From 718c87f9150e388184ea5ce493f58830794093f2 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 17 Feb 2016 15:40:36 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14653
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Manual.html                   |  61 +-----
 doc/Section_packages.html         | 298 +++++++++++++++---------------
 doc/Section_packages.txt          | 164 ++++++++--------
 doc/_sources/Section_packages.txt | 166 +++++++++--------
 doc/_sources/fix_langevin.txt     |   4 +-
 doc/fix_langevin.html             |   8 +-
 doc/fix_langevin.txt              |   4 +-
 doc/searchindex.js                |   2 +-
 8 files changed, 334 insertions(+), 373 deletions(-)

diff --git a/doc/Manual.html b/doc/Manual.html
index 2857967f53..40201cc6b7 100644
--- a/doc/Manual.html
+++ b/doc/Manual.html
@@ -220,66 +220,7 @@ it gives quick access to documentation for all LAMMPS commands.</p>
 </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#asphere-package">4.2. ASPHERE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#body-package">4.3. BODY package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#class2-package">4.4. CLASS2 package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#colloid-package">4.5. COLLOID package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#compress-package">4.6. COMPRESS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#coreshell-package">4.7. CORESHELL package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#dipole-package">4.8. DIPOLE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#fld-package">4.9. FLD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#gpu-package">4.10. GPU package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#granular-package">4.11. GRANULAR package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#kim-package">4.12. KIM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#kokkos-package">4.13. KOKKOS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#kspace-package">4.14. KSPACE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#manybody-package">4.15. MANYBODY package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#mc-package">4.16. MC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#meam-package">4.17. MEAM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#misc-package">4.18. MISC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#molecule-package">4.19. MOLECULE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#mpiio-package">4.20. MPIIO package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#opt-package">4.21. OPT package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#peri-package">4.22. PERI package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#poems-package">4.23. POEMS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#python-package">4.24. PYTHON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#qeq-package">4.25. QEQ package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#reax-package">4.26. REAX package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#replica-package">4.27. REPLICA package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#rigid-package">4.28. RIGID package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#shock-package">4.29. SHOCK package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#snap-package">4.30. SNAP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#srd-package">4.31. SRD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#voronoi-package">4.32. VORONOI package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#xtc-package">4.33. XTC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.34. User packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.35. USER-ATC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.36. USER-AWPMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.37. USER-CG-CMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.38. USER-COLVARS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.39. USER-CUDA package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.40. USER-DIFFRACTION package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-dpd-package">4.41. USER-DPD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.42. USER-DRUDE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.43. USER-EFF package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.44. USER-FEP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.45. USER-H5MD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.46. USER-INTEL package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.47. USER-LB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-mgpt-package">4.48. USER-MGPT package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.49. USER-MISC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.50. USER-MOLFILE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.51. USER-OMP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.52. USER-PHONON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.53. USER-QMMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.54. USER-QTB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-quip-package">4.55. USER-QUIP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.56. USER-REAXC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.57. USER-SMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smtbq-package">4.58. USER-SMTBQ package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.59. USER-SPH package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-tally-package">4.60. USER-TALLY package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-vtk-package">4.61. USER-VTK package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.2. User packages</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a><ul>
diff --git a/doc/Section_packages.html b/doc/Section_packages.html
index eb4594c24b..183dc7d4fa 100644
--- a/doc/Section_packages.html
+++ b/doc/Section_packages.html
@@ -78,67 +78,71 @@
 <li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. 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="#asphere-package">4.2. ASPHERE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#body-package">4.3. BODY package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#class2-package">4.4. CLASS2 package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#colloid-package">4.5. COLLOID package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#compress-package">4.6. COMPRESS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#coreshell-package">4.7. CORESHELL package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#dipole-package">4.8. DIPOLE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#fld-package">4.9. FLD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#gpu-package">4.10. GPU package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#granular-package">4.11. GRANULAR package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#kim-package">4.12. KIM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#kokkos-package">4.13. KOKKOS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#kspace-package">4.14. KSPACE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#manybody-package">4.15. MANYBODY package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#mc-package">4.16. MC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#meam-package">4.17. MEAM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#misc-package">4.18. MISC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#molecule-package">4.19. MOLECULE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#mpiio-package">4.20. MPIIO package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#opt-package">4.21. OPT package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#peri-package">4.22. PERI package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#poems-package">4.23. POEMS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#python-package">4.24. PYTHON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#qeq-package">4.25. QEQ package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#reax-package">4.26. REAX package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#replica-package">4.27. REPLICA package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#rigid-package">4.28. RIGID package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#shock-package">4.29. SHOCK package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#snap-package">4.30. SNAP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#srd-package">4.31. SRD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#voronoi-package">4.32. VORONOI package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#xtc-package">4.33. XTC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.34. User packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-atc-package">4.35. USER-ATC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-awpmd-package">4.36. USER-AWPMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-cg-cmm-package">4.37. USER-CG-CMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-colvars-package">4.38. USER-COLVARS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-cuda-package">4.39. USER-CUDA package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-diffraction-package">4.40. USER-DIFFRACTION package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-dpd-package">4.41. USER-DPD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-drude-package">4.42. USER-DRUDE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-eff-package">4.43. USER-EFF package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-fep-package">4.44. USER-FEP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-h5md-package">4.45. USER-H5MD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-intel-package">4.46. USER-INTEL package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-lb-package">4.47. USER-LB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-mgpt-package">4.48. USER-MGPT package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.49. USER-MISC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.50. USER-MOLFILE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.51. USER-OMP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.52. USER-PHONON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.53. USER-QMMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.54. USER-QTB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-quip-package">4.55. USER-QUIP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.56. USER-REAXC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-smd-package">4.57. USER-SMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-smtbq-package">4.58. USER-SMTBQ package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.59. USER-SPH package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-tally-package">4.60. USER-TALLY package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-vtk-package">4.61. USER-VTK package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#standard-packages">4.1. Standard packages</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#asphere-package">4.1.1. ASPHERE package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#body-package">4.1.2. BODY package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#class2-package">4.1.3. CLASS2 package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#colloid-package">4.1.4. COLLOID package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#compress-package">4.1.5. COMPRESS package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#coreshell-package">4.1.6. CORESHELL package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#dipole-package">4.1.7. DIPOLE package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#fld-package">4.1.8. FLD package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#gpu-package">4.1.9. GPU package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#granular-package">4.1.10. GRANULAR package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#kim-package">4.1.11. KIM package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#kokkos-package">4.1.12. KOKKOS package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#kspace-package">4.1.13. KSPACE package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#manybody-package">4.1.14. MANYBODY package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#mc-package">4.1.15. MC package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#meam-package">4.1.16. MEAM package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#misc-package">4.1.17. MISC package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#molecule-package">4.1.18. MOLECULE package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#mpiio-package">4.1.19. MPIIO package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#opt-package">4.1.20. OPT package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#peri-package">4.1.21. PERI package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#poems-package">4.1.22. POEMS package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#python-package">4.1.23. PYTHON package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#qeq-package">4.1.24. QEQ package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#reax-package">4.1.25. REAX package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#replica-package">4.1.26. REPLICA package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#rigid-package">4.1.27. RIGID package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#shock-package">4.1.28. SHOCK package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#snap-package">4.1.29. SNAP package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#srd-package">4.1.30. SRD package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#voronoi-package">4.1.31. VORONOI package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#xtc-package">4.1.32. XTC package</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.2. User packages</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#user-atc-package">4.2.1. USER-ATC package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-awpmd-package">4.2.2. USER-AWPMD package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-cg-cmm-package">4.2.3. USER-CG-CMM package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-colvars-package">4.2.4. USER-COLVARS package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-cuda-package">4.2.5. USER-CUDA package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-diffraction-package">4.2.6. USER-DIFFRACTION package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-dpd-package">4.2.7. USER-DPD package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-drude-package">4.2.8. USER-DRUDE package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-eff-package">4.2.9. USER-EFF package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-fep-package">4.2.10. USER-FEP package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-h5md-package">4.2.11. USER-H5MD package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-intel-package">4.2.12. USER-INTEL package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-lb-package">4.2.13. USER-LB package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-mgpt-package">4.2.14. USER-MGPT package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-misc-package">4.2.15. USER-MISC package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-molfile-package">4.2.16. USER-MOLFILE package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-omp-package">4.2.17. USER-OMP package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-phonon-package">4.2.18. USER-PHONON package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-qmmm-package">4.2.19. USER-QMMM package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-qtb-package">4.2.20. USER-QTB package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-quip-package">4.2.21. USER-QUIP package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-reaxc-package">4.2.22. USER-REAXC package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-smd-package">4.2.23. USER-SMD package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-smtbq-package">4.2.24. USER-SMTBQ package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-sph-package">4.2.25. USER-SPH package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-tally-package">4.2.26. USER-TALLY package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#user-vtk-package">4.2.27. USER-VTK package</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
@@ -200,26 +204,35 @@
             
   <div class="section" id="packages">
 <h1>4. Packages<a class="headerlink" href="#packages" title="Permalink to this headline">¶</a></h1>
-<p>This section gives an overview of the add-on packages that extend
-LAMMPS functionality.  Two tables, for standard and user packages, are
-below.  A brief sub-section for each package follows, with a summary
-of what the package contains, how to install it, and pointers to
-examples of its use or documentation provided in the LAMMPS
-distribution.</p>
+<p>This section gives an overview of the add-on optional packages that
+extend LAMMPS functionality.  Packages are groups of files that enable
+a specific set of features.  For example, force fields for molecular
+systems or granular systems are in packages.  You can see the list of
+all packages by typing &#8220;make package&#8221; from within the src directory of
+the LAMMPS distribution.</p>
+<p>Here are links for two tables below, which list standard and user
+packages.</p>
 <div class="line-block">
 <div class="line">4.1 <a class="reference internal" href="#pkg-1"><span>Standard packages</span></a></div>
 <div class="line">4.2 <a class="reference internal" href="#pkg-2"><span>User packages</span></a></div>
 <div class="line"><br /></div>
 </div>
-<p>LAMMPS includes many optional packages, which are groups of files that
-enable a specific set of features.  For example, force fields for
-molecular systems or granular systems are in packages.  You can see
-the list of all packages by typing &#8220;make package&#8221; from within the src
-directory of the LAMMPS distribution.</p>
-<p>See <a class="reference internal" href="Section_start.html#start-3"><span>Section_start 3</span></a> of the manual for
-details on how to include/exclude specific packages as part of the
-LAMMPS build process, and for more details about the differences
-between standard packages and user packages.</p>
+<p><a class="reference internal" href="Section_start.html#start-3"><span>Section_start 3</span></a> of the manual describes
+the difference between standard packages and user packages.  It also
+has general details on how to include/exclude specific packages as
+part of the LAMMPS build process, and on how to build auxiliary
+libraries or modify a machine Makefile if a package requires it.</p>
+<p>Following the two tables below, is a sub-section for each package.  It
+has a summary of what the package contains.  It has specific
+instructions on how to install it, build or obtain any auxiliary
+library it requires, and any Makefile.machine changes it requires.  It
+also lists pointers to examples of its use or documentation provided
+in the LAMMPS distribution.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">The sub-sections below are still being filled in, as of Feb
+2016.</p>
+</div>
 <p>Unless otherwise noted below, every package is independent of all the
 others.  I.e. any package can be included or excluded in a LAMMPS
 build, independent of all other packages.  However, note that some
@@ -232,15 +245,11 @@ package is not also installed, since it contains the pair
 lj/cut/coul/long command.  If you later install the KSPACE pacakge and
 the USER-OMP package is already installed, both the pair
 lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.</p>
-<p>The two tables below list currently available packages in LAMMPS, with
-a one-line descriptions of each.  The sub-sections below give more
-details.</p>
 <hr class="docutils" />
 <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>
 <p>The current list of standard packages is as follows.  Each package
-name links to a sub-section below with more details on how to build
-with the package and pointers to additional info.</p>
+name links to a sub-section below with more details.</p>
 <table border="1" class="docutils">
 <colgroup>
 <col width="16%" />
@@ -630,11 +639,11 @@ lib/package, then the code for the library is under the lib directory
 of the LAMMPS distribution.  See the lib/package/README file for info
 on how to build the library.  If it is not listed as lib/package, then
 it is a third-party library not included in the LAMMPS distribution.
-See details on all of this below for individual packages.</p>
+See details on all of this below for individual packages.
+p.s.: are we ever going to get commit messages from you? ;-)</p>
 <hr class="docutils" />
-</div>
 <div class="section" id="asphere-package">
-<span id="asphere"></span><h2>4.2. ASPHERE package<a class="headerlink" href="#asphere-package" title="Permalink to this headline">¶</a></h2>
+<span id="asphere"></span><h3>4.1.1. ASPHERE package<a class="headerlink" href="#asphere-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
 triangles.</p>
 <p>To install via make or Make.py:</p>
@@ -658,7 +667,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="body-package">
-<span id="body"></span><h2>4.3. BODY package<a class="headerlink" href="#body-package" title="Permalink to this headline">¶</a></h2>
+<span id="body"></span><h3>4.1.2. BODY package<a class="headerlink" href="#body-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-body
@@ -680,7 +689,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="class2-package">
-<span id="class2"></span><h2>4.4. CLASS2 package<a class="headerlink" href="#class2-package" title="Permalink to this headline">¶</a></h2>
+<span id="class2"></span><h3>4.1.3. CLASS2 package<a class="headerlink" href="#class2-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-class2
@@ -702,7 +711,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="colloid-package">
-<span id="colloid"></span><h2>4.5. COLLOID package<a class="headerlink" href="#colloid-package" title="Permalink to this headline">¶</a></h2>
+<span id="colloid"></span><h3>4.1.4. COLLOID package<a class="headerlink" href="#colloid-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-colloid
@@ -724,7 +733,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="compress-package">
-<span id="compress"></span><h2>4.6. COMPRESS package<a class="headerlink" href="#compress-package" title="Permalink to this headline">¶</a></h2>
+<span id="compress"></span><h3>4.1.5. COMPRESS package<a class="headerlink" href="#compress-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-compress
@@ -746,7 +755,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="coreshell-package">
-<span id="coreshell"></span><h2>4.7. CORESHELL package<a class="headerlink" href="#coreshell-package" title="Permalink to this headline">¶</a></h2>
+<span id="coreshell"></span><h3>4.1.6. CORESHELL package<a class="headerlink" href="#coreshell-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-coreshell
@@ -768,7 +777,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="dipole-package">
-<span id="dipole"></span><h2>4.8. DIPOLE package<a class="headerlink" href="#dipole-package" title="Permalink to this headline">¶</a></h2>
+<span id="dipole"></span><h3>4.1.7. DIPOLE package<a class="headerlink" href="#dipole-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-dipole
@@ -790,7 +799,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="fld-package">
-<span id="fld"></span><h2>4.9. FLD package<a class="headerlink" href="#fld-package" title="Permalink to this headline">¶</a></h2>
+<span id="fld"></span><h3>4.1.8. FLD package<a class="headerlink" href="#fld-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-fld
@@ -812,7 +821,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="gpu-package">
-<span id="gpu"></span><h2>4.10. GPU package<a class="headerlink" href="#gpu-package" title="Permalink to this headline">¶</a></h2>
+<span id="gpu"></span><h3>4.1.9. GPU package<a class="headerlink" href="#gpu-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-gpu
@@ -834,7 +843,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="granular-package">
-<span id="granular"></span><h2>4.11. GRANULAR package<a class="headerlink" href="#granular-package" title="Permalink to this headline">¶</a></h2>
+<span id="granular"></span><h3>4.1.10. GRANULAR package<a class="headerlink" href="#granular-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-granular
@@ -856,7 +865,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="kim-package">
-<span id="kim"></span><h2>4.12. KIM package<a class="headerlink" href="#kim-package" title="Permalink to this headline">¶</a></h2>
+<span id="kim"></span><h3>4.1.11. KIM package<a class="headerlink" href="#kim-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-kim
@@ -878,7 +887,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="kokkos-package">
-<span id="kokkos"></span><h2>4.13. KOKKOS package<a class="headerlink" href="#kokkos-package" title="Permalink to this headline">¶</a></h2>
+<span id="kokkos"></span><h3>4.1.12. KOKKOS package<a class="headerlink" href="#kokkos-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-kokkow
@@ -920,7 +929,7 @@ Makefile.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="kspace-package">
-<span id="kspace"></span><h2>4.14. KSPACE package<a class="headerlink" href="#kspace-package" title="Permalink to this headline">¶</a></h2>
+<span id="kspace"></span><h3>4.1.13. KSPACE package<a class="headerlink" href="#kspace-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-kspace
@@ -944,7 +953,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="manybody-package">
-<span id="manybody"></span><h2>4.15. MANYBODY package<a class="headerlink" href="#manybody-package" title="Permalink to this headline">¶</a></h2>
+<span id="manybody"></span><h3>4.1.14. MANYBODY package<a class="headerlink" href="#manybody-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-manybody
@@ -967,7 +976,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="mc-package">
-<span id="mc"></span><h2>4.16. MC package<a class="headerlink" href="#mc-package" title="Permalink to this headline">¶</a></h2>
+<span id="mc"></span><h3>4.1.15. MC package<a class="headerlink" href="#mc-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-mc
@@ -989,7 +998,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="meam-package">
-<span id="meam"></span><h2>4.17. MEAM package<a class="headerlink" href="#meam-package" title="Permalink to this headline">¶</a></h2>
+<span id="meam"></span><h3>4.1.16. MEAM package<a class="headerlink" href="#meam-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-meam
@@ -1011,7 +1020,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="misc-package">
-<span id="misc"></span><h2>4.18. MISC package<a class="headerlink" href="#misc-package" title="Permalink to this headline">¶</a></h2>
+<span id="misc"></span><h3>4.1.17. MISC package<a class="headerlink" href="#misc-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-misc
@@ -1033,7 +1042,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="molecule-package">
-<span id="molecule"></span><h2>4.19. MOLECULE package<a class="headerlink" href="#molecule-package" title="Permalink to this headline">¶</a></h2>
+<span id="molecule"></span><h3>4.1.18. MOLECULE package<a class="headerlink" href="#molecule-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-molecule
@@ -1055,7 +1064,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="mpiio-package">
-<span id="mpiio"></span><h2>4.20. MPIIO package<a class="headerlink" href="#mpiio-package" title="Permalink to this headline">¶</a></h2>
+<span id="mpiio"></span><h3>4.1.19. MPIIO package<a class="headerlink" href="#mpiio-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-mpiio
@@ -1077,7 +1086,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="opt-package">
-<span id="opt"></span><h2>4.21. OPT package<a class="headerlink" href="#opt-package" title="Permalink to this headline">¶</a></h2>
+<span id="opt"></span><h3>4.1.20. OPT package<a class="headerlink" href="#opt-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-opt
@@ -1104,7 +1113,7 @@ settings for CCFLAGS.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="peri-package">
-<span id="peri"></span><h2>4.22. PERI package<a class="headerlink" href="#peri-package" title="Permalink to this headline">¶</a></h2>
+<span id="peri"></span><h3>4.1.21. PERI package<a class="headerlink" href="#peri-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-peri
@@ -1126,7 +1135,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="poems-package">
-<span id="poems"></span><h2>4.23. POEMS package<a class="headerlink" href="#poems-package" title="Permalink to this headline">¶</a></h2>
+<span id="poems"></span><h3>4.1.22. POEMS package<a class="headerlink" href="#poems-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-poems
@@ -1148,7 +1157,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="python-package">
-<span id="python"></span><h2>4.24. PYTHON package<a class="headerlink" href="#python-package" title="Permalink to this headline">¶</a></h2>
+<span id="python"></span><h3>4.1.23. PYTHON package<a class="headerlink" href="#python-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-python
@@ -1170,7 +1179,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="qeq-package">
-<span id="qeq"></span><h2>4.25. QEQ package<a class="headerlink" href="#qeq-package" title="Permalink to this headline">¶</a></h2>
+<span id="qeq"></span><h3>4.1.24. QEQ package<a class="headerlink" href="#qeq-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-qeq
@@ -1192,7 +1201,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="reax-package">
-<span id="reax"></span><h2>4.26. REAX package<a class="headerlink" href="#reax-package" title="Permalink to this headline">¶</a></h2>
+<span id="reax"></span><h3>4.1.25. REAX package<a class="headerlink" href="#reax-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-reax
@@ -1214,7 +1223,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="replica-package">
-<span id="replica"></span><h2>4.27. REPLICA package<a class="headerlink" href="#replica-package" title="Permalink to this headline">¶</a></h2>
+<span id="replica"></span><h3>4.1.26. REPLICA package<a class="headerlink" href="#replica-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-replica
@@ -1236,7 +1245,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="rigid-package">
-<span id="rigid"></span><h2>4.28. RIGID package<a class="headerlink" href="#rigid-package" title="Permalink to this headline">¶</a></h2>
+<span id="rigid"></span><h3>4.1.27. RIGID package<a class="headerlink" href="#rigid-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-rigid
@@ -1258,7 +1267,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="shock-package">
-<span id="shock"></span><h2>4.29. SHOCK package<a class="headerlink" href="#shock-package" title="Permalink to this headline">¶</a></h2>
+<span id="shock"></span><h3>4.1.28. SHOCK package<a class="headerlink" href="#shock-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-shock
@@ -1280,7 +1289,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="snap-package">
-<span id="snap"></span><h2>4.30. SNAP package<a class="headerlink" href="#snap-package" title="Permalink to this headline">¶</a></h2>
+<span id="snap"></span><h3>4.1.29. SNAP package<a class="headerlink" href="#snap-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-snap
@@ -1302,7 +1311,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="srd-package">
-<span id="srd"></span><h2>4.31. SRD package<a class="headerlink" href="#srd-package" title="Permalink to this headline">¶</a></h2>
+<span id="srd"></span><h3>4.1.30. SRD package<a class="headerlink" href="#srd-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-srd
@@ -1324,7 +1333,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="voronoi-package">
-<span id="voronoi"></span><h2>4.32. VORONOI package<a class="headerlink" href="#voronoi-package" title="Permalink to this headline">¶</a></h2>
+<span id="voronoi"></span><h3>4.1.31. VORONOI package<a class="headerlink" href="#voronoi-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-voronoi
@@ -1346,7 +1355,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="xtc-package">
-<span id="xtc"></span><h2>4.33. XTC package<a class="headerlink" href="#xtc-package" title="Permalink to this headline">¶</a></h2>
+<span id="xtc"></span><h3>4.1.32. XTC package<a class="headerlink" href="#xtc-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-xtc
@@ -1367,8 +1376,9 @@ make machine
 <p>Supporting info:</p>
 <hr class="docutils" />
 </div>
+</div>
 <div class="section" id="user-packages">
-<span id="pkg-2"></span><h2>4.34. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
+<span id="pkg-2"></span><h2>4.2. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
 <p>The current list of user-contributed packages is as follows:</p>
 <table border="1" class="docutils">
 <colgroup>
@@ -1785,9 +1795,8 @@ on how to build the library.  If it is not listed as lib/package, then
 it is a third-party library not included in the LAMMPS distribution.
 See details on all of this below for individual packages.</p>
 <hr class="docutils" />
-</div>
 <div class="section" id="user-atc-package">
-<span id="user-atc"></span><h2>4.35. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-atc"></span><h3>4.2.1. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -1812,7 +1821,7 @@ you have questions.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-awpmd-package">
-<span id="user-awpmd"></span><h2>4.36. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-awpmd"></span><h3>4.2.2. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -1832,7 +1841,7 @@ have questions.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-cg-cmm-package">
-<span id="user-cg-cmm"></span><h2>4.37. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-cg-cmm"></span><h3>4.2.3. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-body
@@ -1886,7 +1895,7 @@ simulation systems.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-colvars-package">
-<span id="user-colvars"></span><h2>4.38. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-colvars"></span><h3>4.2.4. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -1924,7 +1933,7 @@ beta quality.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-cuda-package">
-<span id="user-cuda"></span><h2>4.39. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-cuda"></span><h3>4.2.5. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h3>
 <p>This package provides acceleration of various LAMMPS pair styles, fix
 styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
 GPUs.</p>
@@ -1947,7 +1956,7 @@ tu-ilmenau.de).  Contact him directly if you have questions.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-diffraction-package">
-<span id="user-diffraction"></span><h2>4.40. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-diffraction"></span><h3>4.2.6. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h3>
 <p>This package contains the commands neeed to calculate x-ray and
 electron diffraction intensities based on kinematic diffraction
 theory.</p>
@@ -1982,7 +1991,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-dpd-package">
-<span id="user-dpd"></span><h2>4.41. USER-DPD package<a class="headerlink" href="#user-dpd-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-dpd"></span><h3>4.2.7. USER-DPD package<a class="headerlink" href="#user-dpd-package" title="Permalink to this headline">¶</a></h3>
 <p>This package implements the dissipative particle dynamics (DPD) method
 under isothermal, isoenergetic, isobaric and isenthalpic conditions.
 The DPD equations of motion are integrated efficiently through the
@@ -2023,7 +2032,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-drude-package">
-<span id="user-drude"></span><h2>4.42. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-drude"></span><h3>4.2.8. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2065,7 +2074,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-eff-package">
-<span id="user-eff"></span><h2>4.43. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-eff"></span><h3>4.2.9. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2120,7 +2129,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-fep-package">
-<span id="user-fep"></span><h2>4.44. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-fep"></span><h3>4.2.10. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2156,7 +2165,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-h5md-package">
-<span id="user-h5md"></span><h2>4.45. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-h5md"></span><h3>4.2.11. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2174,7 +2183,7 @@ directly if you have questions.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-intel-package">
-<span id="user-intel"></span><h2>4.46. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-intel"></span><h3>4.2.12. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2209,7 +2218,7 @@ your Makefile.machine for CCFLAGS and LINKFLAGS.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-lb-package">
-<span id="user-lb"></span><h2>4.47. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-lb"></span><h3>4.2.13. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2242,7 +2251,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-mgpt-package">
-<span id="user-mgpt"></span><h2>4.48. USER-MGPT package<a class="headerlink" href="#user-mgpt-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-mgpt"></span><h3>4.2.14. USER-MGPT package<a class="headerlink" href="#user-mgpt-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2286,7 +2295,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-misc-package">
-<span id="user-misc"></span><h2>4.49. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-misc"></span><h3>4.2.15. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2324,7 +2333,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-molfile-package">
-<span id="user-molfile"></span><h2>4.50. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-molfile"></span><h3>4.2.16. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2347,7 +2356,7 @@ application itself.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-omp-package">
-<span id="user-omp"></span><h2>4.51. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-omp"></span><h3>4.2.17. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2369,7 +2378,7 @@ settings for CCFLAGS and LINKFLAGS.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-phonon-package">
-<span id="user-phonon"></span><h2>4.52. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-phonon"></span><h3>4.2.18. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h3>
 <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>
@@ -2398,7 +2407,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-qmmm-package">
-<span id="user-qmmm"></span><h2>4.53. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-qmmm"></span><h3>4.2.19. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2419,7 +2428,7 @@ without changes to LAMMPS itself.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-qtb-package">
-<span id="user-qtb"></span><h2>4.54. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-qtb"></span><h3>4.2.20. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2462,7 +2471,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-quip-package">
-<span id="user-quip"></span><h2>4.55. USER-QUIP package<a class="headerlink" href="#user-quip-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-quip"></span><h3>4.2.21. USER-QUIP package<a class="headerlink" href="#user-quip-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2471,7 +2480,7 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-reaxc-package">
-<span id="user-reaxc"></span><h2>4.56. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-reaxc"></span><h3>4.2.22. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-body
@@ -2518,7 +2527,7 @@ questions.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-smd-package">
-<span id="user-smd"></span><h2>4.57. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-smd"></span><h3>4.2.23. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
@@ -2547,7 +2556,7 @@ you have questions.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-smtbq-package">
-<span id="user-smtbq"></span><h2>4.58. USER-SMTBQ package<a class="headerlink" href="#user-smtbq-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-smtbq"></span><h3>4.2.24. USER-SMTBQ package<a class="headerlink" href="#user-smtbq-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-body
@@ -2580,7 +2589,7 @@ them directly if you have any questions.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-sph-package">
-<span id="user-sph"></span><h2>4.59. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-sph"></span><h3>4.2.25. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-body
@@ -2621,7 +2630,7 @@ you have questions.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-tally-package">
-<span id="user-tally"></span><h2>4.60. USER-TALLY package<a class="headerlink" href="#user-tally-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-tally"></span><h3>4.2.26. USER-TALLY package<a class="headerlink" href="#user-tally-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <div class="highlight-python"><div class="highlight"><pre>make yes-body
@@ -2644,13 +2653,14 @@ make machine
 <hr class="docutils" />
 </div>
 <div class="section" id="user-vtk-package">
-<span id="user-vtk"></span><h2>4.61. USER-VTK package<a class="headerlink" href="#user-vtk-package" title="Permalink to this headline">¶</a></h2>
+<span id="user-vtk"></span><h3>4.2.27. USER-VTK package<a class="headerlink" href="#user-vtk-package" title="Permalink to this headline">¶</a></h3>
 <p>Contents:</p>
 <p>To install via make or Make.py:</p>
 <p>To un-install via make or Make.py:</p>
 <p>Supporting info:</p>
 <p>Examples: examples/USER/tally</p>
 </div>
+</div>
 </div>
 
 
diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt
index 43c7a2579f..cf19f9ef68 100644
--- a/doc/Section_packages.txt
+++ b/doc/Section_packages.txt
@@ -10,26 +10,34 @@ Section"_Section_accelerate.html :c
 
 4. Packages :h3
 
-This section gives an overview of the add-on packages that extend
-LAMMPS functionality.  Two tables, for standard and user packages, are
-below.  A brief sub-section for each package follows, with a summary
-of what the package contains, how to install it, and pointers to
-examples of its use or documentation provided in the LAMMPS
-distribution.
+This section gives an overview of the add-on optional packages that
+extend LAMMPS functionality.  Packages are groups of files that enable
+a specific set of features.  For example, force fields for molecular
+systems or granular systems are in packages.  You can see the list of
+all packages by typing "make package" from within the src directory of
+the LAMMPS distribution.
+
+Here are links for two tables below, which list standard and user
+packages.
 
 4.1 "Standard packages"_#pkg_1
 4.2 "User packages"_#pkg_2 :all(b)
 
-LAMMPS includes many optional packages, which are groups of files that
-enable a specific set of features.  For example, force fields for
-molecular systems or granular systems are in packages.  You can see
-the list of all packages by typing "make package" from within the src
-directory of the LAMMPS distribution.
+"Section_start 3"_Section_start.html#start_3 of the manual describes
+the difference between standard packages and user packages.  It also
+has general details on how to include/exclude specific packages as
+part of the LAMMPS build process, and on how to build auxiliary
+libraries or modify a machine Makefile if a package requires it.
 
-See "Section_start 3"_Section_start.html#start_3 of the manual for
-details on how to include/exclude specific packages as part of the
-LAMMPS build process, and for more details about the differences
-between standard packages and user packages.
+Following the two tables below, is a sub-section for each package.  It
+has a summary of what the package contains.  It has specific
+instructions on how to install it, build or obtain any auxiliary
+library it requires, and any Makefile.machine changes it requires.  It
+also lists pointers to examples of its use or documentation provided
+in the LAMMPS distribution.
+
+NOTE: The sub-sections below are still being filled in, as of Feb
+2016.
 
 Unless otherwise noted below, every package is independent of all the
 others.  I.e. any package can be included or excluded in a LAMMPS
@@ -44,17 +52,12 @@ lj/cut/coul/long command.  If you later install the KSPACE pacakge and
 the USER-OMP package is already installed, both the pair
 lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
 
-The two tables below list currently available packages in LAMMPS, with
-a one-line descriptions of each.  The sub-sections below give more
-details.
-
 :line
 
 4.1 Standard packages :h4,link(pkg_1)
 
 The current list of standard packages is as follows.  Each package
-name links to a sub-section below with more details on how to build
-with the package and pointers to additional info.
+name links to a sub-section below with more details.
 
 Package, Description, Author(s), Doc page, Example, Library
 "ASPHERE"_#ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, -
@@ -121,10 +124,11 @@ of the LAMMPS distribution.  See the lib/package/README file for info
 on how to build the library.  If it is not listed as lib/package, then
 it is a third-party library not included in the LAMMPS distribution.
 See details on all of this below for individual packages.
+p.s.: are we ever going to get commit messages from you? ;-)
 
 :line
 
-ASPHERE package :link(ASPHERE),h4
+ASPHERE package :link(ASPHERE),h5
 
 Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
 triangles.
@@ -148,7 +152,7 @@ Supporting info: examples/ASPHERE, examples/ellipse, Section howto
 
 :line
 
-BODY package :link(BODY),h4
+BODY package :link(BODY),h5
 
 Contents:
 
@@ -170,7 +174,7 @@ Supporting info: examples/body
 
 :line
  
-CLASS2 package :link(CLASS2),h4
+CLASS2 package :link(CLASS2),h5
 
 Contents:
 
@@ -192,7 +196,7 @@ Supporting info:
  
 :line
  
-COLLOID package :link(COLLOID),h4
+COLLOID package :link(COLLOID),h5
 
 Contents:
 
@@ -214,7 +218,7 @@ Supporting info: examples/colloid, examples/srd
  
 :line
  
-COMPRESS package :link(COMPRESS),h4
+COMPRESS package :link(COMPRESS),h5
  
 Contents:
 
@@ -236,7 +240,7 @@ Supporting info:
 
 :line
  
-CORESHELL package :link(CORESHELL),h4
+CORESHELL package :link(CORESHELL),h5
 
 Contents:
 
@@ -258,7 +262,7 @@ Supporting info: examples/coreshell, Section howto 6.26
 
 :line
  
-DIPOLE package :link(DIPOLE),h4
+DIPOLE package :link(DIPOLE),h5
 
 Contents:
 
@@ -280,7 +284,7 @@ Supporting info: examples/dipole
  
 :line
  
-FLD package :link(FLD),h4
+FLD package :link(FLD),h5
 
 Contents:
 
@@ -302,7 +306,7 @@ Supporting info:
  
 :line
  
-GPU package :link(GPU),h4
+GPU package :link(GPU),h5
 
 Contents:
 
@@ -324,7 +328,7 @@ Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER
  
 :line
  
-GRANULAR package :link(GRANULAR),h4
+GRANULAR package :link(GRANULAR),h5
 
 Contents:
 
@@ -346,7 +350,7 @@ Supporting info: examples/pour, bench/in.chute, Section howto 6.6
  
 :line
  
-KIM package :link(KIM),h4
+KIM package :link(KIM),h5
 
 Contents:
 
@@ -368,7 +372,7 @@ Supporting info: examples/kim
  
 :line
  
-KOKKOS package :link(KOKKOS),h4
+KOKKOS package :link(KOKKOS),h5
 
 Contents:
 
@@ -412,7 +416,7 @@ Examples: examples/accelerate, bench/FERMI, bench/KEPLER
  
 :line
  
-KSPACE package :link(KSPACE),h4
+KSPACE package :link(KSPACE),h5
 
 Contents:
 
@@ -438,7 +442,7 @@ Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9
 
 :line
  
-MANYBODY package :link(MANYBODY),h4
+MANYBODY package :link(MANYBODY),h5
 
 Contents:
 
@@ -462,7 +466,7 @@ Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta
 
 :line
  
-MC package :link(MC),h4
+MC package :link(MC),h5
 
 Contents:
 
@@ -484,7 +488,7 @@ Supporting info:
  
 :line
  
-MEAM package :link(MEAM),h4
+MEAM package :link(MEAM),h5
 
 Contents:
 
@@ -506,7 +510,7 @@ Supporting info: examples/meam
  
 :line
  
-MISC package :link(MISC),h4
+MISC package :link(MISC),h5
 
 Contents:
 
@@ -528,7 +532,7 @@ Supporting info: examples/misc
  
 :line
  
-MOLECULE package :link(MOLECULE),h4
+MOLECULE package :link(MOLECULE),h5
 
 Contents:
 
@@ -550,7 +554,7 @@ Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rh
  
 :line
  
-MPIIO package :link(MPIIO),h4
+MPIIO package :link(MPIIO),h5
 
 Contents:
 
@@ -572,7 +576,7 @@ Supporting info:
  
 :line
  
-OPT package :link(OPT),h4
+OPT package :link(OPT),h5
 
 Contents:
 
@@ -599,7 +603,7 @@ CCFLAGS: add -restrict :ul
 
 :line
  
-PERI package :link(PERI),h4
+PERI package :link(PERI),h5
 
 Contents:
 
@@ -621,7 +625,7 @@ Supporting info: examples/peri
  
 :line
  
-POEMS package :link(POEMS),h4
+POEMS package :link(POEMS),h5
 
 Contents:
 
@@ -643,7 +647,7 @@ Supporting info: examples/rigid
 
 :line
  
-PYTHON package :link(PYTHON),h4
+PYTHON package :link(PYTHON),h5
 
 Contents:
 
@@ -665,7 +669,7 @@ Supporting info: examples/python
  
 :line
  
-QEQ package :link(QEQ),h4
+QEQ package :link(QEQ),h5
 
 Contents:
 
@@ -687,7 +691,7 @@ Supporting info: examples/qeq
  
 :line
  
-REAX package :link(REAX),h4
+REAX package :link(REAX),h5
 
 Contents:
 
@@ -709,7 +713,7 @@ Supporting info: examples/reax
  
 :line
  
-REPLICA package :link(REPLICA),h4
+REPLICA package :link(REPLICA),h5
 
 Contents:
 
@@ -731,7 +735,7 @@ Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5
 
 :line
  
-RIGID package :link(RIGID),h4
+RIGID package :link(RIGID),h5
 
 Contents:
 
@@ -753,7 +757,7 @@ Supporting info: examples/ASPHERE, examples/rigid
 
 :line
  
-SHOCK package :link(SHOCK),h4
+SHOCK package :link(SHOCK),h5
 
 Contents:
 
@@ -775,7 +779,7 @@ Supporting info: examples/hugoniostat, examples/msst
  
 :line
  
-SNAP package :link(SNAP),h4
+SNAP package :link(SNAP),h5
 
 Contents:
 
@@ -797,7 +801,7 @@ Supporting info: examples/snap
  
 :line
  
-SRD package :link(SRD),h4
+SRD package :link(SRD),h5
 
 Contents:
 
@@ -819,7 +823,7 @@ Supporting info:
  
 :line
  
-VORONOI package :link(VORONOI),h4
+VORONOI package :link(VORONOI),h5
 
 Contents:
 
@@ -841,7 +845,7 @@ Supporting info: examples/voronoi
  
 :line
  
-XTC package :link(XTC),h4
+XTC package :link(XTC),h5
 
 Contents:
 
@@ -946,7 +950,7 @@ See details on all of this below for individual packages.
 
 :line
 
-USER-ATC package :link(USER-ATC),h4
+USER-ATC package :link(USER-ATC),h5
 
 Contents:
  
@@ -981,7 +985,7 @@ Examples: examples/USER/atc
 
 :line
 
-USER-AWPMD package :link(USER-AWPMD),h4
+USER-AWPMD package :link(USER-AWPMD),h5
 
 Contents:
  
@@ -1011,7 +1015,7 @@ Examples: examples/USER/awpmd
 
 :line
 
-USER-CG-CMM package :link(USER-CG-CMM),h4
+USER-CG-CMM package :link(USER-CG-CMM),h5
 
 Contents:
  
@@ -1072,7 +1076,7 @@ Examples: examples/USER/cg-cmm
 
 :line
 
-USER-COLVARS package :link(USER-COLVARS),h4
+USER-COLVARS package :link(USER-COLVARS),h5
 
 Contents:
  
@@ -1124,7 +1128,7 @@ Supporting info:
  
 :line
 
-USER-CUDA package :link(USER-CUDA),h4
+USER-CUDA package :link(USER-CUDA),h5
 
 This package provides acceleration of various LAMMPS pair styles, fix
 styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
@@ -1158,7 +1162,7 @@ Supporting info:
  
 :line
 
-USER-DIFFRACTION package :link(USER-DIFFRACTION),h4
+USER-DIFFRACTION package :link(USER-DIFFRACTION),h5
 
 This package contains the commands neeed to calculate x-ray and
 electron diffraction intensities based on kinematic diffraction 
@@ -1196,7 +1200,7 @@ Supporting info:
  
 :line
 
-USER-DPD package :link(USER-DPD),h4
+USER-DPD package :link(USER-DPD),h5
 
 This package implements the dissipative particle dynamics (DPD) method
 under isothermal, isoenergetic, isobaric and isenthalpic conditions.
@@ -1239,7 +1243,7 @@ Examples: examples/USER/dpd
 
 :line
 
-USER-DRUDE package :link(USER-DRUDE),h4
+USER-DRUDE package :link(USER-DRUDE),h5
 
 Contents:
  
@@ -1288,7 +1292,7 @@ Doc: Section howto 6.27
 
 :line
 
-USER-EFF package :link(USER-EFF),h4
+USER-EFF package :link(USER-EFF),h5
 
 Contents:
  
@@ -1353,7 +1357,7 @@ Examples: examples/USER/eff
 
 :line
 
-USER-FEP package :link(USER-FEP),h4
+USER-FEP package :link(USER-FEP),h5
 
 Contents:
  
@@ -1394,7 +1398,7 @@ Examples: examples/USER/fep
 
 :line
 
-USER-H5MD package :link(USER-H5MD),h4
+USER-H5MD package :link(USER-H5MD),h5
 
 Contents:
  
@@ -1421,7 +1425,7 @@ directly if you have questions.
 
 :line
 
-USER-INTEL package :link(USER-INTEL),h4
+USER-INTEL package :link(USER-INTEL),h5
 
 Contents:
  
@@ -1466,7 +1470,7 @@ Examples: examples/accelerate, bench/KEPLER
 
 :line
 
-USER-LB package :link(USER-LB),h4
+USER-LB package :link(USER-LB),h5
 
 Contents:
  
@@ -1506,7 +1510,7 @@ Examples: examples/USER/lb
 
 :line
 
-USER-MGPT package :link(USER-MGPT),h4
+USER-MGPT package :link(USER-MGPT),h5
 
 Contents:
  
@@ -1558,7 +1562,7 @@ Examples: examples/USER/mgpt
 
 :line
 
-USER-MISC package :link(USER-MISC),h4
+USER-MISC package :link(USER-MISC),h5
 
 Contents:
  
@@ -1605,7 +1609,7 @@ Examples: examples/USER/misc
 
 :line
 
-USER-MOLFILE package :link(USER-MOLFILE),h4
+USER-MOLFILE package :link(USER-MOLFILE),h5
 
 Contents:
  
@@ -1637,7 +1641,7 @@ The person who created this package is Axel Kohlmeyer at Temple U
 
 :line
 
-USER-OMP package :link(USER-OMP),h4
+USER-OMP package :link(USER-OMP),h5
 
 Contents:
  
@@ -1668,7 +1672,7 @@ Examples: examples/accelerate, bench/KEPLER
 
 :line
 
-USER-PHONON package :link(USER-PHONON),h4
+USER-PHONON package :link(USER-PHONON),h5
 
 This package contains a fix phonon command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
@@ -1700,7 +1704,7 @@ Examples: examples/USER/phonon
 
 :line
 
-USER-QMMM package :link(USER-QMMM),h4
+USER-QMMM package :link(USER-QMMM),h5
 
 Contents:
  
@@ -1733,7 +1737,7 @@ The person who created this package is Axel Kohlmeyer at Temple U
 
 :line
  
-USER-QTB package :link(USER-QTB),h4
+USER-QTB package :link(USER-QTB),h5
  
 Contents:
  
@@ -1784,7 +1788,7 @@ Examples: examples/USER/qtb
 
 :line
 
-USER-QUIP package :link(USER-QUIP),h4
+USER-QUIP package :link(USER-QUIP),h5
 
 Contents:
  
@@ -1798,7 +1802,7 @@ Examples: examples/USER/quip
 
 :line
 
-USER-REAXC package :link(USER-REAXC),h4
+USER-REAXC package :link(USER-REAXC),h5
 
 Contents:
  
@@ -1853,7 +1857,7 @@ Examples: examples/reax
 
 :line
 
-USER-SMD package :link(USER-SMD),h4
+USER-SMD package :link(USER-SMD),h5
 
 Contents:
  
@@ -1894,7 +1898,7 @@ Examples: examples/USER/smd
 
 :line
 
-USER-SMTBQ package :link(USER-SMTBQ),h4
+USER-SMTBQ package :link(USER-SMTBQ),h5
 
 Contents:
  
@@ -1933,7 +1937,7 @@ Examples: examples/USER/smtbq
 
 :line
 
-USER-SPH package :link(USER-SPH),h4
+USER-SPH package :link(USER-SPH),h5
 
 Contents:
  
@@ -1982,7 +1986,7 @@ Examples: examples/USER/sph
 
 :line
 
-USER-TALLY package :link(USER-TALLY),h4
+USER-TALLY package :link(USER-TALLY),h5
 
 Contents:
 
@@ -2006,7 +2010,7 @@ Examples: examples/USER/tally
 
 :line
 
-USER-VTK package :link(USER-VTK),h4
+USER-VTK package :link(USER-VTK),h5
 
 Contents:
 
diff --git a/doc/_sources/Section_packages.txt b/doc/_sources/Section_packages.txt
index 8dc9b753d7..e58582c947 100644
--- a/doc/_sources/Section_packages.txt
+++ b/doc/_sources/Section_packages.txt
@@ -1,27 +1,37 @@
 Packages
 ========
 
-This section gives an overview of the add-on packages that extend
-LAMMPS functionality.  Two tables, for standard and user packages, are
-below.  A brief sub-section for each package follows, with a summary
-of what the package contains, how to install it, and pointers to
-examples of its use or documentation provided in the LAMMPS
-distribution.
+This section gives an overview of the add-on optional packages that
+extend LAMMPS functionality.  Packages are groups of files that enable
+a specific set of features.  For example, force fields for molecular
+systems or granular systems are in packages.  You can see the list of
+all packages by typing "make package" from within the src directory of
+the LAMMPS distribution.
+
+Here are links for two tables below, which list standard and user
+packages.
 
 | 4.1 :ref:`Standard packages <pkg_1>`
 | 4.2 :ref:`User packages <pkg_2>` 
 | 
 
-LAMMPS includes many optional packages, which are groups of files that
-enable a specific set of features.  For example, force fields for
-molecular systems or granular systems are in packages.  You can see
-the list of all packages by typing "make package" from within the src
-directory of the LAMMPS distribution.
+:ref:`Section_start 3 <start_3>` of the manual describes
+the difference between standard packages and user packages.  It also
+has general details on how to include/exclude specific packages as
+part of the LAMMPS build process, and on how to build auxiliary
+libraries or modify a machine Makefile if a package requires it.
 
-See :ref:`Section_start 3 <start_3>` of the manual for
-details on how to include/exclude specific packages as part of the
-LAMMPS build process, and for more details about the differences
-between standard packages and user packages.
+Following the two tables below, is a sub-section for each package.  It
+has a summary of what the package contains.  It has specific
+instructions on how to install it, build or obtain any auxiliary
+library it requires, and any Makefile.machine changes it requires.  It
+also lists pointers to examples of its use or documentation provided
+in the LAMMPS distribution.
+
+.. note::
+
+   The sub-sections below are still being filled in, as of Feb
+   2016.
 
 Unless otherwise noted below, every package is independent of all the
 others.  I.e. any package can be included or excluded in a LAMMPS
@@ -36,10 +46,6 @@ lj/cut/coul/long command.  If you later install the KSPACE pacakge and
 the USER-OMP package is already installed, both the pair
 lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
 
-The two tables below list currently available packages in LAMMPS, with
-a one-line descriptions of each.  The sub-sections below give more
-details.
-
 
 ----------
 
@@ -50,8 +56,7 @@ Standard packages
 -----------------------------
 
 The current list of standard packages is as follows.  Each package
-name links to a sub-section below with more details on how to build
-with the package and pointers to additional info.
+name links to a sub-section below with more details.
 
 +------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
 | Package                      | Description                          | Author(s)                              | Doc page                                           | Example   | Library    |
@@ -150,6 +155,7 @@ of the LAMMPS distribution.  See the lib/package/README file for info
 on how to build the library.  If it is not listed as lib/package, then
 it is a third-party library not included in the LAMMPS distribution.
 See details on all of this below for individual packages.
+p.s.: are we ever going to get commit messages from you? ;-)
 
 
 ----------
@@ -158,7 +164,7 @@ See details on all of this below for individual packages.
 .. _ASPHERE:
 
 ASPHERE package
----------------
+^^^^^^^^^^^^^^^
 
 Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
 triangles.
@@ -195,7 +201,7 @@ Supporting info: examples/ASPHERE, examples/ellipse, Section howto
 .. _BODY:
 
 BODY package
-------------
+^^^^^^^^^^^^
 
 Contents:
 
@@ -230,7 +236,7 @@ Supporting info: examples/body
 .. _CLASS2:
 
 CLASS2 package
---------------
+^^^^^^^^^^^^^^
 
 Contents:
 
@@ -265,7 +271,7 @@ Supporting info:
 .. _COLLOID:
 
 COLLOID package
----------------
+^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -300,7 +306,7 @@ Supporting info: examples/colloid, examples/srd
 .. _COMPRESS:
 
 COMPRESS package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -335,7 +341,7 @@ Supporting info:
 .. _CORESHELL:
 
 CORESHELL package
------------------
+^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -370,7 +376,7 @@ Supporting info: examples/coreshell, Section howto 6.26
 .. _DIPOLE:
 
 DIPOLE package
---------------
+^^^^^^^^^^^^^^
 
 Contents:
 
@@ -405,7 +411,7 @@ Supporting info: examples/dipole
 .. _FLD:
 
 FLD package
------------
+^^^^^^^^^^^
 
 Contents:
 
@@ -440,7 +446,7 @@ Supporting info:
 .. _GPU:
 
 GPU package
------------
+^^^^^^^^^^^
 
 Contents:
 
@@ -475,7 +481,7 @@ Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER
 .. _GRANULAR:
 
 GRANULAR package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -510,7 +516,7 @@ Supporting info: examples/pour, bench/in.chute, Section howto 6.6
 .. _KIM:
 
 KIM package
------------
+^^^^^^^^^^^
 
 Contents:
 
@@ -545,7 +551,7 @@ Supporting info: examples/kim
 .. _KOKKOS:
 
 KOKKOS package
---------------
+^^^^^^^^^^^^^^
 
 Contents:
 
@@ -604,7 +610,7 @@ Examples: examples/accelerate, bench/FERMI, bench/KEPLER
 .. _KSPACE:
 
 KSPACE package
---------------
+^^^^^^^^^^^^^^
 
 Contents:
 
@@ -643,7 +649,7 @@ Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9
 .. _MANYBODY:
 
 MANYBODY package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -680,7 +686,7 @@ Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta
 .. _MC:
 
 MC package
-----------
+^^^^^^^^^^
 
 Contents:
 
@@ -715,7 +721,7 @@ Supporting info:
 .. _MEAM:
 
 MEAM package
-------------
+^^^^^^^^^^^^
 
 Contents:
 
@@ -750,7 +756,7 @@ Supporting info: examples/meam
 .. _MISC:
 
 MISC package
-------------
+^^^^^^^^^^^^
 
 Contents:
 
@@ -785,7 +791,7 @@ Supporting info: examples/misc
 .. _MOLECULE:
 
 MOLECULE package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -820,7 +826,7 @@ Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rh
 .. _MPIIO:
 
 MPIIO package
--------------
+^^^^^^^^^^^^^
 
 Contents:
 
@@ -855,7 +861,7 @@ Supporting info:
 .. _OPT:
 
 OPT package
------------
+^^^^^^^^^^^
 
 Contents:
 
@@ -895,7 +901,7 @@ settings for CCFLAGS.
 .. _PERI:
 
 PERI package
-------------
+^^^^^^^^^^^^
 
 Contents:
 
@@ -930,7 +936,7 @@ Supporting info: examples/peri
 .. _POEMS:
 
 POEMS package
--------------
+^^^^^^^^^^^^^
 
 Contents:
 
@@ -965,7 +971,7 @@ Supporting info: examples/rigid
 .. _PYTHON:
 
 PYTHON package
---------------
+^^^^^^^^^^^^^^
 
 Contents:
 
@@ -1000,7 +1006,7 @@ Supporting info: examples/python
 .. _QEQ:
 
 QEQ package
------------
+^^^^^^^^^^^
 
 Contents:
 
@@ -1035,7 +1041,7 @@ Supporting info: examples/qeq
 .. _REAX:
 
 REAX package
-------------
+^^^^^^^^^^^^
 
 Contents:
 
@@ -1070,7 +1076,7 @@ Supporting info: examples/reax
 .. _REPLICA:
 
 REPLICA package
----------------
+^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -1105,7 +1111,7 @@ Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5
 .. _RIGID:
 
 RIGID package
--------------
+^^^^^^^^^^^^^
 
 Contents:
 
@@ -1140,7 +1146,7 @@ Supporting info: examples/ASPHERE, examples/rigid
 .. _SHOCK:
 
 SHOCK package
--------------
+^^^^^^^^^^^^^
 
 Contents:
 
@@ -1175,7 +1181,7 @@ Supporting info: examples/hugoniostat, examples/msst
 .. _SNAP:
 
 SNAP package
-------------
+^^^^^^^^^^^^
 
 Contents:
 
@@ -1210,7 +1216,7 @@ Supporting info: examples/snap
 .. _SRD:
 
 SRD package
------------
+^^^^^^^^^^^
 
 Contents:
 
@@ -1245,7 +1251,7 @@ Supporting info:
 .. _VORONOI:
 
 VORONOI package
----------------
+^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -1280,7 +1286,7 @@ Supporting info: examples/voronoi
 .. _XTC:
 
 XTC package
------------
+^^^^^^^^^^^
 
 Contents:
 
@@ -1447,7 +1453,7 @@ See details on all of this below for individual packages.
 .. _USER-ATC:
 
 USER-ATC package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -1487,7 +1493,7 @@ Examples: examples/USER/atc
 .. _USER-AWPMD:
 
 USER-AWPMD package
-------------------
+^^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -1522,7 +1528,7 @@ Examples: examples/USER/awpmd
 .. _USER-CG-CMM:
 
 USER-CG-CMM package
--------------------
+^^^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -1596,7 +1602,7 @@ Examples: examples/USER/cg-cmm
 .. _USER-COLVARS:
 
 USER-COLVARS package
---------------------
+^^^^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -1653,7 +1659,7 @@ Supporting info:
 .. _USER-CUDA:
 
 USER-CUDA package
------------------
+^^^^^^^^^^^^^^^^^
 
 This package provides acceleration of various LAMMPS pair styles, fix
 styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
@@ -1692,7 +1698,7 @@ Supporting info:
 .. _USER-DIFFRACTION:
 
 USER-DIFFRACTION package
-------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^
 
 This package contains the commands neeed to calculate x-ray and
 electron diffraction intensities based on kinematic diffraction 
@@ -1743,7 +1749,7 @@ Supporting info:
 .. _USER-DPD:
 
 USER-DPD package
-----------------
+^^^^^^^^^^^^^^^^
 
 This package implements the dissipative particle dynamics (DPD) method
 under isothermal, isoenergetic, isobaric and isenthalpic conditions.
@@ -1799,7 +1805,7 @@ Examples: examples/USER/dpd
 .. _USER-DRUDE:
 
 USER-DRUDE package
-------------------
+^^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -1861,7 +1867,7 @@ Doc: Section howto 6.27
 .. _USER-EFF:
 
 USER-EFF package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -1939,7 +1945,7 @@ Examples: examples/USER/eff
 .. _USER-FEP:
 
 USER-FEP package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -1993,7 +1999,7 @@ Examples: examples/USER/fep
 .. _USER-H5MD:
 
 USER-H5MD package
------------------
+^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2026,7 +2032,7 @@ directly if you have questions.
 .. _USER-INTEL:
 
 USER-INTEL package
-------------------
+^^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2078,7 +2084,7 @@ Examples: examples/accelerate, bench/KEPLER
 .. _USER-LB:
 
 USER-LB package
----------------
+^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2131,7 +2137,7 @@ Examples: examples/USER/lb
 .. _USER-MGPT:
 
 USER-MGPT package
------------------
+^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2196,7 +2202,7 @@ Examples: examples/USER/mgpt
 .. _USER-MISC:
 
 USER-MISC package
------------------
+^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2256,7 +2262,7 @@ Examples: examples/USER/misc
 .. _USER-MOLFILE:
 
 USER-MOLFILE package
---------------------
+^^^^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2293,7 +2299,7 @@ The person who created this package is Axel Kohlmeyer at Temple U
 .. _USER-OMP:
 
 USER-OMP package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2329,7 +2335,7 @@ Examples: examples/accelerate, bench/KEPLER
 .. _USER-PHONON:
 
 USER-PHONON package
--------------------
+^^^^^^^^^^^^^^^^^^^
 
 This package contains a fix phonon command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
@@ -2374,7 +2380,7 @@ Examples: examples/USER/phonon
 .. _USER-QMMM:
 
 USER-QMMM package
------------------
+^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2414,7 +2420,7 @@ The person who created this package is Axel Kohlmeyer at Temple U
 .. _USER-QTB:
 
 USER-QTB package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2478,7 +2484,7 @@ Examples: examples/USER/qtb
 .. _USER-QUIP:
 
 USER-QUIP package
------------------
+^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2497,7 +2503,7 @@ Examples: examples/USER/quip
 .. _USER-REAXC:
 
 USER-REAXC package
-------------------
+^^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2565,7 +2571,7 @@ Examples: examples/reax
 .. _USER-SMD:
 
 USER-SMD package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2611,7 +2617,7 @@ Examples: examples/USER/smd
 .. _USER-SMTBQ:
 
 USER-SMTBQ package
-------------------
+^^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2663,7 +2669,7 @@ Examples: examples/USER/smtbq
 .. _USER-SPH:
 
 USER-SPH package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2725,7 +2731,7 @@ Examples: examples/USER/sph
 .. _USER-TALLY:
 
 USER-TALLY package
-------------------
+^^^^^^^^^^^^^^^^^^
 
 Contents:
 
@@ -2762,7 +2768,7 @@ Examples: examples/USER/tally
 .. _USER-VTK:
 
 USER-VTK package
-----------------
+^^^^^^^^^^^^^^^^
 
 Contents:
 
diff --git a/doc/_sources/fix_langevin.txt b/doc/_sources/fix_langevin.txt
index 5c100703b9..a789f45acb 100644
--- a/doc/_sources/fix_langevin.txt
+++ b/doc/_sources/fix_langevin.txt
@@ -23,9 +23,9 @@ Syntax
 * keyword = *angmom* or *omega* or *scale* or *tally* or *zero*
 .. parsed-literal::
 
-     *angmom* value = *no* or scale
+     *angmom* value = *no* or factor
        *no* = do not thermostat rotational degrees of freedom via the angular momentum
-       factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
+       factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
      *gjf* value = *no* or *yes*
        *no* = use standard formulation
        *yes* = use Gronbech-Jensen/Farago formulation
diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html
index efb8c12082..a3192dc1e8 100644
--- a/doc/fix_langevin.html
+++ b/doc/fix_langevin.html
@@ -145,9 +145,9 @@
 <li>keyword = <em>angmom</em> or <em>omega</em> or <em>scale</em> or <em>tally</em> or <em>zero</em></li>
 </ul>
 <pre class="literal-block">
-<em>angmom</em> value = <em>no</em> or scale
+<em>angmom</em> value = <em>no</em> or factor
   <em>no</em> = do not thermostat rotational degrees of freedom via the angular momentum
-  factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
+  factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
 <em>gjf</em> value = <em>no</em> or <em>yes</em>
   <em>no</em> = use standard formulation
   <em>yes</em> = use Gronbech-Jensen/Farago formulation
@@ -175,7 +175,7 @@ fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333
 </div>
 <div class="section" id="description">
 <h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
-<p>Apply a Langevin thermostat as described in <a class="reference internal" href="fix_langevin_eff.html#schneider"><span>(Schneider)</span></a>
+<p>Apply a Langevin thermostat as described in <a class="reference internal" href="#schneider"><span>(Schneider)</span></a>
 to a group of atoms which models an interaction with a background
 implicit solvent.  Used with <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, this command
 performs Brownian dynamics (BD), since the total force on each atom
@@ -203,7 +203,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired
 temperature, m is the mass of the particle, dt is the timestep size,
 and damp is the damping factor.  Random numbers are used to randomize
 the direction and magnitude of this force as described in
-<a class="reference internal" href="fix_langevin_eff.html#dunweg"><span>(Dunweg)</span></a>, where a uniform random number is used (instead of
+<a class="reference internal" href="#dunweg"><span>(Dunweg)</span></a>, where a uniform random number is used (instead of
 a Gaussian random number) for speed.</p>
 <p>Note that unless you use the <em>omega</em> or <em>angmom</em> keywords, the
 thermostat effect of this fix is applied to only the translational
diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt
index 14245ac0f6..8b86d763a3 100644
--- a/doc/fix_langevin.txt
+++ b/doc/fix_langevin.txt
@@ -21,9 +21,9 @@ damp = damping parameter (time units) :l
 seed = random number seed to use for white noise (positive integer) :l
 zero or more keyword/value pairs may be appended :l
 keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l
-  {angmom} value = {no} or scale
+  {angmom} value = {no} or factor
     {no} = do not thermostat rotational degrees of freedom via the angular momentum
-    factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
+    factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below
   {gjf} value = {no} or {yes}
     {no} = use standard formulation
     {yes} = use Gronbech-Jensen/Farago formulation
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 0423e42e7c..856689cf5c 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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[3,6,320],advertis:8,advis:[371,438],afer:3,affect:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,196,197,202,209,210,212,213,214,215,218,219,220,221,223,224,234,240,242,244,250,257,261,262,263,264,266,267,268,274,279,280,281,283,304,305,318,332,342,355,361,367,368,369,371,372,373,376,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,223,376,391],afil:238,aforement:18,afresh:[292,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,198,200,201,202,206,207,209,210,217,218,219,220,221,223,227,236,247,248,249,250,251,256,257,258,260,266,267,268,274,279,280,281,283,286,290,294,302,304,307,316,321,323,324,325,327,328,329,330,331,335,337,339,343,346,347,353,360,366,367,369,370,372,374,375,376,377,378,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,457,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,197,223,240,290,346,360,371,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,224,371,439,440],aggreg:[6,12,65,68,69,79,95,112,119,240,256,302,304,318,471,503],aggress:[240,490],agilio:[9,13],agre:[3,8,190,369,378,411,440],agreement:[5,7],ahd:408,ahead:339,aidan:[0,5,7,9,13,364],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:196,akohlmei:[7,9,13,198,241],aktulga:[7,9,297,440],al2o3:447,al2o3_001:[122,305],al3:169,ala:[247,447],alain:9,alat:[285,426],alb:[437,460,462],albeit:303,albert:9,alchem:[89,164],alcohol:335,alcu:[377,382],alcu_eam:437,alderton:395,alejandr:[260,261],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,197,206,217,220,223,247,249,250,274,287,295,304,307,308,327,328,332,335,340,367,368,369,373,376,398,402,424,429,444,446,471,473,490],alia:[9,12,16],alias:[1,362],aliceblu:197,align:[6,12,29,41,71,172,190,213,217,242,364,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,198,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,229,230,231,232,233,234,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,253,255,256,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,305,306,307,308,309,310,311,312,316,317,319,320,321,322,323,324,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,351,356,359,360,361,362,363,364,366,369,370,371,372,373,375,376,377,378,379,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:344,alloc:[3,5,6,8,9,11,12,60,234,334,370,372,376,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,194,196,197,198,200,201,203,205,206,207,209,210,211,212,213,214,215,217,219,220,221,222,223,224,228,229,234,236,237,238,239,241,244,247,250,251,255,257,260,261,285,289,290,291,292,293,294,298,304,305,307,309,311,312,316,320,327,328,329,330,332,333,334,335,336,337,343,345,347,356,361,362,364,369,370,371,372,375,376,379,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,242,294,332,362,373,376,456],alo:392,alon:[6,7,220,300,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,196,209,220,242,247,248,252,257,259,294,304,307,309,313,317,318,327,331,332,338,341,343,364,367,368,369,371,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,201,247,286,294,295,299,369,377,380,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,200,347,356,370,389,457,476],alphanum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8,11,12,15,17,39,41,71,93,190,207,213,217,218,219,224,233,236,242,243,290,303,307,320,328,330,335,343,345,360,369,370,371,372,373,376,399,410,413,431,440,471,473,474,476,484,490,493,494,502],checkf:190,checkqeq:440,checku:190,chem:[6,13,20,21,25,39,40,43,45,46,89,90,110,116,145,176,177,187,211,222,227,237,238,245,247,259,260,261,281,282,287,291,294,296,304,308,309,320,323,324,327,328,329,330,337,346,355,357,361,362,368,371,378,383,387,388,391,392,393,395,396,398,402,404,405,407,408,414,418,419,422,426,430,431,434,447,456,463,485,488,490,497],chemic:[9,122,164,169,193,194,206,207,236,295,300,301,327,362,439,440,452],chemistri:[9,294,295,297,382,402,439,440],chen:332,cheng:391,chenoweth:[439,440],chenoweth_2008:[439,440],chi:[95,159,192,285,295,297,403,405,503],chiefli:438,child:8,chip:[7,9,12,17,18,376,489],chipot:222,chiral:355,chmod:[11,12],cho:426,chocol:[7,197],choic:[3,6,9,12,15,16,18,40,41,54,89,145,148,149,163,174,190,209,213,214,217,220,223,224,238,244,247,258,260,287,295,304,327,356,362,367,368,371,373,376,409,422,431,435,476,485,486,489,490,496,497,501],choos:[1,3,6,7,8,12,16,17,18,29,39,54,89,121,160,161,196,218,219,220,221,224,233,244,247,258,260,262,263,264,265,266,267,268,290,291,308,320,324,338,361,362,368,466,471,473,485,491],chose:[460,462],chosen:[2,3,6,12,17,144,170,173,182,190,196,202,207,221,224,233,236,237,245,247,258,260,265,287,290,301,320,324,327,328,333,335,336,342,362,363,368,376,397,398,402,406,413,416,442,460,471,485,490,497],chri:168,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,92,96,107,109,118,150,165,167,209],chute:[4,9,10,239],ciccotti:307,cieplak:[6,176,488],cii:210,cij:210,ciko:2,circl:[42,71,316],circular:[3,6,148,191],circumst:18,circumv:[94,110,299],citat:[],cite:[3,7,8,12,244,447],civ:9,ckio:2,cko:2,cl1:169,clarendon:[29,395],clarifi:[7,460,462],clariti:345,clark:434,class2:[],classic:[0,3,5,6,7,8,9,234,287,294,299,332,357,402],classifi:[9,457,465],claus:474,clean:[6,12,14,15,17,484],cleanli:[475,505],clear:[],clearli:7,clebsch:144,clermont:[9,13],clever:480,click:[2,11,22,37,44,55,170,178,189,196,241,347,356,371,389,457],client:[241,243],climb:[259,371,490],clinic:[7,13],clo:[159,192,503],clock:[12,471,490],clockwis:338,close:[3,6,11,12,13,39,41,67,71,145,173,193,219,220,221,238,245,247,260,281,304,307,338,341,360,362,365,367,368,371,376,378,382,392,393,412,426,431,443,445,462,480,486,497,499],closer:[3,41,120,168,192,193,217,221,225,329,371],closest:[219,285,304,335,405,441,456,466],cloud:[447,497],clovertown:18,clsuter:72,clump1:[289,304],clump2:[289,304],clump3:[289,304],clump:304,cluster:[],clutter:[3,9],cmap:476,cmatrix:238,cmax:426,cmd:[11,12,287,487],cmdarg:11,cmin:426,cmm:[],cmoput:137,cn1:210,cn2:210,cna:[],cnn:210,cnr:[9,13],cnt:[409,480],co2:[40,169,307,370],coars:[7,9,29,36,40,54,182,289,304,320,407,442,485,488],coarser:[362,502],coarsest:144,code:[],coeff:[3,7,8,12,21,22,33,44,50,176,177,178,183,346,347,353,389,409,413,431,444,446,449,476],coeffcient:476,coeffici:[],coefficienct:396,coefficient0:400,coefficient1:400,coeffieci:[6,380,412],coeffincientn:400,coexist:[9,236,402],cohes:[6,403,426],coincid:[126,341,387,423,424,471],colberg:195,cold:[6,155,236,240,372,497],coldest:328,coleman8:9,coleman:[9,122,169,305],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,85,92,96,101,107,109,118,150,158,165,167,170,193,194,197,209,222,250,256,289,299,302,304,343,361,370,372,390,476,483,489,495,506],collid:[228,320,342],colliex:169,collinear:[3,289],collis:[3,247,320,338,342,399,406,469],colllis:320,colloid:[],colombo:39,colon:[198,343,477],color1:197,color2:197,color:[3,9,41,193,196,197,217,237,294,299],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,83,92,94,95,96,107,109,110,112,114,117,118,119,120,121,123,144,145,150,158,165,167,168,169,190,193,194,197,200,208,209,210,212,213,214,215,250,257,258,294,304,321,322,332,342,404,408,439,440,477,491,493,502],columnar:168,colvar:[],colvarmodul:12,com:[],comamnd:223,comand:220,comannd:376,comb3:[],comb:[],comb_1:296,comb_2:296,combiant:393,combin:[3,6,7,9,11,13,36,40,63,65,69,79,89,95,106,112,119,148,149,163,193,196,206,212,241,250,260,287,293,308,324,333,341,344,346,361,362,364,368,376,390,392,393,398,402,403,409,421,422,448,458,460,462,465,468,479,484,489,497,502],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,195,241,243,244,362,371,376,396,431,436,459,478],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,176,190,193,232,245,304,332,370,371,377,400,401,403,413,426,433,440,447,448,458,459,460,461,462,465,473,474,476,497,502],commerci:7,commmand:[3,6,12,59,111,282,412,470,471,473,490,505],common:[],commonli:[3,6,12,17,25,57,59,108,110,172,193,196,198,357,407,416,448,460,462,476,479,488],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,173,174,196,197,217,218,219,221,222,223,241,243,247,249,250,251,260,286,293,295,296,297,304,308,320,332,343,359,361,372,373,374,376,398,399,435,473,474,485,486,502,504,506],communc:361,comp:[7,195,243,244,307,362,371,402,431,436,441,455,459,461],compact:[63,200,389,457],compani:[5,7],compar:[1,3,4,6,8,12,17,39,88,114,122,153,169,178,189,197,227,295,343,345,361,362,369,371,426,447,471,490,491,497,501],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,346,347,356,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,198,202,208,209,210,212,213,214,215,217,286,298,324,327,334,337,340,361,376,410,429,431,459,473,474,502],compens:[6,218,219,302,372,402],compet:331,competit:362,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,195,196,198,241,331,362,376,429,476,477,481,502],compl:17,complain:[11,12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,197,213,217,222,250,287,290,293,320,331,333,344,345,360,371,376,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,247,316,341,359,371,402,429,459,474,476,479,502],compli:[327,331],complic:[6,7,9,12,13,207,236,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,194,196,197,203,204,208,209,210,211,212,213,214,215,216,220,221,223,224,229,234,239,243,244,247,250,252,256,257,259,260,261,265,266,267,268,279,280,281,283,284,286,287,288,291,302,304,306,307,309,313,314,317,320,323,324,325,327,334,335,340,341,342,361,364,368,369,370,371,376,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,207,247,400],compound:[391,402,403,465],compres:[71,118,209],compress:[],compris:[40,341,441,464],compton:[122,169],comptu:3,compuat:362,comput:[],computation:[3,6,218,219,332,382],computational:497,compute_arrai:8,compute_fep:[202,422],compute_group_group:236,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,305],compute_scalar:8,compute_temp:8,compute_ti:202,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:341,concentr:[71,400],concept:[6,150,160,209,485],conceptu:[3,6,71,158,221,223,371,392,409,426,481],concern:[6,73,89,195,237],concetr:71,concis:[11,331],conclud:12,concret:8,concurr:[9,16,362,502],conden:[332,460,462],condens:[6,152,332,378,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:222,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,196,200,221,222,223,224,228,236,243,244,274,287,295,331,359,369,371,378,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,194,431,474],conform:[3,6,13,59,220,221,259,303,309,331,355,371,402,488],confus:[3,465],conjuct:396,conjug:[7,8,244,368,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,197,201,202,244,247,251,274,290,291,295,296,297,299,304,308,320,328,335,340,361,362,371,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,220,241,289,304,307,317,371,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,197,201,202,224,241,242,392,414,418,471,477,479],consequ:[1,6,207,332,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,194,197,201,202,208,210,213,217,219,220,224,248,261,286,304,327,328,331,332,335,362,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,244,245,323,324,325,376,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,198,203,204,209,223,224,227,229,234,237,244,245,246,257,260,262,263,264,265,266,267,268,269,270,272,273,274,275,277,278,279,280,281,282,283,291,294,299,301,303,304,323,324,325,326,336,361,362,364,370,371,376,378,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:206,consit:304,constant:[],constitu:[3,6,250,304,337,341,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,200,209,224,236,237,242,250,254,289,290,302,304,307,318,328,335,369,370,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,221,260,286,303,341,372,376,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,299,435,502],consumpt:359,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,194,196,197,198,200,201,202,206,208,209,210,212,213,214,215,217,222,224,229,232,238,242,243,244,247,258,274,285,286,289,290,292,294,297,301,304,305,310,320,327,331,332,341,342,345,360,362,370,371,374,375,377,378,379,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[9,12,18,440,492,494],context:[3,6,8,12,17,120,121,197,218,219,224,289,301,336,368,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,197,200,201,202,207,209,210,211,212,213,214,215,217,220,221,222,223,224,236,237,238,240,241,242,244,245,246,252,257,258,260,262,263,264,265,266,267,268,279,280,281,282,283,288,290,293,294,304,305,309,319,320,322,329,330,332,338,341,345,360,375,376,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,206,332,444,446],contour_integr:206,contract:[59,221,223,260,291,304],contradictori:3,contrain:307,contraint:274,contrari:[238,245],contrast:[1,6,42,55,64,152,155,194,223,343,444,446,468,505],contrib:332,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,202,207,208,209,210,212,213,214,215,221,236,244,247,250,251,255,261,281,282,289,290,298,301,304,305,307,334,361,369,371,379,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,194,196,200,206,207,217,221,222,223,240,241,244,245,260,262,263,264,265,266,267,268,291,296,304,311,312,323,324,325,332,336,359,361,373,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:206,controlfil:440,convect:93,conveni:[6,12,29,193,198,215,305,364,448,502],convent:[3,8,9,29,181,188,189,194,197,303,317,344,400,402,502],converg:[3,6,41,90,193,194,196,198,203,217,220,221,229,234,265,294,296,299,303,307,367,368,369,371,391,392,414,447,471,483,490],convers:[3,8,144,196,197,207,210,291,361,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,196,197,215,258,290,343,346,348,352,355,364,371,377,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,341],convinc:[7,12],cook:9,cooki:7,cool:[7,160,240,302],cooordin:[193,194],cooper:[5,7],coord123:118,coord1:[3,118,209,213,214],coord2:[3,118,209,213,214],coord3:[3,118,209,213,214],coord:[],coordb:447,coordbb:447,coordiat:369,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,198,200,203,208,209,212,213,214,217,218,219,220,221,222,223,224,227,229,230,234,236,239,240,241,242,243,244,245,257,259,260,262,263,264,266,267,268,281,284,285,286,289,290,291,301,302,304,306,307,309,314,317,318,319,320,322,330,331,332,339,340,342,343,364,369,370,371,376,377,378,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,209],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,196,332,371,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,376,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,289],coral:197,core:[],core_shel:152,coreshel:[6,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,196,341,342,364,464,476],cornflowerblu:197,cornsilk:197,corp:[],corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,194,196,223,236,238,244,260,261,281,289,291,294,331,337,341,361,371,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:206,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,197,203,224,229,234,245,254,260,261,297,304,307,317,319,338,341,371,372,376,394,424,429,473,474,476,486,501,503],correl:[],correpond:232,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,194,196,197,201,202,203,209,211,212,213,214,216,219,221,223,230,234,235,239,244,247,248,256,257,258,260,262,263,264,265,266,267,268,269,270,274,277,279,280,281,283,286,287,291,296,304,306,307,323,325,327,336,337,338,340,341,342,344,346,347,348,349,351,352,355,357,362,366,368,370,371,377,378,380,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],corrupt:3,cosin:[],cosineshift:27,cosmo:[238,243],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,196,197,209,213,214,217,218,219,233,260,296,332,361,362,374,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,238,372],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,194,196,197,201,202,209,210,213,217,223,234,243,293,294,295,299,302,304,306,320,321,327,331,332,333,337,341,343,345,353,358,360,367,369,372,376,379,404,408,409,412,439,440,472,473,474,476,478,480,483,484,491,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,295,297,333,361,362,369,376,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,203,204,207,209,212,213,214,216,217,224,229,233,236,242,260,274,290,307,323,324,341,362,369,370,371,373,376,404,408,431,494,502],counter:[3,338,471,482,484,490],counteract:236,counterbal:240,counterbalanc:29,counterpart:[193,304,471],counterproduct:18,coupl:[],courant:310,cours:[3,8,130,132,164,193,201,202,237,303,317,331,337,339,340,342,343,362,423,449,473,476,489,497,502,504],courtesi:364,cov:447,coval:[6,29,402,426,447,497],covari:238,cover:[6,71,190,197,206,247,402,464],coverag:[71,213],cpc:243,cpp:[1,3,6,8,9,11,12,13,89,193,201,202,234,307],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,197,211,227,245,333,359,362,376,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,372],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,372,497],craympi:376,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:206,create_faceset:206,create_group:195,create_nodeset:206,createatom:[],creation:[],crimson:197,critchlei:289,criteria:[3,120,171,196,197,218,219,220,255,369,436,464,478,481,502],criterion:[12,41,125,170,173,207,217,220,236,274,296,310,338,343,369,371,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,258,327,332,369],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,194,196,208,213,219,223,257,259,281,304,313,317,319,328,335,347,364,371,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:294,crystal:[4,6,13,73,110,285,286,330,364,372,480,494,497],crystallin:[6,106,286,364,461,497],crystallis:327,crystallogr:[122,169],crystallograph:[364,494],crystallographi:[122,169,364],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[377,400],ctemp_cor:227,cterm:309,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,217,227,341,364,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,215,218,219,220,222,233,238,244,246,320,323,324,325,326,328,335,408,494],cumul:[6,207,209,212,213,214,228,236,244,258,260,265,274,304,305,371],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,198,201,202,206,209,213,214,215,217,218,219,220,221,222,223,224,228,229,234,236,238,241,242,244,250,257,260,261,266,267,268,274,279,280,281,283,289,290,295,296,298,301,302,303,304,307,308,309,310,311,312,313,314,316,318,319,320,323,324,325,331,332,335,336,337,338,339,340,342,343,345,359,360,361,362,365,366,368,369,370,371,376,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,236,286],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[285,297],cutinn:[384,423,424],cutlo:[285,297],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,219,220,225,232,285,294,295,297,299,301,304,308,320,333,337,341,343,359,361,362,369,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:[],cutoff_inn:[],cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:327,cvel:309,cvff:[],cwiggl:[3,257,337,340,342,502],cyan:[2,196,197],cycl:[3,236,258,260,261,265],cyclic:[3,190],cygwin:12,cylind:[3,4,71,196,209,242,290,338,341,479],cylindr:[6,242,317,338],cypress:376,cyrot:382,cyrstal:286,d3q15:247,d3q19:247,d_double_doubl:15,d_e:332,d_flag2:293,d_flag:293,d_name:[117,193,293,322,486],d_single_doubl:15,d_single_singl:15,d_sx:293,d_sy:293,d_sz:293,daan:330,dai:12,daili:12,daivi:281,damag:[],dammak:299,damp:[3,6,200,205,244,245,246,251,260,261,265,291,294,295,299,304,323,324,336,338,339,368,369,371,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:245,damp_drud:245,dampen:[304,497],dampflag:[338,406],dan:17,danger:[3,12,236,343,396,494],dangl:173,daniel:9,darden:[362,395],darkblu:197,darkcyan:197,darken:196,darkgoldenrod:197,darkgrai:197,darkgreen:197,darkkhaki:197,darkmagenta:197,darkolivegreen:197,darkorang:197,darkorchid:197,darkr:197,darksalmon:197,darkseagreen:197,darkslateblu:197,darkslategrai:197,darkturquois:197,darkviolet:197,dasgupta:295,dash:[406,493],dat:[6,93,190,206,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,305],dataset:305,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,210],davenport:425,davi:337,david:[9,19,361,362,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,195,196,197,198,287,477,481],ddim:192,deactiv:422,dealt:243,debug:[6,7,11,12,13,14,17,122,126,169,170,287,292,359,361,376,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,257,293,304,333,491],decipher:364,declar:195,declin:320,decod:196,decompos:[89,448],decomposit:[3,5,7,18,62,206,287,308],decoupl:[6,497],decreas:[3,193,194,203,204,211,220,223,229,234,236,244,331,361],decrement:309,deepli:358,deeppink:197,deepskyblu:197,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,217,218,219,220,221,223,224,227,228,229,231,234,235,236,239,242,243,244,245,246,247,255,257,259,260,261,262,263,264,265,266,267,268,270,271,272,275,277,278,279,280,281,282,283,285,286,287,289,290,291,293,295,297,302,304,305,306,307,310,314,318,320,322,323,324,325,326,328,329,330,332,334,335,337,338,339,340,341,342,343,345,346,347,348,349,350,351,352,355,356,357,359,361,362,364,366,368,369,370,371,372,373,374,375,376,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,197,209,210,211,212,213,214,215,223,231,242,265,305,322,334,337,340,342,344,356,359,370,379,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,289],degrad:[8,18,286,362,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,196,209,220,227,236,238,239,244,245,250,260,261,265,266,267,268,279,280,281,283,287,289,303,304,307,323,324,325,330,346,348,352,355,357,369,395,400,408,486,494,497,503],degress:[150,209],del:490,delai:[3,6,12,372,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,200,209,210,212,213,214,215,218,220,233,236,260,305,323,324,343,345,360,370,372,375,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:206,deli:192,delimit:[474,502],deloc:[261,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:[],delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:[],delx:192,delz:192,dem:[],demand:299,demo:11,demon:284,demonstr:[294,426],den:290,dendrim:408,denniston:[9,247,249,250,251,286],denomin:[7,175],denot:[122,227,245,286,297,299,392,407,409,440,444,446],dens:[71,220,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,201,202,206,209,213,214,217,223,234,247,250,253,254,286,290,291,295,332,337,364,366,370,377,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[258,294],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,196,197,200,201,202,203,204,207,209,211,212,213,215,216,217,219,221,223,229,230,235,238,239,240,242,244,245,247,249,250,257,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,285,296,299,301,304,306,307,308,314,320,323,324,325,327,329,331,332,334,336,337,340,341,342,343,345,346,347,348,349,351,352,355,357,362,364,369,370,372,373,374,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:224,deposit:[],deprec:[3,295,439],depth:[51,148,196,332,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,210,221,223,236,244,257,260,262,263,264,265,266,267,268,285,291,295,299,329,330,332,337,338,341,368,370,378,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:285,descend:197,descent:[7,368],descib:[40,196,295],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,195,200,201,202,209,210,211,212,213,214,215,217,220,221,222,223,224,226,227,232,237,238,241,242,243,244,245,246,247,249,250,251,255,259,260,261,265,273,282,285,287,292,293,294,295,296,297,304,309,317,320,321,322,323,324,325,326,327,328,329,330,335,337,338,340,345,361,362,364,367,368,369,370,371,375,378,379,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:362,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,206,220,226,227,260,261,285,286,305,327,332,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,209,215,221,223,234,236,237,244,245,246,250,260,281,289,290,291,292,295,299,304,307,320,323,324,325,326,331,338,353,358,361,362,364,367,369,370,371,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,196],despit:497,destabil:382,destre:355,destroi:[11,39,218,219],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,194,196,197,200,201,202,206,209,210,211,212,213,215,217,219,220,221,222,223,224,234,236,237,238,239,241,242,244,246,247,251,257,258,259,260,261,262,263,264,265,266,267,268,272,274,279,280,281,282,283,286,289,290,291,293,294,296,297,298,304,307,308,320,323,324,325,326,327,328,330,331,332,333,334,335,336,343,345,347,356,361,362,365,369,370,372,373,376,377,378,379,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,235,290,331,371,391,408,413,471,473,476,487,490,502],determ:376,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,194,196,197,198,199,203,204,205,208,209,210,211,212,213,214,215,216,217,221,223,224,227,229,236,239,240,242,244,245,250,255,257,258,260,266,267,268,279,280,281,283,285,287,290,291,294,301,302,303,304,305,306,310,312,314,320,323,324,325,327,333,334,337,338,339,340,341,342,343,356,361,362,364,370,372,373,376,378,379,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:308,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,241,265,289,294,295,298,378,382,402,428,429,447,465,478],devemi:9,deviat:[258,265,285,404],deviator:9,devic:[1,3,12,15,17,241,376],device_typ:376,devin:[296,391],devis:428,dfactor:196,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,362],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,298,429],dhi:[59,192,223,290],dhug:[258,294],dhugoniot:[258,294],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,221,260,291,304,335,444,446],diagonalstyl:448,diagram:[41,122,169,189,217,287],diallo:408,diam:[196,197,290,370],diamet:[3,6,40,42,117,170,193,194,196,197,201,202,244,290,304,320,322,336,338,370,390,405,406,416,441,464,468,476,477,486],diamond:[364,402,426],diamter:[40,290],dick:6,dicsuss:257,dictat:[207,258],did:[3,12,369,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,334,361],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,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245,304,307,329,330,471],elj:395,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,71,84,148,191],ellipsoid:[3,4,6,7,9,13,40,42,71,84,117,134,148,170,191,192,193,194,244,257,262,266,270,271,279,304,320,366,369,405,424,441,457,476,486,504],ellipsoidflag:476,elong:[227,245,494],elp:[439,440],els:[3,7,8,12,71,111,120,121,123,195,196,208,209,210,212,213,214,215,236,260,304,320,332,333,334,343,345,361,409,475,487,502,505],elsewher:[8,257,320,426,438,439,440,488,494,502],elt:426,emac:[],email:[0,3,5,7,8,9,11,403],emb:[3,9,341],emb_lin_neg:426,embed:[3,5,7,11,12,13,29,90,146,168,332,377,400,403,422,426,427,428,437,457,466,474],embt:177,emi:[7,9],emil:9,emol:[439,440,494],emphas:406,empir:[206,324,378,402],emploi:[9,286,295,299,461],empti:[3,57,71,168,172,304,361,372,413,476,487,488,502],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,85,89,99,100,101,102,103,104,108,113,115,116,122,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,146,147,148,149,152,154,156,157,161,162,164,168,169,176,177,179,180,181,182,183,184,185,187,188,189,190,193,194,195,197,198,200,201,202,203,204,205,207,211,214,216,218,219,220,222,223,224,229,230,233,234,235,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,253,254,256,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,277,278,279,280,281,282,283,285,286,287,289,290,294,295,296,297,298,299,300,301,303,304,306,307,309,310,311,312,313,314,316,317,319,320,323,325,326,327,328,329,330,332,333,335,336,337,338,339,340,341,344,346,348,349,351,352,353,355,356,357,362,369,371,375,376,377,378,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,427,428,429,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,467,468,469,474,477,478,479,483,485,495,502,506],enclos:[2,6,12,172,193,292,345,426,447,472,474,484,502],encod:[13,39,42,193,196,197,293,409],encompass:[3,6,40,42,57,59,120,171,316,334,457,479],encount:[3,8,12,59,110,212,375,481,502],encourag:[7,8,298,318],end12i:117,end12x:117,end12z:117,end1i:117,end1x:117,end1z:117,end2i:117,end2x:117,end2z:117,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,42,57,59,71,117,173,174,177,192,193,194,196,197,198,201,202,210,212,214,215,220,223,237,242,244,246,259,260,261,274,291,303,304,309,320,323,324,325,326,328,331,332,335,339,342,343,360,361,370,371,375,376,396,400,405,412,425,429,441,444,446,448,449,466,471,474,476,477,478,479,481,483,484,488,492,494,497,502,506],end_of_step:8,endbondtors:[3,177,183,476],endif:8,energet:[220,378,440],energi:[],energy_compon:447,energy_update_freq:440,enforc:[6,57,58,107,192,193,194,195,196,198,200,207,220,223,260,284,286,296,304,307,345,361,414,473,502,503],enforce2d:[],eng:[11,65,69,112,193,234,343,345,391,428],eng_previ:345,engil:9,engilitycorp:9,engin:[206,223,289,309,329,400,427],engr:[439,440],enhanc:[202,206,471],enlarg:[59,196],enough:[3,40,61,88,170,171,173,174,217,245,290,294,299,304,333,337,338,341,372,376,392,435,476,480,481],enpub:400,enrti:[],ensembl:[],ensight:6,ensur:[3,6,144,193,194,207,211,221,236,237,260,310,331,362,382,399,422,458,465],enter:[57,160,403,429,465,490],enthalpi:[127,262,263,264,400,493,494,502],entir:[0,2,3,6,11,14,15,41,42,63,82,83,90,113,114,116,120,122,145,150,169,170,197,200,201,202,209,213,214,217,220,222,233,236,237,240,244,245,256,260,262,263,264,265,266,267,268,285,287,289,302,304,318,332,334,345,376,395,418,431,459,476,484,485],entireti:464,entiti:[6,8,40,42,193,304],entri:[3,8,12,38,42,56,65,69,79,95,112,119,122,131,134,135,136,137,138,140,141,142,168,190,194,197,212,213,214,222,232,294,343,370,382,401,426,433,440,448,458,459,460,461,462,465,502],entropi:490,entry1:[38,56,197,389,459],entry2:197,entryn:197,enumer:[171,193],enumuer:6,env:376,environ:[1,3,6,11,12,16,17,18,196,238,243,285,376,377,382,389,391,401,402,437,460,473,487,502],epair:[111,197,404,408,439,440,494],epen:[439,440],epfl:[238,243],epp:395,epq:395,eps0:468,eps14:422,epsilon0:462,epsilon:[3,6,36,45,46,50,53,54,89,176,201,202,236,304,320,337,341,367,369,381,387,388,390,392,393,394,395,405,407,408,409,412,413,414,415,416,417,418,419,420,421,422,425,430,434,441,442,452,458,464,467,468,485,497,501],epsilon_0:469,epsilon_14:387,epsilon_:441,epsilon_d:393,epsilon_i:[405,431,441],epsilon_i_:441,epsilon_i_a:[405,441],epsilon_i_b:[405,441],epsilon_i_c:[405,441],epsilon_ij:431,epsilon_j:[405,431,441],epsilon_j_:441,epsilon_j_a:[405,441],epsilon_j_b:[405,441],epsilon_j_c:[405,441],epsilon_lj:441,epton:436,eqch:165,eqeq:[439,440],eqp:395,eqq:395,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,71,76,79,88,89,93,95,112,114,119,121,123,145,148,164,166,168,170,192,196,197,200,201,202,203,204,207,210,211,212,215,216,217,221,223,224,229,236,237,239,240,242,244,245,247,250,251,257,258,265,276,285,287,290,292,294,295,296,299,301,303,304,306,309,314,316,323,324,325,328,329,330,332,334,335,337,340,342,343,345,360,364,369,371,372,373,375,376,391,396,398,404,405,408,412,423,429,430,437,439,440,441,443,444,445,447,448,449,459,464,465,469,472,473,474,476,478,479,483,484,487,490,492,494,502,503],equat:[3,6,7,8,9,93,110,116,122,169,178,189,200,221,227,228,231,232,238,244,245,247,250,258,259,260,261,265,281,285,287,294,295,299,307,308,320,328,332,335,337,338,340,342,355,361,362,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:261,equidist:259,equil:[3,295,365,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,200,207,210,220,221,236,258,260,261,281,282,294,295,296,297,328,329,330,335,391,392,439,440,472,486],equilibria:335,equilibribum:[218,219],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,221,223,236,237,238,245,247,260,265,281,294,295,299,303,307,309,317,320,327,328,330,335,346,348,352,355,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:206,equival:[6,12,13,29,59,61,128,129,137,142,168,172,197,212,215,221,223,236,244,260,281,291,303,304,340,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[295,297],er3:169,eradiu:[40,117,194,402,476],eras:[306,329],erat:[223,424],erc:392,erfc:[392,414,431],erforc:[117,194],erg:501,erhart:[207,400,460,462],ermscal:379,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:337,erron:3,error:[],erta:406,ervel:[117,194,476],escap:[224,497],especi:[8,16,158,170,200,207,217,236,294,299,302,303,376,473],espresso:[9,298],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,210,265,286,336,362,378,392,414,462,481,494],essex:29,establish:[89,240],estim:[1,3,6,10,12,38,41,56,93,145,206,217,228,258,320,327,361,362,367,431,440,459,490,494],esu:501,esub:426,eta:[6,247,260,294,295,297,336,401,403,405,437,461,465,501],eta_dot:260,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:260,etap_dot:260,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,194,196,197,200,201,206,207,208,209,212,213,214,215,218,219,223,224,234,236,237,244,260,290,301,305,332,333,341,345,360,361,369,370,371,372,374,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[369,371,471,490],etot0:294,etot:[6,97,99,100,114,145,156,197,227,245,258,294,493,494],eu2:169,eu3:169,euler:[369,371],eulerian:206,euqat:450,europhi:247,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,194,196,197,201,202,203,204,206,208,209,210,211,212,213,214,215,216,223,229,237,239,240,242,243,244,245,286,292,295,306,310,314,323,324,325,334,337,340,342,343,345,361,362,367,369,376,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[345,474],evan:[158,281],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,369],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,194,197,200,201,202,207,208,209,212,213,214,215,217,218,219,221,223,224,227,242,245,258,260,261,286,290,299,301,304,305,316,320,328,332,335,337,341,343,354,361,367,369,371,376,381,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,217,247,412,466],event:[],eventu:[3,6,12,15,172,295,490],ever:[54,56,243,320],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,198,200,201,202,203,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,228,233,234,236,238,240,241,242,247,248,256,260,261,265,284,285,286,290,291,292,293,294,295,296,297,299,301,302,304,305,307,309,320,322,323,324,325,326,327,328,331,332,333,334,335,343,345,360,362,371,372,373,376,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[238,247,287,471],evolv:[247,287,333],ewald:[2,3,5,6,7,8,12,90,114,122,145,333,361,362,369,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,217,220,237,238,244,245,246,290,299,300,320,332,347,361,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,201,202,212,217,223,228,232,237,244,245,246,261,273,274,282,286,294,320,325,326,339,376,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,220,286],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,208,209,212,213,214,215,217,221,223,228,233,260,286,301,305,311,312,320,369,376,476,502],exceed:[3,41,59,217,223,260,320,484],excel:402,except:[1,2,5,6,8,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,197,200,203,209,210,212,216,217,221,223,230,235,236,239,242,244,246,260,261,262,263,264,265,266,267,268,269,270,273,274,277,279,280,281,282,283,287,296,297,304,306,307,317,320,323,325,326,332,336,340,343,344,345,346,347,348,349,351,352,355,356,357,361,362,364,366,370,371,372,374,375,376,377,378,380,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[211,402],exchang:[2,3,6,8,9,61,62,200,206,207,236,244,296,304,328,332,335,361,376,402,491],exchange:361,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,209,213,218,219,248,256,289,302,304,327,338,343,369,370,372,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,376,391,429,431,485,495],excurs:[260,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,196,241,298,345,360,363,375,472,474,484,487,490,502],exempl:447,exemplari:237,exemplifi:402,exert:[6,242,245,299,339,340,341,362],exhaust:[206,375,502],exhibit:[94,260,368,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,195,196,197,200,205,216,219,221,224,236,289,290,292,343,344,346,348,349,350,352,356,365,370,376,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,217,232,360,375,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,217,229,236,238,257,285,291,293,294,299,304,343,362,372,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,197,285,289,304,332,343,361,362,372,376,474],experi:[6,13,15,17,216,224,241,250,259,291,303,304,367,371,396,431,485,490],experienc:[6,12,249,250],experiment:[236,361,376,490],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,194,196,197,200,209,210,215,217,219,221,223,260,285,293,304,317,343,345,360,361,364,370,371,375,381,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,194,209,259,285,409,470,473,474,476,485],explanatori:[3,8,121,193,194,208,209,212,213,214,304,370,473,502],explantori:[3,300],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,201,202,223,311,312,347,366,378,379,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,194,197,203,213,216,223,230,235,237,239,244,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,293,294,296,304,306,307,323,325,326,332,336,340,346,348,349,351,352,355,357,370,376,377,378,380,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,287],explor:[122,169],expon:[3,295,297,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[206,396,399],express:[6,144,156,170,201,202,221,257,285,295,332,338,345,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,194,200,203,204,207,215,216,222,225,229,234,235,236,238,239,240,242,244,246,258,260,265,274,285,286,302,303,304,306,309,314,317,319,323,324,325,326,327,329,330,332,334,337,341,342,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,205,213,217,242,339,342,361,364,378,443,445,459,473,476,479],exterior:[3,6,168,341],extern:[],extra:[3,6,8,11,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,197,212,217,219,260,292,293,294,304,320,369,370,373,374,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,201,202,297,371,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,196,211,221,223,260,330,402,461,497],extrema:422,extrins:206,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,334],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:294,f_harm:330,f_i:[29,437],f_id:[6,71,121,123,193,194,200,208,209,210,211,212,213,214,215,255,322,334,494,502],f_ij:437,f_indent:215,f_int:329,f_j:29,f_jj:93,f_k:437,f_langevin:332,f_max:[294,299],f_msst:258,f_r:[245,460,461,462],f_sigma:382,f_solid:330,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,205,213,214,337,339,340,341,342,364,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,238,290,320,330,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,196,197,201,202,210,217,221,223,224,236,241,244,246,247,258,260,261,265,287,291,295,303,307,310,312,320,324,328,335,336,337,341,352,362,364,370,376,378,379,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:361,fail:[3,11,12,59,174,221,224,361,369,371,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:241,fall:[3,6,197,212,290,474,502],fals:[88,343,345,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,194,197,198,217,218,219,221,224,260,285,303,304,320,337,348,352,367,371,372,464,474,476,481,494],farago:244,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,197,200,201,202,207,213,217,219,224,236,238,242,257,258,260,262,263,264,265,266,267,268,276,279,280,281,282,283,293,294,296,304,309,313,319,322,330,332,336,337,338,340,342,371,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,194,271,294,333,361,362,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,194,197,203,216,217,223,230,235,239,243,244,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,291,295,296,304,306,307,320,323,325,327,329,332,336,340,346,348,349,351,352,355,357,361,362,373,374,376,377,378,380,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,213,332,333,376,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:220,favorit:7,fbmc:327,fcc:[],fcm:[276,502],fdirect:227,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:206,featu:8,featur:[],fecr:400,feedback:[7,241],feel:[7,241,242,250,285,341,343,371,431],felling:428,felt:341,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,9,12,15,156,376,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,18,39,63,198,208,209,210,212,213,214,215,245,260,290,293,295,307,334,361,369,370,371,378,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,250,485],fewest:3,fextern:234,feynman:287,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,196],ffplai:196,fft:[1,3,7,11,12,14,15,90,113,114,145,286,361,362,485],fft_inc:[12,362],fft_lib:12,fft_path:12,fftbench:[361,495],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:456,fictiti:[6,203,204,229,234,238,287,303,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[317,433],figur:[1,3,8,12,294,473,474],fij:395,file0:285,file1:[11,13,285,331,345,370,481,483,487],file2:[11,13,331,345,370,481,483,487],file:[],file_from:195,filen:370,filenam:[3,12,13,38,41,56,190,193,194,196,197,198,206,209,210,211,212,213,214,215,217,222,232,285,289,292,295,296,297,300,301,304,305,331,332,358,359,360,370,371,377,378,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,194,197,478,483,506],filepo:301,fill:[7,9,170,196,290,332,364,372,382,429,440,479],filter:[197,206],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,198,207,220,221,232,233,236,259,285,290,291,299,303,367,369,371,372,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,203,229,330,372,376,502],finer:[144,170,502],finest:361,finger:[170,192,257,479],finish:[6,11,41,217,345,358,360,361,373,375,376,464,481,502,503],finit:[],finni:[7,400,457],finvers:227,fiorin:[9,222],fire:[],firebrick:197,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,198,200,201,209,210,212,213,214,215,217,220,223,232,236,237,242,247,257,258,259,260,285,287,292,293,294,296,301,304,307,309,317,318,320,321,322,329,330,331,332,334,338,343,345,346,353,364,369,370,371,372,375,376,377,378,381,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,232,303,320,378,382,411,426,431,452,459,461,484,502],five:[73,156,294,370,382,427,476,490],fix:[],fix_adapt:[164,202,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,207,290],fix_eo:9,fix_evapor:207,fix_flux:206,fix_gcmc:[207,370],fix_gl:238,fix_gld:238,fix_grav:290,fix_id:[3,221,258,260,262,263,264,265,266,267,268,291,294],fix_modifi:[],fix_mov:[192,338],fix_nh:8,fix_npt:238,fix_nvt:[207,236],fix_poem:[3,6],fix_pour:[3,224],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:307,fix_reax_bond:439,fix_rigid:[250,381],fix_saed_vtk:305,fix_setforc:8,fix_shak:307,fix_shardlow:9,fix_srd:3,fix_styl:265,fix_temp_rescal:326,fixedpoint:[221,260],fixextern:234,fixid:206,fji:395,flag1:[226,374],flag2:[226,374],flag:[3,8,9,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,194,196,197,198,215,220,222,226,241,244,248,250,256,257,286,293,304,317,319,320,327,331,340,343,359,362,370,374,375,376,378,408,413,426,429,456,471,473,474,476,477,478,480,481,482,486,502],flag_buck:386,flag_coul:[386,395,418],flag_lj:[395,418],flagfld:[384,423,424],flaghi:[3,384,423,424],flaglog:[384,423,424],flagn:226,flagvf:[384,423,424],flat:[6,332,337,338,342],flavor:[2,7,12],fld:[337,384,423,424],flen:379,flex_press:379,flexibl:[3,6,8,171,196,209,213,222,238,261,328,335,402,461,494],flip:[3,6,223,260,339,340],floor:502,flop:12,floralwhit:197,flow:[],fluctuat:[6,64,89,221,236,237,244,247,260,265,285,286,308,330,332,355,398],fluid:[],fluid_veloc:251,flush:[3,197,493],flux:[],flv:196,fly:[7,9,12,41,196,200,206,211,224,227,304,307,333,382,429,494,497],fmackai:9,fmag:225,fmass:287,fmax:[369,494],fmomentum:227,fmsec:[2,197,244,245,257,260,291,304,323,324,485,496,501,503],fname:360,fno:[9,12,16],fnorm:[369,494],fnpt:227,fnvt:227,foce:409,fock:379,focu:307,fogarti:[9,297,440],foil:[144,285,448],fold:[318,485],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,40,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,82,93,94,99,100,110,117,120,121,123,144,145,148,149,150,156,158,163,166,168,170,171,176,179,180,181,182,184,185,187,188,190,193,195,196,197,200,206,207,208,209,210,211,212,213,214,215,217,222,223,224,227,228,231,232,234,236,237,238,241,243,244,245,247,250,258,260,265,266,267,268,279,280,281,283,286,287,289,292,293,294,295,297,299,301,303,304,305,307,322,323,324,325,328,329,330,331,332,334,335,343,344,348,349,350,351,352,355,357,359,364,366,369,370,371,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,436,437,438,439,440,441,442,444,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,467,468,469,471,473,474,476,477,479,481,483,484,485,488,490,491,492,497,502,503,505],foo:[4,8,11,12,193,196,234,474,487,502],foot:6,footprint:[12,376],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:250,forcefield:[303,408],forcegroup:247,forcezero:367,ford:395,forestgreen:197,forev:71,forget:[245,497],forgiv:260,fork:[12,193],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,89,91,92,94,96,106,107,109,120,144,145,164,165,174,178,197,200,201,202,219,237,238,244,246,250,257,281,286,297,299,303,304,332,337,341,346,347,350,355,366,368,370,371,378,379,382,389,397,398,400,402,404,408,409,413,425,426,428,429,433,434,437,439,440,441,447,448,449,457,459,460,461,462,468,470,473,474,476,481,486,493,497,502],formal:[6,78,80,93,237,238,244,260,287,320,328,447],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,178,190,193,194,195,196,197,198,209,212,213,214,215,217,219,232,286,289,293,295,297,300,304,305,316,331,332,343,344,347,366,370,371,377,378,382,389,400,403,413,426,428,438,439,440,442,448,459,465,466,473,474,476,477,478,481,492,493,494,502,504],former:[6,12,16,39,41,197,217,332,336,382,384,482,488,502],formerli:[7,13],formul:[1,40,64,145,203,229,244,260,281,295,297,303,307,331,361,378,382,400,402,405,426,436],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,89,91,92,93,97,99,100,109,116,122,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,169,170,175,177,178,189,192,193,201,202,203,204,209,210,211,212,215,216,223,229,239,240,242,244,245,257,285,286,292,301,306,314,318,320,323,324,325,334,337,340,342,343,345,346,347,349,356,364,370,378,379,381,382,387,388,389,390,395,396,400,401,405,406,407,408,410,413,414,416,417,418,420,421,423,424,426,430,431,432,441,442,449,457,458,460,461,462,465,467,468,472,476,479,486,493,494,501,502,503],forth:[1,6,11,12,13,14,15,375,474,479,483],fortran:[3,6,9,11,12,13,234,400,409,426,439,440],fortun:8,forward:[3,8,89,360,371,376],foster:[382,436,437],foul:173,found:[3,6,9,12,73,164,193,220,222,236,241,247,286,327,333,345,360,372,389,392,395,471,477,478,493],four:[6,11,54,81,106,107,144,166,258,332,355,370,371,429,471],fourier:[],fourth:[6,108,303,317,327,387,433,447],fox:[6,122,176,455,488],fphi:[38,56,459],fpic:12,fplo:[38,56,459],fprime:459,fqdn:243,fqq:395,frac:[],fraction:[1,3,6,8,12,16,39,41,80,113,145,173,192,196,197,207,218,219,220,221,258,290,294,301,302,320,325,326,364,371,376,382,384,406,423,424,481,486],fragment:[42,241,301],fraig:42,frame:[85,144,197,206,258,294,339,405],framer:[196,197],framewo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inner:[3,8,16,193,242,345,360,367,368,369,371,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,464,465,466,467,468,469,485,490,502],inner_distance_cutoff:408,innergroup:250,innermost:[38,56,71,374,459,485],innernod:250,innner:420,inordin:333,inorgan:[6,465],inp:[222,345,448,465],input1:[65,68,69,79,95,112,117,118,119,121,123,322],input2:[65,68,69,79,95,112,117,118,119,121,123,322],input:[],input_doubl:3,inquir:310,insensit:12,insert:[3,5,7,8,12,59,170,200,224,236,242,290,361,448,456,474,480,497],insid:[2,3,6,8,11,71,133,139,170,193,194,197,208,213,214,224,225,233,236,242,247,250,290,304,320,337,339,340,341,342,343,359,364,416,474,475,476,478,479,486,490,502],insight:[6,13],instabl:[247,395,446],instal:[],instanc:[6,11,201,222,238,339,404,409,431,437,474,497],instantan:[6,63,220,221,237,238,260,265,286,291,294,299,301,304,327,482,494],instanti:[6,11,12,206,409,473],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,92,106,121,148,152,174,190,193,194,202,209,212,213,214,215,217,221,222,236,244,247,250,251,286,292,302,304,322,340,359,361,362,365,372,376,385,386,400,413,415,422,426,429,471,479,483,490,492,497,502],institut:[9,241,289],instruct:[],insuffici:[3,6,12],insult:260,insur:[3,6,11,12,17,39,40,61,73,105,107,170,171,190,193,194,196,197,203,218,219,224,229,230,233,234,236,239,244,256,292,293,302,304,320,332,337,341,342,343,345,360,370,372,376,390,405,409,435,441,459,473,474,476,477,481,484,485,493,494,502,503],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,110,117,119,121,123,144,168,170,173,174,176,180,181,185,190,192,193,196,197,207,209,213,214,218,219,220,224,226,234,236,237,238,241,244,245,246,247,286,289,290,293,294,299,304,320,322,324,327,331,332,351,361,364,384,396,398,399,412,426,439,440,444,446,448,471,473,474,475,476,484,485,486,490,493,502,503],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,211,237,438,476],intens:[1,3,6,9,63,66,74,75,88,91,92,93,96,106,107,108,109,116,118,120,121,122,123,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,167,169,200,209,210,212,213,214,215,217,218,219,220,228,233,240,250,258,260,265,301,304,305,320,328,332,334,335,493,494],intepol:502,inter:[14,18,42,61,62,150,173,174,193,220,244,246,259,296,304,361,371,382,486,497,502,504,506],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,89,90,94,95,110,111,112,114,116,119,120,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,144,145,146,148,149,163,164,168,171,172,173,174,175,176,178,182,183,189,193,194,200,201,202,218,219,220,235,236,241,242,244,246,250,274,285,287,289,290,295,297,303,304,311,312,320,321,327,332,336,337,338,341,342,347,348,349,350,352,356,361,362,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,440,441,442,444,446,447,448,449,456,457,458,460,461,462,463,464,465,466,467,468,469,471,474,476,478,480,481,485,486,488,493,494,497,504],interatom:[3,4,7,170,193,259,329,330,377,382,400,402,410,426,429,447,461,502],intercept:122,interchang:6,interconnect:18,interconvert:402,intereract:39,interesect:341,interest:[1,5,7,8,9,11,13,71,169,287,327,330,362,401,424,439,440,474,502],interf:376,interfac:[],interfer:[12,260,378],interg:[6,497],intergr:[485,489],interi:424,interior:[3,6,41,341,479],interlac:426,interleav:[6,170,484],intermedi:[6,12,59,196,259,285,355,371,474,475,484,488],intermix:471,intermolecular:378,intern:[],internal_element_set:206,internal_quadratur:206,internet:243,interpenetr:426,interpentr:[451,452,454],interpol:[6,15,38,56,103,190,196,197,206,232,247,285,361,362,371,382,431,440,453,459,460],interpret:[2,6,11,196,212,406,449,471,474,490,502],interrupt:294,intersect:[3,6,122,197,341,343,479],intersert:341,interspers:369,interstiti:[168,429],intertia:[3,96],interv:[3,6,93,195,210,244,260,294,299,300,312,447,453,471,490,502],intestieti:122,intial:[6,376,378],intiial:[41,481],intiti:[3,319],intra:304,intra_energi:236,intramolecular:[29,236],introduc:[6,9,94,110,196,260,294,299,304,355,361,377,392,402,414,418,422,458,490,502],introduct:[],intsal:[],intuit:364,inv:[122,169,305],invalid:[3,12,71,91,173,274,371,423,424,478],invari:[110,137,142,144],invent:307,invers:[],invert:[1,6,174,286],invis:341,invoc:[168,220,376,444,446,474],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,89,90,91,92,96,106,107,109,113,114,115,116,121,147,157,164,165,168,170,171,173,174,176,177,179,180,181,182,184,185,187,188,190,193,194,196,197,198,200,201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5,7,9,13,200,295,297,300,301,409,439,440,457,488],rebal:[41,217],rebalanc:[41,217],rebo:[],rebuild:[11,12,14,15,16,236,372,396,494],rebuilt:[3,12,193,194,195,196,198,372,376],recalcul:[71,89,320],receiv:[3,216,241,243,285,473],recent:[],reciproc:[6,12,122,168,169,286,361,383,385,386,392,395,402,414,418,434,442,490],recog:12,recoginz:3,recogn:[3,12,16,73,172,218,219,260,370,400,426,439,474,476,483,484,497],recomend:6,recommend:[7,9,12,14,16,196,197,294,330,361,402,409,423,424,429,440,441,444,446,447,485,495],recompil:[1,3,9,12,198,307],recomput:[105,132,174,228,309,399,488],reconstruct:[3,222,447],record:[198,222,309],recov:[221,260],recreat:344,rectangl:[41,217,364],rectangular:[7,41,62,172,217,236,364,476,478,480],rectilinear:[122,169,194],rector:53,recurs:[41,217,382,464],recust:41,recv:473,red:[2,10,196,197,220,287],redefin:[3,478,484,502],redirect:12,redo:12,reduc:[],reduct:[18,19,121,122,169,258,294,361],redund:403,ree:452,reed:[258,294],rees:[7,9,13],ref:[329,330,368],refactor:6,refer:[],referenc:[3,6,12,63,68,71,118,193,194,200,210,215,236,293,334,362,392,408,433,441,474,494,502],reflect:[],reformat:7,refresh:206,reg:479,regard:[6,59,257,307,308,313,436,440],regardless:[15,71,170,173,192,212,213,223,244,260,262,263,264,266,267,268,291,304,314,320,376,473,479,486],regim:[6,328,335,393,485],region:[],region_spher:8,region_styl:341,regist:[8,120,146,316,439,440],regoin:6,regress:502,regspher:170,regstrip:343,regul:6,regular:[1,3,9,41,62,90,168,172,193,196,207,217,236,332,362,393,412,473,476,478,480],reigon:502,reinhardt:[329,330],reject:[170,220,439,491],rel:[1,6,14,27,36,41,59,71,94,106,126,134,144,148,152,153,155,170,179,197,200,207,213,217,223,224,227,236,242,245,256,257,281,285,290,299,301,302,309,317,320,322,327,328,332,339,343,361,362,369,402,405,406,423,424,426,441,468,477,485,490,494,497,503],relat:[],relatic:[],relationship:[6,232,295,345,361,447,468,497,502],relax:[],releas:[0,5,7,8,13,218],relect:[3,431],reles:42,relev:[2,6,12,41,78,80,115,132,170,174,197,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,223,224,225,228,230,233,235,236,237,240,241,247,248,249,251,252,253,254,256,257,259,269,270,271,272,273,274,275,276,277,278,284,288,289,290,292,293,296,298,300,301,302,305,306,307,309,314,318,320,321,322,327,328,331,332,333,334,335,336,337,338,339,340,342,343,361,369,379,380,384,390,392,393,395,396,399,402,404,405,406,407,408,413,415,416,417,419,420,421,423,424,431,432,436,441,449,456,459,467,468,469,473,489,503],reli:[3,12,296,402,440,469,476,486],reloc:12,remain:[7,12,33,37,41,50,55,59,71,89,107,150,151,152,153,157,158,159,160,162,173,183,189,190,193,201,202,207,209,210,213,214,221,223,244,245,252,260,261,266,267,268,279,280,281,283,288,289,312,320,323,324,325,331,332,343,345,353,356,370,382,402,409,422,429,431,457,471,476,477,481,486,488,490,494,497,502,503],remaina:382,remaind:[170,193,224,290,320,333,462,476],remap:[3,6,12,59,61,71,153,170,192,213,223,242,257,281,361,476,477,478],remedi:[6,497],rememb:2,remov:[2,3,6,8,9,13,54,71,72,77,94,110,118,120,144,148,149,150,151,152,153,157,158,159,160,162,163,170,173,174,194,200,209,213,218,233,244,245,250,256,258,260,266,267,268,279,280,281,283,289,295,304,305,307,320,323,324,325,327,343,361,371,395,424,429,476,479,487,488,502,503],remove_bia:8,remove_bias_al:8,remove_molecul:206,remove_sourc:206,remove_speci:206,ren:169,renam:[12,344,487],render:[12,13,193,196,197],rendon:[260,261],reneighbor:[3,8,12,39,57,71,213,217,236,320,333,343,396,493,494],renssela:289,renumb:71,reorder:[3,12,39,473],rep:491,repeat:[2,6,196,197,213,220,221,236,313,364,382,460,462,464,471,490],repeatedli:2,repel:242,repes:193,replac:[2,3,6,11,12,41,63,91,92,121,147,148,149,150,151,152,153,156,157,158,159,160,162,163,193,194,196,197,198,209,210,212,213,214,215,217,220,224,244,265,292,299,301,392,416,477,478,483,484,494,502,503,504,506],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,410,438,439,440],reprens:332,repres:[1,3,6,8,9,12,15,40,41,42,59,67,71,92,117,120,182,190,193,194,196,209,210,211,212,213,214,215,221,227,237,239,244,247,260,287,289,291,299,304,305,309,317,332,334,341,362,371,377,382,405,412,422,423,424,426,427,428,434,437,439,440,463,464,471,473,476,486,488,491,497,502,504],represent:[3,6,8,9,57,59,138,172,193,237,238,287,332,382,402,405,429,441,476,479,497],reprocess:481,reproduc:[3,260,338,392,400,406],repul:426,repuls:[6,7,9,36,40,45,46,112,242,295,337,338,341,378,382,390,392,396,402,406,408,422,426,430,447,456,462,465,468,469,486],reqir:[295,297],request:[3,6,8,12,41,106,173,190,193,241,247,302,308,320,322,359,361,431,439,440,471,481,486,490,502,503,504],requir:[],rerun:[],rescal:[],research:[5,7,82,83,231,247,251,308,429,471,490],resembl:299,reserv:[12,241,497],reservoir:[93,236,240,244,332],reset:[],reset_atomic_reference_posit:206,reset_dt:8,reset_target:8,reset_tim:206,reset_timestep:[],resid:13,residu:241,residue1:372,resist:[6,241],resolut:[211,447,459],resolv:[221,287,320,424],resort:3,resourc:[7,377,400],respa:[3,16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ranarayan:[7,289],ruiz:207,rule:[],run1:[6,375,502],run2:[6,358,360,375,502],run3:[6,375,502],run4:[6,375,502],run5:[6,375,502],run6:[6,375,502],run7:[6,375,476,477,481,502],run8:[6,375,502],run:[],run_styl:[],runloop:360,runtim:[12,17,196,376],russia:9,rutherford:332,rutuparna:[460,462],ryan:9,ryckaert:[307,355],rycroft:168,rydberg:429,s00:436,s0st:6,s2050:1,s2629:400,s319:206,s_fact:310,s_i:[6,402],s_ij:6,sack:7,saddl:[259,371],saddlebrown:197,sadigh:[207,400,427,428],saed_vtk:122,safe:[12,196,227,245,376],safe_zon:3,safest:[3,320],safeti:310,safezon:440,safran:468,sagui:[362,395],sai:[1,3,12,13,197,439,440,474],said:369,sakai:461,sall:[9,447],salmon:197,salt:[393,404,426,476],salter:447,same:[1,2,3,4,6,8,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,41,43,44,45,46,47,48,49,50,51,53,54,56,57,59,62,63,65,69,71,72,77,79,81,84,86,87,89,90,91,92,93,94,95,97,100,106,107,108,110,112,113,114,116,117,119,120,121,144,145,146,147,148,149,150,151,152,153,156,157,158,159,160,162,163,164,166,168,170,171,172,173,174,176,177,178,179,180,181,182,183,184,185,187,188,190,191,192,193,194,195,196,197,200,201,202,203,206,207,209,212,213,214,215,216,217,218,219,220,221,223,224,228,229,230,235,236,237,238,239,240,241,242,243,244,245,246,247,250,257,260,262,263,264,265,266,267,268,269,270,277,279,280,281,282,283,285,286,287,289,290,291,294,295,296,297,299,300,301,302,303,304,306,307,309,314,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,334,335,336,338,339,340,341,343,344,345,346,347,348,349,351,352,355,357,361,362,364,365,366,370,371,372,373,374,375,376,377,378,380,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,416,417,418,419,420,421,422,423,424,426,427,430,431,432,433,434,436,437,441,442,447,449,456,457,458,459,460,461,462,465,467,468,469,471,473,474,476,477,478,479,481,484,485,486,487,488,489,490,494,497,501,502,503,505],sampl:[1,2,4,6,9,10,11,12,14,93,106,148,149,163,168,192,196,200,209,210,213,214,222,224,234,236,238,240,260,261,287,290,299,301,305,317,318,320,324,327,330,342,372,382,399,476,490],sample_frequ:206,san:436,sandia:[0,5,7,9,13,14,17,70,115,403,426,436],sandybrown:197,saniti:[303,372],satellit:[6,152],satifsi:502,satisfi:[3,12,73,122,144,169,221,247,265,307,340,369,372,406,490],satur:393,save:[6,8,12,19,40,59,190,194,196,211,220,237,238,244,245,246,290,299,332,344,362,372,374,382,478,481,488],sb3:169,sb5:169,sc3:169,scalabl:[],scalar:[],scale:[0,1,3,4,5,6,9,10,13,18,40,59,63,71,72,93,117,120,121,144,156,164,190,192,193,194,196,197,200,201,202,206,207,210,221,223,236,240,241,242,244,246,247,258,260,262,263,264,265,266,267,268,287,291,294,295,304,311,312,320,322,324,327,329,330,332,336,343,361,362,364,370,373,377,378,379,393,399,402,406,409,423,424,426,429,436,443,445,463,477,479,481,485,488,490,493,494,502,503],scale_factor:[443,445],scalegamma:247,scalexi:[3,221,260,265],scalexz:[221,260,265],scaleyz:[221,260,265],scan:[197,219,360,477],scatter:[11,122,169],scatter_atom:11,scatter_coord:11,scenario:[6,40,61,220,293,302,320,333,341,372,480,481,485,493],scf:497,schaik:422,schedul:471,schell:461,schemat:220,scheme:[6,9,18,237,238,260,287,299,307,332,361,463],schlitter1:331,schlitter2:331,schlitter:331,schmid:396,schneider:[244,246],schoen:361,schr:497,schroding:402,schroeder:[110,497],schulten:[245,309,362,497],schunk:320,schwen:9,sci:[73,340,391,428,437,447],scienc:[8,206,220,241,309,329,400,427,447,461],scientif:[144,400],scm:11,scratch:[12,41,217],screen:[],screenshot:11,scripe:11,script:[],scripta:67,scsl:12,sdk:[],sea:11,seagreen:197,seamlessli:293,search:[0,2,3,8,12,94,110,171,173,197,198,320,367,368,369,371,373,471,477,478,490,502],seashel:197,sec:[12,496,501],second:[1,3,6,9,10,11,12,16,54,57,59,61,71,90,93,106,108,110,116,137,138,142,145,146,158,164,168,169,171,172,173,192,193,197,200,201,209,210,212,213,214,215,220,236,237,242,257,259,287,301,303,304,307,309,317,318,320,329,330,332,343,361,364,368,369,371,372,376,381,382,383,385,386,391,392,400,402,403,406,407,409,412,413,416,426,431,433,447,458,461,462,463,465,469,471,472,473,474,476,478,483,485,489,490,494,497,501,502,503,504,506],second_mo:447,secondari:[3,182],sectinn:505,section:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,58,59,63,64,65,66,67,68,69,71,74,75,78,79,80,81,82,85,88,89,90,91,92,93,95,96,99,100,101,102,103,104,106,107,108,109,111,112,113,115,116,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,146,147,148,149,150,151,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168,169,171,176,177,178,179,180,181,182,183,184,185,187,188,189,190,192,193,194,195,196,198,200,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,226,227,229,230,232,233,235,236,237,238,239,241,243,244,245,246,247,248,249,250,251,253,254,257,258,259,260,261,262,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/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 hexorder/atom 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 orientorder/atom 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 smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body 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 custom/vtk command","dump h5md 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/correlate/long 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 eos/cv command","fix eos/table 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/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body 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/body 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 shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface 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 distance 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 dpd/conservative command","pair_style dpd/fdt 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 lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","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 smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq 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_style vashishta 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","timer command","timestep command","&lt;no title&gt;","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":218,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,194,196,197,198,199,201,202,203,205,206,207,209,213,214,215,218,219,221,222,223,224,228,233,236,237,242,244,245,246,247,248,250,255,258,260,261,265,281,282,286,287,290,291,292,293,294,296,299,301,302,304,305,320,322,327,328,329,330,333,335,337,339,343,356,359,361,362,364,365,367,368,370,372,373,374,376,379,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[211,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[201,202],addforc:203,addit:[12,13],addtorqu:204,adiabat:6,adjust_dt:310,adp:377,airebo:378,alloi:400,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:205,arrai:6,aspher:[6,9,84,148,262,266,270,271,279],atc:[9,206],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,205,207,208,293,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:216,awpmd:[9,379],balanc:[41,217],barostat:6,basal:67,beck:380,berendsen:[291,323],between:6,binary2txt:13,bodi:[6,8,9,42,68,149,263,267,272,280,381],bond:[8,13,69,218,219,220,300],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,221],brownian:384,buck:[385,386,394,425],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,209],citat:7,class2:[9,21,43,177,346,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[9,337,390,468],colvar:[9,13,222],com:[74,75,151],comb3:391,comb:[296,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,328],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,coreshel:9,correl:[210,211],cosin:[23,24,25,26,27,28,179],cossq:348,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:219,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:324,csvr:324,cubic:416,cuda:[9,14,113,116,147,157,203,216,230,235,239,260,269,306,307,323,325,336,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:[8,193,194],cut:[49,379,385,388,392,395,402,404,414,415,422,430,434],cvff:349,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,223],delete_atom:173,delete_bond:174,delta:24,deposit:224,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,9,29,395],direct:227,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:350,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:225,dreid:[6,408],drude:[6,9,155,226,227,245],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,196,198],dump_modifi:197,dynam:295,eam:[13,400],echo:199,edip:401,eff:[9,13,99,100,154,156,161,246,261,273,282,326,402],efield:229,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:230,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:233,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:234,fcc:285,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,202],field:[6,7],file:6,finit:6,fire:295,fix:[2,6,8,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,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[3,6,320],advertis:8,advis:[371,438],afer:3,affect:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,196,197,202,209,210,212,213,214,215,218,219,220,221,223,224,234,240,242,244,250,257,261,262,263,264,266,267,268,274,279,280,281,283,304,305,318,332,342,355,361,367,368,369,371,372,373,376,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,223,376,391],afil:238,aforement:18,afresh:[292,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,198,200,201,202,206,207,209,210,217,218,219,220,221,223,227,236,247,248,249,250,251,256,257,258,260,266,267,268,274,279,280,281,283,286,290,294,302,304,307,316,321,323,324,325,327,328,329,330,331,335,337,339,343,346,347,353,360,366,367,369,370,372,374,375,376,377,378,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,457,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,197,223,240,290,346,360,371,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,224,371,439,440],aggreg:[6,12,65,68,69,79,95,112,119,240,256,302,304,318,471,503],aggress:[240,490],agilio:[9,13],agre:[3,8,190,369,378,411,440],agreement:[5,7],ahd:408,ahead:339,aidan:[0,5,7,9,13,364],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:196,akohlmei:[7,9,13,198,241],aktulga:[7,9,297,440],al2o3:447,al2o3_001:[122,305],al3:169,ala:[247,447],alain:9,alat:[285,426],alb:[437,460,462],albeit:303,albert:9,alchem:[89,164],alcohol:335,alcu:[377,382],alcu_eam:437,alderton:395,alejandr:[260,261],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,197,206,217,220,223,247,249,250,274,287,295,304,307,308,327,328,332,335,340,367,368,369,373,376,398,402,424,429,444,446,471,473,490],alia:[9,12,16],alias:[1,362],aliceblu:197,align:[6,12,29,41,71,172,190,213,217,242,364,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,198,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,229,230,231,232,233,234,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,253,255,256,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,305,306,307,308,309,310,311,312,316,317,319,320,321,322,323,324,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,351,356,359,360,361,362,363,364,366,369,370,371,372,373,375,376,377,378,379,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:344,alloc:[3,5,6,8,9,11,12,60,234,334,370,372,376,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,194,196,197,198,200,201,203,205,206,207,209,210,211,212,213,214,215,217,219,220,221,222,223,224,228,229,234,236,237,238,239,241,244,247,250,251,255,257,260,261,285,289,290,291,292,293,294,298,304,305,307,309,311,312,316,320,327,328,329,330,332,333,334,335,336,337,343,345,347,356,361,362,364,369,370,371,372,375,376,379,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,242,294,332,362,373,376,456],alo:392,alon:[6,7,220,300,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,196,209,220,242,247,248,252,257,259,294,304,307,309,313,317,318,327,331,332,338,341,343,364,367,368,369,371,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,201,247,286,294,295,299,369,377,380,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,200,347,356,370,389,457,476],alphanum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11,12,15,17,39,41,71,93,190,207,213,217,218,219,224,233,236,242,243,290,303,307,320,328,330,335,343,345,360,369,370,371,372,373,376,399,410,413,431,440,471,473,474,476,484,490,493,494,502],checkf:190,checkqeq:440,checku:190,chem:[6,13,20,21,25,39,40,43,45,46,89,90,110,116,145,176,177,187,211,222,227,237,238,245,247,259,260,261,281,282,287,291,294,296,304,308,309,320,323,324,327,328,329,330,337,346,355,357,361,362,368,371,378,383,387,388,391,392,393,395,396,398,402,404,405,407,408,414,418,419,422,426,430,431,434,447,456,463,485,488,490,497],chemic:[9,122,164,169,193,194,206,207,236,295,300,301,327,362,439,440,452],chemistri:[9,294,295,297,382,402,439,440],chen:332,cheng:391,chenoweth:[439,440],chenoweth_2008:[439,440],chi:[95,159,192,285,295,297,403,405,503],chiefli:438,child:8,chip:[7,9,12,17,18,376,489],chipot:222,chiral:355,chmod:[11,12],cho:426,chocol:[7,197],choic:[3,6,9,12,15,16,18,40,41,54,89,145,148,149,163,174,190,209,213,214,217,220,223,224,238,244,247,258,260,287,295,304,327,356,362,367,368,371,373,376,409,422,431,435,476,485,486,489,490,496,497,501],choos:[1,3,6,7,8,12,16,17,18,29,39,54,89,121,160,161,196,218,219,220,221,224,233,244,247,258,260,262,263,264,265,266,267,268,290,291,308,320,324,338,361,362,368,466,471,473,485,491],chose:[460,462],chosen:[2,3,6,12,17,144,170,173,182,190,196,202,207,221,224,233,236,237,245,247,258,260,265,287,290,301,320,324,327,328,333,335,336,342,362,363,368,376,397,398,402,406,413,416,442,460,471,485,490,497],chri:168,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,92,96,107,109,118,150,165,167,209],chute:[4,9,10,239],ciccotti:307,cieplak:[6,176,488],cii:210,cij:210,ciko:2,circl:[42,71,316],circular:[3,6,148,191],circumst:18,circumv:[94,110,299],citat:[],cite:[3,7,8,12,244,447],civ:9,ckio:2,cko:2,cl1:169,clarendon:[29,395],clarifi:[7,460,462],clariti:345,clark:434,class2:[],classic:[0,3,5,6,7,8,9,234,287,294,299,332,357,402],classifi:[9,457,465],claus:474,clean:[6,12,14,15,17,484],cleanli:[475,505],clear:[],clearli:7,clebsch:144,clermont:[9,13],clever:480,click:[2,11,22,37,44,55,170,178,189,196,241,347,356,371,389,457],client:[241,243],climb:[259,371,490],clinic:[7,13],clo:[159,192,503],clock:[12,471,490],clockwis:338,close:[3,6,11,12,13,39,41,67,71,145,173,193,219,220,221,238,245,247,260,281,304,307,338,341,360,362,365,367,368,371,376,378,382,392,393,412,426,431,443,445,462,480,486,497,499],closer:[3,41,120,168,192,193,217,221,225,329,371],closest:[219,285,304,335,405,441,456,466],cloud:[447,497],clovertown:18,clsuter:72,clump1:[289,304],clump2:[289,304],clump3:[289,304],clump:304,cluster:[],clutter:[3,9],cmap:476,cmatrix:238,cmax:426,cmd:[11,12,287,487],cmdarg:11,cmin:426,cmm:[],cmoput:137,cn1:210,cn2:210,cna:[],cnn:210,cnr:[9,13],cnt:[409,480],co2:[40,169,307,370],coars:[7,9,29,36,40,54,182,289,304,320,407,442,485,488],coarser:[362,502],coarsest:144,code:[],coeff:[3,7,8,12,21,22,33,44,50,176,177,178,183,346,347,353,389,409,413,431,444,446,449,476],coeffcient:476,coeffici:[],coefficienct:396,coefficient0:400,coefficient1:400,coeffieci:[6,380,412],coeffincientn:400,coexist:[9,236,402],cohes:[6,403,426],coincid:[126,341,387,423,424,471],colberg:195,cold:[6,155,236,240,372,497],coldest:328,coleman8:9,coleman:[9,122,169,305],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,85,92,96,101,107,109,118,150,158,165,167,170,193,194,197,209,222,250,256,289,299,302,304,343,361,370,372,390,476,483,489,495,506],collid:[228,320,342],colliex:169,collinear:[3,289],collis:[3,247,320,338,342,399,406,469],colllis:320,colloid:[],colombo:39,colon:[198,343,477],color1:197,color2:197,color:[3,9,41,193,196,197,217,237,294,299],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,83,92,94,95,96,107,109,110,112,114,117,118,119,120,121,123,144,145,150,158,165,167,168,169,190,193,194,197,200,208,209,210,212,213,214,215,250,257,258,294,304,321,322,332,342,404,408,439,440,477,491,493,502],columnar:168,colvar:[],colvarmodul:12,com:[],comamnd:223,comand:220,comannd:376,comb3:[],comb:[],comb_1:296,comb_2:296,combiant:393,combin:[3,6,7,9,11,13,36,40,63,65,69,79,89,95,106,112,119,148,149,163,193,196,206,212,241,250,260,287,293,308,324,333,341,344,346,361,362,364,368,376,390,392,393,398,402,403,409,421,422,448,458,460,462,465,468,479,484,489,497,502],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,195,241,243,244,362,371,376,396,431,436,459,478],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,176,190,193,232,245,304,332,370,371,377,400,401,403,413,426,433,440,447,448,458,459,460,461,462,465,473,474,476,497,502],commerci:7,commit:9,commmand:[3,6,12,59,111,282,412,470,471,473,490,505],common:[],commonli:[3,6,12,17,25,57,59,108,110,172,193,196,198,357,407,416,448,460,462,476,479,488],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,168,173,174,196,197,217,218,219,221,222,223,241,243,247,249,250,251,260,286,293,295,296,297,304,308,320,332,343,359,361,372,373,374,376,398,399,435,473,474,485,486,502,504,506],communc:361,comp:[7,195,243,244,307,362,371,402,431,436,441,455,459,461],compact:[63,200,389,457],compani:[5,7],compar:[1,3,4,6,8,12,17,39,88,114,122,153,169,178,189,197,227,295,343,345,361,362,369,371,426,447,471,490,491,497,501],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,346,347,356,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,198,202,208,209,210,212,213,214,215,217,286,298,324,327,334,337,340,361,376,410,429,431,459,473,474,502],compens:[6,218,219,302,372,402],compet:331,competit:362,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,195,196,198,241,331,362,376,429,476,477,481,502],compl:17,complain:[11,12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,197,213,217,222,250,287,290,293,320,331,333,344,345,360,371,376,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,247,316,341,359,371,402,429,459,474,476,479,502],compli:[327,331],complic:[6,7,9,12,13,207,236,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,194,196,197,203,204,208,209,210,211,212,213,214,215,216,220,221,223,224,229,234,239,243,244,247,250,252,256,257,259,260,261,265,266,267,268,279,280,281,283,284,286,287,288,291,302,304,306,307,309,313,314,317,320,323,324,325,327,334,335,340,341,342,361,364,368,369,370,371,376,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,207,247,400],compound:[391,402,403,465],compres:[71,118,209],compress:[],compris:[40,341,441,464],compton:[122,169],comptu:3,compuat:362,comput:[],computation:[3,6,218,219,332,382],computational:497,compute_arrai:8,compute_fep:[202,422],compute_group_group:236,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,305],compute_scalar:8,compute_temp:8,compute_ti:202,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:341,concentr:[71,400],concept:[6,150,160,209,485],conceptu:[3,6,71,158,221,223,371,392,409,426,481],concern:[6,73,89,195,237],concetr:71,concis:[11,331],conclud:12,concret:8,concurr:[9,16,362,502],conden:[332,460,462],condens:[6,152,332,378,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:222,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,196,200,221,222,223,224,228,236,243,244,274,287,295,331,359,369,371,378,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,194,431,474],conform:[3,6,13,59,220,221,259,303,309,331,355,371,402,488],confus:[3,465],conjuct:396,conjug:[7,8,244,368,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,197,201,202,244,247,251,274,290,291,295,296,297,299,304,308,320,328,335,340,361,362,371,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,220,241,289,304,307,317,371,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,197,201,202,224,241,242,392,414,418,471,477,479],consequ:[1,6,207,332,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,194,197,201,202,208,210,213,217,219,220,224,248,261,286,304,327,328,331,332,335,362,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,244,245,323,324,325,376,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,198,203,204,209,223,224,227,229,234,237,244,245,246,257,260,262,263,264,265,266,267,268,269,270,272,273,274,275,277,278,279,280,281,282,283,291,294,299,301,303,304,323,324,325,326,336,361,362,364,370,371,376,378,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:206,consit:304,constant:[],constitu:[3,6,250,304,337,341,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,200,209,224,236,237,242,250,254,289,290,302,304,307,318,328,335,369,370,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,221,260,286,303,341,372,376,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,299,435,502],consumpt:359,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,194,196,197,198,200,201,202,206,208,209,210,212,213,214,215,217,222,224,229,232,238,242,243,244,247,258,274,285,286,289,290,292,294,297,301,304,305,310,320,327,331,332,341,342,345,360,362,370,371,374,375,377,378,379,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[9,12,18,440,492,494],context:[3,6,8,12,17,120,121,197,218,219,224,289,301,336,368,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,197,200,201,202,207,209,210,211,212,213,214,215,217,220,221,222,223,224,236,237,238,240,241,242,244,245,246,252,257,258,260,262,263,264,265,266,267,268,279,280,281,282,283,288,290,293,294,304,305,309,319,320,322,329,330,332,338,341,345,360,375,376,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,206,332,444,446],contour_integr:206,contract:[59,221,223,260,291,304],contradictori:3,contrain:307,contraint:274,contrari:[238,245],contrast:[1,6,42,55,64,152,155,194,223,343,444,446,468,505],contrib:332,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,202,207,208,209,210,212,213,214,215,221,236,244,247,250,251,255,261,281,282,289,290,298,301,304,305,307,334,361,369,371,379,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,194,196,200,206,207,217,221,222,223,240,241,244,245,260,262,263,264,265,266,267,268,291,296,304,311,312,323,324,325,332,336,359,361,373,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:206,controlfil:440,convect:93,conveni:[6,12,29,193,198,215,305,364,448,502],convent:[3,8,9,29,181,188,189,194,197,303,317,344,400,402,502],converg:[3,6,41,90,193,194,196,198,203,217,220,221,229,234,265,294,296,299,303,307,367,368,369,371,391,392,414,447,471,483,490],convers:[3,8,144,196,197,207,210,291,361,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,196,197,215,258,290,343,346,348,352,355,364,371,377,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,341],convinc:[7,12],cook:9,cooki:7,cool:[7,160,240,302],cooordin:[193,194],cooper:[5,7],coord123:118,coord1:[3,118,209,213,214],coord2:[3,118,209,213,214],coord3:[3,118,209,213,214],coord:[],coordb:447,coordbb:447,coordiat:369,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,198,200,203,208,209,212,213,214,217,218,219,220,221,222,223,224,227,229,230,234,236,239,240,241,242,243,244,245,257,259,260,262,263,264,266,267,268,281,284,285,286,289,290,291,301,302,304,306,307,309,314,317,318,319,320,322,330,331,332,339,340,342,343,364,369,370,371,376,377,378,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,209],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,196,332,371,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,376,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,289],coral:197,core:[],core_shel:152,coreshel:[6,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,196,341,342,364,464,476],cornflowerblu:197,cornsilk:197,corp:[],corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,194,196,223,236,238,244,260,261,281,289,291,294,331,337,341,361,371,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:206,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,197,203,224,229,234,245,254,260,261,297,304,307,317,319,338,341,371,372,376,394,424,429,473,474,476,486,501,503],correl:[],correpond:232,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,194,196,197,201,202,203,209,211,212,213,214,216,219,221,223,230,234,235,239,244,247,248,256,257,258,260,262,263,264,265,266,267,268,269,270,274,277,279,280,281,283,286,287,291,296,304,306,307,323,325,327,336,337,338,340,341,342,344,346,347,348,349,351,352,355,357,362,366,368,370,371,377,378,380,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],corrupt:3,cosin:[],cosineshift:27,cosmo:[238,243],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,196,197,209,213,214,217,218,219,233,260,296,332,361,362,374,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,238,372],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,194,196,197,201,202,209,210,213,217,223,234,243,293,294,295,299,302,304,306,320,321,327,331,332,333,337,341,343,345,353,358,360,367,369,372,376,379,404,408,409,412,439,440,472,473,474,476,478,480,483,484,491,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,295,297,333,361,362,369,376,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,203,204,207,209,212,213,214,216,217,224,229,233,236,242,260,274,290,307,323,324,341,362,369,370,371,373,376,404,408,431,494,502],counter:[3,338,471,482,484,490],counteract:236,counterbal:240,counterbalanc:29,counterpart:[193,304,471],counterproduct:18,coupl:[],courant:310,cours:[3,8,130,132,164,193,201,202,237,303,317,331,337,339,340,342,343,362,423,449,473,476,489,497,502,504],courtesi:364,cov:447,coval:[6,29,402,426,447,497],covari:238,cover:[6,71,190,197,206,247,402,464],coverag:[71,213],cpc:243,cpp:[1,3,6,8,9,11,12,13,89,193,201,202,234,307],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,197,211,227,245,333,359,362,376,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,372],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,372,497],craympi:376,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:206,create_faceset:206,create_group:195,create_nodeset:206,createatom:[],creation:[],crimson:197,critchlei:289,criteria:[3,120,171,196,197,218,219,220,255,369,436,464,478,481,502],criterion:[12,41,125,170,173,207,217,220,236,274,296,310,338,343,369,371,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,258,327,332,369],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,194,196,208,213,219,223,257,259,281,304,313,317,319,328,335,347,364,371,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:294,crystal:[4,6,13,73,110,285,286,330,364,372,480,494,497],crystallin:[6,106,286,364,461,497],crystallis:327,crystallogr:[122,169],crystallograph:[364,494],crystallographi:[122,169,364],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[377,400],ctemp_cor:227,cterm:309,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,217,227,341,364,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,215,218,219,220,222,233,238,244,246,320,323,324,325,326,328,335,408,494],cumul:[6,207,209,212,213,214,228,236,244,258,260,265,274,304,305,371],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,198,201,202,206,209,213,214,215,217,218,219,220,221,222,223,224,228,229,234,236,238,241,242,244,250,257,260,261,266,267,268,274,279,280,281,283,289,290,295,296,298,301,302,303,304,307,308,309,310,311,312,313,314,316,318,319,320,323,324,325,331,332,335,336,337,338,339,340,342,343,345,359,360,361,362,365,366,368,369,370,371,376,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,236,286],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[285,297],cutinn:[384,423,424],cutlo:[285,297],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,219,220,225,232,285,294,295,297,299,301,304,308,320,333,337,341,343,359,361,362,369,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:[],cutoff_inn:[],cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:327,cvel:309,cvff:[],cwiggl:[3,257,337,340,342,502],cyan:[2,196,197],cycl:[3,236,258,260,261,265],cyclic:[3,190],cygwin:12,cylind:[3,4,71,196,209,242,290,338,341,479],cylindr:[6,242,317,338],cypress:376,cyrot:382,cyrstal:286,d3q15:247,d3q19:247,d_double_doubl:15,d_e:332,d_flag2:293,d_flag:293,d_name:[117,193,293,322,486],d_single_doubl:15,d_single_singl:15,d_sx:293,d_sy:293,d_sz:293,daan:330,dai:12,daili:12,daivi:281,damag:[],dammak:299,damp:[3,6,200,205,244,245,246,251,260,261,265,291,294,295,299,304,323,324,336,338,339,368,369,371,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:245,damp_drud:245,dampen:[304,497],dampflag:[338,406],dan:17,danger:[3,12,236,343,396,494],dangl:173,daniel:9,darden:[362,395],darkblu:197,darkcyan:197,darken:196,darkgoldenrod:197,darkgrai:197,darkgreen:197,darkkhaki:197,darkmagenta:197,darkolivegreen:197,darkorang:197,darkorchid:197,darkr:197,darksalmon:197,darkseagreen:197,darkslateblu:197,darkslategrai:197,darkturquois:197,darkviolet:197,dasgupta:295,dash:[406,493],dat:[6,93,190,206,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,305],dataset:305,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,210],davenport:425,davi:337,david:[9,19,361,362,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,195,196,197,198,287,477,481],ddim:192,deactiv:422,dealt:243,debug:[6,7,11,12,13,14,17,122,126,169,170,287,292,359,361,376,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,257,293,304,333,491],decipher:364,declar:195,declin:320,decod:196,decompos:[89,448],decomposit:[3,5,7,18,62,206,287,308],decoupl:[6,497],decreas:[3,193,194,203,204,211,220,223,229,234,236,244,331,361],decrement:309,deepli:358,deeppink:197,deepskyblu:197,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,217,218,219,220,221,223,224,227,228,229,231,234,235,236,239,242,243,244,245,246,247,255,257,259,260,261,262,263,264,265,266,267,268,270,271,272,275,277,278,279,280,281,282,283,285,286,287,289,290,291,293,295,297,302,304,305,306,307,310,314,318,320,322,323,324,325,326,328,329,330,332,334,335,337,338,339,340,341,342,343,345,346,347,348,349,350,351,352,355,356,357,359,361,362,364,366,368,369,370,371,372,373,374,375,376,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,197,209,210,211,212,213,214,215,223,231,242,265,305,322,334,337,340,342,344,356,359,370,379,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,289],degrad:[8,18,286,362,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,196,209,220,227,236,238,239,244,245,250,260,261,265,266,267,268,279,280,281,283,287,289,303,304,307,323,324,325,330,346,348,352,355,357,369,395,400,408,486,494,497,503],degress:[150,209],del:490,delai:[3,6,12,372,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,200,209,210,212,213,214,215,218,220,233,236,260,305,323,324,343,345,360,370,372,375,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:206,deli:192,delimit:[474,502],deloc:[261,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:[],delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:[],delx:192,delz:192,dem:[],demand:299,demo:11,demon:284,demonstr:[294,426],den:290,dendrim:408,denniston:[9,247,249,250,251,286],denomin:[7,175],denot:[122,227,245,286,297,299,392,407,409,440,444,446],dens:[71,220,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,201,202,206,209,213,214,217,223,234,247,250,253,254,286,290,291,295,332,337,364,366,370,377,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[258,294],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,196,197,200,201,202,203,204,207,209,211,212,213,215,216,217,219,221,223,229,230,235,238,239,240,242,244,245,247,249,250,257,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,285,296,299,301,304,306,307,308,314,320,323,324,325,327,329,331,332,334,336,337,340,341,342,343,345,346,347,348,349,351,352,355,357,362,364,369,370,372,373,374,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:224,deposit:[],deprec:[3,295,439],depth:[51,148,196,332,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,210,221,223,236,244,257,260,262,263,264,265,266,267,268,285,291,295,299,329,330,332,337,338,341,368,370,378,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:285,descend:197,descent:[7,368],descib:[40,196,295],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,195,200,201,202,209,210,211,212,213,214,215,217,220,221,222,223,224,226,227,232,237,238,241,242,243,244,245,246,247,249,250,251,255,259,260,261,265,273,282,285,287,292,293,294,295,296,297,304,309,317,320,321,322,323,324,325,326,327,328,329,330,335,337,338,340,345,361,362,364,367,368,369,370,371,375,378,379,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:362,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,206,220,226,227,260,261,285,286,305,327,332,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,209,215,221,223,234,236,237,244,245,246,250,260,281,289,290,291,292,295,299,304,307,320,323,324,325,326,331,338,353,358,361,362,364,367,369,370,371,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,196],despit:497,destabil:382,destre:355,destroi:[11,39,218,219],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,194,196,197,200,201,202,206,209,210,211,212,213,215,217,219,220,221,222,223,224,234,236,237,238,239,241,242,244,246,247,251,257,258,259,260,261,262,263,264,265,266,267,268,272,274,279,280,281,282,283,286,289,290,291,293,294,296,297,298,304,307,308,320,323,324,325,326,327,328,330,331,332,333,334,335,336,343,345,347,356,361,362,365,369,370,372,373,376,377,378,379,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,235,290,331,371,391,408,413,471,473,476,487,490,502],determ:376,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,194,196,197,198,199,203,204,205,208,209,210,211,212,213,214,215,216,217,221,223,224,227,229,236,239,240,242,244,245,250,255,257,258,260,266,267,268,279,280,281,283,285,287,290,291,294,301,302,303,304,305,306,310,312,314,320,323,324,325,327,333,334,337,338,339,340,341,342,343,356,361,362,364,370,372,373,376,378,379,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:308,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,241,265,289,294,295,298,378,382,402,428,429,447,465,478],devemi:9,deviat:[258,265,285,404],deviator:9,devic:[1,3,12,15,17,241,376],device_typ:376,devin:[296,391],devis:428,dfactor:196,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,362],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,298,429],dhi:[59,192,223,290],dhug:[258,294],dhugoniot:[258,294],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,221,260,291,304,335,444,446],diagonalstyl:448,diagram:[41,122,169,189,217,287],diallo:408,diam:[196,197,290,370],diamet:[3,6,40,42,117,170,193,194,196,197,201,202,244,290,304,320,322,336,338,370,390,405,406,416,441,464,468,476,477,486],diamond:[364,402,426],diamter:[40,290],dick:6,dicsuss:257,dictat:[207,258],did:[3,12,369,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,334,361],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,196,197,200,202,205,207,209,212,217,218,219,220,221,222,223,227,232,235,236,237,238,239,240,241,244,245,247,257,260,261,262,263,264,266,267,268,270,272,275,277,278,279,280,283,285,287,289,291,294,295,296,299,302,304,307,309,317,318,320,323,324,325,328,329,330,332,335,336,337,338,341,345,346,356,358,360,361,362,364,365,367,368,370,371,373,374,375,376,377,378,382,386,387,389,390,391,396,397,398,400,402,405,406,407,409,412,414,415,417,418,425,426,427,428,430,431,433,437,439,440,441,442,443,444,446,447,448,449,457,458,459,460,462,464,465,468,470,471,473,474,476,478,479,480,481,484,485,486,488,490,491,493,494,495,497,501,502,503,504],differenti:[1,3,6,29,190,361,392,437,461],difficult:[221,287,376,408,485],difficulti:[94,110,307,439],diffract:[],diffus:[],digit:[2,3,197,345,429],dih_table1:190,dih_table2:190,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:219,dihydrid:402,dij:307,dilat:[],dim1:3,dim2:3,dim:[3,59,71,147,151,152,153,156,157,158,159,160,162,170,192,213,223,242,338,364,426,479,501,502,503],dimdim:502,dimems:286,dimens:[],dimensinon:71,dimension:[3,39,94,116,122,144,147,150,151,152,153,156,157,158,159,160,162,169,191,209,213,259,286,332,364,367,371,437,476,486],dimensionless:[108,125,126,128,131,133,135,140,144,332,362,448,468],diment:3,dimentionless:139,dimer:[6,304,426],dimgrai:197,dimstr:[41,217],dinola:[291,323],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,193,194,322,497],dir1:487,dir2:487,dir:[1,3,4,8,11,12,258,285,294,319,437,439,440,474,487,502],dirac:144,direc:437,direct:[],directli:[3,6,8,9,11,12,89,117,144,146,193,194,195,196,203,229,238,242,247,286,305,324,336,338,339,340,341,364,368,376,377,378,383,385,386,392,395,400,402,414,418,431,434,442,456,474,486,487,488,494,502],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,194,198,222,243,289,295,298,308,316,320,329,330,371,375,377,378,382,389,391,392,400,401,403,410,411,422,426,427,428,429,433,437,438,439,440,447,448,458,460,461,462,465,474,476,477,478,487,502],disabl:[3,12,16,332,413,474,489,502],disadvantag:[6,217],disallow:[193,223,260],disappear:478,discard:[2,3,41,71,211,213,217,333,341,473,478,479],discontinu:[9,190,369,420],discourag:426,discov:[13,333],discret:[6,8,40,42,196,197,244,247],discuss:[],disk:[6,86,87,94,163,191,224,236,290,474],disloc:[70,429],disord:[39,70,429],disp:[],dispar:441,disperion:[395,418],dispers:[3,6,7,9,168,286,361,362,386,395,418,423,431,440,459,465],displac:[],displace_atom:[],displace_box:59,displacemet:479,displai:[11,13,22,37,44,55,178,189,193,196,347,356,389,457],dispters:3,disregard:429,dissip:[6,9,40,82,83,231,237,244,286,308,329,330,384,396,397,398,406,423,424,457],dissolut:218,dist:[6,69,93,112,121,193,287,303,399,456,471,503],distanc:[],distinct:[6,227,301,361,441],distinguish:[6,88,144,250,402,475],distort:[168,377],distrbut:377,distribut:[],distro:[115,389,436,437],ditto:[8,12,14,15,16,17,18,42,119,219,469,474],div:8,divd:121,diverg:[3,12,39,304,330,478,497,504],divid:[3,6,16,41,93,116,121,130,132,145,167,168,178,189,197,209,210,212,217,223,285,328,335,340,361,369,371,403,440,447,465,485,493,502],divis:[6,247,382,412,422,473,494,502],dl_poli:[6,7],dlambda:164,dlammps_async_imd:241,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,196],dlammps_gzip:[3,12,193,196,331,476,477,481],dlammps_jpeg:[3,12,196],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,16],dlammps_png:[3,12,196],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,193],dlen:486,dlmp_intel_offload:[9,12,16],dlo:[59,192,223,290],dlopen:6,dlvo:[7,390,468],dm_lb:247,dmax:[320,367],dmpvtk:194,dmpvtp:194,dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,89,92,96,105,107,108,109,111,113,115,116,118,121,123,145,148,149,150,163,165,167,170,171,172,178,189,192,193,194,195,196,197,198,200,201,202,207,208,209,210,211,212,213,214,215,224,236,244,245,255,260,261,266,267,268,272,279,280,281,282,283,290,293,304,317,320,323,324,325,334,338,341,343,345,347,356,360,369,370,371,376,377,378,381,389,391,392,400,401,403,408,409,411,412,426,427,428,431,433,436,437,438,448,457,458,460,462,464,465,474,476,477,478,479,481,484,485,486,493,494,502,503,504,505],docuement:441,dodd:42,dodgerblu:197,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,42,50,54,56,59,62,63,67,70,71,72,89,90,93,107,114,120,121,122,146,148,150,152,153,158,160,164,169,170,171,172,174,176,178,183,189,190,192,193,194,195,196,197,200,206,207,209,213,216,217,219,220,221,223,227,229,232,233,236,237,240,242,244,245,247,250,256,260,261,262,263,264,266,267,268,279,280,281,282,283,291,292,293,297,299,302,304,320,323,325,327,328,332,335,336,337,340,341,342,343,348,349,350,352,353,355,360,361,362,363,364,370,371,372,377,378,379,380,381,382,384,386,387,388,390,391,392,393,395,396,399,400,401,402,404,405,406,407,409,410,411,412,413,416,417,419,420,421,423,424,426,427,428,429,431,437,438,439,440,441,443,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37,244,245,304,307,329,330,471],elj:395,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,71,84,148,191],ellipsoid:[3,4,6,7,9,13,40,42,71,84,117,134,148,170,191,192,193,194,244,257,262,266,270,271,279,304,320,366,369,405,424,441,457,476,486,504],ellipsoidflag:476,elong:[227,245,494],elp:[439,440],els:[3,7,8,12,71,111,120,121,123,195,196,208,209,210,212,213,214,215,236,260,304,320,332,333,334,343,345,361,409,475,487,502,505],elsewher:[8,257,320,426,438,439,440,488,494,502],elt:426,emac:[],email:[0,3,5,7,8,9,11,403],emb:[3,9,341],emb_lin_neg:426,embed:[3,5,7,11,12,13,29,90,146,168,332,377,400,403,422,426,427,428,437,457,466,474],embt:177,emi:[7,9],emil:9,emol:[439,440,494],emphas:406,empir:[206,324,378,402],emploi:[9,286,295,299,461],empti:[3,57,71,168,172,304,361,372,413,476,487,488,502],enabl:[3,6,8,9,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,37,38,39,40,43,45,46,47,48,49,50,51,53,54,55,56,60,61,62,64,67,78,80,85,89,99,100,101,102,103,104,108,113,115,116,122,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,146,147,148,149,152,154,156,157,161,162,164,168,169,176,177,179,180,181,182,183,184,185,187,188,189,190,193,194,195,197,198,200,201,202,203,204,205,207,211,214,216,218,219,220,222,223,224,229,230,233,234,235,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,253,254,256,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,277,278,279,280,281,282,283,285,286,287,289,290,294,295,296,297,298,299,300,301,303,304,306,307,309,310,311,312,313,314,316,317,319,320,323,325,326,327,328,329,330,332,333,335,336,337,338,339,340,341,344,346,348,349,351,352,353,355,356,357,362,369,371,375,376,377,378,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,426,427,428,429,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,467,468,469,474,477,478,479,483,485,495,502,506],enclos:[2,6,12,172,193,292,345,426,447,472,474,484,502],encod:[13,39,42,193,196,197,293,409],encompass:[3,6,40,42,57,59,120,171,316,334,457,479],encount:[3,8,12,59,110,212,375,481,502],encourag:[7,8,298,318],end12i:117,end12x:117,end12z:117,end1i:117,end1x:117,end1z:117,end2i:117,end2x:117,end2z:117,end:[1,2,3,5,6,8,11,12,15,16,17,18,19,38,40,41,42,57,59,71,117,173,174,177,192,193,194,196,197,198,201,202,210,212,214,215,220,223,237,242,244,246,259,260,261,274,291,303,304,309,320,323,324,325,326,328,331,332,335,339,342,343,360,361,370,371,375,376,396,400,405,412,425,429,441,444,446,448,449,466,471,474,476,477,478,479,481,483,484,488,492,494,497,502,506],end_of_step:8,endbondtors:[3,177,183,476],endif:8,energet:[220,378,440],energi:[],energy_compon:447,energy_update_freq:440,enforc:[6,57,58,107,192,193,194,195,196,198,200,207,220,223,260,284,286,296,304,307,345,361,414,473,502,503],enforce2d:[],eng:[11,65,69,112,193,234,343,345,391,428],eng_previ:345,engil:9,engilitycorp:9,engin:[206,223,289,309,329,400,427],engr:[439,440],enhanc:[202,206,471],enlarg:[59,196],enough:[3,40,61,88,170,171,173,174,217,245,290,294,299,304,333,337,338,341,372,376,392,435,476,480,481],enpub:400,enrti:[],ensembl:[],ensight:6,ensur:[3,6,144,193,194,207,211,221,236,237,260,310,331,362,382,399,422,458,465],enter:[57,160,403,429,465,490],enthalpi:[127,262,263,264,400,493,494,502],entir:[0,2,3,6,11,14,15,41,42,63,82,83,90,113,114,116,120,122,145,150,169,170,197,200,201,202,209,213,214,217,220,222,233,236,237,240,244,245,256,260,262,263,264,265,266,267,268,285,287,289,302,304,318,332,334,345,376,395,418,431,459,476,484,485],entireti:464,entiti:[6,8,40,42,193,304],entri:[3,8,12,38,42,56,65,69,79,95,112,119,122,131,134,135,136,137,138,140,141,142,168,190,194,197,212,213,214,222,232,294,343,370,382,401,426,433,440,448,458,459,460,461,462,465,502],entropi:490,entry1:[38,56,197,389,459],entry2:197,entryn:197,enumer:[171,193],enumuer:6,env:376,environ:[1,3,6,11,12,16,17,18,196,238,243,285,376,377,382,389,391,401,402,437,460,473,487,502],epair:[111,197,404,408,439,440,494],epen:[439,440],epfl:[238,243],epp:395,epq:395,eps0:468,eps14:422,epsilon0:462,epsilon:[3,6,36,45,46,50,53,54,89,176,201,202,236,304,320,337,341,367,369,381,387,388,390,392,393,394,395,405,407,408,409,412,413,414,415,416,417,418,419,420,421,422,425,430,434,441,442,452,458,464,467,468,485,497,501],epsilon_0:469,epsilon_14:387,epsilon_:441,epsilon_d:393,epsilon_i:[405,431,441],epsilon_i_:441,epsilon_i_a:[405,441],epsilon_i_b:[405,441],epsilon_i_c:[405,441],epsilon_ij:431,epsilon_j:[405,431,441],epsilon_j_:441,epsilon_j_a:[405,441],epsilon_j_b:[405,441],epsilon_j_c:[405,441],epsilon_lj:441,epton:436,eqch:165,eqeq:[439,440],eqp:395,eqq:395,equal:[2,3,6,8,11,12,17,39,41,54,63,65,68,69,71,76,79,88,89,93,95,112,114,119,121,123,145,148,164,166,168,170,192,196,197,200,201,202,203,204,207,210,211,212,215,216,217,221,223,224,229,236,237,239,240,242,244,245,247,250,251,257,258,265,276,285,287,290,292,294,295,296,299,301,303,304,306,309,314,316,323,324,325,328,329,330,332,334,335,337,340,342,343,345,360,364,369,371,372,373,375,376,391,396,398,404,405,408,412,423,429,430,437,439,440,441,443,444,445,447,448,449,459,464,465,469,472,473,474,476,478,479,483,484,487,490,492,494,502,503],equat:[3,6,7,8,9,93,110,116,122,169,178,189,200,221,227,228,231,232,238,244,245,247,250,258,259,260,261,265,281,285,287,294,295,299,307,308,320,328,332,335,337,338,340,342,355,361,362,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:261,equidist:259,equil:[3,295,365,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,200,207,210,220,221,236,258,260,261,281,282,294,295,296,297,328,329,330,335,391,392,439,440,472,486],equilibria:335,equilibribum:[218,219],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,221,223,236,237,238,245,247,260,265,281,294,295,299,303,307,309,317,320,327,328,330,335,346,348,352,355,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:206,equival:[6,12,13,29,59,61,128,129,137,142,168,172,197,212,215,221,223,236,244,260,281,291,303,304,340,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[295,297],er3:169,eradiu:[40,117,194,402,476],eras:[306,329],erat:[223,424],erc:392,erfc:[392,414,431],erforc:[117,194],erg:501,erhart:[207,400,460,462],ermscal:379,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:337,erron:3,error:[],erta:406,ervel:[117,194,476],escap:[224,497],especi:[8,16,158,170,200,207,217,236,294,299,302,303,376,473],espresso:[9,298],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,210,265,286,336,362,378,392,414,462,481,494],essex:29,establish:[89,240],estim:[1,3,6,10,12,38,41,56,93,145,206,217,228,258,320,327,361,362,367,431,440,459,490,494],esu:501,esub:426,eta:[6,247,260,294,295,297,336,401,403,405,437,461,465,501],eta_dot:260,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:260,etap_dot:260,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,194,196,197,200,201,206,207,208,209,212,213,214,215,218,219,223,224,234,236,237,244,260,290,301,305,332,333,341,345,360,361,369,370,371,372,374,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[369,371,471,490],etot0:294,etot:[6,97,99,100,114,145,156,197,227,245,258,294,493,494],eu2:169,eu3:169,euler:[369,371],eulerian:206,euqat:450,europhi:247,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,194,196,197,201,202,203,204,206,208,209,210,211,212,213,214,215,216,223,229,237,239,240,242,243,244,245,286,292,295,306,310,314,323,324,325,334,337,340,342,343,345,361,362,367,369,376,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[345,474],evan:[158,281],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,369],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,194,197,200,201,202,207,208,209,212,213,214,215,217,218,219,221,223,224,227,242,245,258,260,261,286,290,299,301,304,305,316,320,328,332,335,337,341,343,354,361,367,369,371,376,381,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,217,247,412,466],event:[],eventu:[3,6,12,15,172,295,490],ever:[9,54,56,243,320],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,198,200,201,202,203,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,228,233,234,236,238,240,241,242,247,248,256,260,261,265,284,285,286,290,291,292,293,294,295,296,297,299,301,302,304,305,307,309,320,322,323,324,325,326,327,328,331,332,333,334,335,343,345,360,362,371,372,373,376,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[238,247,287,471],evolv:[247,287,333],ewald:[2,3,5,6,7,8,12,90,114,122,145,333,361,362,369,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,217,220,237,238,244,245,246,290,299,300,320,332,347,361,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,201,202,212,217,223,228,232,237,244,245,246,261,273,274,282,286,294,320,325,326,339,376,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,220,286],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,208,209,212,213,214,215,217,221,223,228,233,260,286,301,305,311,312,320,369,376,476,502],exceed:[3,41,59,217,223,260,320,484],excel:402,except:[1,2,5,6,8,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,197,200,203,209,210,212,216,217,221,223,230,235,236,239,242,244,246,260,261,262,263,264,265,266,267,268,269,270,273,274,277,279,280,281,282,283,287,296,297,304,306,307,317,320,323,325,326,332,336,340,343,344,345,346,347,348,349,351,352,355,356,357,361,362,364,366,370,371,372,374,375,376,377,378,380,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[211,402],exchang:[2,3,6,8,9,61,62,200,206,207,236,244,296,304,328,332,335,361,376,402,491],exchange:361,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,209,213,218,219,248,256,289,302,304,327,338,343,369,370,372,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,376,391,429,431,485,495],excurs:[260,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,196,241,298,345,360,363,375,472,474,484,487,490,502],exempl:447,exemplari:237,exemplifi:402,exert:[6,242,245,299,339,340,341,362],exhaust:[206,375,502],exhibit:[94,260,368,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,195,196,197,200,205,216,219,221,224,236,289,290,292,343,344,346,348,349,350,352,356,365,370,376,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,217,232,360,375,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,217,229,236,238,257,285,291,293,294,299,304,343,362,372,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,197,285,289,304,332,343,361,362,372,376,474],experi:[6,13,15,17,216,224,241,250,259,291,303,304,367,371,396,431,485,490],experienc:[6,12,249,250],experiment:[236,361,376,490],expert:12,expertis:7,explain:[1,3,6,8,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,194,196,197,200,209,210,215,217,219,221,223,260,285,293,304,317,343,345,360,361,364,370,371,375,381,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,194,209,259,285,409,470,473,474,476,485],explanatori:[3,8,121,193,194,208,209,212,213,214,304,370,473,502],explantori:[3,300],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,201,202,223,311,312,347,366,378,379,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,194,197,203,213,216,223,230,235,237,239,244,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,293,294,296,304,306,307,323,325,326,332,336,340,346,348,349,351,352,355,357,370,376,377,378,380,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,287],explor:[122,169],expon:[3,295,297,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[206,396,399],express:[6,144,156,170,201,202,221,257,285,295,332,338,345,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,194,200,203,204,207,215,216,222,225,229,234,235,236,238,239,240,242,244,246,258,260,265,274,285,286,302,303,304,306,309,314,317,319,323,324,325,326,327,329,330,332,334,337,341,342,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,205,213,217,242,339,342,361,364,378,443,445,459,473,476,479],exterior:[3,6,168,341],extern:[],extra:[3,6,8,11,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,197,212,217,219,260,292,293,294,304,320,369,370,373,374,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,201,202,297,371,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,196,211,221,223,260,330,402,461,497],extrema:422,extrins:206,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,334],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:294,f_harm:330,f_i:[29,437],f_id:[6,71,121,123,193,194,200,208,209,210,211,212,213,214,215,255,322,334,494,502],f_ij:437,f_indent:215,f_int:329,f_j:29,f_jj:93,f_k:437,f_langevin:332,f_max:[294,299],f_msst:258,f_r:[245,460,461,462],f_sigma:382,f_solid:330,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,205,213,214,337,339,340,341,342,364,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,238,290,320,330,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,196,197,201,202,210,217,221,223,224,236,241,244,246,247,258,260,261,265,287,291,295,303,307,310,312,320,324,328,335,336,337,341,352,362,364,370,376,378,379,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:361,fail:[3,11,12,59,174,221,224,361,369,371,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:241,fall:[3,6,197,212,290,474,502],fals:[88,343,345,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,194,197,198,217,218,219,221,224,260,285,303,304,320,337,348,352,367,371,372,464,474,476,481,494],farago:244,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,197,200,201,202,207,213,217,219,224,236,238,242,257,258,260,262,263,264,265,266,267,268,276,279,280,281,282,283,293,294,296,304,309,313,319,322,330,332,336,337,338,340,342,371,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,194,271,294,333,361,362,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,194,197,203,216,217,223,230,235,239,243,244,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,291,295,296,304,306,307,320,323,325,327,329,332,336,340,346,348,349,351,352,355,357,361,362,373,374,376,377,378,380,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,213,332,333,376,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:220,favorit:7,fbmc:327,fcc:[],fcm:[276,502],fdirect:227,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:206,featu:8,featur:[],fecr:400,feedback:[7,241],feel:[7,241,242,250,285,341,343,371,431],felling:428,felt:341,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,9,12,15,156,376,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,10,11,12,13,14,18,39,63,198,208,209,210,212,213,214,215,245,260,290,293,295,307,334,361,369,370,371,378,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,250,485],fewest:3,fextern:234,feynman:287,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,196],ffplai:196,fft:[1,3,7,11,12,14,15,90,113,114,145,286,361,362,485],fft_inc:[12,362],fft_lib:12,fft_path:12,fftbench:[361,495],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:456,fictiti:[6,203,204,229,234,238,287,303,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[317,433],figur:[1,3,8,12,294,473,474],fij:395,file0:285,file1:[11,13,285,331,345,370,481,483,487],file2:[11,13,331,345,370,481,483,487],file:[],file_from:195,filen:370,filenam:[3,12,13,38,41,56,190,193,194,196,197,198,206,209,210,211,212,213,214,215,217,222,232,285,289,292,295,296,297,300,301,304,305,331,332,358,359,360,370,371,377,378,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,194,197,478,483,506],filepo:301,fill:[7,9,170,196,290,332,364,372,382,429,440,479],filter:[197,206],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,198,207,220,221,232,233,236,259,285,290,291,299,303,367,369,371,372,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,203,229,330,372,376,502],finer:[144,170,502],finest:361,finger:[170,192,257,479],finish:[6,11,41,217,345,358,360,361,373,375,376,464,481,502,503],finit:[],finni:[7,400,457],finvers:227,fiorin:[9,222],fire:[],firebrick:197,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,198,200,201,209,210,212,213,214,215,217,220,223,232,236,237,242,247,257,258,259,260,285,287,292,293,294,296,301,304,307,309,317,318,320,321,322,329,330,331,332,334,338,343,345,346,353,364,369,370,371,372,375,376,377,378,381,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,232,303,320,378,382,411,426,431,452,459,461,484,502],five:[73,156,294,370,382,427,476,490],fix:[],fix_adapt:[164,202,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,207,290],fix_eo:9,fix_evapor:207,fix_flux:206,fix_gcmc:[207,370],fix_gl:238,fix_gld:238,fix_grav:290,fix_id:[3,221,258,260,262,263,264,265,266,267,268,291,294],fix_modifi:[],fix_mov:[192,338],fix_nh:8,fix_npt:238,fix_nvt:[207,236],fix_poem:[3,6],fix_pour:[3,224],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:307,fix_reax_bond:439,fix_rigid:[250,381],fix_saed_vtk:305,fix_setforc:8,fix_shak:307,fix_shardlow:9,fix_srd:3,fix_styl:265,fix_temp_rescal:326,fixedpoint:[221,260],fixextern:234,fixid:206,fji:395,flag1:[226,374],flag2:[226,374],flag:[3,8,9,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,194,196,197,198,215,220,222,226,241,244,248,250,256,257,286,293,304,317,319,320,327,331,340,343,359,362,370,374,375,376,378,408,413,426,429,456,471,473,474,476,477,478,480,481,482,486,502],flag_buck:386,flag_coul:[386,395,418],flag_lj:[395,418],flagfld:[384,423,424],flaghi:[3,384,423,424],flaglog:[384,423,424],flagn:226,flagvf:[384,423,424],flat:[6,332,337,338,342],flavor:[2,7,12],fld:[337,384,423,424],flen:379,flex_press:379,flexibl:[3,6,8,171,196,209,213,222,238,261,328,335,402,461,494],flip:[3,6,223,260,339,340],floor:502,flop:12,floralwhit:197,flow:[],fluctuat:[6,64,89,221,236,237,244,247,260,265,285,286,308,330,332,355,398],fluid:[],fluid_veloc:251,flush:[3,197,493],flux:[],flv:196,fly:[7,9,12,41,196,200,206,211,224,227,304,307,333,382,429,494,497],fmackai:9,fmag:225,fmass:287,fmax:[369,494],fmomentum:227,fmsec:[2,197,244,245,257,260,291,304,323,324,485,496,501,503],fname:360,fno:[9,12,16],fnorm:[369,494],fnpt:227,fnvt:227,foce:409,fock:379,focu:307,fogarti:[9,297,440],foil:[144,285,448],fold:[318,485],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,40,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,82,93,94,99,100,110,117,120,121,123,144,145,148,149,150,156,158,163,166,168,170,171,176,179,180,181,182,184,185,187,188,190,193,195,196,197,200,206,207,208,209,210,211,212,213,214,215,217,222,223,224,227,228,231,232,234,236,237,238,241,243,244,245,247,250,258,260,265,266,267,268,279,280,281,283,286,287,289,292,293,294,295,297,299,301,303,304,305,307,322,323,324,325,328,329,330,331,332,334,335,343,344,348,349,350,351,352,355,357,359,364,366,369,370,371,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,436,437,438,439,440,441,442,444,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,467,468,469,471,473,474,476,477,479,481,483,484,485,488,490,491,492,497,502,503,505],foo:[4,8,11,12,193,196,234,474,487,502],foot:6,footprint:[12,376],fopenmp:[9,12,16,18],forc:[],force_uvm:17,forceatom:250,forcefield:[303,408],forcegroup:247,forcezero:367,ford:395,forestgreen:197,forev:71,forget:[245,497],forgiv:260,fork:[12,193],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,89,91,92,94,96,106,107,109,120,144,145,164,165,174,178,197,200,201,202,219,237,238,244,246,250,257,281,286,297,299,303,304,332,337,341,346,347,350,355,366,368,370,371,378,379,382,389,397,398,400,402,404,408,409,413,425,426,428,429,433,434,437,439,440,441,447,448,449,457,459,460,461,462,468,470,473,474,476,481,486,493,497,502],formal:[6,78,80,93,237,238,244,260,287,320,328,447],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,178,190,193,194,195,196,197,198,209,212,213,214,215,217,219,232,286,289,293,295,297,300,304,305,316,331,332,343,344,347,366,370,371,377,378,382,389,400,403,413,426,428,438,439,440,442,448,459,465,466,473,474,476,477,478,481,492,493,494,502,504],former:[6,12,16,39,41,197,217,332,336,382,384,482,488,502],formerli:[7,13],formul:[1,40,64,145,203,229,244,260,281,295,297,303,307,331,361,378,382,400,402,405,426,436],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,89,91,92,93,97,99,100,109,116,122,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,169,170,175,177,178,189,192,193,201,202,203,204,209,210,211,212,215,216,223,229,239,240,242,244,245,257,285,286,292,301,306,314,318,320,323,324,325,334,337,340,342,343,345,346,347,349,356,364,370,378,379,381,382,387,388,389,390,395,396,400,401,405,406,407,408,410,413,414,416,417,418,420,421,423,424,426,430,431,432,441,442,449,457,458,460,461,462,465,467,468,472,476,479,486,493,494,501,502,503],forth:[1,6,11,12,13,14,15,375,474,479,483],fortran:[3,6,9,11,12,13,234,400,409,426,439,440],fortun:8,forward:[3,8,89,360,371,376],foster:[382,436,437],foul:173,found:[3,6,9,12,73,164,193,220,222,236,241,247,286,327,333,345,360,372,389,392,395,471,477,478,493],four:[6,11,54,81,106,107,144,166,258,332,355,370,371,429,471],fourier:[],fourth:[6,108,303,317,327,387,433,447],fox:[6,122,176,455,488],fphi:[38,56,459],fpic:12,fplo:[38,56,459],fprime:459,fqdn:243,fqq:395,frac:[],fraction:[1,3,6,8,12,16,39,41,80,113,145,173,192,196,197,207,218,219,220,221,258,290,294,301,302,320,325,326,364,371,376,382,384,406,423,424,481,486],fragment:[42,241,301],fraig:42,frame:[85,144,197,206,258,294,339,405],framer:[196,197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:[387,407],inner:[3,8,16,193,242,345,360,367,368,369,371,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,464,465,466,467,468,469,485,490,502],inner_distance_cutoff:408,innergroup:250,innermost:[38,56,71,374,459,485],innernod:250,innner:420,inordin:333,inorgan:[6,465],inp:[222,345,448,465],input1:[65,68,69,79,95,112,117,118,119,121,123,322],input2:[65,68,69,79,95,112,117,118,119,121,123,322],input:[],input_doubl:3,inquir:310,insensit:12,insert:[3,5,7,8,12,59,170,200,224,236,242,290,361,448,456,474,480,497],insid:[2,3,6,8,11,71,133,139,170,193,194,197,208,213,214,224,225,233,236,242,247,250,290,304,320,337,339,340,341,342,343,359,364,416,474,475,476,478,479,486,490,502],insight:[6,13],instabl:[247,395,446],instal:[],instanc:[6,11,201,222,238,339,404,409,431,437,474,497],instantan:[6,63,220,221,237,238,260,265,286,291,294,299,301,304,327,482,494],instanti:[6,11,12,206,409,473],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,92,106,121,148,152,174,190,193,194,202,209,212,213,214,215,217,221,222,236,244,247,250,251,286,292,302,304,322,340,359,361,362,365,372,376,385,386,400,413,415,422,426,429,471,479,483,490,492,497,502],institut:[9,241,289],instruct:[],insuffici:[3,6,12],insult:260,insur:[3,6,11,12,17,39,40,61,73,105,107,170,171,190,193,194,196,197,203,218,219,224,229,230,233,234,236,239,244,256,292,293,302,304,320,332,337,341,342,343,345,360,370,372,376,390,405,409,435,441,459,473,474,476,477,481,484,485,493,494,502,503],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,110,117,119,121,123,144,168,170,173,174,176,180,181,185,190,192,193,196,197,207,209,213,214,218,219,220,224,226,234,236,237,238,241,244,245,246,247,286,289,290,293,294,299,304,320,322,324,327,331,332,351,361,364,384,396,398,399,412,426,439,440,444,446,448,471,473,474,475,476,484,485,486,490,493,502,503],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,211,237,438,476],intens:[1,3,6,9,63,66,74,75,88,91,92,93,96,106,107,108,109,116,118,120,121,122,123,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,167,169,200,209,210,212,213,214,215,217,218,219,220,228,233,240,250,258,260,265,301,304,305,320,328,332,334,335,493,494],intepol:502,inter:[14,18,42,61,62,150,173,174,193,220,244,246,259,296,304,361,371,382,486,497,502,504,506],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,89,90,94,95,110,111,112,114,116,119,120,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,144,145,146,148,149,163,164,168,171,172,173,174,175,176,178,182,183,189,193,194,200,201,202,218,219,220,235,236,241,242,244,246,250,274,285,287,289,290,295,297,303,304,311,312,320,321,327,332,336,337,338,341,342,347,348,349,350,352,356,361,362,369,370,371,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,440,441,442,444,446,447,448,449,456,457,458,460,461,462,463,464,465,466,467,468,469,471,474,476,478,480,481,485,486,488,493,494,497,504],interatom:[3,4,7,170,193,259,329,330,377,382,400,402,410,426,429,447,461,502],intercept:122,interchang:6,interconnect:18,interconvert:402,intereract:39,interesect:341,interest:[1,5,7,8,9,11,13,71,169,287,327,330,362,401,424,439,440,474,502],interf:376,interfac:[],interfer:[12,260,378],interg:[6,497],intergr:[485,489],interi:424,interior:[3,6,41,341,479],interlac:426,interleav:[6,170,484],intermedi:[6,12,59,196,259,285,355,371,474,475,484,488],intermix:471,intermolecular:378,intern:[],internal_element_set:206,internal_quadratur:206,internet:243,interpenetr:426,interpentr:[451,452,454],interpol:[6,15,38,56,103,190,196,197,206,232,247,285,361,362,371,382,431,440,453,459,460],interpret:[2,6,11,196,212,406,449,471,474,490,502],interrupt:294,intersect:[3,6,122,197,341,343,479],intersert:341,interspers:369,interstiti:[168,429],intertia:[3,96],interv:[3,6,93,195,210,244,260,294,299,300,312,447,453,471,490,502],intestieti:122,intial:[6,376,378],intiial:[41,481],intiti:[3,319],intra:304,intra_energi:236,intramolecular:[29,236],introduc:[6,9,94,110,196,260,294,299,304,355,361,377,392,402,414,418,422,458,490,502],introduct:[],intsal:[],intuit:364,inv:[122,169,305],invalid:[3,12,71,91,173,274,371,423,424,478],invari:[110,137,142,144],invent:307,invers:[],invert:[1,6,174,286],invis:341,invoc:[168,220,376,444,446,474],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,89,90,91,92,96,106,107,109,113,114,115,116,121,147,157,164,165,168,170,171,173,174,176,177,179,180,181,182,184,185,187,188,190,193,194,196,197,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eaxff:[3,4,5,7,9,13,200,295,297,300,301,409,439,440,457,488],rebal:[41,217],rebalanc:[41,217],rebo:[],rebuild:[11,12,14,15,16,236,372,396,494],rebuilt:[3,12,193,194,195,196,198,372,376],recalcul:[71,89,320],receiv:[3,216,241,243,285,473],recent:[],reciproc:[6,12,122,168,169,286,361,383,385,386,392,395,402,414,418,434,442,490],recog:12,recoginz:3,recogn:[3,12,16,73,172,218,219,260,370,400,426,439,474,476,483,484,497],recomend:6,recommend:[7,9,12,14,16,196,197,294,330,361,402,409,423,424,429,440,441,444,446,447,485,495],recompil:[1,3,9,12,198,307],recomput:[105,132,174,228,309,399,488],reconstruct:[3,222,447],record:[198,222,309],recov:[221,260],recreat:344,rectangl:[41,217,364],rectangular:[7,41,62,172,217,236,364,476,478,480],rectilinear:[122,169,194],rector:53,recurs:[41,217,382,464],recust:41,recv:473,red:[2,10,196,197,220,287],redefin:[3,478,484,502],redirect:12,redo:12,reduc:[],reduct:[18,19,121,122,169,258,294,361],redund:403,ree:452,reed:[258,294],rees:[7,9,13],ref:[329,330,368],refactor:6,refer:[],referenc:[3,6,12,63,68,71,118,193,194,200,210,215,236,293,334,362,392,408,433,441,474,494,502],reflect:[],reformat:7,refresh:206,reg:479,regard:[6,59,257,307,308,313,436,440],regardless:[15,71,170,173,192,212,213,223,244,260,262,263,264,266,267,268,291,304,314,320,376,473,479,486],regim:[6,328,335,393,485],region:[],region_spher:8,region_styl:341,regist:[8,120,146,316,439,440],regoin:6,regress:502,regspher:170,regstrip:343,regul:6,regular:[1,3,9,41,62,90,168,172,193,196,207,217,236,332,362,393,412,473,476,478,480],reigon:502,reinhardt:[329,330],reject:[170,220,439,491],rel:[1,6,14,27,36,41,59,71,94,106,126,134,144,148,152,153,155,170,179,197,200,207,213,217,223,224,227,236,242,245,256,257,281,285,290,299,301,302,309,317,320,322,327,328,332,339,343,361,362,369,402,405,406,423,424,426,441,468,477,485,490,494,497,503],relat:[],relatic:[],relationship:[6,232,295,345,361,447,468,497,502],relax:[],releas:[0,5,7,8,13,218],relect:[3,431],reles:42,relev:[2,6,12,41,78,80,115,132,170,174,197,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,223,224,225,228,230,233,235,236,237,240,241,247,248,249,251,252,253,254,256,257,259,269,270,271,272,273,274,275,276,277,278,284,288,289,290,292,293,296,298,300,301,302,305,306,307,309,314,318,320,321,322,327,328,331,332,333,334,335,336,337,338,339,340,342,343,361,369,379,380,384,390,392,393,395,396,399,402,404,405,406,407,408,413,415,416,417,419,420,421,423,424,431,432,436,441,449,456,459,467,468,469,473,489,503],reli:[3,12,296,402,440,469,476,486],reloc:12,remain:[7,12,33,37,41,50,55,59,71,89,107,150,151,152,153,157,158,159,160,162,173,183,189,190,193,201,202,207,209,210,213,214,221,223,244,245,252,260,261,266,267,268,279,280,281,283,288,289,312,320,323,324,325,331,332,343,345,353,356,370,382,402,409,422,429,431,457,471,476,477,481,486,488,490,494,497,502,503],remaina:382,remaind:[170,193,224,290,320,333,462,476],remap:[3,6,12,59,61,71,153,170,192,213,223,242,257,281,361,476,477,478],remedi:[6,497],rememb:2,remov:[2,3,6,8,9,13,54,71,72,77,94,110,118,120,144,148,149,150,151,152,153,157,158,159,160,162,163,170,173,174,194,200,209,213,218,233,244,245,250,256,258,260,266,267,268,279,280,281,283,289,295,304,305,307,320,323,324,325,327,343,361,371,395,424,429,476,479,487,488,502,503],remove_bia:8,remove_bias_al:8,remove_molecul:206,remove_sourc:206,remove_speci:206,ren:169,renam:[12,344,487],render:[12,13,193,196,197],rendon:[260,261],reneighbor:[3,8,12,39,57,71,213,217,236,320,333,343,396,493,494],renssela:289,renumb:71,reorder:[3,12,39,473],rep:491,repeat:[2,6,196,197,213,220,221,236,313,364,382,460,462,464,471,490],repeatedli:2,repel:242,repes:193,replac:[2,3,6,11,12,41,63,91,92,121,147,148,149,150,151,152,153,156,157,158,159,160,162,163,193,194,196,197,198,209,210,212,213,214,215,217,220,224,244,265,292,299,301,392,416,477,478,483,484,494,502,503,504,506],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,410,438,439,440],reprens:332,repres:[1,3,6,8,9,12,15,40,41,42,59,67,71,92,117,120,182,190,193,194,196,209,210,211,212,213,214,215,221,227,237,239,244,247,260,287,289,291,299,304,305,309,317,332,334,341,362,371,377,382,405,412,422,423,424,426,427,428,434,437,439,440,463,464,471,473,476,486,488,491,497,502,504],represent:[3,6,8,9,57,59,138,172,193,237,238,287,332,382,402,405,429,441,476,479,497],reprocess:481,reproduc:[3,260,338,392,400,406],repul:426,repuls:[6,7,9,36,40,45,46,112,242,295,337,338,341,378,382,390,392,396,402,406,408,422,426,430,447,456,462,465,468,469,486],reqir:[295,297],request:[3,6,8,12,41,106,173,190,193,241,247,302,308,320,322,359,361,431,439,440,471,481,486,490,502,503,504],requir:[],rerun:[],rescal:[],research:[5,7,82,83,231,247,251,308,429,471,490],resembl:299,reserv:[12,241,497],reservoir:[93,236,240,244,332],reset:[],reset_atomic_reference_posit:206,reset_dt:8,reset_target:8,reset_tim:206,reset_timestep:[],resid:13,residu:241,residue1:372,resist:[6,241],resolut:[211,447,459],resolv:[221,287,320,424],resort:3,resourc:[7,377,400],respa:[3,16,228,241,260,374,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,429,430,432,434,436,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,464,465,467,468,469,484,485,496,502],respecifi:429,respect:[1,6,9,10,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,45,46,47,48,49,51,53,54,56,59,70,71,89,91,99,100,113,116,122,126,147,152,155,157,164,168,169,176,177,179,180,181,182,184,185,187,188,190,194,196,197,213,214,219,220,221,223,239,242,244,245,247,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,295,296,304,305,309,317,319,332,337,340,346,348,349,351,352,355,357,359,361,362,366,369,370,375,376,377,378,380,382,383,384,385,386,387,388,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,441,442,446,447,448,449,458,459,460,461,462,463,465,467,468,469,473,477,486,489,497,502,504,506],respon:9,respond:[6,7,153,223,402,436],respons:[6,7,258,328,335],resquar:[],rest:[6,8,12,293,297,303,382,424,426,493,494,497],restart1:287,restart2:287,restart2data:[],restart:[],restartfil:[12,13],restor:[3,8,60,61,106,170,201,202,293,309,317,322,344,493,494],restore_bia:8,restore_bias_al:8,restrain:[],restraint:[9,222,258,303,319,413],restratin:303,restrict:[],result:[1,2,3,6,7,9,11,12,13,15,16,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,45,46,47,48,49,51,53,54,56,63,64,66,67,71,75,89,92,93,96,106,107,109,113,114,116,118,119,120,121,122,123,145,147,150,153,157,164,165,167,169,170,173,176,177,179,180,181,182,184,185,187,188,190,192,193,194,196,197,200,203,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,227,230,232,235,236,237,239,244,245,247,251,258,260,262,263,264,265,266,267,268,269,270,277,279,280,281,282,283,286,287,295,296,301,302,304,306,307,320,323,325,328,329,330,332,333,334,336,337,338,340,342,345,346,348,349,351,352,355,357,361,362,371,374,376,377,378,380,383,384,385,386,387,388,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,426,427,429,431,432,433,434,436,440,441,442,449,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,480,481,485,486,487,488,490,501,502,503],resum:502,retain:[2,218,219,382,429,473],retart:[33,50,183,353],retir:[3,439],retreiv:8,retriev:[6,8,234,427,428,502],reus:[3,488],rev:[6,13,64,70,94,110,114,144,145,158,207,238,244,246,258,260,261,265,281,286,296,299,304,309,320,324,327,329,330,335,368,382,390,391,392,395,400,401,402,405,406,411,416,423,424,425,426,428,437,441,448,458,460,461,462,465,471],revers:[2,6,8,89,181,220,242,260,284,285,295,313,328,329,335,371,422,485,497],review:[144,295,309,327,429,438,448,471,490,497],rewind:360,rewrap:193,rewrit:[5,12],rewritten:19,rezwanur:436,rfac0:[144,448],rfactor:320,rfile:304,rg0:318,rgb:197,rh3:169,rh4:169,rhaphson:3,rheolog:6,rhi:459,rho0:[426,444,446,454,455],rho0_meam:426,rho:[],rho_0:[454,455],rho_alpha_beta:400,rho_bkgd:426,rho_colloid:337,rho_e:332,rho_fin:331,rho_i:[427,428],rho_initi:331,rho_ref_meam:426,rho_wal:337,rhodo:[9,10],rhodopsin:[1,10],rhohi:290,rholo:290,rhosum:[],ribier:368,richard:9,richardson:304,richi:[9,19],rick:[295,296,391,447],rick_and_stuart:296,ridg:[9,19],right:[3,6,11,12,41,146,170,188,189,192,194,217,220,242,247,257,284,345,364,392,476,479,486,502],rightmost:[41,217],rigid:[],rigidifi:304,rii:[91,92],rij:[94,110,218,219,285,396,397,398,456],rin:[408,419,420],ring:[],rino:[73,465],rinv:361,rirj:[338,406],rise:[],risi:[144,448],risk:[8,303,485],rix:[91,92],rjk:[218,219],rjone:[7,9,13],rlo:459,rmask:[3,502],rmass:3,rmax:[71,171,218],rmdir:487,rmin0:[144,448],rmin:[71,171,219,416],rmsd:331,rnemd:6,robert:9,robin:197,robust:[367,368,369],rock:426,rockett:437,rod:304,rodata:12,rodnei:299,roi:7,role:327,roll:12,ronchetti:110,room:[57,59],root:[11,89,91,92,195,327,331,376,400,483],rosati:39,rose:426,ross:426,rosski:287,rosybrown:197,rot:[6,93,287,303,327,503],rotat:[],rotation:110,rotaton:479,rough:[6,170,196,342],roughli:[7,10,12,41,153,196,211,236,244,245,259,260,274,291,304,320,323,324,327,362,371,376,443,445,478,485],round:[],rous:237,rout:[89,408,422],routin:[5,6,8,11,15,16,38,39,56,90,174,176,247,429,438,459,489],roux:[6,227,245,463,497],row:[6,65,66,68,69,75,79,92,95,96,107,109,112,118,119,120,123,150,158,165,167,168,169,209,210,212,213,214,215,250,304,332,334,342,402],royalblu:197,rozero:426,rperp:[257,313],rpi:289,rpm:12,rrespa:[1,3,5,7,8,16,201,202,257,260,372,377,378,379,380,381,383,384,385,386,387,388,390,391,392,393,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,428,430,432,434,436,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,464,465,467,468,469,485],rspace:3,rsq:[459,466],rsurfac:332,ru3:169,ru4:169,rub:20,rubia:[427,428],rudd:[431,459],rudr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23],tensor:[3,6,8,63,84,85,91,92,93,96,109,116,131,134,135,136,137,140,141,142,144,145,146,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,221,247,250,260,261,265,289,291,304,335,361,362,370,402,423,424,429,444,446,494,502],tenth:[131,360],term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,40,45,46,61,89,90,91,93,114,116,145,146,148,149,158,163,164,177,178,179,190,197,201,202,208,210,212,215,223,229,237,238,239,244,245,246,247,259,260,261,262,263,264,265,266,267,268,279,280,281,283,287,291,294,303,304,318,323,324,325,332,334,336,338,346,347,357,361,369,372,377,378,382,383,384,385,386,387,388,390,391,392,393,394,395,396,397,398,400,401,402,403,405,406,407,414,418,421,422,423,424,426,427,428,429,431,434,441,447,456,458,460,461,462,465,468,485,486,488,494,497],termin:[122,260,369,371,444,446,475,484],termostat:324,terrel:368,terri:7,tersoff:[],tersoff_1:[460,461,462],tersoff_2:[460,461,462],tersoff_mod:461,tertiari:182,tessel:[9,168],test:[],test_descriptor_str:3,testf:190,testu:190,tether:[6,302,309,317,319,330,404],tetot:[9,447],tex:8,texa:436,texas_holdem:303,text:[2,3,4,6,7,8,12,13,38,41,56,190,193,194,196,197,200,206,209,210,211,212,213,214,215,217,222,232,241,292,331,332,344,362,364,371,400,403,413,426,448,459,472,476,477,493,502,504],textur:17,tfac_insert:236,tfactor:[3,197],tfinal:502,tfix:303,tflag:196,tfmc:[],th4:169,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,39,40,41,42,56,57,58,59,61,63,68,71,76,88,90,94,108,110,112,116,119,120,123,145,168,171,172,173,179,190,192,193,195,197,200,205,207,209,212,213,214,215,217,218,219,220,221,223,224,225,228,232,233,236,237,238,239,242,243,244,247,258,285,286,290,291,292,293,294,295,297,299,302,303,304,305,308,309,310,316,317,318,320,324,325,327,328,332,335,336,337,338,339,340,341,342,343,345,361,362,367,368,369,370,371,372,373,376,381,382,383,385,386,387,400,402,405,406,412,423,424,426,431,439,440,441,447,449,456,457,458,459,462,464,466,468,469,471,472,473,474,476,477,478,479,480,481,484,485,488,490,491,493,502,503,504],thank:[241,460,462],thb:440,thb_cutoff:440,thb_cutoff_sq:440,thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,39,40,41,42,43,45,46,47,48,49,51,53,54,55,56,57,59,61,63,64,66,68,70,71,74,75,81,84,86,89,91,92,93,96,106,107,109,112,113,116,118,119,120,121,123,144,147,148,150,152,153,156,157,163,165,167,168,170,172,173,174,176,177,179,180,181,182,184,185,187,188,189,190,193,194,196,197,200,201,202,203,205,208,209,210,212,213,214,215,216,217,218,219,220,221,223,224,229,230,235,236,237,239,240,241,244,245,247,250,257,260,262,263,264,265,266,267,268,269,270,271,272,277,279,280,281,283,289,290,291,292,293,295,296,303,304,305,306,307,320,321,323,324,325,327,331,332,334,335,336,338,340,341,343,344,345,346,348,349,350,351,352,355,356,357,359,361,362,364,366,368,369,370,371,372,375,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,432,433,434,436,437,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,464,465,466,467,468,469,472,474,476,477,478,479,480,481,485,486,488,489,494,497,502,504,505],them:[1,2,3,4,6,7,8,9,11,12,13,14,17,39,40,41,54,59,71,93,106,111,118,121,123,146,172,177,193,196,197,198,208,209,210,212,213,214,215,217,220,221,223,233,241,244,245,256,260,262,263,264,265,266,267,268,279,280,283,285,291,293,301,302,303,304,307,320,323,324,325,327,331,332,334,338,339,340,342,343,346,362,364,370,371,372,376,377,382,389,400,403,405,409,412,431,441,449,464,471,474,476,483,488,491,497,502,503],themselv:[6,11,173,201,202,217,245,361,362,371,373,377,382,392,400,422,426,427,428,448,502],theor:327,theorem:[237,244,308,382,398],theoret:[108,241,294,458],theori:[3,6,9,12,40,144,206,222,238,260,286,361,362,382,429,468,490],thereaft:[71,252,288,304,328,335,474],therebi:[333,423,424],therefor:[3,6,12,64,89,155,227,236,245,247,307,327,362,394,438,440,458,463,485,497],therein:[6,426],thereof:89,thermal:[],thermo:[],thermo_modifi:[],thermo_p:[3,63,113,474,494],thermo_press:[63,116,221,227,260,262,263,264,265,266,267,268,291,493,494,497],thermo_styl:[],thermo_temp:[63,116,147,220,221,236,260,262,263,264,265,266,267,268,279,280,281,283,286,291,323,324,325,493,494,497],thermoberendsen:6,thermochem:501,thermochemistri:402,thermodyam:[494,501],thermodyanm:[63,220,320,343,485],thermodynam:[],thermophys:431,thermost:[6,152,205,222,227,245,339,497],thermostat:[],thermostatequ:6,thesi:[361,362,423,438],thess:383,theta0:[20,21,24,26,27,28,32,33,35,36,144,179,303,355],theta0max:144,theta10:382,theta1:[177,346,382],theta2:[177,346,382],theta3:[346,382],theta4:382,theta5:382,theta6:382,theta7:382,theta8:382,theta9:382,theta:[3,6,26,27,37,38,63,65,80,94,110,144,169,170,179,192,196,239,299,303,332,346,355,408,437,461,476,479,486],theta_0:433,theta_:[355,382],theta_c:408,theta_ijk:382,theta_ijl:346,theta_jik:[427,428],theta_pi:382,theta_sigma:382,thex:295,thi:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/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 hexorder/atom 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 orientorder/atom 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 smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body 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 custom/vtk command","dump h5md 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/correlate/long 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 eos/cv command","fix eos/table 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/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body 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/body 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 shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface 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 distance 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 dpd/conservative command","pair_style dpd/fdt 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 lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","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 smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq 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_style vashishta 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","timer command","timestep command","&lt;no title&gt;","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":218,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,194,196,197,198,199,201,202,203,205,206,207,209,213,214,215,218,219,221,222,223,224,228,233,236,237,242,244,245,246,247,248,250,255,258,260,261,265,281,282,286,287,290,291,292,293,294,296,299,301,302,304,305,320,322,327,328,329,330,333,335,337,339,343,356,359,361,362,364,365,367,368,370,372,373,374,376,379,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[211,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[201,202],addforc:203,addit:[12,13],addtorqu:204,adiabat:6,adjust_dt:310,adp:377,airebo:378,alloi:400,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:205,arrai:6,aspher:[6,9,84,148,262,266,270,271,279],atc:[9,206],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,205,207,208,293,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:216,awpmd:[9,379],balanc:[41,217],barostat:6,basal:67,beck:380,berendsen:[291,323],between:6,binary2txt:13,bodi:[6,8,9,42,68,149,263,267,272,280,381],bond:[8,13,69,218,219,220,300],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,221],brownian:384,buck:[385,386,394,425],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,209],citat:7,class2:[9,21,43,177,346,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[9,337,390,468],colvar:[9,13,222],com:[74,75,151],comb3:391,comb:[296,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,328],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,coreshel:9,correl:[210,211],cosin:[23,24,25,26,27,28,179],cossq:348,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:219,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:324,csvr:324,cubic:416,cuda:[9,14,113,116,147,157,203,216,230,235,239,260,269,306,307,323,325,336,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:[8,193,194],cut:[49,379,385,388,392,395,402,404,414,415,422,430,434],cvff:349,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,223],delete_atom:173,delete_bond:174,delta:24,deposit:224,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,9,29,395],direct:227,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:350,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:225,dreid:[6,408],drude:[6,9,155,226,227,245],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,196,198],dump_modifi:197,dynam:295,eam:[13,400],echo:199,edip:401,eff:[9,13,99,100,154,156,161,246,261,273,282,326,402],efield:229,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:230,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:233,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:234,fcc:285,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,202],field:[6,7],file:6,finit:6,fire:295,fix:[2,6,8,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,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