,426,428,429,431,433,435,437,440,441,443,447,448,449,450,451,452],afterrun:431,afterward:3,afterword:41,ag1:143,ag2:143,again:[6,11,12,17,62,120,124,126,130,138,167,169,194,209,256,304,317,328,378,379,418,420,421,423,425,430,437,439,448,450],against:[11,12,13,64,195,328,392,393],aggreg:[6,12,65,68,69,79,92,108,115,209,225,268,270,276,418,449],aggress:[209,437],agilio:[9,13],agre:[3,8,164,326,335,366,393],agreement:[5,7],ahd:363,ahead:297,aidan:[0,5,7,9,13],aij:13,aim:6,airebo:[2,3,7,189,190,267],ajaramil:[7,9,13],aka:168,akohlmei:[7,9,13,170,210],aktulga:[7,9,263,393],al2o3_001:[118,271],al3:143,ala:216,alain:9,alat:[251,380],alb:[390,408,410],albeit:269,albert:9,alchem:[87,138],alcohol:293,alcu:[334,339],alcu_eam:390,alderton:352,alejandr:[229,230],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,169,178,188,191,194,216,218,219,241,253,270,273,285,286,290,293,298,324,325,326,330,333,357,379,418,420,437],alia:12,alias:[1,319],aliceblu:169,align:[6,12,29,41,71,146,164,184,188,211,321,423,426,443],alkali:357,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,132,137,138,139,140,141,142,143,144,145,146,147,148,150,152,157,163,164,167,168,169,170,172,173,174,175,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,197,198,199,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,222,224,225,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,308,313,316,317,318,319,320,321,323,326,327,328,329,330,332,333,334,335,336,338,339,340,342,343,344,345,346,348,349,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,373,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,430,431,432,433,434,435,436,437,438,440,441,443,447,448,449,450,451,452],allen:[29,87,352,360],allentildeslei:87,allign:3,allindex:302,alloc:[3,5,6,8,9,11,12,60,203,292,327,329,333,388,393,423,431],allocat:3,alloi:[2,12,13,334,339,349],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,123,124,137,142,143,144,146,152,163,164,167,168,169,170,172,173,175,177,178,179,181,182,183,184,185,186,188,190,191,192,193,194,195,199,200,203,205,206,207,208,210,213,216,219,220,224,226,229,230,251,255,257,258,259,260,264,270,271,273,274,278,285,286,287,288,290,291,292,293,294,295,301,303,305,313,318,319,321,326,327,328,329,332,333,336,339,340,341,342,343,344,349,355,357,361,362,363,364,373,378,379,384,390,393,394,404,413,415,418,421,423,425,426,427,428,429,430,433,435,436,437,440,441,448,449],almost:[2,3,12,60,211,260,290,319,330,333,404],alo:349,alon:[6,7,191,266,392,393,421],alond:13,along:[6,8,9,12,29,40,87,118,143,144,166,167,168,191,211,216,217,221,226,228,260,270,273,274,275,276,285,289,290,296,299,301,321,324,325,326,328,349,352,361,364,367,369,373,380,392,393,407,423,426,433,434,448],alonso:[381,382],alpha:[6,51,173,216,252,260,265,326,334,337,340,349,353,355,356,358,363,368,369,380,385,389,409,411,441,443],alpha_:411,alpha_c:377,alpha_i:[396,411],alpha_ialpha_j:411,alpha_lj:377,alphabet:[2,3,22,37,44,55,63,152,163,172,305,313,327,346,405,423],alphanumer:[3,63,172,259,267,303,327,448],alreadi:[3,7,8,12,42,144,145,147,177,181,184,185,188,190,194,220,258,260,278,301,327,328,353,362,364,371,379,404,413,416,419,423,424,428,448],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,120,121,122,123,124,125,126,127,128,130,131,132,133,134,136,137,138,139,140,141,142,144,145,146,147,148,150,152,163,164,165,167,168,169,170,172,173,174,175,177,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,200,203,204,205,206,207,209,210,213,214,215,216,226,227,229,230,231,232,233,234,235,240,243,244,246,247,248,249,251,252,253,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,278,281,282,283,284,285,289,290,291,292,294,296,299,301,303,305,310,313,316,318,319,321,322,323,326,327,328,329,330,332,333,339,343,344,346,350,351,352,353,355,356,357,360,361,363,364,365,373,377,378,380,384,386,388,389,390,391,394,395,399,400,402,403,404,405,406,407,408,409,410,411,418,420,421,422,423,424,425,426,427,428,430,431,432,433,435,436,437,438,441,442,443,444,446,447,448,449,450,452],alter:[3,6,8,9,11,12,41,59,122,123,124,125,127,130,131,132,133,136,137,144,148,167,168,170,173,174,181,189,190,191,192,194,228,229,265,268,270,272,278,286,293,300,325,328,364,423,428,430,433,448,449,452],altern:[1,6,8,11,12,17,18,91,144,172,194,210,214,229,259,270,285,286,293,306,309,318,325,326,334,335,349,355,356,358,366,369,377,380,381,382,386,390,391,396,406,408,410,421,423,424,438,441],although:[29,42,164,219,229,257,261,270,285,317,416,430,443,452],aluminum:416,alwai:[0,6,11,12,17,18,54,57,63,71,142,169,182,184,185,186,190,193,205,207,211,262,265,270,278,295,299,300,304,318,319,324,326,327,329,330,333,342,345,355,372,392,393,397,407,408,410,416,418,423,424,426,428,435,437,440,443,448,449],amap:169,amatrix:207,amaz:11,amazingli:13,amber2lmp:0,amber:0,ambient:168,ambigu:[3,63,172,448],amd:[17,333],amend:11,amino:9,amit:9,among:[16,121,179,216],amorph:[144,409],amount:[1,3,6,12,59,88,115,142,146,166,168,192,193,205,209,213,229,251,257,270,278,283,286,291,293,301,318,333,353,388,423,426],amplitud:[194,226,296,312,426,448],amu:205,analag:[6,448],analalog:6,analog:[6,120,146,164,361,384],analys:[7,428],analysi:[7,9,13,63,64,73,170,266,267,302,396,423,433],analyt:[1,3,13,118,138,143,273,318,339,365,366,371,390],analyz:[6,8,13,328],andersen:273,anderson:[255,353],andr:[7,9,13],andrew:13,andzelm:404,ang:251,angl:[0,1,2,3,6,7],angle1:269,angle2:269,angle_coeff:[2,3,20,21],angle_cosineshift:27,angle_cosineshiftexp:[26,153],angle_cutof:363,angle_cutoff:363,angle_hybrid:29,angle_info:393,angle_styl:0,angle_typ:40,angleangl:[3,304,310,423],angleangletors:[3,151,423],anglecoeff:3,angletors:[3,151,157,423],angletyp:190,angmom:[2,3,6],angmomi:[113,167,280],angmomx:[113,167,280],angmomz:[113,167,280],angstrom:[6,10,59,71,118,133,143,144,166,167,168,169,177,184,185,194,195,205,210,211,226,263,268,295,297,298,300,319,321,324,330,334,335,344,355,377,380,386,391,392,393,410,416,426,432,447,449],angular:[3,6,40,61,66,82,83,84,85,106,113,120,123,136,137,144,167,172,213,219,225,226,231,232,234,235,237,238,239,242,244,245,246,249,268,270,273,280,334,339,348,361,378,379,380,390,405,408,409,423,433,448,449],angularm:238,anharmon:[27,53,153,265,437],ani:[1,3,6,7,8,9,10,11,12,13,14,15,16,17,22,29,38,39,40,41,42,44,55,56,58,59,61,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,147,148,150,152,164,166,167,168,169,172,175,176,177,179,181,182,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,200,202,205,208,209,211,213,216,219,225,226,229,233,251,253,255,256,257,259,261,262,263,265,267,268,270,272,273,274,275,277,278,279,280,289,290,295,296,297,298,299,300,301,302,303,305,317,318,319,321,323,324,326,327,328,330,331,332,333,335,339,343,344,348,349,352,353,355,356,358,360,364,365,366,367,373,384,390,392,393,394,396,405,406,407,408,409,410,411,412,417,418,420,421,423,424,426,427,428,429,430,431,432,433,434,435,436,437,441,443,444,446,447,448,449,450,451,452],anihil:377,anim:[2,4,7,11,13,168,328],anion:358,aniso:[3,192,194,229,230,231,232,233,234,235,257,270],anisotrop:[213,360,394],ann:383,annot:[7,406,408,409,410,423],annual:[418,437],anoth:[1,3,4,6,7,8,11,12,17,29,40,63,71,87,119,168,172,173,179,181,183,184,185,186,191,194,195,206,209,213,214,219,229,230,233,256,259,270,271,281,282,283,290,300,303,324,326,328,329,332,349,353,357,358,360,363,364,368,369,377,392,394,397,404,408,409,410,417,418,421,424,430,432,443,448,452],ansi:12,answer:[3,4,8,12,270,330,331],anthoni:288,antiquewhit:169,antisymmetr:[9,40,336],antisymmetri:357,antonelli:[287,288],antonio:389,anymor:288,anyon:7,anyparticl:86,anyth:[8,11,144,194,212,406,408,410,434],anywai:[147,333,443,450],anywher:[12,144,346,380,396,448],aoff:[327,423],aparam:[87,173,174],apart:[3,145,219,275,329,338,397,423,432],aperiod:252,api:[11,12,170,365,421],appar:3,appear:[2,3,6,11,12,13,39,40,41,77,87,108,115,116,120,127,144,145,147,167,168,169,181,184,185,188,192,195,198,205,210,256,267,268,289,301,303,304,318,326,327,328,347,355,380,384,407,419,420,421,423,424,425,428,430,443,448,452],append:[1,2,3,9,11,12,14,15,16,17,18,19,39,41,58,59,61,65,68,69,71,79,87,88,90,91,92,103,105,108,109,110,112,117,118,119,120,121,123,124,132,133,137,138,142,143,144,146,147,148,166,168,169,172,173,174,175],appendix:[29,352],appl:[192,229,230],appli:[2,3,4,5,6,8,12,17,18,33,41,50,57,59,61,63,71,87,88,105,120,121,124,130,132,134,138,143,144,146,150,152,157,163,167,169,172,173,174,175,176,178,181,187,188,192,193,194,196,199,200,203,204,205,206,207,208,210,211,213,214,215,216,220,229,230,233,234,235,241,246,249,250,251,253,257,260,268,269,270,272,273,274,275,276,277,279,281,282,283,284,286,288,289,290,293,301,318,321,326,327,328,338,340,342,344,349,352,357,361,362,363,364,366,369,375,379,384,387,392,395,404,411,415,423,424,426,427,428,432,435,440,443,448,449,450,451],applic:[1,6,9,12,17,170,178,191,195,196,203,207,210,251,256,269,274,275,286,293,318,333,410,443],applyt:3,appopri:17,approach:[6,7,9,14,178,206,252,253,265,270,285,286,288,290,293,318,339,349,351,354,360,394,404,413],appropri:[1,2,3,6,8,11,12,13,15,17,33,38,42,50,56,61,73,88,91,116,117,123,124,152,157,163,164,167,169,181,182,184,185,186,191,192,194,203,204,207,216,224,226,227,229,231,232,233,234,235,246,247,249,253,256,257,260,265,270,278,281,282,283,286,293,295,296,298,299,300,310,319,328,335,339,343,347,348,349,356,361,364,366,373,377,391,392,393,406,407,408,409,410,413,423,424,425,427,428,436,437,440,448,449],approri:208,approxim:[6,9,118,143,205,207,216,253,271,273,285,318,324,325,326,341,351,357,360,378,379,384,391,394,415,437,443],april:11,aprpopri:418,apu:[378,379],aqua:[168,169],aquamarin:169,ar_therm:178,ar_ttm:178,ara:13,arbitrari:[6,40,58,167,168,170,193,194,208,229,253,261,406,421,434,448],arbitrarili:[11,59,116,120,166,192,229,349,448],arcco:3,arch:[1,12,14,15,17],architect:316,architectur:[16,333],archiv:[6,7,11,12,280,346,430],arcsin:3,area:[6,41,91,112,116,142,188,194,216,286,293,354,361,389,412,420,433],aren:[259,303],arflag:12,arg:[3,11,12,22,40,41,44,55,59,63,71,87,117,132,138,142,144,147,148,152,166,167,169,172,173,174,175,177,179,181,182,183,184,185,186,187,188,189,190,193,194,195,200,203,205,208,209,210,211,219,226,231,232,256,269,270,271,272,285,288,295,296,297,298,300,301,305,316,328,333,340,341,342,344,345,346,351,352,357,362,364,369,373,377,378,379,387,395,405,420,421,423,426,428,430,432,434,441,448,449,451,452],argon:205,argonn:12,argument:[2,3,6,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,63,73,87,91,109,112,116,120,121,122,131,132,133,138,142,144,145,146,148,150,151,152,153,154,155,156,158,159,161,162,164,167,169,172,173,174,175,177,180,181,182,183,184,185,186,187,188,192,193,194,201,203,204,207,208,212,213,219,226,229,231,232,233,234,235,236,244,246,247,249,255,256,258,262,267,270,271,272,273,278,281,283,290,292,294,296,301,303,304,305,306,307,308,309,310,312,314,316,317,319,320,321,323,328,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,351,352,353,355,356,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,389,390,392,393,394,395,396,397,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,423,424,426,428,431,432,433,434,438,440,441,448,449,451],aris:[12,415],arithmet:[3,6,318,344,347,367,372,384,411,412],arkansa:9,arl:9,armv8:17,arnold:318,around:[1,3,4,6,12,42,57,58,59,66,70,73,77,116,120,123,139,142,144,146,166,168,169,176,177,192,194,195,211,226,229,259,261,265,270,275,278,295,296,299,317,327,423,426,433,434,443,448],aroung:3,arrai:3,arrang:120,arrheniu:437,art:[261,418,437],artefact:207,articl:6,articul:[7,255],artifact:[88,142,443],artifici:[227,260,399,400,402],arun:13,arxiv:[120,396],ascend:[41,169,210,219,270,428],asci:7,ascii:[13,271,289,328,355,358,380,423],ash:[378,379],asid:[8,144,380],asin:448,ask:[3,11],askari:389,askoos:13,asoci:168,aspect:[6,7,59,194,205,360,394,412,423,433,437],aspect_ratio:271,asper:4,aspher:[0,2,3],asq:[378,379],assembl:4,assign:[1,2,3,6,7,11,12,14,15,17,18,33,39,40,41,50,57,59,61,63,66,71,72,75,90,93,104,106,110,113,114,118,120,121,124,139,141,143,144,147,157,167,168,169,170,172,173,174,177,181,183,188,190,191,192,195,197,205,210,213,214,215,216,226,229,231,232,233,234,235,244,246,247,248,249,253,256,257,259,261,267,270,271,281,282,283,284,301,310,319,321,323,327,328,332,333,339,355,358,360,363,364,393,394,420,421,423,424,425,426,427,432,433,438,441,448,449],assignemnt:[6,432],assing:259,assist:[7,227],associ:[3,5,6,8,9,12,22,37,39,40,44,55,59,66,74,75,81,87,89,90,93,99,101,103,104,106,139,152,163,167,168,169,173,174,175,179,192,194,200,203,205,206,212,216,226,229,255,265,269,270,271,276,278,302,303,305,313,321,326,328,332,333,346,349,353,354,355,357,363,364,366,369,373,404,405,407,421,424,431,443,445,448],associd:67,assum:[2,3,4,6,11,12,16,39,59,67,71,88,96,102,104,122,123,124,125,126,127,129,130,131,132,133,134,136,137,138,142,144,147,169,173,174,181,182,183,184,185,186,192,194,202,210,212,216,219,231,232,234,235,237,239,242,244,245,246,249,251,252,256,257,258,261,270,272,274,275,286,289,290,295,298,301,318,319,327,328,333,339,341,343,346,347,354,357,363,364,368,373,378,379,412,418,420,421,423,425,428,433,437,440,441,443,449],assumpt:[142,210,334,384],astar:380,astart:397,asterisk:[22,44,77,87,116,138,148,152,169,173,174,219,270,305,323,346,363,404,417,420,433,447],astop:[326,397],asu:355,asub:380,asubrama:13,asymmetr:[298,339,355],asynchron:[15,16],atan2:448,atan:448,atc:[0,2,7],atc_fe_output:178,athomp:[0,7,9,13],atm2pa:6,atmospher:447,atol:12,atom1:[255,269,327,423],atom2:[255,269,327,423],atom3:[255,269,327,423],atom4:[269,327,423],atom:[0,1,2,3,5],atom_element_map:178,atom_forc:393,atom_info:393,atom_modifi:[2,3,11],atom_styl:[2,3,6,9,12,37,39],atom_vec:8,atom_vec_atom:8,atom_vec_electron:8,atom_veloc:393,atom_weight:178,atomey:[6,7,11,13,167,168,169],atomfil:[3,71,259,301,332,433,448],atomic_charg:178,atomic_numb:390,atomid:423,atomist:[6,178,285],atomperbin:3,atomt:169,atomvec:8,attach:[6,185,253,274,275,423],attatch:288,attempt:[3,6,41,59,71,166,179,188,189,190,191,195,205,256,257,278,298,318,322,328,364,421,436,438,441,448],attend:178,attent:[15,18],attogram:447,attrac:380,attract:0,attribut:[3,6,7,8,11,39,40,42,58,63,71,87,113,114,115,117,123,138,167,168,169,172,173,174,180,181,183,184,185,191,192,229,231,232,233,234,235,237,238,246,247,249,257,270,271,280,281,282,283,321,327,339,357,364,423,424,425,433,441,448],atw:[378,379],atwat:409,atwt:380,atyp:[115,138,190,349,369,373,377],au1:143,au3:143,aug:11,augment:[12,113,192,259,380],augt1:380,auo:267,auoh:267,author:[3,8,9,13,355,356,443],auto:[6,8,11,12,91,140,172,182,274,292,318,327,333,420],autocorrel:[63,91,213],autom:[12,168],automag:7,automat:[3,6,12,14,15,16,17,18,19,36,164,177,205,207,216,270,274,291,318,333,348,355,364,380,416,423,436,443],auxiliari:[1,6,9,11,12,13,167,252,270,424,428,450],avail:[1,3,5,6,7,8,9,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,63,87,109,112,113,120,122,131,142,150,151,153,154,155,156,158,159,161,162,164,167,168,172,175,181,183,184,185,186,187,192,193,201,204,206,208,210,213,229,230,231,232,233,234,235,236,244,246,247,249,262,264,270,271,272,273,281,283,288,294,304,306,307,308,309,312,314,316,319,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,381,384,385,386,387,389,390,392,393,394,395,396,397,406,407,408,409,410,412,414,415,416,424,432,436,448],availab:9,ave_chunk:6,aveforc:[2,3,6,172,175],avendano:383,averag:[3,6,7,15,41,63,64,71,87,91,103,105,116,118,124,132,140,143,167,169,172,174,178,180,181,182,183,184,185,186,187,188,192,205,207,209,213,214,219,229,230,233,252,257,260,266,267,270,271,274,304,335,357,380,411,424,428,441,443,448],averi:278,avesq:117,avi:168,avoid:[1,3,6,12,36,39,59,144,145,164,168,177,182,183,186,198,205,207,214,251,253,261,265,270,271,292,299,331,339,357,377,380,393,407,425,431,432,443],awai:[3,6,61,116,167,168,191,195,208,211,228,251,274,275,289,295,329,349,369,373,428],awar:[333,356,420],awpmd:[0,2,7],axel:[7,9,13,18],axi:[3,6,41,118,123,143,144,146,166,168,188,205,208,211,226,256,275,290,296,308,314,321,423,426,433],axial:233,azimuth:[168,208],azur:169,b_k:396,ba2:143,babadi:394,back:[1,6,7,11,12,13,14,15,17,125,126,127,131,132,133,134,136,144,148,167,169,170,173,174,193,198,203,210,211,213,214,229,234,235,246,247,249,268,270,281,282,283,287,288,297,298,300,317,318,319,328,361,421,423,424,425,426,427,430,436,437,449],backbon:[191,273,312],backcolor:[169,451],backend:17,background:[9,87,88,112,121,169,188,194,213,278,286,290,293,328,347,378,379,380],backtrack:[324,326],backward:[9,12,170,328,437],baczewski:206,bad:[3,12,59,61,211,328,423,428,440],badli:[3,192,229],bal:285,balanc:[1,2,3,4,6,7,15,16,18],balasubramanian:248,ball:[120,378,379],ballenegg:318,bammann:178,band:[4,6,7,120,172,228,325,328,339],bandwidth:[1,10,18,40],bandwith:168,bar:[87,168,447],barashev:355,bare:[198,212,214],barost:[198,443],barostat:[0,1,3],barostt:6,barr:348,barrat:265,barrett:67,barrier:[3,4,6,228,314,328,348,359,437],bartel:252,bartok2010:396,bartok2013:396,bartok:[9,120,391,396],bartok_2010:391,bartok_phd:391,bary:447,basal:2,base:[3,4,6,8,9,11,12,13,14,15,20,63,64,71,78,87,91,111,118,124,126,143,144,146,167,168,169,172,178,184,185,188,189,190,194,195,199,210,213,217,219,241,252,253,259,261,263,270,271,274,278,285,319,333,335,337,339,353,357,360,363,365,369,378,381,382,387,389,390,406,409,410,418,420,423,424,425,427,430,433,434,437,438,441,447,448,449,452],bash:346,bashford:[6,20,150,344,435],basi:[3,6,12,40,120,124,144,177,213,215,252,278,295,321,416,433,448],basic:[6,7,8,12,17,41,113,121,168,169,178,188,229,230,251,299,334,336,417,425,443],basin:[86,328,418,437],bask:[355,380,390],bath:[9,260,265],batom1:[69,115,117,167,169],batom2:[69,115,117,167,169],bayli:[6,150,435],bb13:151,bcc:[3,4,7,64,70,73,321,380,382],bcolor:[3,168,169],bdiam:[3,168,169],be2:143,bead:[5,7,10,13,40,45,46,136,176,191,253,404],beam:195,bear:[6,206],becau:13,becaus:[0,1,3,6,8,12,16,17,18,29,40,41,59,64,71,77,116,120,124,129,134,144,145,146,150,167,168,169,170,175,179,181,188,189,190,191,192,194,200,204,206,207,212,213,214,215,226,229,230,241,247,256,260,261,265,270,275,280,285,286,289,290,293,297,298,299,300,301,307,318,324,326,328,329,332,333,344,346,349,351,353,357,358,360,361,362,363,364,367,368,377,378,379,380,384,394,404,405,411,412,420,421,423,425,426,427,430,432,433,435,437,443,448,449,450,452],beck:[2,3],becker:[334,355],beckman:210,becom:[1,2,3,6,7,8,18,39,41,54,57,59,71,146,167,168,169,188,189,190,191,194,205,207,216,228,229,267,268,281,282,295,296,298,299,300,318,319,324,328,335,347,349,355,357,360,369,384,390,394,406,415,423,424,426,433,448],been:[1,2,3,6,7,9,12,13,16,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,45,46,47,48,49,51,53,54,56,57,59,60,63,65,69,71,87,109,112,113,114,115,117,119,122,123,124,125,126,127,131,132,133,134,136,137,145,146,147,148,150,151,153,154,155,156,158,159,161,162,164,166,167,168,169,170,175,177,179,180,181,182,183,184,185,186,187,188,191,192,193,194,195,201,204,205,208,210,211,213,214,216,217,218,219,220,224,226,227,229,231,232,233,234,235,236,244,246,247,249,255,256,257,260,262,264,267,268,270,272,273,279,281,282,283,290,291,292,294,295,296,297,298,300,301,304,306,307,308,309,312,314,317,318,319,326,329,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,354,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,381,382,385,386,387,389,392,393,394,395,397,404,406,407,408,409,410,412,414,415,416,418,420,421,423,424,425,426,427,429,433,437,440,441,448,449,450,451],befor:[1,2,3,6,8,9,12,14,17,22,29,39,40,41,44,59,66,71,74,75,81,89,90,93,103,104,105,106,114,124,127,132,133,139,144,145,147,148,152,165,166,169,173,174,175,176,177,179,181,183,184,185,186,187,188,192,197,198,204,205,210,212,213,214,216,219,226,229,234,235,246,249,252,259,260,261,264,265,270,271,272,279,281,282,283,289,295,296,297,301,305,323,324,326,328,333,358,361,377,380,405,413,418,420,421,424,425,426,427,428,430,431,433,437,440,441,443,448,449,450,451,452],began:[5,12],begin:[3,8,12,38,39,56,71,117,119,145,164,166,167,169,173,174,178,180,181,182,183,184,185,186,188,194,198,214,241,255,268,271,278,280,283,292,297,300,301,315,317,318,319,320,322,325,327,328,329,332,333,355,384,390,397,404,407,411,416,418,423,430,437,439,441,443,447,448,450],behalf:3,behav:[3,27,153,325,326],behavior:[3,148,164,167,168,170,191,192,195,205,206,207,210,213,214,215,229,256,260,265,278,281,282,290,325,339,357,380,417,425,429,448,450],behaviour:[6,213],behind:[8,212,227,260,278,318],beig:169,belak:7,believ:11,bellott:[6,20,150,344,435],bellow:308,belong:[2,3,40,71,147,179,181,184,205,219,270,301,327,423],below:[1,2,3,5,6,8,9,11,12,15,16,17,22,38,39,41,42,44,54,56,59,60,63,65,68,69,71,77,79,91,92,112,113,116,117,118,120,121,124,130,132,138,142,143,144,147,148,150,152,163,164,167,168,169,172,173,175,176,178,181,182,183,184,185,187,188,190,191,192,194,195,200,203,208,209,211,213,214,219,226,227,229,233,234,235,246,249,251,256,259,260,261,268,269,270,272,273,275,278,279,280,281,282,283,286,287,288,290,293,295,296,301,303,305,316,318,321,323,324,326,327,328,330,333,334,335,336,339,340,341,344,345,346,347,349,352,355,357,358,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,383,384,389,392,393,394,395,396,397,405,407,412,414,415,417,418,421,423,424,425,426,428,430,431,433,435,437,439,440,441,442,443,448,449,452],bench:[1,6,11,12],benchmark:[1,7,10,11,12,13,14,15,16,17,18,41,188,318,436],beneath:195,benefici:[61,330],benefit:[1,206,432],bennet:87,beowulf:7,berardi:[360,394],beraun:290,berendsen:[2,3,6,7,125,126,127,131,132,133,134,136,172,179,205,207,229,233],berensen:270,berkelei:142,berkowitz:318,berlin:[7,9,274],bern:[3,253,261,262,348,360,405,432],bernendsen:6,beryllium:357,besid:[8,272,426],best:[1,6,8,14,15,16,17,18,19,229,247,248,269,270,333,339,349,369,373,384,407,424,432,437],beta:[6,9,252,260,334,337,355,356,358,380,408,409,410,441,448],beta_:339,beta_k:396,beta_pi:339,beta_sigma:339,beta_t:409,better:[3,6,7,8,12,14,16,27,120,153,174,188,205,216,229,241,261,268,270,278,319,328,333,408],betwe:338,between:[1,2,3,4,5],beutler:377,bewteen:[108,182,278,286,293,364,420],beyon:432,beyond:[3,5,6,12,17,61,71,87,142,167,169,183,184,205,229,318,330,359,375,384,437,441,448],bgq:17,bi3:143,bi5:143,bia:[3,6,8,112,121,123,124,125,126,127,131,132,133,134,136,137,181,193,194,205,213,214,229,234,235,246,247,249,265,281,282,283,285,449],bias:[6,9,193,449],biaxial:123,biersack:[380,405,410,416],big:[3,4,12,167,260,265,278,329,347],bigbig:[3,12],bigint:[3,203],bilay:[4,10,275],bilayer1:275,bilayer2:275,bill:7,billion:[3,7,10,12,39,205,431],bin:[3,6,11,12,39,63,66,71,75,90,93,104,106,114,116,124,132,139,141,167,169,181,183,184,185,252,260,265,278,329,330,333,354,388,424,451],binari:[3,6,7,12,13,16,33,37,50,55,157,163,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,310,313,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,416,424,425,430,450,452],binary2txt:0,binchunk:181,bind:[17,18,184,339],binsiz:[39,169,329,333],binstyl:132,bio:[40,329],biolog:[6,7],biologi:156,biomolecul:[255,270,318,319,344],biomolecular:432,biophys:210,biosym:13,bird:354,bisect:[41,188,412],bisector:[6,349,369,373],bispectrum:[63,120,396],bisqu:169,bit:[3,12,17,39,203,214,384,407,431,443],bitmap:[3,407,413],bitrat:[168,169],bitzek:325,bkgd_dyn:380,bla:12,black:169,blais:[9,13],blanchedalmond:169,blank:[2,3,12,38,56,107,164,168,255,270,327,328,339,356,380,386,396,406,407,408,409,410,420,421,423,448],blast:290,blend:380,block:[2,3,6,91,120,144,146,147,256,299,321,333,339,357,390,396,426,437,443],blow:[3,241,295,299,397],blown:3,blue:[2,168,169,191],bluegen:[167,318],blueviolet:169,board:[319,352],bodi:[0,2,3,4,5],body_nparticl:8,bodyflag:423,bodyforc:216,bodyforcei:216,bodyforcex:216,bodyforcez:216,bodystyl:[219,270],boff:[327,423],bogaert:285,bogu:[3,127,192],bogusz:88,bohr:[355,357,410,447],boltzmann:[6,7,9,87,91,112,122,124,125,126,127,130,131,132,133,134,136,181,191,213,216,217,218,219,220,233,294,353,438,447],bond:[0,1,2,3,6,7],bond_coeff:[2,3,6,43],bond_graph_cutoff:393,bond_harmon:[8,48,49],bond_harmonicshift:49,bond_info:393,bond_interact:178,bond_styl:0,bond_typ:[148,404],bondangl:[3,21,33,423],bondbond13:[3,151,423],bondbond:[3,21,33,423],bondchk:393,bondcoeff:3,bondtyp:[189,190,327,404],bonu:[3,450],book:415,bookkeep:384,bookmark:0,boost:[1,3,12,64,329],bop:[2,3,267,323],border:[3,7,16,61,290,449],boresch:87,boreschkarplu:87,born:[2,3,6,7,87,138,173,174],boron:357,borrow:274,bose:265,botero:[7,9,13,357],both:[1,3,6,7,8,9,11,12,14,15,16,17,18,27,37,39,54,55,57,59,61,62,63,68,69,71,83,87,88,108,113,115,116,123,124,129,132,134,137,144,146,147,148,153,163,164,167,168,171,172,173,174,179,181,182,184,185,186,189,190,191,192,193,194,199,205,207,209,211,213,214,216,217,225,226,229,230,234,235,241,246,249,255,259,260,261,267,270,273,274,275,278,282,286,287,288,290,293,295,296,298,299,300,303,304,313,319,323,326,327,328,329,331,333,335,339,340,341,342,343,344,345,347,352,353,355,356,357,360,361,363,364,365,369,371,373,374,375,377,378,379,383,384,387,394,395,406,408,409,410,416,418,420,421,423,424,425,426,430,435,440,441,443,448,450,451,452],bottleneck:[1,3,421],bottom:[8,9,127,169,194,204,216,247,286,293,321,435],bottomwal:187,bounc:[3,278],bound:[3,6,17,26,27,41,42,57,59,71,133,146,153,166,167,169,183,184,188,194,195,199,205,214,229,256,278,295,296,297,298,299,300,318,326,357,423,426,437,443,448,449],boundar:3,boundari:[2,3,5,6],boundary_dynam:178,boundary_faceset:178,boundary_integr:178,bount:11,box:[0,1,2,3,4],boxcolor:[168,169],boxxlo:11,bpa:333,bpclermont:[9,13],bptype:404,br1:143,bracket:[2,3,6,41,63,71,117,119,172,180,181,182,183,184,185,186,188,292,441,448],bragg:[118,143],branc:11,branch:11,branicio:73,breakabl:[7,44,55],breakag:[78,189],breakdown:[1,12,15,88,107,392,393,418,437],brennan:404,brenner:[335,405],brick:[3,41,62,132,146,188,423,425,427],brief:[1,5,6,7,8,12,212,335,339,393,437],briefli:[6,10,253,348],brilliantov:361,bristol:[5,7],brittl:389,broader:421,broadli:8,broken:[2,54,65,69,70,78,107,115,148,189,229,339,425,435,450],brook:6,brought:166,brown:[7,9,13,15,16,118,121,169],brownain:341,brownian:[2,3,6,7,105,213,215,270,294],brownw:7,brows:0,browser:[4,168],bryantsev:363,bsd:12,bstyle:[40,42],btype:[69,115,145,167,349,369,373,377,404],buc:342,buck:[2,3,6,87,173,174,291,319,340],buckingham:[7,173,174,261,319,340,342,343,351,405],buffer:[3,8,168,169,440],bufi:168,bug:0,bui:168,build:[0,1,2,3,6,7,8,9],builder:[7,13],built:[1,2,3,4,6,8,9,11,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,43,45,46,47,48,49,50,51,53,54,55,56,64,67,78,80,83,86,87,96,97,98,99,100,101,105,109,111,112,120,122,123,128,130,131,135,136,138,142,150,151,153,154,155,156,157,158,159,161,162,163,164,167,170,172,175,176,177,179,187,189,190,191,193,195,200,201,202,204,205,206,207,208,210,212,213,215,216,217,218,219,220,222,223,227,228,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,251,252,253,255,256,259,260,261,262,263,264,265,266,267,270,272,273,274,278,281,283,284,285,286,287,288,290,291,293,294,296,297,302,303,304,306,307,308,309,310,312,313,314,319,328,329,330,333,334,335,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,385,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,418,421,424,426,432,436,437,438],bulatov:[381,382],bulk:[4,6,10,70,216,251,257,350,380,384,389,427],bullet:7,bump:213,bunch:8,bundl:[9,168,170],burlywood:169,bussi1:282,bussi2:282,bussi:[207,282],bybe:9,c1060:14,c11:[182,380],c12:182,c13:182,c1n:182,c2050:14,c21:182,c22:182,c23:182,c2n:182,c31:182,c32:182,c33:182,c34:182,c3n:182,c41:182,c42:182,c43:182,c44:182,c_0:[290,402,403],c_1:[68,69,117,118,143,167,169,206,259,271,301],c_2:[69,117,118,140,142,143,167,271,292,301],c_3:[117,271],c_cluster:6,c_cstherm:6,c_dist:117,c_doubl:11,c_e:290,c_flux:91,c_forc:117,c_gauss:359,c_hb:363,c_id:[6,63,71,87,117,119,167,180,181,182,183,184,185,186,271,280,292,441,448],c_ij:6,c_ijkl:6,c_index:117,c_k:206,c_ke:286,c_msdmol:119,c_my_stress:180,c_mycentro:[181,184],c_mychunk1:114,c_mychunk2:114,c_mychunk:[6,66,75,90,93,104,106,124,139,141],c_mycom:183,c_mycomput:181,c_myf:[167,451],c_myrdf:[116,186],c_mytemp:[8,182,183,186,292,441,448],c_n_k:206,c_p:121,c_pe:110,c_peratom:[110,121],c_pi:339,c_press:117,c_prop:6,c_radiu:142,c_reax:[392,393],c_sa:271,c_sigma:339,c_size:6,c_stress:167,c_tatom:214,c_tdrude:[198,214,443],c_thermo_press:[8,182,183,186],c_thermo_temp:186,c_xrd:183,ca2:143,cach:[17,39,384,436],cacul:273,cadetblu:169,cai:443,calcforc:216,calclat:91,calcluat:[103,105,110,112,121,349],calcualt:[91,181],calcul:[0,1,3,4],caldwel:[6,150,435],calhoun:253,call:[1,3,6,7,8,11],callabl:[3,11],callback:[3,11,172,203,421],caller:3,calori:447,caltech:[6,7,9,13,357],calucl:6,calul:[11,12,124,319],cambridg:[9,391],campa:252,can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,313,314,315,316,317,318,319,321,322,323,324,326,327,328,329,330,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,435,436,437,438,439,440,441,443,447,448,449,450,451,452],cancel:[172,270,449],candid:[148,179,205],cannot:[1,2,3,6,11,12,13,15,16,17,39,40,41,54,57,58,59,68,71,82,84,88,104,117,119,123,124,145,147,148,166,167,168,169,180,181,182,183,184,185,186,188,191,192,194,195,205,206,207,213,214,215,219,226,229,231,232,234,235,237,238,239,244,246,249,256,257,260,265,267,270,271,272,278,286,290,292,293,295,296,299,300,301,303,318,321,326,328,331,332,333,342,343,345,355,360,362,369,373,375,377,384,387,392,394,395,404,405,407,418,420,421,423,424,426,427,429,432,433,435,437,440,447,448],canon:[172,179,205,207,229,230,246,247,248,249,253,282,285,288,389],cao1:253,cao2:253,cao:253,capabl:[5,7,9,11,14,16,17,18,297,303,319,333,335,345],capac:[9,40,101,130,265,290,399,423,433],capit:[197,423],capolungo:[118,143,271],captur:[6,291,335,343,357,361,373,380,443],carbid:349,carbon:[7,168,312,335,348,366,380],card:[12,14,16,22,44,77,87,116,152,173,174,270,305,323,346,363,417,425,430,450,452],care:[3,6,59,71,144,147,166,181,184,185,189,190,195,207,212,216,229,256,270,285,338,421,423,426,427,432,433],carefulli:[11,12,54,267,301,364,366,428],carlo:[6,7,9,172,179,191,205,270,285,354,405],caro:[179,355],carpent:[7,13],carri:[16,222,259,290,361,393],cart:[3,420],carter:[9,17],cartesian:[3,62,334,420],carv:147,cascad:[199,290],cash:7,cast:[207,448],cat:[15,168],catastroph:261,cate:216,categori:0,cation:358,caus:[1,2,3,6,8,12,16,17,144,146,147,148,167,169,177,192,199,205,241,251,268,270,295,297,298,299,300,303,317,319,326,328,332,363,369,375,378,379,417,421,422,423,424,427,428,430,431,448,452],caution:[1,319],cautiou:[189,190],cautious:335,caveat:[335,432],cbecker:[334,355],cc1:[6,14,66,75,90,93,104,106,114,124,139,141,181,184],cc2:14,ccc:[356,406,408,410],ccflag:[12,16,17,18,19,167],ccm6:355,ccsi:[356,406,408,410],ccu:339,cd2:143,cdeam:355,cdennist:9,cdll:11,cdof:[6,124,181],cdte:339,cdte_bop:339,cdtese:339,cdzn:339,cdznte:339,ce3:143,ce4:143,ceas:325,ceil:448,cell:[3,6,59,88,116,118,142,143,144,167,177,192,193,205,210,227,229,230,233,252,260,263,290,318,319,321,354,357,441],cella:[6,441],cellalpha:[6,441],cellb:[6,441],cellbeta:[6,441],cellc:[6,441],cellgamma:[6,441],center:[3,6,25,42,63,66,71,74,75,86,89,90,98,103,104,105,114,116,118,124,125,126,129,132,136,139,141,144,168,169,172,173,174,176,181,183,184,185,192,194,195,196,198,205,206,211,213,214,219,225,229,234,235,246,247,249,252,256,261,267,268,270,271,274,275,276,278,280,281,282,283,285,286,288,295,299,304,321,327,338,356,357,360,361,367,378,379,380,381,382,406,408,409,410,412,426,433,443,448],centimet:447,central:[3,61,70,76,77,116,120,219,251,273,276,327,386,392,393,423],centro:[2,3,5,6,7,8,63,64,67],centroid:[3,253,412,433],cerda:318,ceriotti2:207,ceriotti:[13,207,212],certain:[1,2,3,6,8,12,17,39,71,113,117,119,148,167,168,180,181,182,183,184,185,186,191,203,204,270,272,279,292,303,310,317,329,364,384,393,411,425,429,443,448],certainli:211,cerutti:319,cfg:[3,6,7,13,167,168,169,170],cfile:393,cfor:274,cg_type:395,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:273,ch2lmp:[0,6],ch3:273,chain3:329,chain:[0,3,4,6,10],challeng:[6,274],chalopin:265,champaign:[210,318,319,378],chandler:[334,355],chandrasekhar:[6,369],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,127,128,144,145,146,148,164,166,167,168,169,170,172,173,174,175,176,178,179,184,185,187,188,189,190,191,192,193,194,195,199,200,202,204,207,209,210,211,213,215,216,217,219,225,226,227,229,230,231,232,233,234,235,241,246,247,248,249,251,252,256,257,259,260,264,267,268,269,270,272,273,274,278,281,282,283,284,286,287,288,289,290,291,293,296,299,301,319,324,326,328,331,333,353,357,361,378,379,380,384,392,393,405,418,419,420,421,423,424,425,426,427,428,429,431,432,433,434,435,438,441,444,446,447,448,449,450],change_box:[2,3,6,57],changeabl:167,channel:[4,175],chapter:[253,319],charact:[2,3,6,12,38,41,56,63,164,167,168,169,170,172,188,259,267,303,327,332,357,368,390,392,393,407,420,421,425,430,431,448,450,451,452],character:[6,67,70,116,120,396,418,437],characterist:[214,278,287],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,143,144,167,170,172,173,174,179,195,200,205,259,261,262,263,267,280,293,318,319,327,340,342,348,349,351,352,355,357,358,364,369,373,377,387,392,393,405,410,411,413,415,416,423,424,428,433,435,443,447,448],charmm2lammp:13,charmm:[0,2,3,5],chartreus:169,cheap:278,cheaper:[199,360,394],check:[3,6,8,11,12,15,17,39,41,71,91,164,179,184,188,189,190,195,202,205,211,212,269,273,278,286,288,293,301,303,317,326,327,328,329,330,333,354,365,368,384,393,404,418,420,421,423,431,437,440,441],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:[0,2,3],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:0,cite:[3,7,8,12,213],cko:2,cl1:143,clarendon:[29,352],clarifi:[7,408,410],clariti:303,clark:387,class2:[2,3,9],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:[2,3,6,8,11],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:[2,3,6,7,12,61,63,71],clutter:[3,9],cmap:423,cmatrix:207,cmax:380,cmd:[11,12,253,434],cmin:380,cmm:[0,7],cn1:182,cn2:182,cna:[2,3,7,63,70],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:[0,1,3,4,5],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:[0,2,3],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:[2,3,4,6,7,9,12,39,147,172,270,278],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:[0,2],colvarmodul:12,com:[2,3,6,7,9,13,15,42,63,71],comamnd:194,comand:[191,425],comannd:333,comb3:[2,3],comb:[2,3,4,7,172,261],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:[0,2,3],comfort:[12,13],comm:[0,3,12,61,73,210,212,213,319,328,333,353,384,389,407],comm_modifi:[2,3,6,39],comm_styl:[2,3,41,61],command:[0,1],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:[0,1],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:0,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:[0,1],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:[2,3,63],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:[2,3,5,6],conducit:6,conduct:[0,2,3],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:[0,3,4],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:[3,5],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:[0,2,3,4,5,8,9,12,13,42,63],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:[2,3,6,7,11,59,63,72,76],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:[0,1,3],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:[2,3,6,91,120,140,172,181],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:[2,6,7,22],cosineshift:27,cosmo:[207,212],cossq:2,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:[2,3,6,9,36,45,46,87,107,138,150,173,174,291,319,326],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:[0,3,4],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:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,38,39,41,56,58,59,62,63,71,81,91,103,108,109,112,115,118,122,127,128,140,144,145,146,147,164,167,168,169,172,177,178,181,183,184,185,186,188,189],create_atom:[2,3,6,7,8,40,41,59,91],create_bond:[2,3],create_box:[2,3,6,22,40,41,44,57,58,59,62,71,91,142,144,145],create_elementset:178,create_faceset:178,create_nodeset:178,createatom:0,creation:[3,5],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:2,cst:355,cstherm:6,cstyle:420,csvr:[2,3,6],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:[3,38,56,164,216,251,278,319,321,355],cuda:[0,1,2,3,4,7],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:[0,3,6],cut0:421,cut1:432,cut2:432,cut:[1,2,3,6,9,12,14,15,16,17,18,19,41],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:[2,7,305],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:[2,3,63],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:0,data:[1,2,3,4],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:0,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:[2,3,7,173,174,265],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:[2,3,6,7,8,40,42,57,59,61,63,80,111,121],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:[2,3,7,144],delete_bond:[2,3,43,45,46,47,48,49,50,51,53,54,55,56,65,69,115,145],delete_el:178,deli:166,delimit:[421,448],deloc:[230,357],delr:380,delt_lo:437,delta:[2,22],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:[2,3,102,146,172],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:[2,3,6,8,9,11,12,13,18],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:[2,5],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:2,dielectr:2,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:[0,7],diffus:[0,4],digit:[2,3,169,303],dih_table1:164,dih_table2:164,dihedr:[0,2,3,7],dihedral_coeff:[2,3,150,151],dihedral_cosineshift:27,dihedral_styl:0,dihedralcoeff:3,dihedraltyp:190,dihydrid:357,dij:273,dilat:[2,3,59,61,63,78],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:[1,2,3,6,7,12,41,57,58,59,61,63,71,91,114,121,124,131,132,133,142,144,146],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:[0,2,3,4],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:[2,3,6,7,12,13,16,18,29,57,71,118,120,143,144,166,167,168,175,176,177,184,185,194,195],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:[0,1,2,3],disk:[6,84,85,137,165,195,205,256,421],disloc:70,disord:[39,70],disp:[0,2,3],dispar:394,disperion:[352,373],dispers:[3,6,7,9,142,252,318,319,343,352,373,378,384,393,407],displac:[2,3,6,7,12,42,59,63],displace_atom:[2,3,7,103],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:[0,1,2,4,5,6],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:[2,3,6,7,206,207,213],dpde:222,dproduct:336,dr_ewald:[118,271],drag:[2,6,91,172],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:[0,2,3,4],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:[0,2],dry:202,dsecriptor:365,dsf:[2,3],dsmc:[2,3],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:[0,1,2,3,4],dump_atom:8,dump_custom:8,dump_modifi:[2,3,6,167,168],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:[0,2,3,4,5,6,7,9,11,12,13,15,16,39,41,59,61,71,102,105,122,123,124,125,127,129,130,131,132,133,134,136,137,142,144,167,168,169,172,175,178,188,191,193,194,195,200,202,205,206,207,212,213,214,215,220,227,229,230,233,238,241,252,253,256,259,260],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:[0,2,3,5,7,8,9,10,12],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:[2,3,11,12,60,118,143],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:[2,7],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:[0,2,7,8],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:[2,3,172,179],eflux:209,eggebrecht:349,ehb:[392,393],eigensolv:3,eigenvalu:[252,253,318],eigtol:3,eik:138,eim:[2,3,4,7],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:[0,4],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:0,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:[2,3,6,165,172],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:6,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:[2,3,6,63],errata:[408,410],erratum:295,erron:3,error:[0,1,2],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:[2,3,57,102,172],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:[2,3,6,8,63],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:0,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:2,expand:[2,3,44],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:[3,6,59,113,120,167,181,228,251,364,384,417,420,421,423,432],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:[0,3,6,7],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:[2,3,9,86,87,168,172,187,192,200],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:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,87,91,102,108,115,118,120,138,143,146,150,161,167,168,169,173,174,182,188,192,194,195,205,210,213,215,216,227,229,230,233,253,257,269,273,278,282,286,293,294,295,299,309,319,321,333,335,336,339,340,342,344,349,350,351,353,357,361,364,368,369,380,384,386,387,393,395,397,406,411,420,423,426,427,432,435,437,438,441,443,447,448],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:[2,3,6,7,64,70,73,91,172],fcm:[243,448],fdirect:198,fdotr:365,fdti:87,fe2:143,fe3:143,fe_md_boundari:178,featu:8,featur:[0,3,5,6],fecr:355,feedback:[7,210],feel:[7,210,211,219,251,299,301,328,384],felling:382,felt:299,femtosecond:447,fene:[2,3,6,7,10,44],fennel:[349,369],fep:[0,2],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:[0,2,3,5],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:[0,1,2,3,4],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:[0,3],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:[0,1],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:[2,3,6,8,126,129,172],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:[3,8,11,12,14,15,16,17,18,40,66,74,75,81,86,89,90,93,103,104,106,118,139,143,147,167,168,169,170,186,191,193,197,210,213,217,219,225,226,252,259,270,275,277,278,285,289,298,301,316,319,327,331,332,333,335,363,368,380,384,404,418,420,421,423,424,425,427,428,429,433,448],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],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:[4,5],fluctuat:[6,64,87,192,205,206,213,216,229,233,251,252,288,290,312],fluid:[2,6,7,9,10,66,75,88,93,106,116,117,124,139,141,192,194,208],fluid_veloc:220,flush:[3,169,440],flux:[2,3,6,63],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:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,120,121,123,124,130,132,137,140,142,144,145,150,153,154,155,156,158,159,161,162,164,167,168,169,172,178,179,180,181,182,183,184,185,186,188,193,194,195,198,199,203,205,206,207,210,212,213,214,216,219,227,229,233,234,235,246,247,249,252,253,255,258,259,260,261,263,265,267,269,270,271,273,280,281,282,283,286,287,288,289,290,292,293,301,302,306,307,308,309,312,314,316,321,323,326,327,328,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,418,420,421,423,424,425,426,428,430,431,432,435,437,438,439,443,448,449,451],foo:[4,8,11,12,167,168,203,421,434,448],foot:6,footprint:[12,333],fopenmp:[12,16,18],forc:[0,1,2,3,5],force_uvm:17,forceatom:219,forcefield:[269,363],forcegroup:216,forcezero:324,ford:352,forestgreen:169,forev:71,forget:[214,443],forgiv:229,form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,120,121,138,139,148,152,169,172,173,174,190,206,207,213,215,219,226,247,252,263,265,269,270,290,295,299,304,305,312,323,325,327,328,335,336,339,346,355,357,359,363,364,368,380,382,386,387,390,392,393,394,396,397,405,407,408,409,410,415,417,420,421,423,428,433,440,443,448],formal:[6,78,80,91,206,207,213,229,253,278,286],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,152,164,167,168,169,170,181,183,184,185,186,188,190,252,255,259,261,263,266,270,271,289,290,301,302,305,323,327,328,334,335,339,346,355,358,368,380,382,391,392,393,395,396,407,413,420,421,423,424,425,428,439,440,441,448,450],former:[6,12,16,39,41,169,188,290,294,339,341,429,435,448],formerli:[7,13],formul:[1,64,121,175,200,213,229,247,261,263,269,273,289,318,335,339,355,357,360,380,389],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,143,144,149,151,152,163,167,173,174,175,176,181,182,183,186,187,194,200,208,209,211,213,214,226,251,252,258,267,272,276,278,281,282,283,292,295,298,300,301,303,304,305,307,313,321,327,335,336,338,339,344,345,346,347,352,353,355,356,360,361,362,363,365,368,369,371,372,373,375,376,378,379,380,383,384,385,394,395,397,405,406,408,409,410,414,415,416,419,423,426,433,440,441,447,448,449],forth:[1,6,11,12,13,14,15,332,421,426,430],fortran:[3,6,9,11,12,13,203,355,364,380,392,393],fortun:8,forward:[3,8,87,317,328,333],foster:[339,389,390],foul:147,found:[3,6,9,12,73,138,167,191,193,205,210,216,252,285,291,303,317,329,346,349,352,418,424,425,440],four:[6,11,54,81,103,104,120,140,227,290,312,327,328,418],fourier:[2,6,12],fourth:[6,105,269,275,285,344,386],fox:[6,118,150,403,435],fphi:[38,56,407],fpic:12,fplo:[38,56,407],fprime:407,fqdn:212,fqq:352,frac:[198,214,411,443],fraction:[1,3,6,8,12,16,39,41,80,109,121,147,166,168,169,179,189,190,191,192,227,256,260,267,268,278,283,284,321,328,333,339,341,361,378,379,428,433],fragment:[42,210,267],frame:[83,120,169,178,227,260,297,360],framer:[168,169],framework:[5,207,334,396],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,138,174,251,278,287,288,289,290,325,328,336,357,377,390,415,420],freedom:[3,6,8,94,96,97,99,101,102,112,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,181,191,198,205,207,213,214,219,229,230,233,234,235,246,247,249,253,255,270,273,281,282,283,288,326,352,441,443,449],freeli:[0,6,7,12,123,137,142,168],freez:[2,3,6,172,177],frenkel:[205,288],freq:177,frequenc:[3,6,16,39,169,241,252,253,260,265,316,353,357,393,418,432,437,448,451],frequent:[3,64,67,70,72,73,77,88,120,169,189,190,202,286,293,384,430],fri:[227,260],friction:[4,5,6,10,42,172,207,213,260,265,270,290,294,296,361],from:[0,1,2,3,5],front:[227,260,297],frontend:[168,264],frozen:[6,112,148,204,206,214,329,359],fs2:[6,91],fscale:210,fstr:448,fstring:421,ftol:[326,328,418,437],fuchsia:169,fuction:349,fudg:273,fugac:205,fugacity_coeff:205,fulfil:6,full:[1,2,6,9,12,17,38,39,40,91,168,182,193,216,251,318,319,333,339,355,357,358,360,411,423,425,430,431,435,437,443,451],full_energi:[3,205],fuller:326,fulli:[3,6,9,78,207,212,251,326,328,349,390,391,450],fulton:355,fumi:340,func:[421,448],funcfl:355,functino:6,functionaliri:193,fund:[0,7],fundament:[278,447],further:[3,6,8,12,13,61,63,71,86,105,107,116,168,169,172,181,183,184,185,186,189,195,199,216,220,253,261,271,278,290,292,301,319,324,326,327,328,329,334,338,348,404,418,437,438,448],furthermor:[27,153,357],furthest:61,futher:3,futur:0,g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:390,g_p:290,ga3:143,gaa:339,gahler:325,gai:[3,360,405],gain:285,gainsboro:169,galindo:383,game:210,gamma0:29,gamma:[3,6,29,213,216,220,252,260,261,263,265,294,353,356,360,380,383,399,402,403,406,408,410,441],gamma_:[3,290,296],gamma_ijk:408,gamma_n:[296,361],gamma_p:[3,290],gamma_t:[296,361],gammaa:383,gammafactor:216,gammar:383,gan:[390,406,408,410],gan_sw:390,gan_tersoff:390,ganzenmuel:[7,9],ganzenmul:9,gao:[6,20,150,344,435],gap:[164,378,379,391,396],gap_2014_5_8_60_17_10_38_466:391,gap_exampl:391,gaseou:7,gass:205,gather:[11,431],gather_atom:11,gather_scatter_loop_unrol:12,gathert_atom:11,gauch:156,gauss:[2,3,107,138,173,174,350],gaussian:[6,40,63,91,103,105,206,207,213,253,269,278,282,300,318,353,354,357,359,391,405,418,448,449],gave:[3,384],gaybern:[2,3,6,7,123,326],gcc:17,gcmc:[2,3,7,9,172,179],gcore:198,gd3:143,gdot:379,gdrude:198,ge4:143,gec:[408,410],gen:[229,230],gener:0,genom:7,gentler:[295,298,300],gentli:356,geom:[6,318,354,418,449],geometr:[3,6,7,8,42,57,59,71,134,135,144,146,167,169,175,184,185,187,188,195,200,209,229,234,235,246,247,249,270,272,281,282,283,299,301,318,321,328,338,341,345,347,349,352,357,360,362,367,369,370,371,372,373,374,375,376,377,378,379,383,384,394,397,411,412,414,415,423,425,426,433,441,448],geometri:[3,6,7,13,25,41,71,132,144,184,188,189,190,192,195,211,321,384,423,426],georg:[7,9],georgia:13,gerber:377,germani:[9,14],germann:[233,371,418,437],germano:360,gerolf:13,get:[0,1,3,4,6,8,9,11],get_natom:[11,421],getenv:448,gettimeofdai:12,gewald:[6,318],gezelt:[349,369],gf100:14,gf104:14,gf200:14,gflop:12,gflp:12,ghost:[3,6,7,12,16,58,61,62,73,142,147,192,194,214,229,259,270,271,318,329,333,353,354,357,361,368,428,433,443],ghostwhit:169,ghz:10,giacomo:9,gif:[4,168],gifsicl:168,gigabit:18,gillan:396,gingold:[399,400,402],gio:2,git:[7,12],github:[13,17,193,207,212,391],give:[0,1,2,3,5,6,7,8,9,10,11,12,14,15,16,17,29,54,71,113,124,127,131,144,167,169,175,177,181,182,183,186,192,194,207,229,247,251,252,257,265,267,270,292,318,319,326,329,330,333,335,339,354,357,363,364,380,384,394,408,409,410,418,420,421,423,433,437,443,449],given:[3,5,6,7,9,10,11,12,16,17,22,27,37,44,55,63,64,67,71,113,120,121,138,142,146,152,153,163,164,167,169,172,179,181,184,189,190,192,194,195,199,205,206,207,208,210,216,223,226,228,229,233,250,251,252,253,260,261,267,269,273,275,276,278,280,285,290,291,294,295,296,299,305,313,318,319,333,334,335,339,340,342,343,345,346,347,348,349,350,353,354,355,357,358,360,363,369,370,371,373,380,381,382,383,384,386,387,390,394,395,396,404,405,416,418,421,423,425,426,433,437,447,451,452],gjf:213,gjwagn:7,gko:2,gld:[2,3,172],gle4md:[207,212],gle:2,glitch:3,glob:434,global:3,glosli:319,glotzer:[270,353],glue:11,gmail:[7,9,13],gmake:[12,17],gmask:[3,448],gnu:[0,7,12,17,18],gnuplot:[11,13],goal:[5,12,39],goddard:[6,9,25,261,262,263,314,357,363,392,393,435],goe:[12,54,120,144,166,226,326,329,352,356,362,371,374,397,416,426,430],gold:[70,169],goldenrod:169,goldman:260,gone:3,good:[1,3,6,12,17,41,73,118,142,143,188,213,227,229,261,267,273,285,318,328,329,334,347,354,355,384,407,418,432,437,441],googl:210,gordan:120,gordon:6,gould:[6,150,435],gov:[0,7,9,13,334,355,358,447],govern:216,gpl:[0,7,8,12],gpu1:333,gpu:[1,2,3,4,7,9,12,14],gpuid:333,gpun:333,grab:[3,6],gracefulli:3,grad:[6,175,200,228],gradient:[6,7,8,12,13,192,200,208,209,228,247,262,286,290,324,325,328,379,393,407],graduat:255,graft:191,grai:169,grain:[5,6,7,9,29,36,40,54,67,144,147,156,172,251,255,270,278,362,395,435],gram:[181,184,185,355,447],grama:[9,263,393],gran:[2,3,6,172,295],grand:[3,172,179,205],granflow:5,granular:[0,3,4,5],graph:11,graphen:427,graphic:11,grasp:5,gravit:208,graviti:[2,3,6,172,179,205],grdient:178,great:[3,13,260],greater:[1,3,10,61,86,142,169,192,206,229,251,283,297,333,338,340,342,343,384,418,420,423,426,432,437,448,449],greathous:13,greatli:[118,437],green:[2,6,91,168,169,252,253,286,339],green_kubo:6,greenyellow:169,greffet:265,greg:[7,9],grest:[45,46,191,278,319,343,361,373,435],grew:71,grid:[3,12,41,62,118,132,143,146,188,216,265,278,290,291,318,319,417,420,423,425,427,432],grigera:6,grime:40,grmask:[3,448],gromac:[2,3,6,7,167,302,326],gronbech:[213,318],groot:353,ground:[6,357],group1:[126,147,329],group2:[88,126,145,147,329],group2ndx:2,group:[2,3,5,6,7,8,9,11,12,13,16,39,41,59,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87],group_id:11,groupbig:278,groupid1:[219,270],groupid2:[219,270],groupid:423,groupnam:329,grouptyp:205,grow:[3,8,177,194,195,211,213,229,251,292,361,423,435],grow_arrai:8,grow_reset:8,growth:[6,285],gsmooth_factor:380,gstyle:[3,420],gtl:7,gtx285:14,gtx450:14,gtx460:14,gtx470:14,gtx560:14,gtx580:14,guarante:[65,69,79,92,108,115,144,147,167,199,261,317,321,433],guess:[3,167,257,424],gui:[7,11],guid:[1,17,40,78,80,99,100,101,172,222,223,291,389,398,399,400,401,402,403,433],guidelin:[1,8,14,15,16,17,18,19,318,407],guidlin:17,gullet:380,gumbsch:325,gunsteren:[257,281,377],gunzenmul:7,gunzip:12,guo:[6,20,150,156,344,435],gwald:3,gyrat:[2,3,6,63],gzip:[3,12,167,168,169,289,328,423,424,428],h12:360,h2o:[40,327],haak:[257,281],had:[3,6,11,13,59,63,167,169,170,183,186,191,192,206,207,209,213,214,215,227,229,231,232,233,234,235,246,247,249,256,257,278,281,282,283,290,353,354,361,404,425,429,432,438,441],hafskjold:6,half:[1,3,6,8,16,17,39,41,58,59,146,168,180,188,194,213,229,290,295,299,329,333,336,339,347,357,423,425,426,433,443],halfwai:[41,168,169],halsei:361,halt:[41,169,188,209,303,440],halv:168,ham:[38,56],hamak:[295,299,347,394],hamilton:70,hamiltonian:[207,229,230,282,357,432],hammond:[318,319],han:355,hand:[3,6,19,54,144,162,166,168,216,226,321,349,357,423,426,433,436],handl:[3,9,16,168,193,263,333,336,357,378,393,421,437],hang:[3,420,421],happen:[3,6,8,12,15,18,61,116,148,169,179,182,329,333,421,424,431],happi:8,haptic:210,hara:409,hard:[1,219,263,269,270,354,426],harden:397,harder:[295,299,443],hardi:[178,214,318,319,443],hardwar:[1,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,175,187,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,294,304,306,307,308,309,312,314,318,319,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,436],hardwir:[3,17,296],hardy2:319,harm:336,harmon:[2,3,4,6,7,8,22],harmonic_fix_wal:379,harpertown:18,harrison:335,hart:278,hartre:[336,355,357,447],hasan:9,hash:[39,423],hassl:269,hat:[6,10,228],have:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,45,46,47,48,49,51,53,54,56,57,59,63,64,65,66,67,69,70,71,72,73,75,77,81,86,90,91,93,103,104,105,106,109,112,113,114,115,116,120,121,122,123,124,125,127,131,133,136,137,139,140,141,142,144,145,146,147,148,150,151,153,154,155,156,158,159,161,162,164,166,167,168,169,170,175,177,179,180,181,182,184,185,186,187,188,189,190,191,192,194,195,200,201,202,204,205,206,207,208,209,210,211,213,214,215,216,219,224,226,227,229,231,232,233,234,235,236,241,244,246,247,248,249,251,253,255,256,257,259,260,261,262,265,268,270,272,273,278,279,281,282,283,284,285,289,290,291,292,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,312,314,318,319,321,324,325,326,327,328,329,330,333,334,335,336,337,339,340,341,342,343,344,345,347,348,349,352,353,354,355,356,358,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,389,390,392,393,394,395,397,406,407,408,409,410,412,414,415,416,417,418,420,421,423,424,425,426,427,428,429,430,431,432,433,435,437,438,440,441,443,447,448,449,450,451,452],haven:421,hayoun:265,hayr:213,hbcut:392,hbnewflag:392,hbond:[2,3,6],hbond_cutoff:393,hcp:[64,67,73,321,380],he1:143,head:[6,21,151,304,359,363,392,393,438],header:[3,6,7,8,12,145,167,168,169,170,181,182,183,184,185,186,227,260,267,271,290,327,334,339,355,420,423,433,440],heal:432,heat:[2,3,6,9,40,63],heatconduct:2,heavi:278,heavili:[41,188],heavisid:290,hecht:278,heenen:9,height:[168,195,256,328,359],heisenberg:9,held:[6,71,278,328,361],helic:156,helium:337,helix:[2,7,152],hello:421,help:[3,8,12,14,15,16,17,18,19,167,192,194,227,316,339,408,410,450],henc:[1,3,13,20,21,26,32,35,36,70,71,108,124,134,151,181,229,263,278,294,295,299,301,304,306,309,312,319,349,359,377,390,425],henderson:53,hendrik:9,henin:[9,193],henkelman1:[228,328],henkelman2:[228,328],henkelman:[228,325,328],here:[1,2,3,4,5,6,7,8,10,11,12,13,14,15,16,17,18,19,22,37,41,44,55,63,68,69,70,71,118,124,142,143,152,155,163,167,168,169,172,181,188,191,194,205,206,214,216,251,260,263,265,271,290,295,298,300,301,303,305,313,317,326,328,332,333,335,336,339,346,358,360,363,364,368,390,394,405,407,416,421,428,443],herist:291,herrmann:278,hertizian:296,hertz:[2,296],hertzian:[6,296,361,405],hertzsch:361,hess:318,hessian:[5,325],heterogen:105,heurist:[291,424],hex:[3,17,144,321],hexagon:[67,380],hey:[110,121],hf4:143,hfo:348,hftn:[325,326,328],hg1:143,hg2:143,hgrid:278,hibb:253,hidden:[17,421],hienergi:301,hierarch:[7,432],hierarchi:[319,343,344,369,370,373,383,432],higdon:[9,378,379],high:[1,3,6,7,9,19,41,164,168,188,192,199,214,227,286,290,293,319,325,326,333,339,357,360,394,407,416,420,432,437,443],higher:[1,14,120,147,169,189,190,195,211,256,265,285,298,300,326,357,365,448],highest:[195,303,327,328,448],highli:[3,6,7,9,144,168,194,213,229,241,260,270,324,326,357,418,437],highlight:[6,7,10,13],hight:359,hilger:[318,319],hill:253,hill_height:13,him:9,hint:12,histo:[2,3,6,63,113,143,172,180,181,182],histogram:[1,6,12,63,116,142,172,182,183,186],histor:358,histori:[0,2,3],hit:[3,278,297],hmaktulga:[7,9],ho3:143,hoc:312,hocknei:[318,319],hoh:[6,349,369,373],hold:[6,33,59,71,157,181,194,221,254,269,270,275,326,328,361,377,415,434],holdem:269,holder2:319,holder:[318,319],hole:275,holian:[233,371],holm:[251,319],holonom:289,home:[11,12,170],homebrew:12,homepag:[168,210],homogen:[247,384],hone:253,honeydew:169,honor:170,hook:[2,6,11,210,296],hookean:361,hoomd:170,hoover:[6,7,8,134,172,198,213,214,229,230,231,232,233,234,235,246,247,248,249,253,257,265,270,281,282,283,288,353,443],hop:[191,328,339],hope:[5,13,17,41,42,188,431],hopefulli:[8,326],horizon:389,horn:6,host:[3,12,16,17,193,333],hot:[6,209,230],hotpink:169,hottest:286,hour:12,hove:380,how:[0,1,2,3,4],howev:[1,2,3,6,7,11,12,15,16,17,36,39,41,71,88,91,104,118,120,143,164,167,168,169,182,186,188,191,192,195,198,205,206,207,212,213,214,215,216,219,229,251,253,256,259,260,265,270,271,278,279,281,282,285,286,290,291,292,293,294,319,321,323,324,328,333,345,347,355,356,361,364,380,388,390,406,407,410,418,420,421,424,431,437,440,441,443,448,449],howto:[6,63,71,122,123,125,127,130,131,132,133,134,136,137,172,213,214,229,257,281,282,283,349,363,369,373,449],hoyt:178,hpc:[1,15],hsw:17,htm:355,html:[0,4,8,11,12,15,212,359,379,432],htmldoc:0,htst:437,http:[0,6,7,11,13,14,15,193,207,210,212,334,355,378,391,392,393],htype:[349,369,373,377],hubbard:350,huge:[12,146,241,278,423,428,440],huggin:[7,340,342,405],hugh:178,hugoniostat:[4,172,233],hugoniot:[227,233,260],hull:142,hummer:318,hundr:[7,14],hura:6,hwloc:[12,17],hybrid:[1,2,3,6,7,9,16,18,22],hydrat:359,hydrocarbon:[335,348,357],hydrodyanm:40,hydrodynam:[7,9,40,99,101,216,218,219,220,341,378,379,405,433],hydrogen:[3,6,7,202,265,335,339,349,357,363,369,373,377,392,393,405,423,432,443],hydrostat:[3,192,229,233,257,270],hynninen:[350,359],hyoungki:382,hyper:253,hyperbol:350,hyperspher:120,hyperthread:[16,17],i_0:290,i_1:390,i_csid:6,i_flag1:259,i_mpi_pin_domain:16,i_myflag1:259,i_myflag2:259,i_n:390,i_nam:[113,167,259,280,433],ialloi:380,iatom1:115,iatom2:115,iatom3:115,iatom4:115,ibar:380,ibead:253,ibm:[167,318],icc:[10,12,16],icm:[9,210],ico:64,icosohedr:73,ictp:13,id1:[270,328,368,423,426],id2:[270,274,275,328,368,423,426],id_press:[192,227,229,231,232,233,234,235,257],id_temp:[191,192,227,229,231,232,233,234,235,246,247,249,257,281,282,283],idea:[1,3,6,11,12,41,121,168,169,188,211,251,274,278,286,319,384,431,443],ideal:[6,9,40,73,116,198,205,251,321,378,399,443],idealga:2,ident:[1,3,9,12,39,40,71,120,167,169,183,192,193,206,207,213,214,226,229,251,253,257,265,267,270,319,327,328,333,340,342,349,351,355,371,377,386,392,393,396,416,418,421,424,437,447,448,449,451],identi:333,identif:67,identifi:[1,3,12,38,40,56,70,142,144,164,267,278,301,363,368,380,407,418,420,423,426,437,438,440],idl:[18,437],idn:[270,328],idr:448,ielement:380,ieni:13,ifdef:[8,12],iff:214,iffp:421,ignor:[3,6,11,16,41,71,83,87,98,107,119,148,167,168,169,173,174,182,183,184,186,188,192,193,194,195,205,208,212,213,226,229,233,238,243,257,259,269,270,271,278,281,282,283,289,290,292,295,299,300,301,310,320,323,327,328,333,334,345,346,347,355,356,358,360,367,368,380,386,390,394,406,407,408,409,410,412,418,420,423,424,428,433,435,437,440,448],ihl:278,iii:[6,9,25,261,263,314,363,435],ijk:[308,312,314,339,390,420],ijl:312,ikeshoji:6,ill:[124,134,181,261],illeg:3,illinoi:[210,318,319,378],illog:421,illustr:[1,6,8,11,12,17,251,253,328,364,421],ilmenau:[7,9,14],ilya:[7,9],imag:[2,3,4,6,11,12,66,74,75,81,89,90,93,103,104,106,113,118,139,144],image2pip:168,imageint:3,imagemagick:[4,168],imagin:[275,289,339,356,364,365,381,382,386,390,406,408,409,410,435],imaginari:[6,205,253,423],imbal:[1,41,188],imbalanc:[41,188],imbu:278,imd:2,img:168,immedi:[0,2,3,8,12,144,189,190,195,273,279,280,297,420,421,423,425,437,448,451],immens:3,immers:[216,270],impact:[1,4,6,8,199,285],impart:[3,6,208,278,300],impei:[6,369],implement:[1,3,6,8,9,12,17,18,27,78,87,118,126,132,143,144,152,153,163,181,193,197,207,210,213,216,218,219,220,227,247,250,252,253,259,260,261,263,264,265,273,274,278,285,290,294,312,317,318,319,326,328,333,334,336,339,348,349,351,353,355,356,357,364,369,373,377,380,389,392,393,394,408,410,420,421,432,437,443,448,450],impli:[3,6,40,59,87,121,168,173,174,175,194,200,213,269,281,283,284,318,321,346,421],implicit:[2,6,7,206,207,213,238,270,294,295],implicitli:8,implict:350,imporop:327,importannt:226,important:288,important_not:59,impos:[2,6,71,112,133,166,172,175,176,187,200,201,203,208,211,220,221,228,241,251,254,272,275,277,278,285,286,287,288,293,294,295,298,299,300,326,328,330,417,431],imposs:1,improp:[0,2,3,7],improper_coeff:[2,3,304],improper_styl:0,impropercoeff:3,impropertyp:190,imprort:97,improt:[173,174],improv:[0,1,9,39,41,169,188,229,252,333,363,369,384,393,406,409],in3:143,inaccur:[1,3,6,147,227,318],inaccuraci:299,inact:363,inappropri:144,incid:[118,143,195],includ:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,61,63,65,66,68,69,70,74,75,77,79,81,83,87,88,89,90,91,92,93,94,97,98,103,104,105,106,108,109,110,111,112,114,115,116,118,120,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,138,139,141,142,143,147,148,150,151,152,153,154,155,156,158,159,161,162,163,164,167,168,169,170,172,173,174,175,176,178,179,181,182,183,184,185,186,187,191,192,194,195,196,198,200,201,203,204,205,206,208,209,210,211,213,214,216,217,219,220,224,225,229,230,231,232,233,234,235,236,244,246,247,248,249,251,252,253,255,256,260,262,265,266,267,269,270,271,272,273,274,275,277,278,279,281,282,283,285,288,289,290,291,292,294,295,296,298,299,300,301,303,304,305,306,307,308,309,312,313,314],includig:[303,317],inclus:[0,3],incom:210,incompat:[3,11,365],incomplet:[3,11,423],incompress:[230,357],inconsist:[3,148,191,424],inconveni:321,incorpor:[260,339,350],incorrect:[3,127,213,380],incorrectli:[3,321,361,448],increas:[1,3,6,10,18,38,56,57,59,109,118,121,164,167,168,169,189,190,191,194,213,257,268,269,270,286,289,293,318,319,328,333,357,360,393,407,409,421,432,437,448],increasingli:357,increment:[3,11,175,176,187,188,195,200,202,229,274,301,317,332,367,418,421,435,437,448],incur:[14,17,181,184,185,202,290,420],inde:127,indefatig:7,indefinit:287,indent:[2,3,4,172,186],independ:[4,6,11,12,16,17,41,59,63,91,117,119,130,144,166,172,180,181,182,183,184,185,186,188,191,192,193,194,195,206,208,213,214,216,219,229,252,257,261,265,270,271,274,277,288,290,321,361,418,421,440,449],indetermin:[167,169],index:[0,3,6,8,11,12,38,39,40,56,68,69,117,119,164,167,169,180,182,210,212,253,271,290,301,302,303,323,332,384,392,393,407,413,423,438,448],indianr:169,indigo:169,indirectli:[6,448],indistinguish:213,indium:396,individu:[0,1],induc:[0,3],industri:7,ineffici:[3,6,40,64,67,70,72,73,77,120,132,168,194,229,252,318,330],inerti:379,inertia:[2,3,6,40,42,63,82,83,84,85],inexpens:[207,432],inf:[2,3,12,293,426],infer:[3,94,96,97,138,175,176,188,189,190,200,210,255,278,286,293,321,346,358,423,435,441],infil:[3,13,270,420],infin:[3,326,428,441],infininti:168,infinit:[3,195,204,211,213,216,252,278,290,296,297,319,321,357,427,447],infinitesim:6,inflect:[350,371],influenc:[3,9,41,80,126,226,256,318,319,384,408,409,410],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,39,41,42,59,61,62,63,68,88,115,117,118,143,144,150,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,203,204,205,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,228,236,237,238,239,240,241,242,243,244,245,250,251,252,254,255,256,257,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,278,279,281,282,283,284,285,286,287,289,292,293,294,295,297,298,299,300,302,316,318,319,322,325,326,327,328,329,331,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,420,421,423,424,425,427,428,430,435,437,438,440,448,450,451,452],infrequ:[6,353,418,437],infti:[350,378,379],ingtegr:339,inher:[318,326,384],inherit:[6,411],inhomogen:[18,290,384],inidividu:326,init:[3,8,12,268],init_fil:290,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,39,40,41,56,57,59,62,71,80,81,86,87,103,104,140,145,146,164,166,167,168,169,170,173,174,177,178,182,188,190,191,192,194,201,205,206,210,211,212,213,214,216,221,225,226,227,228,229,233,241,252,253,254,259,260,265,268,269,270,272,277,278,280,285,287,288,289,290,291,292,295,296,297,298,300,301,303,318,322,325,326,328,335,336,352,353,354,391,392,393,407,418,420,421,423,425,426,428,430,431,433,437,438,441,443,448,449,450,452],initial_integr:8,initial_integrate_respa:8,initialis:391,initialt:290,inlclud:11,inlcud:448,inlin:421,inner2:[344,362],inner:[3,8,16,167,211,303,317,324,325,326,328,332,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,413,414,415,416,432,437],inner_distance_cutoff:363,innergroup:219,innermost:[38,56,331,407,432],innernod:219,innner:375,inordin:291,inorgan:6,inp:[193,303,396],input1:[65,68,69,79,92,108,113,114,115,117,119,280],input2:[65,68,69,79,92,108,113,114,115,117,119,280],input:[0,1],input_doubl:3,insensit:12,insert:[3,5,7,8,12,59,144,172,195,205,211,256,318,396,404,421,427,443],insid:[2,3,6,8,11,71,144,167,169,180,184,185,195,196,202,205,211,216,219,256,270,278,295,297,298,299,300,301,316,321,371,421,422,423,425,426,433,437,448],insight:[6,13],instabl:[216,352],instal:[0,1,3,6,8,9],instanc:[6,11,193,207,297,359,364,384,390,421,443],instantan:[6,63,191,192,206,207,229,233,252,257,260,265,267,270,285,429,441],instanti:[6,11,12,178,364,420],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,63,70,71,90,117,123,126,148,164,167,174,181,183,184,185,186,188,192,193,213,216,219,220,252,258,268,270,280,298,316,318,319,322,329,333,342,343,355,368,370,377,380,418,426,430,437,439,443,448],institut:[9,210,255],instruct:[3,6,8,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,122,131,142,150,151,153,154,155,156,158,159,161,162,164,165,168,175,187,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,294,304,306,307,308,309,312,314,319,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,432,443],insuffici:[3,6,12],insult:229,insur:[3,6,11,12,17,39,40,61,73,102,104,144,145,164,167,168,169,175,189,190,195,200,201,202,203,205,208,213,225,258,259,268,270,278,290,295,299,300,301,303,317,327,329,333,347,360,364,388,394,407,420,421,423,424,428,431,432,440,441,448,449],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,113,115,117,119,120,142,144,147,148,150,154,155,159,164,166,167,168,169,179,181,184,185,189,190,191,195,197,203,205,206,207,210,213,214,215,216,252,255,256,259,260,265,270,278,280,282,285,289,290,308,318,321,341,353,354,367,380,392,393,396,418,420,421,423,431,432,433,437,440,448,449],integr:[2,3,5],intel:[0,1,2,3,4,7],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,8,12,13,36,206,391,423],intens:[1,3,6,9,63,66,74,75,86,89,90,91,93,103,104,105,106,112,114,116,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,143,172,181,182,183,184,185,186,188,189,190,191,199,202,209,219,227,229,233,267,270,271,278,286,290,292,293,440,441],intepol:448,inter:[14,18,42,61,62,124,147,148,167,191,213,215,228,262,270,318,328,339,433,443,448,450,452],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,77,79,87,88,92,107,108,110,112,115,116,120,121,123,137,138,142,145,146,147,148,149,150,152,156,157,163,167,172,173,174,189,190,191,204,205,210,211,213,215,219,241,251,253,255,261,263,269,270,278,279,285,290,294,295,296,299,300,305,306,307,309,313,318,319,326,327,328,329,330,331,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,393,394,395,396,397,404,405,406,408,409,410,411,412,413,414,415,416,418,421,423,425,427,428,432,433,435,440,441,443,450],interatom:[3,4,7,144,167,228,287,288,334,339,355,357,365,380,409,448],intercept:118,interchang:6,interconnect:18,interconvert:357,intereract:39,interesect:299,interest:[1,5,7,8,9,11,13,71,143,253,285,288,319,356,379,392,393,421,448],interf:333,interfac:[0,3],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:0,intsal:16,intuit:321,inv:[118,143,271],invalid:[3,12,71,89,147,241,328,378,379,425],invari:120,invent:273,invers:[3,6,51,118,143,169],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:[2,13],ipp:0,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:[1,3,6,7,9,10,12,13,45,46,64,87,107,110,172,178,257,278,295,299,319,321,326,335,338,342,343,344,345,347,352,360,362,363,364,367,368,369,370,371,373,374,376,377,383,384,390,394,395,400,405,412,435,443],jonsson:[73,228,325,328],jorgensen:[6,161,349,369,373],joul:447,journal:[138,156,178,263,319,355,392,393,399,400,402],jparam:[3,190],jpeg:[3,12,168],jpeglib:12,jpg:[4,8,12,167,168,169,451],jpg_inc:12,jpg_lib:12,jpg_path:12,jpl:[7,9],jth:448,jtype1:116,jtype2:116,jtype:[3,116,190,413],jtypen:116,judg:437,judici:6,julien:9,jump:[2,6,36,233,303,315],june:170,just:[3,6,8,9,11,12,13,17,19,22,29,42,44,59,61,91,107,110,116,121,123,137,152,167,181,184,185,194,198,202,219,226,257,259,270,285,290,301,303,305,327,328,333,335,338,346,364,390,412,421,425,427,428,430,431,443,448,451,452],justo:356,jusufi:[350,359],jut:299,jzimmer:9,k11:91,k22:91,k33:91,k_b:214,k_d:443,k_sigma:339,k_ub:20,kadiri:67,kamberaj:270,kappa:[6,91,286,349,369,414,415],kappa_:290,karplu:87,karttunen:216,kate:0,kayser:350,kbit:169,kboltz:278,kbp:169,kbt:265,kcal2j:91,kcal:[210,432,443,447],kde:13,ke_eta_dot:229,ke_etap_dot:229,ke_omega_dot:229,keblinski:349,kecom:124,keef:118,keep:[3,7,12,59,71,162,184,190,194,211,252,268,288,293,318,326,349,377,396,418,423,429,431,437,441,448],keflag:3,kei:[6,17,59,278,437],keir:13,kelchner:70,kelkar:293,kelvin:447,kemper:[262,348],kepler30:17,kepler32:17,kepler35:17,kepler37:17,kepler:[1,12,14,15,17,333],kept:[6,172,233,287,288,443],kernel:[7,13,17,100,178,206,207,398,399,400,401,402,403],keword:168,keyboard:12,keyword:[3,6,8,12,16,17,38,39,41,56,58,59,61,65,68,69,70,71,77,79,87,88,90,92,94,96,97,102,103,105,108,109,110,112,114,117,118,120,121,123,124,132,133,137,138,142,143,144,146,147,148,164,166,167,168,169,170,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,303,316,318,319,321,322,323,324,326,327,329,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,378,379,380,381,382,383],keywrod:357,kforc:443,khaki:169,khersonskii:120,kick:[175,176,177,200,297],kilogram:447,kim:[2,3,4,7,9,12],kimviri:[3,365],kind:[1,2,3,6,7,8,9,11,12,17,39,40,41,42,61,62,63,73,117,119,124,167,172,179,181,182,183,188,191,193,197,205,208,226,270,273,278,285,300,328,330,332,339,357,392,393,413,418,423,428,429,436,437,443,448],kinemat:[9,378,379],kinet:[3,6,8,9,63,82,83,84,85,87,91,94,95,96,97,98,112,121,122,123,124,125,126,127,129,130,131,132,133,134,136,137,172,179,181,192,198,209,213,225,227,229,230,231,232,233,234,235,257,260,278,286,293,294,326,357,418,437,441,443],kiss:12,kjl:312,klahn:289,klapp:318,klein:[6,9,178,193,229,230,248,270,369,395],kloss:7,kmax:[3,118,271,318],knc:17,knock:290,know:[3,11,12,41,63,107,116,172,198,212,214,241,278,326,356,365,411,421,424,427,432,443],knowledg:[4,8,168,365],known:[3,12,120,168,252,261,270,287,420,437,449],kohlmey:[7,9,13,18,318,319],kokko:[1,2,3,9,12,16],kokkos_arch:17,kokkos_cuda:[12,17],kokkos_cuda_opt:17,kokkos_debug:17,kokkos_devic:17,kokkos_omp:[12,17],kokkos_pg:17,kokkos_phi:[12,17],kokkos_use_tpl:17,kolafa:319,kollman:[6,150,435],kondor:391,kone:[287,288],kong2011:252,kong:[9,13,252],konglt:9,koning00a:287,koning00b:287,koning96:[287,288],koning97:288,koning99:287,kooser:13,koskinen:325,kosztin:274,krau:13,kremer:[45,46,435],kress:[381,382],kspace:[0,1],kspace_modifi:[2,3,6,291],kspace_styl:[0,2,3],kspce:12,kspring:228,kstart:269,kstop:269,kth:[206,253],kub:20,kubo:[6,91,286],kumagai:409,kumar:[9,378,379],kuronen:390,kurt:255,l12:380,l_box:357,l_skin:290,la3:143,lab:[5,7,12,111,389],label:[2,3,12,72,167,169,173,174,189,190,193,252,253,267,303,317],laboratori:[0,227,260],lack:[3,227,357],lackmann:339,ladd:[247,288],lafitt:383,lag:290,lagrangian:[6,178,227,260,261,443],lagrangian_posit:[227,260],lagrangian_spe:[227,260],lai:417,lambda1:[408,409,410],lambda2:[408,409,410],lambda3:[408,410],lambda:[87,111,118,138,143,216,271,287,288,290,334,356,377,406],lambda_fin:287,lambda_initi:287,lamda:[3,53,278],laminar:403,lamm:6,lammps2pdb:[6,13],lammps_clos:6,lammps_command:6,lammps_extract_atom:6,lammps_extract_comput:6,lammps_extract_fix:6,lammps_extract_glob:6,lammps_extract_vari:6,lammps_fil:6,lammps_gather_atom:3,lammps_get_coord:6,lammps_get_natom:6,lammps_n:[6,12],lammps_open:6,lammps_potenti:[346,348,434],lammps_put_coord:6,lammps_quest:[6,203],lammps_scatter_atom:3,lammps_set_vari:6,lammps_sppark:6,lammpsplot:13,lammpspotenti:346,lammpstrj:[424,428,443],lammpsviri:[3,365],lamoureux:[6,198,411,443],lane:1,lang:443,langevin:[2,3,6,9,39,125,126,127,131,132,133,134,136,172,177,179,198,205,206,207,209],langevin_drud:[129,197],languag:[6,11,12,17,421,448],lanl:9,lapack:12,laps:291,laptop:7,larg:[0,1,3,5,6,7,8,9,10,12,13,14,16,18,39,40,41,58,59,70,71,109,116,121,124,127,132,144,145,146,156,164,166,167,168,169,181,184,185,188,191,192,194,195,199,205,216,229,241,247,252,255,256,260,265,267,268,269,270,273,275,278,286,290,291,293,295,299,312,318,319,324,326,329,333,347,353,357,360,361,368,384,388,394,407,418,421,423,425,426,430,432,437,440,443,449,452],larger:[1,2,3,6,11,12,13,39,41,56,59,70,71,116,144,146,168,182,183,186,195,209,216,229,247,248,256,261,265,269,270,271,278,285,290,294,295,296,299,318,319,324,325,326,328,329,330,333,339,347,349,350,357,361,369,373,379,384,388,405,412,423,427,428,431,432,437],largest:[3,6,12,39,71,142,144,199,318,326,330,404,407,423,425,431,432,442,448],laroch:265,laser:290,last:[1,2,3,5,6,11,12,15,16,19,38,56,59,61,71,110,117,121,142,164,167,168,169,170,171,181,182,183,184,185,186,188,199,228,268,271,275,278,303,316,326,327,328,329,333,337,338,339,340,347,348,353,355,359,360,362,363,367,370,372,374,375,376,379,383,385,394,397,404,407,411,412,414,415,418,419,421,423,424,428,430,431,435,437,438,441,448],lat:380,late:5,latenc:[10,210],later:[6,11,12,16,17,40,59,71,104,146,148,182,195,233,247,255,274,285,301,303,318,326,327,332,333,335,339,421,423,425,427,437,440,448,450],latest:[7,181,182,183,184,185,186,271,425],latex:8,latgen:252,latitud:120,lattc:380,latter:[2,6,11,12,14,15,16,17,18,41,42,87,123,169,173,174,180,181,184,185,188,192,211,220,229,231,232,234,235,255,257,259,261,263,270,278,294,299,317,327,339,341,342,343,344,345,352,369,373,377,384,387,395,411,418,420,421,426,429,440,448,451],lattic:[2,3,5,6,7,9,41,59,64,67,70,71,73,91,114,118,133,143,144,145,166,177,181,184,185,188,194,195,199,211,216,217,218,219,220,226,251,252,268,295,297,298,299,300],launch:[1,3,6,11,12,18,333,420,421],laupretr:312,lavend:169,lavenderblush:169,lavgevin:194,law:[6,227,331],lawngreen:169,layer:[6,9,71,172,184,286,290,293],layout:[1,3,17,146,420,423,432],lb_fluid:216,lbl:[7,9,142],lbnl:9,lbtype:216,lcbop:[2,3],ld_library_path:[11,12],ldfftw:12,ldrd:7,lead:[2,3,6,12,22,25,39,41,44,59,61,77,87,116,138,142,148,152,169,173,174,183,188,195,207,216,233,260,270,273,278,285,286,293,305,312,318,323,328,333,346,349,369,373,375,417,423,433,443,448,449],least:[3,6,12,18,71,118,143,179,184,207,255,259,294,329,333,364,407,412,421,448],leav:[3,7,11,12,16,17,21,41,57,121,134,151,188,192,195,229,231,232,234,235,257,270,273,304,384,423,427,435],lechman:278,lectur:274,led:[3,5],lee2:380,lee:[178,380],left:[6,11,12,41,107,163,168,169,191,211,250,278,301,303,321,411,423,425,430,448,452],leftmost:[41,188],legaci:12,legal:7,lehoucq:389,leimkuhl:298,leiu:353,lemonchiffon:169,len:433,lenart:[350,359],length:[3,6,8,11,12,18,21,38,39,40,41,44,53,54,55,56,58,59,61,65,68,69,71,74,79,80,82,87,88,89,90,91,92,103,105,107,108,112,114,115,117,118,119,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,140,142,143,146,151,164,167,168,169,172,179,183,185,186,188,189,190,191,192,194,205,208,216,227,228,229,230,233,241,251,257,267,270,271,273,275,278,285,289,290,292,295,299,319,321,324,326,328,329,331,336,339,340,342,349,350,354,357,359,363,367,369,380,384,392,393,398,407,408,414,415,423,426,431,433,440,441,443,448],lengthi:205,lennard:[1,3,6,7,9,10,12,45,46,87,107,110,172,257,278,295,299,319,321,326,335,338,342,343,344,345,347,352,360,362,363,364,367,368,369,370,371,373,374,376,377,383,384,394,395,400,405,412,435,443],lenoski:[381,382],less:[1,3,6,13,14,15,16,17,18,38,41,56,57,58,59,76,108,115,116,123,137,164,169,181,183,184,185,186,188,190,191,192,194,195,202,211,227,229,251,263,265,271,278,297,298,300,319,321,326,330,333,339,344,360,361,378,379,384,394,406,407,410,415,423,448,449],let:[1,11,12,38,56,127,155,164,182,273,278,296,333,347,407,432,436,443,450],lett:[120,132,207,214,216,227,265,274,287,288,325,339,355,357,360,377,396,443],letter:[2,12,41,57,59,169,188,197,198,214,253,303,332,391],level:[2,3,8,11,12,14,17,167,168,173,174,210,226,228,229,303,319,332,339,343,344,369,370,373,383,392,393,420,432,437,448],lever:404,levin:361,lexicon:7,lgr_po:[227,260],lgr_vel:[227,260],lgvdw:393,li1:143,liang:348,lib:[1,3,9,11,12,14,15,17,264,333,348,365,421,424],libatom:[9,391],libcolvar:12,libdir:11,libfftw3:12,libgpu:15,libjpeg:12,liblammp:[11,12],liblammps_foo:[11,12],liblammps_g:[11,12],liblammpscuda:14,libmpi:11,libmpi_stub:12,libmpich:12,libpackag:12,libpng:12,librari:[0,1,3,4],librt:17,licens:[0,7,8,12,168],lie:[6,205,271],lieu:318,life:7,lifo:8,ligand:275,liggght:7,lightblu:169,lightcor:169,lightcyan:169,lightest:285,lightgoldenrodyellow:169,lightgreen:169,lightgrei:169,lightli:275,lightpink:169,lightsalmon:169,lightseagreen:169,lightskyblu:169,lightslategrai:169,lightsteelblu:169,lightweight:278,lightyellow:169,like:[3,4,6,7,8,9,11,12,14,16,17,18,39,42,54,59,128,135,168,170,175,192,193,195,198,200,210,213,214,215,227,229,230,234,235,240,241,246,247,248,249,251,257,259,260,261,265,270,271,278,280,281,282,283,284,285,286,293,294,295,298,299,300,303,318,321,325,328,333,339,347,352,353,357,358,361,363,364,374,375,380,396,407,410,414,415,420,421,423,424,425,426,428,433,438,441,443,448,449],likelihood:[118,143,191],likewis:[1,6,10,12,15,18,39,41,71,88,115,178,188,189,190,205,213,214,229,230,233,248,265,278,281,282,283,319,328,334,338,339,349,355,358,405,421,423,435,448],lime:169,limegreen:169,limit:[1,2,3,6,7,9,12,16,17,18,27,39,58,59,61,71,118,120,143,144,145,146,153,168,172,184,190,192,193,194,206,213,229],limit_eradiu:357,lindahl:318,line:[0,1,2,3,4,6,7,8,9,11],linear:[2,3,6,25,27,38,44,55,56,102,120,153,164,172,173,174,178,191,192,198,217,221,225,226,229,255,268,269,273,282,286,290,293,295,297,298,300,306,307,309,321,328,361,375],linearli:[10,117,169,194,252,295,297,298,300,327,328,330,423,448],lineflag:[6,423],lineforc:[2,172],linen:169,linesearch:[8,324],ling:[9,13],lingo:[11,365],link:[5,6,7,8,9,11,12,13,14,15,17,18,22,37,44,55,63,152,163,168,172,190,210,214,255,264,266,274,275,305,313,336,346,380,391,392,393,405,411,421],linker:12,linkflag:[12,16],linux:[10,11,12,15,168,170,210],linuxamd64:424,liouvil:229,lip:13,lipid:[4,9,10,13,29,270],lipton:255,liquid:[6,7,9,29,39,40,41,59,87,121,130,142,188,192,194,205,229,257,260,265,285,352,384,387,409,432],lisal:404,lism:9,list:[0,1],listen:[210,212],listfil:368,liter:[423,434],literatur:[8,380,406],lithium:357,littl:[1,3,12,64,229,329,418,426],littmark:[380,405,410,416],liu:[363,393],lj1043:[2,172],lj126:[2,6,172],lj12_4:395,lj12_6:395,lj1d:252,lj6:3,lj93:[2,6,172],lj96:[2,3],lj9_6:395,lj_flag:335,llnl:[5,7],lmp1:11,lmp2:11,lmp2arc:[0,6],lmp2cfg:[0,6],lmp2vmd:0,lmp:[11,421,443],lmp_auto:12,lmp_cuda:[14,17],lmp_foo:12,lmp_g:[6,11,12,13,17,317],lmp_gpu:15,lmp_ibm:[12,317],lmp_inc:12,lmp_intel_cpu:16,lmp_intel_phi:16,lmp_kokkos_cuda:17,lmp_kokkos_omp:17,lmp_kokkos_phi:17,lmp_linux:[4,6,12],lmp_mac:12,lmp_machin:[1,12,14,15,16,18,19,333],lmp_mpi:[12,253],lmp_mvapich:17,lmp_omp:18,lmp_openmpi:17,lmp_opt:19,lmp_win_mpi:12,lmp_win_no:12,lmpptr:[11,421],lmpqst:203,lmpsdata:13,lmptype:[3,12,203],load:[1,3,4,7,9,11,12,16,17,18,41,168,170,172,188,210,260,333,348,420,421],loadabl:11,loca:169,local:[2,3],localhost:210,localized_lambda:178,localonli:12,localvector:63,locat:[3,6,8,9,11,12,27,61,116,118,142,143,153,164,167,195,196,216,277,288,299,324,346,349,358,359,369,371,373,411,420,423,424,426,433,435],lock:[3,332,448],lockstep:[192,229,257,270],log:[1,2,3,4,6,7,8,12,13,15,16,60,171,227,252,260,273,278,316,318],logarithm:448,logfil:[0,3,6,12,258,322,419],logfreq2:448,logfreq:[169,430,439,448],logic:[7,11,12,17,41,144,188,301,303,418,420,421,424,432,437,448],lomdahl:[233,371],london:[13,205,393],lone:[392,393],longer:[1,3,6,8,12,13,54,116,167,169,180,181,182,183,184,185,186,189,205,213,251,255,260,270,273,285,295,299,301,324,333,335,361,420,428,432,437,445],longest:[41,188,189,329,412],longitudin:275,look:[1,3,6,8,11,12,18,54,61,167,168,171,346,396,407,443,448],lookup:[3,39,164,384,407],lookup_t:271,loop:[3,4,6,7,11,12,18,39,42,65,68,69,79,88,92,108,115,116,121,168,181,184,185,189,190,199,285,301,303,317,320,326,328,329,331,332,354,418,419,421,427,428,431,432,437,442,448,449],loopa:[303,317,332],loopb:[303,317,332],loopvar:448,lopez:[229,230],lorant:261,lorentz:143,lose:[6,58,59,146,192,194,214,229,361,423],loss:[6,447],lossi:168,lossless:168,lost:[3,12,13,57,102,195,268,278,384,423,424,425,432,440],lot:[18,274,318],low:[1,3,6,7,12,41,127,142,167,168,188,198,214,247,265,270,286,293,319,393,407,415,437,443],lower:[2,3,6,9,11,12,41,57,59,71,88,133,166,168,169,182,183,184,185,188,192,198,210,213,214,216,229,260,265,286,293,295,296,301,302,318,321,332,350,380,437,444,446,449],lowercas:168,lowest:[120,303,327,433,437,438,448],lsfftw:12,lsurfac:290,lu3:143,lubric:[2,3,6,7,9,173,174,238,341],lubricateu:[2,3,9,295,341,378],lubricuteu:238,lucki:12,luigi:13,lumped_lambda_solv:178,lussetti:286,lustig:[7,13],lybrand:319,lyulin:312,m4v:168,m_c:443,m_d:443,m_eff:[296,361],m_fill:3,m_i:276,m_lambdai:389,m_taubi:389,m_u:216,m_v:216,m_yield_stress:389,mac:[12,14],mac_mpi:12,mach:9,machin:[1,3,4,6,7,10,11,12,14,15,16,17,18,19,167,168,210,291,318,324,326,331,333,420,425,430,431,432,449,452],mackai:[9,216,218,219,220],mackerel:[6,20,150,214,344,435,443],maco:168,macro:17,macroparticl:354,macroscop:[7,208,227,389],made:[3,6,11,12,15,16,33,41,42,50,64,145,157,167,168,170,172,173,174,179,188,195,199,210,219,256,264,268,270,288,301,310,329,333,360,361,364,392,394,397,420,425,427,433,436,444,446,449,450],madura:[6,369],magazin:355,magda:295,magenta:169,magic:[3,11],maginn:[138,293],magnitud:[6,70,105,108,113,144,166,167,169,195,196,208,209,211,213,274,275,277,278,285,296,319,326,352,361,433],mai:[0,1,2,3,6,7,8,11,12,13,14,15,16,17,18,29,38,39,40,41,56,58,59,61,63,65,68,69,71,79,86,87,88,89,90,92,102,103,105,107,108,109,110,112,113,114,115,117,118,119,120,121,123,124,132,133,137,138,142,143,144,145,146,147,148,163,164,166,167,168,169,170,172,173,174,175,177,179,181,182,183,184,185,186,187,188,189,190,192,194,195,198,199,200,202,205,206,207,209,210,211,213,214,215,216,217,219,224,225,226,227,229,230,233,241,244,252,253,256,257,258,259,260,262,265,267,268,269,270,271,272,273,274,278,280,281,282,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,316,317,318,319,321,324,325,326,327,328,329,330,331,333,336,338,339,347,353,357,361,364,365,375,377,379,380,381,382,384,392,393,395,396,404,407,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,435,437,440,441,443,448,449,450,452],mail:[3,7,9,12,301],main:[3,6,8,12,210,216,270,287,288,355,411,421,438],mainboard:1,mainli:[333,387],maintain:[8,9,13,39,129,190,194,247,278,291,325,334,355,432,435],major:12,make:[0,1,2,3,6,7,8,9,11],makefil:[3,7,9,11,12,13,14,15,16,17,18,19,167,319,333,421],makelist:12,maks:361,malloc:[3,12],manag:[5,8,12,167,210,253,280,432],manbi:396,mandadapu:178,mandatori:[8,193],manh:339,mani:[1,2,3,4,5,6,7,8,9,12,13,14,15,16,17,18,38,39,41,42,56,61,63,68,71,88,91,102,116,124,144,145,164,166,167,168,169,170,172,173,174,175,179,180,181,182,183,184,185,186,188,189,190,191,192,194,195,202,205,206,209,210,216,217,225,227,229,230,233,241,250,251,252,256,259,261,262,263,265,267,270,271,273,278,289,290,292,301,303,318,326,327,328,329,331,333,346,348,354,357,359,363,364,396,405,407,408,410,421,423,425,427,428,430,431,432,433,435,436,437,438,448,449,452],manipul:[12,41,188,210,349,390,434],manner:[2,3,6,9,11,17,41,121,140,173,174,175,176,183,188,194,199,200,203,209,213,214,229,234,235,246,247,249,264,281,282,283,286,287,288,293,295,299,303,319,327,328,332,333,355,357,364,367,378,412,418,420,423,424,425,426,428,432,437],manolopoulo:212,mantissa:3,manual:[0,1,3,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,58,63,68,71,109,112,118,122,123,125,126,127,130,131,132,133,134,136,137,143,150,151,153,154,155,156,158,159,161,162,164,167,168,170,175,184,187,201,204,208,212,213,214,228,229,231,232,233,234,235,236,239,242,244,245,246,247,249,257,259,262,270,271,272,273,281,282,283,293,294,303,304,306,307,308,309,312,314,319,328,332,333,334,335,337,338,340,341,342,343,344,345,347,348,349,351,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,418,432,436,437,438,441,448],manybodi:[3,7,8,9,12,121,326,334,335,339,348,355,358,364,366,386,390,406,408,409,410,435],map:[2,3,11,12,17,18,39,59,64,71,118,120,132,143,144,166,168,169,178,184,252,269,318,319,321,328,334,335,339,348,355,356,358,364,365,366,380,381,382,384,386,390,391,392,393,396,404,406,407,408,409,410,420,423,425,437,448],map_fil:252,mapflag:12,march:380,margin:437,mari:13,mark:[362,377],marker:258,maroon:169,maroonmpi:11,marrink:362,marsaglia:[3,206,207,213,214,265],marseil:9,martin:[252,380],martinez:179,martyna:[229,230,270,432],mashayak:17,mask:[3,251,448],mask_direct:178,mass:[2,3,6,8,13,40,42,63,66,74,75,86,87,89,90,91,93,94,95,96,97,98,100,103,104,105,113,124,125,126,129,132,136,139,141,144,147,148,167,170,172,173,174,176,178,179,181,184,185,194,198,204,205,206,208,213,214,216,219,225,227,229,234,235,246,247,249,252,253,256,260,265,267,268,270,273,274,275,276,278,280,281,282,283,285,286,288,290,293,294,296,297],mass_matrix:178,massdelta:273,massiv:[0,168,216,253,286,293],massless:[6,214,319,349,369,373,377,443],masstot:270,master:[3,328,418,437],mat:[67,178,348,409],match:[3,6,8,9,11,12,17,38,41,56,59,71,116,127,164,169,170,188,191,194,210,229,230,247,267,271,278,285,318,319,339,363,375,380,391,392,393,407,416,417,421,423,424,425,428,432,437,443,448],mater:[73,334,382,390],materi:[6,7,9,59,70,147,177,178,194,205,211,227,251,257,265,286,290,296,349,355,356,357,361,365,380,381,389,392,393,418,423,437,443,447],material_fil:178,math:[3,8,169,229,230,430,439],mathemat:[118,120,143,144,173,174,175,176,187,192,200,206,208,209,211,213,214,258,272,281,282,283,295,298,300,396,419,426,433,449],mathrm:214,mathtt:214,matlab:0,matric:[9,120,207,252,360],matrix:[3,6,9,91,142,182,192,207,252,261,318,321],matter:[6,9,12,39,57,59,71,126,184,290,329,335,351,355,357,380,395,408,410,416],mattson:[112,121],max2theta:143,max:[3,6,8,12,15,18,71,117,169,183,188,190,192,195,256,273,278,303,321,324,326,328,329,333,418,423,437,441,448],max_alpha:8,max_cell_s:354,max_group:3,maxangl:205,maxbodi:3,maxbond:[3,190],maxedg:142,maxev:[326,418,437],maxfoo:8,maxim:[285,328],maximum:[3,6,8,15,17,25,41,42,45,53,54,57,59,61,116,117,118,142,143,145,146,166,167,177,182,183,188,190,194,195,199,205,241,251,256,261,273,278,291,318,319,324,328,329,336,339,354,359,378,379,423,426,431,441,448,449],maxit:[261,326,418,437,441],maxsize_restart:8,maxwel:[17,250],maxwell50:17,maxwell52:17,maxwell53:17,maxx:390,mayb:13,mayer:[7,340,342,405],mayo:[6,7,13,25,314,363,435],mbt:151,mbyte:[12,265],mcdlt:[134,209],mcgraw:253,mdash:443,mdregion:178,mdump:[41,188],meain:6,meam:[2,3,4,7,9,12,349,364],meam_sw_splin:382,meamf:380,mean:[1,2,3,4,6,7,8,10,11,12,17,22,34,37,38,39,41,42,44,52,54,55,56,57,59,61,63,68,71,76,77,82,84,85,87,91,103,104,105,112,113,114,115,116,117,120,121,122,123,125,126,127,130,131,132,133,134,136,137,138,144,145,147,148,150,152,160,163,164,165,166,167,168,169,170,172,173,174,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,200,203,205,206,207,208,209,211,213,214,215,219,226,229,231,232,233,234,235,241,246,247,249,251,253,255,256,257,259,265,267,268,270,272,273,274,275,278,280,281,282,283,285,286,289,290,292,293,294,295,296,297,298,299,300,301,305,306,307,309,311,313,318,319,321,323,324,326,327,328,329,331,333,336,340,342,343,344,346,349,353,354,355,357,360,361,363,364,367,369,370,373,380,383,384,387,388,390,392,393,394,395,406,407,408,409,410,412,415,417,418,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,437,438,440,441,443,447,448,449,450,452],meaning:[116,364],meaningless:[67,285],meant:[6,270,411,427],measur:0,mech:389,mechan:[6,8,9,11,12,17,178,209,253,264,339,357,365,371,417,421,423],mechanic:264,media:168,medium:415,mediumaquamarin:169,mediumblu:169,mediumorchid:169,mediumpurpl:169,mediumseagreen:169,mediumslateblu:169,mediumspringgreen:169,mediumturquois:169,mediumvioletr:169,mee:285,meet:[3,12,145,168,169,190,191,291,428],mehl:334,meloni:39,melros:[378,379],melt1:170,melt2:170,melt3:170,melt:[4,10,191,252,339,409],mem:15,member:[147,255,339],membran:[29,250,415],memori:[1,3,5,6,7,8,9,12,15,16,17,18,39,40,60,71,169,181,184,185,206,207,265,290,316,329,333,339,384,388,393,420,423],memory_usag:8,mendelev:355,mention:[1,6,7,11,42,194,209,216,233,295,321,328,335,384,392,393,425,448],menu:[168,210],mep:[228,328],mer:[4,10,191],meremianin:120,merg:[3,5,423],merz:[6,150,435],mescscop:389,mesh:[1,3,6,7,8,10,12,40,41,42,118,143,178,188,216,271,318,319,354],meso:[2,40],meso_:2,meso_cv:433,meso_rho:[2,3],meso_t:2,mesocop:40,mesoscal:7,mesoscop:[7,99,100,101,222],mess:[3,433],messag:[0,2],met:[8,41,116,188,303,317,319,326,328,332,412,431],metadynam:[9,13,193],metal:[3,5,7,10,40,59,71,133,144,177,178,184,185,194,195,209,211,260,261,265,294,295,297,298,300,319,321,330,334,335,339,348,355,356,357,358,364,366,380,381,382,390,391,406,408,409,410,426,440,441,442,447],meter:[330,447],methan:[260,265],methanol:4,methin:312,method:[1,3,5,6,7,8,9,11,12,13,16,17,19,38,39,40,41,56,64,87,91,110,121,164,172,173,174,178,188,193,203,213,216,220,224,227,229,252,253,260,261,262,263,265,270,273,274,285,286,287,288,293,318,319,324,325,326,328,333,334,336,339,348,349,355,357,358,380,381,382,384,390,405,407,418,420,421,423,424,426,437,443],methodolog:[6,73,121,253,318],metin:[7,9],metric:[3,10,64,426,441],metropoli:[179,205,438],mezei:87,mf1:170,mf2:170,mf3:170,mg2:143,mglob_default_function_attr:12,mgoh:386,miai:265,mic:[12,17],micel:[4,13,276],micelle2d:0,michael:[9,13,382],michel:13,micro:[3,447],microcanon:[236,237,239,240,242,244,245],microelast:389,micromet:447,micropor:205,microscal:378,microsec:447,microsecond:447,mid:[5,59,194,404],middl:[3,6,8,16,22,41,44,77,87,116,133,138,142,148,151,152,169,173,174,180,188,256,268,269,270,286,293,304,305,323,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,378,379,380,381,382,383,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,416,417,421,431,432,433],middlebondtors:[3,151,423],midnightblu:169,midpoint:404,mie:[2,3],might:[3,4,6,7,8,12,14,25,71,203,205,207,270,421,431,448],migrat:[3,8,17,41,42,59,61,65,69,79,92,108,115,167,172,188,251,259,265,278,318,330,333,431,450,452],mikami:[6,229,230],mike:[7,9,13,15,16],mil:[9,355],mill:325,miller:270,million:[3,7,10,39,41,71,188],mimic:[6,11,42,54,214,227,256,349,359,369],mimim:[192,328],min2theta:143,min:[3,4,6,8,12,117,120,169,183,318,321,404,418,437,448],min_cap:3,min_cg:8,min_clearstor:8,min_dof:8,min_modifi:[2,192],min_popstor:8,min_post_forc:8,min_pre_forc:8,min_pushstor:8,min_setup:8,min_setup_pre_forc:8,min_step:8,min_stor:8,min_styl:[2,3,220,294,324],minarea:142,mincap:393,mind:[7,206,252],mine:[12,88,134,135,172,301,445],minim:[0,1,2,3,4,5,6,7],minima:[156,314],minimi:[328,412],minimizaiton:328,minimizi:265,minimum:[3,25,26,27,42,45,57,59,86,105,117,142,143,145,147,153,166,167,168,177,183,192,193,199,212,228,267,269,271,278,295,299,303,314,318,321,324,325,326,328,329,344,357,360,362,363,369,371,373,378,379,393,395,404,418,431,437,448,449],minlength:142,minmiz:[8,192],minn:9,minord:[3,318],mintcream:169,mintmir:[7,261,349,405],minu:[12,59,124,194,303,328,448],minut:[4,8],mirror:[61,297],misc:[0,6,8],miscellan:[2,178],mishin:[334,405],mismatch:[3,6],miss:[3,5,12,147,183,205,241,265,278,368,384,440,441],mistak:[3,448],mistakenli:3,mistyp:3,mistyros:169,mitchel:[6,111,126,318,319,351,389],mitchell2011:389,mitchell2011a:389,mitur:337,mivi2:265,mix:[1,3,6,9,14,15,16,71,115,183,184,291,318,319,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,421,423,436,443,450],mixtur:[6,40,229,270,278,300,347,380,423],mixture_ref_t:380,mjpeg:168,mkdir:434,mkl:12,mkmk:252,mkv:168,mldivide3:3,mlpark:7,mlutipl:186,mn2:143,mn3:143,mn4:143,mo3:143,mo5:143,mo6:143,mobil:[6,105,121,122,123,125,130,137,168,270,301,302],moccasin:169,mod:2,mode:[1,3,6,9,11,12,13,14,15,16,17,18,61,66,75,88,90,93,104,106,114,116,117,124,139,141,142,143,167,168,169,183,186,193,194,203,207,229,253,265,274,278,318,330,333,349,357,420,425,430,432,441,447,452],model:[0,1,3,4],model_ar_p_mors:365,modern:[12,213,215],modest:[1,331],modif:[6,13,87,380,394,410,443],modifi:[0,1,2,3,6,7],modify_param:8,modin:178,modul:[3,9,11,12,13,193,265,364,421],modular:8,modulo:[3,448],modulu:[257,361,380,389],mofil:424,mol1:448,mol:[3,9,71,113,144,146,147,167,169,193,195,205,210,213,256,259,270,273,280,352,360,395,432,433,443,448],molchunk:[66,75,90,93,104,106,124,139,141,181],mole:[179,355,447],moleclu:[189,190,195,202],molecul:[2,3,4,6,7,8,9,12,13,20,23,24,25,28,29,32,33,37,38,40,45,46,47,50,51,53,54,55,56,66,71,75,89,90,93,104,106,113,114,121,124,126,139,141,144,145,146,147,150,155,156,157,158,161,163,167,169,172,179,181,189,190,191,195,196,202,205,213,214,219,255,256,259,267,268,269,270,273,275,280,286,293,301,307,309,310,313,314,319],molecular:[0,2,3,5,6,7,8,9,12,13,39,40,53,71,108,113,115,122,123,125,127,130,131,132,133,136,137,144,145,146,147,148,156,167,170,178,190,193,205,212,252,253,260,264,265,269,274,289,290,319,327,336,337,339,343,354,357,364,405,423,424,425,427,428,432,433,435,441,442,443,448],molfil:0,molfrac:[195,256],molnar:274,molp:109,moltempl:0,mom:[6,91,269,449],momementum:[123,231,234,237,238,239,246],momemtum:66,moment:[3,6,40,42,82,84,85,106,113,123,137,144,165,167,213,216,219,244,256,270,276,327,352,356,423,433,443,447],momenta:[207,238,293,357],momentum:[2,3,6,40,61,66,82,86,102,106,113,120,123,144,167,172,178,198,206,209,213,214,216],momon:191,monaghan:[9,399,400,402],monitor:[3,6,96,97,127,192,194,195,202,210,213,227,229,256,258,260,270,273,278,326,328,352,441],mono:[73,378],monodispers:[3,296,341,361,378,379],monom:[13,54,191],monoton:[3,274,289,328,437],monoval:319,mont:[6,7,9,172,179,191,205,270,285,354,405],montalenti:[418,437],month:0,moor:[17,121],more:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,58,59,61,62,63,64,65,67,68,69,70,71,72,77,78,79,80,83,86,87,88,90,92,96,97,98,99,100,101,102,103,105,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,126,127,128,130,131,132,133,135,136,137,138,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,172,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,278,280,281,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,313,314,316,318,319,321,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,418,419,420,421,423,424,426,427,428,429,430,431,432,433,434,435,436,437,438,440,443,448,449,450,451,452],morefoo:8,moreov:[189,190],morri:2,morriss:[132,247],mors:[2,3,6,7,44],morse_f:407,mosel:325,mosi2:380,moskalev:120,most:[0,1,2,3,4,5,6,7,8,10,11,12,15,17,18,19,37,39,41,55,71,108,132,142,163,167,168,169,181,183,184,185,186,188,189,190,192,209,229,230,253,258,259,260,261,270,271,291,293,301,303,313,319,325,329,331,333,335,357,360,380,391,392,393,410,418,419,420,425,432,437,441,448,450],mostli:[8,9,11,13,71,146,168,329,423,432,435,448,451],motiion:6,motion:[3,6,7,9,42,86,97,122,123,125,127,129,130,131,132,133,134,136,137,194,198,207,216,219,220,226,229,230,233,247,251,253,255,265,269,270,286,290,296,299,328,352,357,378,379,426,432,443],motiv:251,mous:210,mov:168,move:[1,2,3,6,8,11,12,14,15,57,59,61,71,86,105,124,127,142,166,172,173,175,176,179,181,183,184,185,186,189,190,192,194,195,199,200,201,203,204,205,209,210,211,212,216,221],movement:[3,6,12,226,285,326,441],movi:[2,3,4,7,9,12],mp4:168,mpeg:168,mpg:168,mpi4pi:11,mpi:[0,1,3,5,6,7],mpi_allreduc:[270,421],mpi_barri:1,mpi_cart:420,mpi_cart_cr:420,mpi_cart_get:420,mpi_cart_rank:420,mpi_cart_shift:420,mpi_comm:6,mpi_comm_world:11,mpi_get_processor_nam:420,mpi_inc:12,mpi_lib:12,mpi_lmp_bigint:3,mpi_lmp_tagint:3,mpi_path:12,mpi_wtim:12,mpicc:11,mpich2:12,mpich:[12,14,15,16,17,18,333],mpicxx:[12,16,17],mpiexec:[12,14,15,16,17,18,333],mpiio:[3,167,169,425,430,452],mpirun:[6,11,12,14,15,16,17,18,19,253,317,333],mplayer:168,msd:[2,3,6,12,63,71,81],msi2lmp:0,msi:13,msm:[2,3,291,318,319],msmse:[118,143,271],msst:[2,3,4,9,172],mtchell2011:389,mtchell2011a:389,mtd:193,mth:[8,119,169,440],mtk:[229,230,233],mtotal:327,mu_j:29,muccioli:360,much:[1,3,6,11,39,167,168,192,260,285,329,330,333,360,394,418,421,437,443,448],mui:[113,167,200,280,423],mukherje:[7,9,255],mulder:289,muller:[6,91,172,286,293,383],mult:8,multi:[0,1,2,3],multibodi:[3,61,255],multicent:357,multicor:[1,420,436],multidimension:13,multielectron:336,multilevel:[318,319],multiphys:11,multipl:[0,1,2,3],multipli:[3,87,91,116,152,163,173,174,182,213,216,251,257,321,326,335,423,448],multiprocessor:333,multiscal:11,multisect:[41,188],multistag:87,multitud:7,mundi:248,munich:9,murdick:339,murti:409,murtola:318,must:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,57,59,61,62,71,82,84,86,87,104,107,109,112,115,116,117,118,119,123,126,133,137,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,164,165,166,167,168,169,170,173,174,175,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,200,203,205,206,207,209,210,211,212,213,214,216,217,218,219,220,224,225,226,227,228,229,230,231,232,233,234,235,237,238,239,241,244,246,249,251,255,256,257,258,259,260,261,263,265,267,268,269,270,271,272,273,275,277,278,281,282,283,285,286,288,289,290,292,293,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,314,318,319,321,323,326,327,328,329,330,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,423,424,425,426,428,430,431,432,433,434,437,438,440,441,443,447,448,449,450,452],mutli:6,mutlipl:423,mutual:[3,321],mutut:432,muvt:205,mux:[113,167,168,200,280,423],muz:[113,167,200,280,423],mv2_comm_world_local_rank:12,mvapich2:[17,333],mvapich:12,mxn:[12,253],my_ga:205,my_one_wat:205,my_post_process:434,my_qeq:261,my_setup:434,my_swap_region:179,myblock:[195,256],mybox:146,mychunk1:114,mychunk2:114,mychunk:[6,66,75,90,93,104,106,124,139,141],mycmap:423,mycom:183,mydump:[167,169],myer:[5,7],myfil:[420,448],myfix:[179,438],myflux:91,myforc:[167,451],myhug:233,myke:91,mymol:[40,273,327],mympi:11,mymultipli:[421,448],myn:421,mype:91,mypi:448,mypress:224,myramp:121,myrdf:[116,186],myregion:301,myrigid:[83,98,256],mysocket:212,myspher:[169,299],mystr:303,mystress:91,mytemp:[2,102,122,123,125,127,128,130,132,137,224,303,317,332,440,449],myz:423,n_dephas:418,n_f:[260,265],n_hbond:363,n_ij:361,n_ion:290,n_k:206,na1:143,nabla:290,nacl:[4,6,380],nacl_cs_x0:6,nakano:[261,263,328],namd:[7,9,167,210],name1:[138,194],name2:[138,194],name:[0,1,2,3,5,6,8,9,11,12,13,33,42,50,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,157,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,231,232,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,252,253,254,255,256,257,258,259,260,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,310,316,317,319,320,322,327,328,332,334,335,339,342,355,356,358,360,361,364,365,366,368,380,381,382,386,390,392,393,396,406,408,409,410,411,413,420,421,423,424,425,426,430,433,436,438,439,441,443,448,449,450,451,452],namespac:[6,8,12],nan:3,nangl:[3,423],nangletyp:[327,423,433],nano:[270,447],nanoindent:70,nanolett:270,nanomet:[167,169,447],nanoparticl:[188,270],nanosec:447,nanosecond:447,nappli:203,narea:3,narrow:[6,164],narulkar:[408,410],nasa:7,nasr:252,natdef:3,nation:[0,7,12,111,389],nativ:[1,6,7,12,16,17,167,170,424],natoli:[9,19],natom1:115,natom2:115,natom:[6,11,39,327,421,423,440,441,448],nattempt:256,natur:[6,9,120,194,229,251,265,296,355,357,358,380,390,420,448],navajowhit:169,navi:[169,355],navier:216,nb3:143,nb3b:[2,3,4],nb3bharmon:386,nb5:143,nbin:[116,183,184,185,286,293],nbodi:[219,270],nbond:[3,113,423],nbondtyp:[169,327,423,433],nbot:339,nbounc:278,nbrhood_cutoff:393,nbtype:115,nbuild:441,ncall:203,nchar:169,nchunk:[3,6,66,71,75,90,93,104,106,114,124,139,141,181],ncoeff:396,ncount:[181,182],nd3:143,ndanger:441,nden:[6,91],ndihedr:[3,423],ndihedraltyp:[327,423],ndim:184,ndirango:270,ndof:[229,233],ndoubl:423,ndp:443,ndx:302,neal:270,nearbi:[7,62,145,195,226,262,278,299,329,335,378,379,405,415,443],nearest:[3,70,71,73,142,145,216,228,251,285,299,318,368,380,407,448],nearli:[6,18,54,59,188,213,278,357,384,418,421,427,435],neb:[2,3,4,6,13,172],neb_combin:328,neb_fin:328,neb_log:437,neb_step:437,neb_styl:437,necessari:[6,9,11,12,13,15,17,33,61,87,152,157,163,170,188,192,193,205,206,264,278,291,301,318,333,377,384,423,424,428,431,432,433,437,443,451],necessarili:[12,265,285,306,307,309,321,384,449],necessit:259,need:[1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,19,33,37,38,39,40,41,42,50,54,55,56,58,61,63,64,67,70,72,73,77,82,91,102,104,109,112,120,121,122,123,124,125,127,130,131,132,133,134,136,137,144,146,150,152,157,163,164,166,167,168,169,173,174,175,176,178,179,181,182,183,184,185,186,188,189,190,192,193,194,198,200,203,204,205,209,210,212,213,214,216,222,223,229,241,252,256,257,259,265,269,270,274,278,286,289,290,292,293,294,295,301,310,313,318,319,327,328,329,330,333,334,335,336,337,339,340,341,342,343,344,345,347,348,349,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,418,421,423,424,425,426,428,430,431,433,435,436,437,443,448,450,451,452],needless:[6,329],neeed:9,neelov:319,neg:[3,6,12,27,46,65,69,89,102,108,115,120,121,146,148,153,155,164,168,192,194,195,206,233,251,274,275,289,293,295,300,318,325,358,372,380,405,423,426],neglect:[363,379],neglig:[11,87,229,406],neigh:[3,12,15,333],neigh_modifi:[2,3,6,12,39,61,148,188,205,241,255,270,278,291,326],neighbor:[1,2,3,6,7,8,9,10,12,14,15,16,17,39,41,42,61,62,63,64,67,70,72,73,76,77,78,80,88,108,115,116,120,121,142,144,145,146,147,148,167,168,170,179,188,189,190,191,193,195,202,205,210,228,241,251,253,256,259,261,263,270,278,285,301,318,327,328,329],neighborhood:[26,396],neighbour:214,neighobr:[6,349,369,373],neither:[2,3,12,41,63,178,191,194,195,335,341,357,378,379,384,428],nelem:396,nelement:[334,355],nemd:[0,4],nest:[2,303,315,332,448],net:[3,6,11,39,86,88,125,136,209,251,261,270,379,393],netpbm:168,network:[189,190,210,420],neumann:318,neutral:[3,88,205,318,349,369],never:[7,12,63,71,172,182,192,205,229,251,273,280,291,295,298,300,318,329,355,380,396,420,423,437,440,448],neveri:[3,8,71,175,180,181,182,183,184,185,186,189,190,191,216,217,252,261,262,263,266,267,271,286,292,293,328,428,437],newatom:195,newer:[12,181,380],newfil:[315,317],newli:[195,443,449],newlin:169,newn:270,newt:131,newtemp:[63,102],newtion:[339,390],newton:[2,3,5,7,14,15,16,17,29,61,113,247,325],newtonian:206,newtyp:[3,190],next:[1,2,3,6,11,12,16,18,38,56,57,65,69,71,79,91,92,108,115,164,168,169,179,181,184,185,195,199,205,206,241,270,273,290,303,317,318,326,327,328,329],neyt:285,nfile:[3,38,56,164,167,169,407,425,430,452],nfirst:428,nfirt:428,nfreak:271,nfreq:[39,71,180,181,182,183,184,185,186,188,267,271,428],nghost:[3,12],ngp:105,ngpu:333,nguyen:[15,339],nharmon:2,nhc:253,nht:270,ni2:143,ni3:143,ni_000:[118,271],nialh_jea:355,nialhjea:[346,364],nice:[6,8],nickla:382,nimprop:[3,423],nimpropertyp:[327,423],nine:358,ninteg:423,nissila:216,nist:[334,355,447],niter:[41,188],nitrid:349,niu3:[346,355,364],nkb:260,nlast:428,nline:327,nlocal:[3,8,11,12,203],nlog:319,nmax:42,nmin:42,nmol:423,nmpimd:253,nn2:380,nneighmaxdef:3,no_affin:[16,333],no_histori:6,noced:326,nocheck:368,nocit:12,nocoeff:450,nodal:[6,38,56,164,178,290,407],node:[1,3,12,14,15,16,17,18,41,118,143,188,210,216,290,333,368,420,436],node_area:216,node_group:178,nodeless:357,nodeset:178,nodeset_to_elementset:178,nof:164,noforc:[2,3,6,172],nois:[6,206,207,213,214,215,216,260,265,270,282,290],nomenclatur:[6,71,184,321],nomin:[167,229],non:[0,1,2,3,4],nonbond:[4,12,386,405],none:[2,3,6,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33],noneq:207,nonequilibrium:[9,287,288,357],nonetheless:213,nongauss:[2,63,103],nongaussian:105,nonlinear:[2,7,44,45,46],nonloc:389,nonperiod:3,nonzero:3,noordhoek:348,nopreliminari:164,nor:[2,3,41,59,178,348,423,426],nord:[390,408,410],norder:420,nordlund:[390,408,410],norm:[6,12,63,117,172,181,184,185,271,326,328,404,440,441,447],normal:[3,6,9,10,11,12,39,41,58,61,63,67,70,71,73,88,91,102,112,116,117,129,132,144,145,146,164,169,172,181,182,183,184,185,188,192,194,195,204,205,209,213,214,226,229,241,251,253,254,261,265,267,268,274,278,279,281,282,283,290,295,296,299,300,304,306,307,309,323,325,326,328,333,347,348,360,361,364,404,416,417,418,421,423,425,426,428,429,433,437,440,441,443,447,448,451],norman:290,nornal:3,nose:[6,7,8,134,172,198,213,214,229,230,231,232,233,234,235,246,247,248,249,253,257,265,270,281,282,283,288,353,443],noskov:[411,443],noslip:[278,300],notabl:[5,39],notat:[6,63,70,120,138,172,226,229,355,448],note:[1,2,3,6,7,8,11,12,13,14,15,16,17,18,22,24,25,28,29,32,33,35,36,37,38,39,40,41,42,44,47,54,55,56,58,59,60,61,62,63,65,66,68,69,71,73,75,79,87,89,90,91,92,93,97,104,105,106,108,110,112,113,114,115,117,118,119,120,121,124,126,127,128,132,134,138,139,141,142,143,144,145,146,147,148,150,152,155,157,161,163,164,167,168,169,170,172,173,174,175,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,199,200,202,203,205,207,208,209,211,212,213,214,215,216,224,225,226,227,229,231,232,233,234,235,241,246,247,249,253,255,256,257,259,260,261,263,268,269,270,271,274,275,276,278,281,282,283,286,289,290,292,293,294,295,296,299,300,301,303,304,305,306,307,309,313,317,318,319,321,323,326,327,328,329,333,334,335,339,340,342,343,344,346,347,349,350,352,353,354,355,358,360,361,362,363,364,367,368,369,371,373,377,378,379,380,381,382,383,384,386,390,392,393,394,395,396,397,400,404,406,407,408,410,412,415,418,420,421,423,424,425,426,427,428,430,431,433,435,437,438,440,441,443,447,448,449,451,452],noth:[179,212,320,333,421,434],notic:[0,6,7,8,12,288,290,443],noutcol:8,noutput:252,noutrow:8,novemb:380,novik:13,novint:210,now:[2,3,6,9,11,12,13,46,61,62,71,167,173,174,190,206,210,211,270,296,299,319,321,355,357,361,392,393,397,419,424,443,449],nowait:210,nozforc:318,np3:143,np4:143,np6:143,npair:[116,182],nparticl:[3,40,42,338],npartit:441,npernod:[14,15,16,17,18,333],nph:[2,3,5,6,7,9,134,172,194,214],nphi:[16,333],nphug:[2,3,172,227],npoli:256,nproc:[3,167],npt:[2,3,5,6,7,8,10,57,59,87,122,125,126,127,128,130,131,132,133,134,136,172,192,194,198,214],npt_aspher:[231,235,246],npt_sphere:[232,249],nrecomput:354,nrepeat:[71,180,181,182,183,184,185,186,267,271,428],nreset:[192,229,230,233],nreset_ref:192,nrho:[334,355],nrl:355,nsampl:354,nsbmax_most:3,nsec:442,nskip:[119,428],nsq:[3,330,388],nstart:[119,182,183,186,271,423,428],nstat:251,nstep:[3,13,192,229,301,401,421,424],nsteplast:421,nstop:[119,428],nswap:[286,293],ntabl:[38,56,164,407],nterm:274,nth:[12,77,116,117,167,169,183,194,428,438],ntheta:339,nthread:[3,333],ntild:252,ntpc:333,ntptask:333,ntype1:115,ntype2:115,ntype:[3,120,144,167,169,179,261,263,357,363,390,423,433],nuclear:[9,96,97,130,207,230,260,265,327,357,416],nuclei:[9,96,97,128,130,135,215,230,240,248,284,336,357,423],nucleu:[96,97,261,410,443],nudg:[4,6,7,172,228,325,328],nulcear:9,num_of_collis:3,numa:[1,3,12,333,420],numactl:16,number:[1,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,27,38,39,40,41,42,44,56,63,64,65,66,68,69,70,71,73,75,76,77,78,79,80,87,90,91,92,93,102,104,106,108,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,129,130,131,132,133,134,136,137,138,139,141,142,143,144,145,146,147,148,152,153,163,164,166,167,168,169,170,172,173,174,177,179,181,182,183,184,185,186,188,189,190,191,193,194,195,202,203,205,206,207,209,210,211,212,213,214,215,216,219,226,229,230,233,241,251,252,253,255,256,259,260,261,265,267,270,273,278,279,280,282,285,286,287,288,290,291,292,293,295,297,298,300,301,303,305,316,318,319,321,323,324,326,327,328,329,330,333,334,335,339,341,346,348,353,354,355,356,357,358,363,364,365,366,367,380,381,382,384,386,390,391,392,393,394,396,404,406,407,408,409,410,412,413,416,417,418,420,421,423,424,425,426,427,429,430,431,432,433,435,437,438,440,441,443,447,448,449,452],number_of_a:3,number_of_b:3,number_of_typ:179,numbond:3,numer:[1,2,3,6,9,12,22,38,41,42,44,56,71,77,87,116,138,148,152,164,167,168,169,173,174,175,177,178,184,200,206,209,213,226,229,253,270,290,295,297,298,300,301,305,323,326,327,346,352,364,380,384,392,393,407,416,417,421,423,430,433,439,440,441,448],numpi:11,nvalu:[181,184,185,186,421],nvaluelast:421,nvc_get_devic:15,nvcc:[1,12,17],nve:[1,2,3,4,5,6,7,8,9,10,39,42,87,91,144,172,178,198,206,207,209,212,213,214,215,219,226,229,233],nve_aspher:[231,234,246],nve_spher:[232,235,249],nvida:17,nvidia:[1,3,9,12,14,15,17,333,436],nvt1:443,nvt2:443,nvt:[2,3,5,6,7,8,87,91,125,126,127,128,131,132,133,134,136,172,178,182,183,186,194,198,205,207,209,213,214,226],nvt_aspher:[231,234,249],nvt_sphere:[232,235],nvtfe:178,nwait:252,nwchem:7,nxnode:290,o_cor:126,o_shel:126,oascr:7,obei:[3,194,321,418],ober:7,obj_shared_foo:12,obj_target:12,object:[6,8,11,12,15,40,42,168,192,210,216,219,256,274,326,421,426],observ:[229,260,281,282,285,286,293],obsolet:13,obstacl:[4,211],obtain:[1,3,9,12,29,73,87,142,170,174,204,207,216,233,252,253,285,318,335,352,380,384,391,408,410,432],obviou:[12,448],obvious:[168,438,448],occ:359,occasion:[3,418],occlus:168,occup:[3,142,359],occur:[1,3,6,9,11,12,14,17,39,57,59,61,62,71,86,105,142,145,147,164,167,169,179,188,191,192,194,205,208,211,219,227,241,261,270,278,287,300,301,303,318,329,333,354,357,377,393,418,420,421,428,432,437,440,448],occurr:[312,423,437,448],octahedr:25,octant:420,odd:[41,169,188,229,270,281,282,290,438],off:[1,3,6,12,14,15,16,17,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,44,45,46,47,48,49,50,51,53,54,55,56,59,61,65,69,71,107,108,109,112,113,115,120,121,122,127,131,142,143,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,167,168,169,172,175,179,186,187,190,191,201,204,205,206,208,210,213,214,219,229,231,232,233,234,235,236,241,244,246,247,249,255,257,258,262,270,272,273,278,281,283,293,294,295,299,304,305,306,307,308,309,310,312,313,314,318,319,326,328,329,331,333,334,335,337,340,341,342,343,344,345,347,348,349,351,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,381,384,385,386,387,389,393,394,395,397,404,405,406,407,408,409,410,412,414,415,416,418,419,420,423,425,430,432,435,436,437,445,447,450,452],offend:[3,421],offer:[6,14,18,147,325,349,418,432],offic:7,offload:[1,12,16,17,210,333],offset:[3,6,57,144,168,194,195,205,256,327,349,369,373,405,423],offsit:8,often:[1,3,6,7,12,13,14,15,16,17,18,37,55,71,138,163,168,175,183,186,188,192,203,210,229,253,271,313,321,325,326,328,329,330,333,348,353,369,408,410,418,437,443,447],ohio:382,old:[3,6,9,172,192,195,229,380,392,397,424,427,431,434,447,450],older:[3,5,12,13,17,169,181,192,229,397],oldlac:169,oleinik:339,olfason:[6,25,314,363,435],oliv:169,olivedrab:169,ollila:[216,218,219,220],olmst:[178,251],omega0:314,omega:[2,3,6,84],omega_dot:229,omega_ijk:410,omega_ik:408,omegai:[113,167,280],omegax:[113,167,280],omegaz:[113,167,280],omgea:6,omiss:[0,7],omit:[164,169,297,343,352,373],omp:[0,1,2,3,7],omp_num_thread:[3,16,18,333],omp_proc_bind:17,ompi_comm_world_local_rank:12,on_the_fli:178,onc:[0,1,2,3,6,11,12,16,40,41,59,60,63,71,91,104,150,168,169,172,173,174,188,189,190,195,203,205,207,214,252,259,270,278,286,291,293,301,324,327,328,329,360,362,364,365,390,394,420,421,430,437,440,443,448],onelevel:420,onewai:[2,3],ongo:210,oniom:[9,264],onli:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,59,60,61,63,64,65,66,67,68,69,70,71,72,73,75,78,79,80,83,86,87,88,90,92,93,96,97,98,99,100,101,102,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,127,128,130,131,132,135,136,137,138,139,141,142,143,144,147,148,150,151,153,154,155,156,157,158,159,161,162,163,164,167,168,169,170,172,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,198,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,270,271,272,273,274,278,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,312,313,314,316,318,319,321,323,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,425,427,428,430,431,432,433,434,435,437,438,439,440,441,443,448,449,450],only_group:142,onn:432,onset:[260,312],ontario:9,onto:[120,146,191,195,216,404],onward:2,open:[0,3,5],opencl:[1,3,7,15,333],opengl:6,openkim:9,openmp:[1,3,7,9,12,16,17,18,333,436],openmpi:[12,14,15,16,17,18,333],opensourc:7,oper:[1,3,6,7,8,11,12,14,16,17,39,41,42,59,71,91,117,119,132,134,135,144,147,148,169,172,179,181,182,183,184,185,186,188,189,190,191,195,205,208,215,225,226,227,229,230,231,232,233,234,235,240,246,247,248,249,256,258,259,268,270,271,273,274,277,278,279,280,284,288,290,294,296,301,303,316,318,319,325,328,330,333,417,418,419,420,421,423,424,425,426,428,429,431,432,436,437,440],opl:[2,7,152],oppos:[6,39,165,167,269,297,319,327,423],opposit:[6,70,177,213,220,251,270,293,328,349,377,411,421],opt:[1,2,9,12,18],optic:123,optim:0,option:[0,1,2,3],optionn:17,orang:[2,168,169],orbit:[261,263,339,349,357,405],orchid:169,order:[1,2,3,6,9,11,12,14,16,27,38,39,41,56,59,65,69,71,79,87,89,90,92,93,108,112,115,120,121,122,123,124,125,126,127,130,131,132,133,134,136,137,148,153,163,164,167,168,169,172,175,180,182,183,184,185,186,187,189,190,191,192,193,198,200,205,207,209,210,212,216,217,219,227,229,251,259,260,264,267,268,269,270,271,272,273,274,279,285,289,290,291,292,302,303,304,306,307,309,312,313,318,327,328,334,335,336,339,348,354,355,357,358,360,361,364,366,369,377,380,392,393,394,405,406,407,408,409,410,411,413,418,420,421,423,424,428,430,432,433,437,440,443,448,452],orderomg:3,ordinari:[111,363,389],org:[6,7,11,12,13,14,391],organ:[0,3,6,7,8,348],organometal:25,orient:[2,3,6,8,13,29,40,42,82,91,113,144,167,172,194,200,205,219,231,234,237,238,239,242,244,245,246],orienti:42,origid:181,origin:[3,6,7,9,12,71,81,103,104,114,118,140,144,146,166,168,169,172,173,174,181,184,185,189,190,194,198,205,214,226,229,247,253,256,266,270,271,277,288,315,317,318,321,325,334,335,337,339,349,352,353,354,355,363,366,380,389,392,393,408,410,411,412,420,423,424,425,426,427,428,447,450],origin_i:185,origin_x:185,origin_z:185,ornl:[7,9,15],orsi:29,ortho:[3,59,146,423],orthogon:[0,3],orthograph:168,orthong:59,orthongon:[59,270],orthonorm:195,orthorhomb:260,os4:143,oscil:[6,9,129,190,194,197,198,214,226,227,229,260,265,270,295,296,298,300,327,336,411,443,448],oscillatori:226,oserror:11,other:[0,1,2,3,5],otherwis:[1,3,12,14,16,17,18,37,39,55,71,102,111,118,123,124,137,145,163,169,170,179,181,189,190,194,203,205,207,214,229,270,313,314,326,333,341,364,368,378,379,390,413,418,421,423,424,443],otyp:[349,369,373,377],ouml:443,our:[5,6,7,8,13,216,273,384,408,410,443],out:[1,2,3,6,7,8,11,12,13,14,18,19,21,41,64,66,71,75,90,91,93,94,97,103,104,105,106,107,114,115,122,123,124,125,127,128,130,131,132,133,134,136,137,139,141,147,151,167,168,169,170,172,184,188,189,190,193,201,204,205,211,213,216,221,241,252,254,255,256,265,266,267,270,275,290,299,301,302,303,304,306,309,316,317,321,324,328,332,357,364,405,417,418,420,421,423,426,427,428,430,431,432,434,437,439,440,441,444,446,448,449,450,451,452],outcom:[270,449],outer2:[344,362],outer:[3,8,16,199,211,303,317,324,326,332,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,413,414,415,416,418,431,432,437,442],outer_distance_cutoff:363,outermost:[38,56,173,174,226,229,329,407,432],outfil:[13,420],outlin:[6,168],outmost:210,outpt:12,output:[0,1,2,3,4,5],output_frequ:178,outsid:[3,57,59,71,134,144,166,167,168,169,170,183,184,195,205,211,270,271,278,283,284,297,298,300,301,316,328,340,342,349,357,369,371,387,395,421,423,424,426,433,440,449],outuput:181,outut:6,outward:[142,295,299,300,423,432],over:[1,3,5,6,7,9,12,16,18,27,39,41,42,55,60,65,68,69,71,79,80,87,88,89,90,92,101,103,105,108,115,116,120,121,124,127,130,138,140,153,164,168,170,172,173,174,180,181,182,183,184,185,186,187,188,189,190,194,195,203,206,207,211,213,214,215,219,227,228,229,230,231,232,234,235,246,247,248,249,251,256,257,260,267,268,269,270,271,274,275,278,281,282,283,284,286,289,292,293,295,297,298,299,300,301,304,317,320,328,329,330,333,347,353,355,356,357,358,363,378,380,390,396,397,405,406,408,409,410,419,420,421,426,428,429,431,432,437,440,441,448,449],overal:[6,18,25,59,138,192,198,229,230,253,273,278,303,324,357,363,364,396],overalap:270,overcom:[241,278],overflow:[3,327,329],overhead:[6,11,19,41,169,181,184,185,188,202,259,329,330,426],overkil:270,overlai:[2,6,9,16,87,107,138,173,174,290,349,353,354,363],overlaid:7,overlap:[3,13,16,62,76,144,147,164,169,177,180,181,183,184,185,186,195,199,241,256,261,267,270,271,278,296,300,318,321,324,326,327,333,353,357,361,364,367,377,397,412,423,426,432],overload:1,overrid:[3,12,14,17,22,44,71,130,144,152,168,169,173,174,192,199,224,229,305,318,329,346,363,364,380,384,392,420,421,433,435,440,448],overridden:[6,144,168,233,270,378,384,397,405,431,448,450],overview:[0,1,2,6,7,8,9],overwrit:[11,12,22,44,152,169,181,182,183,184,185,186,271,305,316,322,346,380,421,424],overwritten:[258,289,316,363,364,418,419,424],own:[3,4,6,7,8,11,12,13,15,17,39,41,59,61,63,65,66,69,71,73,75,79,90,92,93,104,106,113,114,115,117,119,124,127,139,141,142,167,169,172,178,180,181,182,183,184,185,186,188,191,192,194,203,206,207,213,214,216,224,227,229,231,232,233,234,235,246,247,249,253,257,265,270,271,281,282,283,292,318,328,333,335,339,348,356,366,390,392,393,406,408,409,410,420,433,440,449],oxford:[29,87,352],oxid:[348,349],oxygen:[6,40,202,349,369,373,423],oxygen_c:126,p_e:290,p_ik:390,p_pi:339,pacakg:[3,4,12,40,333],pack:[5,8,67,296,333,339,380],pack_bord:8,pack_border_bodi:8,pack_border_hybrid:8,pack_border_vel:8,pack_comm:8,pack_comm_bodi:8,pack_comm_hybrid:8,pack_comm_vel:8,pack_exchang:8,pack_restart:8,pack_revers:8,pack_reverse_comm:8,pack_reverse_hybrid:8,packaag:333,packag:0,packakg:15,packet:[7,9,40,168,336,357],pad:[3,167,168,169,253,448],padua:[9,13],page:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,40,42,44,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,112,114,117,119,121,123,124,137,139,141,144,145,146,152,163,167,168,169,170,172,173,174,179,180,181,182,183,184,185,186,195,205,212,213,214,224,229,230,234,235,239,246,247,248,249,256,259,270,275,278,281,282,283,292,296,299,301,303,305,313,317,326,327,328,329,333,334,335,338,346,348,349,355,356,358,363,364,366,367,380,381,382,384,386,390,391,396,405,406,408,410,412,421,423,424,425,426,428,431,432,433,435,440,441,448,449,450,451],pai:[15,18],pair:[1,2,3,4],pair_:[87,173,174],pair_airebo:366,pair_charmm:377,pair_class:8,pair_coeff:[2,3,6,87,91,108,115,145,150,173,174,190,267,278,334,335,336,337,338,339,340,341,342,343,344,345],pair_eam:334,pair_eff:130,pair_foo:8,pair_hybrid:[384,411],pair_interact:178,pair_list:368,pair_lj:377,pair_lj_cut:8,pair_lj_soft_coul_soft:87,pair_modifi:[2,3,6,87,110,318,326,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383],pair_sph:[398,399,400,401,402,403],pair_styl:[0,1],pair_writ:[2,3,346,375,405,407],paircoeff:3,pairfoo:8,pairij:[3,423],pairkim:3,pairstyl:8,pairwis:[0,1,3,5,6,7],palegoldenrod:169,palegreen:169,paleturquois:169,palevioletr:169,pan:168,panagiotopoulo:[350,359],pandit:[9,263,393],papaconstantopoulo:334,papayawhip:169,paper:[3,6,7,8,9,13,39,40,64,120,132,138,156,213,216,220,228,255,261,263,270,278,286,290,293,318,325,328,335,343,349,361,363,366,371,373,389,392,393,408,410,418,437],paradyn:5,paraemt:394,paragraph:[71,132,295,321,424],parallel:[0,1,2,3,4,5,6,7,8,9,10],parallelepip:[6,146,321,423,426],parallelipip:[146,252],paralleliz:255,param:[3,261,263,420,426],paramet:[0,2,3],parameter:[118,143,335,339,348,349,355,356,357,358,366,380,381,382,390,392,393,406,408,409,410],parameter_fil:178,parameterizaion:349,parametr:[6,9,36,356,391,395],paramt:[105,261,297,394],paramter:348,paratem:377,paraview:271,parent:[3,8,301],parenthes:[38,56,164,361,407,448],parenthesi:[2,181,303,448],parinello:[6,7],pariticl:188,paritlc:3,park:[3,7,9,178,274,382,389],parrinello1981:192,parrinello:[192,207,227,229,230,260,282],pars:0,parser:[12,448],part:[0,1,2,3,6,7,8,9,11,12,17,20,21,23,24,25,26,27,28,29,30,31,32,35,36,37,38,40,41,43,45,46,47,48,49,51,53,54,55,56,64,67,70,71,72,78,80,83,96,97,98,99,100,101,105,107,108,109,111,112,115,120,121,122,123,126,128,130,131,135,136,138,142,147,150,151,153,154,155,156,158,159,161,162,163,164,167,169,170,172,175,176,177,179,185,187,188,189,190,191,192,193,195,197,200,201,202,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,222,223,224,227,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,251,252,253,255,256,260,261,262,263,264,265,266,267,269,270,272,273,274,275,277,278,281,283,284,285,286,287,288,289,290,291,293,294,295,296,297,299,301,302,303,304,306,307,308,309,312,313,314,318,319,326,327,328,329,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,420,421,423,424,425,426,430,431,432,435,441,448,452],partai:[9,391],parti:9,partial:[1,2,3,6,8,63,122,124,130],partic:6,particip:[190,338,367,412],particl:[0,3,4,5],particleenergi:3,particleviri:3,particular:[1,3,6,8,10,12,16,40,63,65,69,70,71,79,92,108,113,115,116,120,144,166,167,172,177,184,188,191,206,211,212,216,226,229,251,256,269,270,273,285,296,301,304,319,321,324,327,333,338,339,340,342,344,345,347,351,356,357,360,362,364,369,373,377,386,387,394,395,405,406,408,409,410,418,420,423,424,425,430,431,433,441,448,449,451,452],particularli:[7,9,12,15,16,25,39,168,192,270,319,357],partilc:278,partit:[2,3,6,7,12,41,62,132,146,169,188,230,253,315,317,322,328,332,343,344,357,369,370,373,383,390],partitoin:62,partner:[3,7,61,189,190,191,214,278,293,411,433,438,443],pascal:[9,13,447],pass:[6,7,8,11,66,74,75,81,89,90,93,103,104,105,106,139,167,169,170,192,193,203,205,226,227,229,259,278,295,317,329,333,364,392,404,421,423,424,428,434,448,451],passphras:12,past:0,patch:[0,12],patchi:270,path:[3,6,7,11,12,13,15,170,212,228,253,274,278,285,290,328,334,335,339,346,355,356,358,366,380,381,382,386,390,391,392,396,406,408,410,424],patient:12,patom1:115,patom2:115,patrick:409,pattern:[3,7,12,62,73,425],pattnaik:270,paul:[0,7,13,213,215],pauli:[9,357],paus:431,paves:253,payn:[120,391,396],pb2:143,pb4:143,pbc:[295,336],pchain:[229,230,233,270],pcie:1,pd2:143,pd4:143,pdamp:[229,230,233,257,270],pdb:[6,13,170],pdf:[0,8,9,13,17,40,99,100,101,111,193,212,222,223,389,398,399,400,401,402,403,433],pdim:293,pdlammp:[78,80,389],pdlammps_ep:[111,389],pdlammps_v:389,pe_eta:229,pe_etap:229,pe_omega:229,pe_strain:229,peachei:13,peachpuff:169,peak:359,pearlman:87,peculiar:12,pedersen:319,peform:[39,262],penalti:[14,392,393],pencil:[6,71,132,184],pend:3,penetr:42,peng:143,penn:13,pentium:10,peopl:[7,8,9,12],peptid:[4,9,193],per:[0,1,3,5],peratom:[3,110,121],perceiv:168,percent:[3,16,192,333,406],percentag:[1,192,229,256,257,270],percol:190,perfect:[6,41,70,73,188,251,328],perfectli:[41,188,424],perfom:[6,328],perform:0,performac:1,pergamon:[380,410,416],perhap:321,peri:[2,3,4,6,7,9,40,78,80,111,113,144,323],peridyma:78,peridynam:[3,4,6,7,9,40,63,78,80,111,389,405,433],perimitt:350,period:[2,3,6,7,8,12,22],perioid:295,perl:[6,13],perm0:447,perman:[3,39,54,71,148,189,190,210,269,301,333,363,427,435],permeabl:250,permiss:[190,421],permit:[6,216],permitt:[350,410,415,416],permut:[12,356,406,408,410],perpendicular:[6,123,168,194,211,221,226,228,251,254,295,296,325,423],perram:[319,360],persepct:168,persist:[3,8,71,203,270,333,420,421,429,448],person:9,persp:[3,168],perspect:168,pertain:[346,405],perturb:[9,13,70,87,225,268,295,298,300,428],peru:169,peskin:216,pessimist:319,petersen:[278,319],pettifor:[339,405],pettifor_1:339,pettifor_2:339,pettifor_3:339,pfactor:168,pforc:421,phantom:210,pharmaceut:7,phase:[3,12,16,229,285,293,339,369,409,420],phd:391,phenol:443,phenomena:357,phi0:[162,269],phi1:151,phi2:[151,356,406],phi3:[151,356,406],phi:[1,3,4,7,9,12,16,17,79,120,163,164,168,208,252,269,307,333,334,339,355,358,380,381,382,436],phi_ij:[339,358,390],philadelphia:9,phillip:[214,353,443],phillpot:[262,348,349],philosoph:355,philosophi:[6,7,212],phonon:[0,2],phophor:396,phosphid:396,phy:[6,7,13,20,21,25,39,43,45,46,64,70,73,87,88,110,112,120,121,126,132,150,151,161,179,192,193,198,206,207,212,213,214,215,216,227,228,229,230,233,247,248,252,253,257,260,262,265,270,273,274,278,281,282,285,286,287,288,290,293,295,304,312,314,318,319,325,328,335,339,340,344,345,347,348,349,350,351,352,353,355,356,357,359,360,361,362,363,366,369,371,373,374,377,378,379,380,382,383,384,387,389,390,394,396,404,406,407,408,409,410,411,418,432,435,437,443],physic:[3,6,9,12,14,16,17,18,40,53,59,138,178,194,207,213,215,216,218,219,220,227,252,261,263,289,290,319,321,328,333,335,337,343,347,355,363,364,391,392,393,399,400,402,403,418,420,432,438,447],physica:[378,379],physik:[7,9],pic:9,picki:8,picocoulomb:447,picogram:447,picosecond:[169,194,441,447],picosend:357,pictur:7,piec:[3,11,120,169,229,430,452],pieter:13,pimd:[2,6,7,13,212],pin:16,pink:169,pipe:[6,168],pipelin:[3,6],pisarev:290,pishevar:353,piston:[2,3,172,177],pitera:6,pixel:168,pizza:[4,6,7,11,13,41,167,168,188],pjintv:13,pka:290,place:[3,6,7,9,11,12,33,41,50,71,87,138,144,148,157,164,167,168,169,171,172,173,174,190,191,194,205,206,207,209,212,213,214,215,217,219,220,229,234,235,246,249,256,259,268,270,281,282,283,290,295,298,300,317,346,363,405,412,420,421,424,431,433,441,448],placehold:[33,157,334,335,348,355,358,365,366,380,381,382,386,390,392,393,396,404,406,408,409,410],placement:[321,369],plai:[168,285],plain:[9,377,421],plan:[3,5,6,16,17,146,423],planar:[6,40,42,211,251,296,312,314],planck:[205,253],plane:[3,6,9,41,42,57,59,67,71,168,172,178,184,188,208,211,221,251,254,264,275,277,290,296,304,306,307,308,309,314,321,379,412,426,433],planeforc:[2,172,221],plasma:[9,88,230,290,357],plastic:[2,3,63,78,80],platform:[1,3,7,9,12,13,15,17,167,168,170,425,430,452],plath:[6,91,172,286,293],player:168,pleas:[0,3,7,11,12,13,178,207,216,220,252,255,266,285,301,356,358,389],plen:336,plimpton:[0,5,7,70,112,121,191,251,278,361,389],plo:29,plog:[3,12,432],ploop:[229,230,233],plot:[7,11,13,260,375,377,407,413],plu:[3,11,12,39,59,68,96,147,169,187,192,194,195,233,270,330,357],plug:9,plugin:[9,13,170,424],plum:169,pm3:143,pmb:2,pme:319,pmf:[193,274,275],png:[3,12,167,168],pni:168,poariz:6,poem:[2,3,6,7,9,12,172],point1:423,point2:423,point3:423,point:[1,2,3,4,6,7,8,9,11,12,18,29,38,40,41,42,56,59,70,71,82,84,85,113,114,118,120,123,137,142,143,144,155,164,165,166,167,168,169,172,177,181,184,188,192,194,195,196,200,204,205,207,210,211,216,219,226,228,229,231,232,234,235,237,238,239,242,244,245,246,247,249,252,253,259,260],point_data:271,pointer:[3,7,8,11,203,421],pois:447,poiseuil:[4,175,208],poisson:[59,194,319,361],poisson_solv:178,polak:325,polar:[6,7,120,143,178,197,348,349,369,411,443],polar_off:348,polar_on:348,polariz:0,poli:[2,3,142,256,321],pollock:[7,319],polya:301,polybond:13,polychain:270,polydispers:[3,341,347,361,378,379,405,415],polygon:[6,142],polym:[0,5,6,7,10],polymer:7,polymorph:[2,7],polynomi:[38,56,164,355,375,384,400,407],polytechn:255,poor:[16,17,41,188,247,248,273,333,375],poorli:[325,326],pop:[3,8],popen:12,popul:[12,265,321,354,423],popular:[12,167,356],pore:275,poros:147,porou:[216,219],port:[210,212],portabl:[7,9,12,167,193,392,425],portion:[1,3,9,11,12,15,16,41,54,71,88,91,107,108,110,113,121,134,167,169,180,181,183,184,185,186,188,192,202,216,229,231,232,234,235,262,267,268,270,271,303,317,329,333,340,342,343,344,345,349,350,352,353,357,359,360,362,363,369,373,377,387,394,395,410,413,422,423,428,432,433,448],poschel:361,posfreq:267,posit:[3,6,14,27,39,40,41,42,46,57,59,70,71,81,89,90,103,104,108,117,118,120,121,127,142,143,144,146,147,148,153,155,164,166,168,169,172,173,175,177,179,180,181,183,184,185,188,189,190,191,192,193,194,195,198,200,205,206,207,208,210,211,213,214,215,216,218,219,222,223,226,227,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,255,256,257,260,261,265,267,268,270,273,274,275,277,278,280,281,282,283,285,287,288,289,290,293,295,296,297,298,299,300,301,304,318,321,328,335,336,338,341,353,354,357,359,367,372,393,404,407,412,418,423,426,433,443,448,449],posix:210,posix_memalign:12,possibl:[1,3,6,8,9,11,12,15,38,40,41,55,59,63,70,71,87,113,115,120,121,123,137,166,167,169,172,174,178,179,184,188,189,190,191,195,197,207,214,251,264,265,267,270,278,280,290,291,308,317,319,326,329,330,333,354,363,380,393,407,421,427,436,437,438,441,443,448,449,451],post:[0,4,6],post_forc:8,post_force_integr:8,post_force_respa:8,post_integrate_respa:8,postit:[184,185,241],postiv:86,postma:[257,281],postprocess:13,pot:[361,393],potentail:358,potenti:0,potentiel:377,potetni:364,potpourri:9,pour:[2,3,4,6,9,102,146,169,172],pourtoi:285,pow:194,powderblu:169,power7:17,power8:17,power:[3,9,11,105,120,169,265,318,333,339,421],pparam:[87,173,174],ppm:[12,167,168],ppn:[14,15,16,17,18,333],pppm:[0,1,2,3,5],pppm_disp:3,pppmdisp:3,pproni:[3,206],pr3:143,pr4:143,practic:[3,12,192,229,230,252,259,420],prb:[408,410],prd:[2,3,4,6,86,194,328],pre:[3,6],pre_exchang:8,pre_forc:8,pre_force_respa:8,pre_neighbor:8,prec_tim:14,preced:[2,6,59,180,181,182,183,184,185,186,212,267,271,303,321,328,333,339,363,437,440,441,448],preceed:[11,12,71,132,182,295,421,448],precipit:142,precis:[1,3,9,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,109,112,122,131,144,150,151,153,154,155,156,158,159,161,162,164,167,169,175,187,192,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,261,262,263,270,272,273,281,283,294,304,306,307,308,309,312,314,318,319,326,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,392,394,395,397,406,407,408,409,410,412,414,415,416,425,432,433,436,441,443,447,448,449],precv:420,predefin:[162,169,301,357],predict:[1,6,10,241,270,333],preexponenti:437,prefactor:[24,25,28,32,35,36,138,152,163,173,174,182,295,306,309,312,326,347,359,386,394,395,397,415],prefer:[7,8,12,269,291,335],prefix:[11,12,168,193,252,417,420],preliminari:[38,56,164,407],prematur:326,prepar:[9,264,278,434,443],prepend:392,preprint:[120,396],preprocessor:210,prerecord:193,prescrib:[6,8,123,124,137,172,173,178,181,195,226,243,291],presenc:[167,189,190,216,219,378,379,415,450],present:[1,3,12,16,18,142,164,168,195,206,207,212,216,217,219,220,265,296,299,348,357,368,377,393,394,420,443],preserv:[3,59,192,194,229,273,278,300,424],press:[2,3,6,9,29,87,96,97,110,121,130,172,192,198,205,207,214,224,227,229,231,232,233,234,235],pressdown:187,pressur:[1,2,3,6,7,8,9,57,63],pressure_with_eviri:357,presum:[73,133,172,173,174,194,328,364,426],prevent:[2,3,6,195,204,278,289,312,318,324,326,328,333,353,364,388,399,400,402,404,421,425,431,443,448],previou:[0,2,3,5,6,8,9,11],previouli:195,previous:[3,11,59,61,71,86,102,117,119,133,144,146,148,166,167,169,177,179,180,181,182,183,184,185,186,194,195,205,211,224,226,256,268,270,272,273,290,292,295,296,297,298,300,301,320,361,405,418,421,425,426,436,438,440,441,444,445,446,448,449],prevoiu:296,price:[6,352],primari:[0,9,290],primarili:[5,7,9,17],primaritli:17,prime:[198,214,362,367,408,410,420],primit:[3,6,298,299,321],princip:[3,210],principl:[6,9,11,210,230,261,357,365,406,420],prinicp:[42,270,327],print:[0,1,2,3,6,7,8,11,12,16,17,18,19,41,91,96,97,117,120,167,168,169,170,172,181,182,183,184,185,186,191,192,195,210,213,216,224,227,229,231,232,233,234,235,243,246,247,249,251,255,256,257],printabl:2,printflag:365,printfluid:216,prior:[142,165,320,451],priori:432,prioriz:333,prism:[3,6,132,146,426],priveleg:3,privileg:[12,210],prob:[189,190],probab:397,probabl:[3,8,12,40,71,134,147,148,150,179,188,189,190,191,195,205,214,229,256,295,301,326,384,418,437,443],problem:[0,1,2],problemat:205,proc:[1,3,8,11,12,15,113,167,317,420],proce:[41,54,148,188,199,328,430,438,441],procedur:[6,12,39,41,169,179,188,205,213,214,215,229,231,232,233,234,235,246,247,248,249,252,281,282,283,284,287,288,326,328,335,341,424,443],proceed:12,procesor:[41,420],process:[1,3,4],processor:[1,2,3,4,6,7,8,10,11,12,13,14,15,17,18,39,40,41,42,58,59,61,62,63,65,68,69,71,79,92,107,108,113,115,116,132,142,144,146,147,148,166,167,168,169,172,178,181,184,185,188,189,190,191,192,194,203,206,207,213,214,216,229,253,259,262,265,270,273,278,290,301,315,317,318,322,328,330,331,332,333,353,354,388,417,418],processsor:[41,188,420],procp1:167,procssor:432,produc:[1,3,4,6,7,12,13,14,15,16,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,45,46,47,48,49,51,53,54,56,63,65,68,69,71,79,92,108,109,110,112,113,114,115,117,119,121,122,131,150,151,153,154,155,156,158,159,161,162,164,167,169,172,175,180,181,182,183,184,185,186,187,188,191,201,203,204,206,207,208,213,214,215,224,226,229,231,232,233,234,235,236,244,246,247,249,256,260,261,262,265,270,271,272,273,279,280,281,283,290,291,292,294,295,298,303,304,306,307,308,309,312,314,319,326,328,331,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,390,393,394,395,397,406,407,408,409,410,412,414,415,416,418,420,425,428,429,432,437,448,449],product:[16,17,18,120,194,247,261,291,333,336,357,393,420,448],proessor:333,prof:255,profi:133,profil:[2,3,6,63,123,124,127],program:[3,4,6,7,9,11,12,13,17,167,168,169,170,172,193,203,210,216,264,355,421,434,448],programm:[13,17],progress:[1,41,188,210,227,260,325,326,328,441,443],prohibit:433,project:[6,7,12,13,14,325,405],promis:7,promot:339,prompt:[8,11,12,210,434],proni:[3,206,207],proofread:8,prop:[6,259],propag:[4,9,177,229,260,357,364],propens:6,proper:[191,251,380,421],properati:259,properli:[175,200,270,327,328,421,449],properti:[0,2,3],propoerti:278,proport:[6,39,41,87,103,104,140,188,213,214,215,260,286,293,294,361],proportion:213,propos:[6,120,179,192,205,229,247,265,369,382,409,411],prospect:7,protect:278,protein:[7,10,144,268,270,276,423,431],protocol:210,proton:[410,416,447],prototyp:[10,42,389],prouduc:[186,292],prove:216,proven:247,provid:[1,3,4,6,7,8,9,11,12,13,14,15,16,17,18,29,40,42,67,70,118,138,143,144,170,180,181,186,191,192,193,194,203,205,210,212,216,220,227,229,252,260,261,264,265,270,274,285,287,288,291,292,303,316,318,319,324,328,333,335,339,341,346,348,349,353,356,357,361,363,366,368,377,378,380,382,390,391,392,393,396,404,405,406,408,409,410,420,425,431,436,437,441,448],proxim:166,psa:298,pscreen:[3,12,432],pscrozi:[0,7,13],psec:[169,194,209,213,214,229,257,270,281,282,442,447],psend:420,pseudo:[357,418,423,428],pseudodynam:285,psf:6,psi:[358,415],psi_ij:358,pstart:[3,229,230,233,257,270],pstop:[3,229,230,233,257,270],pstyle:[87,107,173,174],psu:[392,393],psuedo:428,pt2:143,pt4:143,ptarget:192,pthread:[12,17],ptr:[6,11,203,421],ptype1:115,ptype2:115,pu3:143,pu4:143,pu6:143,publicli:5,publish:[7,216,220,261,349,380,408,410],pull:[274,275],puls:290,pump:[378,379],punctuat:[2,418,437],purchas:168,purdu:[9,13],pure:[11,278,364,381,382,408,410,432],purg:[3,424],purpl:[2,169],purport:11,purpos:[3,6,7,12,42,61,71,118,127,128,143,144,146,148,164,167,184,186,191,192,213,251,253,256,258,269,278,318,333,343,367,373,384,412,423,425,426,430,433,435,436,448,452],push:[3,8,175,187,194,211,228,251,268,274,326,361,397],pushd:211,put:[3,6,8,11,12,13,39,59,132,144,167,195,199,297,298,301,321,392,421,423,427],putenv:[434,448],px1:432,px2:432,pxx:[192,229,257,270,318,319,440,441],pxy:[3,6,441],pxz:[3,6,441],py1:432,py2:432,pydir:11,pyi:[192,229,257,270,318,319,441],pymol:[7,11,13],pymol_aspher:0,pympi:11,pypar:11,python:[0,2,3,6,7,9],pythonpath:11,pyz:[3,6,441],pz1:432,pz2:432,pzz:[192,227,229,257,260,270,318,319,441],q_c:443,q_d:443,q_i:[358,377,411],q_j:377,qbmsst:[2,9],qcore:261,qdist:[349,369,373,377],qeq1:261,qeq2:261,qeq:[2,3,4,6,7,172],qfile:[261,349],qin:209,qmin:325,qmmm:[0,2],qmol:264,qout:209,qtb:[0,2],quad:[12,18,333,420],quadrat:[2,3],quadratur:[87,178],quadrupl:334,quadruplet:[160,163,304,306,307,309,311,312,313],qualifi:[3,212],qualiti:[7,9,168,169],quantit:[74,81,103,104,105,140,361],quantiti:[1,3],quantum:[6,9,120,203,207,253,260,264,265,339,357,405],quantum_temperatur:260,quartic:[2,3,7],quartic_spher:178,quartz:[260,265],quasi:253,quat:433,quaternion:[3,6,40,82,113,123,144,231,234,237,238,239,246,360,423,433],quati:[113,423],quatj:[113,423],quatk:[113,423],quatw:[113,423],queen:13,quench:[301,418,437],queri:[3,11,54,243,421,448],quest:[6,203],question:[8,9,12,13,251,301,389,448],quick:[0,9,12,14,15,16,17,18,19],quickli:[3,4,8,12,13,39,188,194,210,278,325,326,328],quickmin:[324,325,326,328,437],quicktim:[4,168],quip:[2,9],quit:[2,216,285,303,396],quot:[2,3,12,219,258,303,380,418,419,421,431,448],r10:339,r12:360,r_1:120,r_2:120,r_c:[350,352,359,410],r_cut:339,r_d:443,r_e:358,r_ewald:271,r_fu:[378,379],r_i:[29,120],r_ii:120,r_ij:[29,339,357,390,416],r_ik:390,r_j:29,r_jik:390,r_max:185,r_me:350,r_mh:359,r_min:[185,351],r_ub:20,r_x86_64_32:12,ra2:143,rad2theta:143,rad:301,radhi:426,radial:[63,96,97,113,116,120,128,130,135,185,215,230,240,248,275,284,326,357,363,384,423,426],radian:[20,21,24,28,32,35,36,38,143,151,162,164,269,304,306,309,312,423,426],radiat:[118,143,290],radic:[146,423],radii:[76,120,191,195,347,355,360,361,378,379,415,426],radit:357,radiu:[3,6,63,76,84,85,89,90,113,118,120,137,142,167,168,172,185,211,216,230,232,235,240,244,248,249,263,275,276,278,280,295,296,299,301,325,339,341,347,357,358,361,369,377,378,379,380,396,410,415,423,426,433,448],radlo:426,rafferti:293,rahman:[6,7,192,227,229,230,260,389],rai:[9,17,143],ram:410,ramp:[2,3,6,9,63,127,128,132],ran:[3,4,6,10,11],random:[3,6,39,144,147,166,168,177,179,189,190,191,193,195,202,205,206,207,213,214,215,216,225,253,256,260,265,268,270,278,282,285,290,294,297,341,353,354,418,433,438,443,448,449],random_se:418,randomli:[144,147,179,195,205,213,256,278,300,437,438],rang:[1,3,6,7,8,9,10,12,14,15,16,18,38,39,56,71,77,88,108,109,110,112,116,117,120,121,130,138,143,145,148,149,156,164,167,168,169,178,179,190,194,195,205,207,256,271,278,279,285,286,291,293,318,319,326,329,330,333,335,337,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,357,360,362,363,364,366,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,387,390,393,394,395,404,405,407,410,414,415,416,417,421,432,433,441,451],rank:[6,11,12,210,291,316,420],rankin:233,raphson:3,rapid:[4,6,11],rapidli:[3,8,12,71,191,213,227,229,270,281,282,294,349,353],rapp:[261,262,263],rappe_and_goddard:262,rare:6,rasmol:[6,7],rasmussen:360,raster3d:[6,7],rate:[6,12,127,169,178,194,195,209,210,211,256,260,286,287,288,289,293,324,325,354,378,379,418,437,441],rather:[1,2,6,9,12,40,41,62,112,127,168,188,194,206,207,270,282,290,294,296,297,298,301,357,392,407,424,428,433,435,440,448],ratio:[6,10,59,87,101,120,179,188,194,213,215,278,286,293,294,318,331,360,361,394,399,412,420,423,433,437],rational:[291,435],rattl:[3,207],rattle_debug:273,ravelo:[233,371],rayleigh:[227,260],rb1:143,rbg:169,rcb:[3,41,188],rcm:[89,90],rcmx:[89,90],rcmy:[89,90],rcut:61,rcutfac:[120,396],rd1:328,rdc:17,rdf:[2,3,63],rdn:328,rdt:328,rdx:4,reach:[6,12,41,119,188,190,192,214,233,278,285,303,317,332,350,443,448],react:6,reactant:357,reaction:[274,276,289,300,328,357],reactiv:[9,267,335],read:[2,3,6,7,8,9,11,12,13,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,38,40,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,59,115,142,144,145,147,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,167,168,169,170,171,172,178,179,191,192,194,195,205,207,210,226,227,229,231,232,233,234,235,246,247,248,249,252,253,255,256,258,259,263,270,273,274,277,280,288,289,290,296,304,305,306,307,308,309,311,312,313,314,315,317,323,327,328,332,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,418,420,423,424,425,427,428,429,430,431,433,434,435,437,448,449,450,452],read_data:[2,3,6,7,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,57,58,59,62,66,71,74,75,81,82,89,90,93,103,104,106,115,139,142,144,145,146,147,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,167,168,190,191,194,226,253,259,269,289,304,305,306,307,308,309,311,312,313,314,323,327,328,331,332,333,336,337,338,340,341,342,343,344,345,346,347,349,350,352,353,354,357,359,360,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,383,385,387,389,390,392,393,394,395,397,404,405,412,414,415,420],read_dump:[2,3,167,328,423],read_restart:[2,3,6,8,12,13,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,39,40,41,43,44,45,46,47,48,49,51,53,54,55,57,58,59,62,144,150,151,152,153,154,155,156,158,159,161,162,163,172,178,179,192,193,194,195,205,216,226,227,229,231,232,233,234,235,246,247,248,249,253,259,270,274,277,280,290,296,304,305,306,307,308,309,312,313,314,323,328,336,337,338,340,341,342,343,344,345,346,347,349,350,352,353,354,357,359,360,361,362,364,367,369,370,371,372,373,374,375,376,377,378,379,383,385,387,389,394,395,397,404,405,412,414,415,420,423,424],read_restart_set:8,readabl:[168,327,430,452],reader:[3,13,424],readi:[11,12,145,147,148,210,433,443,450,451,452],readm:[1,4,6,8,9,11,12,13,142,167,170,264,365,392,393,421],real:[3,6,7,11,27,30,31,59,71,91,120,133,144,153,166,169,177,184,185,194,195,198,210,211,214,226,253,260,265,268,294,295,297,298,300,308,318,319,321,324,330,349,384,392,393,410,423,426,432,440,442,447,449],realist:[3,195,427],realiz:[71,172,421],realli:[1,3,8,12,112,121,169,211,329,364,435],realloc:3,realtim:210,reamin:[295,299],rearrang:328,reason:[3,6,7,11,12,19,39,125,136,144,181,184,185,213,257,270,287,288,291,301,327,328,333,346,350,357,358,359,379,384,412,413,427,432,449],reax:[0,2,3,4,9,12],reax_def:3,reaxc:[0,7],reaxff:[3,4,5,7,9,13,172,261,263,266,267,364,392,393,405,435],rebal:[41,188],rebalanc:[41,188],rebo:[2,7,267],rebuild:[11,12,14,15,16,205,329,353,441],rebuilt:[3,12,167,168,170,329,333],recalcul:[71,87,278],receiv:[3,187,210,212,251,420],recent:[2,3,11,12,172,181,183,184,185,186,188,189,190,209,225],reciproc:[6,118,143,252,318,340,342,343,349,352,357,369,373,387,395,437],recog:12,recoginz:3,recogn:[3,12,16,73,146,189,190,229,327,355,380,392,421,423,430,431,443],recommend:[7,9,11,12,14,16,168,169,260,288,318,357,378,379,393,394,432],recompil:[1,3,9,12,170,273],recomput:[102,148,199,274,354,435],reconstruct:[3,193],record:[170,193,274],recov:[192,229],rectangl:[41,188,321],rectangular:[7,41,62,146,188,205,321,423,425,427],rectilinear:[118,143],rector:53,recurs:[41,188,339,412],recust:41,recv:420,red:[2,10,168,169,191,253],redefin:[3,425,431,448],redirect:12,redo:12,reduc:[1,2,3,6,9,12,17,18,19,27,41,63,71,88,109,110,112,113,114,115],reduct:[18,19,117,118,143,227,260,318],redund:358,ree:400,reed:[227,260],rees:[7,9,13],ref:[287,288,325],refactor:6,refer:[2,3,6,7,8,9,11,12,15,29,63,68,71,80,83,86,87,102,113,115,117,119,123,124,137,144,167,172,178,180,181,182,183,184,185,186,191,192,194,195,204,227,229,230,233,251,253,255,256,258,260,273,274,285,292,297,303,304,314,318,319,325,329,334,341,354,360,380,382,394,402,403,408,410,418,419,421,428,431,432,433,436,437,441],referenc:[3,6,12,63,68,71,114,167,172,182,186,205,259,292,319,349,363,386,394,421,441,448],reflect:[2,3,6,71,118,120,143,163,168,172,189,190,195,219,227,250,252,270,295,297],reformat:7,refresh:178,reg:426,regard:[6,59,226,273,389,393],regardless:[15,71,144,147,166,183,184,194,213,229,231,232,234,235,257,270,278,333,420,426,433],regim:[6,286,293,350,432],region:[0,2,3,6,7],region_spher:8,region_styl:299,regist:[116,392,393],regoin:6,regress:448,regspher:144,regstrip:301,regul:6,regular:[1,3,9,41,62,88,142,146,179,188,205,290,319,350,404,420,423,425,427],reigon:448,reinhardt:[287,288],reject:[144,191,392,438],rel:[1,6,14,27,36,41,59,71,120,123,126,127,129,144,153,169,172,179,184,188,194,195,198,205,211,225,226,247,251,256,265,267,268,274,275,278,280,285,286,290,297,301,318,319,326,357,360,361,378,379,380,394,415,424,432,437,441,443,449],relat:[1,6,8,9,12],relatic:[198,214],relationship:[6,261,303,318,415,443,448],relax:[2,3,6,7,172],releas:[0,5,7,8,13,189],relect:[3,384],relev:[2,6,12,41,78,80,111,144,148,169,173,174,177,178,179,180,181,182,183,184,185,186,187,188,189,190,194,195,196,199,201,202,204,205,206,209,210,216,217,218,220,221,222,223,225,226,228,236,237,238,239,240,241,242,243,244,245,250,254,255,256,258,259,262,264,266,267,268,271,272,273,274,276,278,279,280,285,286,289,290,291,292,293,294,295,296,297,298,300,301,318,326,336,337,341,347,349,350,352,353,354,357,359,360,361,362,363,368,370,371,372,374,375,376,378,379,384,385,389,394,397,404,407,414,415,416,420,436,449],reli:[3,12,262,357,393,423,433],reloc:12,remain:[7,33,37,41,50,55,59,71,87,104,124,125,126,127,131,132,133,134,136,147,157,163,164,167,173,174,179,181,182,184,185,192,194,213,214,221,229,230,234,235,246,247,249,254,255,278,281,282,283,289,290,301,303,310,313,327,339,357,364,377,405,418,423,424,428,433,435,437,441,443,448,449],remaina:339,remaind:[144,167,195,256,278,291,410,423],remap:[3,6,12,59,61,71,127,144,166,184,194,211,226,247,318,423,424,425],remedi:[6,443],rememb:2,remov:[2,3,6,8,9,13,54,71,77,114,116,120,123,124,125,126,127,131,132,133,134,136,137,144,147,148,172,181,184,189,202,213,214,219,225,227,229,234,235,246,247,249,255,261,270,271,273,278,281,282,283,285,301,318,328,352,379,423,426,434,435,448,449],remove_bia:8,remove_bias_al:8,remove_molecul:178,remove_sourc:178,remove_speci:178,ren:143,renam:[12,302,434],render:[12,13,167,168,169],rendon:[229,230],reneighbor:[3,8,12,39,57,71,184,188,205,278,291,301,353,440,441],renssela:255,renumb:71,reorder:[3,12,39,420],repeat:[2,6,168,169,184,191,192,205,321,339,408,410,412,418,437],repeatedli:2,repel:211,repes:167,replac:[2,3,6,11,12,41,63,89,90,117,122,123,124,125,126,127,130,131,132,133,134,136,137,167,168,169,170,181,182,183,184,185,186,188,191,195,213,233,258,265,267,349,371,424,425,430,431,441,448,449,450,452],replic:[2,3,7,321,420,423],replica:[0,2,3,4],replica_fil:12,report:[0,1],repositori:[7,12,365,391,392,393],reprens:290,repres:[1,3,6,8,9,12,15,40,41,42,59,67,71,90,113,116,156,164,167,168,181,182,183,184,185,186,192,198,206,208,213,216,229,253,255,257,265,270,271,274,275,290,292,299,319,328,334,339,360,367,377,378,379,380,381,382,387,390,392,393,411,412,418,420,423,433,435,438,443,448,450],represent:[3,6,8,57,59,146,167,206,207,253,290,339,357,360,394,423,426,443],reprocess:428,reproduc:[3,229,296,349,355,361],repul:380,repuls:[6,7,9,36,45,46,108,211,261,295,296,299,335,339,347,349,353,357,361,363,377,380,383,404,410,415,416],reqir:[261,263],request:[3,6,8,12,41,147,164,167,210,216,268,278,280,316,318,392,393,418,428,433,436,437,448,449,450],requir:[1,2,3,4,6,7,8,9,11],rerun:[2,3,7,77,116,120,167,168,384,424],rescal:[2,3,6,122,125,126,127,131,132,133,134,136,172,179,182,183,186,205,207,209,213,214,225,229,233,247,255,257,265,270,278,281,282],research:[5,7,216,220,418,437],resembl:265,reserv:[12,210,443],reservoir:[91,205,209,213,290],reset:[2,3,6,8,11,12,61,66,71,74,75,81,89,90,93,103,104,106,139,148,172,173,174,192,194],reset_atomic_reference_posit:178,reset_dt:8,reset_target:8,reset_tim:178,reset_timestep:[2,6,91,424,428],resid:13,residu:210,residue1:329,resist:[6,210],resolut:407,resolv:[192,253,278,379],resort:3,resourc:[7,334,355],respa:[3,16,199,210,229,331,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,378,379,380,381,382,383,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,416,431,432,442],respect:[1,6,9,10,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,45,46,47,48,49,51,53,54,56,59,70,71,87,89,96,97,118,126,129,138,142,143,150,151,153,154,155,156,158,159,161,162,164,168,169,184,185,190,191,192,208,211,213,214,216,229,231,232,233,234,235,236,244,246,247,249,261,262,270,271,274,275,277,290,295,304,306,307,308,309,312,314,316,318,319,323,326,327,332,333,334,335,337,339,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,384,385,386,387,389,394,395,396,397,406,407,408,409,410,411,412,414,415,416,420,424,432,433,436,443,448,450,452],respon:9,respond:[6,7,127,194,357,389],respons:[6,7,227,286,293],resquar:[2,3,6,7,360],rest:[6,8,12,259,263,269,339,379,380,440,441,443],restart1:253,restart2:253,restart2data:[0,12],restart:[0,1,2,3],restartfil:[12,13],restor:[3,8,60,61,144,173,174,259,274,275,280,440,441],restore_bia:8,restore_bias_al:8,restrain:[2,3,29,172,179,205,227],restraint:[9,193,227,269,277,368],restratin:269,restrict:[1,2,3,6,8,12],result:[1,2,3,6,7,9,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,45,46,47,48,49,51,53,54,56,63,64,66,67,71,75,87,90,91,93,104,106,109,110,112,114,115,116,117,118,119,121,122,124,127,131,138,139,141,143,144,147,150,151,153,154,155,156,158,159,161,162,164,167,168,169,172,175,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,198,201,204,205,206,208,213,214,216,220,227,229,231,232,233,234,235,236,244,246,247,248,249,252,253,261,262,267,268,270,272,273,278,281,283,286,287,288,290,291,292,294,295,296,298,300,303,304,306,307,308,309,312,314,318,319,328,331,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,381,384,385,386,387,389,393,394,395,397,406,407,408,409,410,411,412,414,415,416,418,420,423,425,426,427,428,432,433,434,435,437,447,448,449],resum:448,retain:[2,189,190,339,420],retart:[33,50,157,310],retreiv:8,retriev:[6,8,203,381,382,448],reus:[3,435],rev:[6,13,64,70,110,120,121,132,179,207,213,215,227,229,230,233,247,252,262,265,270,274,278,282,285,287,288,293,325,339,347,348,349,352,355,356,357,360,361,366,371,378,379,380,382,390,394,396,406,408,409,410,418],revers:[2,6,8,87,155,191,211,229,250,251,261,286,287,293,328,377,432,443],review:[120,261,274,285,391,396,418,437,443],rewind:317,rewrap:167,rewrit:[5,12],rewritten:19,rezwanur:389,rfac0:[120,396],rfactor:278,rfile:270,rg0:276,rgb:169,rh3:143,rh4:143,rhaphson:3,rheolog:6,rhi:407,rho0:[380,402,403],rho0_meam:380,rho:[40,113,216,289,321,334,340,342,343,355,380,381,382,394,399,401,423,447],rho_0:[402,403],rho_alpha_beta:355,rho_bkgd:380,rho_colloid:295,rho_e:290,rho_fin:289,rho_i:[381,382],rho_initi:289,rho_ref_meam:380,rho_wal:295,rhodo:10,rhodopsin:[1,10],rhosum:[2,100,398,399,400],ribier:325,richardson:270,richi:[9,19],rick:[261,262,348],rick_and_stuart:262,ridg:[9,19],right:[3,6,11,12,41,144,162,163,166,188,191,211,216,226,250,303,321,349,411,423,426,433,448],rightmost:[41,188],rigid:[2,3,4],rigidifi:270,rii:[89,90],rij:[189,190,251,353,404],rin:[363,374,375],ring:[2,3,6,116,253,255],rino:73,rinv:318,rirj:[296,361],rise:29,risi:[120,396],risk:[8,269,432],rix:[89,90],rjk:[189,190],rjone:[7,9,13],rlo:407,rmask:[3,448],rmass:3,rmax:[145,189],rmdir:434,rmin0:[120,396],rmin:[145,190,371],rmsd:289,rnemd:6,robin:169,robust:[324,325,326],rock:380,rockett:390,rod:270,rodata:12,rodnei:265,roi:7,role:285,roll:12,room:[57,59],root:[11,87,89,90,285,289,333,355,430],rosati:39,rose:380,ross:380,rosski:253,rosybrown:169,rot:[6,91,253,269,285,449],rotat:[2,3,4,6,7,9,40,63,82,83,84,85,94,120,123,124],rotaton:426,rough:[6,144,168,300],roughli:[7,10,12,41,127,142,168,205,213,214,228,229,241,257,270,278,281,282,285,319,328,333,425,432],round:[1,3,12,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,71,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,169,175,187,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,294,304,306,307,308,309,312,314,319,331,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,425,432,447,448],rous:206,rout:[87,363,377],routin:[5,6,8,11,15,16,38,39,56,88,148,150,216,391,407,436],roux:[6,198,214,411,443],row:[6,65,66,68,69,75,79,90,92,93,104,106,108,114,115,116,119,124,132,139,141,143,181,182,183,184,185,186,219,270,290,292,300,357],royalblu:169,rozero:380,rperp:226,rpi:255,rpm:12,rrespa:[1,3,5,7,8,16,173,174,226,229,329,334,335,336,337,338,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,378,379,380,381,382,383,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,416,432],rspace:3,rsq:[407,413],rsurfac:290,ru3:143,ru4:143,rub:20,rubia:[381,382],rudd:[384,407],rudra:[7,9],rudranarayan:[7,255],ruiz:179,rule:0,run1:[6,332,448],run2:[6,315,317,332,448],run3:[6,332,448],run4:[6,332,448],run5:[6,332,448],run6:[6,332,448],run7:[6,332,423,424,428,448],run8:[6,332,448],run:[0,1,2,3,4],run_styl:[2,3,7,8,12,16,18,229,230,298,326,329,331,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,378,379,380,381,382,383,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,416,417,418,420,431],runloop:317,runtim:[12,17,168,333],russia:9,rutherford:290,rutuparna:[408,410],ryan:9,ryckaert:[273,312],rycroft:142,s00:389,s0st:6,s2050:1,s2629:355,s319:178,s_i:[6,357],s_ij:6,sack:7,saddl:[228,328],saddlebrown:169,sadigh:[179,355,381,382],saed_vtk:118,safe:[12,168,198,214,333],safe_zon:3,safest:[3,278],safezon:393,safran:415,sagui:[319,352],sai:[1,3,12,13,169,392,393,421],said:326,sakai:409,salmon:169,salt:[350,359,380,423],same:[1,2,3,4,6,8,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,41,43,44,45,46,47,48,49,50,51,53,54,56,57,59,62,63,65,69,71,72,77,79,81,82,84,85,87,88,89,90,91,92,94,97,103,104,105,108,109,110,112,113,115,116,117,120,121,122,123,124,125,126,127,130,131,132,133,134,136,137,138,140,142,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,164,165,166,167,168,169,172,173,174,175,178,179,181,183,184,185,186,187,188,189,190,191,192,194,195,199,200,201,204,205,206,207,208,209,210,211,212,213,214,215,216,219,226,229,231,232,233,234,235,236,244,246,247,248,249,251,252,253,255,256,257,260,261,262,263,265,266,267,268,269,270,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,296,297,298,299,301,303,304,305,306,307,308,309,312,314,318,319,321,322,323,327,328,329,330,331,332,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,389,390,394,395,397,404,405,406,407,408,409,410,412,414,415,416,418,420,421,423,424,425,426,428,431,432,433,434,435,436,437,441,443,447,448,449,451],sampl:[1,2,4,6,9,10,11,12,14,91,123,137,142,166,168,181,182,184,185,193,195,203,205,207,209,229,230,253,256,265,267,271,275,276,278,282,285,288,300,329,339,354,423,437],sample_frequ:178,san:389,sandia:[0,5,7,9,13,14,17,70,111,358,380,389],sandybrown:169,saniti:[269,329],satellit:6,satifsi:448,satisfi:[3,12,73,118,120,142,143,192,216,233,273,298,326,329,361,437],satur:350,save:[6,8,12,19,40,59,164,168,191,206,207,213,214,215,256,265,290,319,329,331,339,425,428,435],sb3:143,sb5:143,sc3:143,scalabl:[0,1,7,9],scalar:3,scale:[0,1,3,4,5,6,9,10,13,18,40,59,63,91,113,116,117,120,130,138,164,167,168,169,172,173,174,178,179,182,192,194,205,209,210,211,213,215,216,227,229,231,232,233,234,235,253,257,260,261,270,278,280,282,285,287,288,290,294,301,318,319,321,330,334,335,336,350,354,357,361,378,379,380,389,411,424,426,428,432,435,437,440,441,448,449],scalegamma:216,scalexi:[3,192,229,233],scalexz:[192,229,233],scaleyz:[192,229,233],scan:[169,190,317,424],scatter:[11,118,143],scatter_atom:11,scatter_coord:11,scenario:[6,40,61,191,259,268,278,291,299,329,427,428,432,440],scf:443,schaik:377,schedul:418,schell:409,schemat:191,scheme:[6,9,18,206,207,229,253,265,273,290,318,411],schlitter1:289,schlitter2:289,schlitter:289,schmid:353,schneider:[213,215],schoen:318,schr:443,schroding:357,schroeder:443,schulten:[214,274,319,443],schunk:278,schwen:9,sci:[73,298,348,382,390],scienc:[8,178,191,210,274,287,355,381,409],scientif:[120,355],scm:11,scratch:[12,41,188],screen:[0,1,3,6,8,11],screenshot:11,scripe:11,script:[0,1],scripta:67,scsl:12,sdk:[2,9,14,15],sea:11,seagreen:169,seamlessli:259,search:[0,2,3,8,12,145,147,169,170,278,324,325,326,328,330,418,424,425,437,448],seashel:169,sec:[12,442,447],second:[1,3,6,9,10,11,12,16,17,54,57,59,61,71,88,91,105,112,121,132,138,142,143,145,146,147,166,167,169,172,181,182,183,184,185,186,191,205,206,211,226,228,253,267,269,270,273,274,275,276,278,287,288,290,301,318,321,325,326,328,329,333,338,339,340,342,343,348,349,355,357,358,361,362,364,368,371,380,384,386,406,409,410,411,418,419,420,421,423,425,430,432,436,437,441,443,447,448,449,450,452],secondari:[3,156],sectinn:451,section:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,58,59,63,64,65,66,67,68,69,71,74,75,78,79,80,81,83,86,87,88,89,90,91,92,93,96,97,98,99,100,101,103,104,105,106,107,108,109,111,112,113,114,115,118,119,120,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,145,150,151,152,153,154,155,156,157,158,159,161,162,163,164,167,168,170,172,175,176,177,178,179,181,182,183,184,185,186,187,188,189,190,191,193,194,195,197,198,200,201,202,204,205,206,207,208,210,212,213,214,215,216,217,218,219,220,222,223,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,251,252,253,255,256,257,259,260,261,262,263,264,265,266,267,270,272,273,274,278,281,282,283,284,285,286,287,288,289,290,291,293,294,296,297,301,302,304,305,306,307,308,309,310,312,313,314,319,320,321,323,327,328,330,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,423,424,428,431,432,433,434,436,437,438,441,443,448,449],section_acceler:[9,12,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,175,187,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,294,304,306,307,308,309,312,314,319,334,335,337,340,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,432],section_accerl:355,section_command:[0,1,9,303],section_error:[7,12],section_exampl:[2,6],section_histori:[7,12],section_howto:[6,8,9,11,12,40,42,57,59,64,66,67,68,70,71,72,73,75,76,77,78,80,81,82,83,84,85,86,87,89,90,93,94,95,96,97,98,99,100,101,104,106,109,110,111,114,116,117,120,121,124,126,138,139,141,142,146,165,181,228,239,242,245,293,338,351,418,423,426,437],section_modifi:[6,7,42,167,168,441],section_packag:12,section_perf:7,section_python:[6,12],section_start:[3,4,6,9,11,322,328,417,418,432,438,441],section_tool:[6,7],see:[1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,57,58,59,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,244,245,246,247,248,249,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,275,277,278,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,299,301,302,303,304,305,306,307,308,309,310,312,313,314,315,318,319,321,322,323,325,326,327,328,329,330,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,423,424,425,426,428,429,430,431,432,433,435,437,438,439,440,441,442,443,448,449,450,451,452],seed1:438,seed2:438,seed:[3,144,147,166,168,177,179,189,190,191,193,195,202,205,206,207,213,214,215,216,253,256,260,265,270,278,282,285,290,297,341,353,354,418,433,438,443,448,449],seed_com:214,seed_drud:214,seek:[41,188],seem:[6,192,291,325,380,432],seen:[12,216,299],segement:3,segment:[3,4,6,7,40,42,82,113,172,242,270,278,353,367,393,404,405,423,431,433],select:[6,12,15,17,59,71,117,118,133,138,143,144,164,168,170,177,179,184,185,194,195,202,205,210,211,226,274,277,285,286,291,293,295,297,298,300,316,318,324,328,330,333,363,368,380,420,424,426,432,433,437,448],self:[2,3,4,6,8,9,12,117,167,172,175,180,181,183,184,185,196,198,200,214,260,261,263,265,266,269,270,274,275,276],sellerio:13,semi:[3,170,178,179,250,252,424],semiax:123,semimet:357,send:[0,3,5,7,8,11,12,169,210,420],sender:[3,420],sens:[1,3,6,7,18,39,41,42,59,163,167,181,183,184,185,186,188,191,194,206,207,212,213,214,215,256,260,265,271,278,285,286,290,293,301,328,349,369,373,408,409,410,418,423,428,432,435,440],sensabl:210,sensibl:104,sensit:[2,6,73,192,265,449],sent:[169,210,316],separ:[2,6,7,12,13,40,41,76,116,120,142,144,147,169,170,178,182,188,189,190,191,192,195,198,205,213,214,229,241,253,256,257,259,261,265,270,273,278,281,282,283,286,293,301,319,333,340,342,349,350,352,378,379,380,386,391,396,405,406,407,410,415,421,423,424,425,432,435,440,443,449,450,451],seper:350,sequec:448,sequenc:[2,3,12,41,59,167,168,169,170,188,207,228,301,321,328,364,390,438,448],sequenti:[59,60,169,390,424],sequestr:7,ser:252,seri:[3,4,6,13,18,120,167,168,169,182,186,206,207,256,332,335,360,380,384,394,397,407,421,430,431,440,441,448],serial:[1,5,7,10],serial_icc:12,serious:8,serv:[6,146,278,404],server:[1,212,333],set:[0,1,2,3],set_callback:203,set_energi:203,set_vari:[6,11,421],setarea:216,sete:[181,191],setenv:[11,12,346],setfl:[13,334,355],setforc:[2,3,6,172,175,187,204,243,270],setgamma:216,setmask:8,settl:192,setup:[3,4,6,7,8,11,12,13,16,37,40,55,59,71,87,91,132,145,146,147,148,163,169,178,191,194,278,291,313,329,330,333,405,420,423,431,450,452],setup_pre_exchang:8,setup_pre_forc:8,setup_pre_force_respa:8,seven:382,sever:[1,4,5,6,7,8,10,11,12,13,15,18,39,40,63,71,87,138,145,148,163,167,170,172,178,189,190,192,207,213,216,220,229,255,257,259,270,274,278,285,294,316,321,326,333,336,339,343,354,355,364,373,377,380,384,390,392,393,418,421,425,429,437,441,443,448,449],sfactor:[3,168,169],sfftw:12,sgi:12,sgmc:179,sgrid:278,sgroup:142,shade:168,shake:[2,3,5,6,7,8,29,38,56,65,69,112,115,121,122,123,124,125,127,130,131,132,133,134,136,137,148,172,181,195,205,207,241,256,270],shan:[17,262,348],shanghai:[9,13],shape:[3,6,8,40,41,58,59,62,71,82,113,123,127,128,144,146,166,168,169,172,173,184,188,192,194,213,227,229,231,234,237,238,246,247,260,278,291,299,338,360,394,420,423,424,425,433],shapei:[113,423],shapex:[113,423],shapez:[113,423],shapshot:428,share:[0,1,3,6,7],shared0:12,sharon:270,sharp:[299,380,410],shawn:9,shear:[3,4,5,6,7,9,59,61,127,166,192,194,216,229,247,278,293,296,361,378,379,389],sheet:427,shell:[0,2,3],shen:9,shenderova:335,sheppard:325,shflag:12,shield:[2,3,7,172],shift:[1,2,3,6],shiftse:278,shiga:[6,229,230],shini:[168,451],shinoda:[6,9,229,230,395],shiny:168,ship:170,shlib:[11,12],shlibflag:12,shock:[4,9,172,177,227,233,260,297,371],shockvel:[227,260],shortcut:[192,229,257,270],shorter:[3,119,205,251,330,384,431],shortest:[168,330,336,432],shorthand:169,shoul:412,should:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,61,70,71,73,81,83,87,91,96,97,98,102,103,109,110,112,121,122,123,126,127,130,131,132,134,137,140,142,144,146,148,150,151,152,153,154,155,156,158,159,161,162,164,165,166,167,168,169,173,174,175,176,179,187,188,189,190,191,192,194,195,197,198,200,201,202,203,204,205,206,207,208,209,211,213,214,215,216,218,219,220,221,226,229,231,232,233,234,235,236,241,244,246,247,249,251,252,253,254,255,256,257,258,260,261,262,263,264,265,266,267,268,269,270,272,273,275,278,279,281,282,283,284,285,286,289,290,291,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,312,314,319,321,322,324,326,327,328,329,330,331,333,334,335,337,338,340,341,342,343,344,345,346,347,348,349,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,379,380,381,384,385,386,387,388,389,391,392,394,395,397,404,406,407,408,409,410,411,412,414,415,416,418,419,420,421,423,424,425,426,427,428,430,431,432,433,435,439,440,441,443,448,449,450],shouldn:[3,8],show:[6,11,12,116,251,328,363,380,384,407],shown:[1,12,17,41,96,97,118,120,130,143,163,188,191,213,229,247,253,256,265,285,318,357,358,360,361,377,394,423],shrank:71,shrink:[3,6,41,57,59,71,146,166,167,168,173,174,177,188,194,195,211,216,251,278,297,301,318,319,326,349,369,373,384,423,424],shrunk:71,shut:[6,11,329,422],si4:143,siam:298,sic:[4,349,364,380,386,406,408,410],sic_tersoff:390,sicc:[356,406,408,410],sicg:[408,410],sicsi:[356,406,408,410],side1:426,side2:426,side3:426,side4:426,side:[3,8,41,57,61,134,144,179,180,188,191,195,205,211,216,226,251,256,264,275,295,299,300,301,328,349,360,361,394,412,421,423,426,433],sidewai:4,sienna:169,siepmann:293,sigam:347,sigam_ii:367,sige:[408,410],sigma0:339,sigma14:377,sigma1:339,sigma2:339,sigma:[3,6,10,45,46,50,54,87,150,167,169,173,174,205,216,251,278,294,295,299,321,330,333,335,338,339,340,344,345,347,352,353,354,356,357,360,362,363,367,368,369,370,371,372,373,374,375,376,377,383,384,394,395,400,406,412,432,447,448,449],sigma_14:344,sigma_:350,sigma_c:347,sigma_cc:[335,347],sigma_h:359,sigma_i:[358,384],sigma_ii:[367,412],sigma_ij:[367,384,412],sigma_j:384,sigma_max:354,sigma_ss:347,sign:[3,6,12,155,163,250,275,298,303,431,440,448],signicantli:17,signifi:[3,66,75,90,93,104,106,114,124,139,141],signific:[7,12,18,86,206,227,230,265,278,291,357,360,380,450],significantli:[1,6,39,121,142,216,229,269,357,406],sij:182,sikandar:17,silbert:361,silent:[169,421,434],silicon:[356,380,406,423],sill:389,silver:169,sim:[9,395],similar:[5,6,7,8,9,12,17,18,40,41,46,59,68,87,112,115,121,144,145,167,169,172,173,174,181,188,203,204,206,213,219,220,230,259,260,265,269,270,282,285,295,296,298,300,319,324,325,327,335,338,339,353,355,357,361,377,378,389,390,420,425,430,432,437,439,441,443,448,449,450,452],similarli:[3,6,7,8,59,112,140,146,148,166,167,168,169,180,181,183,184,185,186,190,194,200,211,229,231,232,234,235,255,257,270,271,273,278,285,286,293,299,304,319,321,328,331,343,361,373,406,420,423,426,427,432,433,437,451],simluat:[6,39,169,278,378,424,425],simlul:[270,290],simmul:293,simpl:[1,2,6,7,8,11,12,13],simpler:[8,42,169,270],simplest:[3,8,40,66,75,90,93,104,106,114,116,124,139,141,261,443],simpli:[1,3,6,8,11,12,14,17,66,71,75,88,90,93,95,104,106,113,114,119,124,139,141,147,148,169,172,173,174,181,183,184,185,186,190,192,194,198,203,212,214,219,229,253,257,268,270,271,286,292,293,318,319,321,327,328,333,343,352,364,373,380,384,420,421,428,431,438,441,447,448],simplif:357,simplifi:[179,269],simplist:11,simualt:319,simul:[0,1,2,3,4],simulatan:333,simulation_nam:393,simulatoin:[12,424],simult:333,simultan:[6,7,15,16,194],sin:[194,226,295,298,300,390,423,426,433,448],sinc:[0,1,2,3,6,8,9,10,11,12,13,15,16,21,22,33,39,41,44,54,59,64,67,71,73,89,90,110,116,118,123,124,134,142,146,147,149,150,152,157,167,168,169,172,173,174,175,176,179,180,181,182,183,184,185,186,187,188,191,192,193,194,195,199,200,205,207,209,212,213,215,216,226,229,231,232,233,234,235,238,241,247,251,253,256,258,259,265,268,270,274,277,278,286,290,291,292,293,295,296,299,300,301,302,304,305,317,319,326,327,328,329,332,333,334,335,339,342,343,344,345,347,348,352,353,354,355,356,360,361,362,364,365,366,368,369,371,372,373,374,375,376,377,378,379,380,381,382,384,387,390,391,392,393,394,395,396,397,406,407,408,409,410,416,418,420,421,423,424,425,426,428,431,432,433,434,435,437,441,443,447,448,449,451],sinclair:[7,355,405],sine:390,singapor:120,singh:334,singl:[1,2,3,6,7,8,9,11,12,14,15,16,17,18,40,41,42,57,59,61,63,65,66,68,69,75,77,79,87,88,90,92,93,104,106,108,113,114,115,116,117,119,124,139,141,142,144,167,168,169,170,172,177,180,181,182,183,184,185,186,188,190,191,192,195,198,202,204,209,216,219,226,229,230,233,241,253,255,256,258,269,270,271,273,278,280,290,292,295,296,298,300,301,303,318,319,324,327,328,329,330,332,333,334,335,339,344,346,348,354,355,356,357,358,361,362,363,364,365,366,380,381,382,384,386,387,390,391,392,393,394,396,397,406,408,409,410,418,419,421,423,430,431,432,433,434,435,436,437,440,448,451,452],singleel:339,singular:[377,378,379],sinnott:[262,335,348],sinusoid:[144,194,295,296,298,300],sio:348,sirk:[121,404],sisic:[356,406,408,410],sisisi:[356,406,408,409,410],sister:346,sit:[252,423],site:[0,1,2,3,4,5,6,7,8,10,11,12,13,14,15,16,17,67,70,87,210,216,217,273,319,334,339,349,355,359,369,373,377,387,392,393,411],situat:[9,192,205,216,229,253,271,325,339],sival:143,six:[6,120,182,183,386,390],sixth:386,sixthpow:[345,384],size:[0,1,3],size_restart:8,sizex:235,sjplimp:[0,7,11,12],sjtu:9,skew:[3,6,58,59,146,168,194,229,423,426],skin:[3,12,39,61,73,115,145,147,205,241,270,290,329,330,333,388,441,447],skip:[12,16,33,157,255,317,327,332,368,423,428,431,440,448],skyblu:169,slab:[3,6,71,132,184,256,275,318,319,329,384],slateblu:169,slategrai:169,slater:[2,3,7,172],sleight:54,slepoi:380,slice:[2,3,6,63,118],slider:11,slight:[3,12,290],slightli:[1,6,39,40,167,168,170,265,270,319,335,349,367,369,373,408,410,418,431,450],sligthli:352,sliozberg:404,slip:[3,172,278,294,300],sllod:[2,3,6,127,128,172,194],slope:[6,103,104,286,288,293,350,448],slot:1,slow:[3,6,7,12,39,206,210,213,214,227,278,285,318,328,333,384,432,443,449],slower:[1,10,17,39,214,319,333,339],slowest:[290,420],slowli:[12,71,188,294,326,397,425],slurm:12,slurm_localid:12,sm3:143,small:[1,2,3,4,6,7,8,9,12,15,17,18,39,40,41,58,70,80,87,110,118,121,124,127,142,143,146,167,172,181,188,189,190,191,195,196,198,205,206,213,214,227,229,247,251,256,257,259,260,261,265,267,268],smallbig:3,smaller:[1,3,6,12,16,17,39,56,59,61,71,119,142,146,167,168,169,179,195,199,205,216,252,270,278,288,303,318,319,324,333,367,384,405,412,413,423,430,432,452],smallest:[3,70,72,142,227,267,448],smallint:3,smallq:319,smallsmal:[3,12],smart:207,smd:[2,193,196],smi:[3,333],smirichinski:9,smit:205,smith:387,smmoth:433,smooth:[2,6,9,40,99,101,299,300,318,339,344,349,362,371,374],smoother:144,smoothli:[54,120,286,293,344,362,375,377,410,416],smpd:12,sn2:143,sn4:143,sna:[2,3,63],snad:[2,3,63],snap:[2,3,4,7,9,120,167,168],snapcoeff:396,snaphot:428,snapparam:396,snapshot:[0,1,3,4],snav:[2,3,63],snb:17,snow:169,soc:363,socket:[12,17,18,212,420],soft:[2,3,7,9,11,12,13,87,173,174,241,298,326,353],softer:[295,299],softwar:[1,6,11,12,14,15,16,17,18,19,142,210,255,271],sole:[189,190,328,390],solid:[4,6,7,10,39,40,41,59,70,73,91,121,142,178,188,192,194,199,219,229,231,232,234,235,251,252,257,270,285,288,319,321,340,371,389,423],solut:[3,6,13,142,192,199,227,268,273,278,299,448],solv:[3,12,18,216,261,273,288,290,319,325,379],solvat:[4,10,144],solvent:[4,7,13,61,71,145,147,188,202,206,207,213,229,268,270,275,278,286,293,294,344,347,349,350,359,369,378,379,394,405,423,433],solver:[0,1],some:[1,2,3,4,6,7,8,10,11,12,13,16,17,18,39,40,41,55,61,63,71,102,105,107,113,117,119,123,124,125,136,137,138,144,147,152,155,163,165,167,168,169,172,173,174,177,179,180,181,182,183,184,185,186,188,190,191,192,193,202,205,227,229,230,258,259,261,263,270,274,279,285,290,291,292,294,295,301,316,317,318,319,324,325,326,327,328,329,330,333,336,338,339,346,349,355,357,364,384,392,393,405,407,418,420,421,422,423,425,428,429,430,431,432,433,435,437,440,441,447,448,449,452],somehow:3,someindex:302,someon:[7,11,326],someth:[2,3,7,8,11,12,59,192,229,295,298,300,329,364,421,430],sometim:[2,3,6,8,12,18,184,192,229,286,293,318,330],somewhat:[7,9,12,70,124,134,181,229,318],somewher:[17,230,357],soon:[179,191,202,205,210],sophist:7,sorensen:437,sort:[3,13,16,39,71,167,169,170,210,328,329,333,354,424,425,451],sound:[216,227,402,403],soundspe:[402,403],sourc:[0,3,5],source_integr:178,sourceforg:11,south:120,souza:286,space:[2,3,6,8,11,12,18,41,59,71,118,120,133,138,143,144,164,166,168,173,174,177,183,184,185,188,190,194,195,211,216,223,226,229,252,253,268,271,278,295,297,298,300,303,318,319,321,327,328,329,340,342,343,349,352,355,357,367,369,373,380,387,390,395,407,413,415,420,423,426,435,441,443,448,449],spahn:361,span:[2,12,38,71,173,174,184,211,270,318,334,335,339,348,355,358,365,366,380,381,382,386,390,396,406,408,409,410,417,418,426,427,448],spars:[71,164],spatial:[2,3,5,6,7,18,39,41,59,63,66,71,75,90,93,104,106,113,114,124,127,132,139,141,167,172,175,178,180,181,182,183],spawn:210,spc:0,spcpu:441,speak:[17,278,285],spearot:[118,143,271],specfi:[12,107,211,426],speci:[2,120,212,266],special:[2,3,6],special_bond:[2,3,6,12,16,37,45,46,54,55,77,108,115,116,120,145,147,148,150,163,189,190,191,313,327,329,351,363,364,384,411,423,425],specif:[1,2,3,6,7,8,9,10,12,13,15,17,18,22,29,33,40,41,42,50,63,71,108,113,115,116,124,126,129,144,152,157,167,168,169,170,172,173,174,177,178,181,182,183,184,185,186,188,191,193,202,203,205,206,210,216,224,256,258,259,262,270,285,290,291,295,301,305,319,326,328,333,335,338,339,351,355,360,361,364,365,366,367,380,384,392,393,394,405,406,411,412,420,423,424,428,429,430,432,433,439,440,441,447,448,449,450],specifi:[2,3,6,7,8,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,63,65,66,68,69,70,71,73,75,76,77,78,79,80,81,83,85,86,87,88,90,91,92,93,94,95,96,97,98,99,100,101,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,124,126,131,132,133,138,139,140,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,204,205,206,207,208,209,211,212,213,214,216,217,218,219,221,224,225,226,227,228,229,230,231,232,233,234,235,236,241,244,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,285,288,289,290,292,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,313,314,317,318,319,321,322,323,326,327,328,329,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,447,448,449,450,451,452],specifii:[207,216],speciti:432,spectral:396,spectrum:[9,120,260,265],sped:[39,227],speed:[1,3,6,9,12,14,15,16,17,18,19,39,41,169,188,213,216,227,260,278,285,291,297,318,319,328,333,339,349,384,402,403,408,418,432,438],speedup:[1,18,319,432],spefici:[144,168,363],speicifi:327,spell:426,spellmey:[6,150,435],spend:180,spent:[1,12,13,15,418,437],sph:[0,2,7],sph_lammps_userguid:9,sphere1:216,sphere:[2,3,6,40,42,63,71,76,82],spheric:[0,3,4],spheriod:[3,6],spherioid:278,spheroid:[6,270,278],spike:116,spin:[9,40,113,296,336,357,423],spirit:7,spit:3,spline:[2,3,38,56,164,326,335,339,363,380],split:[1,3,6,12,18,41,181,184,188,214,229,298,318,333,412,417,420,432],splittol:[6,318],sppark:6,spread:[1,6,12,303,431],spring:[2,3,5,6,7,10,13,26,27,40,45,46,48,49,53,153,172,175,191,196,200,228,253,268,274],springer:274,springgreen:169,sptial:71,sputter:195,sq2:[3,321],sqrt:[2,3,59,81,89,205,213,214,215,251,278,294,296,321,347,353,355,359,361,380,384,448],squar:[2,3,6,7,12,22,24],squeez:[192,211,378,379],squibb:[5,7],sr2:143,src:[0,1,3,4,6,7,8,9,11,12,14,15,16,17,18,19,142,167,203,273],srd:[2,3,4,7,9,172],srolovitz:355,srp:[2,353],srun:12,ssao:[168,451],stabil:[6,213,229,339,392],stabl:[6,64,216,233,269,339,443],stabli:206,stack:[3,8,70],stage:[3,87,172,203,228,264,301,328,418,437,448],stagger:[1,3,169,319,430,439,448],stai:[3,14,17,173,174,227,243,260,333,423],stamp:[285,424],stamped:12,stan:17,stand:[0,6,7,13,266,392,393,421],standard:[0,1,3,6,8],stanford:9,starikov:290,start:[0,3,4,6,8,9],start_6:359,start_7:432,startstep:448,stat:[12,54,148,251,265,326,353],statcoul:447,statcoulomb:447,state:[2,3,6,7,9,11,12,13,59,61,63,70,73,80,81,86,87,103,111,156,172,179,191,192,193,195,205,206,207,213,214,215,227,228,229,231,232,233,234,235,246,247,248,249,252,256,260,265,270],statement:[3,421,422],stationari:[2,216,222],statist:[3,6,12,39,41,64,189,190,191,206,207,213,214,215,255,256,260,265,270,273,278,289,290,291,326,328,335,353,354,361,378,415,418,425,431,433,437,440,441],statu:[3,12,54,60,148,193,198,214,348,437],statvolt:447,std:12,stdin:[3,12,317],steadi:[6,227,233,260],steelblu:169,steep:407,steepest:[7,325],steer:[7,9,193,196,274],stegailov:290,steinhaus:443,stencil:[3,216,318],step:[1,2,3,6,8,10,11,12,13,14,15,16,17,18,19,39,71,91,96,97,110,116,117,121,130,140,142,167,168,169,170,172,173,174,178,179,181,182,183,184,185,186,188,189,190,191,192,194,195,198,199,202,203,205,207,210,211,214,227,241,251,252,258,259,260,261,262,263,271,273,274,278,280,283,284,285,286,287,288,289,290,291,292,293,300,301,303,317,318,324,326,328,329,353,359,363,380,392,393,418,420,421,425,427,428,430,431,432,437,438,440,441,443,448,452],stepani:274,stepwis:87,stesman:285,steve:[0,5,7,13],steven:191,stiff:[6,40,51,189,190,252,253,326,389,443],stile:350,still:[1,3,6,9,11,12,13,14,17,18,38,41,61,71,108,116,142,148,164,165,167,169,173,174,188,209,213,241,261,265,278,290,303,318,319,324,345,355,360,361,364,368,378,388,392,394,397,405,423,425,431],stilling:[3,5,7,15,88,356,382,390,405,406,435],stipul:210,stl:71,stochast:[4,7,9,172,207,278,285,300,354],stoddard:352,stoke:[216,294],stoll:[213,215],stone:[9,19,319,352],stop:[3,6,11,12,41,54,119],stopstep:448,stopthresh:[41,188],storag:[3,12,15,292,333,435],store:[2,3,6,7,8,11,12,17,33,37,38,39,40,42,50,55,56,59,61,62,63,65,68,69,71,76,79,81,82,84,86,89,91,92,103,104,107,108,112,113,114,115,117,119,121,122,123,124,125,126,127,131,132,133,134,136,137,140,142,144,147,157,163,164,165,167,168,169,170,172,173,174,177,178,180,181,182,183,186,189,190,194,195,199,201,203,206,210,216,217,218,219,220,221,222,223,225,226,228,229,231,232,233,234,235,236,237,238,239,240,242,243,244,245,246,249,250,251,252,253,254,255,256,257,258,259,261,262,263,264,266,267,270,271,273,274,275,276,277,278],store_st:279,storm:12,stouch:7,str:448,straatsma:6,straddl:[3,59,61,134,211,270,275,301,423,427,433],straight:270,straightforward:[13,357,443],strain:[3,6,59,80,166,192,194,227,229,233,378,379],strang:[164,168,448],strategi:0,stratford:216,strcmp:303,stream:[3,6,112,121,124,127,128,168,178,194,206,207,213,214,247,256,265,278,449],streamlin:[12,431],streitz:[2,3,7,261],streiz:349,strength:[3,120,138,149,168,269,295,299,364,393,394,435],stress:[2,3,5,6,7,42,63,91,110,112],stretch:[3,54,59,117,189,274],strict:396,strictli:[6,41,164,188,227,260,285,423],stride2:448,stride:[169,207,430,439,448],strietz:349,strike:195,string:[2,3,6,11,12,41,144,167,169,181,182,183,184,185,186,188,205,258,271,303,320,332,380,390,391,392,396,419,421,423,433,434,440,441,448],strip:448,strong:[261,335],stronger:6,strongest:[378,379],strongli:[1,6,13,195,270,273,290,443],structrur:3,structur:0,structured_point:271,strucur:73,stuart:[261,262,335,348,405],stub:12,stuck:192,student:255,studi:[6,105,371],studio:12,stukowski:[179,355],style1:[33,50,157,310,364,423],style2:[33,50,157,310,364,423],style:0,style_nam:[229,230],stylist:8,sub1:434,sub:[1,3,4,6,7,8,9,11,12,13,18,33,37,39,40,41,42,50,55,58,61,63,68,87,91,107,120,138,146,157,163,168,169,173,174,188,192,194,229,230,233,252,260,265,270,273,290,291,299,301,310,313,321,323,333,338,348,354,360,361,363,364,384,392,393,394,411,412,420,423,426,432,440],subbox:[117,168,169],subdirectori:4,subdivis:216,subdomain:216,subequ:11,subgroup:[167,451],subject:[6,41,147,188,411],submit:0,subramaniyan:13,subroutin:333,subscript:[11,290,304,358,448],subsequ:[6,11,12,41,59,145,169,188,192,205,285,290,291,292,321,332,355,384,405,421,423,424,430,433,434,442,448,452],subset:[6,11,12,16,41,80,120,167,169,188,225,229,231,232,233,234,235,256,257,261,270,328,333,335,339,364,384,417,420,423,425,428,432,448],substanti:[6,16,406,432],substep:229,substitut:[1,2,3,12,167,212,328,332,357,421,434,448],substract:349,substrat:[146,192,229,231,232,234,235,257,270,423],substyl:[377,432],subsystem:290,subtl:[94,96,97,207],subtleti:130,subtract:[3,6,54,63,91,94,97,102,103,105,112,121,122,123,124,125,126,127,128,130,131,132,133,134,136,137,167,172,181,205,206,209,213,214,215,217,221,225,247,254,270,301,329,376,423,433,441,448,449],succe:12,succeed:182,succesfulli:3,success:[2,6,11,12,14,15,116,167,169,179,182,192,195,205,241,256,270,278,285,303,326,328,421,430,431],successfulli:[3,11,167,195,421,434],successulli:11,successv:428,sucessfulli:3,sudden:36,suddenli:299,sudo:[11,12],sufac:42,suffer:[16,17,18,293,299,333],suffici:[2,3,7,17,18,41,61,71,184,188,227,229,252,278,285,292,295,303,368,423,443],suffix2:12,suffix:[1,2,3,6,9,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,167,168,175,187,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,289,294,304,306,307,308,309,312,314,318,319,328,333,334,335,337,339,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,382,385,386,387,389,390,394,395,397,406,407,408,409,410,412,414,415,416,421,423,424,432],suggest:[0,7,12,227,260,421,443],suit:[7,9,13,174,216,357],suitabl:[4,12,13,17,54,87,167,191,259,282,339,346,361,377,380,392,393,418,437],sum:[3,6,8,9,12,40,70,71,76,80,83,88,89,90,94,98,103,105,107,109,110,112,116,117,120,121,122,124,125,126,127,130,131,132,133,134,136,138,140,141,142,181,182,183,184,185,186,195,203,206,213,214,219,251,252,256,260,265,270,271,274,277,288,290,292,295,299,301,318,319,326,338,349,353,357,358,367,369,372,380,392,393,396,412,421,441,443,448,449],summar:[6,358],summari:1,summat:[6,9,42,70,88,318,319,343,349,355,356,369,373,406,408,409,410],summer:[3,13,184,392,393],sumsq:117,sun:[21,43,151,304,345,384,393],sunderland:17,sup:[252,260,265,348,443],supercomput:[12,17,18,421],superpos:[364,405],superposit:7,supplement:[207,392,393],supplementari:[193,360,394],suppli:[12,164,205,227,290],support:[1,3,6,7,8,9,11,12,13,14,15,16,17,18,19,40,41,42,87,88,102,107,167,168,169,170,173,174,175,176,181,188,191,192,193,200,203,207,208,211,213,214,215,216,224,227,229,231,232,233,234,235,246,247,248,249,251,252,257,260,262,264,269,270,275,277,281,282,283,284,288,293,295,299,316,317,318,319,325,326,327,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,420,424,425,430,432,433,434,436,437,443,447,451,452],suppos:[3,8,358,448],suppress:[6,12,142],sure:[6,8,11,13,14,164,173,174,192,270,273,300,355,407],surf:145,surfac:[3,4,6,8,40,42,57,70,118,120,142,144,147,168,172,195,202,211,216,219,251,262,269,275,278,285,290,295,299,300,328,339,364,378,379,412,415,420,426],surface_mov:290,surfact:[350,359],surpris:357,surrog:9,surround:[38,56,70,144,164,169,192,229,231,232,234,235,251,257,270,407,443],suspect:3,suspens:[378,379],sustain:[167,192,361],suzuki:[229,270],svg:6,svn:[7,11,12],sw_exampl:391,swamp:270,swap:[2,3,6,7,172],swegat:289,swiggl:[3,226,295,298,300,426,448],swiler:[120,396],switch7_section_start:359,switchflag:[120,396],swm4:443,swol:53,swope:6,sxx:169,sy0302:9,symbol:[6,12,118,143,267,339,357,396],symmetr:[6,70,87,93,112,121,173,174,192,229,230,286,293,334,346,352,355,408,410,448],symmetri:[3,5,6,7,8,63,64,70,146,167,227,251,304,319,334,423,443],sync:[3,6],synchron:[1,207,328],synechococcu:7,syntax:[1,2,3,7,8,11,12,13,14,15,16,18],sysdim:252,sysstem:339,system:[0,1,2,3,4,5],system_:253,systemat:[6,213],systemx:3,t10:438,t11:438,t12:438,t13:438,t14:438,t15:438,t3e:12,t_chain:3,t_corr:3,t_correl:418,t_dephas:418,t_e:290,t_e_min:290,t_equil:[287,288],t_event:[3,418,437],t_hi:437,t_infil:290,t_init:[260,290],t_iter:3,t_lb:216,t_lo:437,t_order:3,t_oufil:290,t_out:290,t_outfil:290,t_qm:260,t_switch:[287,288],t_target:341,ta06a:396,ta5:143,tab:[2,423],tabbernor:118,tabinn:384,tabul:[3,7,13,22,37,38,44,55,56,65,71,79,92,164,278,318,334,339,340,342,343,344,345,346,349,355,357,369,373,387,390,393,395,405,407,408,413,425],tabular:390,tabulate_long_rang:393,tad:[2,3,4,6,9,86,418],tadmor:9,tag:[178,197,443],tagint:3,tail:[3,87,110,138,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,425,441],tailor:[71,291],tait:[9,402,403],taitwat:[2,401],take:[1,2,3,6,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,77,87,89,91,109,112,113,116,117,121,122,131,138,142,148,150,151,152,153,154,155,156,158,159,161,162,164,167,168,169,173,174,175,187,188,192,194,201,204,208,212,213,214,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,275,276,277,278,280,281,282,283,291,294,301,304,305,306,307,308,309,312,314,318,319,323,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,355,356,358,359,360,361,362,363,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,392,393,394,395,397,404,406,407,408,409,410,411,412,414,415,416,417,421,424,431,432,433,440,441,448],taken:[6,59,144,166,191,195,205,206,207,213,214,215,216,256,260,263,290,308,355,357,360,406,418,432,433],talk:[6,7],talli:[3,6,8,41,107,113,181,183,184,185,188,190,213,215,230,278,286,293,357,359,363,392,393,448],tan:[169,448],tandem:[4,16,270],tangent:228,tangenti:[6,108,278,296,300,361],tanh:290,tantalum:[4,396],taper:[3,263],tar:12,tarbal:[0,8,11,12],target:[3,6,7,8,11,12,17,39,41,169,177,188,192,193,195,205,206,207,213,214,215,229,230,231,232,233,234,235,246,247,248,249,253,257,260,265,270,274,276,281,282,283,284,289,290,293,294,297,316,319,341,353,418,429,431,449],target_fil:289,task:[1,6,7,12,13,14,15,16,17,18,54,169,210,253,291,333,421],taskset:16,tatb:[4,266],tatom:443,tau:[3,133,213,214,216,229,257,270,281,282,287,288,290,442,447],tau_1:206,tau_k:206,tau_n_k:206,tb3:143,tbead:136,tbp:339,tchain:[229,230,233,247,248,270],tcl:265,tcom:214,tcsh:[11,12,346],tdamp:[213,229,230,233,270,281,282],tdephas:418,tdrude:[129,198,214,443],teal:169,tech:[7,9,13],technic:[6,7,9,216,263,278,393],techniqu:[6,7,9,87,172,192,227,260,270,294,297,319,384,407,443],technolgi:9,technolog:[9,14,19,210],tell:[2,6,11,12,37,55,163,172,252,313,329,392,393,405,421,425,443],telsa:17,temeperatur:11,temp:[2,3,6,9,13,63,87,91,94,96,97,102,110,112,117,121],temp_drud:443,temp_eff:97,tempcom:[123,137],temper:[2,3,6,7,328,418,431,437],temperar:253,temperatur:[0,2,3,4,5],temperature_definit:178,tempfix:438,templ:[7,9,18],templat:[3,8,13,17,19,40,144,145,147,195,205,256,270,273,327,423],templeton2010:178,templeton2011:178,templeton:[9,178],tempor:206,temporari:[2,430],temporarili:[164,269,436,437],ten:14,tend:[29,229,251],tensil:[7,194],tensor:[3,6,8,63,82,83,89,90,91,93,106,112,120,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,192,216,219,229,230,233,255,257,270,293,318,319,327,357,378,379,441,448],tenth:317,term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,40,45,46,61,87,88,89,91,110,112,121,123,132,137,138,151,152,153,164,169,173,174,180,182,183,186,194,200,206,207,208,213,214,215,216,228,229,230,231,232,233,234,235,246,247,249,253,257,260,269,270,276,281,282,283,290,292,294,296,304,305,314,318,326,329,334,335,339,340,341,342,343,344,345,347,348,349,350,351,352,353,355,356,357,358,360,361,362,369,373,376,377,378,379,380,381,382,384,387,394,404,406,408,409,410,415,432,433,435,441,443],termin:[118,229,326,328,422,431],termostat:282,terrel:325,terri:7,tersoff:[2,3,5,7,8,9,88,110,121,189,190,349,356,364,390,405],tersoff_1:[408,409,410],tersoff_2:[408,409,410],tersoff_mod:409,tertiari:156,tessel:[9,142],test:[0,4,6,7,9],test_descriptor_str:3,testf:164,testu:164,tether:[6,268,274,275,277,288,359],tex:8,texa:389,texas_holdem:269,text:[2,3,4,6,7,8,12,13,38,41,56,164,167,168,169,172,178,181,182,183,184,185,186,188,193,210,258,289,290,302,319,321,328,355,358,368,380,396,407,419,423,424,440,448,450],textur:17,tfactor:[3,169],tfinal:448,tfix:269,tfmc:[2,3,7],th4:143,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,39,40,41,42,56,57,58,59,61,63,68,71,76,86,88,105,108,112,115,116,119,121,142,145,146,147,153,164,166,167,169,172,177,179,181,183,184,185,186,188,189,190,191,192,194,195,196,199,202,205,206,207,208,211,212,213,216,227,251,252,256,257,258,259,260,261,263,265,268,269,270,271,274,275,276,278,282,283,285,286,290,293,294,295,296,297,298,299,300,301,303,318,319,324,325,326,327,328,329,330,333,338,339,340,342,343,344,355,357,360,361,367,378,379,380,384,392,393,394,397,405,406,407,410,412,413,415,418,419,420,421,423,424,425,426,427,428,431,432,435,437,438,440,448,449,450],thank:[210,408,410],thb:393,thb_cutoff:393,thb_cutoff_sq:393,thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,39,40,41,42,43,45,46,47,48,49,51,53,54,55,56,57,59,61,63,64,66,68,70,71,74,75,81,82,84,87,89,90,91,93,103,104,106,108,109,112,114,115,116,117,119,120,122,123,124,127,130,131,137,139,141,144,146,147,148,150,151,153,154,155,156,158,159,161,162,163,164,167,168,169,172,173,174,175,177,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,200,201,204,205,206,208,209,210,213,214,216,219,226,229,231,232,233,234,235,236,237,238,239,244,246,247,249,255,256,257,258,259,261,262,269,270,271,272,273,278,279,281,282,283,285,289,290,292,293,294,296,298,299,301,303,304,306,307,308,309,312,313,314,316,318,319,321,323,325,326,327,328,329,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,385,386,387,389,390,392,393,394,395,396,397,404,405,406,407,408,409,410,411,412,413,414,415,416,419,421,423,424,425,426,427,428,432,433,435,436,441,443,448,450,451],them:[1,2,3,4,6,7,8,9,11,12,13,14,39,40,41,54,59,71,91,107,114,117,119,146,151,167,168,169,170,180,181,182,183,184,185,186,188,191,192,194,202,210,213,214,225,229,231,232,233,234,235,246,249,251,257,259,267,268,269,270,273,278,281,282,283,285,289,290,292,296,297,298,300,301,304,319,321,327,328,329,333,334,339,346,355,358,360,384,394,397,412,418,421,423,430,435,438,443,448,449],themselv:[6,11,147,173,174,188,214,318,319,328,330,334,339,349,355,377,380,381,382,396,448],theor:285,theorem:[206,213,339],theoret:[105,210,260,406],theori:[3,9,12,40,120,178,193,207,229,252,318,319,339,415,437],thereaft:[71,221,254,270,286,293,421],therebi:[291,378,379],therefor:[3,6,12,64,87,129,179,198,205,214,216,273,285,319,351,391,393,406,411,416,432,443],therein:[6,380],thereof:87,thermal:[0,2,3],thermo:[0,1,2,3],thermo_modifi:[2,3,6,57,63,96,97,117,122,125,127,128,130,131,132,133,134,135,136,172,192,195,229,404,439],thermo_p:[3,63,109,421,441],thermo_press:[63,112,192,198,229,231,232,233,234,235,257,440,441,443],thermo_styl:[2,3,6,8,63,91,94,96,97,109,110,112,117,121,122,130,140,144,167,172,173,174,175,176,181,182,184,185,186,187,191,192,194,198,199,200,208,209,211,213,214,224,227,229,231,232,233,234,235,246,247,249,257,260,272,281,282,283,292,295,298,300,301,326,359,363,384,392,393,426,428,433,439,440],thermo_temp:[63,112,122,191,192,205,229,231,232,233,234,235,246,247,249,252,257,281,282,283,440,441,443],thermoberendsen:6,thermochem:447,thermochemistri:357,thermodyam:[441,447],thermodyanm:[63,191,278,301,432],thermodynam:[0,3],thermophys:384,thermost:[6,126,177,193,198,214,297,443],thermostat:[0,3],thermostatequ:6,thesi:[318,319,378,391],thess:340,theta0:[20,21,24,26,27,28,32,33,35,36,120,153,269,312],theta0max:120,theta10:339,theta1:[151,304,339],theta2:[151,304,339],theta3:[304,339],theta4:339,theta5:339,theta6:339,theta7:339,theta8:339,theta9:339,theta:[3,6,26,27,37,38,63,65,80,120,143,144,153,166,168,208,265,269,290,304,312,363,390,409,423,426,433],theta_0:386,theta_:[312,339],theta_c:363,theta_ijk:339,theta_ijl:304,theta_jik:[381,382],theta_pi:339,theta_sigma:339,thex:261,thi:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,447,448,449,450,451,452],thick:[71,118,168,184,426],thie:110,thijss:285,thin:[116,168],thing:[3,6,11,12,54,68,71,192,229,257,270,278,420,421,425,448],think:[3,6,7,8,11,13,169,270,301,306,309,321,326,364,392,393,407,421,425,428,448],third:[6,9,29,91,120,121,142,181,182,183,184,185,186,206,267,275,276,290,348,358,380,386,411,418,419,421,423,426],thirumalai:156,thistl:169,tho:356,thole:[2,6,9,129,197,198,214],thompson:[0,5,7,9,13,112,120,121,396],thoroughli:9,those:[1,2,3,4,5,6,7,8,12,13,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,43,45,46,47,48,49,50,51,53,54,56,61,71,77,87,91,108,109,110,112,116,120,121,124,134,144,148,150,151,153,154,155,156,157,158,159,161,162,164,166,167,168,169,179,180,181,182,184,185,186,192,194,195,202,205,208,210,211,212,213,219,228,229,231,232,233,234,235,236,244,246,247,249,256,259,262,270,280,287,288,292,296,297,298,301,302,304,306,307,308,309,310,312,314,318,319,326,328,329,333,334,335,337,340,341,342,343,344,345,346,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,384,385,386,387,389,392,393,394,395,396,397,405,406,407,408,409,410,412,414,415,416,418,420,421,423,425,426,427,428,430,432,433,435,437,440,441,443,448,451,452],though:[6,8,12,16,39,40,63,71,91,104,144,167,169,179,184,189,190,192,194,199,230,268,270,272,286,293,303,318,321,328,353,354,355,357,358,360,361,377,378,384,418,423,425,426,431,435,448],thought:[127,213,247,270,294,295,325,361,368,443],thread:[1,3,9,12,16,17,18,210,291,333,436],threads_per_atom:3,three:[3,6,54,63,74,87,91,105,117,118,119,120,123,143,144,156,172,191,192,197,217,229,233,252,257,270,278,285,287,290,308,312,318,319,327,333,334,335,339,355,356,358,360,361,365,368,380,381,382,386,390,393,394,396,406,408,409,410,421,423,426,448],threebodi:406,thresh:[41,167,168,169,188,421],threshhold:[3,41,168,188,301,421],threshold:[3,41,86,169,188,251,329,393,418,437],thrid:421,through:[3,6,7,9,11,12,63,144,167,170,192,203,205,210,211,216,218,219,220,229,230,253,261,285,290,295,317,324,335,356,357,361,369,395,397,404,411,418,421,424,434,440,443],throughout:[6,16,116,118,291,333,423],thru:[3,6,7,11,12,66,74,75,81,89,90,93,103,104,105,106,139,166,167,169,183,226,278,298,303,317,326,332,426],thrust:1,thu:[1,2,3,6,8,9,11,12,18,33,38,39,41,42,50,59,61,63,64,66,67,70,71,72,73,75,77,81,88,90,91,93,103,104,106,108,109,113,114,115,116,117,120,121,124,127,132,134,139,140,141,144,146,147,148,152,157,163,164,166,167,168,169,170,172,173,174,175,176,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,200,202,206,207,208,209,210,211,213,214,219,224,229,233,243,251,257,259,261,265,268,270,271,272,273,274,275,276,277,278,279,281,282,283,285,286,289,290,292,293,294,295,298,299,300,301,303,304,310,318,319,321,324,326,327,328,332,333,334,335,338,339,340,341,342,343,344,345,346,347,348,349,353,354,355,356,357,358,359,360,361,364,365,366,367,369,373,377,378,379,380,381,382,384,385,387,389,390,391,392,393,394,396,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,418,420,421,423,424,425,426,427,428,430,431,432,433,435,437,438,439,440,441,443,447,448,449,450,451],thumb:[8,10,17,144,166,226,270,333,347,426,432],thz:265,ti2:143,ti3:143,ti4:143,tight:339,tightli:259,tij:352,tildeslei:[29,87,352],tile:[3,6,41,62,144,188,367,412,420],tilt:[3,6,57,58,59,71,132,146,167,169,184,192,194,195,208,227,229,230,251,260,319,321,423,426,441],time:[0,1,2,3],time_integr:178,timedelta:182,timelin:5,timer:[1,12,14,17],timescal:[3,180,181,182,183,184,185,186,227,260,265,357,418,432],timespan:[213,214,229,257,270,281,282],timestamp:[3,428],timestep:[1,2,3,6,7,8,10,11,12,14,15,17,39,41,57,61,62,63,65,69,71,79,91,92,104,108,109,110,115,117,119,121,124,132,167,168,169,170,172,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,199,200,202,203,205,206,208,209,211,213,214,216,217,222,223,225,226,227,229,230,231,232,233,234,235,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,255,256,257,258,259,261,262,266,267,268,269,270,271,272,273,275,277,278,279,280,281,282,283,285,287,288,289,290,292,295,296,297,298,300,301,303,317,318,319,324,325,326,328,329,330,331,333,339,353,354,357,363,378,379,393,397,401,418,421,424,425,426,428,429,430,431,432,433,437,438,439,440,441],timesteppnig:273,tin:[348,349],tine:182,tinfoil:319,tini:[144,326,339,449],tinker:7,tip3p:0,tip4:6,tip4p:[0,2,3],tip:0,tirrel:295,titan:15,titer:270,titl:[181,182,183,184,185,186,258,393],title1:[181,182,183,184,185,186],title2:[181,182,183,184,185,186],title3:[181,182,183,184,185,186],tji:352,tl1:143,tl3:143,tlbr_msw:390,tlo:437,tloop:[229,230,233],tm3:143,tmax:[3,199,437],tmd:[2,3,172],tmd_dump_fil:289,tmdatom:289,tmin:199,tmp1:[183,186,434],tmp2:[183,186,434],tmp3:434,tmp:[6,12,41,66,68,69,75,90,93,104,106,114,116,124,139,141,167,168,169,188,259,270,286,293,332,430,434,448],tobia:[229,230,270],todd:247,toe:138,toff:[327,423],togeth:[2,3,6,11,12,17,39,41,71,115,121,124,138,145,167,173,174,181,183,188,192,198,207,214,229,257,270,274,275,278,296,300,301,359,364,421,426,431,443,451],toggl:[59,148,430],togheth:3,togther:3,tol:[273,278,318,406],toler:[3,192,261,262,263,273,278,326,328,406,418,437],tomato:169,tong:[9,13],too:[1,3,6,7,39,41,64,67,70,72,73,77,88,120,132,145,147,168,188,189,190,192,195,202,205,209,229,252,257,261,265,267,273,278,285,286,290,293,319,328,329,333,353,418,426,437,440,443,448],took:[71,397],tool:[0,1,4,6,7,8,9,11,12],toolkit:[6,7,13,14,15],top:[0,3,8,9,11,12,13,59,127,166,172,187,194,209,216,228,247,271,297,298,300,328,333,392,393,396,423,427,433],topic:[448,451],toplog:[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:[2,3,6,29,40,63,113,123,137],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:[2,6,9,12,57,59,87,129,138,146,167,194,197],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:[2,3,4,6,11,16,40,82,172,179,192,202,205,229,230,233],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:[0,1,3],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:[2,3,6,193,206,207,213,278],tstop:[206,207,213,215,229,230,270,281,282,283,284,353,429,437],tsuzuki:73,ttm:[2,3,172],ttm_mod:290,tucker:[120,396],tuckerman2006:229,tuckerman:[229,230,248,253,270,432],tune:[2,3,6,15,16,172],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:[1,3,6],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],ubiquit:[11,339],uhf:336,uiuc:[9,17],uloop:[3,253,328,332,448],ultim:437,ultra:142,umbrella:[2,6,7,9,193,275,305,313],umin:[26,27,48,49,153],unabl:[3,11,41,188],unaffect:[167,192,229,270,424,435,440],unalt:[173,174,241],unambigu:[71,184],unari:[303,448],unbalanc:3,unbias:[132,357],unbond:[190,423],unbroken:80,uncertainti:40,unchang:[59,192,195,228,229,231,232,234,235,243,257,270,423,424,427,433],uncharg:[40,319],uncom:[1,4],uncompress:[12,71,168],uncomput:[2,3,63],uncorrel:[206,285,418],uncoupl:253,undefin:[3,12],under:[0,5,6,7,8,9,10,12,18,21,22,44,120,151,152,168,210,227,256,260,261,304,305,323,357,377,393,396,421,437,443],underestim:142,underflow:168,undergo:[6,86,87,132,206,213,214,274,278],undergon:[191,278],underli:[12,17,70,168,229,290,321],undermin:39,underpredict:6,underscor:[2,3,63,172,191,192,227,229,231,232,233,234,235,246,247,249,257,259,281,282,283,303,327,448],understand:[1,6,8,205,230],understood:[167,339],undesir:[59,192,194,229,270],undetermin:278,undisturb:[378,379],undo:[148,210],undump:[2,3,59,167,168,169,170,317],unexpect:[3,429],unfix:[2,3,6,59,91,172,178,181,182,183,184,185,186,261,269,271,287],unfix_flux:178,unfold:276,unfortun:[291,431,432],uniaxi:[3,123,233],uniform:[7,16,41,88,116,178,188,189,190,213,216,219,230,285,354,360,394,418,420,448,449],uniformli:[59,116,166,216,256,290,390,407,449],uninstal:12,uninterrupt:[179,195,205,226,227,229,231,232,233,234,235,246,247,248,249,259,260,270,274,277,280,288,290,296],union:[3,6,40,169,299,301,423,426],uniqu:[3,6,7,8,9,12,39,71,206,207,213,214,233,259,265,267,328,355,357,423,448,449],unit:[2,3,5,6,7,8,20,21,32,35,36,38,39,56,59,61,65,66,67,68,69,71,72,73,74,75,77,81,82,83,84,85,86,87,88,89,90,91,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,112,113,114,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,142,143,144,147,151,164,166,167,168,169,175,176,177,179,181,182,184,185,187,189,190,191,192,194,195,196,199,200,203,205,206,207,208,209,210,211,213,214,215,216,226,227,228,229,230,233,241,251,252,253,256,257,260,261,263,265,268,269,270,271,274,275,276,277,278,281,282,283,284,285,286,288,289,290,293,294,295,296,297,298,299,300,304,306,309,312,316,318,319,321,323,324,326,327,328,329,330,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,413,414,415,416,421,423,425,426,432,433,437,440,441,442,443],unit_styl:3,uniti:[356,384,400],unitless:[64,67,70,71,114,149,181,184,185,194,205,227,229,260,296,326,336,361,387,389,406,408,409,410,447],unitlesss:[78,80,111],univ:[9,13],univers:[3,6,9,12,13,18,87,210,318,319,328,332,378,382,389,391,410,417,420,448],universit:[9,13],unix:[12,17,212,434],unknown:[3,12,64,73,423],unless:[2,3,11,12,15,16,18,55,57,67,118,129,143,144,167,169,170,177,192,195,205,213,229,231,232,234,235,256,257,270,278,289,320,326,347,384,407,421,426,430,435,448],unlik:[12,33,50,59,89,104,134,144,157,167,213,229,233,257,263,265,281,282,283,310,317,318,334,339,355,358,363,364,368,380,381,382,393,396,405,420,425,430,435,448,452],unlimit:390,unlucki:3,unmark:7,unmodifi:279,unnecessari:16,unoccupi:290,unoptim:168,unpack:[0,8,11,333],unpack_bord:8,unpack_border_bodi:8,unpack_border_hybrid:8,unpack_border_vel:8,unpack_comm:8,unpack_comm_bodi:8,unpack_comm_hybrid:8,unpack_comm_vel:8,unpack_exchang:8,unpack_restart:8,unpack_revers:8,unpack_reverse_comm:8,unpack_reverse_hybrid:8,unpad:169,unperturb:87,unphys:[3,6,214,229,270,423],unpredict:[268,433],unrecogn:3,unrel:[8,9,13,150],unreli:384,unrestrain:269,unrestrict:336,unscal:[3,113,138,167,280,424],unset:[318,357],unshift:352,unsmooth:375,unsolv:[330,344],unsort:169,unspecifi:[194,423],unsplit:443,unstabl:[3,216],unstrain:194,unsuccess:[3,256],unsupport:3,untar:12,until:[2,3,6,12,14,38,39,41,56,71,119,164,168,188,192,195,205,210,256,278,280,287,303,317,318,329,332,333,339,361,407,418,424,428,429,431,437,447,448],untilt:426,unus:339,unusu:[3,8,329],unwant:[3,144,318],unwrap:[3,66,74,75,81,89,90,93,103,104,106,113,121,139,167,169,170,180,191,193,210,226,270,275,280,423,424,427,433],unwrapexpand:167,unzip:12,up_intern:168,updat:[0,3,6,8,12,13,167,172,189,190,198,203,206,213,214,216,218,219,222,223,226,227,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,255,257,259,260,265,270,280,281,282,283,285,290,301,333,339,352,384,392,393,418,423,425,433,434,437,443],upenn:[11,13],upgrad:12,upon:[6,179,210,339,411,437],upper:[2,3,41,57,59,71,88,103,105,133,140,166,169,182,184,185,188,192,198,214,216,229,260,265,295,296,301,302,326,361,426,449],upsid:6,upsilon:360,upto:[3,425,431],upward:195,urbana:[210,318,319,378],urey_bradlei:20,usa:9,usabl:[12,205,355],usag:[3,6,8,214,251,265,278,364,377,423],use_ldg:17,useful:333,user:[0,1,2,3,4,5,6,7,8],user_misc:[30,31,35,154,159,162,308],userguid:9,usr:[11,12,14,424],usual:[2,3,6,9,12,14,17,18,24,28,32,35,36,47,71,87,117,123,124,129,137,142,161,167,173,174,179,181,191,192,193,194,205,208,213,215,227,233,252,260,261,267,269,270,278,286,290,293,295,299,303,309,316,328,329,333,344,347,350,352,360,364,365,368,377,378,379,386,396,406,411,418,424,428,432,434,437,440,441,448,452],util:[17,18,333,360],utilizi:12,utsa:389,uttormark:13,uuml:252,uwo:9,v11:6,v22:6,v33:6,v_0:[3,290],v_a:[8,194],v_abc:[421,441,448],v_area:[2,448],v_atomfil:433,v_c:138,v_cluster:259,v_dc:138,v_delta:87,v_dhug:[227,260],v_diff:[140,292],v_displac:194,v_dk:138,v_dlj:138,v_drai:[227,260],v_dx:[226,426],v_dy:[226,426],v_dz:226,v_e_hbond:363,v_ea:[392,393],v_eb:[392,393],v_eqeq:[392,393],v_espac:175,v_f:421,v_fac:421,v_flux:209,v_foo:[421,448],v_ij:390,v_increas:208,v_integr:292,v_jx:91,v_jy:91,v_jz:91,v_k11:91,v_k22:91,v_k33:91,v_k:138,v_ke:[167,451],v_left:426,v_lgr_po:[227,260],v_lgr_vel:[227,260],v_linear:[295,298,300],v_lj:138,v_mol:169,v_mu:378,v_myi:226,v_myindex:448,v_myke:117,v_mystep:430,v_myvar:[8,169],v_myx:226,v_n:216,v_name1:[138,194],v_name2:[138,194],v_name:[3,6,71,87,117,167,168,169,173,174,175,176,180,181,182,183,184,185,186,187,200,208,209,211,213,214,226,272,280,281,282,283,292,295,298,300,421,426,430,433,439,441,448,449],v_nstep:301,v_occ:359,v_omega:226,v_oscil:[175,176,187,200,272],v_phi:208,v_prefactor:[173,174,397],v_press:121,v_pressdown:[298,300],v_push:175,v_pxy:6,v_pxz:6,v_pyz:6,v_r0:211,v_r1:142,v_r2:142,v_r:[142,211],v_rad:301,v_radiu:211,v_ramp:[295,298,300],v_rate:[194,211],v_scale1:[173,174],v_scale2:[173,174],v_size:[173,174],v_t_qm:260,v_temp:286,v_theta:[208,426],v_tp:194,v_up:426,v_v0:448,v_v11:6,v_v22:6,v_v33:6,v_v:[226,448],v_valu:[168,421],v_vx:226,v_vy:226,v_vz:[226,449],v_wiggl:[295,298,300],v_x:[2,144,211,226,295,298,300,421,426,448],v_xave:6,v_xmax:6,v_xx:144,v_y:[144,211,426],v_yi:144,v_z:426,vacanc:[4,142,287],vacf:[2,3,6,63],vacuum:[290,319,350,410,416],valanc:339,vale:3,valenc:[263,339,357,392,393],valent:339,valeriu:9,valid:[2,3,6,9,11,12,71,118,130,143,168,169,192,205,213,251,270,278,301,303,316,321,355,357,360,390,423,424,431,433,448],vallon:380,valon:380,valu:[2,3],value0:448,value1:[12,124,180,181,182,183,184,185,186,233,292,301,434],value2:[12,124,180,181,182,183,184,185,186,233,292,301,434],valuei:182,valuej:182,valuev:[7,9],valus:259,van:[9,53,87,107,257,261,266,281,347,348,377,380,392,393,415,449],vanderwa:[384,441],vanilla:[6,8,12],vanillia:42,vanish:[198,265,273],vapor:[41,188,205,440],vapour:285,var1:434,var2:434,varaibl:[3,426],vare:290,vari:[1,18,41,61,62,71,87,118,132,134,143,173,174,178,181,182,184,188,192,194,227,229,257,269,270,281,282,290,295,318,344,353,362,375,378,389,397,407,420],variabl:[0,2,3],variable_hill_factor:13,variable_nam:393,varianc:[117,353,448],variant:[1,3,6,12,83,98,233,270,318,325,333,381,382,408,410,432,436,449],variat:[41,188,448],varieti:[1,2,6,7,13,15,71,168,210,321,364,380,392,393,405,448],variou:0,varreturn:421,varshalovich:120,varshnei:13,vartiabl:3,vbia:6,vcm:[2,3,6,63,98],vdim:[133,286,293,449],vdisplac:[3,211,226,295,298,300,448],vdw:[3,348,393],vec1:[117,259],vec2:[117,259],vec:251,vector:[1,2,3],vel:[3,6,61,181,184,185,194,214,256,274,297,353,357,361,418,425,426,428,443],veld:[13,278,319,343,373],veloc:[2,3,6,7,8,14,39,40,61,63,66,82,83,84,85,91,94,95,96,97,98,102,106,112,113,117,121,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,140,141,144,167,168,169,172,173,179,180,181,183,184,185,192,194,195,198,199,201,205,209,211,213,214,215,216,217,218,219,220,221,222,223,225,226,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,253,254,255,256,257,260,265,268,269,270,272,273,274,278,279,280,281,282,283,284,285,286,288,290,292,293,294,295,296,297,298,300,301,321,323,325,326,328,353,354,357,361,378,379,393,418,423,424,425,426,427,428,432,433,440,441,443,447,448],velocit:[209,353,357,361],velocity_bottom:216,velocity_temp:449,velocity_top:216,vendor:12,verbatim:421,verbos:12,veri:[1,3,6,7,8,9,10,12,13,17,41,71,87,117,167,168,169,180,181,182,183,184,185,186,188,189,190,192,205,219,229,230,241,253,268,273,281,282,292,328,329,330,333,357,361,378,379,389,396,397,407,431,441,443,447,450],verifi:[8,333,384,432,438],verlag:274,verlet:[1,3,7,8,12,18,178,213,229,241,247,253,273,279,290,298,301,417,420,432],versa:[3,6,13,59,138,146,191,211,213,214,270,423,424,443],versu:[6,14,15,16,18,39,41,80,103,104,116,140,169,188,270,273,319,343,352,361,373,384,441,448],vertic:[41,168,188,195,448],vfinal:448,vfrac:113,vhi:[133,449],via:[0,1,2,3,4,6,7,8,9,11],vibrat:[6,9,195,207,251,260,265,312,357,418,432],vice:[3,6,13,59,138,146,191,211,213,214,270,423,424,443],video:168,view:[4,6,7,9,13,167,168,278,339,357,358],viewer:[167,168],viewpoint:168,vij:353,vika:13,vim:0,vincent:[9,19],violat:285,violet:169,virial:[3,63,91,112,120,121,138,173,174,192,198,229,230,231,232,233,234,235,255,257,270,273,318,333,336,353,354,357,365],virialmod:365,virtual:[6,7,8,12,406],virut:9,visa:7,viscoelast:[111,361,389],viscoelsat:389,viscos:[0,2,3],viscou:[2,6,172,206,207,209,213,216],viscous:270,visit:[271,392,393],vista:167,visual:[0,3,4],viz:[11,13],viz_tool:11,vizplotgui_tool:11,vizualiziton:271,vlo:[133,449],vmax:[192,278],vmd:[6,7,9,11,13,167,170,210,424],vmdarch:170,vmdhome:170,vname:[144,448],voigt:[6,120],vol:[6,8,91,121,198,214,256,380,410,419,441,448],volfactor:318,volt:[391,447],volum:[2,3,6,40,41,58,59,63,80,87,91,100,112,116,118,121,142,143,144,147,179,181,184,185,188,192,194,195,205,216,227,229,230,233,236,237,239,240,242,244,245,246,247,248,249,256,257,260,270,274,290,295,299,301,318,321,327,341,378,379,389,402,403,416,419,420,423,426,433,441,443,447,448],volumetr:80,voro:[3,9,142],vorobyov:443,voronoi:[2,3,9,12,63,121],voter2:[418,437],voter:[381,382,418,437],voth:[40,253],vpz:297,vratio:448,vri:362,vrpn:210,vshear:296,vstream:6,vtarget:[3,293],vtk:[2,6,9,118],vv0210:13,vx0:140,vxcm:270,vxhi:[195,256],vxlo:[195,256],vy0:140,vycm:270,vyhi:[195,256],vylo:[195,256],vz0:140,vzcm:270,vzhi:195,vzi:297,vzlo:195,w_1:120,w_2:120,w_i:120,w_ik:390,waal:[87,107,347,348,377,392,393,415],wadlei:[13,339],wag:[7,9,13],wagner:[7,9,178,216,380],wai:[1,2,3,6,7,8,11,12,15,18,22,44,59,63,65,66,69,71,75,77,79,87,90,91,92,93,104,106,108,114,115,116,120,121,122,123,124,125,126,127,130,131,132,133,134,136,137,138,139,141,144,147,152,164,166,167,168,169,172,173,174,181,183,184,186,187,190,191,192,194,203,206,211,213,214,216,227,229,233,241,253,257,259,268,270,271,274,275,278,280,281,282,283,286,289,290,292,295,298,300,301,305,306,307,309,312,319,321,323,326,328,329,333,334,335,346,349,350,353,354,355,356,358,360,363,364,366,369,380,381,382,384,386,390,391,394,396,397,404,406,408,410,417,418,421,423,424,426,427,428,431,432,433,448,449],wait:[1,12,210,252,418,420],walk:[3,206,213,214],wall:[0,2,3,5],wallhi:295,wallstyl:296,wander:275,wang:[319,380,390],want:[0,1,2,3,5,6,7,8,9,11,12,17,38,40,56,63,66,68,71,75,81,90,93,103,104,106,107,109,110,112,114,116,121,124,139,140,141,144,147,150,164,167,168,169,172,173,174,175,180,181,188,191,194,195,198,200,203,205,211,214,224,243,251,256,259,269,270,272,275,277,279,286,288,293,295,299,301,303,319,321,328,334,335,339,347,348,353,355,358,364,365,366,380,384,386,390,392,393,397,406,407,408,410,412,419,421,423,424,425,426,428,430,431,441,443,448,450,452],ward:339,warm:[16,357],warn:[0,2],warner:334,warp:[5,380],warranti:7,warren:353,wasn:3,wast:3,watanab:[287,288],watch:328,water:[0,3],watkin:161,wave:[7,9,40,177,227,264,297,336,357],wavefunct:[9,336,357],wavelength:[118,143],wavepacket:[40,336,357,423],wavevector:252,wbodi:83,weak:261,web:[1,8,14,15,16,17,346],webb:178,weber:[3,5,7,15,88,356,382,390,405,406,435],websit:8,weckner:389,weight:[2,3,6,37,55,87,108,115,116,120,143,145,148,150,163],welcom:421,well:[1,3,6,7,8,9,11,12,13,15,16,17,18,27,40,51,67,71,112,121,123,130,144,153,168,169,175,179,181,186,188,189,190,192,195,200,205,209,213,216,220,226,229,233,256,270,272,285,288,296,326,328,333,338,359,360,363,364,365,378,379,380,394,397,408,409,410,421,423,425,427,432,437,443,447,451],wennberg:318,went:[3,11],were:[3,4,5,6,7,11,12,13,15,16,18,19,34,41,42,52,56,60,70,71,109,112,116,122,124,144,147,148,160,167,169,172,175,181,183,184,185,186,188,194,200,202,209,210,241,247,271,296,297,301,311,318,330,332,357,361,364,368,389,393,418,420,421,423,424,425,426,428,430,438,441,448,449,451,452],weren:428,western:9,westview:415,what:[0,1,2,3,6],whatev:[8,12,14,15,108,113,116,117,119,168,169,173,174,192,205,229,257,259,296,321,325,326,328,333,345,347,392,393,437,443,448],wheat:169,whelan:143,when:[0,1,2,3,4,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,59,61,62,63,71,81,86,88,103,104,105,107,109,112,113,117,119,122,123,127,131,132,140,142,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,167,168,169,170,172,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,199,200,201,202,203,204,205,207,208,210,213,216,217,219,220,224,229,230,231,232,233,234,235,236,241,243,244,246,247,249,251,255,256,257,258,259,260,262,263,264,265,269,270,271,272,273,274,275,276,278,279,280,281,283,285,286,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,312,313,314,315,316,317,318,319,321,324,325,326,327,328,329,330,332,333,334,335,337,340,341,342,343,344,345,346,347,348,349,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,389,390,392,393,394,395,396,397,404,406,407,408,409,410,412,414,415,416,418,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,447,448,449,450,452],whenev:[0,8,12,14,71,169,180,185,270,321,363,421,432,436,448,452],whenth:3,where:[1,3,6,8,9,10,11,12,14,15,18,21,23,24,25,26,27,28,29,32,35,36,37,39,40,41,43,47,48,49,51,55,61,63,65,66,68,69,70,71,73,75,79,80,82,83,84,85,87,88,89,90,92,93,94,95,96,97,98,104,106,108,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,130,131,132,133,134,136,137,138,139,141,143,145,147,148,151,153,163,167,168,169,172,173,174,175,176,179,181,182,184,187,188,191,192,194,195,199,200,202,203,205,206,207,208,209,211,213,214,215,216,219,220,222,224,226,227,230,233,241,244,250,251,252,253,256,258,259,260,263,265,270,271,272,273,274,275,277,280,281,282,283,286,287,288,290,293,294,295,296,298,299,300,301,304,306,307,308,309,312,313,314,316,319,321,325,326,327,328,329,330,333,334,335,338,339,340,342,346,347,348,349,350,351,352,353,355,356,357,358,359,360,361,362,363,364,365,366,369,373,378,379,380,381,382,384,386,387,389,390,391,392,393,394,396,399,402,403,404,405,406,407,408,409,410,415,416,417,418,420,421,423,425,426,427,428,430,432,433,435,437,438,439,440,441,443,447,448,449,450,452],wherea:[6,11,179,206,229,261,285,290,443],wherebi:262,wherev:209,whether:[6,8,11,12,16,17,39,40,54,59,61,63,70,71,102,107,109,131,132,164,168,169,171,172,173,174,181,186,189,190,191,192,193,194,198,202,205,214,226,229,233,259,273,278,286,292,293,301,303,316,318,319,327,331,333,342,344,348,362,364,368,378,379,380,384,393,405,418,421,423,424,426,428,435,436,437,440,448,449],which:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,28,29,32,33,37,38,39,40,41,42,44,45,46,47,50,51,53,54,55,56,58,59,61,63,64,66,67,70,71,72,73,74,75,76,77,78,80,81,82,83,85,87,88,89,90,91,93,95,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,112,113,114,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,150,151,152,155,156,157,158,161,163,164,166,167,168,169,170,172,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,219,220,223,224,226,227,228,229,230,231,232,233,234,235,237,239,241,242,244,245,246,247,248,249,251,252,253,255,256,257,258,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,303,304,305,307,309,310,313,314,316,317,318,319,321,323,324,325,326,327,328,329,330,332,333,334,335,336,338,339,340,342,343,344,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,371,372,373,375,377,378,379,380,381,382,384,386,387,388,390,391,392,393,394,395,396,397,400,405,406,407,408,409,410,411,412,415,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,448,449,450,451,452],whichev:[12,332,418,437],white:[169,206,213,214,215,270,282,290,423,448,451],whitesmok:169,whitespac:[2,3,169,327,423],who:[0,3,6,7,8,9,13,334,355],whole:[198,210,252,265,274,443],wholli:195,whose:[3,6,7,8,19,38,39,56,59,76,87,129,147,164,168,169,194,211,212,226,229,231,232,234,235,251,252,268,269,273,278,292,299,301,321,328,329,357,371,406,407,408,410,443,448,449],why:[3,6,214,286,293],wide:[1,6,7,9,61,63,172,286,293,321,330,344,347,357,392,393],wider:1,width:[168,169,336,359],wiggl:[3,194,226,295,296,298,300,426],wigner:120,wih:6,wiki:14,wikipedia:[6,14],wild:[3,12,22,44,77,87,116,152,173,174,270,305,323,346,363,417,425,430,450,452],wildcard:[3,12,138,148,167,168,169,267,346,430,433,451,452],wildli:229,win:333,window:[3,4,12,13,71,167,168,170,181,182,183,184,185,186,210,271,283,284,346,424],wipe:[172,364,405,444,446],wire:269,wirt:169,wisconsin:13,wise:[3,12,353,406,432],wish:[2,3,5,6,7,8,11,12,14,17,57,58,59,71,117,121,124,145,146,148,150,167,169,180,181,182,184,185,186,190,194,195,202,205,211,216,220,256,259,270,273,278,279,295,296,321,328,333,342,363,364,380,384,392,407,421,423,424,425,431,435,441,448,449,452],within:[1,2,3,6,8,9,11,12,13,15,16,17,29,39,40,41,42,55,59,61,63,65,69,70,71,72,73,77,79,92,108,112,115,116,117,119,120,135,144,147,168,169,173,174,179,180,181,183,184,185,186,188,189,190,191,195,197,202,205,211,213,251,255,256,257,259,261,270,271,273,275,279,290,293,295,299,301,303,317,321,326,327,328,329,330,333,338,340,342,349,354,355,356,357,359,364,365,368,369,380,387,388,389,394,395,405,406,408,409,410,411,418,420,421,423,431,432,435,437,443,447,448],without:[1,2,3,4,6,7,8,9,11,12,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,59,87,109,112,122,131,145,150,151,153,154,155,156,158,159,161,162,164,167,168,169,170,172,175,181,183,184,185,186,187,192,194,201,204,206,208,210,213,226,229,231,232,233,234,235,236,244,246,247,248,249,256,259,261,262,264,268,270,271,272,273,278,281,283,294,298,302,304,306,307,308,309,312,314,317,318,319,328,329,333,334,335,337,340,341,342,343,344,345,346,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,393,394,395,397,405,406,407,408,409,410,412,414,415,416,421,423,431,432,441,443,447,448],witht:9,witi:15,wolf:[2,3,7],wolff:[384,407],won:[3,268,379],wong:[178,339],word:[2,3,6,8,12,29,63,169,172,179,180,181,182,184,185,186,193,211,238,243,258,263,269,292,303,317,347,384,419,421,423,448,449],work:[1,3,6,7,8,9,11,12,14,16,18,39,54,59,60,88,117,118,123,125,126,127,131,132,133,134,136,137,142,143,167,168,170,173,174,181,184,185,191,203,212,213,214,216,220,226,229,234,235,246,247,248,249,267,269,271,273,281,282,283,288,317,329,333,346,348,351,353,364,378,379,380,384,418,420,421,424,425,427,431,432,434,437],workaround:[270,449],worker:[12,392,393],workhors:8,workstat:[333,421],world:[3,12,120,317,328,332,417,420,421,438,448],worlei:353,worri:17,worsen:18,worst:299,worth:[181,182,183,184,185,186,260,271],would:[1,3,4,5,6,7,8,11,12,22,29,37,40,41,42,44,55,70,71,89,91,116,121,124,132,144,145,146,147,152,163,167,169,170,172,173,174,176,179,181,188,191,193,194,198,199,202,205,208,209,210,214,226,229,230,241,251,253,257,259,261,265,268,278,285,289,297,298,301,303,304,305,306,307,309,310,313,318,321,323,325,326,328,329,332,333,334,335,339,346,347,348,349,353,354,355,356,358,364,365,366,380,381,382,386,390,392,393,396,406,408,409,410,418,421,423,426,427,428,430,431,432,433,434,438,440,441,443,448,449,451,452],wrap:[1,3,6,11,12,57,59,144,146,166,167,169,170,180,185,193,194,195,210,216,226,270,275,278,295,297,299,318,319,328,421,423,424,426,431],wrapper:[0,6,7],wrigger:274,wright:326,writabl:3,write:3,write_atom_weight:178,write_data:[2,3,8,12,13,423],write_dump:2,write_freq:393,write_head:8,write_restart:[2,3,8,13,172,178,216,425,430,450],writen:271,written:[3,5,6,7,8,9,12,13,14,17,65,69,115,120,142,167,168,169,170,172,173,174,175,176,177,178,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,196,198,199,200,201,202,203,204,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,228,236,237,238,239,240,241,242,243,244,245,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,278,279,281,282,283,284,285,286,287,289,290,292,293,294,295,297,298,299,300,302,316,321,329,355,364,413,415,418,419,421,424,425,429,430,437,438,439,440,448,450,451,452],wrong:[3,11,192,229,250,295,299,300,329,393,425,430],wrote:[3,425],wt2:384,wt3:384,www:[0,2,3,4,5,6,7,8,10,11,12,13,15,334,355,378,391,392,393,447],x86:12,x_ij:390,x_ijkl:304,x_kjli:304,x_ljik:304,xave:6,xavx:16,xcm:[8,270,448],xdr:[12,167],xeon:[1,4,7,9,12,16,17,18,333,436],xflag:[131,132,217,219,225,270,285],xhe:103,xhi:[2,6,57,59,146,167,194,289,295,298,300,423,426,441,448],xhi_bound:[6,167],xhi_new:423,xhost:[12,16],xi_ij:390,xiaowang:[13,358,408,410],xiij:251,xlat:[144,194,211,441],xlo:[2,6,11,57,59,146,167,194,211,289,295,298,300,423,426,441,448],xlo_bound:[6,167],xlo_new:423,xmax:[6,177,199,241,448],xmgrace:0,xmin:448,xml:[170,391],xml_label:391,xmovi:[0,4,6,7],xmu:[296,361],xplane:296,xplor:167,xpo:144,xrd:[2,9,118],xsph:9,xsu:[3,167,424],xt3:167,xt4:[18,167],xt5:[18,167],xtc:[3,6,7,9,12,167,168,169,170],xtcdump:169,xvf:12,xwall:[297,298,300],xxx:12,xyz:[3,6,7,13,42,66,71,106,108,132,139,144,167,168,169,170,184,192,219,229,230,233,257,267,268,270,275,277,296,298,300,320,327,420,424,449,451],xzhou:[13,358],xzy:420,yang:390,yb2:143,yb3:143,ybox:194,ycm:270,year:[5,7],yeh:318,yellow:[168,169],yellowgreen:169,yet:[3,7,9,17,39,168,173,261,267,295,319,325,326,333,345,347,348,357,415,421,423,424,448,450,451],yflag:[131,132,217,219,225,270,285],yhi:[6,59,146,167,194,289,295,298,300,423,426,441],yhi_bound:[6,167],yield:[6,91,110,117,121,127,132,169,182,192,198,229,247,261,286,292,293,296,301,318,338,353,361,384,389,441,448],yip:287,ylat:[144,194,211,441],ylo:[6,59,146,167,194,289,295,298,300,423,426,441],ylo_bound:[6,167],ymax:[177,448],ymin:448,york:[253,319],yoshida:[229,270],you:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,56,57,58,59,61,63,66,68,71,73,74,75,77,81,87,88,89,90,91,93,102,103,104,106,107,109,110,112,114,116,117,120,121,122,123,124,127,131,132,137,138,139,140,141,142,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,172,173,174,175,176,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,224,226,229,231,232,233,234,235,236,241,243,244,246,247,248,249,252,253,255,256,257,259,261,262,265,268,269,270,272,273,274,275,277,278,279,281,282,283,284,286,287,288,289,290,292,293,294,295,296,298,299,300,301,303,304,306,307,308,309,310,312,314,317,318,319,321,323,325,326,327,328,329,332,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,406,407,408,409,410,412,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,443,447,448,449,450,452],young:361,your:[0,1,2,3,4,5,6,7,8,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,59,61,107,109,112,122,123,127,131,137,142,144,145,146,147,148,150,151,153,154,155,156,158,159,161,162,164,166,167,168,175,178,182,183,186,187,189,190,191,192,195,201,204,205,208,210,213,226,229,231,232,233,234,235,236,244,246,247,249,256,259,262,268,270,272,273,274,280,281,283,286,290,292,293,294,295,296,299,300,301,304,306,307,308,309,312,314,319,321,327,328,329,332,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,354,355,356,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,389,390,392,393,394,395,397,406,407,408,409,410,412,414,415,416,417,420,421,423,425,426,427,430,431,432,433,434,435,436,440,441,447,448,450,452],yourself:[6,8,12,13,192,327],yplane:296,ypo:144,ysu:[3,167,424],yuan:9,yukawa:[2,3,7,347,405],yukawa_1_1:413,yxz:420,yzx:420,z_i:[357,410,416],z_j:[410,416],z_meam:380,zachari:13,zannoni:360,zbl:[2,3,380,396,405],zblcut:410,zblcutinn:396,zblcutout:396,zblexpscal:410,zblz:396,zcm:270,zcylind:296,zepeda:179,zero:[3,4,6,9,11,12,26,27,39,41,48,49,59,61,63,66,71,75,87,88,90,93,102,103,104,105,106,108,109,110,112,113,114,115,116,117,118,120,121,123,124,125,132,133,136,137,139,141,142,143,144,146,147,148,150,153,162,164,166,167,168,169,172,173,174,175,177,179,180,181,182,183,184,185,186,187,188,189,190,192,194,199,200,201,202,204,205,206,207,209,213,214,215,216,217,219,225,226,227,229,233,241,244,253,258,259,260,261,262,265,267,268,270,271,272,273,278,280,285,286,288,290,293,294,295,296,297,298,300,301,302,303,308,321,324,326,327,328,329,333,336,339,340,342,343,344,347,349,352,353,357,360,362,363,365,369,371,373,374,377,379,380,384,389,393,394,395,404,407,411,416,418,419,420,423,424,426,428,430,431,432,433,437,438,441,443,448,449,450,452],zeta:[3,216,261,358],zfactor:168,zflag:[131,132,217,219,225,270,285],zhang:[270,286,361],zhi:[3,6,146,167,177,289,295,298,300,423,426,441],zhi_bound:[6,167],zhou:[13,339,358,390,408,410],zhu:403,ziegenhain:13,ziegler:[255,380,405,410,416],zimmerman2004:178,zimmerman2010:178,zimmerman:[9,70,178,339],zlat:[194,211,441],zlo:[3,6,146,167,177,289,295,297,298,300,423,426,441],zlo_bound:[6,167],zmax:[177,216,448],zmin:[216,448],zn2:143,zone:[118,271],zoom:[3,167,168,169],zplane:296,zr4:143,zrest:277,zsu:[3,167,424],zwall:295,zwall_veloc:216,zxy:420,zybin:393,zyx:420},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & 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","<no title>","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:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],diagnost:7,diel:350,dielectr:149,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:152,dihedral_styl:[2,150,151,153,154,155,156,157,158,159,160,161,162,163,164],dilat:80,dimens:165,dipol:[6,29,352],direct:198,discuss:6,disp:6,displac:[81,86],displace_atom:166,distribut:[7,12],document:0,dpd:353,drag:196,dreid:[6,363],drude:[6,9,129,197,198,214],dsf:[349,369],dsmc:354,dump:[6,8,167,168,170],dump_modifi:169,dynam:261,eam:[13,355],echo:171,edip:356,eff:[9,13,96,97,128,130,135,215,230,240,248,284,357],efield:200,eim:358,elast:6,emac:13,enforce2d:201,ensembl:7,erot:[82,83,84,85],error:3,evapor:202,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],exp:[27,153],expand:[46,372],extend:[8,11],extern:203,fcc:251,featur:[7,8],fene:[45,46],fep:[9,13,87,174],field:[6,7],file:6,finit:6,fix:[2,6,8,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,448],fix_modifi:[173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300],flow:6,fluid:216,flux:91,forc:[6,7,279],fourier:[30,31,154,308],freez:204,from:[6,11],futur:5,gauss:359,gaybern:360,gcmc:205,gener:[1,6,7,13],get:12,gld:206,gle:207,global:6,gpu:[15,337,340,342,344,345,347,349,352,353,355,359,360,362,369,370,372,383,385,394,395,397,406,407,414,415],gran:[296,361],granular:6,graviti:208,gromac:362,group2ndx:302,group:[88,301,448],gyrat:[89,90],harmon:[32,47,48,49,155,158,295,309,386],hbond:363,heat:[91,209],heatconduct:398,helix:156,hertz:361,histo:183,histori:[5,361],hook:361,how:6,hybrid:[33,50,157,310,364],idealga:399,imag:[167,168],imd:210,implicit:344,improp:[8,92],improper_coeff:305,improper_styl:[2,304,306,307,308,309,310,311,312,313,314],includ:315,inclus:8,indent:211,indic:0,individu:2,induc:6,inertia:93,info:[0,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,316],input:[2,6,8],instal:11,integr:[6,7],intel:[9,16,344,360,369,406],interfac:[6,11],introduct:7,invers:198,ipi:212,ipp:13,jul:0,jump:317,kate:13,keyword:384,kim:365,kokko:17,kspace:[2,8,291],kspace_modifi:318,kspace_styl:[6,319],label:320,lammp:[0,1,2,6,7,8,11,12],langevin:[213,214,215],lattic:321,lcbop:366,librari:[6,11,12],limit:[241,283],line:[12,242,367],linear:376,lineforc:221,list:[2,368],lj1043:295,lj126:295,lj93:295,lj96:370,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:322,lubric:378,lubricateu:379,make:12,mass:323,math:448,matlab:13,meam:[380,381,382],measur:1,meso:[222,223],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:383,min_modifi:324,min_styl:325,minim:[8,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,326],misc:9,mod:[290,409],model:[6,7],modifi:8,molecul:327,molfil:[9,167,170],moltempl:13,momentum:[217,225],morri:403,mors:[51,363,385],move:226,movi:[167,168],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[340,342,344,349,369],msst:227,multi:[6,7,158],multipl:6,nb3b:386,neb:[228,328],neigh_modifi:329,neighbor:330,nemd:6,newton:331,next:332,nharmon:159,noforc:[238,243],non:[6,7],none:[34,52,160,311,388],nongauss:105,nonlinear:53,nph:[229,230,231,232,270],nphug:233,npt:[229,230,234,235,270],nve:[236,237,238,239,240,241,242,243,244,245,270],nvt:[229,230,246,247,248,249,270],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,150,151,153,154,155,156,158,159,161,162,164,208,229,231,232,233,234,235,236,244,246,247,249,262,304,306,307,308,309,312,314,334,335,337,340,341,342,343,344,345,347,348,349,350,352,353,355,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,382,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416],onewai:250,open:7,oper:448,opl:161,opt:[19,344,355,369,373,385],optim:1,option:[6,8,12],orient:251,orthogon:6,other:6,output:[6,7,8,12,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300],overlai:364,overview:11,packag:[1,9,12,14,15,16,17,18,19,333],pair:[6,107,108,384],pair_coeff:346,pair_modifi:384,pair_styl:[2,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416],pair_writ:413,pairwis:8,parallel:11,paramet:6,pars:2,partial:131,particl:[6,7,42],partit:417,past:5,per:6,perform:[1,10],peri:389,period:25,phonon:[9,13,252],pimd:253,piston:297,planeforc:254,plastic:111,pmb:389,poem:255,point:261,polariz:6,poli:[341,378,379],polym:13,polymorph:390,post:7,potenti:[2,6,8],pour:256,pppm:6,prd:418,pre:7,press:257,pressur:112,previou:12,print:[258,419],problem:[3,4],process:[6,7],processor:420,profil:132,properti:[6,113,114,115,259],pymol_aspher:13,python:[11,13,421],qbmsst:260,qeq:[261,262,263],qmmm:[9,264],qtb:[9,265],quadrat:162,quantiti:6,quartic:[35,54],quip:391,quit:422,ramp:133,rattl:273,rdf:116,read_data:423,read_dump:424,read_restart:425,reax:[13,263,266,267,392,393],reaxc:9,rebo:335,recent:268,reduc:117,refer:448,reflect:298,region:[8,117,134,135,299,426,448],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,162,163,164,165,166,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,202,204,205,206,207,208,209,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,265,266,267,268,270,271,272,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,313,314,315,316,317,318,319,321,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,429,430,431,432,433,435,436,437,438,439,440,441,442,444,445,446,448,449,450,451,452],relax:192,replic:427,replica:[6,7],report:3,requir:12,rerun:428,rescal:[283,284],reset:199,reset_timestep:429,resquar:394,restart2data:13,restart:[6,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,430],restrain:269,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],rhosum:401,rigid:[6,83,98,219,270],ring:312,rotat:136,rule:2,run:[6,11,12,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,431],run_styl:432,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,395],self:277,serial:11,set:[6,433],setforc:272,shake:273,share:[11,12],shell:[6,434],shield:261,shift:[26,27,48,49,153],simpl:31,simul:6,size:6,slater:261,slice:119,sllod:[247,248],small:270,smd:274,smooth:[375,376],sna:120,snad:120,snap:396,snapshot:6,snav:120,soft:[377,397],solver:2,sourc:7,spatial:[184,185],spc:6,speci:267,special:[7,448],special_bond:435,sph:[9,398,399,400,401,402,403],sphere:[84,85,137,185,219,232,235,244,249],spheric:6,spline:[381,382],spring:[275,276,277,288],squar:28,srd:[278,300],srp:404,standard:9,start:[12,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300],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
+Search.setIndex({envversion:47,filenames:["Manual","Section_accelerate","Section_commands","Section_errors","Section_example","Section_history","Section_howto","Section_intro","Section_modify","Section_packages","Section_perf","Section_python","Section_start","Section_tools","accelerate_cuda","accelerate_gpu","accelerate_intel","accelerate_kokkos","accelerate_omp","accelerate_opt","angle_charmm","angle_class2","angle_coeff","angle_cosine","angle_cosine_delta","angle_cosine_periodic","angle_cosine_shift","angle_cosine_shift_exp","angle_cosine_squared","angle_dipole","angle_fourier","angle_fourier_simple","angle_harmonic","angle_hybrid","angle_none","angle_quartic","angle_sdk","angle_style","angle_table","atom_modify","atom_style","balance","body","bond_class2","bond_coeff","bond_fene","bond_fene_expand","bond_harmonic","bond_harmonic_shift","bond_harmonic_shift_cut","bond_hybrid","bond_morse","bond_none","bond_nonlinear","bond_quartic","bond_style","bond_table","boundary","box","change_box","clear","comm_modify","comm_style","compute","compute_ackland_atom","compute_angle_local","compute_angmom_chunk","compute_basal_atom","compute_body_local","compute_bond_local","compute_centro_atom","compute_chunk_atom","compute_cluster_atom","compute_cna_atom","compute_com","compute_com_chunk","compute_contact_atom","compute_coord_atom","compute_damage_atom","compute_dihedral_local","compute_dilatation_atom","compute_displace_atom","compute_erotate_asphere","compute_erotate_rigid","compute_erotate_sphere","compute_erotate_sphere_atom","compute_event_displace","compute_fep","compute_group_group","compute_gyration","compute_gyration_chunk","compute_heat_flux","compute_improper_local","compute_inertia_chunk","compute_ke","compute_ke_atom","compute_ke_atom_eff","compute_ke_eff","compute_ke_rigid","compute_meso_e_atom","compute_meso_rho_atom","compute_meso_t_atom","compute_modify","compute_msd","compute_msd_chunk","compute_msd_nongauss","compute_omega_chunk","compute_pair","compute_pair_local","compute_pe","compute_pe_atom","compute_plasticity_atom","compute_pressure","compute_property_atom","compute_property_chunk","compute_property_local","compute_rdf","compute_reduce","compute_saed","compute_slice","compute_sna_atom","compute_stress_atom","compute_temp","compute_temp_asphere","compute_temp_chunk","compute_temp_com","compute_temp_cs","compute_temp_deform","compute_temp_deform_eff","compute_temp_drude","compute_temp_eff","compute_temp_partial","compute_temp_profile","compute_temp_ramp","compute_temp_region","compute_temp_region_eff","compute_temp_rotate","compute_temp_sphere","compute_ti","compute_torque_chunk","compute_vacf","compute_vcm_chunk","compute_voronoi_atom","compute_xrd","create_atoms","create_bonds","create_box","delete_atoms","delete_bonds","dielectric","dihedral_charmm","dihedral_class2","dihedral_coeff","dihedral_cosine_shift_exp","dihedral_fourier","dihedral_harmonic","dihedral_helix","dihedral_hybrid","dihedral_multi_harmonic","dihedral_nharmonic","dihedral_none","dihedral_opls","dihedral_quadratic","dihedral_style","dihedral_table","dimension","displace_atoms","dump","dump_image","dump_modify","dump_molfile","echo","fix","fix_adapt","fix_adapt_fep","fix_addforce","fix_addtorque","fix_append_atoms","fix_atc","fix_atom_swap","fix_ave_atom","fix_ave_chunk","fix_ave_correlate","fix_ave_histo","fix_ave_spatial","fix_ave_spatial_sphere","fix_ave_time","fix_aveforce","fix_balance","fix_bond_break","fix_bond_create","fix_bond_swap","fix_box_relax","fix_colvars","fix_deform","fix_deposit","fix_drag","fix_drude","fix_drude_transform","fix_dt_reset","fix_efield","fix_enforce2d","fix_evaporate","fix_external","fix_freeze","fix_gcmc","fix_gld","fix_gle","fix_gravity","fix_heat","fix_imd","fix_indent","fix_ipi","fix_langevin","fix_langevin_drude","fix_langevin_eff","fix_lb_fluid","fix_lb_momentum","fix_lb_pc","fix_lb_rigid_pc_sphere","fix_lb_viscous","fix_lineforce","fix_meso","fix_meso_stationary","fix_modify","fix_momentum","fix_move","fix_msst","fix_neb","fix_nh","fix_nh_eff","fix_nph_asphere","fix_nph_sphere","fix_nphug","fix_npt_asphere","fix_npt_sphere","fix_nve","fix_nve_asphere","fix_nve_asphere_noforce","fix_nve_body","fix_nve_eff","fix_nve_limit","fix_nve_line","fix_nve_noforce","fix_nve_sphere","fix_nve_tri","fix_nvt_asphere","fix_nvt_sllod","fix_nvt_sllod_eff","fix_nvt_sphere","fix_oneway","fix_orient_fcc","fix_phonon","fix_pimd","fix_planeforce","fix_poems","fix_pour","fix_press_berendsen","fix_print","fix_property_atom","fix_qbmsst","fix_qeq","fix_qeq_comb","fix_qeq_reax","fix_qmmm","fix_qtb","fix_reax_bonds","fix_reaxc_species","fix_recenter","fix_restrain","fix_rigid","fix_saed_vtk","fix_setforce","fix_shake","fix_smd","fix_spring","fix_spring_rg","fix_spring_self","fix_srd","fix_store_force","fix_store_state","fix_temp_berendsen","fix_temp_csvr","fix_temp_rescale","fix_temp_rescale_eff","fix_tfmc","fix_thermal_conductivity","fix_ti_rs","fix_ti_spring","fix_tmd","fix_ttm","fix_tune_kspace","fix_vector","fix_viscosity","fix_viscous","fix_wall","fix_wall_gran","fix_wall_piston","fix_wall_reflect","fix_wall_region","fix_wall_srd","group","group2ndx","if","improper_class2","improper_coeff","improper_cossq","improper_cvff","improper_fourier","improper_harmonic","improper_hybrid","improper_none","improper_ring","improper_style","improper_umbrella","include","info","jump","kspace_modify","kspace_style","label","lattice","log","mass","min_modify","min_style","minimize","molecule","neb","neigh_modify","neighbor","newton","next","package","pair_adp","pair_airebo","pair_awpmd","pair_beck","pair_body","pair_bop","pair_born","pair_brownian","pair_buck","pair_buck_long","pair_charmm","pair_class2","pair_coeff","pair_colloid","pair_comb","pair_coul","pair_coul_diel","pair_cs","pair_dipole","pair_dpd","pair_dsmc","pair_eam","pair_edip","pair_eff","pair_eim","pair_gauss","pair_gayberne","pair_gran","pair_gromacs","pair_hbond_dreiding","pair_hybrid","pair_kim","pair_lcbop","pair_line_lj","pair_list","pair_lj","pair_lj96","pair_lj_cubic","pair_lj_expand","pair_lj_long","pair_lj_sf","pair_lj_smooth","pair_lj_smooth_linear","pair_lj_soft","pair_lubricate","pair_lubricateU","pair_meam","pair_meam_spline","pair_meam_sw_spline","pair_mie","pair_modify","pair_morse","pair_nb3b_harmonic","pair_nm","pair_none","pair_peri","pair_polymorphic","pair_quip","pair_reax","pair_reax_c","pair_resquared","pair_sdk","pair_snap","pair_soft","pair_sph_heatconduction","pair_sph_idealgas","pair_sph_lj","pair_sph_rhosum","pair_sph_taitwater","pair_sph_taitwater_morris","pair_srp","pair_style","pair_sw","pair_table","pair_tersoff","pair_tersoff_mod","pair_tersoff_zbl","pair_thole","pair_tri_lj","pair_write","pair_yukawa","pair_yukawa_colloid","pair_zbl","partition","prd","print","processors","python","quit","read_data","read_dump","read_restart","region","replicate","rerun","reset_timestep","restart","run","run_style","set","shell","special_bonds","suffix","tad","temper","thermo","thermo_modify","thermo_style","timestep","tutorial_drude","uncompute","undump","unfix","units","variable","velocity","write_data","write_dump","write_restart"],objects:{},objnames:{},objtypes:{},terms:{"00a":287,"00b":287,"02214e23":91,"03275e":447,"0b1":11,"0e20":[303,426,448],"0e4":[227,296,361],"0e5":227,"0x98b5e0":168,"100k":1,"1024x1024":168,"10e":351,"10f":3,"10g":448,"10th":[418,424,437],"10x":[3,325,326,328,329,339],"10x10x10":132,"10x20x20":321,"11e":10,"15g":[169,448],"16x":1,"18986e":326,"18e":10,"1_prop":6,"1st":[2,6,8,12,20,22,38,44,56,57,58,60,87,138,150,152,164,173,174,181,182,183,184,185,186,190,194,229,258,268,289,301,305,323,329,334,335,339,346,348,355,357,358,365,366,375,376,380,381,382,386,390,396,406,407,408,409,410,417,423,431,432,435,448],"1x2x2":420,"2000k":168,"20x":339,"23899e":326,"2400k":168,"256k":10,"25x":10,"298k":350,"2k_ss":357,"2nd":[2,3,6,11,12,15,17,38,45,46,56,57,60,71,77,88,133,164,169,181,182,183,184,185,186,190,192,194,229,270,274,275,301,304,310,317,326,327,328,329,333,335,348,357,363,364,380,396,405,406,407,408,409,410,423,430,432,435,448],"2pi":164,"2theta":143,"2x1x2":420,"2x2x1":420,"2x2x2":420,"2x4x10":420,"2x5":357,"300k":[207,270,449],"32k":10,"3419e":227,"3806504e":[6,91],"38e":10,"3n_k":206,"3nk":260,"3nkb":265,"3rd":[15,17,20,38,56,71,105,114,164,181,182,183,184,185,186,190,270,271,301,327,331,333,348,357,363,364,396,406,407,408,409,410,423,430,435,448],"3x3":[91,321],"4857990943e":357,"4_94":11,"4th":[6,38,56,81,103,104,116,140,150,164,169,275,301,319,332,334,335,339,355,358,365,380,386,390,396,406,407,408,410,423,430,435,438,452],"4x10":317,"4x2x10":420,"4x6x10":420,"50k":1,"53xx":18,"54xx":18,"55e":10,"5_1":339,"5kx":[175,200],"5nlog_2":12,"5th":[116,326,440],"6021765e":447,"6863e22":389,"6x6":6,"72360e":227,"7797e":227,"8032044e":447,"8x1":6,"8x2":[6,12],"9e18":[12,39],"9e9":389,"9jan09":[296,361],"9th":328,"__main__":421,"__pthread_key_cr":12,"_j1m1m1":120,"_j2m2m2":120,"_serial":12,"abstract":17,"boolean":[3,301,303],"break":[],"byte":[3,12,440],"case":[1,2,3,6,8,11,12,13,15,16,17,18,39,40,41,45,46,59,61,63,71,73,104,108,114,116,117,122,123,124,125,127,130,131,132,133,134,136,137,138,142,144,146,147,148,150,167,168,169,175,176,180,181,182,183,184,185,186,187,188,190,192,194,198,200,202,205,208,209,211,212,213,214,216,227,229,230,231,232,233,234,235,246,247,249,251,252,257,259,260,261,262,269,270,272,274,275,278,281,282,283,285,286,290,292,293,295,296,298,299,300,301,303,317,318,319,321,323,325,326,327,328,330,332,333,335,344,347,349,351,355,357,360,361,363,364,365,367,377,378,379,380,384,386,390,393,397,407,408,410,418,421,423,425,426,430,431,433,435,437,439,440,441,443,447,448,449,451,452],"catch":[1,3,421],"char":[6,8],"class":[1,3,5,6,7,8,9,11,12,13,22,37,44,55,152,163,203,259,305,313,345,364,392,393,405,421,423],"default":[],"export":[168,346],"final":[3,5,6,7,8,11,12,17,41,59,87,121,169,180,181,182,183,184,185,186,188,192,194,205,228,229,233,260,264,270,271,274,287,289,290,297,303,326,328,334,335,339,355,358,365,377,380,386,390,391,406,407,408,410,418,431,437,443,448,450],"float":[3,6,8,12,40,42,71,113,167,169,210,259,271,280,357,421,423,433,440,448],"function":[],"import":[1,2,3,6,11,17,71,87,105,144,155,172,181,184,192,208,213,214,229,265,270,281,282,283,285,290,300,302,328,364,377,421,423,432,440,443],"int":[3,6,8,11,101,203,205,213,215,265,290,440],"long":[],"new":[],"null":[3,6,91,112,121,144,172,187,193,196,199,226,259,268,272,274,275,276,296,334,335,348,355,358,361,364,365,366,380,381,382,386,390,392,393,396,406,408,409,410,423,426,431,433,449],"public":[0,7,8,12,203,212,358,391],"return":[2,3,6,8,11,14,15,16,17,18,19,41,71,108,117,142,144,169,181,184,185,194,203,303,315,317,361,420,421,430,433,439,448],"short":[1,3,6,7,13,16,142,229,270,278,291,319,329,330,333,335,339,340,342,343,344,348,349,351,357,364,369,373,377,380,384,387,395,407,411,418,421,431,437,443],"static":[],"switch":[1,3,6,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,91,109,112,120,122,131,143,150,151,153,154,155,156,158,159,161,162,164,168,171,175,179,187,201,204,208,212,213,216,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,287,288,294,304,306,307,308,309,312,314,315,317,319,322,328,332,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,417,418,420,423,425,430,432,436,438,448,450,452],"throw":440,"true":[6,12,13,17,108,115,167,188,190,194,229,230,251,252,253,257,270,285,289,301,303,333,357,361,406,421,425,433,448],"try":[1,3,8,12,17,19,181,210,216,286,287,288,293,421,448],"var":[3,11,12,144,301,317,434,448],"void":[4,6,7,8,41,147,188,203,426],"while":[3,9,10,11,12,13,14,18,71,105,120,127,142,155,167,170,185,192,194,198,206,207,212,213,214,216,229,247,260,265,267,291,319,326,333,339,350,355,393,408,410,418,421,432,437,443],a10:303,a123:303,a12:394,a2m:[6,91],a_0:[216,290,339],a_0_real:216,a_1:290,a_2:290,a_3:290,a_4:290,a_c:347,a_cc:347,a_f:410,a_i:411,a_ij:339,a_j:411,a_pi:339,a_sigma:339,a_ss:347,aacut:252,aat:151,aatom1:115,aatom2:115,aatom3:115,ab_23_cd:303,abbrevi:12,abc:[3,12,303,421,448],abf:193,abf_integr:13,abi:170,abil:[3,9,192,229,257,270,357],abl:[3,8,11,12,39,86,167,170,191,200,204,286,293,333,421,448,451],ablat:290,about:[0,1,3,4,6,8,9,10,11,12,13,17,39,41,42,61,63,78,108,115,116,118,138,144,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,196,198,199,200,201,202,203,204,205,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,228,233,236,237,238,239,240,241,242,243,244,245,250,251,252,254,255,256,257,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,278,279,281,282,283,284,285,286,287,288,289,290,292,293,294,295,297,298,299,300,301,316,319,325,326,328,333,338,344,349,364,389,393,415,421,424,425,430,431,433,438,448,450,452],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,57,63,64,68,70,71,72,73,76,77,86,87,89,90,91,93,94,96,97,112,114,116,118,120,121,122,123,124,125,126,127,130,131,132,133,134,136,137,138,142,143,144,146,147,150,151,152,153,154,155,156,157,158,159,161,162,164,167,168,169,172,173,174,175,176,181,182,183,184,185,186,188,191,192,194,195,200,203,205,209,211,213,214,215,219,228,229,233,253,256,258,263,269,270,274,275,278,281,282,283,284,301,303,304,305,306,307,308,309,310,312,314,319,321,323,327,328,332,333,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,387,389,390,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,423,424,425,426,427,430,431,432,433,434,437,438,441,443,448,449,451,452],abscissa:407,absenc:176,absent:443,absolut:[3,169,193,194,198,274,280,318,319,326,361,369,424],absorb:290,absoult:319,ac3:143,academ:205,acc:285,acceler:[],accelri:[6,13],accept:[7,87,144,169,179,191,194,205,285,343,373,431,438],acceptor:363,access:[0,3,6,7,8,9,11,12,16,40,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,85,88,89,90,91,92,93,95,96,99,100,101,103,104,105,106,107,108,110,111,112,113,114,115,117,118,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,143,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,210,211,213,215,216,217,218,219,220,221,222,223,225,226,227,228,229,233,236,237,238,239,240,241,242,243,244,245,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,286,287,288,289,290,292,293,294,295,296,297,298,299,300,318,333,359,361,363,364,380,392,393,397,420,421,424,429,441,448],accidenti:312,accler:16,accommod:177,accomod:229,accompani:8,accomplish:[16,194,217,243],accord:[64,71,168,179,189,190,216,229,252,260,274,287,288,290,295,296,298,299,300,329,333,357,361,372,375,390,397,399,400,402,403,404,432,437,448],accordingli:[11,14,123,137,148,329,378,379],account:[3,6,9,87,118,142,143,152,163,182,183,199,210,211,213,229,234,235,246,247,249,251,255,261,270,271,273,275,276,277,278,281,282,283,286,290,293,308,327,349,361,369,373,378,379,380,420,437,449],accuml:[3,270,286,293],accumul:[1,6,8,15,71,172,182,213,270,274,292,316,333,429,447],accur:[1,3,6,15,17,38,41,56,127,188,227,265,270,273,278,286,293,299,301,319,339,357,360,361,384,394,405,407,408,410,437,448],accuraci:[1,3,6,12,41,167,169,188,207,229,262,273,291,301,318,319,325,357,384,392,393,407,413,432,437,443,448,451],ach:318,achiev:[1,3,6,16,17,18,41,188,207,229,230,252,253,260,318,432],achiv:18,acid:9,ackland1:355,ackland2:355,ackland:[],acknowledg:[],acml:12,aco:448,acolor:[168,169],acoust:252,acquir:[3,6,58,61,62,147,190,192,194,229,388,428,443],across:[1,2,3,6,9,12,13,15,41,57,61,65,68,69,71,79,92,107,108,115,117,132,146,148,181,183,184,185,188,199,209,270,271,286,290,293,299,303,328,333,418,423,426,427,431,440],act:[3,6,108,129,198,208,211,212,213,214,216,219,228,270,285,287,288,290,299,300,301,326,341,352,360,361,363,394,404],acta:[118,143,334],action:[2,6,11,12,71,206,211,288,443],activ:[5,8,11,12,13,14,55,59,87,142,179,193,206,210,213,219,228,250,270,289,316,377,405,417,445,448],actual:[1,3,6,8,12,56,62,127,167,169,173,174,187,189,190,198,213,214,247,251,257,265,274,278,280,281,282,283,285,291,300,301,318,329,360,362,372,378,379,420,421,432,433,441,448],adam:[318,319],adapt:[],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,19,40,42,71,87,91,102,114,117,119,142,144,145,167,168,172,173,174,175,176,178,180,181,182,183,184,185,186,190,193,198,200,203,207,208,209,211,213,215,216,220,227,228,229,230,231,232,233,234,235,246,247,248,249,251,259,269,270,272,273,275,277,281,283,284,288,289,290,292,294,295,299,301,319,321,325,327,335,340,342,345,349,357,364,369,380,384,387,393,395,421,423,424,429,431,433,435,443],add_molecul:178,add_speci:178,add_to_nodeset:178,addforc:[],addit:[],addition:[6,8,16,278,300,360,394],address:[7,8,11,168,212],addtorqu:[],adequ:[278,291,318,328,432],adher:29,adhikari:216,adiabat:[],adiam:[168,169],adjac:[39,144,328,384,407,408,437,438],adjiman:383,adjust:[3,6,16,17,41,59,118,123,124,127,128,131,132,137,138,143,148,167,168,181,188,192,194,210,213,217,221,225,226,229,230,233,247,251,254,256,257,260,261,262,263,268,270,278,282,286,291,293,294,295,297,298,300,318,319,326,328,333,335,354,378,379,410,433,449],admiss:233,adof:[124,181],adopt:[269,443],adp:[],adri:[9,266,392,393],adust:138,advanc:[3,210,339,418,429],advantag:[1,6,8,11,14,18,39,40,41,188,333,356,432,437],advect:[3,6,278],advertis:8,advis:[328,391],afer:3,affect:[1,6,10,14,15,16,17,40,60,61,71,88,117,121,128,142,148,169,174,181,182,183,184,185,186,189,190,191,192,194,195,203,209,211,213,219,226,230,231,232,234,235,241,246,247,249,270,271,276,290,300,312,318,324,325,326,328,329,330,333,357,378,379,384,420,421,423,426,428,431,433],affin:[16,17,18,194,333,348],afil:207,aforement:18,afresh:[258,431,448],afshar:353,after:[2,3,5,6,8,9,11,12,15,16,21,22,33,39,40,41,44,50,57,58,59,61,63,71,123,124,125,126,127,128,131,132,133,134,136,137,144,145,147,148,151,152,157,166,167,168,169,170,172,173,174,178,179,181,182,188,189,190,191,192,194,198,205,216,217,218,219,220,225,226,227,229,234,235,241,246,247,249,252,256,260,268,270,273,279,281,282,283,285,286,287,288,289,293,295,297,301,304,305,310,317,323,324,326,327,329,331,332,333,334,335,339,346,348,355,356,357,358,364,365,366,377,378,379,380,381,382,386,390,392,393,396,406,408,409,410,418,420,422,423,424,425,426,428,429,431,433,435,437,440,441,443,447,448,449,450,451,452],afterrun:431,afterward:3,afterword:41,ag1:143,ag2:143,again:[6,11,12,17,62,120,124,126,130,138,167,169,194,209,256,304,317,328,378,379,418,420,421,423,425,430,437,439,448,450],against:[11,12,13,64,195,328,392,393],aggreg:[6,12,65,68,69,79,92,108,115,209,225,268,270,276,418,449],aggress:[209,437],agilio:[9,13],agre:[3,8,164,326,335,366,393],agreement:[5,7],ahd:363,ahead:297,aidan:[0,5,7,9,13],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:168,akohlmei:[7,9,13,170,210],aktulga:[7,9,263,393],al2o3_001:[118,271],al3:143,ala:216,alain:9,alat:[251,380],alb:[390,408,410],albeit:269,albert:9,alchem:[87,138],alcohol:293,alcu:[334,339],alcu_eam:390,alderton:352,alejandr:[229,230],alessandro:13,algorithm:[0,1,6,7,8,9,41,61,169,178,188,191,194,216,218,219,241,253,270,273,285,286,290,293,298,324,325,326,330,333,357,379,418,420,437],alia:12,alias:[1,319],aliceblu:169,align:[6,12,29,41,71,146,164,184,188,211,321,423,426,443],alkali:357,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,132,137,138,139,140,141,142,143,144,145,146,147,148,150,152,157,163,164,167,168,169,170,172,173,174,175,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,197,198,199,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,222,224,225,227,229,230,231,232,233,234,235,236,237,238,239,240,241,242,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,308,313,316,317,318,319,320,321,323,326,327,328,329,330,332,333,334,335,336,338,339,340,342,343,344,345,346,348,349,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,373,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,430,431,432,433,434,435,436,437,438,440,441,443,447,448,449,450,451,452],allen:[29,87,352,360],allentildeslei:87,allign:3,allindex:302,alloc:[3,5,6,8,9,11,12,60,203,292,327,329,333,388,393,423,431],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,108,123,124,137,142,143,144,146,152,163,164,167,168,169,170,172,173,175,177,178,179,181,182,183,184,185,186,188,190,191,192,193,194,195,199,200,203,205,206,207,208,210,213,216,219,220,224,226,229,230,251,255,257,258,259,260,264,270,271,273,274,278,285,286,287,288,290,291,292,293,294,295,301,303,305,313,318,319,321,326,327,328,329,332,333,336,339,340,341,342,343,344,349,355,357,361,362,363,364,373,378,379,384,390,393,394,404,413,415,418,421,423,425,426,427,428,429,430,433,435,436,437,440,441,448,449],almost:[2,3,12,60,211,260,290,319,330,333,404],alo:349,alon:[6,7,191,266,392,393,421],alond:13,along:[6,8,9,12,29,40,87,118,143,144,166,167,168,191,211,216,217,221,226,228,260,270,273,274,275,276,285,289,290,296,299,301,321,324,325,326,328,349,352,361,364,367,369,373,380,392,393,407,423,426,433,434,448],alonso:[381,382],alpha:[6,51,173,216,252,260,265,326,334,337,340,349,353,355,356,358,363,368,369,380,385,389,409,411,441,443],alpha_:411,alpha_c:377,alpha_i:[396,411],alpha_ialpha_j:411,alpha_lj:377,alphabet:[2,3,22,37,44,55,63,152,163,172,305,313,327,346,405,423],alphanumer:[3,63,172,259,267,303,327,448],alreadi:[3,7,8,12,42,144,145,147,177,181,184,185,188,190,194,220,258,260,278,301,327,328,353,362,364,371,379,404,413,416,419,423,424,428,448],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,73,75,77,81,87,89,90,93,103,104,105,106,107,112,114,116,117,119,120,121,122,123,124,125,126,127,128,130,131,132,133,134,136,137,138,139,140,141,142,144,145,146,147,148,150,152,163,164,165,167,168,169,170,172,173,174,175,177,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,200,203,204,205,206,207,209,210,213,214,215,216,226,227,229,230,231,232,233,234,235,240,243,244,246,247,248,249,251,252,253,255,256,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,278,281,282,283,284,285,289,290,291,292,294,296,299,301,303,305,310,313,316,318,319,321,322,323,326,327,328,329,330,332,333,339,343,344,346,350,351,352,353,355,356,357,360,361,363,364,365,373,377,378,380,384,386,388,389,390,391,394,395,399,400,402,403,404,405,406,407,408,409,410,411,418,420,421,422,423,424,425,426,427,428,430,431,432,433,435,436,437,438,441,442,443,444,446,447,448,449,450,452],alter:[3,6,8,9,11,12,41,59,122,123,124,125,127,130,131,132,133,136,137,144,148,167,168,170,173,174,181,189,190,191,192,194,228,229,265,268,270,272,278,286,293,300,325,328,364,423,428,430,433,448,449,452],altern:[1,6,8,11,12,17,18,91,144,172,194,210,214,229,259,270,285,286,293,306,309,318,325,326,334,335,349,355,356,358,366,369,377,380,381,382,386,390,391,396,406,408,410,421,423,424,438,441],although:[29,42,164,219,229,257,261,270,285,317,416,430,443,452],aluminum:416,alwai:[0,6,11,12,17,18,54,57,63,71,142,169,182,184,185,186,190,193,205,207,211,262,265,270,278,295,299,300,304,318,319,324,326,327,329,330,333,342,345,355,372,392,393,397,407,408,410,416,418,423,424,426,428,435,437,440,443,448,449],amap:169,amatrix:207,amaz:11,amazingli:13,amber2lmp:[],amber:[],ambient:168,ambigu:[3,63,172,448],amd:[17,333],amend:11,amino:9,amit:9,among:[16,121,179,216],amorph:[144,409],amount:[1,3,6,12,59,88,115,142,146,166,168,192,193,205,209,213,229,251,257,270,278,283,286,291,293,301,318,333,353,388,423,426],amplitud:[194,226,296,312,426,448],amu:205,analag:[6,448],analalog:6,analog:[6,120,146,164,361],analys:[7,428],analysi:[7,9,13,63,64,73,170,266,267,302,396,423,433],analyt:[1,3,13,118,138,143,273,318,339,365,366,371,390],analyz:[6,8,13,328],andersen:273,anderson:[255,353],andr:[7,9,13],andrew:13,andzelm:404,ang:251,angl:[],angle1:269,angle2:269,angle_coeff:[],angle_cosineshift:27,angle_cosineshiftexp:[26,153],angle_cutof:363,angle_cutoff:363,angle_hybrid:29,angle_info:393,angle_styl:[],angle_typ:40,angleangl:[3,304,310,423],angleangletors:[3,151,423],anglecoeff:3,angletors:[3,151,157,423],angletyp:190,angmom:[],angmomi:[113,167,280],angmomx:[113,167,280],angmomz:[113,167,280],angstrom:[6,10,59,71,118,133,143,144,166,167,168,169,177,184,185,194,195,205,210,211,226,263,268,295,297,298,300,319,321,324,330,334,335,344,355,377,380,386,391,392,393,410,416,426,432,447,449],angular:[3,6,40,61,66,82,83,84,85,106,113,120,123,136,137,144,167,172,213,219,225,226,231,232,234,235,237,238,239,242,244,245,246,249,268,270,273,280,334,339,348,361,378,379,380,390,405,408,409,423,433,448,449],angularm:238,anharmon:[27,53,153,265,437],ani:[1,3,6,7,8,9,10,11,12,13,14,15,16,17,22,29,38,39,40,41,42,44,55,56,58,59,61,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,147,148,150,152,164,166,167,168,169,172,175,176,177,179,181,182,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,200,202,205,208,209,211,213,216,219,225,226,229,233,251,253,255,256,257,259,261,262,263,265,267,268,270,272,273,274,275,277,278,279,280,289,290,295,296,297,298,299,300,301,302,303,305,317,318,319,321,323,324,326,327,328,330,331,332,333,335,339,343,344,348,349,352,353,355,356,358,360,364,365,366,367,373,384,390,392,393,394,396,405,406,407,408,409,410,411,412,417,418,420,421,423,424,426,427,428,429,430,431,432,433,434,435,436,437,441,443,444,446,447,448,449,450,451,452],anihil:377,anim:[2,4,7,11,13,168,328],anion:358,aniso:[3,192,194,229,230,231,232,233,234,235,257,270],anisotrop:[213,360,394],ann:383,annot:[7,406,408,409,410,423],annual:[418,437],anoth:[1,3,4,6,7,8,11,12,17,29,40,63,71,87,119,168,172,173,179,181,183,184,185,186,191,194,195,206,209,213,214,219,229,230,233,256,259,270,271,281,282,283,290,300,303,324,326,328,329,332,349,353,357,358,360,363,364,368,369,377,392,394,397,404,408,409,410,417,418,421,424,430,432,443,448,452],ansi:12,answer:[3,4,8,12,270,330,331],anthoni:288,antiquewhit:169,antisymmetr:[9,40,336],antisymmetri:357,antonelli:[287,288],antonio:389,anymor:288,anyon:7,anyparticl:86,anyth:[8,11,144,194,212,406,408,410,434],anywai:[147,333,443,450],anywher:[12,144,346,380,396,448],aoff:[327,423],aparam:[87,173,174],apart:[3,145,219,275,329,338,397,423,432],aperiod:252,api:[11,12,170,365,421],appar:3,appear:[2,3,6,11,12,13,39,40,41,77,87,108,115,116,120,127,144,145,147,167,168,169,181,184,185,188,192,195,198,205,210,256,267,268,289,301,303,304,318,326,327,328,347,355,380,384,407,419,420,421,423,424,425,428,430,443,448,452],append:[],appendix:[29,352],appl:[192,229,230],appli:[2,3,4,5,6,8,12,17,18,33,41,50,57,59,61,63,71,87,88,105,120,121,124,130,132,134,138,143,144,146,150,152,157,163,167,169,172,173,174,175,176,178,181,187,188,192,193,194,196,199,200,203,204,205,206,207,208,210,211,213,214,215,216,220,229,230,233,234,235,241,246,249,250,251,253,257,260,268,269,270,272,273,274,275,276,277,279,281,282,283,284,286,288,289,290,293,301,318,321,326,327,328,338,340,342,344,349,352,357,361,362,363,364,366,369,375,379,384,387,392,395,404,411,415,423,424,426,427,428,432,435,440,443,448,449,450,451],applic:[1,6,9,12,17,170,178,191,195,196,203,207,210,251,256,269,274,275,286,293,318,333,410,443],applyt:3,appopri:17,approach:[6,7,9,14,178,206,252,253,265,270,285,286,288,290,293,318,339,349,351,354,360,394,404,413],appropri:[1,2,3,6,8,11,12,13,15,17,33,38,42,50,56,61,73,88,91,116,117,123,124,152,157,163,164,167,169,181,182,184,185,186,191,192,194,203,204,207,216,224,226,227,229,231,232,233,234,235,246,247,249,253,256,257,260,265,270,278,281,282,283,286,293,295,296,298,299,300,310,319,328,335,339,343,347,348,349,356,361,364,366,373,377,391,392,393,406,407,408,409,410,413,423,424,425,427,428,436,437,440,448,449],approri:208,approxim:[6,9,118,143,205,207,216,253,271,273,285,318,324,325,326,341,351,357,360,378,379,384,391,394,415,437,443],april:11,aprpopri:418,apu:[378,379],aqua:[168,169],aquamarin:169,ar_therm:178,ar_ttm:178,ara:13,arbitrari:[6,40,58,167,168,170,193,194,208,229,253,261,406,421,434,448],arbitrarili:[11,59,116,120,166,192,229,349,448],arcco:3,arch:[1,12,14,15,17],architect:316,architectur:[16,333],archiv:[6,7,11,12,280,346,430],arcsin:3,area:[6,41,91,112,116,142,188,194,216,286,293,354,361,389,412,420,433],aren:[259,303],arflag:12,arg:[3,11,12,22,40,41,44,55,59,63,71,87,117,132,138,142,144,147,148,152,166,167,169,172,173,174,175,177,179,181,182,183,184,185,186,187,188,189,190,193,194,195,200,203,205,208,209,210,211,219,226,231,232,256,269,270,271,272,285,288,295,296,297,298,300,301,305,316,328,333,340,341,342,344,345,346,351,352,357,362,364,369,373,377,378,379,387,395,405,420,421,423,426,428,430,432,434,441,448,449,451,452],argon:205,argonn:12,argument:[2,3,6,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,63,73,87,91,109,112,116,120,121,122,131,132,133,138,142,144,145,146,148,150,151,152,153,154,155,156,158,159,161,162,164,167,169,172,173,174,175,177,180,181,182,183,184,185,186,187,188,192,193,194,201,203,204,207,208,212,213,219,226,229,231,232,233,234,235,236,244,246,247,249,255,256,258,262,267,270,271,272,273,278,281,283,290,292,294,296,301,303,304,305,306,307,308,309,310,312,314,316,317,319,320,321,323,328,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,351,352,353,355,356,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,389,390,392,393,394,395,396,397,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,423,424,426,428,431,432,433,434,438,440,441,448,449,451],aris:[12,415],arithmet:[3,6,318,344,347,367,372,384,411,412],arkansa:9,arl:9,armv8:17,arnold:318,around:[1,3,4,6,12,42,57,58,59,66,70,73,77,116,120,123,139,142,144,146,166,168,169,176,177,192,194,195,211,226,229,259,261,265,270,275,278,295,296,299,317,327,423,426,433,434,443,448],aroung:3,arrai:[],arrang:120,arrheniu:437,art:[261,418,437],artefact:207,articl:6,articul:[7,255],artifact:[88,142,443],artifici:[227,260,399,400,402],arun:13,arxiv:[120,396],ascend:[41,169,210,219,270,428],asci:7,ascii:[13,271,289,328,355,358,380,423],ash:[378,379],asid:[8,144,380],asin:448,ask:[3,11],askari:389,askoos:13,asoci:168,aspect:[6,7,59,194,205,360,394,412,423,433,437],aspect_ratio:271,asper:4,aspher:[],asq:[378,379],assembl:4,assign:[1,2,3,6,7,11,12,14,15,17,18,33,39,40,41,50,57,59,61,63,66,71,72,75,90,93,104,106,110,113,114,118,120,121,124,139,141,143,144,147,157,167,168,169,170,172,173,174,177,181,183,188,190,191,192,195,197,205,210,213,214,215,216,226,229,231,232,233,234,235,244,246,247,248,249,253,256,257,259,261,267,270,271,281,282,283,284,301,310,319,321,323,327,328,332,333,339,355,358,360,363,364,393,394,420,421,423,424,425,426,427,432,433,438,441,448,449],assignemnt:[6,432],assing:259,assist:[7,227],associ:[3,5,6,8,9,12,22,37,39,40,44,55,59,66,74,75,81,87,89,90,93,99,101,103,104,106,139,152,163,167,168,169,173,174,175,179,192,194,200,203,205,206,212,216,226,229,255,265,269,270,271,276,278,302,303,305,313,321,326,328,332,333,346,349,353,354,355,357,363,364,366,369,373,404,405,407,421,424,431,443,445,448],associd:67,assum:[2,3,4,6,11,12,16,39,59,67,71,88,96,102,104,122,123,124,125,126,127,129,130,131,132,133,134,136,137,138,142,144,147,169,173,174,181,182,183,184,185,186,192,194,202,210,212,216,219,231,232,234,235,237,239,242,244,245,246,249,251,252,256,257,258,261,270,272,274,275,286,289,290,295,298,301,318,319,327,328,333,339,341,343,346,347,354,357,363,364,368,373,378,379,412,418,420,421,423,425,428,433,437,440,441,443,449],assumpt:[142,210,334,384],astar:380,astart:397,asterisk:[22,44,77,87,116,138,148,152,169,173,174,219,270,305,323,346,363,404,417,420,433,447],astop:[326,397],asu:355,asub:380,asubrama:13,asymmetr:[298,339,355],asynchron:[15,16],atan2:448,atan:448,atc:[],atc_fe_output:178,athomp:[0,7,9,13],atm2pa:6,atmospher:447,atol:12,atom1:[255,269,327,423],atom2:[255,269,327,423],atom3:[255,269,327,423],atom4:[269,327,423],atom:[],atom_element_map:178,atom_forc:393,atom_info:393,atom_modifi:[],atom_styl:[],atom_vec:8,atom_vec_atom:8,atom_vec_electron:8,atom_veloc:393,atom_weight:178,atomey:[6,7,11,13,167,168,169],atomfil:[3,71,259,301,332,433,448],atomic_charg:178,atomic_numb:390,atomid:423,atomist:[6,178,285],atomperbin:3,atomt:169,atomvec:8,attach:[6,185,253,274,275,423],attatch:288,attempt:[3,6,41,59,71,166,179,188,189,190,191,195,205,256,257,278,298,318,322,328,364,421,436,438,441,448],attend:178,attent:[15,18],attogram:447,attrac:380,attract:[],attribut:[3,6,7,8,11,39,40,42,58,63,71,87,113,114,115,117,123,138,167,168,169,172,173,174,180,181,183,184,185,191,192,229,231,232,233,234,235,237,238,246,247,249,257,270,271,280,281,282,283,321,327,339,357,364,423,424,425,433,441,448],atw:[378,379],atwat:409,atwt:380,atyp:[115,138,190,349,369,373,377],au1:143,au3:143,aug:11,augment:[12,113,192,259,380],augt1:380,auo:267,auoh:267,author:[3,8,9,13,355,356,443],auto:[6,8,11,12,91,140,172,182,274,292,318,327,333,420],autocorrel:[63,91,213],autom:[12,168],automag:7,automat:[3,6,12,14,15,16,17,18,19,36,164,177,205,207,216,270,274,291,318,333,348,355,364,380,416,423,436,443],auxiliari:[1,6,9,11,12,13,167,252,270,424,428,450],avail:[1,3,5,6,7,8,9,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,63,87,109,112,113,120,122,131,142,150,151,153,154,155,156,158,159,161,162,164,167,168,172,175,181,183,184,185,186,187,192,193,201,204,206,208,210,213,229,230,231,232,233,234,235,236,244,246,247,249,262,264,270,271,272,273,281,283,288,294,304,306,307,308,309,312,314,316,319,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,381,384,385,386,387,389,390,392,393,394,395,396,397,406,407,408,409,410,412,414,415,416,424,432,436,448],availab:9,ave_chunk:6,aveforc:[],avendano:383,averag:[3,6,7,15,41,63,64,71,87,91,103,105,116,118,124,132,140,143,167,169,172,174,178,180,181,182,183,184,185,186,187,188,192,205,207,209,213,214,219,229,230,233,252,257,260,266,267,270,271,274,304,335,357,380,411,424,428,441,443,448],averi:278,avesq:117,avi:168,avoid:[1,3,6,12,36,39,59,144,145,164,168,177,182,183,186,198,205,207,214,251,253,261,265,270,271,292,299,331,339,357,377,380,393,407,425,431,432,443],awai:[3,6,61,116,167,168,191,195,208,211,228,251,274,275,289,295,329,349,369,373,428],awar:[333,356,420],awpmd:[],axel:[7,9,13,18],axi:[3,6,41,118,123,143,144,146,166,168,188,205,208,211,226,256,275,290,296,308,314,321,423,426,433],axial:233,azimuth:[168,208],azur:169,b_k:396,ba2:143,babadi:394,back:[1,6,7,11,12,13,14,15,17,125,126,127,131,132,133,134,136,144,148,167,169,170,173,174,193,198,203,210,211,213,214,229,234,235,246,247,249,268,270,281,282,283,287,288,297,298,300,317,318,319,328,361,421,423,424,425,426,427,430,436,437,449],backbon:[191,273,312],backcolor:[169,451],backend:17,background:[9,87,88,112,121,169,188,194,213,278,286,290,293,328,347,378,379,380],backtrack:[324,326],backward:[9,12,170,328,437],baczewski:206,bad:[3,12,59,61,211,328,423,428,440],badli:[3,192,229],bal:285,balanc:[],balasubramanian:248,ball:[120,378,379],ballenegg:318,bammann:178,band:[4,6,7,120,172,228,325,328,339],bandwidth:[1,10,18,40],bandwith:168,bar:[87,168,447],barashev:355,bare:[198,212,214],barost:[198,443],barostat:[],barostt:6,barr:348,barrat:265,barrett:67,barrier:[3,4,6,228,314,328,348,359,437],bartel:252,bartok2010:396,bartok2013:396,bartok:[9,120,391,396],bartok_2010:391,bartok_phd:391,bary:447,basal:[],base:[3,4,6,8,9,11,12,13,14,15,20,63,64,71,78,87,91,111,118,124,126,143,144,146,167,168,169,172,178,184,185,188,189,190,194,195,199,210,213,217,219,241,252,253,259,261,263,270,271,274,278,285,319,333,335,337,339,353,357,360,363,365,369,378,381,382,387,389,390,406,409,410,418,420,423,424,425,427,430,433,434,437,438,441,447,448,449,452],bash:346,bashford:[6,20,150,344,435],basi:[3,6,12,40,120,124,144,177,213,215,252,278,295,321,416,433,448],basic:[6,7,8,12,17,41,113,121,168,169,178,188,229,230,251,299,334,336,417,425,443],basin:[86,328,418,437],bask:[355,380,390],bath:[9,260,265],batom1:[69,115,117,167,169],batom2:[69,115,117,167,169],bayli:[6,150,435],bb13:151,bcc:[3,4,7,64,70,73,321,380,382],bcolor:[3,168,169],bdiam:[3,168,169],be2:143,bead:[5,7,10,13,40,45,46,136,176,191,253,404],beam:195,bear:[6,206],becau:13,becaus:[0,1,3,6,8,12,16,17,18,29,40,41,59,64,71,77,116,120,124,129,134,144,145,146,150,167,168,169,170,175,179,181,188,189,190,191,192,194,200,204,206,207,212,213,214,215,226,229,230,241,247,256,260,261,265,270,275,280,285,286,289,290,293,297,298,299,300,301,307,318,324,326,328,329,332,333,344,346,349,351,353,357,358,360,361,362,363,364,367,368,377,378,379,380,384,394,404,405,411,412,420,421,423,425,426,427,430,432,433,435,437,443,448,449,450,452],beck:[],becker:[334,355],beckman:210,becom:[1,2,3,6,7,8,18,39,41,54,57,59,71,146,167,168,169,188,189,190,191,194,205,207,216,228,229,267,268,281,282,295,296,298,299,300,318,319,324,328,335,347,349,355,357,360,369,384,390,394,406,415,423,424,426,433,448],been:[1,2,3,6,7,9,12,13,16,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,45,46,47,48,49,51,53,54,56,57,59,60,63,65,69,71,87,109,112,113,114,115,117,119,122,123,124,125,126,127,131,132,133,134,136,137,145,146,147,148,150,151,153,154,155,156,158,159,161,162,164,166,167,168,169,170,175,177,179,180,181,182,183,184,185,186,187,188,191,192,193,194,195,201,204,205,208,210,211,213,214,216,217,218,219,220,224,226,227,229,231,232,233,234,235,236,244,246,247,249,255,256,257,260,262,264,267,268,270,272,273,279,281,282,283,290,291,292,294,295,296,297,298,300,301,304,306,307,308,309,312,314,317,318,319,326,329,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,354,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,381,382,385,386,387,389,392,393,394,395,397,404,406,407,408,409,410,412,414,415,416,418,420,421,423,424,425,426,427,429,433,437,440,441,448,449,450,451],befor:[1,2,3,6,8,9,12,14,17,22,29,39,40,41,44,59,66,71,74,75,81,89,90,93,103,104,105,106,114,124,127,132,133,139,144,145,147,148,152,165,166,169,173,174,175,176,177,179,181,183,184,185,186,187,188,192,197,198,204,205,210,212,213,214,216,219,226,229,234,235,246,249,252,259,260,261,264,265,270,271,272,279,281,282,283,289,295,296,297,301,305,323,324,326,328,333,358,361,377,380,405,413,418,420,421,424,425,426,427,428,430,431,433,437,440,441,443,448,449,450,451,452],began:[5,12],begin:[3,8,12,38,39,56,71,117,119,145,164,166,167,169,173,174,178,180,181,182,183,184,185,186,188,194,198,214,241,255,268,271,278,280,283,292,297,300,301,315,317,318,319,320,322,325,327,328,329,332,333,355,384,390,397,404,407,411,416,418,423,430,437,439,441,443,447,448,450],behalf:3,behav:[3,27,153,325,326],behavior:[3,148,164,167,168,170,191,192,195,205,206,207,210,213,214,215,229,256,260,265,278,281,282,290,325,339,357,380,417,425,429,448,450],behaviour:[6,213],behind:[8,212,227,260,278,318],beig:169,belak:7,believ:11,bellott:[6,20,150,344,435],bellow:308,belong:[2,3,40,71,147,179,181,184,205,219,270,301,327,423],below:[1,2,3,5,6,8,9,11,12,15,16,17,22,38,39,41,42,44,54,56,59,60,63,65,68,69,71,77,79,91,92,112,113,116,117,118,120,121,124,130,132,138,142,143,144,147,148,150,152,163,164,167,168,169,172,173,175,176,178,181,182,183,184,185,187,188,190,191,192,194,195,200,203,208,209,211,213,214,219,226,227,229,233,234,235,246,249,251,256,259,260,261,268,269,270,272,273,275,278,279,280,281,282,283,286,287,288,290,293,295,296,301,303,305,316,318,321,323,324,326,327,328,330,333,334,335,336,339,340,341,344,345,346,347,349,352,355,357,358,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,383,384,389,392,393,394,395,396,397,405,407,412,414,415,417,418,421,423,424,425,426,428,430,431,433,435,437,439,440,441,442,443,448,449,452],bench:[1,6,11,12],benchmark:[1,7,10,11,12,13,14,15,16,17,18,41,188,318,436],beneath:195,benefici:[61,330],benefit:[1,206,432],bennet:87,beowulf:7,berardi:[360,394],beraun:290,berendsen:[],berensen:270,berkelei:142,berkowitz:318,berlin:[7,9,274],bern:[3,253,261,262,348,360,405,432],bernendsen:6,beryllium:357,besid:[8,272,426],best:[1,6,8,14,15,16,17,18,19,229,247,248,269,270,333,339,349,369,373,384,407,424,432,437],beta:[6,9,252,260,334,337,355,356,358,380,408,409,410,441,448],beta_:339,beta_k:396,beta_pi:339,beta_sigma:339,beta_t:409,better:[3,6,7,8,12,14,16,27,120,153,174,188,205,216,229,241,261,268,270,278,319,328,333,408],betwe:338,between:[],beutler:377,bewteen:[108,182,278,286,293,364,420],beyon:432,beyond:[3,5,6,12,17,61,71,87,142,167,169,183,184,205,229,318,330,359,375,384,437,441,448],bgq:17,bi3:143,bi5:143,bia:[3,6,8,112,121,123,124,125,126,127,131,132,133,134,136,137,181,193,194,205,213,214,229,234,235,246,247,249,265,281,282,283,285,449],bias:[6,9,193,449],biaxial:123,biersack:[380,405,410,416],big:[3,4,12,167,260,265,278,329,347],bigbig:[3,12],bigint:[3,203],bilay:[4,10,275],bilayer1:275,bilayer2:275,bill:7,billion:[3,7,10,12,39,205,431],bin:[3,6,11,12,39,63,66,71,75,90,93,104,106,114,116,124,132,139,141,167,169,181,183,184,185,252,260,265,278,329,330,333,354,388,424,451],binari:[3,6,7,12,13,16,33,37,50,55,157,163,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,310,313,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,416,424,425,430,450,452],binary2txt:[],binchunk:181,bind:[17,18,184,339],binsiz:[39,169,329,333],binstyl:132,bio:[40,329],biolog:[6,7],biologi:156,biomolecul:[255,270,318,319,344],biomolecular:432,biophys:210,biosym:13,bird:354,bisect:[41,188,412],bisector:[6,349,369,373],bispectrum:[63,120,396],bisqu:169,bit:[3,12,17,39,203,214,384,407,431,443],bitmap:[3,407,413],bitrat:[168,169],bitzek:325,bkgd_dyn:380,bla:12,black:169,blais:[9,13],blanchedalmond:169,blank:[2,3,12,38,56,107,164,168,255,270,327,328,339,356,380,386,396,406,407,408,409,410,420,421,423,448],blast:290,blend:380,block:[2,3,6,91,120,144,146,147,256,299,321,333,339,357,390,396,426,437,443],blow:[3,241,295,299,397],blown:3,blue:[2,168,169,191],bluegen:[167,318],blueviolet:169,board:[319,352],bodi:[],body_nparticl:8,bodyflag:423,bodyforc:216,bodyforcei:216,bodyforcex:216,bodyforcez:216,bodystyl:[219,270],boff:[327,423],bogaert:285,bogu:[3,127,192],bogusz:88,bohr:[355,357,410,447],boltzmann:[6,7,9,87,91,112,122,124,125,126,127,130,131,132,133,134,136,181,191,213,216,217,218,219,220,233,294,353,438,447],bond:[],bond_coeff:[],bond_graph_cutoff:393,bond_harmon:[8,48,49],bond_harmonicshift:49,bond_info:393,bond_interact:178,bond_styl:[],bond_typ:[148,404],bondangl:[3,21,33,423],bondbond13:[3,151,423],bondbond:[3,21,33,423],bondchk:393,bondcoeff:3,bondtyp:[189,190,327,404],bonu:[3,450],book:415,bookkeep:384,bookmark:0,boost:[1,3,12,64,329],bop:[],border:[3,7,16,61,290,449],boresch:87,boreschkarplu:87,born:[],boron:357,borrow:274,bose:265,botero:[7,9,13,357],both:[1,3,6,7,8,9,11,12,14,15,16,17,18,27,37,39,54,55,57,59,61,62,63,68,69,71,83,87,88,108,113,115,116,123,124,129,132,134,137,144,146,147,148,153,163,164,167,168,171,172,173,174,179,181,182,184,185,186,189,190,191,192,193,194,199,205,207,209,211,213,214,216,217,225,226,229,230,234,235,241,246,249,255,259,260,261,267,270,273,274,275,278,282,286,287,288,290,293,295,296,298,299,300,303,304,313,319,323,326,327,328,329,331,333,335,339,340,341,342,343,344,345,347,352,353,355,356,357,360,361,363,364,365,369,371,373,374,375,377,378,379,383,384,387,394,395,406,408,409,410,416,418,420,421,423,424,425,426,430,435,440,441,443,448,450,451,452],bottleneck:[1,3,421],bottom:[8,9,127,169,194,204,216,247,286,293,321,435],bottomwal:187,bounc:[3,278],bound:[3,6,17,26,27,41,42,57,59,71,133,146,153,166,167,169,183,184,188,194,195,199,205,214,229,256,278,295,296,297,298,299,300,318,326,357,423,426,437,443,448,449],boundar:3,boundari:[],boundary_dynam:178,boundary_faceset:178,boundary_integr:178,bount:11,box:[],boxcolor:[168,169],boxxlo:11,bpa:333,bpclermont:[9,13],bptype:404,br1:143,bracket:[2,3,6,41,63,71,117,119,172,180,181,182,183,184,185,186,188,292,441,448],bragg:[118,143],branc:11,branch:11,branicio:73,breakabl:[7,44,55],breakag:[78,189],breakdown:[1,12,15,88,107,392,393,418,437],brennan:404,brenner:[335,405],brick:[3,41,62,132,146,188,423,425,427],brief:[1,5,6,7,8,12,212,335,339,393,437],briefli:[6,10,253,348],brilliantov:361,bristol:[5,7],brittl:389,broader:421,broadli:8,broken:[2,54,65,69,70,78,107,115,148,189,229,339,425,435,450],brook:6,brought:166,brown:[7,9,13,15,16,118,121,169],brownain:341,brownian:[],brownw:7,brows:0,browser:[4,168],bryantsev:363,bsd:12,bstyle:[40,42],btype:[69,115,145,167,349,369,373,377,404],buc:342,buck:[],buckingham:[7,173,174,261,319,340,342,343,351,405],buffer:[3,8,168,169,440],bufi:168,bug:[],bui:168,build:[],builder:[7,13],built:[1,2,3,4,6,8,9,11,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,43,45,46,47,48,49,50,51,53,54,55,56,64,67,78,80,83,86,87,96,97,98,99,100,101,105,109,111,112,120,122,123,128,130,131,135,136,138,142,150,151,153,154,155,156,157,158,159,161,162,163,164,167,170,172,175,176,177,179,187,189,190,191,193,195,200,201,202,204,205,206,207,208,210,212,213,215,216,217,218,219,220,222,223,227,228,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,251,252,253,255,256,259,260,261,262,263,264,265,266,267,270,272,273,274,278,281,283,284,285,286,287,288,290,291,293,294,296,297,302,303,304,306,307,308,309,310,312,313,314,319,328,329,330,333,334,335,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,385,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,418,421,424,426,432,436,437,438],bulatov:[381,382],bulk:[4,6,10,70,216,251,257,350,380,384,389,427],bullet:7,bump:213,bunch:8,bundl:[9,168,170],burlywood:169,bussi1:282,bussi2:282,bussi:[207,282],bybe:9,c1060:14,c11:[182,380],c12:182,c13:182,c1n:182,c2050:14,c21:182,c22:182,c23:182,c2n:182,c31:182,c32:182,c33:182,c34:182,c3n:182,c41:182,c42:182,c43:182,c44:182,c_0:[290,402,403],c_1:[68,69,117,118,143,167,169,206,259,271,301],c_2:[69,117,118,140,142,143,167,271,292,301],c_3:[117,271],c_cluster:6,c_cstherm:6,c_dist:117,c_doubl:11,c_e:290,c_flux:91,c_forc:117,c_gauss:359,c_hb:363,c_id:[6,63,71,87,117,119,167,180,181,182,183,184,185,186,271,280,292,441,448],c_ij:6,c_ijkl:6,c_index:117,c_k:206,c_ke:286,c_msdmol:119,c_my_stress:180,c_mycentro:[181,184],c_mychunk1:114,c_mychunk2:114,c_mychunk:[6,66,75,90,93,104,106,124,139,141],c_mycom:183,c_mycomput:181,c_myf:[167,451],c_myrdf:[116,186],c_mytemp:[8,182,183,186,292,441,448],c_n_k:206,c_p:121,c_pe:110,c_peratom:[110,121],c_pi:339,c_press:117,c_prop:6,c_radiu:142,c_reax:[392,393],c_sa:271,c_sigma:339,c_size:6,c_stress:167,c_tatom:214,c_tdrude:[198,214,443],c_thermo_press:[8,182,183,186],c_thermo_temp:186,c_xrd:183,ca2:143,cach:[17,39,384,436],cacul:273,cadetblu:169,cai:443,calcforc:216,calclat:91,calcluat:[103,105,110,112,121,349],calcualt:[91,181],calcul:[],caldwel:[6,150,435],calhoun:253,call:[],callabl:[3,11],callback:[3,11,172,203,421],caller:3,calori:447,caltech:[6,7,9,13,357],calucl:6,calul:[11,12,124,319],cambridg:[9,391],campa:252,can:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,313,314,315,316,317,318,319,321,322,323,324,326,327,328,329,330,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,435,436,437,438,439,440,441,443,447,448,449,450,451,452],cancel:[172,270,449],candid:[148,179,205],cannot:[1,2,3,6,11,12,13,15,16,17,39,40,41,54,57,58,59,68,71,82,84,88,104,117,119,123,124,145,147,148,166,167,168,169,180,181,182,183,184,185,186,188,191,192,194,195,205,206,207,213,214,215,219,226,229,231,232,234,235,237,238,239,244,246,249,256,257,260,265,267,270,271,272,278,286,290,292,293,295,296,299,300,301,303,318,321,326,328,331,332,333,342,343,345,355,360,362,369,373,375,377,384,387,392,394,395,404,405,407,418,420,421,423,424,426,427,429,432,433,435,437,440,447,448],canon:[172,179,205,207,229,230,246,247,248,249,253,282,285,288,389],cao1:253,cao2:253,cao:253,capabl:[5,7,9,11,14,16,17,18,297,303,319,333,335,345],capac:[9,40,101,130,265,290,399,423,433],capit:[197,423],capolungo:[118,143,271],captur:[6,291,335,343,357,361,373,380,443],carbid:349,carbon:[7,168,312,335,348,366,380],card:[12,14,16,22,44,77,87,116,152,173,174,270,305,323,346,363,417,425,430,450,452],care:[3,6,59,71,144,147,166,181,184,185,189,190,195,207,212,216,229,256,270,285,338,421,423,426,427,432,433],carefulli:[11,12,54,267,301,364,366,428],carlo:[6,7,9,172,179,191,205,270,285,354,405],caro:[179,355],carpent:[7,13],carri:[16,222,259,290,361,393],cart:[3,420],carter:[9,17],cartesian:[3,62,334,420],carv:147,cascad:[199,290],cash:7,cast:[207,448],cat:[15,168],catastroph:261,cate:216,categori:[],cation:358,caus:[1,2,3,6,8,12,16,17,144,146,147,148,167,169,177,192,199,205,241,251,268,270,295,297,298,299,300,303,317,319,326,328,332,363,369,375,378,379,417,421,422,423,424,427,428,430,431,448,452],caution:[1,319],cautiou:[189,190],cautious:335,caveat:[335,432],cbecker:[334,355],cc1:[6,14,66,75,90,93,104,106,114,124,139,141,181,184],cc2:14,ccc:[356,406,408,410],ccflag:[12,16,17,18,19,167],ccm6:355,ccsi:[356,406,408,410],ccu:339,cd2:143,cdeam:355,cdennist:9,cdll:11,cdof:[6,124,181],cdte:339,cdte_bop:339,cdtese:339,cdzn:339,cdznte:339,ce3:143,ce4:143,ceas:325,ceil:448,cell:[3,6,59,88,116,118,142,143,144,167,177,192,193,205,210,227,229,230,233,252,260,263,290,318,319,321,354,357,441],cella:[6,441],cellalpha:[6,441],cellb:[6,441],cellbeta:[6,441],cellc:[6,441],cellgamma:[6,441],center:[3,6,25,42,63,66,71,74,75,86,89,90,98,103,104,105,114,116,118,124,125,126,129,132,136,139,141,144,168,169,172,173,174,176,181,183,184,185,192,194,195,196,198,205,206,211,213,214,219,225,229,234,235,246,247,249,252,256,261,267,268,270,271,274,275,276,278,280,281,282,283,285,286,288,295,299,304,321,327,338,356,357,360,361,367,378,379,380,381,382,406,408,409,410,412,426,433,443,448],centimet:447,central:[3,61,70,76,77,116,120,219,251,273,276,327,386,392,393,423],centro:[],centroid:[3,253,412,433],cerda:318,ceriotti2:207,ceriotti:[13,207,212],certain:[1,2,3,6,8,12,17,39,71,113,117,119,148,167,168,180,181,182,183,184,185,186,191,203,204,270,272,279,292,303,310,317,329,364,384,393,411,425,429,443,448],certainli:211,cerutti:319,cfg:[3,6,7,13,167,168,169,170],cfile:393,cfor:274,cg_type:395,cgiko:2,cgikot:2,cgkio:2,cgko:2,cgkot:2,cgo:2,cgot:2,ch2:273,ch2lmp:[],ch3:273,chain3:329,chain:[],challeng:[6,274],chalopin:265,champaign:[210,318,319,378],chandler:[334,355],chandrasekhar:[6,369],chang:[1,2,3,6,8,9,11,12,14,15,16,17,39,40,41,46,55,57,59,62,71,80,87,116,126,127,128,144,145,146,148,164,166,167,168,169,170,172,173,174,175,176,178,179,184,185,187,188,189,190,191,192,193,194,195,199,200,202,204,207,209,210,211,213,215,216,217,219,225,226,227,229,230,231,232,233,234,235,241,246,247,248,249,251,252,256,257,259,260,264,267,268,269,270,272,273,274,278,281,282,283,284,286,287,288,289,290,291,293,296,299,301,319,324,326,328,331,333,353,357,361,364,378,379,380,384,392,393,405,418,419,420,421,423,424,425,426,427,428,429,431,432,433,434,435,438,441,444,446,447,448,449,450],change_box:[],changeabl:167,channel:[4,175],chapter:[253,319],charact:[2,3,6,12,38,41,56,63,164,167,168,169,170,172,188,259,267,303,327,332,357,368,390,392,393,407,420,421,425,430,431,448,450,451,452],character:[6,67,70,116,120,396,418,437],characterist:[214,278,287],charg:[1,3,4,5,6,7,9,11,15,40,87,88,113,118,143,144,167,170,172,173,174,179,195,200,205,259,261,262,263,267,280,293,318,319,327,340,342,348,349,351,352,355,357,358,364,369,373,377,387,392,393,405,410,411,413,415,416,423,424,428,433,435,443,447,448],charmm2lammp:13,charmm:[],chartreus:169,cheap:278,cheaper:[199,360,394],check:[3,6,8,11,12,15,17,39,41,71,91,164,179,184,188,189,190,195,202,205,211,212,269,273,278,286,288,293,301,303,317,326,327,328,329,330,333,354,365,368,384,393,404,418,420,421,423,431,437,440,441],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:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,96,97,113,116,117,119,120,121,123,124,130,132,137,140,142,144,145,150,153,154,155,156,158,159,161,162,164,167,168,169,172,178,179,180,181,182,183,184,185,186,188,193,194,195,198,199,203,205,206,207,210,212,213,214,216,219,227,229,233,234,235,246,247,249,252,253,255,258,259,260,261,263,265,267,269,270,271,273,280,281,282,283,286,287,288,289,290,292,293,301,302,306,307,308,309,312,314,316,321,323,326,327,328,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,418,420,421,423,424,425,426,428,430,431,432,435,437,438,439,443,448,449,451],foo:[4,8,11,12,167,168,203,421,434,448],foot:6,footprint:[12,333],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:219,forcefield:[269,363],forcegroup:216,forcezero:324,ford:352,forestgreen:169,forev:71,forget:[214,443],forgiv:229,form:[2,3,6,8,12,16,19,22,44,54,63,66,74,75,77,81,87,89,90,93,103,104,106,116,120,121,138,139,148,152,169,172,173,174,190,206,207,213,215,219,226,247,252,263,265,269,270,290,295,299,304,305,312,323,325,327,328,335,336,339,346,355,357,359,363,364,368,380,382,386,387,390,392,393,394,396,397,405,407,408,409,410,415,417,420,421,423,428,433,440,443,448],formal:[6,78,80,91,206,207,213,229,253,278,286],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,152,164,167,168,169,170,181,183,184,185,186,188,190,252,255,259,261,263,266,270,271,289,290,301,302,305,323,327,328,334,335,339,346,355,358,368,380,382,384,391,392,393,395,396,407,413,420,421,423,424,425,428,439,440,441,448,450],former:[6,12,16,39,41,169,188,290,294,339,341,429,435,448],formerli:[7,13],formul:[1,64,121,175,200,213,229,247,261,263,269,273,289,318,335,339,355,357,360,380,389],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,94,96,97,106,112,118,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,143,144,149,151,152,163,167,173,174,175,176,181,182,183,186,187,194,200,208,209,211,213,214,226,251,252,258,267,272,276,278,281,282,283,292,295,298,300,301,303,304,305,307,313,321,327,335,336,338,339,344,345,346,347,352,353,355,356,360,361,362,363,365,368,369,371,372,373,375,376,378,379,380,383,384,385,394,395,397,405,406,408,409,410,414,415,416,419,423,426,433,440,441,447,448,449],forth:[1,6,11,12,13,14,15,332,421,426,430],fortran:[3,6,9,11,12,13,203,355,364,380,392,393],fortun:8,forward:[3,8,87,317,328,333],foster:[339,389,390],foul:147,found:[3,6,9,12,73,138,167,191,193,205,210,216,252,285,291,303,317,329,346,349,352,418,424,425,440],four:[6,11,54,81,103,104,120,140,227,290,312,327,328,418],fourier:[],fourth:[6,105,269,275,285,344,386],fox:[6,118,150,403,435],fphi:[38,56,407],fpic:12,fplo:[38,56,407],fprime:407,fqdn:212,fqq:352,frac:[198,214,411,443],fraction:[1,3,6,8,12,16,39,41,80,109,121,147,166,168,169,179,189,190,191,192,227,256,260,267,268,278,283,284,321,328,333,339,341,361,378,379,428,433],fragment:[42,210,267],frame:[83,120,169,178,227,260,297,360],framer:[168,169],framework:[5,207,334,396],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,138,174,251,278,287,288,289,290,325,328,336,357,377,390,415,420],freedom:[3,6,8,94,96,97,99,101,102,112,122,123,124,125,126,127,128,129,130,131,132,133,134,136,137,181,191,198,205,207,213,214,219,229,230,233,234,235,246,247,249,253,255,270,273,281,282,283,288,326,352,441,443,449],freeli:[0,6,7,12,123,137,142,168],freez:[],frenkel:[205,288],freq:177,frequenc:[3,6,16,39,169,241,252,253,260,265,316,353,357,393,418,432,437,448,451],frequent:[3,64,67,70,72,73,77,88,120,169,189,190,202,286,293,384,430],fri:[227,260],friction:[4,5,6,10,42,172,207,213,260,265,270,290,294,296,361],from:[],front:[227,260,297],frontend:[168,264],frozen:[6,112,148,204,206,214,329,359],fs2:[6,91],fscale:210,fstr:448,fstring:421,ftol:[326,328,418,437],fuchsia:169,fuction:349,fudg:273,fugac:205,fugacity_coeff:205,fulfil:6,full:[1,2,6,9,12,17,38,39,40,91,168,182,193,216,251,318,319,333,339,355,357,358,360,411,423,425,430,431,435,437,443,451],full_energi:[3,205],fuller:326,fulli:[3,6,9,78,207,212,251,326,328,349,390,391,450],fulton:355,fumi:340,func:[421,448],funcfl:355,functino:6,functionaliri:193,fund:[0,7],fundament:[278,447],further:[3,6,8,12,13,61,63,71,86,105,107,116,168,169,172,181,183,184,185,186,189,195,199,216,220,253,261,271,278,290,292,301,319,324,326,327,328,329,334,338,348,404,418,437,438,448],furthermor:[27,153,357],furthest:61,futher:3,futur:[],g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:390,g_p:290,ga3:143,gaa:339,gahler:325,gai:[3,360,405],gain:285,gainsboro:169,galindo:383,game:210,gamma0:29,gamma:[3,6,29,213,216,220,252,260,261,263,265,294,353,356,360,380,383,399,402,403,406,408,410,441],gamma_:[3,290,296],gamma_ijk:408,gamma_n:[296,361],gamma_p:[3,290],gamma_t:[296,361],gammaa:383,gammafactor:216,gammar:383,gan:[390,406,408,410],gan_sw:390,gan_tersoff:390,ganzenmuel:[7,9],ganzenmul:9,gao:[6,20,150,344,435],gap:[164,378,379,391,396],gap_2014_5_8_60_17_10_38_466:391,gap_exampl:391,gaseou:7,gass:205,gather:[11,431],gather_atom:11,gather_scatter_loop_unrol:12,gathert_atom:11,gauch:156,gauss:[],gaussian:[6,40,63,91,103,105,206,207,213,253,269,278,282,300,318,353,354,357,359,391,405,418,448,449],gave:[3,384],gaybern:[],gcc:17,gcmc:[],gcore:198,gd3:143,gdot:379,gdrude:198,ge4:143,gec:[408,410],gen:[229,230],gener:[],genom:7,gentler:[295,298,300],gentli:356,geom:[6,318,354,418,449],geometr:[3,6,7,8,42,57,59,71,134,135,144,146,167,169,175,184,185,187,188,195,200,209,229,234,235,246,247,249,270,272,281,282,283,299,301,318,321,328,338,341,345,347,349,352,357,360,362,367,369,370,371,372,373,374,375,376,377,378,379,383,384,394,397,411,412,414,415,423,425,426,433,441,448],geometri:[3,6,7,13,25,41,71,132,144,184,188,189,190,192,195,211,321,384,423,426],georg:[7,9],georgia:13,gerber:377,germani:[9,14],germann:[233,371,418,437],germano:360,gerolf:13,get:[],get_natom:[11,421],getenv:448,gettimeofdai:12,gewald:[6,318],gezelt:[349,369],gf100:14,gf104:14,gf200:14,gflop:12,gflp:12,ghost:[3,6,7,12,16,58,61,62,73,142,147,192,194,214,229,259,270,271,318,329,333,353,354,357,361,368,428,433,443],ghostwhit:169,ghz:10,giacomo:9,gif:[4,168],gifsicl:168,gigabit:18,gillan:396,gingold:[399,400,402],gio:2,git:[7,12],github:[13,17,193,207,212,391],give:[0,1,2,3,5,6,7,8,9,10,11,12,14,15,16,17,29,54,71,113,124,127,131,144,167,169,175,177,181,182,183,186,192,194,207,229,247,251,252,257,265,267,270,292,318,319,326,329,330,333,335,339,354,357,363,364,380,384,394,408,409,410,418,420,421,423,433,437,443,449],given:[3,5,6,7,9,10,11,12,16,17,22,27,37,44,55,63,64,67,71,113,120,121,138,142,146,152,153,163,164,167,169,172,179,181,184,189,190,192,194,195,199,205,206,207,208,210,216,223,226,228,229,233,250,251,252,253,260,261,267,269,273,275,276,278,280,285,290,291,294,295,296,299,305,313,318,319,333,334,335,339,340,342,343,345,346,347,348,349,350,353,354,355,357,358,360,363,369,370,371,373,380,381,382,383,384,386,387,390,394,395,396,404,405,416,418,421,423,425,426,433,437,447,451,452],gjf:213,gjwagn:7,gko:2,gld:[],gle4md:[207,212],gle:[],glitch:3,glob:434,global:[],glosli:319,glotzer:[270,353],glue:11,gmail:[7,9,13],gmake:[12,17],gmask:[3,448],gnu:[0,7,12,17,18],gnuplot:[11,13],goal:[5,12,39],goddard:[6,9,25,261,262,263,314,357,363,392,393,435],goe:[12,54,120,144,166,226,326,329,352,356,362,371,374,397,416,426,430],gold:[70,169],goldenrod:169,goldman:260,gone:3,good:[1,3,6,12,17,41,73,118,142,143,188,213,227,229,261,267,273,285,318,328,329,334,347,354,355,384,407,418,432,437,441],googl:210,gordan:120,gordon:6,gould:[6,150,435],gov:[0,7,9,13,334,355,358,447],govern:216,gpl:[0,7,8,12],gpu1:333,gpu:[],gpuid:333,gpun:333,grab:[3,6],gracefulli:3,grad:[6,175,200,228],gradient:[6,7,8,12,13,192,200,208,209,228,247,262,286,290,324,325,328,379,393,407],graduat:255,graft:191,grai:169,grain:[5,6,7,9,29,36,40,54,67,144,147,156,172,251,255,270,278,362,395,435],gram:[181,184,185,355,447],grama:[9,263,393],gran:[],grand:[3,172,179,205],granflow:5,granular:[],graph:11,graphen:427,graphic:11,grasp:5,gravit:208,graviti:[],grdient:178,great:[3,13,260],greater:[1,3,10,61,86,142,169,192,206,229,251,283,297,333,338,340,342,343,384,418,420,423,426,432,437,448,449],greathous:13,greatli:[118,437],green:[2,6,91,168,169,252,253,286,339],green_kubo:6,greenyellow:169,greffet:265,greg:[7,9],grest:[45,46,191,278,319,343,361,373,435],grew:71,grid:[3,12,41,62,118,132,143,146,188,216,265,278,290,291,318,319,417,420,423,425,427,432],grigera:6,grime:40,grmask:[3,448],gromac:[],gronbech:[213,318],groot:353,ground:[6,357],group1:[126,147,329],group2:[88,126,145,147,329],group2ndx:[],group:[],group_id:11,groupbig:278,groupid1:[219,270],groupid2:[219,270],groupid:423,groupnam:329,grouptyp:205,grow:[3,8,177,194,195,211,213,229,251,292,361,423,435],grow_arrai:8,grow_reset:8,growth:[6,285],gsmooth_factor:380,gstyle:[3,420],gtl:7,gtx285:14,gtx450:14,gtx460:14,gtx470:14,gtx560:14,gtx580:14,guarante:[65,69,79,92,108,115,144,147,167,199,261,317,321,433],guess:[3,167,257,424],gui:[7,11],guid:[1,17,40,78,80,99,100,101,172,222,223,291,389,398,399,400,401,402,403,433],guidelin:[1,8,14,15,16,17,18,19,318,407],guidlin:17,gullet:380,gumbsch:325,gunsteren:[257,281,377],gunzenmul:7,gunzip:12,guo:[6,20,150,156,344,435],gwald:3,gyrat:[],gzip:[3,12,167,168,169,289,328,423,424,428],h12:360,h2o:[40,327],haak:[257,281],had:[3,6,11,13,59,63,167,169,170,183,186,191,192,206,207,209,213,214,215,227,229,231,232,233,234,235,246,247,249,256,257,278,281,282,283,290,353,354,361,404,425,429,432,438,441],hafskjold:6,half:[1,3,6,8,16,17,39,41,58,59,146,168,180,188,194,213,229,290,295,299,329,333,336,339,347,357,423,425,426,433,443],halfwai:[41,168,169],halsei:361,halt:[41,169,188,209,303,440],halv:168,ham:[38,56],hamak:[295,299,347,394],hamilton:70,hamiltonian:[207,229,230,282,357,432],hammond:[318,319],han:355,hand:[3,6,19,54,144,162,166,168,216,226,321,349,357,423,426,433,436],handl:[3,9,16,168,193,263,333,336,357,378,393,421,437],hang:[3,420,421],happen:[3,6,8,12,15,18,61,116,148,169,179,182,329,333,421,424,431],happi:8,haptic:210,hara:409,hard:[1,219,263,269,270,354,426],harden:397,harder:[295,299,443],hardi:[178,214,318,319,443],hardwar:[1,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,175,187,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,294,304,306,307,308,309,312,314,318,319,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,436],hardwir:[3,17,296],hardy2:319,harm:336,harmon:[],harmonic_fix_wal:379,harpertown:18,harrison:335,hart:278,hartre:[336,355,357,447],hasan:9,hash:[39,423],hassl:269,hat:[6,10,228],have:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,45,46,47,48,49,51,53,54,56,57,59,63,64,65,66,67,69,70,71,72,73,75,77,81,86,90,91,93,103,104,105,106,109,112,113,114,115,116,120,121,122,123,124,125,127,131,133,136,137,139,140,141,142,144,145,146,147,148,150,151,153,154,155,156,158,159,161,162,164,166,167,168,169,170,175,177,179,180,181,182,184,185,186,187,188,189,190,191,192,194,195,200,201,202,204,205,206,207,208,209,210,211,213,214,215,216,219,224,226,227,229,231,232,233,234,235,236,241,244,246,247,248,249,251,253,255,256,257,259,260,261,262,265,268,270,272,273,278,279,281,282,283,284,285,289,290,291,292,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,312,314,318,319,321,324,325,326,327,328,329,330,333,334,335,336,337,339,340,341,342,343,344,345,347,348,349,352,353,354,355,356,358,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,389,390,392,393,394,395,397,406,407,408,409,410,412,414,415,416,417,418,420,421,423,424,425,426,427,428,429,430,431,432,433,435,437,438,440,441,443,447,448,449,450,451,452],haven:421,hayoun:265,hayr:213,hbcut:392,hbnewflag:392,hbond:[],hbond_cutoff:393,hcp:[64,67,73,321,380],he1:143,head:[6,21,151,304,359,363,392,393,438],header:[3,6,7,8,12,145,167,168,169,170,181,182,183,184,185,186,227,260,267,271,290,327,334,339,355,420,423,433,440],heal:432,heat:[],heatconduct:[],heavi:278,heavili:[41,188],heavisid:290,hecht:278,heenen:9,height:[168,195,256,328,359],heisenberg:9,held:[6,71,278,328,361],helic:156,helium:337,helix:[],hello:421,help:[3,8,12,14,15,16,17,18,19,167,192,194,227,316,339,408,410,450],henc:[1,3,13,20,21,26,32,35,36,70,71,108,124,134,151,181,229,263,278,294,295,299,301,304,306,309,312,319,349,359,377,390,425],henderson:53,hendrik:9,henin:[9,193],henkelman1:[228,328],henkelman2:[228,328],henkelman:[228,325,328],here:[1,2,3,4,5,6,7,8,10,11,12,13,14,15,16,17,18,19,22,37,41,44,55,63,68,69,70,71,118,124,142,143,152,155,163,167,168,169,172,181,188,191,194,205,206,214,216,251,260,263,265,271,290,295,298,300,301,303,305,313,317,326,328,332,333,335,336,339,346,358,360,363,364,368,390,394,405,407,416,421,428,443],herist:291,herrmann:278,hertizian:296,hertz:[],hertzian:[6,296,361,405],hertzsch:361,hess:318,hessian:[5,325],heterogen:105,heurist:[291,424],hex:[3,17,144,321],hexagon:[67,380],hey:[110,121],hf4:143,hfo:348,hftn:[325,326,328],hg1:143,hg2:143,hgrid:278,hibb:253,hidden:[17,421],hienergi:301,hierarch:[7,432],hierarchi:[319,343,344,369,370,373,383,432],higdon:[9,378,379],high:[1,3,6,7,9,19,41,164,168,188,192,199,214,227,286,290,293,319,325,326,333,339,357,360,394,407,416,420,432,437,443],higher:[1,14,120,147,169,189,190,195,211,256,265,285,298,300,326,357,365,448],highest:[195,303,327,328,448],highli:[3,6,7,9,144,168,194,213,229,241,260,270,324,326,357,418,437],highlight:[6,7,10,13],hight:359,hilger:[318,319],hill:253,hill_height:13,him:9,hint:12,histo:[],histogram:[1,6,12,63,116,142,172,182,183,186],histor:358,histori:[],hit:[3,278,297],hmaktulga:[7,9],ho3:143,hoc:312,hocknei:[318,319],hoh:[6,349,369,373],hold:[6,33,59,71,157,181,194,221,254,269,270,275,326,328,361,377,415,434],holdem:269,holder2:319,holder:[318,319],hole:275,holian:[233,371],holm:[251,319],holonom:289,home:[11,12,170],homebrew:12,homepag:[168,210],homogen:[247,384],hone:253,honeydew:169,honor:170,hook:[],hookean:361,hoomd:170,hoover:[6,7,8,134,172,198,213,214,229,230,231,232,233,234,235,246,247,248,249,253,257,265,270,281,282,283,288,353,443],hop:[191,328,339],hope:[5,13,17,41,42,188,431],hopefulli:[8,326],horizon:389,horn:6,host:[3,12,16,17,193,333],hot:[6,209,230],hotpink:169,hottest:286,hour:12,hove:380,how:[],howev:[1,2,3,6,7,11,12,15,16,17,36,39,41,71,88,91,104,118,120,143,164,167,168,169,182,186,188,191,192,195,198,205,206,207,212,213,214,215,216,219,229,251,253,256,259,260,265,270,271,278,279,281,282,285,286,290,291,292,293,294,319,321,323,324,328,333,345,347,355,356,361,364,380,388,390,406,407,410,418,420,421,424,431,437,440,441,443,448,449],howto:[6,63,71,122,123,125,127,130,131,132,133,134,136,137,172,213,214,229,257,281,282,283,349,363,369,373,449],hoyt:178,hpc:[1,15],hsw:17,htm:355,html:[0,4,8,11,12,15,212,359,379,432],htmldoc:0,htst:437,http:[0,6,7,11,13,14,15,193,207,210,212,334,355,378,391,392,393],htype:[349,369,373,377],hubbard:350,huge:[12,146,241,278,423,428,440],huggin:[7,340,342,405],hugh:178,hugoniostat:[4,172,233],hugoniot:[227,233,260],hull:142,hummer:318,hundr:[7,14],hura:6,hwloc:[12,17],hybrid:[],hydrat:359,hydrocarbon:[335,348,357],hydrodyanm:40,hydrodynam:[7,9,40,99,101,216,218,219,220,341,378,379,405,433],hydrogen:[3,6,7,202,265,335,339,349,357,363,369,373,377,392,393,405,423,432,443],hydrostat:[3,192,229,233,257,270],hynninen:[350,359],hyoungki:382,hyper:253,hyperbol:350,hyperspher:120,hyperthread:[16,17],i_0:290,i_1:390,i_csid:6,i_flag1:259,i_mpi_pin_domain:16,i_myflag1:259,i_myflag2:259,i_n:390,i_nam:[113,167,259,280,433],ialloi:380,iatom1:115,iatom2:115,iatom3:115,iatom4:115,ibar:380,ibead:253,ibm:[167,318],icc:[10,12,16],icm:[9,210],ico:64,icosohedr:73,ictp:13,id1:[270,328,368,423,426],id2:[270,274,275,328,368,423,426],id_press:[192,227,229,231,232,233,234,235,257],id_temp:[191,192,227,229,231,232,233,234,235,246,247,249,257,281,282,283],idea:[1,3,6,11,12,41,121,168,169,188,211,251,274,278,286,319,384,431,443],ideal:[6,9,40,73,116,198,205,251,321,378,399,443],idealga:[],ident:[1,3,9,12,39,40,71,120,167,169,183,192,193,206,207,213,214,226,229,251,253,257,265,267,270,319,327,328,333,340,342,349,351,355,371,377,386,392,393,396,416,418,421,424,437,447,448,449,451],identi:333,identif:67,identifi:[1,3,12,38,40,56,70,142,144,164,267,278,301,363,368,380,407,418,420,423,426,437,438,440],idl:[18,437],idn:[270,328],idr:448,ielement:380,ieni:13,ifdef:[8,12],iff:214,iffp:421,ignor:[3,6,11,16,41,71,83,87,98,107,119,148,167,168,169,173,174,182,183,184,186,188,192,193,194,195,205,208,212,213,226,229,233,238,243,257,259,269,270,271,278,281,282,283,289,290,292,295,299,300,301,310,320,323,327,328,333,334,345,346,347,355,356,358,360,367,368,380,386,390,394,406,407,408,409,410,412,418,420,423,424,428,433,435,437,440,448],ihl:278,iii:[6,9,25,261,263,314,363,435],ijk:[308,312,314,339,390,420],ijl:312,ikeshoji:6,ill:[124,134,181,261],illeg:3,illinoi:[210,318,319,378],illog:421,illustr:[1,6,8,11,12,17,251,253,328,364,421],ilmenau:[7,9,14],ilya:[7,9],imag:[],image2pip:168,imageint:3,imagemagick:[4,168],imagin:[275,289,339,356,364,365,381,382,386,390,406,408,409,410,435],imaginari:[6,205,253,423],imbal:[1,41,188],imbalanc:[41,188],imbu:278,imd:[],img:168,immedi:[0,2,3,8,12,144,189,190,195,273,279,280,297,420,421,423,425,437,448,451],immens:3,immers:[216,270],impact:[1,4,6,8,199,285],impart:[3,6,208,278,300],impei:[6,369],implement:[1,3,6,8,9,12,17,18,27,78,87,118,126,132,143,144,152,153,163,181,193,197,207,210,213,216,218,219,220,227,247,250,252,253,259,260,261,263,264,265,273,274,278,285,290,294,312,317,318,319,326,328,333,334,336,339,348,349,351,353,355,356,357,364,369,373,377,380,389,392,393,394,408,410,420,421,432,437,443,448,450],impli:[3,6,40,59,87,121,168,173,174,175,194,200,213,269,281,283,284,318,321,346,421],implicit:[],implicitli:8,implict:350,imporop:327,importannt:226,important:288,important_not:59,impos:[2,6,71,112,133,166,172,175,176,187,200,201,203,208,211,220,221,228,241,251,254,272,275,277,278,285,286,287,288,293,294,295,298,299,300,326,328,330,417,431],imposs:1,improp:[],improper_coeff:[],improper_styl:[],impropercoeff:3,impropertyp:190,imprort:97,improt:[173,174],improv:[0,1,9,39,41,169,188,229,252,333,363,369,384,393,406,409],in3:143,inaccur:[1,3,6,147,227,318],inaccuraci:299,inact:363,inappropri:144,incid:[118,143,195],includ:[],includig:[303,317],inclus:[],incom:210,incompat:[3,11,365],incomplet:[3,11,423],incompress:[230,357],inconsist:[3,148,191,424],inconveni:321,incorpor:[260,339,350],incorrect:[3,127,213,380],incorrectli:[3,321,361,448],increas:[1,3,6,10,18,38,56,57,59,109,118,121,164,167,168,169,189,190,191,194,213,257,268,269,270,286,289,293,318,319,328,333,357,360,393,407,409,421,432,437,448],increasingli:357,increment:[3,11,175,176,187,188,195,200,202,229,274,301,317,332,367,418,421,435,437,448],incur:[14,17,181,184,185,202,290,420],inde:127,indefatig:7,indefinit:287,indent:[],independ:[4,6,11,12,16,17,41,59,63,91,117,119,130,144,166,172,180,181,182,183,184,185,186,188,191,192,193,194,195,206,208,213,214,216,219,229,252,257,261,265,270,271,274,277,288,290,321,361,418,421,440,449],indetermin:[167,169],index:[0,3,6,8,11,12,38,39,40,56,68,69,117,119,164,167,169,180,182,210,212,253,271,290,301,302,303,323,332,384,392,393,407,413,423,438,448],indianr:169,indigo:169,indirectli:[6,448],indistinguish:213,indium:396,individu:[],induc:[],industri:7,ineffici:[3,6,40,64,67,70,72,73,77,120,132,168,194,229,252,318,330],inerti:379,inertia:[],inexpens:[207,432],inf:[2,3,12,293,426],infer:[3,94,96,97,138,175,176,188,189,190,200,210,255,278,286,293,321,346,358,423,435,441],infil:[3,13,270,420],infin:[3,326,428,441],infininti:168,infinit:[3,195,204,211,213,216,252,278,290,296,297,319,321,357,427,447],infinitesim:6,inflect:[350,371],influenc:[3,9,41,80,126,226,256,318,319,384,408,409,410],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,39,41,42,59,61,62,63,68,88,115,117,118,143,144,150,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,203,204,205,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,228,236,237,238,239,240,241,242,243,244,245,250,251,252,254,255,256,257,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,278,279,281,282,283,284,285,286,287,289,292,293,294,295,297,298,299,300,302,316,318,319,322,325,326,327,328,329,331,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,420,421,423,424,425,427,428,430,435,437,438,440,448,450,451,452],infrequ:[6,353,418,437],infti:[350,378,379],ingtegr:339,inher:[318,326,384],inherit:[6,411],inhomogen:[18,290,384],inidividu:326,init:[3,8,12,268],init_fil:290,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,39,40,41,56,57,59,62,71,80,81,86,87,103,104,140,145,146,164,166,167,168,169,170,173,174,177,178,182,188,190,191,192,194,201,205,206,210,211,212,213,214,216,221,225,226,227,228,229,233,241,252,253,254,259,260,265,268,269,270,272,277,278,280,285,287,288,289,290,291,292,295,296,297,298,300,301,303,318,322,325,326,328,335,336,352,353,354,391,392,393,407,418,420,421,423,425,426,428,430,431,433,437,438,441,443,448,449,450,452],initial_integr:8,initial_integrate_respa:8,initialis:391,initialt:290,inlclud:11,inlcud:448,inlin:421,inner2:[344,362],inner:[3,8,16,167,211,303,317,324,325,326,328,332,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,413,414,415,416,432,437],inner_distance_cutoff:363,innergroup:219,innermost:[38,56,331,407,432],innernod:219,innner:375,inordin:291,inorgan:6,inp:[193,303,396],input1:[65,68,69,79,92,108,113,114,115,117,119,280],input2:[65,68,69,79,92,108,113,114,115,117,119,280],input:[],input_doubl:3,insensit:12,insert:[3,5,7,8,12,59,144,172,195,205,211,256,318,396,404,421,427,443],insid:[2,3,6,8,11,71,144,167,169,180,184,185,195,196,202,205,211,216,219,256,270,278,295,297,298,299,300,301,316,321,371,421,422,423,425,426,433,437,448],insight:[6,13],instabl:[216,352],instal:[],instanc:[6,11,193,207,297,359,364,384,390,421,443],instantan:[6,63,191,192,206,207,229,233,252,257,260,265,267,270,285,429,441],instanti:[6,11,12,178,364,420],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,63,70,71,90,117,123,126,148,164,167,174,181,183,184,185,186,188,192,193,213,216,219,220,252,258,268,270,280,298,316,318,319,322,329,333,342,343,355,368,370,377,380,418,426,430,437,439,443,448],institut:[9,210,255],instruct:[3,6,8,11,12,13,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,122,131,142,150,151,153,154,155,156,158,159,161,162,164,165,168,175,187,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,294,304,306,307,308,309,312,314,319,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,432,443],insuffici:[3,6,12],insult:229,insur:[3,6,11,12,17,39,40,61,73,102,104,144,145,164,167,168,169,175,189,190,195,200,201,202,203,205,208,213,225,258,259,268,270,278,290,295,299,300,301,303,317,327,329,333,347,360,364,388,394,407,420,421,423,424,428,431,432,440,441,448,449],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,113,115,117,119,120,142,144,147,148,150,154,155,159,164,166,167,168,169,179,181,184,185,189,190,191,195,197,203,205,206,207,210,213,214,215,216,252,255,256,259,260,265,270,278,280,282,285,289,290,308,318,321,341,353,354,367,380,392,393,396,418,420,421,423,431,432,433,437,440,448,449],integr:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,8,12,13,36,206,391,423],intens:[1,3,6,9,63,66,74,75,86,89,90,91,93,103,104,105,106,112,114,116,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,139,140,141,143,172,181,182,183,184,185,186,188,189,190,191,199,202,209,219,227,229,233,267,270,271,278,286,290,292,293,440,441],intepol:448,inter:[14,18,42,61,62,124,147,148,167,191,213,215,228,262,270,318,328,339,433,443,448,450,452],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,77,79,87,88,92,107,108,110,112,115,116,120,121,123,137,138,142,145,146,147,148,149,150,152,156,157,163,167,172,173,174,189,190,191,204,205,210,211,213,215,219,241,251,253,255,261,263,269,270,278,279,285,290,294,295,296,299,300,305,306,307,309,313,318,319,326,327,328,329,330,331,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,393,394,395,396,397,404,405,406,408,409,410,411,412,413,414,415,416,418,421,423,425,427,428,432,433,435,440,441,443,450],interatom:[3,4,7,144,167,228,287,288,334,339,355,357,365,380,409,448],intercept:118,interchang:6,interconnect:18,interconvert:357,intereract:39,interesect:299,interest:[1,5,7,8,9,11,13,71,143,253,285,288,319,356,379,392,393,421,448],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:[1,3,6,7,9,10,12,13,45,46,64,87,107,110,172,178,257,278,295,299,319,321,326,335,338,342,343,344,345,347,352,360,362,363,364,367,368,369,370,371,373,374,376,377,383,384,390,394,395,400,405,412,435,443],jonsson:[73,228,325,328],jorgensen:[6,161,349,369,373],joul:447,journal:[138,156,178,263,319,355,392,393,399,400,402],jparam:[3,190],jpeg:[3,12,168],jpeglib:12,jpg:[4,8,12,167,168,169,451],jpg_inc:12,jpg_lib:12,jpg_path:12,jpl:[7,9],jth:448,jtype1:116,jtype2:116,jtype:[3,116,190,413],jtypen:116,judg:437,judici:6,julien:9,jump:[],june:170,just:[3,6,8,9,11,12,13,17,19,22,29,42,44,59,61,91,107,110,116,121,123,137,152,167,181,184,185,194,198,202,219,226,257,259,270,285,290,301,303,305,327,328,333,335,338,346,364,390,412,421,425,427,428,430,431,443,448,451,452],justo:356,jusufi:[350,359],jut:299,jzimmer:9,k11:91,k22:91,k33:91,k_b:214,k_d:443,k_sigma:339,k_ub:20,kadiri:67,kamberaj:270,kappa:[6,91,286,349,369,414,415],kappa_:290,karplu:87,karttunen:216,kate:[],kayser:350,kbit:169,kboltz:278,kbp:169,kbt:265,kcal2j:91,kcal:[210,432,443,447],kde:13,ke_eta_dot:229,ke_etap_dot:229,ke_omega_dot:229,keblinski:349,kecom:124,keef:118,keep:[3,7,12,59,71,162,184,190,194,211,252,268,288,293,318,326,349,377,396,418,423,429,431,437,441,448],keflag:3,kei:[6,17,59,278,437],keir:13,kelchner:70,kelkar:293,kelvin:447,kemper:[262,348],kepler30:17,kepler32:17,kepler35:17,kepler37:17,kepler:[1,12,14,15,17,333],kept:[6,172,233,287,288,443],kernel:[7,13,17,100,178,206,207,398,399,400,401,402,403],keword:168,keyboard:12,keyword:[],keywrod:357,kforc:443,khaki:169,khersonskii:120,kick:[175,176,177,200,297],kilogram:447,kim:[],kimviri:[3,365],kind:[1,2,3,6,7,8,9,11,12,17,39,40,41,42,61,62,63,73,117,119,124,167,172,179,181,182,183,188,191,193,197,205,208,226,270,273,278,285,300,328,330,332,339,357,392,393,413,418,423,428,429,436,437,443,448],kinemat:[9,378,379],kinet:[3,6,8,9,63,82,83,84,85,87,91,94,95,96,97,98,112,121,122,123,124,125,126,127,129,130,131,132,133,134,136,137,172,179,181,192,198,209,213,225,227,229,230,231,232,233,234,235,257,260,278,286,293,294,326,357,418,437,441,443],kiss:12,kjl:312,klahn:289,klapp:318,klein:[6,9,178,193,229,230,248,270,369,395],kloss:7,kmax:[3,118,271,318],knc:17,knock:290,know:[3,11,12,41,63,107,116,172,198,212,214,241,278,326,356,365,411,421,424,427,432,443],knowledg:[4,8,168,365],known:[3,12,120,168,252,261,270,287,420,437,449],kohlmey:[7,9,13,18,318,319],kokko:[],kokkos_arch:17,kokkos_cuda:[12,17],kokkos_cuda_opt:17,kokkos_debug:17,kokkos_devic:17,kokkos_omp:[12,17],kokkos_pg:17,kokkos_phi:[12,17],kokkos_use_tpl:17,kolafa:319,kollman:[6,150,435],kondor:391,kone:[287,288],kong2011:252,kong:[9,13,252],konglt:9,koning00a:287,koning00b:287,koning96:[287,288],koning97:288,koning99:287,kooser:13,koskinen:325,kosztin:274,krau:13,kremer:[45,46,435],kress:[381,382],kspace:[],kspace_modifi:[],kspace_styl:[],kspce:12,kspring:228,kstart:269,kstop:269,kth:[206,253],kub:20,kubo:[6,91,286],kumagai:409,kumar:[9,378,379],kuronen:390,kurt:255,l12:380,l_box:357,l_skin:290,la3:143,lab:[5,7,12,111,389],label:[],laboratori:[0,227,260],lack:[3,227,357],lackmann:339,ladd:[247,288],lafitt:383,lag:290,lagrangian:[6,178,227,260,261,443],lagrangian_posit:[227,260],lagrangian_spe:[227,260],lai:417,lambda1:[408,409,410],lambda2:[408,409,410],lambda3:[408,410],lambda:[87,111,118,138,143,216,271,287,288,290,334,356,377,406],lambda_fin:287,lambda_initi:287,lamda:[3,53,278],laminar:403,lamm:6,lammps2pdb:[6,13],lammps_clos:6,lammps_command:6,lammps_extract_atom:6,lammps_extract_comput:6,lammps_extract_fix:6,lammps_extract_glob:6,lammps_extract_vari:6,lammps_fil:6,lammps_gather_atom:3,lammps_get_coord:6,lammps_get_natom:6,lammps_n:[6,12],lammps_open:6,lammps_potenti:[346,348,434],lammps_put_coord:6,lammps_quest:[6,203],lammps_scatter_atom:3,lammps_set_vari:6,lammps_sppark:6,lammpsplot:13,lammpspotenti:346,lammpstrj:[424,428,443],lammpsviri:[3,365],lamoureux:[6,198,411,443],lane:1,lang:443,langevin:[],langevin_drud:[129,197],languag:[6,11,12,17,421,448],lanl:9,lapack:12,laps:291,laptop:7,larg:[0,1,3,5,6,7,8,9,10,12,13,14,16,18,39,40,41,58,59,70,71,109,116,121,124,127,132,144,145,146,156,164,166,167,168,169,181,184,185,188,191,192,194,195,199,205,216,229,241,247,252,255,256,260,265,267,268,269,270,273,275,278,286,290,291,293,295,299,312,318,319,324,326,329,333,347,353,357,360,361,368,384,388,394,407,418,421,423,425,426,430,432,437,440,443,449,452],larger:[1,2,3,6,11,12,13,39,41,56,59,70,71,116,144,146,168,182,183,186,195,209,216,229,247,248,256,261,265,269,270,271,278,285,290,294,295,296,299,318,319,324,325,326,328,329,330,333,339,347,349,350,357,361,369,373,379,384,388,405,412,423,427,428,431,432,437],largest:[3,6,12,39,71,142,144,199,318,326,330,404,407,423,425,431,432,442,448],laroch:265,laser:290,last:[1,2,3,5,6,11,12,15,16,19,38,56,59,61,71,110,117,121,142,164,167,168,169,170,171,181,182,183,184,185,186,188,199,228,268,271,275,278,303,316,326,327,328,329,333,337,338,339,340,347,348,353,355,359,360,362,363,367,370,372,374,375,376,379,383,384,385,394,397,404,407,411,412,414,415,418,419,421,423,424,428,430,431,435,437,438,441,448],lat:380,late:5,latenc:[10,210],later:[6,11,12,16,17,40,59,71,104,146,148,182,195,233,247,255,274,285,301,303,318,326,327,332,333,335,339,421,423,425,427,437,440,448,450],latest:[7,181,182,183,184,185,186,271,425],latex:8,latgen:252,latitud:120,lattc:380,latter:[2,6,11,12,14,15,16,17,18,41,42,87,123,169,173,174,180,181,184,185,188,192,211,220,229,231,232,234,235,255,257,259,261,263,270,278,294,299,317,327,339,341,342,343,344,345,352,369,373,377,387,395,411,418,420,421,426,429,440,448,451],lattic:[],launch:[1,3,6,11,12,18,333,420,421],laupretr:312,lavend:169,lavenderblush:169,lavgevin:194,law:[6,227,331],lawngreen:169,layer:[6,9,71,172,184,286,290,293],layout:[1,3,17,146,420,423,432],lb_fluid:216,lbl:[7,9,142],lbnl:9,lbtype:216,lcbop:[],ld_library_path:[11,12],ldfftw:12,ldrd:7,lead:[2,3,6,12,22,25,39,41,44,59,61,77,87,116,138,142,148,152,169,173,174,183,188,195,207,216,233,260,270,273,278,285,286,293,305,312,318,323,328,333,346,349,369,373,375,417,423,433,443,448,449],least:[3,6,12,18,71,118,143,179,184,207,255,259,294,329,333,364,407,412,421,448],leav:[3,7,11,12,16,17,21,41,57,121,134,151,188,192,195,229,231,232,234,235,257,270,273,304,384,423,427,435],lechman:278,lectur:274,led:[3,5],lee2:380,lee:[178,380],left:[6,11,12,41,107,163,168,169,191,211,250,278,301,303,321,411,423,425,430,448,452],leftmost:[41,188],legaci:12,legal:7,lehoucq:389,leimkuhl:298,leiu:353,lemonchiffon:169,len:433,lenart:[350,359],length:[3,6,8,11,12,18,21,38,39,40,41,44,53,54,55,56,58,59,61,65,68,69,71,74,79,80,82,87,88,89,90,91,92,103,105,107,108,112,114,115,117,118,119,122,123,124,125,126,127,128,129,131,132,133,134,135,136,137,140,142,143,146,151,164,167,168,169,172,179,183,185,186,188,189,190,191,192,194,205,208,216,227,228,229,230,233,241,251,257,267,270,271,273,275,278,285,289,290,292,295,299,319,321,324,326,328,329,331,336,339,340,342,349,350,354,357,359,363,367,369,380,384,392,393,398,407,408,414,415,423,426,431,433,440,441,443,448],lengthi:205,lennard:[1,3,6,7,9,10,12,45,46,87,107,110,172,257,278,295,299,319,321,326,335,338,342,343,344,345,347,352,360,362,363,364,367,368,369,370,371,373,374,376,377,383,384,394,395,400,405,412,435,443],lenoski:[381,382],less:[1,3,6,13,14,15,16,17,18,38,41,56,57,58,59,76,108,115,116,123,137,164,169,181,183,184,185,186,188,190,191,192,194,195,202,211,227,229,251,263,265,271,278,297,298,300,319,321,326,330,333,339,344,360,361,378,379,384,394,406,407,410,415,423,448,449],let:[1,11,12,38,56,127,155,164,182,273,278,296,333,347,407,432,436,443,450],lett:[120,132,207,214,216,227,265,274,287,288,325,339,355,357,360,377,396,443],letter:[2,12,41,57,59,169,188,197,198,214,253,303,332,391],level:[2,3,8,11,12,14,17,167,168,173,174,210,226,228,229,303,319,332,339,343,344,369,370,373,383,392,393,420,432,437,448],lever:404,levin:361,lexicon:7,lgr_po:[227,260],lgr_vel:[227,260],lgvdw:393,li1:143,liang:348,lib:[1,3,9,11,12,14,15,17,264,333,348,365,421,424],libatom:[9,391],libcolvar:12,libdir:11,libfftw3:12,libgpu:15,libjpeg:12,liblammp:[11,12],liblammps_foo:[11,12],liblammps_g:[11,12],liblammpscuda:14,libmpi:11,libmpi_stub:12,libmpich:12,libpackag:12,libpng:12,librari:[],librt:17,licens:[0,7,8,12,168],lie:[6,205,271],lieu:318,life:7,lifo:8,ligand:275,liggght:7,lightblu:169,lightcor:169,lightcyan:169,lightest:285,lightgoldenrodyellow:169,lightgreen:169,lightgrei:169,lightli:275,lightpink:169,lightsalmon:169,lightseagreen:169,lightskyblu:169,lightslategrai:169,lightsteelblu:169,lightweight:278,lightyellow:169,like:[3,4,6,7,8,9,11,12,14,16,17,18,39,42,54,59,128,135,168,170,175,192,193,195,198,200,210,213,214,215,227,229,230,234,235,240,241,246,247,248,249,251,257,259,260,261,265,270,271,278,280,281,282,283,284,285,286,293,294,295,298,299,300,303,318,321,325,328,333,339,347,352,353,357,358,361,363,364,374,375,380,384,396,407,410,414,415,420,421,423,424,425,426,428,433,438,441,443,448,449],likelihood:[118,143,191],likewis:[1,6,10,12,15,18,39,41,71,88,115,178,188,189,190,205,213,214,229,230,233,248,265,278,281,282,283,319,328,334,338,339,349,355,358,405,421,423,435,448],lime:169,limegreen:169,limit:[],limit_eradiu:357,lindahl:318,line:[],linear:[],linearli:[10,117,169,194,252,295,297,298,300,327,328,330,423,448],lineflag:[6,423],lineforc:[],linen:169,linesearch:[8,324],ling:[9,13],lingo:[11,365],link:[5,6,7,8,9,11,12,13,14,15,17,18,22,37,44,55,63,152,163,168,172,190,210,214,255,264,266,274,275,305,313,336,346,380,391,392,393,405,411,421],linker:12,linkflag:[12,16],linux:[10,11,12,15,168,170,210],linuxamd64:424,liouvil:229,lip:13,lipid:[4,9,10,13,29,270],lipton:255,liquid:[6,7,9,29,39,40,41,59,87,121,130,142,188,192,194,205,229,257,260,265,285,352,384,387,409,432],lisal:404,lism:9,list:[],listen:[210,212],listfil:368,liter:[423,434],literatur:[8,380,406],lithium:357,littl:[1,3,12,64,229,329,418,426],littmark:[380,405,410,416],liu:[363,393],lj1043:[],lj126:[],lj12_4:395,lj12_6:395,lj1d:252,lj6:3,lj93:[],lj96:[],lj9_6:395,lj_flag:335,llnl:[5,7],lmp1:11,lmp2:11,lmp2arc:[],lmp2cfg:[],lmp2vmd:[],lmp:[11,421,443],lmp_auto:12,lmp_cuda:[14,17],lmp_foo:12,lmp_g:[6,11,12,13,17,317],lmp_gpu:15,lmp_ibm:[12,317],lmp_inc:12,lmp_intel_cpu:16,lmp_intel_phi:16,lmp_kokkos_cuda:17,lmp_kokkos_omp:17,lmp_kokkos_phi:17,lmp_linux:[4,6,12],lmp_mac:12,lmp_machin:[1,12,14,15,16,18,19,333],lmp_mpi:[12,253],lmp_mvapich:17,lmp_omp:18,lmp_openmpi:17,lmp_opt:19,lmp_win_mpi:12,lmp_win_no:12,lmpptr:[11,421],lmpqst:203,lmpsdata:13,lmptype:[3,12,203],load:[1,3,4,7,9,11,12,16,17,18,41,168,170,172,188,210,260,333,348,420,421],loadabl:11,loca:169,local:[],localhost:210,localized_lambda:178,localonli:12,localvector:63,locat:[3,6,8,9,11,12,27,61,116,118,142,143,153,164,167,195,196,216,277,288,299,324,346,349,358,359,369,371,373,411,420,423,424,426,433,435],lock:[3,332,448],lockstep:[192,229,257,270],log:[],logarithm:448,logfil:[0,3,6,12,258,322,419],logfreq2:448,logfreq:[169,430,439,448],logic:[7,11,12,17,41,144,188,301,303,418,420,421,424,432,437,448],lomdahl:[233,371],london:[13,205,393],lone:[392,393],longer:[1,3,6,8,12,13,54,116,167,169,180,181,182,183,184,185,186,189,205,213,251,255,260,270,273,285,295,299,301,324,333,335,361,420,428,432,437,445],longest:[41,188,189,329,412],longitudin:275,look:[1,3,6,8,11,12,18,54,61,167,168,171,346,396,407,443,448],lookup:[3,39,164,384,407],lookup_t:271,loop:[3,4,6,7,11,12,18,39,42,65,68,69,79,88,92,108,115,116,121,168,181,184,185,189,190,199,285,301,303,317,320,326,328,329,331,332,354,418,419,421,427,428,431,432,437,442,448,449],loopa:[303,317,332],loopb:[303,317,332],loopvar:448,lopez:[229,230],lorant:261,lorentz:143,lose:[6,58,59,146,192,194,214,229,361,423],loss:[6,447],lossi:168,lossless:168,lost:[3,12,13,57,102,195,268,278,384,423,424,425,432,440],lot:[18,274,318],low:[1,3,6,7,12,41,127,142,167,168,188,198,214,247,265,270,286,293,319,393,407,415,437,443],lower:[2,3,6,9,11,12,41,57,59,71,88,133,166,168,169,182,183,184,185,188,192,198,210,213,214,216,229,260,265,286,293,295,296,301,302,318,321,332,350,380,437,444,446,449],lowercas:168,lowest:[120,303,327,433,437,438,448],lsfftw:12,lsurfac:290,lu3:143,lubric:[],lubricateu:[],lubricuteu:238,lucki:12,luigi:13,lumped_lambda_solv:178,lussetti:286,lustig:[7,13],lybrand:319,lyulin:312,m4v:168,m_c:443,m_d:443,m_eff:[296,361],m_fill:3,m_i:276,m_lambdai:389,m_taubi:389,m_u:216,m_v:216,m_yield_stress:389,mac:[12,14],mac_mpi:12,mach:9,machin:[1,3,4,6,7,10,11,12,14,15,16,17,18,19,167,168,210,291,318,324,326,331,333,420,425,430,431,432,449,452],mackai:[9,216,218,219,220],mackerel:[6,20,150,214,344,435,443],maco:168,macro:17,macroparticl:354,macroscop:[7,208,227,389],made:[3,6,11,12,15,16,33,41,42,50,64,145,157,167,168,170,172,173,174,179,188,195,199,210,219,256,264,268,270,288,301,310,329,333,360,361,364,392,394,397,420,425,427,433,436,444,446,449,450],madura:[6,369],magazin:355,magda:295,magenta:169,magic:[3,11],maginn:[138,293],magnitud:[6,70,105,108,113,144,166,167,169,195,196,208,209,211,213,274,275,277,278,285,296,319,326,352,361,433],mai:[0,1,2,3,6,7,8,11,12,13,14,15,16,17,18,29,38,39,40,41,56,58,59,61,63,65,68,69,71,79,86,87,88,89,90,92,102,103,105,107,108,109,110,112,113,114,115,117,118,119,120,121,123,124,132,133,137,138,142,143,144,145,146,147,148,163,164,166,167,168,169,170,172,173,174,175,177,179,181,182,183,184,185,186,187,188,189,190,192,194,195,198,199,200,202,205,206,207,209,210,211,213,214,215,216,217,219,224,225,226,227,229,230,233,241,244,252,253,256,257,258,259,260,262,265,267,268,269,270,271,272,273,274,278,280,281,282,285,286,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,316,317,318,319,321,324,325,326,327,328,329,330,331,333,336,338,339,347,353,357,361,364,365,375,377,379,380,381,382,384,392,393,395,396,404,407,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,435,437,440,441,443,448,449,450,452],mail:[3,7,9,12,301],main:[3,6,8,12,210,216,270,287,288,355,411,421,438],mainboard:1,mainli:[333,387],maintain:[8,9,13,39,129,190,194,247,278,291,325,334,355,432,435],major:12,make:[],makefil:[3,7,9,11,12,13,14,15,16,17,18,19,167,319,333,421],makelist:12,maks:361,malloc:[3,12],manag:[5,8,12,167,210,253,280,432],manbi:396,mandadapu:178,mandatori:[8,193],manh:339,mani:[1,2,3,4,5,6,7,8,9,12,13,14,15,16,17,18,38,39,41,42,56,61,63,68,71,88,91,102,116,124,144,145,164,166,167,168,169,170,172,173,174,175,179,180,181,182,183,184,185,186,188,189,190,191,192,194,195,202,205,206,209,210,216,217,225,227,229,230,233,241,250,251,252,256,259,261,262,263,265,267,270,271,273,278,289,290,292,301,303,318,326,327,328,329,331,333,346,348,354,357,359,363,364,396,405,407,408,410,421,423,425,427,428,430,431,432,433,435,436,437,438,448,449,452],manipul:[12,41,188,210,349,390,434],manner:[2,3,6,9,11,17,41,121,140,173,174,175,176,183,188,194,199,200,203,209,213,214,229,234,235,246,247,249,264,281,282,283,286,287,288,293,295,299,303,319,327,328,332,333,355,357,364,367,378,412,418,420,423,424,425,426,428,432,437],manolopoulo:212,mantissa:3,manual:[0,1,3,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,58,63,68,71,109,112,118,122,123,125,126,127,130,131,132,133,134,136,137,143,150,151,153,154,155,156,158,159,161,162,164,167,168,170,175,184,187,201,204,208,212,213,214,228,229,231,232,233,234,235,236,239,242,244,245,246,247,249,257,259,262,270,271,272,273,281,282,283,293,294,303,304,306,307,308,309,312,314,319,328,332,333,334,335,337,338,340,341,342,343,344,345,347,348,349,351,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,418,432,436,437,438,441,448],manybodi:[3,7,8,9,12,121,326,334,335,339,348,355,358,364,366,386,390,406,408,409,410,435],map:[2,3,11,12,17,18,39,59,64,71,118,120,132,143,144,166,168,169,178,184,252,269,318,319,321,328,334,335,339,348,355,356,358,364,365,366,380,381,382,384,386,390,391,392,393,396,404,406,407,408,409,410,420,423,425,437,448],map_fil:252,mapflag:12,march:380,margin:437,mari:13,mark:[362,377],marker:258,maroon:169,maroonmpi:11,marrink:362,marsaglia:[3,206,207,213,214,265],marseil:9,martin:[252,380],martinez:179,martyna:[229,230,270,432],mashayak:17,mask:[3,251,448],mask_direct:178,mass:[],mass_matrix:178,massdelta:273,massiv:[0,168,216,253,286,293],massless:[6,214,319,349,369,373,377,443],masstot:270,master:[3,328,418,437],mat:[67,178,348,409],match:[3,6,8,9,11,12,17,38,41,56,59,71,116,127,164,169,170,188,191,194,210,229,230,247,267,271,278,285,318,319,339,363,375,380,391,392,393,407,416,417,421,423,424,425,428,432,437,443,448],mater:[73,334,382,390],materi:[6,7,9,59,70,147,177,178,194,205,211,227,251,257,265,286,290,296,349,355,356,357,361,365,380,381,389,392,393,418,423,437,443,447],material_fil:178,math:[],mathemat:[118,120,143,144,173,174,175,176,187,192,200,206,208,209,211,213,214,258,272,281,282,283,295,298,300,396,419,426,433,449],mathrm:214,mathtt:214,matlab:[],matric:[9,120,207,252,360],matrix:[3,6,9,91,142,182,192,207,252,261,318,321],matter:[6,9,12,39,57,59,71,126,184,290,329,335,351,355,357,380,395,408,410,416],mattson:[112,121],max2theta:143,max:[3,6,8,12,15,18,71,117,169,183,188,190,192,195,256,273,278,303,321,324,326,328,329,333,418,423,437,441,448],max_alpha:8,max_cell_s:354,max_group:3,maxangl:205,maxbodi:3,maxbond:[3,190],maxedg:142,maxev:[326,418,437],maxfoo:8,maxim:[285,328],maximum:[3,6,8,15,17,25,41,42,45,53,54,57,59,61,116,117,118,142,143,145,146,166,167,177,182,183,188,190,194,195,199,205,241,251,256,261,273,278,291,318,319,324,328,329,336,339,354,359,378,379,423,426,431,441,448,449],maxit:[261,326,418,437,441],maxsize_restart:8,maxwel:[17,250],maxwell50:17,maxwell52:17,maxwell53:17,maxx:390,mayb:13,mayer:[7,340,342,405],mayo:[6,7,13,25,314,363,435],mbt:151,mbyte:[12,265],mcdlt:[134,209],mcgraw:253,mdash:443,mdregion:178,mdump:[41,188],meain:6,meam:[],meam_sw_splin:382,meamf:380,mean:[1,2,3,4,6,7,8,10,11,12,17,22,34,37,38,39,41,42,44,52,54,55,56,57,59,61,63,68,71,76,77,82,84,85,87,91,103,104,105,112,113,114,115,116,117,120,121,122,123,125,126,127,130,131,132,133,134,136,137,138,144,145,147,148,150,152,160,163,164,165,166,167,168,169,170,172,173,174,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,200,203,205,206,207,208,209,211,213,214,215,219,226,229,231,232,233,234,235,241,246,247,249,251,253,255,256,257,259,265,267,268,270,272,273,274,275,278,280,281,282,283,285,286,289,290,292,293,294,295,296,297,298,299,300,301,305,306,307,309,311,313,318,319,321,323,324,326,327,328,329,331,333,336,340,342,343,344,346,349,353,354,355,357,360,361,363,364,367,369,370,373,380,383,384,387,388,390,392,393,394,395,406,407,408,409,410,412,415,417,418,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,437,438,440,441,443,447,448,449,450,452],meaning:[116,364],meaningless:[67,285],meant:[6,270,411,427],measur:[],mech:389,mechan:[6,8,9,11,12,17,178,209,253,264,339,357,365,371,417,421,423],mechanic:264,media:168,medium:415,mediumaquamarin:169,mediumblu:169,mediumorchid:169,mediumpurpl:169,mediumseagreen:169,mediumslateblu:169,mediumspringgreen:169,mediumturquois:169,mediumvioletr:169,mee:285,meet:[3,12,145,168,169,190,191,291,428],mehl:334,meloni:39,melros:[378,379],melt1:170,melt2:170,melt3:170,melt:[4,10,191,252,339,409],mem:15,member:[147,255,339],membran:[29,250,415],memori:[1,3,5,6,7,8,9,12,15,16,17,18,39,40,60,71,169,181,184,185,206,207,265,290,316,329,333,339,384,388,393,420,423],memory_usag:8,mendelev:355,mention:[1,6,7,11,42,194,209,216,233,295,321,328,335,392,393,425,448],menu:[168,210],mep:[228,328],mer:[4,10,191],meremianin:120,merg:[3,5,423],merz:[6,150,435],mescscop:389,mesh:[1,3,6,7,8,10,12,40,41,42,118,143,178,188,216,271,318,319,354],meso:[],meso_:[],meso_cv:433,meso_rho:[],meso_t:[],mesocop:40,mesoscal:7,mesoscop:[7,99,100,101,222],mess:[3,433],messag:[],met:[8,41,116,188,303,317,319,326,328,332,412,431],metadynam:[9,13,193],metal:[3,5,7,10,40,59,71,133,144,177,178,184,185,194,195,209,211,260,261,265,294,295,297,298,300,319,321,330,334,335,339,348,355,356,357,358,364,366,380,381,382,390,391,406,408,409,410,426,440,441,442,447],meter:[330,447],methan:[260,265],methanol:4,methin:312,method:[1,3,5,6,7,8,9,11,12,13,16,17,19,38,39,40,41,56,64,87,91,110,121,164,172,173,174,178,188,193,203,213,216,220,224,227,229,252,253,260,261,262,263,265,270,273,274,285,286,287,288,293,318,319,324,325,326,328,333,334,336,339,348,349,355,357,358,380,381,382,384,390,405,407,418,420,421,423,424,426,437,443],methodolog:[6,73,121,253,318],metin:[7,9],metric:[3,10,64,426,441],metropoli:[179,205,438],mezei:87,mf1:170,mf2:170,mf3:170,mg2:143,mglob_default_function_attr:12,mgoh:386,miai:265,mic:[12,17],micel:[4,13,276],micelle2d:[],michael:[9,13,382],michel:13,micro:[3,447],microcanon:[236,237,239,240,242,244,245],microelast:389,micromet:447,micropor:205,microscal:378,microsec:447,microsecond:447,mid:[5,59,194,404],middl:[3,6,8,16,22,41,44,77,87,116,133,138,142,148,151,152,169,173,174,180,188,256,268,269,270,286,293,304,305,323,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,378,379,380,381,382,383,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,416,417,421,431,432,433],middlebondtors:[3,151,423],midnightblu:169,midpoint:404,mie:[],might:[3,4,6,7,8,12,14,25,71,203,205,207,270,421,431,448],migrat:[3,8,17,41,42,59,61,65,69,79,92,108,115,167,172,188,251,259,265,278,318,330,333,431,450,452],mikami:[6,229,230],mike:[7,9,13,15,16],mil:[9,355],mill:325,miller:270,million:[3,7,10,39,41,71,188],mimic:[6,11,42,54,214,227,256,349,359,369],mimim:[192,328],min2theta:143,min:[3,4,6,8,12,117,120,169,183,318,321,404,418,437,448],min_cap:3,min_cg:8,min_clearstor:8,min_dof:8,min_modifi:[],min_popstor:8,min_post_forc:8,min_pre_forc:8,min_pushstor:8,min_setup:8,min_setup_pre_forc:8,min_step:8,min_stor:8,min_styl:[],minarea:142,mincap:393,mind:[7,206,252],mine:[12,88,134,135,172,301,445],minim:[],minima:[156,314],minimi:[328,412],minimizaiton:328,minimizi:265,minimum:[3,25,26,27,42,45,57,59,86,105,117,142,143,145,147,153,166,167,168,177,183,192,193,199,212,228,267,269,271,278,295,299,303,314,318,321,324,325,326,328,329,344,357,360,362,363,369,371,373,378,379,393,395,404,418,431,437,448,449],minlength:142,minmiz:[8,192],minn:9,minord:[3,318],mintcream:169,mintmir:[7,261,349,405],minu:[12,59,124,194,303,328,448],minut:[4,8],mirror:[61,297],misc:[],miscellan:[2,178],mishin:[334,405],mismatch:[3,6],miss:[3,5,12,147,183,205,241,265,278,368,384,440,441],mistak:[3,448],mistakenli:3,mistyp:3,mistyros:169,mitchel:[6,111,126,318,319,351,389],mitchell2011:389,mitchell2011a:389,mitur:337,mivi2:265,mix:[1,3,6,9,14,15,16,71,115,183,184,291,318,319,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,421,423,436,443,450],mixtur:[6,40,229,270,278,300,347,380,423],mixture_ref_t:380,mjpeg:168,mkdir:434,mkl:12,mkmk:252,mkv:168,mldivide3:3,mlpark:7,mlutipl:186,mn2:143,mn3:143,mn4:143,mo3:143,mo5:143,mo6:143,mobil:[6,105,121,122,123,125,130,137,168,270,301,302],moccasin:169,mod:[],mode:[1,3,6,9,11,12,13,14,15,16,17,18,61,66,75,88,90,93,104,106,114,116,117,124,139,141,142,143,167,168,169,183,186,193,194,203,207,229,253,265,274,278,318,330,333,349,357,420,425,430,432,441,447,452],model:[],model_ar_p_mors:365,modern:[12,213,215],modest:[1,331],modif:[6,13,87,380,394,410,443],modifi:[],modify_param:8,modin:178,modul:[3,9,11,12,13,193,265,421],modular:8,modulo:[3,448],modulu:[257,361,380,389],mofil:424,mol1:448,mol:[3,9,71,113,144,146,147,167,169,193,195,205,210,213,256,259,270,273,280,352,360,395,432,433,443,448],molchunk:[66,75,90,93,104,106,124,139,141,181],mole:[179,355,447],moleclu:[189,190,195,202],molecul:[],molecular:[0,2,3,5,6,7,8,9,12,13,39,40,53,71,108,113,115,122,123,125,127,130,131,132,133,136,137,144,145,146,147,148,156,167,170,178,190,193,205,212,252,253,260,264,265,269,274,289,290,319,327,336,337,339,343,354,357,364,405,423,424,425,427,428,432,433,435,441,442,443,448],molfil:[],molfrac:[195,256],molnar:274,molp:109,moltempl:[],mom:[6,91,269,449],momementum:[123,231,234,237,238,239,246],momemtum:66,moment:[3,6,40,42,82,84,85,106,113,123,137,144,165,167,213,216,219,244,256,270,276,327,352,356,423,433,443,447],momenta:[207,238,293,357],momentum:[],momon:191,monaghan:[9,399,400,402],monitor:[3,6,96,97,127,192,194,195,202,210,213,227,229,256,258,260,270,273,278,326,328,352,441],mono:[73,378],monodispers:[3,296,341,361,378,379],monom:[13,54,191],monoton:[3,274,289,328,437],monoval:319,mont:[6,7,9,172,179,191,205,270,285,354,405],montalenti:[418,437],month:0,moor:[17,121],more:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,58,59,61,62,63,64,65,67,68,69,70,71,72,77,78,79,80,83,86,87,88,90,92,96,97,98,99,100,101,102,103,105,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,126,127,128,130,131,132,133,135,136,137,138,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,172,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,278,280,281,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,313,314,316,318,319,321,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,418,419,420,421,423,424,426,427,428,429,430,431,432,433,434,435,436,437,438,440,443,448,449,450,451,452],morefoo:8,moreov:[189,190],morri:[],morriss:[132,247],mors:[],morse_f:407,mosel:325,mosi2:380,moskalev:120,most:[0,1,2,3,4,5,6,7,8,10,11,12,15,17,18,19,37,39,41,55,71,108,132,142,163,167,168,169,181,183,184,185,186,188,189,190,192,209,229,230,253,258,259,260,261,270,271,291,293,301,303,313,319,325,329,331,333,335,357,360,380,391,392,393,410,418,419,420,425,432,437,441,448,450],mostli:[8,9,11,13,71,146,168,329,423,432,435,448,451],motiion:6,motion:[3,6,7,9,42,86,97,122,123,125,127,129,130,131,132,133,134,136,137,194,198,207,216,219,220,226,229,230,233,247,251,253,255,265,269,270,286,290,296,299,328,352,357,378,379,426,432,443],motiv:251,mous:210,mov:168,move:[],movement:[3,6,12,226,285,326,441],movi:[],mp4:168,mpeg:168,mpg:168,mpi4pi:11,mpi:[],mpi_allreduc:[270,421],mpi_barri:1,mpi_cart:420,mpi_cart_cr:420,mpi_cart_get:420,mpi_cart_rank:420,mpi_cart_shift:420,mpi_comm:6,mpi_comm_world:11,mpi_get_processor_nam:420,mpi_inc:12,mpi_lib:12,mpi_lmp_bigint:3,mpi_lmp_tagint:3,mpi_path:12,mpi_wtim:12,mpicc:11,mpich2:12,mpich:[12,14,15,16,17,18,333],mpicxx:[12,16,17],mpiexec:[12,14,15,16,17,18,333],mpiio:[3,167,169,425,430,452],mpirun:[6,11,12,14,15,16,17,18,19,253,317,333],mplayer:168,msd:[],msi2lmp:[],msi:13,msm:[],msmse:[118,143,271],msst:[],mtchell2011:389,mtchell2011a:389,mtd:193,mth:[8,119,169,440],mtk:[229,230,233],mtotal:327,mu_j:29,muccioli:360,much:[1,3,6,11,39,167,168,192,260,285,329,330,333,360,394,418,421,437,443,448],mui:[113,167,200,280,423],mukherje:[7,9,255],mulder:289,muller:[6,91,172,286,293,383],mult:8,multi:[],multibodi:[3,61,255],multicent:357,multicor:[1,420,436],multidimension:13,multielectron:336,multilevel:[318,319],multiphys:11,multipl:[],multipli:[3,87,91,116,152,163,173,174,182,213,216,251,257,321,326,335,423,448],multiprocessor:333,multiscal:11,multisect:[41,188],multistag:87,multitud:7,mundi:248,munich:9,murdick:339,murti:409,murtola:318,must:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,57,59,61,62,71,82,84,86,87,104,107,109,112,115,116,117,118,119,123,126,133,137,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,164,165,166,167,168,169,170,173,174,175,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,200,203,205,206,207,209,210,211,212,213,214,216,217,218,219,220,224,225,226,227,228,229,230,231,232,233,234,235,237,238,239,241,244,246,249,251,255,256,257,258,259,260,261,263,265,267,268,269,270,271,272,273,275,277,278,281,282,283,285,286,288,289,290,292,293,295,296,297,298,299,300,301,303,304,305,306,307,308,309,310,312,314,318,319,321,323,326,327,328,329,330,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,423,424,425,426,428,430,431,432,433,434,437,438,440,441,443,447,448,449,450,452],mutli:6,mutlipl:423,mutual:[3,321],mutut:432,muvt:205,mux:[113,167,168,200,280,423],muz:[113,167,200,280,423],mv2_comm_world_local_rank:12,mvapich2:[17,333],mvapich:12,mxn:[12,253],my_ga:205,my_one_wat:205,my_post_process:434,my_qeq:261,my_setup:434,my_swap_region:179,myblock:[195,256],mybox:146,mychunk1:114,mychunk2:114,mychunk:[6,66,75,90,93,104,106,124,139,141],mycmap:423,mycom:183,mydump:[167,169],myer:[5,7],myfil:[420,448],myfix:[179,438],myflux:91,myforc:[167,451],myhug:233,myke:91,mymol:[40,273,327],mympi:11,mymultipli:[421,448],myn:421,mype:91,mypi:448,mypress:224,myramp:121,myrdf:[116,186],myregion:301,myrigid:[83,98,256],mysocket:212,myspher:[169,299],mystr:303,mystress:91,mytemp:[2,102,122,123,125,127,128,130,132,137,224,303,317,332,440,449],myz:423,n_dephas:418,n_f:[260,265],n_hbond:363,n_ij:361,n_ion:290,n_k:206,na1:143,nabla:290,nacl:[4,6,380],nacl_cs_x0:6,nakano:[261,263,328],namd:[7,9,167,210],name1:[138,194],name2:[138,194],name:[0,1,2,3,5,6,8,9,11,12,13,33,42,50,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,157,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,231,232,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,252,253,254,255,256,257,258,259,260,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,291,292,293,294,295,296,297,298,299,300,301,302,303,310,316,317,319,320,322,327,328,332,334,335,339,342,355,356,358,360,361,364,365,366,368,380,381,382,386,390,392,393,396,406,408,409,410,411,413,420,421,423,424,425,426,430,433,436,438,439,441,443,448,449,450,451,452],namespac:[6,8,12],nan:3,nangl:[3,423],nangletyp:[327,423,433],nano:[270,447],nanoindent:70,nanolett:270,nanomet:[167,169,447],nanoparticl:[188,270],nanosec:447,nanosecond:447,nappli:203,narea:3,narrow:[6,164],narulkar:[408,410],nasa:7,nasr:252,natdef:3,nation:[0,7,12,111,389],nativ:[1,6,7,12,16,17,167,170,424],natoli:[9,19],natom1:115,natom2:115,natom:[6,11,39,327,421,423,440,441,448],nattempt:256,natur:[6,9,120,194,229,251,265,296,355,357,358,380,390,420,448],navajowhit:169,navi:[169,355],navier:216,nb3:143,nb3b:[],nb3bharmon:386,nb5:143,nbin:[116,183,184,185,286,293],nbodi:[219,270],nbond:[3,113,423],nbondtyp:[169,327,423,433],nbot:339,nbounc:278,nbrhood_cutoff:393,nbtype:115,nbuild:441,ncall:203,nchar:169,nchunk:[3,6,66,71,75,90,93,104,106,114,124,139,141,181],ncoeff:396,ncount:[181,182],nd3:143,ndanger:441,nden:[6,91],ndihedr:[3,423],ndihedraltyp:[327,423],ndim:184,ndirango:270,ndof:[229,233],ndoubl:423,ndp:443,ndx:302,neal:270,nearbi:[7,62,145,195,226,262,278,299,329,335,378,379,405,415,443],nearest:[3,70,71,73,142,145,216,228,251,285,299,318,368,380,407,448],nearli:[6,18,54,59,188,213,278,357,384,418,421,427,435],neb:[],neb_combin:328,neb_fin:328,neb_log:437,neb_step:437,neb_styl:437,necessari:[6,9,11,12,13,15,17,33,61,87,152,157,163,170,188,192,193,205,206,264,278,291,301,318,333,377,384,423,424,428,431,432,433,437,443,451],necessarili:[12,265,285,306,307,309,321,384,449],necessit:259,need:[1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,19,33,37,38,39,40,41,42,50,54,55,56,58,61,63,64,67,70,72,73,77,82,91,102,104,109,112,120,121,122,123,124,125,127,130,131,132,133,134,136,137,144,146,150,152,157,163,164,166,167,168,169,173,174,175,176,178,179,181,182,183,184,185,186,188,189,190,192,193,194,198,200,203,204,205,209,210,212,213,214,216,222,223,229,241,252,256,257,259,265,269,270,274,278,286,289,290,292,293,294,295,301,310,313,318,319,327,328,329,330,333,334,335,336,337,339,340,341,342,343,344,345,347,348,349,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,418,421,423,424,425,426,428,430,431,433,435,436,437,443,448,450,451,452],needless:[6,329],neeed:9,neelov:319,neg:[3,6,12,27,46,65,69,89,102,108,115,120,121,146,148,153,155,164,168,192,194,195,206,233,251,274,275,289,293,295,300,318,325,358,372,380,405,423,426],neglect:[363,379],neglig:[11,87,229,406],neigh:[3,12,15,333],neigh_modifi:[],neighbor:[],neighborhood:[26,396],neighbour:214,neighobr:[6,349,369,373],neither:[2,3,12,41,63,178,191,194,195,335,341,357,378,379,428],nelem:396,nelement:[334,355],nemd:[],nest:[2,303,315,332,448],net:[3,6,11,39,86,88,125,136,209,251,261,270,379,393],netpbm:168,network:[189,190,210,420],neumann:318,neutral:[3,88,205,318,349,369],never:[7,12,63,71,172,182,192,205,229,251,273,280,291,295,298,300,318,329,355,380,396,420,423,437,440,448],neveri:[3,8,71,175,180,181,182,183,184,185,186,189,190,191,216,217,252,261,262,263,266,267,271,286,292,293,328,428,437],newatom:195,newer:[12,181,380],newfil:[315,317],newli:[195,443,449],newlin:169,newn:270,newt:131,newtemp:[63,102],newtion:[339,390],newton:[],newtonian:206,newtyp:[3,190],next:[],neyt:285,nfile:[3,38,56,164,167,169,407,425,430,452],nfirst:428,nfirt:428,nfreak:271,nfreq:[39,71,180,181,182,183,184,185,186,188,267,271,428],nghost:[3,12],ngp:105,ngpu:333,nguyen:[15,339],nharmon:[],nhc:253,nht:270,ni2:143,ni3:143,ni_000:[118,271],nialh_jea:355,nialhjea:[346,364],nice:[6,8],nickla:382,nimprop:[3,423],nimpropertyp:[327,423],nine:358,ninteg:423,nissila:216,nist:[334,355,447],niter:[41,188],nitrid:349,niu3:[346,355,364],nkb:260,nlast:428,nline:327,nlocal:[3,8,11,12,203],nlog:319,nmax:42,nmin:42,nmol:423,nmpimd:253,nn2:380,nneighmaxdef:3,no_affin:[16,333],no_histori:6,noced:326,nocheck:368,nocit:12,nocoeff:450,nodal:[6,38,56,164,178,290,407],node:[1,3,12,14,15,16,17,18,41,118,143,188,210,216,290,333,368,420,436],node_area:216,node_group:178,nodeless:357,nodeset:178,nodeset_to_elementset:178,nof:164,noforc:[],nois:[6,206,207,213,214,215,216,260,265,270,282,290],nomenclatur:[6,71,184,321],nomin:[167,229],non:[],nonbond:[4,12,386,405],none:[],noneq:207,nonequilibrium:[9,287,288,357],nonetheless:213,nongauss:[],nongaussian:105,nonlinear:[],nonloc:389,nonperiod:3,nonzero:3,noordhoek:348,nopreliminari:164,nor:[2,3,41,59,178,348,423,426],nord:[390,408,410],norder:420,nordlund:[390,408,410],norm:[6,12,63,117,172,181,184,185,271,326,328,404,440,441,447],normal:[3,6,9,10,11,12,39,41,58,61,63,67,70,71,73,88,91,102,112,116,117,129,132,144,145,146,164,169,172,181,182,183,184,185,188,192,194,195,204,205,209,213,214,226,229,241,251,253,254,261,265,267,268,274,278,279,281,282,283,290,295,296,299,300,304,306,307,309,323,325,326,328,333,347,348,360,361,364,404,416,417,418,421,423,425,426,428,429,433,437,440,441,443,447,448,451],norman:290,nornal:3,nose:[6,7,8,134,172,198,213,214,229,230,231,232,233,234,235,246,247,248,249,253,257,265,270,281,282,283,288,353,443],noskov:[411,443],noslip:[278,300],notabl:[5,39],notat:[6,63,70,120,138,172,226,229,355,448],note:[1,2,3,6,7,8,11,12,13,14,15,16,17,18,22,24,25,28,29,32,33,35,36,37,38,39,40,41,42,44,47,54,55,56,58,59,60,61,62,63,65,66,68,69,71,73,75,79,87,89,90,91,92,93,97,104,105,106,108,110,112,113,114,115,117,118,119,120,121,124,126,127,128,132,134,138,139,141,142,143,144,145,146,147,148,150,152,155,157,161,163,164,167,168,169,170,172,173,174,175,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,199,200,202,203,205,207,208,209,211,212,213,214,215,216,224,225,226,227,229,231,232,233,234,235,241,246,247,249,253,255,256,257,259,260,261,263,268,269,270,271,274,275,276,278,281,282,283,286,289,290,292,293,294,295,296,299,300,301,303,304,305,306,307,309,313,317,318,319,321,323,326,327,328,329,333,334,335,339,340,342,343,344,346,347,349,350,352,353,354,355,358,360,361,362,363,364,367,368,369,371,373,377,378,379,380,381,382,383,384,386,390,392,393,394,395,396,397,400,404,406,407,408,410,412,415,418,420,421,423,424,425,426,427,428,430,431,433,435,437,438,440,441,443,447,448,449,451,452],noth:[179,212,320,333,421,434],notic:[0,6,7,8,12,288,290,443],noutcol:8,noutput:252,noutrow:8,novemb:380,novik:13,novint:210,now:[2,3,6,9,11,12,13,46,61,62,71,167,173,174,190,206,210,211,270,296,299,319,321,355,357,361,392,393,397,419,424,443,449],nowait:210,nozforc:318,np3:143,np4:143,np6:143,npair:[116,182],nparticl:[3,40,42,338],npartit:441,npernod:[14,15,16,17,18,333],nph:[],nphi:[16,333],nphug:[],npoli:256,nproc:[3,167],npt:[],npt_aspher:[231,235,246],npt_sphere:[232,249],nrecomput:354,nrepeat:[71,180,181,182,183,184,185,186,267,271,428],nreset:[192,229,230,233],nreset_ref:192,nrho:[334,355],nrl:355,nsampl:354,nsbmax_most:3,nsec:442,nskip:[119,428],nsq:[3,330,388],nstart:[119,182,183,186,271,423,428],nstat:251,nstep:[3,13,192,229,301,401,421,424],nsteplast:421,nstop:[119,428],nswap:[286,293],ntabl:[38,56,164,407],nterm:274,nth:[12,77,116,117,167,169,183,194,428,438],ntheta:339,nthread:[3,333],ntild:252,ntpc:333,ntptask:333,ntype1:115,ntype2:115,ntype:[3,120,144,167,169,179,261,263,357,363,390,423,433],nuclear:[9,96,97,130,207,230,260,265,327,357,416],nuclei:[9,96,97,128,130,135,215,230,240,248,284,336,357,423],nucleu:[96,97,261,410,443],nudg:[4,6,7,172,228,325,328],nulcear:9,num_of_collis:3,numa:[1,3,12,333,420],numactl:16,number:[1,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,22,27,38,39,40,41,42,44,56,63,64,65,66,68,69,70,71,73,75,76,77,78,79,80,87,90,91,92,93,102,104,106,108,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,129,130,131,132,133,134,136,137,138,139,141,142,143,144,145,146,147,148,152,153,163,164,166,167,168,169,170,172,173,174,177,179,181,182,183,184,185,186,188,189,190,191,193,194,195,202,203,205,206,207,209,210,211,212,213,214,215,216,219,226,229,230,233,241,251,252,253,255,256,259,260,261,265,267,270,273,278,279,280,282,285,286,287,288,290,291,292,293,295,297,298,300,301,303,305,316,318,319,321,323,324,326,327,328,329,330,333,334,335,339,341,346,348,353,354,355,356,357,358,363,364,365,366,367,380,381,382,384,386,390,391,392,393,394,396,404,406,407,408,409,410,412,413,416,417,418,420,421,423,424,425,426,427,429,430,431,432,433,435,437,438,440,441,443,447,448,449,452],number_of_a:3,number_of_b:3,number_of_typ:179,numbond:3,numer:[1,2,3,6,9,12,22,38,41,42,44,56,71,77,87,116,138,148,152,164,167,168,169,173,174,175,177,178,184,200,206,209,213,226,229,253,270,290,295,297,298,300,301,305,323,326,327,346,352,364,380,384,392,393,407,416,417,421,423,430,433,439,440,441,448],numpi:11,nvalu:[181,184,185,186,421],nvaluelast:421,nvc_get_devic:15,nvcc:[1,12,17],nve:[],nve_aspher:[231,234,246],nve_spher:[232,235,249],nvida:17,nvidia:[1,3,9,12,14,15,17,333,436],nvt1:443,nvt2:443,nvt:[],nvt_aspher:[231,234,249],nvt_sphere:[232,235],nvtfe:178,nwait:252,nwchem:7,nxnode:290,o_cor:126,o_shel:126,oascr:7,obei:[3,194,321,418],ober:7,obj_shared_foo:12,obj_target:12,object:[6,8,11,12,15,40,42,168,192,210,216,219,256,274,326,421,426],observ:[229,260,281,282,285,286,293],obsolet:13,obstacl:[4,211],obtain:[1,3,9,12,29,73,87,142,170,174,204,207,216,233,252,253,285,318,335,352,380,384,391,408,410,432],obviou:[12,448],obvious:[168,438,448],occ:359,occasion:[3,418],occlus:168,occup:[3,142,359],occur:[1,3,6,9,11,12,14,17,39,57,59,61,62,71,86,105,142,145,147,164,167,169,179,188,191,192,194,205,208,211,219,227,241,261,270,278,287,300,301,303,318,329,333,354,357,377,393,418,420,421,428,432,437,440,448],occurr:[312,423,437,448],octahedr:25,octant:420,odd:[41,169,188,229,270,281,282,290,438],off:[1,3,6,12,14,15,16,17,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,44,45,46,47,48,49,50,51,53,54,55,56,59,61,65,69,71,107,108,109,112,113,115,120,121,122,127,131,142,143,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,167,168,169,172,175,179,186,187,190,191,201,204,205,206,208,210,213,214,219,229,231,232,233,234,235,236,241,244,246,247,249,255,257,258,262,270,272,273,278,281,283,293,294,295,299,304,305,306,307,308,309,310,312,313,314,318,319,326,328,329,331,333,334,335,337,340,341,342,343,344,345,347,348,349,351,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,381,384,385,386,387,389,393,394,395,397,404,405,406,407,408,409,410,412,414,415,416,418,419,420,423,425,430,432,435,436,437,445,447,450,452],offend:[3,421],offer:[6,14,18,147,325,349,418,432],offic:7,offload:[1,12,16,17,210,333],offset:[3,6,57,144,168,194,195,205,256,327,349,369,373,405,423],offsit:8,often:[1,3,6,7,12,13,14,15,16,17,18,37,55,71,138,163,168,175,183,186,188,192,203,210,229,253,271,313,321,325,326,328,329,330,333,348,353,369,408,410,418,437,443,447],ohio:382,old:[3,6,9,172,192,195,229,380,392,397,424,427,431,434,447,450],older:[3,5,12,13,17,169,181,192,229,397],oldlac:169,oleinik:339,olfason:[6,25,314,363,435],oliv:169,olivedrab:169,ollila:[216,218,219,220],olmst:[178,251],omega0:314,omega:[],omega_dot:229,omega_ijk:410,omega_ik:408,omegai:[113,167,280],omegax:[113,167,280],omegaz:[113,167,280],omgea:6,omiss:[0,7],omit:[164,169,297,343,352,373],omp:[],omp_num_thread:[3,16,18,333],omp_proc_bind:17,ompi_comm_world_local_rank:12,on_the_fli:178,onc:[0,1,2,3,6,11,12,16,40,41,59,60,63,71,91,104,150,168,169,172,173,174,188,189,190,195,203,205,207,214,252,259,270,278,286,291,293,301,324,327,328,329,360,362,364,365,390,394,420,421,430,437,440,443,448],onelevel:420,onewai:[],ongo:210,oniom:[9,264],onli:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,59,60,61,63,64,65,66,67,68,69,70,71,72,73,75,78,79,80,83,86,87,88,90,92,93,96,97,98,99,100,101,102,104,105,106,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,127,128,130,131,132,135,136,137,138,139,141,142,143,144,147,148,150,151,153,154,155,156,157,158,159,161,162,163,164,167,168,169,170,172,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,198,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,250,251,252,253,254,255,256,257,259,260,261,262,263,264,265,266,267,270,271,272,273,274,278,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,312,313,314,316,318,319,321,323,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,423,424,425,427,428,430,431,432,433,434,435,437,438,439,440,441,443,448,449,450],only_group:142,onn:432,onset:[260,312],ontario:9,onto:[120,146,191,195,216,404],onward:2,open:[],opencl:[1,3,7,15,333],opengl:6,openkim:9,openmp:[1,3,7,9,12,16,17,18,333,436],openmpi:[12,14,15,16,17,18,333],opensourc:7,oper:[],opl:[],oppos:[6,39,165,167,269,297,319,327,423],opposit:[6,70,177,213,220,251,270,293,328,349,377,411,421],opt:[],optic:123,optim:[],option:[],optionn:17,orang:[2,168,169],orbit:[261,263,339,349,357,405],orchid:169,order:[1,2,3,6,9,11,12,14,16,27,38,39,41,56,59,65,69,71,79,87,89,90,92,93,108,112,115,120,121,122,123,124,125,126,127,130,131,132,133,134,136,137,148,153,163,164,167,168,169,172,175,180,182,183,184,185,186,187,189,190,191,192,193,198,200,205,207,209,210,212,216,217,219,227,229,251,259,260,264,267,268,269,270,271,272,273,274,279,285,289,290,291,292,302,303,304,306,307,309,312,313,318,327,328,334,335,336,339,348,354,355,357,358,360,361,364,366,369,377,380,392,393,394,405,406,407,408,409,410,411,413,418,420,421,423,424,428,430,432,433,437,440,443,448,452],orderomg:3,ordinari:[111,363,389],org:[6,7,11,12,13,14,391],organ:[0,3,6,7,8,348],organometal:25,orient:[],orienti:42,origid:181,origin:[3,6,7,9,12,71,81,103,104,114,118,140,144,146,166,168,169,172,173,174,181,184,185,189,190,194,198,205,214,226,229,247,253,256,266,270,271,277,288,315,317,318,321,325,334,335,337,339,349,352,353,354,355,363,366,380,389,392,393,408,410,411,412,420,423,424,425,426,427,428,447,450],origin_i:185,origin_x:185,origin_z:185,ornl:[7,9,15],orsi:29,ortho:[3,59,146,423],orthogon:[],orthograph:168,orthong:59,orthongon:[59,270],orthonorm:195,orthorhomb:260,os4:143,oscil:[6,9,129,190,194,197,198,214,226,227,229,260,265,270,295,296,298,300,327,336,411,443,448],oscillatori:226,oserror:11,other:[],otherwis:[1,3,12,14,16,17,18,37,39,55,71,102,111,118,123,124,137,145,163,169,170,179,181,189,190,194,203,205,207,214,229,270,313,314,326,333,341,364,368,378,379,390,413,418,421,423,424,443],otyp:[349,369,373,377],ouml:443,our:[5,6,7,8,13,216,273,384,408,410,443],out:[1,2,3,6,7,8,11,12,13,14,18,19,21,41,64,66,71,75,90,91,93,94,97,103,104,105,106,107,114,115,122,123,124,125,127,128,130,131,132,133,134,136,137,139,141,147,151,167,168,169,170,172,184,188,189,190,193,201,204,205,211,213,216,221,241,252,254,255,256,265,266,267,270,275,290,299,301,302,303,304,306,309,316,317,321,324,328,332,357,364,405,417,418,420,421,423,426,427,428,430,431,432,434,437,439,440,441,444,446,448,449,450,451,452],outcom:[270,449],outer2:[344,362],outer:[3,8,16,199,211,303,317,324,326,332,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,413,414,415,416,418,431,432,437,442],outer_distance_cutoff:363,outermost:[38,56,173,174,226,229,329,407,432],outfil:[13,420],outlin:[6,168],outmost:210,outpt:12,output:[],output_frequ:178,outsid:[3,57,59,71,134,144,166,167,168,169,170,183,184,195,205,211,270,271,278,283,284,297,298,300,301,316,328,340,342,349,357,369,371,387,395,421,423,424,426,433,440,449],outuput:181,outut:6,outward:[142,295,299,300,423,432],over:[1,3,5,6,7,9,12,16,18,27,39,41,42,55,60,65,68,69,71,79,80,87,88,89,90,92,101,103,105,108,115,116,120,121,124,127,130,138,140,153,164,168,170,172,173,174,180,181,182,183,184,185,186,187,188,189,190,194,195,203,206,207,211,213,214,215,219,227,228,229,230,231,232,234,235,246,247,248,249,251,256,257,260,267,268,269,270,271,274,275,278,281,282,283,284,286,289,292,293,295,297,298,299,300,301,304,317,320,328,329,330,333,347,353,355,356,357,358,363,378,380,390,396,397,405,406,408,409,410,419,420,421,426,428,429,431,432,437,440,441,448,449],overal:[6,18,25,59,138,192,198,229,230,253,273,278,303,324,357,363,364,396],overalap:270,overcom:[241,278],overflow:[3,327,329],overhead:[6,11,19,41,169,181,184,185,188,202,259,329,330,426],overkil:270,overlai:[],overlaid:7,overlap:[3,13,16,62,76,144,147,164,169,177,180,181,183,184,185,186,195,199,241,256,261,267,270,271,278,296,300,318,321,324,326,327,333,353,357,361,364,367,377,397,412,423,426,432],overload:1,overrid:[3,12,14,17,22,44,71,130,144,152,168,169,173,174,192,199,224,229,305,318,329,346,363,364,380,384,392,420,421,433,435,440,448],overridden:[6,144,168,233,270,378,384,397,405,431,448,450],overview:[],overwrit:[11,12,22,44,152,169,181,182,183,184,185,186,271,305,316,322,346,380,421,424],overwritten:[258,289,316,363,364,418,419,424],own:[3,4,6,7,8,11,12,13,15,17,39,41,59,61,63,65,66,69,71,73,75,79,90,92,93,104,106,113,114,115,117,119,124,127,139,141,142,167,169,172,178,180,181,182,183,184,185,186,188,191,192,194,203,206,207,213,214,216,224,227,229,231,232,233,234,235,246,247,249,253,257,265,270,271,281,282,283,292,318,328,333,335,339,348,356,366,390,392,393,406,408,409,410,420,433,440,449],oxford:[29,87,352],oxid:[348,349],oxygen:[6,40,202,349,369,373,423],oxygen_c:126,p_e:290,p_ik:390,p_pi:339,pacakg:[3,4,12,40,333],pack:[5,8,67,296,333,339,380],pack_bord:8,pack_border_bodi:8,pack_border_hybrid:8,pack_border_vel:8,pack_comm:8,pack_comm_bodi:8,pack_comm_hybrid:8,pack_comm_vel:8,pack_exchang:8,pack_restart:8,pack_revers:8,pack_reverse_comm:8,pack_reverse_hybrid:8,packaag:333,packag:[],packakg:15,packet:[7,9,40,168,336,357],pad:[3,167,168,169,253,448],padua:[9,13],page:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,37,40,42,44,55,57,59,63,66,68,75,87,90,93,102,104,105,106,107,109,112,114,117,119,121,123,124,137,139,141,144,145,146,152,163,167,168,169,170,172,173,174,179,180,181,182,183,184,185,186,195,205,212,213,214,224,229,230,234,235,239,246,247,248,249,256,259,270,275,278,281,282,283,292,296,299,301,303,305,313,317,326,327,328,329,333,334,335,338,346,348,349,355,356,358,363,364,366,367,380,381,382,384,386,390,391,396,405,406,408,410,412,421,423,424,425,426,428,431,432,433,435,440,441,448,449,450,451],pai:[15,18],pair:[],pair_:[87,173,174],pair_airebo:366,pair_charmm:377,pair_class:8,pair_coeff:[],pair_eam:334,pair_eff:130,pair_foo:8,pair_hybrid:[384,411],pair_interact:178,pair_list:368,pair_lj:377,pair_lj_cut:8,pair_lj_soft_coul_soft:87,pair_modifi:[],pair_sph:[398,399,400,401,402,403],pair_styl:[],pair_writ:[],paircoeff:3,pairfoo:8,pairij:[3,423],pairkim:3,pairstyl:8,pairwis:[],palegoldenrod:169,palegreen:169,paleturquois:169,palevioletr:169,pan:168,panagiotopoulo:[350,359],pandit:[9,263,393],papaconstantopoulo:334,papayawhip:169,paper:[3,6,7,8,9,13,39,40,64,120,132,138,156,213,216,220,228,255,261,263,270,278,286,290,293,318,325,328,335,343,349,361,363,366,371,373,389,392,393,408,410,418,437],paradyn:5,paraemt:394,paragraph:[71,132,295,321,424],parallel:[],parallelepip:[6,146,321,423,426],parallelipip:[146,252],paralleliz:255,param:[3,261,263,420,426],paramet:[],parameter:[118,143,335,339,348,349,355,356,357,358,366,380,381,382,390,392,393,406,408,409,410],parameter_fil:178,parameterizaion:349,parametr:[6,9,36,356,391,395],paramt:[105,261,297,394],paramter:348,paratem:377,paraview:271,parent:[3,8,301],parenthes:[38,56,164,361,407,448],parenthesi:[2,181,303,448],parinello:[6,7],pariticl:188,paritlc:3,park:[3,7,9,178,274,382,389],parrinello1981:192,parrinello:[192,207,227,229,230,260,282],pars:[],parser:[12,448],part:[0,1,2,3,6,7,8,9,11,12,17,20,21,23,24,25,26,27,28,29,30,31,32,35,36,37,38,40,41,43,45,46,47,48,49,51,53,54,55,56,64,67,70,71,72,78,80,83,96,97,98,99,100,101,105,107,108,109,111,112,115,120,121,122,123,126,128,130,131,135,136,138,142,147,150,151,153,154,155,156,158,159,161,162,163,164,167,169,170,172,175,176,177,179,185,187,188,189,190,191,192,193,195,197,200,201,202,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,222,223,224,227,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,251,252,253,255,256,260,261,262,263,264,265,266,267,269,270,272,273,274,275,277,278,281,283,284,285,286,287,288,289,290,291,293,294,295,296,297,299,301,302,303,304,306,307,308,309,312,313,314,318,319,326,327,328,329,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,420,421,423,424,425,426,430,431,432,435,441,448,452],partai:[9,391],parti:9,partial:[],partic:6,particip:[190,338,367,412],particl:[],particleenergi:3,particleviri:3,particular:[1,3,6,8,10,12,16,40,63,65,69,70,71,79,92,108,113,115,116,120,144,166,167,172,177,184,188,191,206,211,212,216,226,229,251,256,269,270,273,285,296,301,304,319,321,324,327,333,338,339,340,342,344,345,347,351,356,357,360,362,364,369,373,377,386,387,394,395,405,406,408,409,410,418,420,423,424,425,430,431,433,441,448,449,451,452],particularli:[7,9,12,15,16,25,39,168,192,270,319,357],partilc:278,partit:[],partitoin:62,partner:[3,7,61,189,190,191,214,278,293,411,433,438,443],pascal:[9,13,447],pass:[6,7,8,11,66,74,75,81,89,90,93,103,104,105,106,139,167,169,170,192,193,203,205,226,227,229,259,278,295,317,329,333,364,392,404,421,423,424,428,434,448,451],passphras:12,past:[],patch:[0,12],patchi:270,path:[3,6,7,11,12,13,15,170,212,228,253,274,278,285,290,328,334,335,339,346,355,356,358,366,380,381,382,386,390,391,392,396,406,408,410,424],patient:12,patom1:115,patom2:115,patrick:409,pattern:[3,7,12,62,73,425],pattnaik:270,paul:[0,7,13,213,215],pauli:[9,357],paus:431,paves:253,payn:[120,391,396],pb2:143,pb4:143,pbc:[295,336],pchain:[229,230,233,270],pcie:1,pd2:143,pd4:143,pdamp:[229,230,233,257,270],pdb:[6,13,170],pdf:[0,8,9,13,17,40,99,100,101,111,193,212,222,223,389,398,399,400,401,402,403,433],pdim:293,pdlammp:[78,80,389],pdlammps_ep:[111,389],pdlammps_v:389,pe_eta:229,pe_etap:229,pe_omega:229,pe_strain:229,peachei:13,peachpuff:169,peak:359,pearlman:87,peculiar:12,pedersen:319,peform:[39,262],penalti:[14,392,393],pencil:[6,71,132,184],pend:3,penetr:42,peng:143,penn:13,pentium:10,peopl:[7,8,9,12],peptid:[4,9,193],per:[],peratom:[3,110,121],perceiv:168,percent:[3,16,192,333,406],percentag:[1,192,229,256,257,270],percol:190,perfect:[6,41,70,73,188,251,328],perfectli:[41,188,424],perfom:[6,328],perform:[],performac:1,pergamon:[380,410,416],perhap:321,peri:[],peridyma:78,peridynam:[3,4,6,7,9,40,63,78,80,111,389,405,433],perimitt:350,period:[],perioid:295,perl:[6,13],perm0:447,perman:[3,39,54,71,148,189,190,210,269,301,333,363,427,435],permeabl:250,permiss:[190,421],permit:[6,216],permitt:[350,410,415,416],permut:[12,356,406,408,410],perpendicular:[6,123,168,194,211,221,226,228,251,254,295,296,325,423],perram:[319,360],persepct:168,persist:[3,8,71,203,270,333,420,421,429,448],person:9,persp:[3,168],perspect:168,pertain:[346,405],perturb:[9,13,70,87,225,268,295,298,300,428],peru:169,peskin:216,pessimist:319,petersen:[278,319],pettifor:[339,405],pettifor_1:339,pettifor_2:339,pettifor_3:339,pfactor:168,pforc:421,phantom:210,pharmaceut:7,phase:[3,12,16,229,285,293,339,369,409,420],phd:391,phenol:443,phenomena:357,phi0:[162,269],phi1:151,phi2:[151,356,406],phi3:[151,356,406],phi:[1,3,4,7,9,12,16,17,79,120,163,164,168,208,252,269,307,333,334,339,355,358,380,381,382,436],phi_ij:[339,358,390],philadelphia:9,phillip:[214,353,443],phillpot:[262,348,349],philosoph:355,philosophi:[6,7,212],phonon:[],phophor:396,phosphid:396,phy:[6,7,13,20,21,25,39,43,45,46,64,70,73,87,88,110,112,120,121,126,132,150,151,161,179,192,193,198,206,207,212,213,214,215,216,227,228,229,230,233,247,248,252,253,257,260,262,265,270,273,274,278,281,282,285,286,287,288,290,293,295,304,312,314,318,319,325,328,335,339,340,344,345,347,348,349,350,351,352,353,355,356,357,359,360,361,362,363,366,369,371,373,374,377,378,379,380,382,383,384,387,389,390,394,396,404,406,407,408,409,410,411,418,432,435,437,443],physic:[3,6,9,12,14,16,17,18,40,53,59,138,178,194,207,213,215,216,218,219,220,227,252,261,263,289,290,319,321,328,333,335,337,343,347,355,363,364,391,392,393,399,400,402,403,418,420,432,438,447],physica:[378,379],physik:[7,9],pic:9,picki:8,picocoulomb:447,picogram:447,picosecond:[169,194,441,447],picosend:357,pictur:7,piec:[3,11,120,169,229,430,452],pieter:13,pimd:[],pin:16,pink:169,pipe:[6,168],pipelin:[3,6],pisarev:290,pishevar:353,piston:[],pitera:6,pixel:168,pizza:[4,6,7,11,13,41,167,168,188],pjintv:13,pka:290,place:[3,6,7,9,11,12,33,41,50,71,87,138,144,148,157,164,167,168,169,171,172,173,174,190,191,194,205,206,207,209,212,213,214,215,217,219,220,229,234,235,246,249,256,259,268,270,281,282,283,290,295,298,300,317,346,363,405,412,420,421,424,431,433,441,448],placehold:[33,157,334,335,348,355,358,365,366,380,381,382,386,390,392,393,396,404,406,408,409,410],placement:[321,369],plai:[168,285],plain:[9,377,421],plan:[3,5,6,16,17,146,423],planar:[6,40,42,211,251,296,312,314],planck:[205,253],plane:[3,6,9,41,42,57,59,67,71,168,172,178,184,188,208,211,221,251,254,264,275,277,290,296,304,306,307,308,309,314,321,379,412,426,433],planeforc:[],plasma:[9,88,230,290,357],plastic:[],platform:[1,3,7,9,12,13,15,17,167,168,170,425,430,452],plath:[6,91,172,286,293],player:168,pleas:[0,3,7,11,12,13,178,207,216,220,252,255,266,285,301,356,358,389],plen:336,plimpton:[0,5,7,70,112,121,191,251,278,361,389],plo:29,plog:[3,12,432],ploop:[229,230,233],plot:[7,11,13,260,375,377,407,413],plu:[3,11,12,39,59,68,96,147,169,187,192,194,195,233,270,330,357],plug:9,plugin:[9,13,170,424],plum:169,pm3:143,pmb:[],pme:319,pmf:[193,274,275],png:[3,12,167,168],pni:168,poariz:6,poem:[],point1:423,point2:423,point3:423,point:[],point_data:271,pointer:[3,7,8,11,203,421],pois:447,poiseuil:[4,175,208],poisson:[59,194,319,361],poisson_solv:178,polak:325,polar:[6,7,120,143,178,197,348,349,369,411,443],polar_off:348,polar_on:348,polariz:[],poli:[],pollock:[7,319],polya:301,polybond:13,polychain:270,polydispers:[3,341,347,361,378,379,405,415],polygon:[6,142],polym:[],polymer:7,polymorph:[],polynomi:[38,56,164,355,375,384,400,407],polytechn:255,poor:[16,17,41,188,247,248,273,333,375],poorli:[325,326],pop:[3,8],popen:12,popul:[12,265,321,354,423],popular:[12,167,356],pore:275,poros:147,porou:[216,219],port:[210,212],portabl:[7,9,12,167,193,392,425],portion:[1,3,9,11,12,15,16,41,54,71,88,91,107,108,110,113,121,134,167,169,180,181,183,184,185,186,188,192,202,216,229,231,232,234,235,262,267,268,270,271,303,317,329,333,340,342,343,344,345,349,350,352,353,357,359,360,362,363,369,373,377,387,394,395,410,413,422,423,428,432,433,448],poschel:361,posfreq:267,posit:[3,6,14,27,39,40,41,42,46,57,59,70,71,81,89,90,103,104,108,117,118,120,121,127,142,143,144,146,147,148,153,155,164,166,168,169,172,173,175,177,179,180,181,183,184,185,188,189,190,191,192,193,194,195,198,200,205,206,207,208,210,211,213,214,215,216,218,219,222,223,226,227,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,255,256,257,260,261,265,267,268,270,273,274,275,277,278,280,281,282,283,285,287,288,289,290,293,295,296,297,298,299,300,301,304,318,321,328,335,336,338,341,353,354,357,359,367,372,393,404,407,412,418,423,426,433,443,448,449],posix:210,posix_memalign:12,possibl:[1,3,6,8,9,11,12,15,38,40,41,55,59,63,70,71,87,113,115,120,121,123,137,166,167,169,172,174,178,179,184,188,189,190,191,195,197,207,214,251,264,265,267,270,278,280,290,291,308,317,319,326,329,330,333,354,363,380,393,407,421,427,436,437,438,441,443,448,449,451],post:[],post_forc:8,post_force_integr:8,post_force_respa:8,post_integrate_respa:8,postit:[184,185,241],postiv:86,postma:[257,281],postprocess:13,pot:[361,393],potentail:358,potenti:[],potentiel:377,potetni:364,potpourri:9,pour:[],pourtoi:285,pow:194,powderblu:169,power7:17,power8:17,power:[3,9,11,105,120,169,265,318,333,339,421],pparam:[87,173,174],ppm:[12,167,168],ppn:[14,15,16,17,18,333],pppm:[],pppm_disp:3,pppmdisp:3,pproni:[3,206],pr3:143,pr4:143,practic:[3,12,192,229,230,252,259,420],prb:[408,410],prd:[],pre:[],pre_exchang:8,pre_forc:8,pre_force_respa:8,pre_neighbor:8,prec_tim:14,preced:[2,6,59,180,181,182,183,184,185,186,212,267,271,303,321,328,333,339,363,437,440,441,448],preceed:[11,12,71,132,182,295,421,448],precipit:142,precis:[1,3,9,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,109,112,122,131,144,150,151,153,154,155,156,158,159,161,162,164,167,169,175,187,192,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,261,262,263,270,272,273,281,283,294,304,306,307,308,309,312,314,318,319,326,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,392,394,395,397,406,407,408,409,410,412,414,415,416,425,432,433,436,441,443,447,448,449],precv:420,predefin:[162,169,301,357],predict:[1,6,10,241,270,333],preexponenti:437,prefactor:[24,25,28,32,35,36,138,152,163,173,174,182,295,306,309,312,326,347,359,386,394,395,397,415],prefer:[7,8,12,269,291,335],prefix:[11,12,168,193,252,417,420],preliminari:[38,56,164,407],prematur:326,prepar:[9,264,278,434,443],prepend:392,preprint:[120,396],preprocessor:210,prerecord:193,prescrib:[6,8,123,124,137,172,173,178,181,195,226,243,291],presenc:[167,189,190,216,219,378,379,415,450],present:[1,3,12,16,18,142,164,168,195,206,207,212,216,217,219,220,265,296,299,348,357,368,377,393,394,420,443],preserv:[3,59,192,194,229,273,278,300,424],press:[],pressdown:187,pressur:[],pressure_with_eviri:357,presum:[73,133,172,173,174,194,328,364,426],prevent:[2,3,6,195,204,278,289,312,318,324,326,328,333,353,364,388,399,400,402,404,421,425,431,443,448],previou:[],previouli:195,previous:[3,11,59,61,71,86,102,117,119,133,144,146,148,166,167,169,177,179,180,181,182,183,184,185,186,194,195,205,211,224,226,256,268,270,272,273,290,292,295,296,297,298,300,301,320,361,405,418,421,425,426,436,438,440,441,444,445,446,448,449],prevoiu:296,price:[6,352],primari:[0,9,290],primarili:[5,7,9,17],primaritli:17,prime:[198,214,362,367,408,410,420],primit:[3,6,298,299,321],princip:[3,210],principl:[6,9,11,210,230,261,357,365,406,420],prinicp:[42,270,327],print:[],printabl:2,printflag:365,printfluid:216,prior:[142,165,320,451],priori:432,prioriz:333,prism:[3,6,132,146,426],priveleg:3,privileg:[12,210],prob:[189,190],probab:397,probabl:[3,8,12,40,71,134,147,148,150,179,188,189,190,191,195,205,214,229,256,295,301,326,384,418,437,443],problem:[],problemat:205,proc:[1,3,8,11,12,15,113,167,317,420],proce:[41,54,148,188,199,328,430,438,441],procedur:[6,12,39,41,169,179,188,205,213,214,215,229,231,232,233,234,235,246,247,248,249,252,281,282,283,284,287,288,326,328,335,341,424,443],proceed:12,procesor:[41,420],process:[],processor:[],processsor:[41,188,420],procp1:167,procssor:432,produc:[1,3,4,6,7,12,13,14,15,16,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,45,46,47,48,49,51,53,54,56,63,65,68,69,71,79,92,108,109,110,112,113,114,115,117,119,121,122,131,150,151,153,154,155,156,158,159,161,162,164,167,169,172,175,180,181,182,183,184,185,186,187,188,191,201,203,204,206,207,208,213,214,215,224,226,229,231,232,233,234,235,236,244,246,247,249,256,260,261,262,265,270,271,272,273,279,280,281,283,290,291,292,294,295,298,303,304,306,307,308,309,312,314,319,326,328,331,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,390,393,394,395,397,406,407,408,409,410,412,414,415,416,418,420,425,428,429,432,437,448,449],product:[16,17,18,120,194,247,261,291,333,336,357,393,420,448],proessor:333,prof:255,profi:133,profil:[],program:[3,4,6,7,9,11,12,13,17,167,168,169,170,172,193,203,210,216,264,355,421,434,448],programm:[13,17],progress:[1,41,188,210,227,260,325,326,328,441,443],prohibit:433,project:[6,7,12,13,14,325,405],promis:7,promot:339,prompt:[8,11,12,210,434],proni:[3,206,207],proofread:8,prop:[6,259],propag:[4,9,177,229,260,357,364],propens:6,proper:[191,251,380,421],properati:259,properli:[175,200,270,327,328,421,449],properti:[],propoerti:278,proport:[6,39,41,87,103,104,140,188,213,214,215,260,286,293,294,361],proportion:213,propos:[6,120,179,192,205,229,247,265,369,382,409,411],prospect:7,protect:278,protein:[7,10,144,268,270,276,423,431],protocol:210,proton:[410,416,447],prototyp:[10,42,389],prouduc:[186,292],prove:216,proven:247,provid:[1,3,4,6,7,8,9,11,12,13,14,15,16,17,18,29,40,42,67,70,118,138,143,144,170,180,181,186,191,192,193,194,203,205,210,212,216,220,227,229,252,260,261,264,265,270,274,285,287,288,291,292,303,316,318,319,324,328,333,335,339,341,346,348,349,353,356,357,361,363,366,368,377,378,380,382,390,391,392,393,396,404,405,406,408,409,410,420,425,431,436,437,441,448],proxim:166,psa:298,pscreen:[3,12,432],pscrozi:[0,7,13],psec:[169,194,209,213,214,229,257,270,281,282,442,447],psend:420,pseudo:[357,418,423,428],pseudodynam:285,psf:6,psi:[358,415],psi_ij:358,pstart:[3,229,230,233,257,270],pstop:[3,229,230,233,257,270],pstyle:[87,107,173,174],psu:[392,393],psuedo:428,pt2:143,pt4:143,ptarget:192,pthread:[12,17],ptr:[6,11,203,421],ptype1:115,ptype2:115,pu3:143,pu4:143,pu6:143,publicli:5,publish:[7,216,220,261,349,380,408,410],pull:[274,275],puls:290,pump:[378,379],punctuat:[2,418,437],purchas:168,purdu:[9,13],pure:[11,278,364,381,382,408,410,432],purg:[3,424],purpl:[2,169],purport:11,purpos:[3,6,7,12,42,61,71,118,127,128,143,144,146,148,164,167,184,186,191,192,213,251,253,256,258,269,278,318,333,343,367,373,384,412,423,425,426,430,433,435,436,448,452],push:[3,8,175,187,194,211,228,251,268,274,326,361,397],pushd:211,put:[3,6,8,11,12,13,39,59,132,144,167,195,199,297,298,301,321,392,421,423,427],putenv:[434,448],px1:432,px2:432,pxx:[192,229,257,270,318,319,440,441],pxy:[3,6,441],pxz:[3,6,441],py1:432,py2:432,pydir:11,pyi:[192,229,257,270,318,319,441],pymol:[7,11,13],pymol_aspher:[],pympi:11,pypar:11,python:[],pythonpath:11,pyz:[3,6,441],pz1:432,pz2:432,pzz:[192,227,229,257,260,270,318,319,441],q_c:443,q_d:443,q_i:[358,377,411],q_j:377,qbmsst:[],qcore:261,qdist:[349,369,373,377],qeq1:261,qeq2:261,qeq:[],qfile:[261,349],qin:209,qmin:325,qmmm:[],qmol:264,qout:209,qtb:[],quad:[12,18,333,420],quadrat:[],quadratur:[87,178],quadrupl:334,quadruplet:[160,163,304,306,307,309,311,312,313],qualifi:[3,212],qualiti:[7,9,168,169],quantit:[74,81,103,104,105,140,361],quantiti:[],quantum:[6,9,120,203,207,253,260,264,265,339,357,405],quantum_temperatur:260,quartic:[],quartic_spher:178,quartz:[260,265],quasi:253,quat:433,quaternion:[3,6,40,82,113,123,144,231,234,237,238,239,246,360,423,433],quati:[113,423],quatj:[113,423],quatk:[113,423],quatw:[113,423],queen:13,quench:[301,418,437],queri:[3,11,54,243,421,448],quest:[6,203],question:[8,9,12,13,251,301,389,448],quick:[0,9,12,14,15,16,17,18,19],quickli:[3,4,8,12,13,39,188,194,210,278,325,326,328],quickmin:[324,325,326,328,437],quicktim:[4,168],quip:[],quit:[],quot:[2,3,12,219,258,303,380,418,419,421,431,448],r10:339,r12:360,r_1:120,r_2:120,r_c:[350,352,359,410],r_cut:339,r_d:443,r_e:358,r_ewald:271,r_fu:[378,379],r_i:[29,120],r_ii:120,r_ij:[29,339,357,390,416],r_ik:390,r_j:29,r_jik:390,r_max:185,r_me:350,r_mh:359,r_min:[185,351],r_ub:20,r_x86_64_32:12,ra2:143,rad2theta:143,rad:301,radhi:426,radial:[63,96,97,113,116,120,128,130,135,185,215,230,240,248,275,284,326,357,363,384,423,426],radian:[20,21,24,28,32,35,36,38,143,151,162,164,269,304,306,309,312,423,426],radiat:[118,143,290],radic:[146,423],radii:[76,120,191,195,347,355,360,361,378,379,415,426],radit:357,radiu:[3,6,63,76,84,85,89,90,113,118,120,137,142,167,168,172,185,211,216,230,232,235,240,244,248,249,263,275,276,278,280,295,296,299,301,325,339,341,347,357,358,361,369,377,378,379,380,396,410,415,423,426,433,448],radlo:426,rafferti:293,rahman:[6,7,192,227,229,230,260,389],rai:[9,17,143],ram:410,ramp:[],ran:[3,4,6,10,11],random:[3,6,39,144,147,166,168,177,179,189,190,191,193,195,202,205,206,207,213,214,215,216,225,253,256,260,265,268,270,278,282,285,290,294,297,341,353,354,418,433,438,443,448,449],random_se:418,randomli:[144,147,179,195,205,213,256,278,300,437,438],rang:[1,3,6,7,8,9,10,12,14,15,16,18,38,39,56,71,77,88,108,109,110,112,116,117,120,121,130,138,143,145,148,149,156,164,167,168,169,178,179,190,194,195,205,207,256,271,278,279,285,286,291,293,318,319,326,329,330,333,335,337,339,340,341,342,343,344,345,347,349,350,351,352,353,354,355,357,360,362,363,364,366,369,370,371,372,373,374,375,376,377,378,379,380,383,384,385,387,390,393,394,395,404,405,407,410,414,415,416,417,421,432,433,441,451],rank:[6,11,12,210,291,316,420],rankin:233,raphson:3,rapid:[4,6,11],rapidli:[3,8,12,71,191,213,227,229,270,281,282,294,349,353],rapp:[261,262,263],rappe_and_goddard:262,rare:6,rasmol:[6,7],rasmussen:360,raster3d:[6,7],rate:[6,12,127,169,178,194,195,209,210,211,256,260,286,287,288,289,293,324,325,354,378,379,418,437,441],rather:[1,2,6,9,12,40,41,62,112,127,168,188,194,206,207,270,282,290,294,296,297,298,301,357,392,407,424,428,433,435,440,448],ratio:[6,10,59,87,101,120,179,188,194,213,215,278,286,293,294,318,331,360,361,394,399,412,420,423,433,437],rational:[291,435],rattl:[],rattle_debug:273,ravelo:[233,371],rayleigh:[227,260],rb1:143,rbg:169,rcb:[3,41,188],rcm:[89,90],rcmx:[89,90],rcmy:[89,90],rcut:61,rcutfac:[120,396],rd1:328,rdc:17,rdf:[],rdn:328,rdt:328,rdx:4,reach:[6,12,41,119,188,190,192,214,233,278,285,303,317,332,350,443,448],react:6,reactant:357,reaction:[274,276,289,300,328,357],reactiv:[9,267,335],read:[2,3,6,7,8,9,11,12,13,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,37,38,40,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,59,115,142,144,145,147,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,167,168,169,170,171,172,178,179,191,192,194,195,205,207,210,226,227,229,231,232,233,234,235,246,247,248,249,252,253,255,256,258,259,263,270,273,274,277,280,288,289,290,296,304,305,306,307,308,309,311,312,313,314,315,317,323,327,328,332,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,418,420,423,424,425,427,428,429,430,431,433,434,435,437,448,449,450,452],read_data:[],read_dump:[],read_restart:[],read_restart_set:8,readabl:[168,327,430,452],reader:[3,13,424],readi:[11,12,145,147,148,210,433,443,450,451,452],readm:[1,4,6,8,9,11,12,13,142,167,170,264,365,392,393,421],real:[3,6,7,11,27,30,31,59,71,91,120,133,144,153,166,169,177,184,185,194,195,198,210,211,214,226,253,260,265,268,294,295,297,298,300,308,318,319,321,324,330,349,384,392,393,410,423,426,432,440,442,447,449],realist:[3,195,427],realiz:[71,172,421],realli:[1,3,8,12,112,121,169,211,329,364,435],realloc:3,realtim:210,reamin:[295,299],rearrang:328,reason:[3,6,7,11,12,19,39,125,136,144,181,184,185,213,257,270,287,288,291,301,327,328,333,346,350,357,358,359,379,384,412,413,427,432,449],reax:[],reax_def:3,reaxc:[],reaxff:[3,4,5,7,9,13,172,261,263,266,267,364,392,393,405,435],rebal:[41,188],rebalanc:[41,188],rebo:[],rebuild:[11,12,14,15,16,205,329,353,441],rebuilt:[3,12,167,168,170,329,333],recalcul:[71,87,278],receiv:[3,187,210,212,251,420],recent:[],reciproc:[6,118,143,252,318,340,342,343,349,352,357,369,373,387,395,437],recog:12,recoginz:3,recogn:[3,12,16,73,146,189,190,229,327,355,380,392,421,423,430,431,443],recommend:[7,9,11,12,14,16,168,169,260,288,318,357,378,379,393,394,432],recompil:[1,3,9,12,170,273],recomput:[102,148,199,274,354,435],reconstruct:[3,193],record:[170,193,274],recov:[192,229],rectangl:[41,188,321],rectangular:[7,41,62,146,188,205,321,423,425,427],rectilinear:[118,143],rector:53,recurs:[41,188,339,412],recust:41,recv:420,red:[2,10,168,169,191,253],redefin:[3,425,431,448],redirect:12,redo:12,reduc:[],reduct:[18,19,117,118,143,227,260,318],redund:358,ree:400,reed:[227,260],rees:[7,9,13],ref:[287,288,325],refactor:6,refer:[],referenc:[3,6,12,63,68,71,114,167,172,182,186,205,259,292,319,349,363,386,394,421,441,448],reflect:[],reformat:7,refresh:178,reg:426,regard:[6,59,226,273,389,393],regardless:[15,71,144,147,166,183,184,194,213,229,231,232,234,235,257,270,278,333,420,426,433],regim:[6,286,293,350,432],region:[],region_spher:8,region_styl:299,regist:[116,392,393],regoin:6,regress:448,regspher:144,regstrip:301,regul:6,regular:[1,3,9,41,62,88,142,146,179,188,205,290,319,350,404,420,423,425,427],reigon:448,reinhardt:[287,288],reject:[144,191,392,438],rel:[1,6,14,27,36,41,59,71,120,123,126,127,129,144,153,169,172,179,184,188,194,195,198,205,211,225,226,247,251,256,265,267,268,274,275,278,280,285,286,290,297,301,318,319,326,357,360,361,378,379,380,394,415,424,432,437,441,443,449],relat:[],relatic:[198,214],relationship:[6,261,303,318,415,443,448],relax:[],releas:[0,5,7,8,13,189],relect:[3,384],relev:[2,6,12,41,78,80,111,144,148,169,173,174,177,178,179,180,181,182,183,184,185,186,187,188,189,190,194,195,196,199,201,202,204,205,206,209,210,216,217,218,220,221,222,223,225,226,228,236,237,238,239,240,241,242,243,244,245,250,254,255,256,258,259,262,264,266,267,268,271,272,273,274,276,278,279,280,285,286,289,290,291,292,293,294,295,296,297,298,300,301,318,326,336,337,341,347,349,350,352,353,354,357,359,360,361,362,363,368,370,371,372,374,375,376,378,379,384,385,389,394,397,404,407,414,415,416,420,436,449],reli:[3,12,262,357,393,423,433],reloc:12,remain:[7,33,37,41,50,55,59,71,87,104,124,125,126,127,131,132,133,134,136,147,157,163,164,167,173,174,179,181,182,184,185,192,194,213,214,221,229,230,234,235,246,247,249,254,255,278,281,282,283,289,290,301,303,310,313,327,339,357,364,377,384,405,418,423,424,428,433,435,437,441,443,448,449],remaina:339,remaind:[144,167,195,256,278,291,410,423],remap:[3,6,12,59,61,71,127,144,166,184,194,211,226,247,318,423,424,425],remedi:[6,443],rememb:2,remov:[2,3,6,8,9,13,54,71,77,114,116,120,123,124,125,126,127,131,132,133,134,136,137,144,147,148,172,181,184,189,202,213,214,219,225,227,229,234,235,246,247,249,255,261,270,271,273,278,281,282,283,285,301,318,328,352,379,423,426,434,435,448,449],remove_bia:8,remove_bias_al:8,remove_molecul:178,remove_sourc:178,remove_speci:178,ren:143,renam:[12,302,434],render:[12,13,167,168,169],rendon:[229,230],reneighbor:[3,8,12,39,57,71,184,188,205,278,291,301,353,440,441],renssela:255,renumb:71,reorder:[3,12,39,420],repeat:[2,6,168,169,184,191,192,205,321,339,408,410,412,418,437],repeatedli:2,repel:211,repes:167,replac:[2,3,6,11,12,41,63,89,90,117,122,123,124,125,126,127,130,131,132,133,134,136,137,167,168,169,170,181,182,183,184,185,186,188,191,195,213,233,258,265,267,349,371,424,425,430,431,441,448,449,450,452],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,365,391,392,393],reprens:290,repres:[1,3,6,8,9,12,15,40,41,42,59,67,71,90,113,116,156,164,167,168,181,182,183,184,185,186,192,198,206,208,213,216,229,253,255,257,265,270,271,274,275,290,292,299,319,328,334,339,360,367,377,378,379,380,381,382,387,390,392,393,411,412,418,420,423,433,435,438,443,448,450],represent:[3,6,8,57,59,146,167,206,207,253,290,339,357,360,394,423,426,443],reprocess:428,reproduc:[3,229,296,349,355,361],repul:380,repuls:[6,7,9,36,45,46,108,211,261,295,296,299,335,339,347,349,353,357,361,363,377,380,383,404,410,415,416],reqir:[261,263],request:[3,6,8,12,41,147,164,167,210,216,268,278,280,316,318,392,393,418,428,433,436,437,448,449,450],requir:[],rerun:[],rescal:[],research:[5,7,216,220,418,437],resembl:265,reserv:[12,210,443],reservoir:[91,205,209,213,290],reset:[],reset_atomic_reference_posit:178,reset_dt:8,reset_target:8,reset_tim:178,reset_timestep:[],resid:13,residu:210,residue1:329,resist:[6,210],resolut:407,resolv:[192,253,278,379],resort:3,resourc:[7,334,355],respa:[3,16,199,210,229,331,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,378,379,380,381,382,383,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,416,431,432,442],respect:[1,6,9,10,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,45,46,47,48,49,51,53,54,56,59,70,71,87,89,96,97,118,126,129,138,142,143,150,151,153,154,155,156,158,159,161,162,164,168,169,184,185,190,191,192,208,211,213,214,216,229,231,232,233,234,235,236,244,246,247,249,261,262,270,271,274,275,277,290,295,304,306,307,308,309,312,314,316,318,319,323,326,327,332,333,334,335,337,339,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,384,385,386,387,389,394,395,396,397,406,407,408,409,410,411,412,414,415,416,420,424,432,433,436,443,448,450,452],respon:9,respond:[6,7,127,194,357,389],respons:[6,7,227,286,293],resquar:[],rest:[6,8,12,259,263,269,339,379,380,440,441,443],restart1:253,restart2:253,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,60,61,144,173,174,259,274,275,280,440,441],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,193,227,269,277,368],restratin:269,restrict:[],result:[1,2,3,6,7,9,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,45,46,47,48,49,51,53,54,56,63,64,66,67,71,75,87,90,91,93,104,106,109,110,112,114,115,116,117,118,119,121,122,124,127,131,138,139,141,143,144,147,150,151,153,154,155,156,158,159,161,162,164,167,168,169,172,175,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,198,201,204,205,206,208,213,214,216,220,227,229,231,232,233,234,235,236,244,246,247,248,249,252,253,261,262,267,268,270,272,273,278,281,283,286,287,288,290,291,292,294,295,296,298,300,303,304,306,307,308,309,312,314,318,319,328,331,333,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,379,380,381,384,385,386,387,389,393,394,395,397,406,407,408,409,410,411,412,414,415,416,418,420,423,425,426,427,428,432,433,434,435,437,447,448,449],resum:448,retain:[2,189,190,339,420],retart:[33,50,157,310],retreiv:8,retriev:[6,8,203,381,382,448],reus:[3,435],rev:[6,13,64,70,110,120,121,132,179,207,213,215,227,229,230,233,247,252,262,265,270,274,278,282,285,287,288,293,325,339,347,348,349,352,355,356,357,360,361,366,371,378,379,380,382,390,394,396,406,408,409,410,418],revers:[2,6,8,87,155,191,211,229,250,251,261,286,287,293,328,377,432,443],review:[120,261,274,285,391,396,418,437,443],rewind:317,rewrap:167,rewrit:[5,12],rewritten:19,rezwanur:389,rfac0:[120,396],rfactor:278,rfile:270,rg0:276,rgb:169,rh3:143,rh4:143,rhaphson:3,rheolog:6,rhi:407,rho0:[380,402,403],rho0_meam:380,rho:[40,113,216,289,321,334,340,342,343,355,380,381,382,394,399,401,423,447],rho_0:[402,403],rho_alpha_beta:355,rho_bkgd:380,rho_colloid:295,rho_e:290,rho_fin:289,rho_i:[381,382],rho_initi:289,rho_ref_meam:380,rho_wal:295,rhodo:10,rhodopsin:[1,10],rhosum:[],ribier:325,richardson:270,richi:[9,19],rick:[261,262,348],rick_and_stuart:262,ridg:[9,19],right:[3,6,11,12,41,144,162,163,166,188,191,211,216,226,250,303,321,349,411,423,426,433,448],rightmost:[41,188],rigid:[],rigidifi:270,rii:[89,90],rij:[189,190,251,353,404],rin:[363,374,375],ring:[],rino:73,rinv:318,rirj:[296,361],rise:29,risi:[120,396],risk:[8,269,432],rix:[89,90],rjk:[189,190],rjone:[7,9,13],rlo:407,rmask:[3,448],rmass:3,rmax:[145,189],rmdir:434,rmin0:[120,396],rmin:[145,190,371],rmsd:289,rnemd:6,robin:169,robust:[324,325,326],rock:380,rockett:390,rod:270,rodata:12,rodnei:265,roi:7,role:285,roll:12,room:[57,59],root:[11,87,89,90,285,289,333,355,430],rosati:39,rose:380,ross:380,rosski:253,rosybrown:169,rot:[6,91,253,269,285,449],rotat:[],rotaton:426,rough:[6,144,168,300],roughli:[7,10,12,41,127,142,168,205,213,214,228,229,241,257,270,278,281,282,285,319,328,333,425,432],round:[1,3,12,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,71,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,169,175,187,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,294,304,306,307,308,309,312,314,319,331,334,335,337,340,341,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,425,432,447,448],rous:206,rout:[87,363,377],routin:[5,6,8,11,15,16,38,39,56,88,148,150,216,391,407,436],roux:[6,198,214,411,443],row:[6,65,66,68,69,75,79,90,92,93,104,106,108,114,115,116,119,124,132,139,141,143,181,182,183,184,185,186,219,270,290,292,300,357],royalblu:169,rozero:380,rperp:226,rpi:255,rpm:12,rrespa:[1,3,5,7,8,16,173,174,226,229,329,334,335,336,337,338,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,378,379,380,381,382,383,385,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,412,414,415,416,432],rspace:3,rsq:[407,413],rsurfac:290,ru3:143,ru4:143,rub:20,rubia:[381,382],rudd:[384,407],rudra:[7,9],rudranarayan:[7,255],ruiz:179,rule:[],run1:[6,332,448],run2:[6,315,317,332,448],run3:[6,332,448],run4:[6,332,448],run5:[6,332,448],run6:[6,332,448],run7:[6,332,423,424,428,448],run8:[6,332,448],run:[],run_styl:[],runloop:317,runtim:[12,17,168,333],russia:9,rutherford:290,rutuparna:[408,410],ryan:9,ryckaert:[273,312],rycroft:142,s00:389,s0st:6,s2050:1,s2629:355,s319:178,s_i:[6,357],s_ij:6,sack:7,saddl:[228,328],saddlebrown:169,sadigh:[179,355,381,382],saed_vtk:118,safe:[12,168,198,214,333],safe_zon:3,safest:[3,278],safezon:393,safran:415,sagui:[319,352],sai:[1,3,12,13,169,392,393,421],said:326,sakai:409,salmon:169,salt:[350,359,380,423],same:[1,2,3,4,6,8,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,41,43,44,45,46,47,48,49,50,51,53,54,56,57,59,62,63,65,69,71,72,77,79,81,82,84,85,87,88,89,90,91,92,94,97,103,104,105,108,109,110,112,113,115,116,117,120,121,122,123,124,125,126,127,130,131,132,133,134,136,137,138,140,142,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,164,165,166,167,168,169,172,173,174,175,178,179,181,183,184,185,186,187,188,189,190,191,192,194,195,199,200,201,204,205,206,207,208,209,210,211,212,213,214,215,216,219,226,229,231,232,233,234,235,236,244,246,247,248,249,251,252,253,255,256,257,260,261,262,263,265,266,267,268,269,270,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,296,297,298,299,301,303,304,305,306,307,308,309,312,314,318,319,321,322,323,327,328,329,330,331,332,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,389,390,394,395,397,404,405,406,407,408,409,410,412,414,415,416,418,420,421,423,424,425,426,428,431,432,433,434,435,436,437,441,443,447,448,449,451],sampl:[1,2,4,6,9,10,11,12,14,91,123,137,142,166,168,181,182,184,185,193,195,203,205,207,209,229,230,253,256,265,267,271,275,276,278,282,285,288,300,329,339,354,423,437],sample_frequ:178,san:389,sandia:[0,5,7,9,13,14,17,70,111,358,380,389],sandybrown:169,saniti:[269,329],satellit:6,satifsi:448,satisfi:[3,12,73,118,120,142,143,192,216,233,273,298,326,329,361,437],satur:350,save:[6,8,12,19,40,59,164,168,191,206,207,213,214,215,256,265,290,319,329,331,339,425,428,435],sb3:143,sb5:143,sc3:143,scalabl:[],scalar:[],scale:[0,1,3,4,5,6,9,10,13,18,40,59,63,91,113,116,117,120,130,138,164,167,168,169,172,173,174,178,179,182,192,194,205,209,210,211,213,215,216,227,229,231,232,233,234,235,253,257,260,261,270,278,280,282,285,287,288,290,294,301,318,319,321,330,334,335,336,350,354,357,361,378,379,380,389,411,424,426,428,432,435,437,440,441,448,449],scalegamma:216,scalexi:[3,192,229,233],scalexz:[192,229,233],scaleyz:[192,229,233],scan:[169,190,317,424],scatter:[11,118,143],scatter_atom:11,scatter_coord:11,scenario:[6,40,61,191,259,268,278,291,299,329,427,428,432,440],scf:443,schaik:377,schedul:418,schell:409,schemat:191,scheme:[6,9,18,206,207,229,253,265,273,290,318,411],schlitter1:289,schlitter2:289,schlitter:289,schmid:353,schneider:[213,215],schoen:318,schr:443,schroding:357,schroeder:443,schulten:[214,274,319,443],schunk:278,schwen:9,sci:[73,298,348,382,390],scienc:[8,178,191,210,274,287,355,381,409],scientif:[120,355],scm:11,scratch:[12,41,188],screen:[],screenshot:11,scripe:11,script:[],scripta:67,scsl:12,sdk:[],sea:11,seagreen:169,seamlessli:259,search:[0,2,3,8,12,145,147,169,170,278,324,325,326,328,330,418,424,425,437,448],seashel:169,sec:[12,442,447],second:[1,3,6,9,10,11,12,16,17,54,57,59,61,71,88,91,105,112,121,132,138,142,143,145,146,147,166,167,169,172,181,182,183,184,185,186,191,205,206,211,226,228,253,267,269,270,273,274,275,276,278,287,288,290,301,318,321,325,326,328,329,333,338,339,340,342,343,348,349,355,357,358,361,362,364,368,371,380,384,386,406,409,410,411,418,419,420,421,423,425,430,432,436,437,441,443,447,448,449,450,452],secondari:[3,156],sectinn:451,section:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,58,59,63,64,65,66,67,68,69,71,74,75,78,79,80,81,83,86,87,88,89,90,91,92,93,96,97,98,99,100,101,103,104,105,106,107,108,109,111,112,113,114,115,118,119,120,122,123,124,125,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,145,150,151,152,153,154,155,156,157,158,159,161,162,163,164,167,168,170,172,175,176,177,178,179,181,182,183,184,185,186,187,188,189,190,191,193,194,195,197,198,200,201,202,204,205,206,207,208,210,212,213,214,215,216,217,218,219,220,222,223,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,242,244,245,246,247,248,249,251,252,253,255,256,257,259,260,261,262,263,264,265,266,267,270,272,273,274,278,281,282,283,284,285,286,287,288,289,290,291,293,294,296,297,301,302,304,305,306,307,308,309,310,312,313,314,319,320,321,323,327,328,330,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,423,424,428,431,432,433,434,436,437,438,441,443,448,449],section_acceler:[9,12,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,109,112,122,131,150,151,153,154,155,156,158,159,161,162,164,175,187,201,204,208,213,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,281,283,294,304,306,307,308,309,312,314,319,334,335,337,340,342,343,344,345,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,381,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416,432],section_accerl:355,section_command:[0,1,9,303],section_error:[7,12],section_exampl:[2,6],section_histori:[7,12],section_howto:[6,8,9,11,12,40,42,57,59,64,66,67,68,70,71,72,73,75,76,77,78,80,81,82,83,84,85,86,87,89,90,93,94,95,96,97,98,99,100,101,104,106,109,110,111,114,116,117,120,121,124,126,138,139,141,142,146,165,181,228,239,242,245,293,338,351,418,423,426,437],section_modifi:[6,7,42,167,168,441],section_packag:12,section_perf:7,section_python:[6,12],section_start:[3,4,6,9,11,322,328,417,418,432,438,441],section_tool:[6,7],see:[1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,57,58,59,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,244,245,246,247,248,249,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,275,277,278,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,299,301,302,303,304,305,306,307,308,309,310,312,313,314,315,318,319,321,322,323,325,326,327,328,329,330,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416,417,418,419,420,421,423,424,425,426,428,429,430,431,432,433,435,437,438,439,440,441,442,443,448,449,450,451,452],seed1:438,seed2:438,seed:[3,144,147,166,168,177,179,189,190,191,193,195,202,205,206,207,213,214,215,216,253,256,260,265,270,278,282,285,290,297,341,353,354,418,433,438,443,448,449],seed_com:214,seed_drud:214,seek:[41,188],seem:[6,192,291,325,380,432],seen:[12,216,299],segement:3,segment:[3,4,6,7,40,42,82,113,172,242,270,278,353,367,393,404,405,423,431,433],select:[6,12,15,17,59,71,117,118,133,138,143,144,164,168,170,177,179,184,185,194,195,202,205,210,211,226,274,277,285,286,291,293,295,297,298,300,316,318,324,328,330,333,363,368,380,420,424,426,432,433,437,448],self:[],sellerio:13,semi:[3,170,178,179,250,252,424],semiax:123,semimet:357,send:[0,3,5,7,8,11,12,169,210,420],sender:[3,420],sens:[1,3,6,7,18,39,41,42,59,163,167,181,183,184,185,186,188,191,194,206,207,212,213,214,215,256,260,265,271,278,285,286,290,293,301,328,349,369,373,408,409,410,418,423,428,432,435,440],sensabl:210,sensibl:104,sensit:[2,6,73,192,265,449],sent:[169,210,316],separ:[2,6,7,12,13,40,41,76,116,120,142,144,147,169,170,178,182,188,189,190,191,192,195,198,205,213,214,229,241,253,256,257,259,261,265,270,273,278,281,282,283,286,293,301,319,333,340,342,349,350,352,378,379,380,386,391,396,405,406,407,410,415,421,423,424,425,432,435,440,443,449,450,451],seper:350,sequec:448,sequenc:[2,3,12,41,59,167,168,169,170,188,207,228,301,321,328,364,390,438,448],sequenti:[59,60,169,390,424],sequestr:7,ser:252,seri:[3,4,6,13,18,120,167,168,169,182,186,206,207,256,332,335,360,380,384,394,397,407,421,430,431,440,441,448],serial:[],serial_icc:12,serious:8,serv:[6,146,278,404],server:[1,212,333],set:[],set_callback:203,set_energi:203,set_vari:[6,11,421],setarea:216,sete:[181,191],setenv:[11,12,346],setfl:[13,334,355],setforc:[],setgamma:216,setmask:8,settl:192,setup:[3,4,6,7,8,11,12,13,16,37,40,55,59,71,87,91,132,145,146,147,148,163,169,178,191,194,278,291,313,329,330,333,405,420,423,431,450,452],setup_pre_exchang:8,setup_pre_forc:8,setup_pre_force_respa:8,seven:382,sever:[1,4,5,6,7,8,10,11,12,13,15,18,39,40,63,71,87,138,145,148,163,167,170,172,178,189,190,192,207,213,216,220,229,255,257,259,270,274,278,285,294,316,321,326,333,336,339,343,354,355,364,373,377,380,384,390,392,393,418,421,425,429,437,441,443,448,449],sfactor:[3,168,169],sfftw:12,sgi:12,sgmc:179,sgrid:278,sgroup:142,shade:168,shake:[],shan:[17,262,348],shanghai:[9,13],shape:[3,6,8,40,41,58,59,62,71,82,113,123,127,128,144,146,166,168,169,172,173,184,188,192,194,213,227,229,231,234,237,238,246,247,260,278,291,299,338,360,394,420,423,424,425,433],shapei:[113,423],shapex:[113,423],shapez:[113,423],shapshot:428,share:[],shared0:12,sharon:270,sharp:[299,380,410],shawn:9,shear:[3,4,5,6,7,9,59,61,127,166,192,194,216,229,247,278,293,296,361,378,379,389],sheet:427,shell:[],shen:9,shenderova:335,sheppard:325,shflag:12,shield:[],shift:[],shiftse:278,shiga:[6,229,230],shini:[168,451],shinoda:[6,9,229,230,395],shiny:168,ship:170,shlib:[11,12],shlibflag:12,shock:[4,9,172,177,227,233,260,297,371],shockvel:[227,260],shortcut:[192,229,257,270],shorter:[3,119,205,251,330,384,431],shortest:[168,330,336,432],shorthand:169,shoul:412,should:[1,2,3,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,61,70,71,73,81,83,87,91,96,97,98,102,103,109,110,112,121,122,123,126,127,130,131,132,134,137,140,142,144,146,148,150,151,152,153,154,155,156,158,159,161,162,164,165,166,167,168,169,173,174,175,176,179,187,188,189,190,191,192,194,195,197,198,200,201,202,203,204,205,206,207,208,209,211,213,214,215,216,218,219,220,221,226,229,231,232,233,234,235,236,241,244,246,247,249,251,252,253,254,255,256,257,258,260,261,262,263,264,265,266,267,268,269,270,272,273,275,278,279,281,282,283,284,285,286,289,290,291,293,294,295,296,297,298,299,300,301,303,304,305,306,307,308,309,312,314,319,321,322,324,326,327,328,329,330,331,333,334,335,337,338,340,341,342,343,344,345,346,347,348,349,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,379,380,381,384,385,386,387,388,389,391,392,394,395,397,404,406,407,408,409,410,411,412,414,415,416,418,419,420,421,423,424,425,426,427,428,430,431,432,433,435,439,440,441,443,448,449,450],shouldn:[3,8],show:[6,11,12,116,251,328,363,380,384,407],shown:[1,12,17,41,96,97,118,120,130,143,163,188,191,213,229,247,253,256,265,285,318,357,358,360,361,377,394,423],shrank:71,shrink:[3,6,41,57,59,71,146,166,167,168,173,174,177,188,194,195,211,216,251,278,297,301,318,319,326,349,369,373,384,423,424],shrunk:71,shut:[6,11,329,422],si4:143,siam:298,sic:[4,349,364,380,386,406,408,410],sic_tersoff:390,sicc:[356,406,408,410],sicg:[408,410],sicsi:[356,406,408,410],side1:426,side2:426,side3:426,side4:426,side:[3,8,41,57,61,134,144,179,180,188,191,195,205,211,216,226,251,256,264,275,295,299,300,301,328,349,360,361,394,412,421,423,426,433],sidewai:4,sienna:169,siepmann:293,sigam:347,sigam_ii:367,sige:[408,410],sigma0:339,sigma14:377,sigma1:339,sigma2:339,sigma:[3,6,10,45,46,50,54,87,150,167,169,173,174,205,216,251,278,294,295,299,321,330,333,335,338,339,340,344,345,347,352,353,354,356,357,360,362,363,367,368,369,370,371,372,373,374,375,376,377,383,384,394,395,400,406,412,432,447,448,449],sigma_14:344,sigma_:350,sigma_c:347,sigma_cc:[335,347],sigma_h:359,sigma_i:[358,384],sigma_ii:[367,412],sigma_ij:[367,384,412],sigma_j:384,sigma_max:354,sigma_ss:347,sign:[3,6,12,155,163,250,275,298,303,431,440,448],signicantli:17,signifi:[3,66,75,90,93,104,106,114,124,139,141],signific:[7,12,18,86,206,227,230,265,278,291,357,360,380,450],significantli:[1,6,39,121,142,216,229,269,357,406],sij:182,sikandar:17,silbert:361,silent:[169,421,434],silicon:[356,380,406,423],sill:389,silver:169,sim:[9,395],similar:[5,6,7,8,9,12,17,18,40,41,46,59,68,87,112,115,121,144,145,167,169,172,173,174,181,188,203,204,206,213,219,220,230,259,260,265,269,270,282,285,295,296,298,300,319,324,325,327,335,338,339,353,355,357,361,377,378,384,389,390,420,425,430,432,437,439,441,443,448,449,450,452],similarli:[3,6,7,8,59,112,140,146,148,166,167,168,169,180,181,183,184,185,186,190,194,200,211,229,231,232,234,235,255,257,270,271,273,278,285,286,293,299,304,319,321,328,331,343,361,373,406,420,423,426,427,432,433,437,451],simluat:[6,39,169,278,378,424,425],simlul:[270,290],simmul:293,simpl:[],simpler:[8,42,169,270],simplest:[3,8,40,66,75,90,93,104,106,114,116,124,139,141,261,443],simpli:[1,3,6,8,11,12,14,17,66,71,75,88,90,93,95,104,106,113,114,119,124,139,141,147,148,169,172,173,174,181,183,184,185,186,190,192,194,198,203,212,214,219,229,253,257,268,270,271,286,292,293,318,319,321,327,328,333,343,352,364,373,380,384,420,421,428,431,438,441,447,448],simplif:357,simplifi:[179,269],simplist:11,simualt:319,simul:[],simulatan:333,simulation_nam:393,simulatoin:[12,424],simult:333,simultan:[6,7,15,16,194],sin:[194,226,295,298,300,390,423,426,433,448],sinc:[0,1,2,3,6,8,9,10,11,12,13,15,16,21,22,33,39,41,44,54,59,64,67,71,73,89,90,110,116,118,123,124,134,142,146,147,149,150,152,157,167,168,169,172,173,174,175,176,179,180,181,182,183,184,185,186,187,188,191,192,193,194,195,199,200,205,207,209,212,213,215,216,226,229,231,232,233,234,235,238,241,247,251,253,256,258,259,265,268,270,274,277,278,286,290,291,292,293,295,296,299,300,301,302,304,305,317,319,326,327,328,329,332,333,334,335,339,342,343,344,345,347,348,352,353,354,355,356,360,361,362,364,365,366,368,369,371,372,373,374,375,376,377,378,379,380,381,382,384,387,390,391,392,393,394,395,396,397,406,407,408,409,410,416,418,420,421,423,424,425,426,428,431,432,433,434,435,437,441,443,447,448,449,451],sinclair:[7,355,405],sine:390,singapor:120,singh:334,singl:[1,2,3,6,7,8,9,11,12,14,15,16,17,18,40,41,42,57,59,61,63,65,66,68,69,75,77,79,87,88,90,92,93,104,106,108,113,114,115,116,117,119,124,139,141,142,144,167,168,169,170,172,177,180,181,182,183,184,185,186,188,190,191,192,195,198,202,204,209,216,219,226,229,230,233,241,253,255,256,258,269,270,271,273,278,280,290,292,295,296,298,300,301,303,318,319,324,327,328,329,330,332,333,334,335,339,344,346,348,354,355,356,357,358,361,362,363,364,365,366,380,381,382,384,386,387,390,391,392,393,394,396,397,406,408,409,410,418,419,421,423,430,431,432,433,434,435,436,437,440,448,451,452],singleel:339,singular:[377,378,379],sinnott:[262,335,348],sinusoid:[144,194,295,296,298,300],sio:348,sirk:[121,404],sisic:[356,406,408,410],sisisi:[356,406,408,409,410],sister:346,sit:[252,423],site:[0,1,2,3,4,5,6,7,8,10,11,12,13,14,15,16,17,67,70,87,210,216,217,273,319,334,339,349,355,359,369,373,377,387,392,393,411],situat:[9,192,205,216,229,253,271,325,339],sival:143,six:[6,120,182,183,386,390],sixth:386,sixthpow:[345,384],size:[],size_restart:8,sizex:235,sjplimp:[0,7,11,12],sjtu:9,skew:[3,6,58,59,146,168,194,229,423,426],skin:[3,12,39,61,73,115,145,147,205,241,270,290,329,330,333,388,441,447],skip:[12,16,33,157,255,317,327,332,368,423,428,431,440,448],skyblu:169,slab:[3,6,71,132,184,256,275,318,319,329,384],slateblu:169,slategrai:169,slater:[],sleight:54,slepoi:380,slice:[],slider:11,slight:[3,12,290],slightli:[1,6,39,40,167,168,170,265,270,319,335,349,367,369,373,408,410,418,431,450],sligthli:352,sliozberg:404,slip:[3,172,278,294,300],sllod:[],slope:[6,103,104,286,288,293,350,448],slot:1,slow:[3,6,7,12,39,206,210,213,214,227,278,285,318,328,333,384,432,443,449],slower:[1,10,17,39,214,319,333,339],slowest:[290,420],slowli:[12,71,188,294,326,397,425],slurm:12,slurm_localid:12,sm3:143,small:[],smallbig:3,smaller:[1,3,6,12,16,17,39,56,59,61,71,119,142,146,167,168,169,179,195,199,205,216,252,270,278,288,303,318,319,324,333,367,384,405,412,413,423,430,432,452],smallest:[3,70,72,142,227,267,448],smallint:3,smallq:319,smallsmal:[3,12],smart:207,smd:[],smi:[3,333],smirichinski:9,smit:205,smith:387,smmoth:433,smooth:[],smoother:144,smoothli:[54,120,286,293,344,362,375,377,410,416],smpd:12,sn2:143,sn4:143,sna:[],snad:[],snap:[],snapcoeff:396,snaphot:428,snapparam:396,snapshot:[],snav:[],snb:17,snow:169,soc:363,socket:[12,17,18,212,420],soft:[],softer:[295,299],softwar:[1,6,11,12,14,15,16,17,18,19,142,210,255,271],sole:[189,190,328,390],solid:[4,6,7,10,39,40,41,59,70,73,91,121,142,178,188,192,194,199,219,229,231,232,234,235,251,252,257,270,285,288,319,321,340,371,389,423],solut:[3,6,13,142,192,199,227,268,273,278,299,448],solv:[3,12,18,216,261,273,288,290,319,325,379],solvat:[4,10,144],solvent:[4,7,13,61,71,145,147,188,202,206,207,213,229,268,270,275,278,286,293,294,344,347,349,350,359,369,378,379,394,405,423,433],solver:[],some:[1,2,3,4,6,7,8,10,11,12,13,16,17,18,39,40,41,55,61,63,71,102,105,107,113,117,119,123,124,125,136,137,138,144,147,152,155,163,165,167,168,169,172,173,174,177,179,180,181,182,183,184,185,186,188,190,191,192,193,202,205,227,229,230,258,259,261,263,270,274,279,285,290,291,292,294,295,301,316,317,318,319,324,325,326,327,328,329,330,333,336,338,339,346,349,355,357,364,384,392,393,405,407,418,420,421,422,423,425,428,429,430,431,432,433,435,437,440,441,447,448,449,452],somehow:3,someindex:302,someon:[7,11,326],someth:[2,3,7,8,11,12,59,192,229,295,298,300,329,364,421,430],sometim:[2,3,6,8,12,18,184,192,229,286,293,318,330],somewhat:[7,9,12,70,124,134,181,229,318],somewher:[17,230,357],soon:[179,191,202,205,210],sophist:7,sorensen:437,sort:[3,13,16,39,71,167,169,170,210,328,329,333,354,424,425,451],sound:[216,227,402,403],soundspe:[402,403],sourc:[],source_integr:178,sourceforg:11,south:120,souza:286,space:[2,3,6,8,11,12,18,41,59,71,118,120,133,138,143,144,164,166,168,173,174,177,183,184,185,188,190,194,195,211,216,223,226,229,252,253,268,271,278,295,297,298,300,303,318,319,321,327,328,329,340,342,343,349,352,355,357,367,369,373,380,387,390,395,407,413,415,420,423,426,435,441,443,448,449],spahn:361,span:[2,12,38,71,173,174,184,211,270,318,334,335,339,348,355,358,365,366,380,381,382,386,390,396,406,408,409,410,417,418,426,427,448],spars:[71,164],spatial:[],spawn:210,spc:[],spcpu:441,speak:[17,278,285],spearot:[118,143,271],specfi:[12,107,211,426],speci:[],special:[],special_bond:[],specif:[1,2,3,6,7,8,9,10,12,13,15,17,18,22,29,33,40,41,42,50,63,71,108,113,115,116,124,126,129,144,152,157,167,168,169,170,172,173,174,177,178,181,182,183,184,185,186,188,191,193,202,203,205,206,210,216,224,256,258,259,262,270,285,290,291,295,301,305,319,326,328,333,335,338,339,351,355,360,361,364,365,366,367,380,384,392,393,394,405,406,411,412,420,423,424,428,429,430,432,433,439,440,441,447,448,449,450],specifi:[2,3,6,7,8,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,63,65,66,68,69,70,71,73,75,76,77,78,79,80,81,83,85,86,87,88,90,91,92,93,94,95,96,97,98,99,100,101,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,121,122,124,126,131,132,133,138,139,140,141,142,143,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,201,204,205,206,207,208,209,211,212,213,214,216,217,218,219,221,224,225,226,227,228,229,230,231,232,233,234,235,236,241,244,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,285,288,289,290,292,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,313,314,317,318,319,321,322,323,326,327,328,329,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,447,448,449,450,451,452],specifii:[207,216],speciti:432,spectral:396,spectrum:[9,120,260,265],sped:[39,227],speed:[1,3,6,9,12,14,15,16,17,18,19,39,41,169,188,213,216,227,260,278,285,291,297,318,319,328,333,339,349,384,402,403,408,418,432,438],speedup:[1,18,319,432],spefici:[144,168,363],speicifi:327,spell:426,spellmey:[6,150,435],spend:180,spent:[1,12,13,15,418,437],sph:[],sph_lammps_userguid:9,sphere1:216,sphere:[],spheric:[],spheriod:[3,6],spherioid:278,spheroid:[6,270,278],spike:116,spin:[9,40,113,296,336,357,423],spirit:7,spit:3,spline:[],split:[1,3,6,12,18,41,181,184,188,214,229,298,318,333,412,417,420,432],splittol:[6,318],sppark:6,spread:[1,6,12,303,431],spring:[],springer:274,springgreen:169,sptial:71,sputter:195,sq2:[3,321],sqrt:[2,3,59,81,89,205,213,214,215,251,278,294,296,321,347,353,355,359,361,380,384,448],squar:[],squeez:[192,211,378,379],squibb:[5,7],sr2:143,src:[0,1,3,4,6,7,8,9,11,12,14,15,16,17,18,19,142,167,203,273],srd:[],srolovitz:355,srp:[],srun:12,ssao:[168,451],stabil:[6,213,229,339,392],stabl:[6,64,216,233,269,339,443],stabli:206,stack:[3,8,70],stage:[3,87,172,203,228,264,301,328,418,437,448],stagger:[1,3,169,319,430,439,448],stai:[3,14,17,173,174,227,243,260,333,423],stamp:[285,424],stamped:12,stan:17,stand:[0,6,7,13,266,392,393,421],standard:[],stanford:9,starikov:290,start:[],start_6:359,start_7:432,startstep:448,stat:[12,54,148,251,265,326,353],statcoul:447,statcoulomb:447,state:[],statement:[3,421,422],stationari:[],statist:[3,6,12,39,41,64,189,190,191,206,207,213,214,215,255,256,260,265,270,273,278,289,290,291,326,328,335,353,354,361,378,415,418,425,431,433,437,440,441],statu:[3,12,54,60,148,193,198,214,348,437],statvolt:447,std:12,stdin:[3,12,317],steadi:[6,227,233,260],steelblu:169,steep:407,steepest:[7,325],steer:[7,9,193,196,274],stegailov:290,steinhaus:443,stencil:[3,216,318],step:[1,2,3,6,8,10,11,12,13,14,15,16,17,18,19,39,71,91,96,97,110,116,117,121,130,140,142,167,168,169,170,172,173,174,178,179,181,182,183,184,185,186,188,189,190,191,192,194,195,198,199,202,203,205,207,210,211,214,227,241,251,252,258,259,260,261,262,263,271,273,274,278,280,283,284,285,286,287,288,289,290,291,292,293,300,301,303,317,318,324,326,328,329,353,359,363,380,392,393,418,420,421,425,427,428,430,431,432,437,438,440,441,443,448,452],stepani:274,stepwis:87,stesman:285,steve:[0,5,7,13],steven:191,stiff:[6,40,51,189,190,252,253,326,389,443],stile:350,still:[1,3,6,9,11,12,13,14,17,18,38,41,61,71,108,116,142,148,164,165,167,169,173,174,188,209,213,241,261,265,278,290,303,318,319,324,345,355,360,361,364,368,378,388,392,394,397,405,423,425,431],stilling:[3,5,7,15,88,356,382,390,405,406,435],stipul:210,stl:71,stochast:[4,7,9,172,207,278,285,300,354],stoddard:352,stoke:[216,294],stoll:[213,215],stone:[9,19,319,352],stop:[],stopstep:448,stopthresh:[41,188],storag:[3,12,15,292,333,435],store:[],store_st:279,storm:12,stouch:7,str:448,straatsma:6,straddl:[3,59,61,134,211,270,275,301,423,427,433],straight:270,straightforward:[13,357,443],strain:[3,6,59,80,166,192,194,227,229,233,378,379],strang:[164,168,448],strategi:[],stratford:216,strcmp:303,stream:[3,6,112,121,124,127,128,168,178,194,206,207,213,214,247,256,265,278,449],streamlin:[12,431],streitz:[],streiz:349,strength:[3,120,138,149,168,269,295,299,364,393,394,435],stress:[],stretch:[3,54,59,117,189,274],strict:396,strictli:[6,41,164,188,227,260,285,423],stride2:448,stride:[169,207,430,439,448],strietz:349,strike:195,string:[2,3,6,11,12,41,144,167,169,181,182,183,184,185,186,188,205,258,271,303,320,332,380,390,391,392,396,419,421,423,433,434,440,441,448],strip:448,strong:[261,335],stronger:6,strongest:[378,379],strongli:[1,6,13,195,270,273,290,443],structrur:3,structur:[],structured_point:271,strucur:73,stuart:[261,262,335,348,405],stub:12,stuck:192,student:255,studi:[6,105,371],studio:12,stukowski:[179,355],style1:[33,50,157,310,364,423],style2:[33,50,157,310,364,423],style:[],style_nam:[229,230],stylist:8,sub1:434,sub:[1,3,4,6,7,8,9,11,12,13,18,33,37,39,40,41,42,50,55,58,61,63,68,87,91,107,120,138,146,157,163,168,169,173,174,188,192,194,229,230,233,252,260,265,270,273,290,291,299,301,310,313,321,323,333,338,348,354,360,361,363,364,384,392,393,394,411,412,420,423,426,432,440],subbox:[117,168,169],subdirectori:4,subdivis:216,subdomain:216,subequ:11,subgroup:[167,451],subject:[6,41,147,188,411],submit:[],subramaniyan:13,subroutin:333,subscript:[11,290,304,358,448],subsequ:[6,11,12,41,59,145,169,188,192,205,285,290,291,292,321,332,355,405,421,423,424,430,433,434,442,448,452],subset:[6,11,12,16,41,80,120,167,169,188,225,229,231,232,233,234,235,256,257,261,270,328,333,335,339,364,384,417,420,423,425,428,432,448],substanti:[6,16,406,432],substep:229,substitut:[1,2,3,12,167,212,328,332,357,421,434,448],substract:349,substrat:[146,192,229,231,232,234,235,257,270,423],substyl:[377,432],subsystem:290,subtl:[94,96,97,207],subtleti:130,subtract:[3,6,54,63,91,94,97,102,103,105,112,121,122,123,124,125,126,127,128,130,131,132,133,134,136,137,167,172,181,205,206,209,213,214,215,217,221,225,247,254,270,301,329,376,423,433,441,448,449],succe:12,succeed:182,succesfulli:3,success:[2,6,11,12,14,15,116,167,169,179,182,192,195,205,241,256,270,278,285,303,326,328,421,430,431],successfulli:[3,11,167,195,421,434],successulli:11,successv:428,sucessfulli:3,sudden:36,suddenli:299,sudo:[11,12],sufac:42,suffer:[16,17,18,293,299,333],suffici:[2,3,7,17,18,41,61,71,184,188,227,229,252,278,285,292,295,303,368,423,443],suffix2:12,suffix:[],suggest:[0,7,12,227,260,421,443],suit:[7,9,13,174,216,357],suitabl:[4,12,13,17,54,87,167,191,259,282,339,346,361,377,380,392,393,418,437],sum:[3,6,8,9,12,40,70,71,76,80,83,88,89,90,94,98,103,105,107,109,110,112,116,117,120,121,122,124,125,126,127,130,131,132,133,134,136,138,140,141,142,181,182,183,184,185,186,195,203,206,213,214,219,251,252,256,260,265,270,271,274,277,288,290,292,295,299,301,318,319,326,338,349,353,357,358,367,369,372,380,392,393,396,412,421,441,443,448,449],summar:[6,358],summari:[],summat:[6,9,42,70,88,318,319,343,349,355,356,369,373,406,408,409,410],summer:[3,13,184,392,393],sumsq:117,sun:[21,43,151,304,345,384,393],sunderland:17,sup:[252,260,265,348,443],supercomput:[12,17,18,421],superpos:[364,405],superposit:7,supplement:[207,392,393],supplementari:[193,360,394],suppli:[12,164,205,227,290],support:[1,3,6,7,8,9,11,12,13,14,15,16,17,18,19,40,41,42,87,88,102,107,167,168,169,170,173,174,175,176,181,188,191,192,193,200,203,207,208,211,213,214,215,216,224,227,229,231,232,233,234,235,246,247,248,249,251,252,257,260,262,264,269,270,275,277,281,282,283,284,288,293,295,299,316,317,318,319,325,326,327,333,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,410,411,412,414,415,416,420,424,425,430,432,433,434,436,437,443,447,451,452],suppos:[3,8,358,448],suppress:[6,12,142],sure:[6,8,11,13,14,164,173,174,192,270,273,300,355,407],surf:145,surfac:[3,4,6,8,40,42,57,70,118,120,142,144,147,168,172,195,202,211,216,219,251,262,269,275,278,285,290,295,299,300,328,339,364,378,379,412,415,420,426],surface_mov:290,surfact:[350,359],surpris:357,surrog:9,surround:[38,56,70,144,164,169,192,229,231,232,234,235,251,257,270,407,443],suspect:3,suspens:[378,379],sustain:[167,192,361],suzuki:[229,270],svg:6,svn:[7,11,12],sw_exampl:391,swamp:270,swap:[],swegat:289,swiggl:[3,226,295,298,300,426,448],swiler:[120,396],switch7_section_start:359,switchflag:[120,396],swm4:443,swol:53,swope:6,sxx:169,sy0302:9,symbol:[6,12,118,143,267,339,357,396],symmetr:[6,70,87,93,112,121,173,174,192,229,230,286,293,334,346,352,355,408,410,448],symmetri:[3,5,6,7,8,63,64,70,146,167,227,251,304,319,334,423,443],sync:[3,6],synchron:[1,207,328],synechococcu:7,syntax:[],sysdim:252,sysstem:339,system:[],system_:253,systemat:[6,213],systemx:3,t10:438,t11:438,t12:438,t13:438,t14:438,t15:438,t3e:12,t_chain:3,t_corr:3,t_correl:418,t_dephas:418,t_e:290,t_e_min:290,t_equil:[287,288],t_event:[3,418,437],t_hi:437,t_infil:290,t_init:[260,290],t_iter:3,t_lb:216,t_lo:437,t_order:3,t_oufil:290,t_out:290,t_outfil:290,t_qm:260,t_switch:[287,288],t_target:341,ta06a:396,ta5:143,tab:[2,423],tabbernor:118,tabinn:384,tabul:[3,7,13,22,37,38,44,55,56,65,71,79,92,164,278,318,334,339,340,342,343,344,345,346,349,355,357,369,373,387,390,393,395,405,407,408,413,425],tabular:390,tabulate_long_rang:393,tad:[],tadmor:9,tag:[178,197,443],tagint:3,tail:[3,87,110,138,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,352,353,354,355,356,357,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,425,441],tailor:[71,291],tait:[9,402,403],taitwat:[],take:[1,2,3,6,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,77,87,89,91,109,112,113,116,117,121,122,131,138,142,148,150,151,152,153,154,155,156,158,159,161,162,164,167,168,169,173,174,175,187,188,192,194,201,204,208,212,213,214,229,231,232,233,234,235,236,244,246,247,249,262,270,272,273,275,276,277,278,280,281,282,283,291,294,301,304,305,306,307,308,309,312,314,318,319,323,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,355,356,358,359,360,361,362,363,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,392,393,394,395,397,404,406,407,408,409,410,411,412,414,415,416,417,421,424,431,432,433,440,441,448],taken:[6,59,144,166,191,195,205,206,207,213,214,215,216,256,260,263,290,308,355,357,360,406,418,432,433],talk:[6,7],talli:[3,6,8,41,107,113,181,183,184,185,188,190,213,215,230,278,286,293,357,359,363,392,393,448],tan:[169,448],tandem:[4,16,270],tangent:228,tangenti:[6,108,278,296,300,361],tanh:290,tantalum:[4,396],taper:[3,263],tar:12,tarbal:[0,8,11,12],target:[3,6,7,8,11,12,17,39,41,169,177,188,192,193,195,205,206,207,213,214,215,229,230,231,232,233,234,235,246,247,248,249,253,257,260,265,270,274,276,281,282,283,284,289,290,293,294,297,316,319,341,353,418,429,431,449],target_fil:289,task:[1,6,7,12,13,14,15,16,17,18,54,169,210,253,291,333,421],taskset:16,tatb:[4,266],tatom:443,tau:[3,133,213,214,216,229,257,270,281,282,287,288,290,442,447],tau_1:206,tau_k:206,tau_n_k:206,tb3:143,tbead:136,tbp:339,tchain:[229,230,233,247,248,270],tcl:265,tcom:214,tcsh:[11,12,346],tdamp:[213,229,230,233,270,281,282],tdephas:418,tdrude:[129,198,214,443],teal:169,tech:[7,9,13],technic:[6,7,9,216,263,278,393],techniqu:[6,7,9,87,172,192,227,260,270,294,297,319,384,407,443],technolgi:9,technolog:[9,14,19,210],tell:[2,6,11,12,37,55,163,172,252,313,329,392,393,405,421,425,443],telsa:17,temeperatur:11,temp:[],temp_drud:443,temp_eff:97,tempcom:[123,137],temper:[],temperar:253,temperatur:[],temperature_definit:178,tempfix:438,templ:[7,9,18],templat:[3,8,13,17,19,40,144,145,147,195,205,256,270,273,327,423],templeton2010:178,templeton2011:178,templeton:[9,178],tempor:206,temporari:[2,430],temporarili:[164,269,436,437],ten:14,tend:[29,229,251],tensil:[7,194],tensor:[3,6,8,63,82,83,89,90,91,93,106,112,120,121,122,123,124,125,126,127,128,130,131,132,133,134,135,136,137,192,216,219,229,230,233,255,257,270,293,318,319,327,357,378,379,441,448],tenth:317,term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,40,45,46,61,87,88,89,91,110,112,121,123,132,137,138,151,152,153,164,169,173,174,180,182,183,186,194,200,206,207,208,213,214,215,216,228,229,230,231,232,233,234,235,246,247,249,253,257,260,269,270,276,281,282,283,290,292,294,296,304,305,314,318,326,329,334,335,339,340,341,342,343,344,345,347,348,349,350,351,352,353,355,356,357,358,360,361,362,369,373,376,377,378,379,380,381,382,384,387,394,404,406,408,409,410,415,432,433,435,441,443],termin:[118,229,326,328,422,431],termostat:282,terrel:325,terri:7,tersoff:[],tersoff_1:[408,409,410],tersoff_2:[408,409,410],tersoff_mod:409,tertiari:156,tessel:[9,142],test:[],test_descriptor_str:3,testf:164,testu:164,tether:[6,268,274,275,277,288,359],tex:8,texa:389,texas_holdem:269,text:[2,3,4,6,7,8,12,13,38,41,56,164,167,168,169,172,178,181,182,183,184,185,186,188,193,210,258,289,290,302,319,321,328,355,358,368,380,396,407,419,423,424,440,448,450],textur:17,tfactor:[3,169],tfinal:448,tfix:269,tfmc:[],th4:143,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,39,40,41,42,56,57,58,59,61,63,68,71,76,86,88,105,108,112,115,116,119,121,142,145,146,147,153,164,166,167,169,172,177,179,181,183,184,185,186,188,189,190,191,192,194,195,196,199,202,205,206,207,208,211,212,213,216,227,251,252,256,257,258,259,260,261,263,265,268,269,270,271,274,275,276,278,282,283,285,286,290,293,294,295,296,297,298,299,300,301,303,318,319,324,325,326,327,328,329,330,333,338,339,340,342,343,344,355,357,360,361,367,378,379,380,384,392,393,394,397,405,406,407,410,412,413,415,418,419,420,421,423,424,425,426,427,428,431,432,435,437,438,440,448,449,450],thank:[210,408,410],thb:393,thb_cutoff:393,thb_cutoff_sq:393,thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,39,40,41,42,43,45,46,47,48,49,51,53,54,55,56,57,59,61,63,64,66,68,70,71,74,75,81,82,84,87,89,90,91,93,103,104,106,108,109,112,114,115,116,117,119,120,122,123,124,127,130,131,137,139,141,144,146,147,148,150,151,153,154,155,156,158,159,161,162,163,164,167,168,169,172,173,174,175,177,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,200,201,204,205,206,208,209,210,213,214,216,219,226,229,231,232,233,234,235,236,237,238,239,244,246,247,249,255,256,257,258,259,261,262,269,270,271,272,273,278,279,281,282,283,285,289,290,292,293,294,296,298,299,301,303,304,306,307,308,309,312,313,314,316,318,319,321,323,325,326,327,328,329,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,348,349,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,385,386,387,389,390,392,393,394,395,396,397,404,405,406,407,408,409,410,411,412,413,414,415,416,419,421,423,424,425,426,427,428,432,433,435,436,441,443,448,450,451],them:[1,2,3,4,6,7,8,9,11,12,13,14,39,40,41,54,59,71,91,107,114,117,119,146,151,167,168,169,170,180,181,182,183,184,185,186,188,191,192,194,202,210,213,214,225,229,231,232,233,234,235,246,249,251,257,259,267,268,269,270,273,278,281,282,283,285,289,290,292,296,297,298,300,301,304,319,321,327,328,329,333,334,339,346,355,358,360,384,394,397,412,418,421,423,430,435,438,443,448,449],themselv:[6,11,147,173,174,188,214,318,319,328,330,334,339,349,355,377,380,381,382,396,448],theor:285,theorem:[206,213,339],theoret:[105,210,260,406],theori:[3,9,12,40,120,178,193,207,229,252,318,319,339,415,437],thereaft:[71,221,254,270,286,293,421],therebi:[291,378,379],therefor:[3,6,12,64,87,129,179,198,205,214,216,273,285,319,351,391,393,406,411,416,432,443],therein:[6,380],thereof:87,thermal:[],thermo:[],thermo_modifi:[],thermo_p:[3,63,109,421,441],thermo_press:[63,112,192,198,229,231,232,233,234,235,257,440,441,443],thermo_styl:[],thermo_temp:[63,112,122,191,192,205,229,231,232,233,234,235,246,247,249,252,257,281,282,283,440,441,443],thermoberendsen:6,thermochem:447,thermochemistri:357,thermodyam:[441,447],thermodyanm:[63,191,278,301,432],thermodynam:[],thermophys:384,thermost:[6,126,177,193,198,214,297,443],thermostat:[],thermostatequ:6,thesi:[318,319,378,391],thess:340,theta0:[20,21,24,26,27,28,32,33,35,36,120,153,269,312],theta0max:120,theta10:339,theta1:[151,304,339],theta2:[151,304,339],theta3:[304,339],theta4:339,theta5:339,theta6:339,theta7:339,theta8:339,theta9:339,theta:[3,6,26,27,37,38,63,65,80,120,143,144,153,166,168,208,265,269,290,304,312,363,390,409,423,426,433],theta_0:386,theta_:[312,339],theta_c:363,theta_ijk:339,theta_ijl:304,theta_jik:[381,382],theta_pi:339,theta_sigma:339,thex:261,thi:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,444,445,446,447,448,449,450,451,452],thick:[71,118,168,184,426],thie:110,thijss:285,thin:[116,168],thing:[3,6,11,12,54,68,71,192,229,257,270,278,420,421,425,448],think:[3,6,7,8,11,13,169,270,301,306,309,321,326,364,392,393,407,421,425,428,448],third:[6,9,29,91,120,121,142,181,182,183,184,185,186,206,267,275,276,290,348,358,380,386,411,418,419,421,423,426],thirumalai:156,thistl:169,tho:356,thole:[],thompson:[0,5,7,9,13,112,120,121,396],thoroughli:9,those:[1,2,3,4,5,6,7,8,12,13,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,43,45,46,47,48,49,50,51,53,54,56,61,71,77,87,91,108,109,110,112,116,120,121,124,134,144,148,150,151,153,154,155,156,157,158,159,161,162,164,166,167,168,169,179,180,181,182,184,185,186,192,194,195,202,205,208,210,211,212,213,219,228,229,231,232,233,234,235,236,244,246,247,249,256,259,262,270,280,287,288,292,296,297,298,301,302,304,306,307,308,309,310,312,314,318,319,326,328,329,333,334,335,337,340,341,342,343,344,345,346,347,348,349,352,353,355,356,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,380,381,384,385,386,387,389,392,393,394,395,396,397,405,406,407,408,409,410,412,414,415,416,418,420,421,423,425,426,427,428,430,432,433,435,437,440,441,443,448,451,452],though:[6,8,12,16,39,40,63,71,91,104,144,167,169,179,184,189,190,192,194,199,230,268,270,272,286,293,303,318,321,328,353,354,355,357,358,360,361,377,378,384,418,423,425,426,431,435,448],thought:[127,213,247,270,294,295,325,361,368,443],thread:[1,3,9,12,16,17,18,210,291,333,436],threads_per_atom:3,three:[3,6,54,63,74,87,91,105,117,118,119,120,123,143,144,156,172,191,192,197,217,229,233,252,257,270,278,285,287,290,308,312,318,319,327,333,334,335,339,355,356,358,360,361,365,368,380,381,382,386,390,393,394,396,406,408,409,410,421,423,426,448],threebodi:406,thresh:[41,167,168,169,188,421],threshhold:[3,41,168,188,301,421],threshold:[3,41,86,169,188,251,329,393,418,437],thrid:421,through:[3,6,7,9,11,12,63,144,167,170,192,203,205,210,211,216,218,219,220,229,230,253,261,285,290,295,317,324,335,356,357,361,369,395,397,404,411,418,421,424,434,440,443],throughout:[6,16,116,118,291,333,423],thru:[3,6,7,11,12,66,74,75,81,89,90,93,103,104,105,106,139,166,167,169,183,226,278,298,303,317,326,332,426],thrust:1,thu:[1,2,3,6,8,9,11,12,18,33,38,39,41,42,50,59,61,63,64,66,67,70,71,72,73,75,77,81,88,90,91,93,103,104,106,108,109,113,114,115,116,117,120,121,124,127,132,134,139,140,141,144,146,147,148,152,157,163,164,166,167,168,169,170,172,173,174,175,176,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,200,202,206,207,208,209,210,211,213,214,219,224,229,233,243,251,257,259,261,265,268,270,271,272,273,274,275,276,277,278,279,281,282,283,285,286,289,290,292,293,294,295,298,299,300,301,303,304,310,318,319,321,324,326,327,328,332,333,334,335,338,339,340,341,342,343,344,345,346,347,348,349,353,354,355,356,357,358,359,360,361,364,365,366,367,369,373,377,378,379,380,381,382,384,385,387,389,390,391,392,393,394,396,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,418,420,421,423,424,425,426,427,428,430,431,432,433,435,437,438,439,440,441,443,447,448,449,450,451],thumb:[8,10,17,144,166,226,270,333,347,426,432],thz:265,ti2:143,ti3:143,ti4:143,tight:339,tightli:259,tij:352,tildeslei:[29,87,352],tile:[3,6,41,62,144,188,367,412,420],tilt:[3,6,57,58,59,71,132,146,167,169,184,192,194,195,208,227,229,230,251,260,319,321,423,426,441],time:[],time_integr:178,timedelta:182,timelin:5,timer:[1,12,14,17],timescal:[3,180,181,182,183,184,185,186,227,260,265,357,418,432],timespan:[213,214,229,257,270,281,282],timestamp:[3,428],timestep:[],timesteppnig:273,tin:[348,349],tine:182,tinfoil:319,tini:[144,326,339,449],tinker:7,tip3p:[],tip4:6,tip4p:[],tip:[],tirrel:295,titan:15,titer:270,titl:[181,182,183,184,185,186,258,393],title1:[181,182,183,184,185,186],title2:[181,182,183,184,185,186],title3:[181,182,183,184,185,186],tji:352,tl1:143,tl3:143,tlbr_msw:390,tlo:437,tloop:[229,230,233],tm3:143,tmax:[3,199,437],tmd:[],tmd_dump_fil:289,tmdatom:289,tmin:199,tmp1:[183,186,434],tmp2:[183,186,434],tmp3:434,tmp:[6,12,41,66,68,69,75,90,93,104,106,114,116,124,139,141,167,168,169,188,259,270,286,293,332,430,434,448],tobia:[229,230,270],todd:247,toe:138,toff:[327,423],togeth:[2,3,6,11,12,17,39,41,71,115,121,124,138,145,167,173,174,181,183,188,192,198,207,214,229,257,270,274,275,278,296,300,301,359,364,421,426,431,443,451],toggl:[59,148,430],togheth:3,togther:3,tol:[273,278,318,406],toler:[3,192,261,262,263,273,278,326,328,406,418,437],tomato:169,tong:[9,13],too:[1,3,6,7,39,41,64,67,70,72,73,77,88,120,132,145,147,168,188,189,190,192,195,202,205,209,229,252,257,261,265,267,273,278,285,286,290,293,319,328,329,333,353,418,426,437,440,443,448],took:[71,397],tool:[],toolkit:[6,7,13,14,15],top:[0,3,8,9,11,12,13,59,127,166,172,187,194,209,216,228,247,271,297,298,300,328,333,392,393,396,423,427,433],topic:[448,451],toplog:[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],ubiquit:[11,339],uhf:336,uiuc:[9,17],uloop:[3,253,328,332,448],ultim:437,ultra:142,umbrella:[],umin:[26,27,48,49,153],unabl:[3,11,41,188],unaffect:[167,192,229,270,424,435,440],unalt:[173,174,241],unambigu:[71,184],unari:[303,448],unbalanc:3,unbias:[132,357],unbond:[190,423],unbroken:80,uncertainti:40,unchang:[59,192,195,228,229,231,232,234,235,243,257,270,423,424,427,433],uncharg:[40,319],uncom:[1,4],uncompress:[12,71,168],uncomput:[],uncorrel:[206,285,418],uncoupl:253,undefin:[3,12],under:[0,5,6,7,8,9,10,12,18,21,22,44,120,151,152,168,210,227,256,260,261,304,305,323,357,377,393,396,421,437,443],underestim:142,underflow:168,undergo:[6,86,87,132,206,213,214,274,278],undergon:[191,278],underli:[12,17,70,168,229,290,321],undermin:39,underpredict:6,underscor:[2,3,63,172,191,192,227,229,231,232,233,234,235,246,247,249,257,259,281,282,283,303,327,448],understand:[1,6,8,205,230],understood:[167,339],undesir:[59,192,194,229,270],undetermin:278,undisturb:[378,379],undo:[148,210],undump:[],unexpect:[3,429],unfix:[],unfix_flux:178,unfold:276,unfortun:[291,431,432],uniaxi:[3,123,233],uniform:[7,16,41,88,116,178,188,189,190,213,216,219,230,285,354,360,394,418,420,448,449],uniformli:[59,116,166,216,256,290,390,407,449],uninstal:12,uninterrupt:[179,195,205,226,227,229,231,232,233,234,235,246,247,248,249,259,260,270,274,277,280,288,290,296],union:[3,6,40,169,299,301,423,426],uniqu:[3,6,7,8,9,12,39,71,206,207,213,214,233,259,265,267,328,355,357,423,448,449],unit:[],unit_styl:3,uniti:[356,384,400],unitless:[64,67,70,71,114,149,181,184,185,194,205,227,229,260,296,326,336,361,387,389,406,408,409,410,447],unitlesss:[78,80,111],univ:[9,13],univers:[3,6,9,12,13,18,87,210,318,319,328,332,378,382,389,391,410,417,420,448],universit:[9,13],unix:[12,17,212,434],unknown:[3,12,64,73,423],unless:[2,3,11,12,15,16,18,55,57,67,118,129,143,144,167,169,170,177,192,195,205,213,229,231,232,234,235,256,257,270,278,289,320,326,347,384,407,421,426,430,435,448],unlik:[12,33,50,59,89,104,134,144,157,167,213,229,233,257,263,265,281,282,283,310,317,318,334,339,355,358,363,364,368,380,381,382,393,396,405,420,425,430,435,448,452],unlimit:390,unlucki:3,unmark:7,unmodifi:279,unnecessari:16,unoccupi:290,unoptim:168,unpack:[0,8,11,333],unpack_bord:8,unpack_border_bodi:8,unpack_border_hybrid:8,unpack_border_vel:8,unpack_comm:8,unpack_comm_bodi:8,unpack_comm_hybrid:8,unpack_comm_vel:8,unpack_exchang:8,unpack_restart:8,unpack_revers:8,unpack_reverse_comm:8,unpack_reverse_hybrid:8,unpad:169,unperturb:87,unphys:[3,6,214,229,270,423],unpredict:[268,433],unrecogn:3,unrel:[8,9,13,150],unreli:384,unrestrain:269,unrestrict:336,unscal:[3,113,138,167,280,424],unset:[318,357],unshift:352,unsmooth:375,unsolv:[330,344],unsort:169,unspecifi:[194,423],unsplit:443,unstabl:[3,216],unstrain:194,unsuccess:[3,256],unsupport:3,untar:12,until:[2,3,6,12,14,38,39,41,56,71,119,164,168,188,192,195,205,210,256,278,280,287,303,317,318,329,332,333,339,361,407,418,424,428,429,431,437,447,448],untilt:426,unus:339,unusu:[3,8,329],unwant:[3,144,318],unwrap:[3,66,74,75,81,89,90,93,103,104,106,113,121,139,167,169,170,180,191,193,210,226,270,275,280,423,424,427,433],unwrapexpand:167,unzip:12,up_intern:168,updat:[0,3,6,8,12,13,167,172,189,190,198,203,206,213,214,216,218,219,222,223,226,227,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,255,257,259,260,265,270,280,281,282,283,285,290,301,333,339,352,384,392,393,418,423,425,433,434,437,443],upenn:[11,13],upgrad:12,upon:[6,179,210,339,411,437],upper:[2,3,41,57,59,71,88,103,105,133,140,166,169,182,184,185,188,192,198,214,216,229,260,265,295,296,301,302,326,361,426,449],upsid:6,upsilon:360,upto:[3,425,431],upward:195,urbana:[210,318,319,378],urey_bradlei:20,usa:9,usabl:[12,205,355],usag:[3,6,8,214,251,265,278,364,377,423],use_ldg:17,useful:333,user:[],user_misc:[30,31,35,154,159,162,308],userguid:9,usr:[11,12,14,424],usual:[2,3,6,9,12,14,17,18,24,28,32,35,36,47,71,87,117,123,124,129,137,142,161,167,173,174,179,181,191,192,193,194,205,208,213,215,227,233,252,260,261,267,269,270,278,286,290,293,295,299,303,309,316,328,329,333,344,347,350,352,360,364,365,368,377,378,379,386,396,406,411,418,424,428,432,434,437,440,441,448,452],util:[17,18,333,360],utilizi:12,utsa:389,uttormark:13,uuml:252,uwo:9,v11:6,v22:6,v33:6,v_0:[3,290],v_a:[8,194],v_abc:[421,441,448],v_area:[2,448],v_atomfil:433,v_c:138,v_cluster:259,v_dc:138,v_delta:87,v_dhug:[227,260],v_diff:[140,292],v_displac:194,v_dk:138,v_dlj:138,v_drai:[227,260],v_dx:[226,426],v_dy:[226,426],v_dz:226,v_e_hbond:363,v_ea:[392,393],v_eb:[392,393],v_eqeq:[392,393],v_espac:175,v_f:421,v_fac:421,v_flux:209,v_foo:[421,448],v_ij:390,v_increas:208,v_integr:292,v_jx:91,v_jy:91,v_jz:91,v_k11:91,v_k22:91,v_k33:91,v_k:138,v_ke:[167,451],v_left:426,v_lgr_po:[227,260],v_lgr_vel:[227,260],v_linear:[295,298,300],v_lj:138,v_mol:169,v_mu:378,v_myi:226,v_myindex:448,v_myke:117,v_mystep:430,v_myvar:[8,169],v_myx:226,v_n:216,v_name1:[138,194],v_name2:[138,194],v_name:[3,6,71,87,117,167,168,169,173,174,175,176,180,181,182,183,184,185,186,187,200,208,209,211,213,214,226,272,280,281,282,283,292,295,298,300,421,426,430,433,439,441,448,449],v_nstep:301,v_occ:359,v_omega:226,v_oscil:[175,176,187,200,272],v_phi:208,v_prefactor:[173,174,397],v_press:121,v_pressdown:[298,300],v_push:175,v_pxy:6,v_pxz:6,v_pyz:6,v_r0:211,v_r1:142,v_r2:142,v_r:[142,211],v_rad:301,v_radiu:211,v_ramp:[295,298,300],v_rate:[194,211],v_scale1:[173,174],v_scale2:[173,174],v_size:[173,174],v_t_qm:260,v_temp:286,v_theta:[208,426],v_tp:194,v_up:426,v_v0:448,v_v11:6,v_v22:6,v_v33:6,v_v:[226,448],v_valu:[168,421],v_vx:226,v_vy:226,v_vz:[226,449],v_wiggl:[295,298,300],v_x:[2,144,211,226,295,298,300,421,426,448],v_xave:6,v_xmax:6,v_xx:144,v_y:[144,211,426],v_yi:144,v_z:426,vacanc:[4,142,287],vacf:[],vacuum:[290,319,350,410,416],valanc:339,vale:3,valenc:[263,339,357,392,393],valent:339,valeriu:9,valid:[2,3,6,9,11,12,71,118,130,143,168,169,192,205,213,251,270,278,301,303,316,321,355,357,360,390,423,424,431,433,448],vallon:380,valon:380,valu:[],value0:448,value1:[12,124,180,181,182,183,184,185,186,233,292,301,434],value2:[12,124,180,181,182,183,184,185,186,233,292,301,434],valuei:182,valuej:182,valuev:[7,9],valus:259,van:[9,53,87,107,257,261,266,281,347,348,377,380,392,393,415,449],vanderwa:[384,441],vanilla:[6,8,12],vanillia:42,vanish:[198,265,273],vapor:[41,188,205,440],vapour:285,var1:434,var2:434,varaibl:[3,426],vare:290,vari:[1,18,41,61,62,71,87,118,132,134,143,173,174,178,181,182,184,188,192,194,227,229,257,269,270,281,282,290,295,318,344,353,362,375,378,389,397,407,420],variabl:[],variable_hill_factor:13,variable_nam:393,varianc:[117,353,448],variant:[1,3,6,12,83,98,233,270,318,325,333,381,382,408,410,432,436,449],variat:[41,188,448],varieti:[1,2,6,7,13,15,71,168,210,321,364,380,392,393,405,448],variou:[],varreturn:421,varshalovich:120,varshnei:13,vartiabl:3,vbia:6,vcm:[],vdim:[133,286,293,449],vdisplac:[3,211,226,295,298,300,448],vdw:[3,348,393],vec1:[117,259],vec2:[117,259],vec:251,vector:[],vel:[3,6,61,181,184,185,194,214,256,274,297,353,357,361,418,425,426,428,443],veld:[13,278,319,343,373],veloc:[],velocit:[209,353,357,361],velocity_bottom:216,velocity_temp:449,velocity_top:216,vendor:12,verbatim:421,verbos:12,veri:[1,3,6,7,8,9,10,12,13,17,41,71,87,117,167,168,169,180,181,182,183,184,185,186,188,189,190,192,205,219,229,230,241,253,268,273,281,282,292,328,329,330,333,357,361,378,379,389,396,397,407,431,441,443,447,450],verifi:[8,333,384,432,438],verlag:274,verlet:[1,3,7,8,12,18,178,213,229,241,247,253,273,279,290,298,301,417,420,432],versa:[3,6,13,59,138,146,191,211,213,214,270,423,424,443],versu:[6,14,15,16,18,39,41,80,103,104,116,140,169,188,270,273,319,343,352,361,373,384,441,448],vertic:[41,168,188,195,448],vfinal:448,vfrac:113,vhi:[133,449],via:[],vibrat:[6,9,195,207,251,260,265,312,357,418,432],vice:[3,6,13,59,138,146,191,211,213,214,270,423,424,443],video:168,view:[4,6,7,9,13,167,168,278,339,357,358],viewer:[167,168],viewpoint:168,vij:353,vika:13,vim:[],vincent:[9,19],violat:285,violet:169,virial:[3,63,91,112,120,121,138,173,174,192,198,229,230,231,232,233,234,235,255,257,270,273,318,333,336,353,354,357,365],virialmod:365,virtual:[6,7,8,12,406],virut:9,visa:7,viscoelast:[111,361,389],viscoelsat:389,viscos:[],viscou:[],viscous:270,visit:[271,392,393],vista:167,visual:[],viz:[11,13],viz_tool:11,vizplotgui_tool:11,vizualiziton:271,vlo:[133,449],vmax:[192,278],vmd:[6,7,9,11,13,167,170,210,424],vmdarch:170,vmdhome:170,vname:[144,448],voigt:[6,120],vol:[6,8,91,121,198,214,256,380,410,419,441,448],volfactor:318,volt:[391,447],volum:[2,3,6,40,41,58,59,63,80,87,91,100,112,116,118,121,142,143,144,147,179,181,184,185,188,192,194,195,205,216,227,229,230,233,236,237,239,240,242,244,245,246,247,248,249,256,257,260,270,274,290,295,299,301,318,321,327,341,378,379,389,402,403,416,419,420,423,426,433,441,443,447,448],volumetr:80,voro:[3,9,142],vorobyov:443,voronoi:[],voter2:[418,437],voter:[381,382,418,437],voth:[40,253],vpz:297,vratio:448,vri:362,vrpn:210,vshear:296,vstream:6,vtarget:[3,293],vtk:[],vv0210:13,vx0:140,vxcm:270,vxhi:[195,256],vxlo:[195,256],vy0:140,vycm:270,vyhi:[195,256],vylo:[195,256],vz0:140,vzcm:270,vzhi:195,vzi:297,vzlo:195,w_1:120,w_2:120,w_i:120,w_ik:390,waal:[87,107,347,348,377,392,393,415],wadlei:[13,339],wag:[7,9,13],wagner:[7,9,178,216,380],wai:[1,2,3,6,7,8,11,12,15,18,22,44,59,63,65,66,69,71,75,77,79,87,90,91,92,93,104,106,108,114,115,116,120,121,122,123,124,125,126,127,130,131,132,133,134,136,137,138,139,141,144,147,152,164,166,167,168,169,172,173,174,181,183,184,186,187,190,191,192,194,203,206,211,213,214,216,227,229,233,241,253,257,259,268,270,271,274,275,278,280,281,282,283,286,289,290,292,295,298,300,301,305,306,307,309,312,319,321,323,326,328,329,333,334,335,346,349,350,353,354,355,356,358,360,363,364,366,369,380,381,382,384,386,390,391,394,396,397,404,406,408,410,417,418,421,423,424,426,427,428,431,432,433,448,449],wait:[1,12,210,252,418,420],walk:[3,206,213,214],wall:[],wallhi:295,wallstyl:296,wander:275,wang:[319,380,390],want:[0,1,2,3,5,6,7,8,9,11,12,17,38,40,56,63,66,68,71,75,81,90,93,103,104,106,107,109,110,112,114,116,121,124,139,140,141,144,147,150,164,167,168,169,172,173,174,175,180,181,188,191,194,195,198,200,203,205,211,214,224,243,251,256,259,269,270,272,275,277,279,286,288,293,295,299,301,303,319,321,328,334,335,339,347,348,353,355,358,364,365,366,380,386,390,392,393,397,406,407,408,410,412,419,421,423,424,425,426,428,430,431,441,443,448,450,452],ward:339,warm:[16,357],warn:[],warner:334,warp:[5,380],warranti:7,warren:353,wasn:3,wast:3,watanab:[287,288],watch:328,water:[],watkin:161,wave:[7,9,40,177,227,264,297,336,357],wavefunct:[9,336,357],wavelength:[118,143],wavepacket:[40,336,357,423],wavevector:252,wbodi:83,weak:261,web:[1,8,14,15,16,17,346],webb:178,weber:[3,5,7,15,88,356,382,390,405,406,435],websit:8,weckner:389,weight:[],welcom:421,well:[1,3,6,7,8,9,11,12,13,15,16,17,18,27,40,51,67,71,112,121,123,130,144,153,168,169,175,179,181,186,188,189,190,192,195,200,205,209,213,216,220,226,229,233,256,270,272,285,288,296,326,328,333,338,359,360,363,364,365,378,379,380,394,397,408,409,410,421,423,425,427,432,437,443,447,451],wennberg:318,went:[3,11],were:[3,4,5,6,7,11,12,13,15,16,18,19,34,41,42,52,56,60,70,71,109,112,116,122,124,144,147,148,160,167,169,172,175,181,183,184,185,186,188,194,200,202,209,210,241,247,271,296,297,301,311,318,330,332,357,361,364,368,389,393,418,420,421,423,424,425,426,428,430,438,441,448,449,451,452],weren:428,western:9,westview:415,what:[],whatev:[8,12,14,15,108,113,116,117,119,168,169,173,174,192,205,229,257,259,296,321,325,326,328,333,345,347,392,393,437,443,448],wheat:169,whelan:143,when:[0,1,2,3,4,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,59,61,62,63,71,81,86,88,103,104,105,107,109,112,113,117,119,122,123,127,131,132,140,142,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,167,168,169,170,172,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,199,200,201,202,203,204,205,207,208,210,213,216,217,219,220,224,229,230,231,232,233,234,235,236,241,243,244,246,247,249,251,255,256,257,258,259,260,262,263,264,265,269,270,271,272,273,274,275,276,278,279,280,281,283,285,286,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,306,307,308,309,310,312,313,314,315,316,317,318,319,321,324,325,326,327,328,329,330,332,333,334,335,337,340,341,342,343,344,345,346,347,348,349,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,379,380,381,382,384,385,386,387,389,390,392,393,394,395,396,397,404,406,407,408,409,410,412,414,415,416,418,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,447,448,449,450,452],whenev:[0,8,12,14,71,169,180,185,270,321,363,421,432,436,448,452],whenth:3,where:[1,3,6,8,9,10,11,12,14,15,18,21,23,24,25,26,27,28,29,32,35,36,37,39,40,41,43,47,48,49,51,55,61,63,65,66,68,69,70,71,73,75,79,80,82,83,84,85,87,88,89,90,92,93,94,95,96,97,98,104,106,108,112,113,114,115,116,117,118,119,121,122,123,124,125,126,127,130,131,132,133,134,136,137,138,139,141,143,145,147,148,151,153,163,167,168,169,172,173,174,175,176,179,181,182,184,187,188,191,192,194,195,199,200,202,203,205,206,207,208,209,211,213,214,215,216,219,220,222,224,226,227,230,233,241,244,250,251,252,253,256,258,259,260,263,265,270,271,272,273,274,275,277,280,281,282,283,286,287,288,290,293,294,295,296,298,299,300,301,304,306,307,308,309,312,313,314,316,319,321,325,326,327,328,329,330,333,334,335,338,339,340,342,346,347,348,349,350,351,352,353,355,356,357,358,359,360,361,362,363,364,365,366,369,373,378,379,380,381,382,384,386,387,389,390,391,392,393,394,396,399,402,403,404,405,406,407,408,409,410,415,416,417,418,420,421,423,425,426,427,428,430,432,433,435,437,438,439,440,441,443,447,448,449,450,452],wherea:[6,11,179,206,229,261,285,290,443],wherebi:262,wherev:209,whether:[6,8,11,12,16,17,39,40,54,59,61,63,70,71,102,107,109,131,132,164,168,169,171,172,173,174,181,186,189,190,191,192,193,194,198,202,205,214,226,229,233,259,273,278,286,292,293,301,303,316,318,319,327,331,333,342,344,348,362,364,368,378,379,380,384,393,405,418,421,423,424,426,428,435,436,437,440,448,449],which:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,28,29,32,33,37,38,39,40,41,42,44,45,46,47,50,51,53,54,55,56,58,59,61,63,64,66,67,70,71,72,73,74,75,76,77,78,80,81,82,83,85,87,88,89,90,91,93,95,96,97,98,99,100,101,102,103,104,105,106,107,108,110,111,112,113,114,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,150,151,152,155,156,157,158,161,163,164,166,167,168,169,170,172,173,174,175,176,177,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,198,199,200,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,219,220,223,224,226,227,228,229,230,231,232,233,234,235,237,239,241,242,244,245,246,247,248,249,251,252,253,255,256,257,258,259,260,261,262,263,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,303,304,305,307,309,310,313,314,316,317,318,319,321,323,324,325,326,327,328,329,330,332,333,334,335,336,338,339,340,342,343,344,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,371,372,373,375,377,378,379,380,381,382,384,386,387,388,390,391,392,393,394,395,396,397,400,405,406,407,408,409,410,411,412,415,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,443,448,449,450,451,452],whichev:[12,332,418,437],white:[169,206,213,214,215,270,282,290,423,448,451],whitesmok:169,whitespac:[2,3,169,327,423],who:[0,3,6,7,8,9,13,334,355],whole:[198,210,252,265,274,443],wholli:195,whose:[3,6,7,8,19,38,39,56,59,76,87,129,147,164,168,169,194,211,212,226,229,231,232,234,235,251,252,268,269,273,278,292,299,301,321,328,329,357,371,406,407,408,410,443,448,449],why:[3,6,214,286,293],wide:[1,6,7,9,61,63,172,286,293,321,330,344,347,357,392,393],wider:1,width:[168,169,336,359],wiggl:[3,194,226,295,296,298,300,426],wigner:120,wih:6,wiki:14,wikipedia:[6,14],wild:[3,12,22,44,77,87,116,152,173,174,270,305,323,346,363,417,425,430,450,452],wildcard:[3,12,138,148,167,168,169,267,346,430,433,451,452],wildli:229,win:333,window:[3,4,12,13,71,167,168,170,181,182,183,184,185,186,210,271,283,284,346,424],wipe:[172,364,405,444,446],wire:269,wirt:169,wisconsin:13,wise:[3,12,353,406,432],wish:[2,3,5,6,7,8,11,12,14,17,57,58,59,71,117,121,124,145,146,148,150,167,169,180,181,182,184,185,186,190,194,195,202,205,211,216,220,256,259,270,273,278,279,295,296,321,328,333,342,363,364,380,384,392,407,421,423,424,425,431,435,441,448,449,452],within:[1,2,3,6,8,9,11,12,13,15,16,17,29,39,40,41,42,55,59,61,63,65,69,70,71,72,73,77,79,92,108,112,115,116,117,119,120,135,144,147,168,169,173,174,179,180,181,183,184,185,186,188,189,190,191,195,197,202,205,211,213,251,255,256,257,259,261,270,271,273,275,279,290,293,295,299,301,303,317,321,326,327,328,329,330,333,338,340,342,349,354,355,356,357,359,364,365,368,369,380,387,388,389,394,395,405,406,408,409,410,411,418,420,421,423,431,432,435,437,443,447,448],without:[1,2,3,4,6,7,8,9,11,12,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,59,87,109,112,122,131,145,150,151,153,154,155,156,158,159,161,162,164,167,168,169,170,172,175,181,183,184,185,186,187,192,194,201,204,206,208,210,213,226,229,231,232,233,234,235,236,244,246,247,248,249,256,259,261,262,264,268,270,271,272,273,278,281,283,294,298,302,304,306,307,308,309,312,314,317,318,319,328,329,333,334,335,337,340,341,342,343,344,345,346,347,348,349,352,353,355,356,357,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,385,386,387,389,393,394,395,397,405,406,407,408,409,410,412,414,415,416,421,423,431,432,441,443,447,448],witht:9,witi:15,wolf:[],wolff:[384,407],won:[3,268,379],wong:[178,339],word:[2,3,6,8,12,29,63,169,172,179,180,181,182,184,185,186,193,211,238,243,258,263,269,292,303,317,347,384,419,421,423,448,449],work:[1,3,6,7,8,9,11,12,14,16,18,39,54,59,60,88,117,118,123,125,126,127,131,132,133,134,136,137,142,143,167,168,170,173,174,181,184,185,191,203,212,213,214,216,220,226,229,234,235,246,247,248,249,267,269,271,273,281,282,283,288,317,329,333,346,348,351,353,364,378,379,380,384,418,420,421,424,425,427,431,432,434,437],workaround:[270,449],worker:[12,392,393],workhors:8,workstat:[333,421],world:[3,12,120,317,328,332,417,420,421,438,448],worlei:353,worri:17,worsen:18,worst:299,worth:[181,182,183,184,185,186,260,271],would:[1,3,4,5,6,7,8,11,12,22,29,37,40,41,42,44,55,70,71,89,91,116,121,124,132,144,145,146,147,152,163,167,169,170,172,173,174,176,179,181,188,191,193,194,198,199,202,205,208,209,210,214,226,229,230,241,251,253,257,259,261,265,268,278,285,289,297,298,301,303,304,305,306,307,309,310,313,318,321,323,325,326,328,329,332,333,334,335,339,346,347,348,349,353,354,355,356,358,364,365,366,380,381,382,386,390,392,393,396,406,408,409,410,418,421,423,426,427,428,430,431,432,433,434,438,440,441,443,448,449,451,452],wrap:[1,3,6,11,12,57,59,144,146,166,167,169,170,180,185,193,194,195,210,216,226,270,275,278,295,297,299,318,319,328,421,423,424,426,431],wrapper:[],wrigger:274,wright:326,writabl:3,write:[],write_atom_weight:178,write_data:[],write_dump:[],write_freq:393,write_head:8,write_restart:[],writen:271,written:[3,5,6,7,8,9,12,13,14,17,65,69,115,120,142,167,168,169,170,172,173,174,175,176,177,178,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,196,198,199,200,201,202,203,204,206,207,208,209,210,211,213,214,215,216,217,218,219,220,221,222,223,225,228,236,237,238,239,240,241,242,243,244,245,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,276,278,279,281,282,283,284,285,286,287,289,290,292,293,294,295,297,298,299,300,302,316,321,329,355,364,413,415,418,419,421,424,425,429,430,437,438,439,440,448,450,451,452],wrong:[3,11,192,229,250,295,299,300,329,393,425,430],wrote:[3,425],wt2:384,wt3:384,www:[0,2,3,4,5,6,7,8,10,11,12,13,15,334,355,378,391,392,393,447],x86:12,x_ij:390,x_ijkl:304,x_kjli:304,x_ljik:304,xave:6,xavx:16,xcm:[8,270,448],xdr:[12,167],xeon:[1,4,7,9,12,16,17,18,333,436],xflag:[131,132,217,219,225,270,285],xhe:103,xhi:[2,6,57,59,146,167,194,289,295,298,300,423,426,441,448],xhi_bound:[6,167],xhi_new:423,xhost:[12,16],xi_ij:390,xiaowang:[13,358,408,410],xiij:251,xlat:[144,194,211,441],xlo:[2,6,11,57,59,146,167,194,211,289,295,298,300,423,426,441,448],xlo_bound:[6,167],xlo_new:423,xmax:[6,177,199,241,448],xmgrace:[],xmin:448,xml:[170,391],xml_label:391,xmovi:[],xmu:[296,361],xplane:296,xplor:167,xpo:144,xrd:[],xsph:9,xsu:[3,167,424],xt3:167,xt4:[18,167],xt5:[18,167],xtc:[3,6,7,9,12,167,168,169,170],xtcdump:169,xvf:12,xwall:[297,298,300],xxx:12,xyz:[3,6,7,13,42,66,71,106,108,132,139,144,167,168,169,170,184,192,219,229,230,233,257,267,268,270,275,277,296,298,300,320,327,420,424,449,451],xzhou:[13,358],xzy:420,yang:390,yb2:143,yb3:143,ybox:194,ycm:270,year:[5,7],yeh:318,yellow:[168,169],yellowgreen:169,yet:[3,7,9,17,39,168,173,261,267,295,319,325,326,333,345,347,348,357,415,421,423,424,448,450,451],yflag:[131,132,217,219,225,270,285],yhi:[6,59,146,167,194,289,295,298,300,423,426,441],yhi_bound:[6,167],yield:[6,91,110,117,121,127,132,169,182,192,198,229,247,261,286,292,293,296,301,318,338,353,361,384,389,441,448],yip:287,ylat:[144,194,211,441],ylo:[6,59,146,167,194,289,295,298,300,423,426,441],ylo_bound:[6,167],ymax:[177,448],ymin:448,york:[253,319],yoshida:[229,270],you:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,56,57,58,59,61,63,66,68,71,73,74,75,77,81,87,88,89,90,91,93,102,103,104,106,107,109,110,112,114,116,117,120,121,122,123,124,127,131,132,137,138,139,140,141,142,144,145,146,147,148,150,151,152,153,154,155,156,157,158,159,161,162,163,164,166,167,168,169,170,172,173,174,175,176,179,180,181,182,183,184,185,186,187,188,189,190,191,192,194,195,198,200,201,202,203,204,205,206,207,208,209,210,211,213,214,215,224,226,229,231,232,233,234,235,236,241,243,244,246,247,248,249,252,253,255,256,257,259,261,262,265,268,269,270,272,273,274,275,277,278,279,281,282,283,284,286,287,288,289,290,292,293,294,295,296,298,299,300,301,303,304,306,307,308,309,310,312,314,317,318,319,321,323,325,326,327,328,329,332,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,406,407,408,409,410,412,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,443,447,448,449,450,452],young:361,your:[0,1,2,3,4,5,6,7,8,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,59,61,107,109,112,122,123,127,131,137,142,144,145,146,147,148,150,151,153,154,155,156,158,159,161,162,164,166,167,168,175,178,182,183,186,187,189,190,191,192,195,201,204,205,208,210,213,226,229,231,232,233,234,235,236,244,246,247,249,256,259,262,268,270,272,273,274,280,281,283,286,290,292,293,294,295,296,299,300,301,304,306,307,308,309,312,314,319,321,327,328,329,332,333,334,335,337,339,340,341,342,343,344,345,346,347,348,349,352,353,354,355,356,358,359,360,361,362,363,364,365,366,367,369,370,371,372,373,374,375,376,377,378,380,381,382,384,385,386,387,389,390,392,393,394,395,397,406,407,408,409,410,412,414,415,416,417,420,421,423,425,426,427,430,431,432,433,434,435,436,440,441,447,448,450,452],yourself:[6,8,12,13,192,327],yplane:296,ypo:144,ysu:[3,167,424],yuan:9,yukawa:[],yukawa_1_1:413,yxz:420,yzx:420,z_i:[357,410,416],z_j:[410,416],z_meam:380,zachari:13,zannoni:360,zbl:[],zblcut:410,zblcutinn:396,zblcutout:396,zblexpscal:410,zblz:396,zcm:270,zcylind:296,zepeda:179,zero:[3,4,6,9,11,12,26,27,39,41,48,49,59,61,63,66,71,75,87,88,90,93,102,103,104,105,106,108,109,110,112,113,114,115,116,117,118,120,121,123,124,125,132,133,136,137,139,141,142,143,144,146,147,148,150,153,162,164,166,167,168,169,172,173,174,175,177,179,180,181,182,183,184,185,186,187,188,189,190,192,194,199,200,201,202,204,205,206,207,209,213,214,215,216,217,219,225,226,227,229,233,241,244,253,258,259,260,261,262,265,267,268,270,271,272,273,278,280,285,286,288,290,293,294,295,296,297,298,300,301,302,303,308,321,324,326,327,328,329,333,336,339,340,342,343,344,347,349,352,353,357,360,362,363,365,369,371,373,374,377,379,380,384,389,393,394,395,404,407,411,416,418,419,420,423,424,426,428,430,431,432,433,437,438,441,443,448,449,450,452],zeta:[3,216,261,358],zfactor:168,zflag:[131,132,217,219,225,270,285],zhang:[270,286,361],zhi:[3,6,146,167,177,289,295,298,300,423,426,441],zhi_bound:[6,167],zhou:[13,339,358,390,408,410],zhu:403,ziegenhain:13,ziegler:[255,380,405,410,416],zimmerman2004:178,zimmerman2010:178,zimmerman:[9,70,178,339],zlat:[194,211,441],zlo:[3,6,146,167,177,289,295,297,298,300,423,426,441],zlo_bound:[6,167],zmax:[177,216,448],zmin:[216,448],zn2:143,zone:[118,271],zoom:[3,167,168,169],zplane:296,zr4:143,zrest:277,zsu:[3,167,424],zwall:295,zwall_veloc:216,zxy:420,zybin:393,zyx:420},titles:["LAMMPS Documentation","Accelerating LAMMPS performance","Commands","Errors","Example problems","Future and history","How-to discussions","Introduction","Modifying & extending LAMMPS","Packages","Performance & 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","<no title>","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:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],diagnost:7,diel:350,dielectr:149,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:152,dihedral_styl:[2,150,151,153,154,155,156,157,158,159,160,161,162,163,164],dilat:80,dimens:165,dipol:[6,29,352],direct:198,discuss:6,disp:6,displac:[81,86],displace_atom:166,distribut:[7,12],document:0,dpd:353,drag:196,dreid:[6,363],drude:[6,9,129,197,198,214],dsf:[349,369],dsmc:354,dump:[6,8,167,168,170],dump_modifi:169,dynam:261,eam:[13,355],echo:171,edip:356,eff:[9,13,96,97,128,130,135,215,230,240,248,284,357],efield:200,eim:358,elast:6,emac:13,enforce2d:201,ensembl:7,erot:[82,83,84,85],error:3,evapor:202,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],exp:[27,153],expand:[46,372],extend:[8,11],extern:203,fcc:251,featur:[7,8],fene:[45,46],fep:[9,13,87,174],field:[6,7],file:6,finit:6,fix:[2,6,8,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,448],fix_modifi:[173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300],flow:6,fluid:216,flux:91,forc:[6,7,279],fourier:[30,31,154,308],freez:204,from:[6,11],futur:5,gauss:359,gaybern:360,gcmc:205,gener:[1,6,7,13],get:12,gld:206,gle:207,global:6,gpu:[15,337,340,342,344,345,347,349,352,353,355,359,360,362,369,370,372,383,385,394,395,397,406,407,414,415],gran:[296,361],granular:6,graviti:208,gromac:362,group2ndx:302,group:[88,301,448],gyrat:[89,90],harmon:[32,47,48,49,155,158,295,309,386],hbond:363,heat:[91,209],heatconduct:398,helix:156,hertz:361,histo:183,histori:[5,361],hook:361,how:6,hybrid:[33,50,157,310,364],idealga:399,imag:[167,168],imd:210,implicit:344,improp:[8,92],improper_coeff:305,improper_styl:[2,304,306,307,308,309,310,311,312,313,314],includ:315,inclus:8,indent:211,indic:0,individu:2,induc:6,inertia:93,info:[0,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,316],input:[2,6,8],instal:11,integr:[6,7],intel:[9,16,344,360,369,406],interfac:[6,11],introduct:7,invers:198,ipi:212,ipp:13,jul:0,jump:317,kate:13,keyword:384,kim:365,kokko:17,kspace:[2,8,291],kspace_modifi:318,kspace_styl:[6,319],label:320,lammp:[0,1,2,6,7,8,11,12],langevin:[213,214,215],lattic:321,lcbop:366,librari:[6,11,12],limit:[241,283],line:[12,242,367],linear:376,lineforc:221,list:[2,368],lj1043:295,lj126:295,lj93:295,lj96:370,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,92,108,115],log:322,lubric:378,lubricateu:379,make:12,mass:323,math:448,matlab:13,meam:[380,381,382],measur:1,meso:[222,223],meso_:99,meso_rho:100,meso_t:101,messag:3,micelle2d:13,mie:383,min_modifi:324,min_styl:325,minim:[8,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,326],misc:9,mod:[290,409],model:[6,7],modifi:8,molecul:327,molfil:[9,167,170],moltempl:13,momentum:[217,225],morri:403,mors:[51,363,385],move:226,movi:[167,168],mpi:11,msd:[103,104,105],msi2lmp:13,msm:[340,342,344,349,369],msst:227,multi:[6,7,158],multipl:6,nb3b:386,neb:[228,328],neigh_modifi:329,neighbor:330,nemd:6,newton:331,next:332,nharmon:159,noforc:[238,243],non:[6,7],none:[34,52,160,311,388],nongauss:105,nonlinear:53,nph:[229,230,231,232,270],nphug:233,npt:[229,230,234,235,270],nve:[236,237,238,239,240,241,242,243,244,245,270],nvt:[229,230,246,247,248,249,270],omega:106,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,150,151,153,154,155,156,158,159,161,162,164,208,229,231,232,233,234,235,236,244,246,247,249,262,304,306,307,308,309,312,314,334,335,337,340,341,342,343,344,345,347,348,349,350,352,353,355,358,359,360,361,362,363,364,367,369,370,371,372,373,374,375,376,377,378,381,382,385,386,387,389,394,395,397,406,407,408,409,410,412,414,415,416],onewai:250,open:7,oper:448,opl:161,opt:[19,344,355,369,373,385],optim:1,option:[6,8,12],orient:251,orthogon:6,other:6,output:[6,7,8,12,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300],overlai:364,overview:11,packag:[1,9,12,14,15,16,17,18,19,333],pair:[6,107,108],pair_coeff:346,pair_modifi:384,pair_styl:[2,334,335,336,337,338,339,340,341,342,343,344,345,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,414,415,416],pair_writ:413,pairwis:8,parallel:11,paramet:6,pars:2,partial:131,particl:[6,7,42],partit:417,past:5,per:6,perform:[1,10],peri:389,period:25,phonon:[9,13,252],pimd:253,piston:297,planeforc:254,plastic:111,pmb:389,poem:255,point:261,polariz:6,poli:[341,378,379],polym:13,polymorph:390,post:7,potenti:[2,6,8],pour:256,pppm:6,prd:418,pre:7,press:257,pressur:112,previou:12,print:[258,419],problem:[3,4],process:[6,7],processor:420,profil:132,properti:[6,113,114,115,259],pymol_aspher:13,python:[11,13,421],qbmsst:260,qeq:[261,262,263],qmmm:[9,264],qtb:[9,265],quadrat:162,quantiti:6,quartic:[35,54],quip:391,quit:422,ramp:133,rattl:273,rdf:116,read_data:423,read_dump:424,read_restart:425,reax:[13,263,266,267,392,393],reaxc:9,rebo:335,recent:268,reduc:117,refer:448,reflect:298,region:[8,117,134,135,299,426,448],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,161,162,163,164,165,166,167,168,169,170,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,202,204,205,206,207,208,209,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,265,266,267,268,270,271,272,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,312,313,314,315,316,317,318,319,321,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,429,430,431,432,433,435,436,437,438,439,440,441,442,444,445,446,448,449,450,451,452],relax:192,replic:427,replica:[6,7],report:3,requir:12,rerun:428,rescal:[283,284],reset:199,reset_timestep:429,resquar:394,restart2data:13,restart:[6,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,430],restrain:269,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,444,445,446,447,448,449,450,451,452],rhosum:401,rigid:[6,83,98,219,270],ring:312,rotat:136,rule:2,run:[6,11,12,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300,431],run_styl:432,scalabl:10,scalar:6,screen:12,script:[2,6,8,11,12],sdk:[36,395],self:277,serial:11,set:[6,433],setforc:272,shake:273,share:[11,12],shell:[6,434],shield:261,shift:[26,27,48,49,153],simpl:31,simul:6,size:6,slater:261,slice:119,sllod:[247,248],small:270,smd:274,smooth:[375,376],sna:120,snad:120,snap:396,snapshot:6,snav:120,soft:[377,397],solver:2,sourc:7,spatial:[184,185],spc:6,speci:267,special:[7,384,448],special_bond:435,sph:[9,398,399,400,401,402,403],sphere:[84,85,137,185,219,232,235,244,249],spheric:6,spline:[381,382],spring:[275,276,277,288],squar:28,srd:[278,300],srp:404,standard:9,start:[12,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,192,193,194,195,196,198,199,200,201,202,203,204,205,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,292,293,294,295,296,297,298,299,300],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 a11c8db6ca01196328045faa127c887b198dd33e..d11e85c32d70dd6e6986f5811a6fae21d0dd67d6 100644
--- a/doc/set.html
+++ b/doc/set.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/shell.html b/doc/shell.html
index 9d94d9da4893e506b881a0595f9e4136cbcae2d6..c88acda77517e985f7cfc679e548364e7101a96b 100644
--- a/doc/shell.html
+++ b/doc/shell.html
@@ -71,22 +71,17 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/special_bonds.html b/doc/special_bonds.html
index 2680144fcda68faed6d20ff510aca624e684192f..27bcb1a79c81458e12ddb156917f864206fb4030 100644
--- a/doc/special_bonds.html
+++ b/doc/special_bonds.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/suffix.html b/doc/suffix.html
index 6ba28b1419a56ea7c590abc179ecb7e66d44f98d..da1e75e1223677d54c84007f39810cd4cfbe2deb 100644
--- a/doc/suffix.html
+++ b/doc/suffix.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/tad.html b/doc/tad.html
index 88d95cc6785e566e5d316c2ab5243186aa3f9ef5..9b9362005736d4e5304db0a6ec3accc5c0b9babb 100644
--- a/doc/tad.html
+++ b/doc/tad.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/temper.html b/doc/temper.html
index 6b85f9b5be11286f398143007450fb07fea8ee42..90a4376a74a1ffaaeb6114ba0aa51bc5c0751b54 100644
--- a/doc/temper.html
+++ b/doc/temper.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/thermo.html b/doc/thermo.html
index 4d167e8596c6bcc7c3be162b33007141cb8d0593..be54e7bebb22c05ca9fedcb2c292f665eae6a77c 100644
--- a/doc/thermo.html
+++ b/doc/thermo.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/thermo_modify.html b/doc/thermo_modify.html
index 8ae6cd9694785da3bc6b03aa975436b29965541e..e5533d60cff0cddcbd522c7c7f158ae0d192747e 100644
--- a/doc/thermo_modify.html
+++ b/doc/thermo_modify.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/thermo_style.html b/doc/thermo_style.html
index 3d6356aa3c7f80bcb7b02d9dda6ca712cb748ec8..4c049f078637798bc727901ded9fbaea7d015d62 100644
--- a/doc/thermo_style.html
+++ b/doc/thermo_style.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/timestep.html b/doc/timestep.html
index 0a1e588a246baa3ae41ed2de601f75b9df78ffa9..d424cc4603c6697e06292cbf4a3f7c144268cd48 100644
--- a/doc/timestep.html
+++ b/doc/timestep.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/tutorial_drude.html b/doc/tutorial_drude.html
index 8e135dc2ee1a7ce9e9ac3ee6b3dd36e71a2beb00..b1e38a2f600b71d9c4d622c614f215ba906ced42 100644
--- a/doc/tutorial_drude.html
+++ b/doc/tutorial_drude.html
@@ -71,22 +71,10 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- Local TOC -->
+ <div class="local-toc"><ul class="simple">
</ul>
-
+</div>
</div>
diff --git a/doc/uncompute.html b/doc/uncompute.html
index c2e18b140b83f3ed878ae726fb9d9d3ff93b3d0d..7b9e01642439eea25b94b3e3a178ec80176c5e00 100644
--- a/doc/uncompute.html
+++ b/doc/uncompute.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/undump.html b/doc/undump.html
index f345273c34d1f6ecab397f5f23472de5c04fda99..2ffbd741a809b5a4b8526c55545023a1486ef8bf 100644
--- a/doc/undump.html
+++ b/doc/undump.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/unfix.html b/doc/unfix.html
index 8ffc18411984eb73b033befb099ddd65c6350c7e..efc91cc3d3e9d2cab821dea6b0a876e4bc534129 100644
--- a/doc/unfix.html
+++ b/doc/unfix.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/units.html b/doc/units.html
index f7fa0f3a52720edd44b52e203db1706b486ceed2..8475208ca52c5b929a9e2c5f21410244a607e84a 100644
--- a/doc/units.html
+++ b/doc/units.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/variable.html b/doc/variable.html
index d76ee57022d350983c907466abd606d4d203e2d1..e0a1d1cb15e9d0e99b32fd9ff7236d899b1e561f 100644
--- a/doc/variable.html
+++ b/doc/variable.html
@@ -71,22 +71,28 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+<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 7b492cc11b5d14898eac0dd821796304a0c2f247..f23a490f5e5eef8bf11b891f383f1ebc6b79ac11 100644
--- a/doc/velocity.html
+++ b/doc/velocity.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/write_data.html b/doc/write_data.html
index 1fed354d061d908afeece0e5500396eace44fa75..c828ed96e028f759be432690e4991e6a461ceb9a 100644
--- a/doc/write_data.html
+++ b/doc/write_data.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/write_dump.html b/doc/write_dump.html
index 29bdfb7200f40ba0bbf723615ef2188761ab1f15..1a8238384dfd182d7a886a11893fadb04984aca1 100644
--- a/doc/write_dump.html
+++ b/doc/write_dump.html
@@ -71,22 +71,19 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>
diff --git a/doc/write_restart.html b/doc/write_restart.html
index d6863eb7c80f7cc69d538563cb28045ef32a71ca..27cb53137c1d6bba45ad6328b005be64f15c271a 100644
--- a/doc/write_restart.html
+++ b/doc/write_restart.html
@@ -71,22 +71,18 @@
- <ul>
-<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
+ <!-- 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>
+</ul>
+</div>
</div>