From eee65e309eddecdeea71d328ef880dab12ff6b8a Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 17 Feb 2016 00:18:50 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14651
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Manual.html                   |   96 +-
 doc/Section_packages.html         | 1535 ++++++++++++++++++---
 doc/Section_packages.txt          | 1454 +++++++++++++++++---
 doc/_sources/Section_packages.txt | 2134 ++++++++++++++++++++++++++---
 doc/improper_distance.html        |    2 +-
 doc/searchindex.js                |    2 +-
 6 files changed, 4600 insertions(+), 623 deletions(-)

diff --git a/doc/Manual.html b/doc/Manual.html
index 61c33b7d0c..2857967f53 100644
--- a/doc/Manual.html
+++ b/doc/Manual.html
@@ -220,42 +220,66 @@ 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#build-instructions-for-compress-package">4.2. Build instructions for COMPRESS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-gpu-package">4.3. Build instructions for GPU package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kim-package">4.4. Build instructions for KIM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kokkos-package">4.5. Build instructions for KOKKOS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-kspace-package">4.6. Build instructions for KSPACE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-meam-package">4.7. Build instructions for MEAM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-poems-package">4.8. Build instructions for POEMS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-python-package">4.9. Build instructions for PYTHON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-reax-package">4.10. Build instructions for REAX package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-voronoi-package">4.11. Build instructions for VORONOI package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#build-instructions-for-xtc-package">4.12. Build instructions for XTC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-packages">4.13. User packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-atc-package">4.14. USER-ATC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-awpmd-package">4.15. USER-AWPMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cg-cmm-package">4.16. USER-CG-CMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-colvars-package">4.17. USER-COLVARS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-cuda-package">4.18. USER-CUDA package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-dpd-package">4.20. USER-DPD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-drude-package">4.21. USER-DRUDE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-eff-package">4.22. USER-EFF package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-fep-package">4.23. USER-FEP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-h5md-package">4.24. USER-H5MD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-intel-package">4.25. USER-INTEL package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-lb-package">4.26. USER-LB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-mgpt-package">4.27. USER-MGPT package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-misc-package">4.28. USER-MISC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-molfile-package">4.29. USER-MOLFILE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-omp-package">4.30. USER-OMP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-phonon-package">4.31. USER-PHONON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qmmm-package">4.32. USER-QMMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-qtb-package">4.33. USER-QTB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-reaxc-package">4.34. USER-REAXC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smd-package">4.35. USER-SMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-smtbq-package">4.36. USER-SMTBQ package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="Section_packages.html#user-sph-package">4.37. USER-SPH package</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>
 </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 62cfaab8dd..eb4594c24b 100644
--- a/doc/Section_packages.html
+++ b/doc/Section_packages.html
@@ -79,42 +79,66 @@
 <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="#build-instructions-for-compress-package">4.2. Build instructions for COMPRESS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-gpu-package">4.3. Build instructions for GPU package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-kim-package">4.4. Build instructions for KIM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-kokkos-package">4.5. Build instructions for KOKKOS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-kspace-package">4.6. Build instructions for KSPACE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-meam-package">4.7. Build instructions for MEAM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-poems-package">4.8. Build instructions for POEMS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-python-package">4.9. Build instructions for PYTHON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-reax-package">4.10. Build instructions for REAX package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-voronoi-package">4.11. Build instructions for VORONOI package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#build-instructions-for-xtc-package">4.12. Build instructions for XTC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-packages">4.13. User packages</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-atc-package">4.14. USER-ATC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-awpmd-package">4.15. USER-AWPMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-cg-cmm-package">4.16. USER-CG-CMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-colvars-package">4.17. USER-COLVARS package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-cuda-package">4.18. USER-CUDA package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-diffraction-package">4.19. USER-DIFFRACTION package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-dpd-package">4.20. USER-DPD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-drude-package">4.21. USER-DRUDE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-eff-package">4.22. USER-EFF package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-fep-package">4.23. USER-FEP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-h5md-package">4.24. USER-H5MD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-intel-package">4.25. USER-INTEL package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-lb-package">4.26. USER-LB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-mgpt-package">4.27. USER-MGPT package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-misc-package">4.28. USER-MISC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-molfile-package">4.29. USER-MOLFILE package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-omp-package">4.30. USER-OMP package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-phonon-package">4.31. USER-PHONON package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-qmmm-package">4.32. USER-QMMM package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-qtb-package">4.33. USER-QTB package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-reaxc-package">4.34. USER-REAXC package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-smd-package">4.35. USER-SMD package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-smtbq-package">4.36. USER-SMTBQ package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#user-sph-package">4.37. USER-SPH package</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>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
@@ -176,8 +200,12 @@
             
   <div class="section" id="packages">
 <h1>4. Packages<a class="headerlink" href="#packages" title="Permalink to this headline">¶</a></h1>
-<p>This section gives a quick overview of the add-on packages that extend
-LAMMPS functionality.</p>
+<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>
 <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>
@@ -205,19 +233,21 @@ 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 sections below give a few more
-details, including instructions for building LAMMPS with the package,
-either via the make command or the Make.py tool described in <a class="reference internal" href="Section_start.html#start-4"><span>Section 2.4</span></a>.</p>
+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.</p>
+<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>
 <table border="1" class="docutils">
 <colgroup>
-<col width="7%" />
-<col width="23%" />
-<col width="24%" />
-<col width="32%" />
-<col width="7%" />
+<col width="16%" />
+<col width="21%" />
+<col width="22%" />
+<col width="28%" />
+<col width="6%" />
 <col width="7%" />
 </colgroup>
 <tbody valign="top">
@@ -228,7 +258,7 @@ either via the make command or the Make.py tool described in <a class="reference
 <td>Example</td>
 <td>Library</td>
 </tr>
-<tr class="row-even"><td>ASPHERE</td>
+<tr class="row-even"><td><a class="reference internal" href="#asphere"><span>ASPHERE</span></a></td>
 <td>aspherical particles</td>
 <td><ul class="first last simple">
 <li></li>
@@ -241,7 +271,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>BODY</td>
+<tr class="row-odd"><td><a class="reference internal" href="#body"><span>BODY</span></a></td>
 <td>body-style particles</td>
 <td><ul class="first last simple">
 <li></li>
@@ -254,7 +284,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>CLASS2</td>
+<tr class="row-even"><td><a class="reference internal" href="#class2"><span>CLASS2</span></a></td>
 <td>class 2 force fields</td>
 <td><ul class="first last simple">
 <li></li>
@@ -270,7 +300,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>COLLOID</td>
+<tr class="row-odd"><td><a class="reference internal" href="#colloid"><span>COLLOID</span></a></td>
 <td>colloidal particles</td>
 <td><ul class="first last simple">
 <li></li>
@@ -283,7 +313,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>COMPRESS</td>
+<tr class="row-even"><td><a class="reference internal" href="#compress"><span>COMPRESS</span></a></td>
 <td>I/O compression</td>
 <td>Axel Kohlmeyer (Temple U)</td>
 <td><a class="reference internal" href="dump.html"><em>dump */gz</em></a></td>
@@ -296,7 +326,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>CORESHELL</td>
+<tr class="row-odd"><td><a class="reference internal" href="#coreshell"><span>CORESHELL</span></a></td>
 <td>adiabatic core/shell model</td>
 <td>Hendrik Heenen (Technical U of Munich)</td>
 <td><a class="reference internal" href="Section_howto.html#howto-25"><span>Section_howto 6.25</span></a></td>
@@ -306,7 +336,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>DIPOLE</td>
+<tr class="row-even"><td><a class="reference internal" href="#dipole"><span>DIPOLE</span></a></td>
 <td>point dipole particles</td>
 <td><ul class="first last simple">
 <li></li>
@@ -319,7 +349,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>FLD</td>
+<tr class="row-odd"><td><a class="reference internal" href="#fld"><span>FLD</span></a></td>
 <td>Fast Lubrication Dynamics</td>
 <td>Kumar &amp; Bybee &amp; Higdon (1)</td>
 <td><a class="reference internal" href="pair_lubricateU.html"><em>pair_style lubricateU</em></a></td>
@@ -332,14 +362,14 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>GPU</td>
+<tr class="row-even"><td><a class="reference internal" href="#gpu"><span>GPU</span></a></td>
 <td>GPU-enabled styles</td>
 <td>Mike Brown (ORNL)</td>
 <td><a class="reference internal" href="accelerate_gpu.html"><em>Section accelerate</em></a></td>
 <td>gpu</td>
 <td>lib/gpu</td>
 </tr>
-<tr class="row-odd"><td>GRANULAR</td>
+<tr class="row-odd"><td><a class="reference internal" href="#granular"><span>GRANULAR</span></a></td>
 <td>granular systems</td>
 <td><ul class="first last simple">
 <li></li>
@@ -352,21 +382,21 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>KIM</td>
+<tr class="row-even"><td><a class="reference internal" href="#kim"><span>KIM</span></a></td>
 <td>openKIM potentials</td>
 <td>Smirichinski &amp; Elliot &amp; Tadmor (3)</td>
 <td><a class="reference internal" href="pair_kim.html"><em>pair_style kim</em></a></td>
 <td>kim</td>
 <td>KIM</td>
 </tr>
-<tr class="row-odd"><td>KOKKOS</td>
+<tr class="row-odd"><td><a class="reference internal" href="#kokkos"><span>KOKKOS</span></a></td>
 <td>Kokkos-enabled styles</td>
 <td>Trott &amp; Edwards (4)</td>
 <td><a class="reference internal" href="accelerate_kokkos.html"><em>Section_accelerate</em></a></td>
 <td>kokkos</td>
 <td>lib/kokkos</td>
 </tr>
-<tr class="row-even"><td>KSPACE</td>
+<tr class="row-even"><td><a class="reference internal" href="#kspace"><span>KSPACE</span></a></td>
 <td>long-range Coulombic solvers</td>
 <td><ul class="first last simple">
 <li></li>
@@ -379,7 +409,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>MANYBODY</td>
+<tr class="row-odd"><td><a class="reference internal" href="#manybody"><span>MANYBODY</span></a></td>
 <td>many-body potentials</td>
 <td><ul class="first last simple">
 <li></li>
@@ -392,14 +422,14 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>MEAM</td>
+<tr class="row-even"><td><a class="reference internal" href="#meam"><span>MEAM</span></a></td>
 <td>modified EAM potential</td>
 <td>Greg Wagner (Sandia)</td>
 <td><a class="reference internal" href="pair_meam.html"><em>pair_style meam</em></a></td>
 <td>meam</td>
 <td>lib/meam</td>
 </tr>
-<tr class="row-odd"><td>MC</td>
+<tr class="row-odd"><td><a class="reference internal" href="#mc"><span>MC</span></a></td>
 <td>Monte Carlo options</td>
 <td><ul class="first last simple">
 <li></li>
@@ -415,7 +445,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>MOLECULE</td>
+<tr class="row-even"><td><a class="reference internal" href="#molecule"><span>MOLECULE</span></a></td>
 <td>molecular system force fields</td>
 <td><ul class="first last simple">
 <li></li>
@@ -428,7 +458,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>OPT</td>
+<tr class="row-odd"><td><a class="reference internal" href="#opt"><span>OPT</span></a></td>
 <td>optimized pair styles</td>
 <td>Fischer &amp; Richie &amp; Natoli (2)</td>
 <td><a class="reference internal" href="accelerate_opt.html"><em>Section accelerate</em></a></td>
@@ -441,7 +471,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>PERI</td>
+<tr class="row-even"><td><a class="reference internal" href="#peri"><span>PERI</span></a></td>
 <td>Peridynamics models</td>
 <td>Mike Parks (Sandia)</td>
 <td><a class="reference internal" href="pair_peri.html"><em>pair_style peri</em></a></td>
@@ -451,14 +481,14 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>POEMS</td>
+<tr class="row-odd"><td><a class="reference internal" href="#poems"><span>POEMS</span></a></td>
 <td>coupled rigid body motion</td>
 <td>Rudra Mukherjee (JPL)</td>
 <td><a class="reference internal" href="fix_poems.html"><em>fix poems</em></a></td>
 <td>rigid</td>
 <td>lib/poems</td>
 </tr>
-<tr class="row-even"><td>PYTHON</td>
+<tr class="row-even"><td><a class="reference internal" href="#python"><span>PYTHON</span></a></td>
 <td>embed Python code in an input script</td>
 <td><ul class="first last simple">
 <li></li>
@@ -468,14 +498,14 @@ either via the make command or the Make.py tool described in <a class="reference
 <td>python</td>
 <td>lib/python</td>
 </tr>
-<tr class="row-odd"><td>REAX</td>
+<tr class="row-odd"><td><a class="reference internal" href="#reax"><span>REAX</span></a></td>
 <td>ReaxFF potential</td>
 <td>Aidan Thompson (Sandia)</td>
 <td><a class="reference internal" href="pair_reax.html"><em>pair_style reax</em></a></td>
 <td>reax</td>
 <td>lib/reax</td>
 </tr>
-<tr class="row-even"><td>REPLICA</td>
+<tr class="row-even"><td><a class="reference internal" href="#replica"><span>REPLICA</span></a></td>
 <td>multi-replica methods</td>
 <td><ul class="first last simple">
 <li></li>
@@ -488,7 +518,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>RIGID</td>
+<tr class="row-odd"><td><a class="reference internal" href="#rigid"><span>RIGID</span></a></td>
 <td>rigid bodies</td>
 <td><ul class="first last simple">
 <li></li>
@@ -501,7 +531,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>SHOCK</td>
+<tr class="row-even"><td><a class="reference internal" href="#shock"><span>SHOCK</span></a></td>
 <td>shock loading methods</td>
 <td><ul class="first last simple">
 <li></li>
@@ -517,7 +547,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>SNAP</td>
+<tr class="row-odd"><td><a class="reference internal" href="#snap"><span>SNAP</span></a></td>
 <td>quantum-fit potential</td>
 <td>Aidan Thompson (Sandia)</td>
 <td><a class="reference internal" href="pair_snap.html"><em>pair snap</em></a></td>
@@ -527,7 +557,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>SRD</td>
+<tr class="row-even"><td><a class="reference internal" href="#srd"><span>SRD</span></a></td>
 <td>stochastic rotation dynamics</td>
 <td><ul class="first last simple">
 <li></li>
@@ -540,7 +570,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>VORONOI</td>
+<tr class="row-odd"><td><a class="reference internal" href="#voronoi"><span>VORONOI</span></a></td>
 <td>Voronoi tesselations</td>
 <td>Daniel Schwen (LANL)</td>
 <td><a class="reference internal" href="compute_voronoi_atom.html"><em>compute voronoi/atom</em></a></td>
@@ -550,7 +580,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </td>
 <td>Voro++</td>
 </tr>
-<tr class="row-even"><td>XTC</td>
+<tr class="row-even"><td><a class="reference internal" href="#xtc"><span>XTC</span></a></td>
 <td>dumps in XTC format</td>
 <td><ul class="first last simple">
 <li></li>
@@ -576,9 +606,7 @@ either via the make command or the Make.py tool described in <a class="reference
 </tbody>
 </table>
 <p>The &#8220;Authors&#8221; column lists a name(s) if a specific person is
-responible for creating and maintaining the package.
-More details on
-multiple authors are give below.</p>
+responible for creating and maintaining the package.</p>
 <p>(1) The FLD package was created by Amit Kumar and Michael Bybee from
 Jonathan Higdon&#8217;s group at UIUC.</p>
 <p>(2) The OPT package was created by James Fischer (High Performance
@@ -589,9 +617,10 @@ and Ellad Tadmor (U Minn).</p>
 <p>(4) The KOKKOS package was created primarily by Christian Trott
 (Sandia).  It uses the Kokkos library which was developed by Carter
 Edwards, Christian, and collaborators at Sandia.</p>
-<p>The &#8220;Doc page&#8221; column links to either a portion of the
+<p>The &#8220;Doc page&#8221; column links to either a sub-section of the
 <a class="reference internal" href="Section_howto.html"><em>Section_howto</em></a> of the manual, or an input script
-command implemented as part of the package.</p>
+command implemented as part of the package, or to additional
+documentation provided within the package.</p>
 <p>The &#8220;Example&#8221; column is a sub-directory in the examples directory of
 the distribution which has an input script that uses the package.
 E.g. &#8220;peptide&#8221; refers to the examples/peptide directory.</p>
@@ -601,74 +630,755 @@ 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 the src/package/README or src/package/Makefile.lammps file for
-info on where to download the library.  <a class="reference internal" href="Section_start.html#start-3-3"><span>Section start</span></a> of the manual also gives details
-on how to build LAMMPS with both kinds of auxiliary libraries.</p>
-<p>Except where explained below, all of these packages can be installed,
-and LAMMPS re-built, by issuing these commands from the src dir.</p>
-<div class="highlight-python"><div class="highlight"><pre>make yes-package
+See details on all of this below for individual packages.</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>
+<p>Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
+triangles.</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-asphere
 make machine
-or
-Make.py -p package -a machine
 </pre></div>
 </div>
-<p>To un-install the package and re-build LAMMPS without it:</p>
-<div class="highlight-python"><div class="highlight"><pre>make no-package
-make machine
-or
-Make.py -p ^package -a machine
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p asphere -a machine
 </pre></div>
 </div>
-<p>&#8220;Package&#8221; is the name of the package in lower-case letters,
-e.g. asphere or rigid, and &#8220;machine&#8221; is the build target, e.g. mpi or
-serial.</p>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-asphere
+make machine
+</pre></div>
 </div>
-<div class="section" id="build-instructions-for-compress-package">
-<h2>4.2. Build instructions for COMPRESS package<a class="headerlink" href="#build-instructions-for-compress-package" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^asphere -a machine
+</pre></div>
 </div>
-<div class="section" id="build-instructions-for-gpu-package">
-<h2>4.3. Build instructions for GPU package<a class="headerlink" href="#build-instructions-for-gpu-package" title="Permalink to this headline">¶</a></h2>
+<p>Supporting info: examples/ASPHERE, examples/ellipse, Section howto
+6.14, pair gayberne</p>
+<hr class="docutils" />
 </div>
-<div class="section" id="build-instructions-for-kim-package">
-<h2>4.4. Build instructions for KIM package<a class="headerlink" href="#build-instructions-for-kim-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
-<div class="section" id="build-instructions-for-kokkos-package">
-<h2>4.5. Build instructions for KOKKOS package<a class="headerlink" href="#build-instructions-for-kokkos-package" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
 </div>
-<div class="section" id="build-instructions-for-kspace-package">
-<h2>4.6. Build instructions for KSPACE package<a class="headerlink" href="#build-instructions-for-kspace-package" title="Permalink to this headline">¶</a></h2>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
 </div>
-<div class="section" id="build-instructions-for-meam-package">
-<h2>4.7. Build instructions for MEAM package<a class="headerlink" href="#build-instructions-for-meam-package" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
 </div>
-<div class="section" id="build-instructions-for-poems-package">
-<h2>4.8. Build instructions for POEMS package<a class="headerlink" href="#build-instructions-for-poems-package" title="Permalink to this headline">¶</a></h2>
+<p>Supporting info: examples/body</p>
+<hr class="docutils" />
 </div>
-<div class="section" id="build-instructions-for-python-package">
-<h2>4.9. Build instructions for PYTHON package<a class="headerlink" href="#build-instructions-for-python-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-class2
+make machine
+</pre></div>
 </div>
-<div class="section" id="build-instructions-for-reax-package">
-<h2>4.10. Build instructions for REAX package<a class="headerlink" href="#build-instructions-for-reax-package" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p class2 -a machine
+</pre></div>
 </div>
-<div class="section" id="build-instructions-for-voronoi-package">
-<h2>4.11. Build instructions for VORONOI package<a class="headerlink" href="#build-instructions-for-voronoi-package" title="Permalink to this headline">¶</a></h2>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-class2
+make machine
+</pre></div>
 </div>
-<div class="section" id="build-instructions-for-xtc-package">
-<h2>4.12. Build instructions for XTC package<a class="headerlink" href="#build-instructions-for-xtc-package" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^class2 -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-colloid
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p colloid -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-colloid
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^colloid -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/colloid, examples/srd</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-compress
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p compress -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-compress
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^compress -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-coreshell
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p coreshell -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-coreshell
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^coreshell -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/coreshell, Section howto 6.26</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-dipole
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p dipole -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-dipole
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^dipole -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/dipole</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-fld
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p fld -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-fld
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^fld -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-gpu
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p gpu -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-gpu
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^gpu -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-granular
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p granular -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-granular
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^granular -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/pour, bench/in.chute, Section howto 6.6</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-kim
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p kim -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-kim
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^kim -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/kim</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-kokkow
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p kokkow -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-kokkow
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^kokkow -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
+<p>For the KOKKOS package, you have 3 choices when building.  You can
+build with OMP or Cuda or Phi support.  Phi support uses Xeon Phi
+chips in &#8220;native&#8221; mode.  This can be done by setting the following
+variables in your Makefile.machine:</p>
+<ul class="simple">
+<li>for OMP support, set OMP = yes</li>
+<li>for Cuda support, set OMP = yes and CUDA = yes</li>
+<li>for Phi support, set OMP = yes and MIC = yes</li>
+</ul>
+<p>These can also be set as additional arguments to the make command, e.g.</p>
+<div class="highlight-python"><div class="highlight"><pre>make g++ OMP=yes MIC=yes
+</pre></div>
+</div>
+<p>Building the KOKKOS package with CUDA support requires a Makefile
+machine that uses the NVIDIA &#8220;nvcc&#8221; compiler, as well as an
+appropriate &#8220;arch&#8221; setting appropriate to the GPU hardware and NVIDIA
+software you have on your machine.  See
+src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
+Makefile.</p>
+<p>Examples: examples/accelerate, bench/FERMI, bench/KEPLER</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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-kspace
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p kspace -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-kspace
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^kspace -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
+<p>Examples: examples/peptide, bench/in.rhodo</p>
+<p>Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-manybody
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p manybody -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-manybody
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^manybody -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
+<p>Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-mc
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p mc -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-mc
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^mc -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-meam
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p meam -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-meam
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^meam -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/meam</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-misc
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p misc -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-misc
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^misc -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/misc</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-molecule
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p molecule -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-molecule
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^molecule -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo, Section howto 6.3</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-mpiio
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p mpiio -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-mpiio
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^mpiio -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-opt
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p opt -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-opt
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^opt -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/accelerate, bench/KEPLER</p>
+<p>For the OPT package, your Makefile.machine needs an additional
+settings for CCFLAGS.</p>
+<ul class="simple">
+<li>CCFLAGS: add -restrict</li>
+</ul>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-peri
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p peri -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-peri
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^peri -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/peri</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-poems
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p poems -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-poems
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^poems -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/rigid</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-python
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p python -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-python
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^python -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/python</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-qeq
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p qeq -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-qeq
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^qeq -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/qeq</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-reax
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p reax -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-reax
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^reax -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/reax</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-replica
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p replica -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-replica
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^replica -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-rigid
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p rigid -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-rigid
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^rigid -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/ASPHERE, examples/rigid</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-shock
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p shock -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-shock
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^shock -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/hugoniostat, examples/msst</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-snap
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p snap -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-snap
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^snap -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/snap</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-srd
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p srd -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-srd
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^srd -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-voronoi
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p voronoi -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-voronoi
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^voronoi -a machine
+</pre></div>
+</div>
+<p>Supporting info: examples/voronoi</p>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-xtc
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p xtc -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-xtc
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^xtc -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="user-packages">
-<span id="pkg-2"></span><h2>4.13. User packages<a class="headerlink" href="#user-packages" title="Permalink to this headline">¶</a></h2>
+<span id="pkg-2"></span><h2>4.34. 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>
-<col width="8%" />
-<col width="21%" />
-<col width="22%" />
-<col width="25%" />
-<col width="8%" />
-<col width="10%" />
-<col width="6%" />
+<col width="18%" />
+<col width="19%" />
+<col width="20%" />
+<col width="23%" />
+<col width="7%" />
+<col width="9%" />
+<col width="5%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>Package</td>
@@ -679,7 +1389,7 @@ serial.</p>
 <td>Pic/movie</td>
 <td>Library</td>
 </tr>
-<tr class="row-even"><td>USER-ATC</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-atc"><span>USER-ATC</span></a></td>
 <td>atom-to-continuum coupling</td>
 <td>Jones &amp; Templeton &amp; Zimmerman (1)</td>
 <td><a class="reference internal" href="fix_atc.html"><em>fix atc</em></a></td>
@@ -687,7 +1397,7 @@ serial.</p>
 <td><a class="reference external" href="http://lammps.sandia.gov/pictures.html#atc">atc</a></td>
 <td>lib/atc</td>
 </tr>
-<tr class="row-odd"><td>USER-AWPMD</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-awpmd"><span>USER-AWPMD</span></a></td>
 <td>wave-packet MD</td>
 <td>Ilya Valuev (JIHT)</td>
 <td><a class="reference internal" href="pair_awpmd.html"><em>pair_style awpmd/cut</em></a></td>
@@ -698,7 +1408,7 @@ serial.</p>
 </td>
 <td>lib/awpmd</td>
 </tr>
-<tr class="row-even"><td>USER-CG-CMM</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-cg-cmm"><span>USER-CG-CMM</span></a></td>
 <td>coarse-graining model</td>
 <td>Axel Kohlmeyer (Temple U)</td>
 <td><a class="reference internal" href="pair_sdk.html"><em>pair_style lj/sdk</em></a></td>
@@ -709,7 +1419,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>USER-COLVARS</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-colvars"><span>USER-COLVARS</span></a></td>
 <td>collective variables</td>
 <td>Fiorin &amp; Henin &amp; Kohlmeyer (2)</td>
 <td><a class="reference internal" href="fix_colvars.html"><em>fix colvars</em></a></td>
@@ -717,7 +1427,7 @@ serial.</p>
 <td><a class="reference external" href="colvars">colvars</a></td>
 <td>lib/colvars</td>
 </tr>
-<tr class="row-even"><td>USER-CUDA</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-cuda"><span>USER-CUDA</span></a></td>
 <td>NVIDIA GPU styles</td>
 <td>Christian Trott (U Tech Ilmenau)</td>
 <td><a class="reference internal" href="accelerate_cuda.html"><em>Section accelerate</em></a></td>
@@ -728,7 +1438,7 @@ serial.</p>
 </td>
 <td>lib/cuda</td>
 </tr>
-<tr class="row-odd"><td>USER-DIFFRACTION</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-diffraction"><span>USER-DIFFRACTION</span></a></td>
 <td>virutal x-ray and electron diffraction</td>
 <td>Shawn Coleman (ARL)</td>
 <td><a class="reference internal" href="compute_xrd.html"><em>compute xrd</em></a></td>
@@ -742,7 +1452,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>USER-DPD</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-dpd"><span>USER-DPD</span></a></td>
 <td>dissipative particle dynamics (DPD)</td>
 <td>Larentzos &amp; Mattox &amp; Brennan (5)</td>
 <td>src/USER-DPD/README</td>
@@ -756,7 +1466,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>USER-DRUDE</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-drude"><span>USER-DRUDE</span></a></td>
 <td>Drude oscillators</td>
 <td>Dequidt &amp; Devemy &amp; Padua (3)</td>
 <td><a class="reference internal" href="tutorial_drude.html"><em>tutorial</em></a></td>
@@ -770,7 +1480,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>USER-EFF</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-eff"><span>USER-EFF</span></a></td>
 <td>electron force field</td>
 <td>Andres Jaramillo-Botero (Caltech)</td>
 <td><a class="reference internal" href="pair_eff.html"><em>pair_style eff/cut</em></a></td>
@@ -781,7 +1491,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>USER-FEP</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-fep"><span>USER-FEP</span></a></td>
 <td>free energy perturbation</td>
 <td>Agilio Padua (U Blaise Pascal Clermont-Ferrand)</td>
 <td><a class="reference internal" href="compute_fep.html"><em>compute fep</em></a></td>
@@ -795,7 +1505,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>USER-H5MD</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-h5md"><span>USER-H5MD</span></a></td>
 <td>dump output via HDF5</td>
 <td>Pierre de Buyl (KU Leuven)</td>
 <td><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a></td>
@@ -809,7 +1519,7 @@ serial.</p>
 </td>
 <td>lib/h5md</td>
 </tr>
-<tr class="row-odd"><td>USER-INTEL</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-intel"><span>USER-INTEL</span></a></td>
 <td>Vectorized CPU and Intel(R) coprocessor styles</td>
 <td><ol class="first last upperalpha simple" start="23">
 <li>Michael Brown (Intel)</li>
@@ -826,7 +1536,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>USER-LB</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-lb"><span>USER-LB</span></a></td>
 <td>Lattice Boltzmann fluid</td>
 <td>Colin Denniston (U Western Ontario)</td>
 <td><a class="reference internal" href="fix_lb_fluid.html"><em>fix lb/fluid</em></a></td>
@@ -840,7 +1550,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>USER-MGPT</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-mgpt"><span>USER-MGPT</span></a></td>
 <td>fast MGPT multi-ion potentials</td>
 <td>Tomas Oppelstrup &amp; John Moriarty (LLNL)</td>
 <td><a class="reference internal" href="pair_mgpt.html"><em>pair_style mgpt</em></a></td>
@@ -854,7 +1564,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>USER-MISC</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-misc"><span>USER-MISC</span></a></td>
 <td>single-file contributions</td>
 <td>USER-MISC/README</td>
 <td>USER-MISC/README</td>
@@ -871,7 +1581,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>USER-MOLFILE</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-molfile"><span>USER-MOLFILE</span></a></td>
 <td><a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molfile plug-ins</td>
 <td>Axel Kohlmeyer (Temple U)</td>
 <td><a class="reference internal" href="dump_molfile.html"><em>dump molfile</em></a></td>
@@ -885,7 +1595,7 @@ serial.</p>
 </td>
 <td>VMD-MOLFILE</td>
 </tr>
-<tr class="row-even"><td>USER-OMP</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-omp"><span>USER-OMP</span></a></td>
 <td>OpenMP threaded styles</td>
 <td>Axel Kohlmeyer (Temple U)</td>
 <td><a class="reference internal" href="accelerate_omp.html"><em>Section accelerate</em></a></td>
@@ -902,7 +1612,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>USER-PHONON</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-phonon"><span>USER-PHONON</span></a></td>
 <td>phonon dynamical matrix</td>
 <td>Ling-Ti Kong (Shanghai Jiao Tong U)</td>
 <td><a class="reference internal" href="fix_phonon.html"><em>fix phonon</em></a></td>
@@ -916,7 +1626,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>USER-QMMM</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-qmmm"><span>USER-QMMM</span></a></td>
 <td>QM/MM coupling</td>
 <td>Axel Kohlmeyer (Temple U)</td>
 <td><a class="reference internal" href="fix_qmmm.html"><em>fix qmmm</em></a></td>
@@ -927,7 +1637,7 @@ serial.</p>
 </td>
 <td>lib/qmmm</td>
 </tr>
-<tr class="row-odd"><td>USER-QTB</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-qtb"><span>USER-QTB</span></a></td>
 <td>quantum nuclear effects</td>
 <td>Yuan Shen (Stanford)</td>
 <td><a class="reference internal" href="fix_qtb.html"><em>fix qtb</em></a> <a class="reference internal" href="fix_qbmsst.html"><em>fix_qbmsst</em></a></td>
@@ -941,7 +1651,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>USER-QUIP</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-quip"><span>USER-QUIP</span></a></td>
 <td>QUIP/libatoms interface</td>
 <td>Albert Bartok-Partay (U Cambridge)</td>
 <td><a class="reference internal" href="pair_quip.html"><em>pair_style quip</em></a></td>
@@ -952,7 +1662,7 @@ serial.</p>
 </td>
 <td>lib/quip</td>
 </tr>
-<tr class="row-odd"><td>USER-REAXC</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-reaxc"><span>USER-REAXC</span></a></td>
 <td>C version of ReaxFF</td>
 <td>Metin Aktulga (LBNL)</td>
 <td><a class="reference internal" href="pair_reax_c.html"><em>pair_style reaxc</em></a></td>
@@ -966,7 +1676,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>USER-SMD</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-smd"><span>USER-SMD</span></a></td>
 <td>smoothed Mach dynamics</td>
 <td>Georg Ganzenmuller (EMI)</td>
 <td><a class="reference external" href="PDF/SMD_LAMMPS_userguide.pdf">userguide.pdf</a></td>
@@ -980,7 +1690,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>USER-SMTBQ</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-smtbq"><span>USER-SMTBQ</span></a></td>
 <td>Second Moment Tight Binding - QEq potential</td>
 <td>Salles &amp; Maras &amp; Politano &amp; Tetot (4)</td>
 <td><a class="reference internal" href="pair_smtbq.html"><em>pair_style smtbq</em></a></td>
@@ -994,7 +1704,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>USER-SPH</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-sph"><span>USER-SPH</span></a></td>
 <td>smoothed particle hydrodynamics</td>
 <td>Georg Ganzenmuller (EMI)</td>
 <td><a class="reference external" href="PDF/SPH_LAMMPS_userguide.pdf">userguide.pdf</a></td>
@@ -1005,7 +1715,7 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-odd"><td>USER-TALLY</td>
+<tr class="row-odd"><td><a class="reference internal" href="#user-tally"><span>USER-TALLY</span></a></td>
 <td>Pairwise tallied computes</td>
 <td>Axel Kohlmeyer (Temple U)</td>
 <td><code class="xref doc docutils literal"><span class="pre">compute</span></code></td>
@@ -1019,7 +1729,21 @@ serial.</p>
 </ul>
 </td>
 </tr>
-<tr class="row-even"><td>&nbsp;</td>
+<tr class="row-even"><td><a class="reference internal" href="#user-vtk"><span>USER-VTK</span></a></td>
+<td>VTK-style dumps</td>
+<td>Berger and Queteschiner (6)</td>
+<td><code class="xref doc docutils literal"><span class="pre">compute</span> <span class="pre">custom/vtk</span></code></td>
+<td><ul class="first last simple">
+<li></li>
+</ul>
+</td>
+<td><ul class="first last simple">
+<li></li>
+</ul>
+</td>
+<td>lib/vtk</td>
+</tr>
+<tr class="row-odd"><td>&nbsp;</td>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
@@ -1041,13 +1765,11 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
 (U Blaise Pascal).</p>
 <p>(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
 Olivier Politano, and Robert Tetot (LAAS-CNRS, France).</p>
-<p>(4) The USER-DPD package was created by James Larentzos, Timothy
-Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).</p>
-<p>If the Library is not listed as lib/package, then it is a third-party
-library not included in the LAMMPS distribution.  See the
-src/package/Makefile.lammps file for info on where to download the
-library from.</p>
-<p>The &#8220;Doc page&#8221; column links to either a portion of the
+<p>(5) The USER-DPD package was created by James Larentzos (ARL), Timothy
+Mattox (Engility), and John Brennan (ARL).</p>
+<p>(6) The USER-VTK package was created by Richard Berger (JKU) and
+Daniel Queteschiner (DCS Computing).</p>
+<p>The &#8220;Doc page&#8221; column links to either a sub-section of the
 <a class="reference internal" href="Section_howto.html"><em>Section_howto</em></a> of the manual, or an input script
 command implemented as part of the package, or to additional
 documentation provided within the package.</p>
@@ -1061,31 +1783,15 @@ 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 the src/package/Makefile.lammps file for info on where to download
-the library.  <a class="reference internal" href="Section_start.html#start-3-3"><span>Section start</span></a> of the
-manual also gives details on how to build LAMMPS with both kinds of
-auxiliary libraries.</p>
-<p>Except where explained below, all of these packages can be installed,
-and LAMMPS re-built, by issuing these commands from the src dir.</p>
-<div class="highlight-python"><div class="highlight"><pre>make yes-user-package
-make machine
-or
-Make.py -p package -a machine
-</pre></div>
-</div>
-<p>To un-install the package and re-build LAMMPS without it:</p>
-<div class="highlight-python"><div class="highlight"><pre>make no-user-package
-make machine
-or
-Make.py -p ^package -a machine
-</pre></div>
-</div>
-<p>&#8220;Package&#8221; is the name of the package (in this case without the user
-prefix) in lower-case letters, e.g. drude or phonon, and &#8220;machine&#8221; is
-the build target, e.g. mpi or serial.</p>
+See details on all of this below for individual packages.</p>
+<hr class="docutils" />
 </div>
 <div class="section" id="user-atc-package">
-<h2>4.14. USER-ATC package<a class="headerlink" href="#user-atc-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package implements a &#8220;fix atc&#8221; command which can be used in a
 LAMMPS input script.  This fix can be employed to either do concurrent
 coupling of MD with FE-based physics surrogates or on-the-fly
@@ -1102,10 +1808,15 @@ libraries.</p>
 sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
 Zimmerman (jzimmer at sandia.gov) at Sandia.  Contact them directly if
 you have questions.</p>
-</div>
+<p>Examples: examples/USER/atc</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-awpmd-package">
-<h2>4.15. USER-AWPMD package<a class="headerlink" href="#user-awpmd-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package contains a LAMMPS implementation of the Antisymmetrized
 Wave Packet Molecular Dynamics (AWPMD) method.</p>
 <p>See the doc page for the pair_style awpmd/cut command to get started.</p>
@@ -1117,10 +1828,29 @@ libraries.</p>
 <p>The person who created this package is Ilya Valuev at the JIHT in
 Russia (valuev at physik.hu-berlin.de).  Contact him directly if you
 have questions.</p>
-</div>
+<p>Examples: examples/USER/awpmd</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-cg-cmm-package">
-<h2>4.16. 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><h2>4.37. USER-CG-CMM package<a class="headerlink" href="#user-cg-cmm-package" title="Permalink to this headline">¶</a></h2>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
 <p>This package implements 3 commands which can be used in a LAMMPS input
 script:</p>
 <ul class="simple">
@@ -1152,10 +1882,15 @@ have not been testing with all kinds of potential parameters and
 simulation systems.</p>
 <p>The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.</p>
-</div>
+<p>Examples: examples/USER/cg-cmm</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-colvars-package">
-<h2>4.17. USER-COLVARS package<a class="headerlink" href="#user-colvars-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package implements the &#8220;fix colvars&#8221; command which can be
 used in a LAMMPS input script.</p>
 <p>This fix allows to use &#8220;collective variables&#8221; to implement
@@ -1181,10 +1916,15 @@ Thus the current version of this package should be considered
 beta quality.</p>
 <p>The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.</p>
-</div>
+<p>Examples: examples/USER/colvars</p>
+<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>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-cuda-package">
-<h2>4.18. USER-CUDA package<a class="headerlink" href="#user-cuda-package" title="Permalink to this headline">¶</a></h2>
+<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>
 <p>This package provides acceleration of various LAMMPS pair styles, fix
 styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
 GPUs.</p>
@@ -1199,10 +1939,15 @@ libraries.</p>
 <p>The person who created this package is Christian Trott at the
 University of Technology Ilmenau, Germany (christian.trott at
 tu-ilmenau.de).  Contact him directly if you have questions.</p>
-</div>
+<p>Examples: examples/accelerate, bench/FERMI, bench/KEPLER</p>
+<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>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-diffraction-package">
-<h2>4.19. USER-DIFFRACTION package<a class="headerlink" href="#user-diffraction-package" title="Permalink to this headline">¶</a></h2>
+<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>
 <p>This package contains the commands neeed to calculate x-ray and
 electron diffraction intensities based on kinematic diffraction
 theory.</p>
@@ -1215,10 +1960,29 @@ theory.</p>
 <p>The person who created this package is Shawn P. Coleman
 (shawn.p.coleman8.ctr at mail.mil) while at the University of
 Arkansas.  Contact him directly if you have questions.</p>
+<p>Examples: examples/USER/diffraction</p>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-dpd-package">
-<h2>4.20. USER-DPD package<a class="headerlink" href="#user-dpd-package" title="Permalink to this headline">¶</a></h2>
+<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>
 <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
@@ -1239,10 +2003,31 @@ Shardlow splitting algorithm.</p>
 (james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at
 engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
 Contact them directly if you have questions.</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Examples: examples/USER/dpd</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-drude-package">
-<h2>4.21. USER-DRUDE package<a class="headerlink" href="#user-drude-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package implements methods for simulating polarizable systems
 in LAMMPS using thermalized Drude oscillators.</p>
 <p>See these doc pages and their related commands to get started:</p>
@@ -1259,10 +2044,32 @@ in LAMMPS using thermalized Drude oscillators.</p>
 Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
 Contact him directly if you have questions. Co-authors: Julien Devemy,
 Agilio Padua.</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Examples: examples/USER/drude</p>
+<p>Doc: Section howto 6.27</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-eff-package">
-<h2>4.22. USER-EFF package<a class="headerlink" href="#user-eff-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package contains a LAMMPS implementation of the electron Force
 Field (eFF) currently under development at Caltech, as described in
 A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
@@ -1293,10 +2100,31 @@ examples/USER/eff.</p>
 <p>The person who created this package is Andres Jaramillo-Botero at
 CalTech (ajaramil at wag.caltech.edu).  Contact him directly if you
 have questions.</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Examples: examples/USER/eff</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-fep-package">
-<h2>4.23. USER-FEP package<a class="headerlink" href="#user-fep-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package provides methods for performing free energy perturbation
 simulations with soft-core pair potentials in LAMMPS.</p>
 <p>See these doc pages and their related commands to get started:</p>
@@ -1308,10 +2136,31 @@ simulations with soft-core pair potentials in LAMMPS.</p>
 <p>The person who created this package is Agilio Padua at Universite
 Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
 Contact him directly if you have questions.</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Examples: examples/USER/fep</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-h5md-package">
-<h2>4.24. USER-H5MD package<a class="headerlink" href="#user-h5md-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package contains a <a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> command for
 performing a dump of atom properties in HDF5 format.  <a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5 files</a> are binary, portable and self-describing and can be
 examined and used by a variety of auxiliary tools.  The output HDF5
@@ -1322,10 +2171,14 @@ citation to a paper describing the format.</p>
 <p>The person who created this package and the underlying H5MD format is
 Pierre de Buyl at KU Leuven (see <a class="reference external" href="http://pdebuyl.be">http://pdebuyl.be</a>).  Contact him
 directly if you have questions.</p>
-</div>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-intel-package">
-<h2>4.25. USER-INTEL package<a class="headerlink" href="#user-intel-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package provides options for performing neighbor list and
 non-bonded force calculations in single, mixed, or double precision
 and also a capability for accelerating calculations with an
@@ -1334,10 +2187,33 @@ Intel(R) Xeon Phi(TM) coprocessor.</p>
 <p><span class="xref std std-ref">Section_accelerate</span></p>
 <p>The person who created this package is W. Michael Brown at Intel
 (michael.w.brown at intel.com).  Contact him directly if you have questions.</p>
-</div>
+<p>For the USER-INTEL package, you have 2 choices when building.  You can
+build with CPU or Phi support.  The latter uses Xeon Phi chips in
+&#8220;offload&#8221; mode.  Each of these modes requires additional settings in
+your Makefile.machine for CCFLAGS and LINKFLAGS.</p>
+<p>For CPU mode (if using an Intel compiler):</p>
+<ul class="simple">
+<li>CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits</li>
+<li>LINKFLAGS: add -fopenmp</li>
+</ul>
+<p>For Phi mode add the following in addition to the CPU mode flags:</p>
+<ul class="simple">
+<li>CCFLAGS: add -DLMP_INTEL_OFFLOAD and</li>
+<li>LINKFLAGS: add -offload</li>
+</ul>
+<p>And also add this to CCFLAGS:</p>
+<pre class="literal-block">
+-offload-option,mic,compiler,&quot;-fp-model fast=2 -mGLOB_default_function_attrs=&quot;gather_scatter_loop_unroll=4&quot;&quot;
+</pre>
+<p>Examples: examples/accelerate, bench/KEPLER</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-lb-package">
-<h2>4.26. USER-LB package<a class="headerlink" href="#user-lb-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package contains a LAMMPS implementation of a background
 Lattice-Boltzmann fluid, which can be used to model MD particles
 influenced by hydrodynamic forces.</p>
@@ -1346,10 +2222,31 @@ influenced by hydrodynamic forces.</p>
 <p>The people who created this package are Frances Mackay (fmackay at
 uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
 Western Ontario.  Contact them directly if you have questions.</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Examples: examples/USER/lb</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-mgpt-package">
-<h2>4.27. USER-MGPT package<a class="headerlink" href="#user-mgpt-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package contains a fast implementation for LAMMPS of
 quantum-based MGPT multi-ion potentials.  The MGPT or model GPT method
 derives from first-principles DFT-based generalized pseudopotential
@@ -1369,10 +2266,31 @@ Oppelstrup at LLNL.</p>
 <p>The persons who created the USER-MGPT package are Tomas Oppelstrup
 (<a class="reference external" href="mailto:oppelstrup2&#37;&#52;&#48;llnl&#46;gov">oppelstrup2<span>&#64;</span>llnl<span>&#46;</span>gov</a>) and John Moriarty (<a class="reference external" href="mailto:moriarty2&#37;&#52;&#48;llnl&#46;gov">moriarty2<span>&#64;</span>llnl<span>&#46;</span>gov</a>)
 Contact them directly if you have any questions.</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Examples: examples/USER/mgpt</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-misc-package">
-<h2>4.28. USER-MISC package<a class="headerlink" href="#user-misc-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>The files in this package are a potpourri of (mostly) unrelated
 features contributed to LAMMPS by users.  Each feature is a single
 pair of files (<a href="#id2"><span class="problematic" id="id3">*</span></a>.cpp and <a href="#id4"><span class="problematic" id="id5">*</span></a>.h).</p>
@@ -1386,10 +2304,31 @@ compute, pair, etc sections.</p>
 src/USER-MISC/README file.</p>
 <p>You should contact the author directly if you have specific questions
 about the feature or its coding.</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Examples: examples/USER/misc</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-molfile-package">
-<h2>4.29. USER-MOLFILE package<a class="headerlink" href="#user-molfile-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package contains a dump molfile command which uses molfile
 plugins that are bundled with the
 <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a> molecular visualization and
@@ -1405,10 +2344,14 @@ application itself.</p>
 <p><span class="xref std std-ref">dump molfile</span></p>
 <p>The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.</p>
-</div>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-omp-package">
-<h2>4.30. USER-OMP package<a class="headerlink" href="#user-omp-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package provides OpenMP multi-threading support and
 other optimizations of various LAMMPS pair styles, dihedral
 styles, and fix styles.</p>
@@ -1416,10 +2359,17 @@ styles, and fix styles.</p>
 <p><span class="xref std std-ref">Section_accelerate</span></p>
 <p>The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.</p>
-</div>
+<p>For the USER-OMP package, your Makefile.machine needs additional
+settings for CCFLAGS and LINKFLAGS.</p>
+<ul class="simple">
+<li>CCFLAGS: add -fopenmp and -restrict</li>
+<li>LINKFLAGS: add -fopenmp</li>
+</ul>
+<p>Examples: examples/accelerate, bench/KEPLER</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-phonon-package">
-<h2>4.31. USER-PHONON package<a class="headerlink" href="#user-phonon-package" title="Permalink to this headline">¶</a></h2>
+<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>
 <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>
@@ -1428,10 +2378,31 @@ relations, directly from molecular dynamics simulations.</p>
 <p>The person who created this package is Ling-Ti Kong (konglt at
 sjtu.edu.cn) at Shanghai Jiao Tong University.  Contact him directly
 if you have questions.</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Examples: examples/USER/phonon</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-qmmm-package">
-<h2>4.32. USER-QMMM package<a class="headerlink" href="#user-qmmm-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package provides a fix qmmm command which allows LAMMPS to be
 used in a QM/MM simulation, currently only in combination with pw.x
 code from the <a class="reference external" href="http://www.quantum-espresso.org">Quantum ESPRESSO</a> package.</p>
@@ -1445,10 +2416,14 @@ without changes to LAMMPS itself.</p>
 <p>as well as the lib/qmmm/README file.</p>
 <p>The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.</p>
-</div>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-qtb-package">
-<h2>4.33. USER-QTB package<a class="headerlink" href="#user-qtb-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package provides a self-consistent quantum treatment of the
 vibrational modes in a classical molecular dynamics simulation.  By
 coupling the MD simulation to a colored thermostat, it introduces zero
@@ -1467,10 +2442,54 @@ bath with the shocked system.</p>
 <p>The person who created this package is Yuan Shen (sy0302 at
 stanford.edu) at Stanford University.  Contact him directly if you
 have questions.</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
 </div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Examples: examples/USER/qtb</p>
 <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>
+<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/quip</p>
+<hr class="docutils" />
+</div>
 <div class="section" id="user-reaxc-package">
-<h2>4.34. USER-REAXC package<a class="headerlink" href="#user-reaxc-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
 <p>This package contains a implementation for LAMMPS of the ReaxFF force
 field.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
@@ -1495,10 +2514,15 @@ of how to use it in LAMMPS.</p>
 at lbl.gov), while at Purdue University.  Contact him directly, or
 Aidan Thompson at Sandia (athomps at sandia.gov), if you have
 questions.</p>
-</div>
+<p>Examples: examples/reax</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-smd-package">
-<h2>4.35. USER-SMD package<a class="headerlink" href="#user-smd-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<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>This package implements smoothed Mach dynamics (SMD) in
 LAMMPS.  Currently, the package has the following features:</p>
 <ul class="simple">
@@ -1519,10 +2543,29 @@ from <a href="#id7"><span class="problematic" id="id8">*</span></a>.STL files.</
 Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
 Germany (georg.ganzenmueller at emi.fhg.de).  Contact him directly if
 you have questions.</p>
-</div>
+<p>Examples: examples/USER/smd</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-smtbq-package">
-<h2>4.36. USER-SMTBQ package<a class="headerlink" href="#user-smtbq-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
 <p>This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
 potential for the description of ionocovalent bonds in oxides.</p>
 <p>There are example scripts for using this package in
@@ -1533,10 +2576,29 @@ examples/USER/smtbq.</p>
 Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
 these email addreses: <a class="reference external" href="mailto:lammps&#37;&#52;&#48;u-bourgogne&#46;fr">lammps<span>&#64;</span>u-bourgogne<span>&#46;</span>fr</a>, <a class="reference external" href="mailto:nsalles&#37;&#52;&#48;laas&#46;fr">nsalles<span>&#64;</span>laas<span>&#46;</span>fr</a>.  Contact
 them directly if you have any questions.</p>
-</div>
+<p>Examples: examples/USER/smtbq</p>
 <hr class="docutils" />
+</div>
 <div class="section" id="user-sph-package">
-<h2>4.37. USER-SPH package<a class="headerlink" href="#user-sph-package" title="Permalink to this headline">¶</a></h2>
+<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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
 <p>This package implements smoothed particle hydrodynamics (SPH) in
 LAMMPS.  Currently, the package has the following features:</p>
 <ul class="simple">
@@ -1555,6 +2617,39 @@ thermo output</li>
 Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
 Germany (georg.ganzenmueller at emi.fhg.de).  Contact him directly if
 you have questions.</p>
+<p>Examples: examples/USER/sph</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>
+<p>Contents:</p>
+<p>To install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make yes-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p body -a machine
+</pre></div>
+</div>
+<p>To un-install via make or Make.py:</p>
+<div class="highlight-python"><div class="highlight"><pre>make no-body
+make machine
+</pre></div>
+</div>
+<div class="highlight-python"><div class="highlight"><pre>Make.py -p ^body -a machine
+</pre></div>
+</div>
+<p>Supporting info:</p>
+<p>Examples: examples/USER/tally</p>
+<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>
+<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>
 
diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt
index 864c0afd92..43c7a2579f 100644
--- a/doc/Section_packages.txt
+++ b/doc/Section_packages.txt
@@ -10,8 +10,12 @@ Section"_Section_accelerate.html :c
 
 4. Packages :h3
 
-This section gives a quick overview of the add-on packages that extend
-LAMMPS functionality.
+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.
 
 4.1 "Standard packages"_#pkg_1
 4.2 "User packages"_#pkg_2 :all(b)
@@ -41,54 +45,51 @@ 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 sections below give a few more
-details, including instructions for building LAMMPS with the package,
-either via the make command or the Make.py tool described in "Section
-2.4"_Section_start.html#start_4.
+a one-line descriptions of each.  The sub-sections below give more
+details.
 
-:line
 :line
 
 4.1 Standard packages :h4,link(pkg_1)
 
-The current list of standard packages is as follows. 
+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.
 
 Package, Description, Author(s), Doc page, Example, Library
-ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, -
-BODY, body-style particles, -, "body"_body.html, body, -
-CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
-COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, -
-COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
-CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section_howto 6.25"_Section_howto.html#howto_25, coreshell, -
-DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
-FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, -
-GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu
-GRANULAR, granular systems, -, "Section_howto 6.6"_Section_howto.html#howto_6, pour, -
-KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
-KOKKOS, Kokkos-enabled styles, Trott & Edwards (4), "Section_accelerate"_accelerate_kokkos.html, kokkos, lib/kokkos
-KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
-MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
-MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
-MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
-MOLECULE, molecular system force fields, -, "Section_howto 6.3"_Section_howto.html#howto_3, peptide, -
-OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, -
-PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
-POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
-PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
-REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax
-REPLICA, multi-replica methods, -, "Section_howto 6.5"_Section_howto.html#howto_5, tad, -
-RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
-SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
-SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, -
-SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
-VORONOI, Voronoi tesselations, Daniel Schwen (LANL), "compute voronoi/atom"_compute_voronoi_atom.html, -, Voro++
-XTC, dumps in XTC format, -, "dump"_dump.html, -, -
+"ASPHERE"_#ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, -
+"BODY"_#BODY, body-style particles, -, "body"_body.html, body, -
+"CLASS2"_#CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
+"COLLOID"_#COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, -
+"COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
+"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section_howto 6.25"_Section_howto.html#howto_25, coreshell, -
+"DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
+"FLD"_#FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, -
+"GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu
+"GRANULAR"_#GRANULAR, granular systems, -, "Section_howto 6.6"_Section_howto.html#howto_6, pour, -
+"KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
+"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Edwards (4), "Section_accelerate"_accelerate_kokkos.html, kokkos, lib/kokkos
+"KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
+"MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
+"MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
+"MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
+"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section_howto 6.3"_Section_howto.html#howto_3, peptide, -
+"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, -
+"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
+"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
+"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
+"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax
+"REPLICA"_#REPLICA, multi-replica methods, -, "Section_howto 6.5"_Section_howto.html#howto_5, tad, -
+"RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
+"SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
+"SNAP"_#SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, -
+"SRD"_#SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
+"VORONOI"_#VORONOI, Voronoi tesselations, Daniel Schwen (LANL), "compute voronoi/atom"_compute_voronoi_atom.html, -, Voro++
+"XTC"_#XTC, dumps in XTC format, -, "dump"_dump.html, -, -
 :tb(ea=c)
 
 The "Authors" column lists a name(s) if a specific person is
 responible for creating and maintaining the package.
-More details on
-multiple authors are give below.
 
 (1) The FLD package was created by Amit Kumar and Michael Bybee from
 Jonathan Higdon's group at UIUC.
@@ -104,9 +105,10 @@ and Ellad Tadmor (U Minn).
 (Sandia).  It uses the Kokkos library which was developed by Carter
 Edwards, Christian, and collaborators at Sandia.
 
-The "Doc page" column links to either a portion of the
+The "Doc page" column links to either a sub-section of the
 "Section_howto"_Section_howto.html of the manual, or an input script
-command implemented as part of the package.
+command implemented as part of the package, or to additional
+documentation provided within the package.
 
 The "Example" column is a sub-directory in the examples directory of
 the distribution which has an input script that uses the package.
@@ -118,76 +120,747 @@ 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 the src/package/README or src/package/Makefile.lammps file for
-info on where to download the library.  "Section
-start"_Section_start.html#start_3_3 of the manual also gives details
-on how to build LAMMPS with both kinds of auxiliary libraries.
-
-Except where explained below, all of these packages can be installed,
-and LAMMPS re-built, by issuing these commands from the src dir.
-
-make yes-package
-make machine
-or
-Make.py -p package -a machine :pre
-
-To un-install the package and re-build LAMMPS without it:
-
-make no-package
-make machine
-or
-Make.py -p ^package -a machine :pre
-
-"Package" is the name of the package in lower-case letters,
-e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or
-serial.
-
-:line
-:line
-
-Build instructions for COMPRESS package :h4
+See details on all of this below for individual packages.
 
 :line
 
-Build instructions for GPU package :h4
+ASPHERE package :link(ASPHERE),h4
+
+Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
+triangles.
+
+To install via make or Make.py:
+
+make yes-asphere
+make machine :pre
+
+Make.py -p asphere -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-asphere
+make machine :pre
+
+Make.py -p ^asphere -a machine :pre
+
+Supporting info: examples/ASPHERE, examples/ellipse, Section howto
+6.14, pair gayberne
 
 :line
 
-Build instructions for KIM package :h4
+BODY package :link(BODY),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Supporting info: examples/body
 
 :line
+ 
+CLASS2 package :link(CLASS2),h4
 
-Build instructions for KOKKOS package :h4
+Contents:
+
+To install via make or Make.py:
+
+make yes-class2
+make machine :pre
+
+Make.py -p class2 -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-class2
+make machine :pre
+
+Make.py -p ^class2 -a machine :pre
+
+Supporting info: 
+ 
+:line
+ 
+COLLOID package :link(COLLOID),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-colloid
+make machine :pre
+
+Make.py -p colloid -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-colloid
+make machine :pre
+
+Make.py -p ^colloid -a machine :pre
+
+Supporting info: examples/colloid, examples/srd
+ 
+:line
+ 
+COMPRESS package :link(COMPRESS),h4
+ 
+Contents:
+
+To install via make or Make.py:
+
+make yes-compress
+make machine :pre
+
+Make.py -p compress -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-compress
+make machine :pre
+
+Make.py -p ^compress -a machine :pre
+
+Supporting info: 
 
 :line
+ 
+CORESHELL package :link(CORESHELL),h4
 
-Build instructions for KSPACE package :h4
+Contents:
+
+To install via make or Make.py:
+
+make yes-coreshell
+make machine :pre
+
+Make.py -p coreshell -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-coreshell
+make machine :pre
+
+Make.py -p ^coreshell -a machine :pre
+
+Supporting info: examples/coreshell, Section howto 6.26
 
 :line
+ 
+DIPOLE package :link(DIPOLE),h4
 
-Build instructions for MEAM package :h4
+Contents:
+
+To install via make or Make.py:
+
+make yes-dipole
+make machine :pre
+
+Make.py -p dipole -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-dipole
+make machine :pre
+
+Make.py -p ^dipole -a machine :pre
+
+Supporting info: examples/dipole
+ 
+:line
+ 
+FLD package :link(FLD),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-fld
+make machine :pre
+
+Make.py -p fld -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-fld
+make machine :pre
+
+Make.py -p ^fld -a machine :pre
+
+Supporting info: 
+ 
+:line
+ 
+GPU package :link(GPU),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-gpu
+make machine :pre
+
+Make.py -p gpu -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-gpu
+make machine :pre
+
+Make.py -p ^gpu -a machine :pre
+
+Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER
+ 
+:line
+ 
+GRANULAR package :link(GRANULAR),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-granular
+make machine :pre
+
+Make.py -p granular -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-granular
+make machine :pre
+
+Make.py -p ^granular -a machine :pre
+
+Supporting info: examples/pour, bench/in.chute, Section howto 6.6
+ 
+:line
+ 
+KIM package :link(KIM),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-kim
+make machine :pre
+
+Make.py -p kim -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-kim
+make machine :pre
+
+Make.py -p ^kim -a machine :pre
+
+Supporting info: examples/kim
+ 
+:line
+ 
+KOKKOS package :link(KOKKOS),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-kokkow
+make machine :pre
+
+Make.py -p kokkow -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-kokkow
+make machine :pre
+
+Make.py -p ^kokkow -a machine :pre
+
+Supporting info: 
+
+For the KOKKOS package, you have 3 choices when building.  You can
+build with OMP or Cuda or Phi support.  Phi support uses Xeon Phi
+chips in "native" mode.  This can be done by setting the following
+variables in your Makefile.machine:
+
+for OMP support, set OMP = yes
+for Cuda support, set OMP = yes and CUDA = yes
+for Phi support, set OMP = yes and MIC = yes :ul
+
+These can also be set as additional arguments to the make command, e.g.
+
+make g++ OMP=yes MIC=yes :pre
+
+Building the KOKKOS package with CUDA support requires a Makefile
+machine that uses the NVIDIA "nvcc" compiler, as well as an
+appropriate "arch" setting appropriate to the GPU hardware and NVIDIA
+software you have on your machine.  See
+src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
+Makefile.
+
+Examples: examples/accelerate, bench/FERMI, bench/KEPLER
+ 
+:line
+ 
+KSPACE package :link(KSPACE),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-kspace
+make machine :pre
+
+Make.py -p kspace -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-kspace
+make machine :pre
+
+Make.py -p ^kspace -a machine :pre
+
+Supporting info: 
+
+Examples: examples/peptide, bench/in.rhodo
+
+Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9
 
 :line
+ 
+MANYBODY package :link(MANYBODY),h4
 
-Build instructions for POEMS package :h4
+Contents:
+
+To install via make or Make.py:
+
+make yes-manybody
+make machine :pre
+
+Make.py -p manybody -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-manybody
+make machine :pre
+
+Make.py -p ^manybody -a machine :pre
+
+Supporting info: 
+ 
+Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta
 
 :line
+ 
+MC package :link(MC),h4
 
-Build instructions for PYTHON package :h4
+Contents:
+
+To install via make or Make.py:
+
+make yes-mc
+make machine :pre
+
+Make.py -p mc -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-mc
+make machine :pre
+
+Make.py -p ^mc -a machine :pre
+
+Supporting info: 
+ 
+:line
+ 
+MEAM package :link(MEAM),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-meam
+make machine :pre
+
+Make.py -p meam -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-meam
+make machine :pre
+
+Make.py -p ^meam -a machine :pre
+
+Supporting info: examples/meam
+ 
+:line
+ 
+MISC package :link(MISC),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-misc
+make machine :pre
+
+Make.py -p misc -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-misc
+make machine :pre
+
+Make.py -p ^misc -a machine :pre
+
+Supporting info: examples/misc
+ 
+:line
+ 
+MOLECULE package :link(MOLECULE),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-molecule
+make machine :pre
+
+Make.py -p molecule -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-molecule
+make machine :pre
+
+Make.py -p ^molecule -a machine :pre
+
+Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo, Section howto 6.3
+ 
+:line
+ 
+MPIIO package :link(MPIIO),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-mpiio
+make machine :pre
+
+Make.py -p mpiio -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-mpiio
+make machine :pre
+
+Make.py -p ^mpiio -a machine :pre
+
+Supporting info: 
+ 
+:line
+ 
+OPT package :link(OPT),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-opt
+make machine :pre
+
+Make.py -p opt -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-opt
+make machine :pre
+
+Make.py -p ^opt -a machine :pre
+
+Supporting info: examples/accelerate, bench/KEPLER
+
+For the OPT package, your Makefile.machine needs an additional
+settings for CCFLAGS.
+
+CCFLAGS: add -restrict :ul
 
 :line
+ 
+PERI package :link(PERI),h4
 
-Build instructions for REAX package :h4
+Contents:
+
+To install via make or Make.py:
+
+make yes-peri
+make machine :pre
+
+Make.py -p peri -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-peri
+make machine :pre
+
+Make.py -p ^peri -a machine :pre
+
+Supporting info: examples/peri
+ 
+:line
+ 
+POEMS package :link(POEMS),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-poems
+make machine :pre
+
+Make.py -p poems -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-poems
+make machine :pre
+
+Make.py -p ^poems -a machine :pre
+
+Supporting info: examples/rigid
 
 :line
+ 
+PYTHON package :link(PYTHON),h4
 
-Build instructions for VORONOI package :h4
+Contents:
+
+To install via make or Make.py:
+
+make yes-python
+make machine :pre
+
+Make.py -p python -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-python
+make machine :pre
+
+Make.py -p ^python -a machine :pre
+
+Supporting info: examples/python
+ 
+:line
+ 
+QEQ package :link(QEQ),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-qeq
+make machine :pre
+
+Make.py -p qeq -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-qeq
+make machine :pre
+
+Make.py -p ^qeq -a machine :pre
+
+Supporting info: examples/qeq
+ 
+:line
+ 
+REAX package :link(REAX),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-reax
+make machine :pre
+
+Make.py -p reax -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-reax
+make machine :pre
+
+Make.py -p ^reax -a machine :pre
+
+Supporting info: examples/reax
+ 
+:line
+ 
+REPLICA package :link(REPLICA),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-replica
+make machine :pre
+
+Make.py -p replica -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-replica
+make machine :pre
+
+Make.py -p ^replica -a machine :pre
+
+Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5
 
 :line
+ 
+RIGID package :link(RIGID),h4
 
-Build instructions for XTC package :h4
+Contents:
+
+To install via make or Make.py:
+
+make yes-rigid
+make machine :pre
+
+Make.py -p rigid -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-rigid
+make machine :pre
+
+Make.py -p ^rigid -a machine :pre
+
+Supporting info: examples/ASPHERE, examples/rigid
 
 :line
+ 
+SHOCK package :link(SHOCK),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-shock
+make machine :pre
+
+Make.py -p shock -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-shock
+make machine :pre
+
+Make.py -p ^shock -a machine :pre
+
+Supporting info: examples/hugoniostat, examples/msst
+ 
+:line
+ 
+SNAP package :link(SNAP),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-snap
+make machine :pre
+
+Make.py -p snap -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-snap
+make machine :pre
+
+Make.py -p ^snap -a machine :pre
+
+Supporting info: examples/snap
+ 
+:line
+ 
+SRD package :link(SRD),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-srd
+make machine :pre
+
+Make.py -p srd -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-srd
+make machine :pre
+
+Make.py -p ^srd -a machine :pre
+
+Supporting info: 
+ 
+:line
+ 
+VORONOI package :link(VORONOI),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-voronoi
+make machine :pre
+
+Make.py -p voronoi -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-voronoi
+make machine :pre
+
+Make.py -p ^voronoi -a machine :pre
+
+Supporting info: examples/voronoi
+ 
+:line
+ 
+XTC package :link(XTC),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-xtc
+make machine :pre
+
+Make.py -p xtc -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-xtc
+make machine :pre
+
+Make.py -p ^xtc -a machine :pre
+
+Supporting info: 
+ 
 :line
 
 4.2 User packages :h4,link(pkg_2)
@@ -195,32 +868,33 @@ Build instructions for XTC package :h4
 The current list of user-contributed packages is as follows:
 
 Package, Description, Author(s), Doc page, Example, Pic/movie, Library
-USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
-USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
-USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
-USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
-USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
-USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
-USER-DPD, dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
-USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
-USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
-USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
-USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
-USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
-USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
-USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -
-USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
-USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
-USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -
-USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
-USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
-USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix_qbmsst"_fix_qbmsst.html, qtb, -, -
-USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip
-USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
-USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, -
-USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, -
-USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
-USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, -
+"USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
+"USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
+"USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
+"USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
+"USER-CUDA"_#USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
+"USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
+"USER-DPD"_#USER-DPD, dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
+"USER-DRUDE"_#USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
+"USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
+"USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
+"USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
+"USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
+"USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
+"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -
+"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
+"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
+"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -
+"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
+"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
+"USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix_qbmsst"_fix_qbmsst.html, qtb, -, -
+"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip
+"USER-REAXC"_#USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
+"USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, -
+"USER-SMTBQ"_#USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, -
+"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
+"USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, -
+"USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_compute_custom_vtk.html, -, -, lib/vtk
 :tb(ea=c)
 
 :link(atc,http://lammps.sandia.gov/pictures.html#atc)
@@ -246,15 +920,13 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
 (4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
 Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
 
-(4) The USER-DPD package was created by James Larentzos, Timothy
-Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).
+(5) The USER-DPD package was created by James Larentzos (ARL), Timothy
+Mattox (Engility), and John Brennan (ARL).
 
-If the Library is not listed as lib/package, then it is a third-party
-library not included in the LAMMPS distribution.  See the
-src/package/Makefile.lammps file for info on where to download the
-library from.
+(6) The USER-VTK package was created by Richard Berger (JKU) and
+Daniel Queteschiner (DCS Computing).
 
-The "Doc page" column links to either a portion of the
+The "Doc page" column links to either a sub-section of the
 "Section_howto"_Section_howto.html of the manual, or an input script
 command implemented as part of the package, or to additional
 documentation provided within the package.
@@ -270,35 +942,20 @@ 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 the src/package/Makefile.lammps file for info on where to download
-the library.  "Section start"_Section_start.html#start_3_3 of the
-manual also gives details on how to build LAMMPS with both kinds of
-auxiliary libraries.
-
-Except where explained below, all of these packages can be installed,
-and LAMMPS re-built, by issuing these commands from the src dir.
-
-make yes-user-package
-make machine
-or
-Make.py -p package -a machine :pre
-
-To un-install the package and re-build LAMMPS without it:
-
-make no-user-package
-make machine
-or
-Make.py -p ^package -a machine :pre
-
-"Package" is the name of the package (in this case without the user
-prefix) in lower-case letters, e.g. drude or phonon, and "machine" is
-the build target, e.g. mpi or serial.
+See details on all of this below for individual packages.
 
-:line
 :line
 
-USER-ATC package :h4
+USER-ATC package :link(USER-ATC),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package implements a "fix atc" command which can be used in a
 LAMMPS input script.  This fix can be employed to either do concurrent
 coupling of MD with FE-based physics surrogates or on-the-fly
@@ -320,10 +977,20 @@ sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
 Zimmerman (jzimmer at sandia.gov) at Sandia.  Contact them directly if
 you have questions.
 
+Examples: examples/USER/atc
+
 :line
 
-USER-AWPMD package :h4
+USER-AWPMD package :link(USER-AWPMD),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package contains a LAMMPS implementation of the Antisymmetrized
 Wave Packet Molecular Dynamics (AWPMD) method.
 
@@ -340,10 +1007,30 @@ The person who created this package is Ilya Valuev at the JIHT in
 Russia (valuev at physik.hu-berlin.de).  Contact him directly if you
 have questions.
 
+Examples: examples/USER/awpmd
+
 :line
 
-USER-CG-CMM package :h4
+USER-CG-CMM package :link(USER-CG-CMM),h4
 
+Contents:
+ 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Supporting info: 
+ 
 This package implements 3 commands which can be used in a LAMMPS input
 script:
 
@@ -381,10 +1068,20 @@ simulation systems.
 The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.
 
+Examples: examples/USER/cg-cmm
+
 :line
 
-USER-COLVARS package :h4
+USER-COLVARS package :link(USER-COLVARS),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package implements the "fix colvars" command which can be
 used in a LAMMPS input script.
 
@@ -415,9 +1112,19 @@ beta quality.
 The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.
 
+Examples: examples/USER/colvars
+
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 :line
 
-USER-CUDA package :h4
+USER-CUDA package :link(USER-CUDA),h4
 
 This package provides acceleration of various LAMMPS pair styles, fix
 styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
@@ -439,9 +1146,19 @@ The person who created this package is Christian Trott at the
 University of Technology Ilmenau, Germany (christian.trott at
 tu-ilmenau.de).  Contact him directly if you have questions.
 
+Examples: examples/accelerate, bench/FERMI, bench/KEPLER
+
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 :line
 
-USER-DIFFRACTION package :h4
+USER-DIFFRACTION package :link(USER-DIFFRACTION),h4
 
 This package contains the commands neeed to calculate x-ray and
 electron diffraction intensities based on kinematic diffraction 
@@ -457,9 +1174,29 @@ The person who created this package is Shawn P. Coleman
 (shawn.p.coleman8.ctr at mail.mil) while at the University of 
 Arkansas.  Contact him directly if you have questions.
 
+Examples: examples/USER/diffraction
+
+Contents:
+ 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Supporting info: 
+ 
 :line
 
-USER-DPD package :h4
+USER-DPD package :link(USER-DPD),h4
 
 This package implements the dissipative particle dynamics (DPD) method
 under isothermal, isoenergetic, isobaric and isenthalpic conditions.
@@ -484,10 +1221,34 @@ The people who created this package are James Larentzos
 engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
 Contact them directly if you have questions.
 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Examples: examples/USER/dpd
+
 :line
 
-USER-DRUDE package :h4
+USER-DRUDE package :link(USER-DRUDE),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package implements methods for simulating polarizable systems
 in LAMMPS using thermalized Drude oscillators.
 
@@ -507,10 +1268,36 @@ Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
 Contact him directly if you have questions. Co-authors: Julien Devemy,
 Agilio Padua.
 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Examples: examples/USER/drude
+
+Doc: Section howto 6.27
+
 :line
 
-USER-EFF package :h4
+USER-EFF package :link(USER-EFF),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package contains a LAMMPS implementation of the electron Force
 Field (eFF) currently under development at Caltech, as described in
 A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
@@ -548,10 +1335,34 @@ The person who created this package is Andres Jaramillo-Botero at
 CalTech (ajaramil at wag.caltech.edu).  Contact him directly if you
 have questions.
 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Examples: examples/USER/eff
+
 :line
 
-USER-FEP package :h4
+USER-FEP package :link(USER-FEP),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package provides methods for performing free energy perturbation
 simulations with soft-core pair potentials in LAMMPS.
 
@@ -565,10 +1376,34 @@ The person who created this package is Agilio Padua at Universite
 Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
 Contact him directly if you have questions.
 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Examples: examples/USER/fep
+
 :line
 
-USER-H5MD package :h4
+USER-H5MD package :link(USER-H5MD),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package contains a "dump h5md"_dump_h5md.html command for
 performing a dump of atom properties in HDF5 format.  "HDF5
 files"_HDF5 are binary, portable and self-describing and can be
@@ -586,8 +1421,16 @@ directly if you have questions.
 
 :line
 
-USER-INTEL package :h4
+USER-INTEL package :link(USER-INTEL),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package provides options for performing neighbor list and
 non-bonded force calculations in single, mixed, or double precision
 and also a capability for accelerating calculations with an
@@ -600,10 +1443,39 @@ See this section of the manual to get started:
 The person who created this package is W. Michael Brown at Intel
 (michael.w.brown at intel.com).  Contact him directly if you have questions.
 
+For the USER-INTEL package, you have 2 choices when building.  You can
+build with CPU or Phi support.  The latter uses Xeon Phi chips in
+"offload" mode.  Each of these modes requires additional settings in
+your Makefile.machine for CCFLAGS and LINKFLAGS.
+
+For CPU mode (if using an Intel compiler):
+
+CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
+LINKFLAGS: add -fopenmp :ul
+
+For Phi mode add the following in addition to the CPU mode flags:
+
+CCFLAGS: add -DLMP_INTEL_OFFLOAD and 
+LINKFLAGS: add -offload :ul
+
+And also add this to CCFLAGS:
+
+-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" :pre
+
+Examples: examples/accelerate, bench/KEPLER
+
 :line
 
-USER-LB package :h4
+USER-LB package :link(USER-LB),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package contains a LAMMPS implementation of a background
 Lattice-Boltzmann fluid, which can be used to model MD particles
 influenced by hydrodynamic forces.
@@ -616,10 +1488,34 @@ The people who created this package are Frances Mackay (fmackay at
 uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
 Western Ontario.  Contact them directly if you have questions.
 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Examples: examples/USER/lb
+
 :line
 
-USER-MGPT package :h4
+USER-MGPT package :link(USER-MGPT),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package contains a fast implementation for LAMMPS of
 quantum-based MGPT multi-ion potentials.  The MGPT or model GPT method
 derives from first-principles DFT-based generalized pseudopotential
@@ -644,10 +1540,34 @@ The persons who created the USER-MGPT package are Tomas Oppelstrup
 (oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov)
 Contact them directly if you have any questions.
 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Examples: examples/USER/mgpt
+
 :line
 
-USER-MISC package :h4
+USER-MISC package :link(USER-MISC),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 The files in this package are a potpourri of (mostly) unrelated
 features contributed to LAMMPS by users.  Each feature is a single
 pair of files (*.cpp and *.h).
@@ -667,10 +1587,34 @@ src/USER-MISC/README file.
 You should contact the author directly if you have specific questions
 about the feature or its coding.
 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Examples: examples/USER/misc
+
 :line
 
-USER-MOLFILE package :h4
+USER-MOLFILE package :link(USER-MOLFILE),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package contains a dump molfile command which uses molfile
 plugins that are bundled with the
 "VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
@@ -693,8 +1637,16 @@ The person who created this package is Axel Kohlmeyer at Temple U
 
 :line
 
-USER-OMP package :h4
+USER-OMP package :link(USER-OMP),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package provides OpenMP multi-threading support and
 other optimizations of various LAMMPS pair styles, dihedral
 styles, and fix styles.
@@ -706,9 +1658,17 @@ See this section of the manual to get started:
 The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.
 
+For the USER-OMP package, your Makefile.machine needs additional
+settings for CCFLAGS and LINKFLAGS.
+
+CCFLAGS: add -fopenmp and -restrict
+LINKFLAGS: add -fopenmp :ul
+
+Examples: examples/accelerate, bench/KEPLER
+
 :line
 
-USER-PHONON package :h4
+USER-PHONON package :link(USER-PHONON),h4
 
 This package contains a fix phonon command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
@@ -722,10 +1682,34 @@ The person who created this package is Ling-Ti Kong (konglt at
 sjtu.edu.cn) at Shanghai Jiao Tong University.  Contact him directly
 if you have questions.
 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Examples: examples/USER/phonon
+
 :line
 
-USER-QMMM package :h4
+USER-QMMM package :link(USER-QMMM),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package provides a fix qmmm command which allows LAMMPS to be
 used in a QM/MM simulation, currently only in combination with pw.x
 code from the "Quantum ESPRESSO"_espresso package.
@@ -748,9 +1732,17 @@ The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.
 
 :line
-
-USER-QTB package :h4
-
+ 
+USER-QTB package :link(USER-QTB),h4
+ 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package provides a self-consistent quantum treatment of the
 vibrational modes in a classical molecular dynamics simulation.  By
 coupling the MD simulation to a colored thermostat, it introduces zero
@@ -774,10 +1766,58 @@ The person who created this package is Yuan Shen (sy0302 at
 stanford.edu) at Stanford University.  Contact him directly if you
 have questions.
 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Examples: examples/USER/qtb
+
 :line
 
-USER-REAXC package :h4
+USER-QUIP package :link(USER-QUIP),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
+Examples: examples/USER/quip
+
+:line
+
+USER-REAXC package :link(USER-REAXC),h4
+
+Contents:
+ 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Supporting info: 
+ 
 This package contains a implementation for LAMMPS of the ReaxFF force
 field.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
@@ -809,10 +1849,20 @@ at lbl.gov), while at Purdue University.  Contact him directly, or
 Aidan Thompson at Sandia (athomps at sandia.gov), if you have
 questions.
 
+Examples: examples/reax
+
 :line
 
-USER-SMD package :h4
+USER-SMD package :link(USER-SMD),h4
 
+Contents:
+ 
+To install via make or Make.py:
+ 
+To un-install via make or Make.py:
+ 
+Supporting info: 
+ 
 This package implements smoothed Mach dynamics (SMD) in
 LAMMPS.  Currently, the package has the following features:
 
@@ -840,10 +1890,30 @@ Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
 Germany (georg.ganzenmueller at emi.fhg.de).  Contact him directly if
 you have questions.
 
+Examples: examples/USER/smd
+
 :line
 
-USER-SMTBQ package :h4
+USER-SMTBQ package :link(USER-SMTBQ),h4
 
+Contents:
+ 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Supporting info: 
+ 
 This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
 potential for the description of ionocovalent bonds in oxides.
 
@@ -859,9 +1929,29 @@ Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
 these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr.  Contact
 them directly if you have any questions.
 
+Examples: examples/USER/smtbq
+
 :line
 
-USER-SPH package :h4
+USER-SPH package :link(USER-SPH),h4
+
+Contents:
+ 
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Supporting info: 
 
 This package implements smoothed particle hydrodynamics (SPH) in
 LAMMPS.  Currently, the package has the following features:
@@ -887,3 +1977,43 @@ The person who created this package is Georg Ganzenmuller at the
 Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
 Germany (georg.ganzenmueller at emi.fhg.de).  Contact him directly if
 you have questions.
+
+Examples: examples/USER/sph
+
+:line
+
+USER-TALLY package :link(USER-TALLY),h4
+
+Contents:
+
+To install via make or Make.py:
+
+make yes-body
+make machine :pre
+
+Make.py -p body -a machine :pre
+
+To un-install via make or Make.py:
+
+make no-body
+make machine :pre
+
+Make.py -p ^body -a machine :pre
+
+Supporting info: 
+
+Examples: examples/USER/tally
+
+:line
+
+USER-VTK package :link(USER-VTK),h4
+
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info: 
+
+Examples: examples/USER/tally
diff --git a/doc/_sources/Section_packages.txt b/doc/_sources/Section_packages.txt
index dee6c8632d..8dc9b753d7 100644
--- a/doc/_sources/Section_packages.txt
+++ b/doc/_sources/Section_packages.txt
@@ -1,8 +1,12 @@
 Packages
 ========
 
-This section gives a quick overview of the add-on packages that extend
-LAMMPS functionality.
+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.
 
 | 4.1 :ref:`Standard packages <pkg_1>`
 | 4.2 :ref:`User packages <pkg_2>` 
@@ -33,12 +37,11 @@ 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 sections below give a few more
-details, including instructions for building LAMMPS with the package,
-either via the make command or the Make.py tool described in :ref:`Section 2.4 <start_4>`.
-
+a one-line descriptions of each.  The sub-sections below give more
+details.
 
 
+----------
 
 
 .. _pkg_1:
@@ -46,76 +49,76 @@ either via the make command or the Make.py tool described in :ref:`Section 2.4 <
 Standard packages
 -----------------------------
 
-The current list of standard packages is as follows.
+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.
 
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| Package   | Description                          | Author(s)                              | Doc page                                           | Example   | Library    |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| ASPHERE   | aspherical particles                 | -                                      | :ref:`Section_howto 6.14 <howto_14>`               | ellipse   | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| BODY      | body-style particles                 | -                                      | :doc:`body <body>`                                 | body      | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| CLASS2    | class 2 force fields                 | -                                      | :doc:`pair_style lj/class2 <pair_class2>`          | -         | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| COLLOID   | colloidal particles                  | -                                      | :doc:`atom_style colloid <atom_style>`             | colloid   | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| COMPRESS  | I/O compression                      | Axel Kohlmeyer (Temple U)              | :doc:`dump */gz <dump>`                            | -         | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| CORESHELL | adiabatic core/shell model           | Hendrik Heenen (Technical U of Munich) | :ref:`Section_howto 6.25 <howto_25>`               | coreshell | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| DIPOLE    | point dipole particles               | -                                      | :doc:`pair_style dipole/cut <pair_dipole>`         | dipole    | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| FLD       | Fast Lubrication Dynamics            | Kumar & Bybee & Higdon (1)             | :doc:`pair_style lubricateU <pair_lubricateU>`     | -         | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| GPU       | GPU-enabled styles                   | Mike Brown (ORNL)                      | :doc:`Section accelerate <accelerate_gpu>`         | gpu       | lib/gpu    |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| GRANULAR  | granular systems                     | -                                      | :ref:`Section_howto 6.6 <howto_6>`                 | pour      | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| KIM       | openKIM potentials                   | Smirichinski & Elliot & Tadmor (3)     | :doc:`pair_style kim <pair_kim>`                   | kim       | KIM        |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| KOKKOS    | Kokkos-enabled styles                | Trott & Edwards (4)                    | :doc:`Section_accelerate <accelerate_kokkos>`      | kokkos    | lib/kokkos |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| KSPACE    | long-range Coulombic solvers         | -                                      | :doc:`kspace_style <kspace_style>`                 | peptide   | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| MANYBODY  | many-body potentials                 | -                                      | :doc:`pair_style tersoff <pair_tersoff>`           | shear     | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| MEAM      | modified EAM potential               | Greg Wagner (Sandia)                   | :doc:`pair_style meam <pair_meam>`                 | meam      | lib/meam   |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| MC        | Monte Carlo options                  | -                                      | :doc:`fix gcmc <fix_gcmc>`                         | -         | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| MOLECULE  | molecular system force fields        | -                                      | :ref:`Section_howto 6.3 <howto_3>`                 | peptide   | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| OPT       | optimized pair styles                | Fischer & Richie & Natoli (2)          | :doc:`Section accelerate <accelerate_opt>`         | -         | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| PERI      | Peridynamics models                  | Mike Parks (Sandia)                    | :doc:`pair_style peri <pair_peri>`                 | peri      | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| POEMS     | coupled rigid body motion            | Rudra Mukherjee (JPL)                  | :doc:`fix poems <fix_poems>`                       | rigid     | lib/poems  |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| PYTHON    | embed Python code in an input script | -                                      | :doc:`python <python>`                             | python    | lib/python |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| REAX      | ReaxFF potential                     | Aidan Thompson (Sandia)                | :doc:`pair_style reax <pair_reax>`                 | reax      | lib/reax   |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| REPLICA   | multi-replica methods                | -                                      | :ref:`Section_howto 6.5 <howto_5>`                 | tad       | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| RIGID     | rigid bodies                         | -                                      | :doc:`fix rigid <fix_rigid>`                       | rigid     | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| SHOCK     | shock loading methods                | -                                      | :doc:`fix msst <fix_msst>`                         | -         | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| SNAP      | quantum-fit potential                | Aidan Thompson (Sandia)                | :doc:`pair snap <pair_snap>`                       | snap      | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| SRD       | stochastic rotation dynamics         | -                                      | :doc:`fix srd <fix_srd>`                           | srd       | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| VORONOI   | Voronoi tesselations                 | Daniel Schwen (LANL)                   | :doc:`compute voronoi/atom <compute_voronoi_atom>` | -         | Voro++     |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-| XTC       | dumps in XTC format                  | -                                      | :doc:`dump <dump>`                                 | -         | -          |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
-|           |                                      |                                        |                                                    |           |            |
-+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| Package                      | Description                          | Author(s)                              | Doc page                                           | Example   | Library    |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`ASPHERE <ASPHERE>`     | aspherical particles                 | -                                      | :ref:`Section_howto 6.14 <howto_14>`               | ellipse   | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`BODY <BODY>`           | body-style particles                 | -                                      | :doc:`body <body>`                                 | body      | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`CLASS2 <CLASS2>`       | class 2 force fields                 | -                                      | :doc:`pair_style lj/class2 <pair_class2>`          | -         | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`COLLOID <COLLOID>`     | colloidal particles                  | -                                      | :doc:`atom_style colloid <atom_style>`             | colloid   | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`COMPRESS <COMPRESS>`   | I/O compression                      | Axel Kohlmeyer (Temple U)              | :doc:`dump */gz <dump>`                            | -         | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`CORESHELL <CORESHELL>` | adiabatic core/shell model           | Hendrik Heenen (Technical U of Munich) | :ref:`Section_howto 6.25 <howto_25>`               | coreshell | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`DIPOLE <DIPOLE>`       | point dipole particles               | -                                      | :doc:`pair_style dipole/cut <pair_dipole>`         | dipole    | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`FLD <FLD>`             | Fast Lubrication Dynamics            | Kumar & Bybee & Higdon (1)             | :doc:`pair_style lubricateU <pair_lubricateU>`     | -         | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`GPU <GPU>`             | GPU-enabled styles                   | Mike Brown (ORNL)                      | :doc:`Section accelerate <accelerate_gpu>`         | gpu       | lib/gpu    |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`GRANULAR <GRANULAR>`   | granular systems                     | -                                      | :ref:`Section_howto 6.6 <howto_6>`                 | pour      | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`KIM <KIM>`             | openKIM potentials                   | Smirichinski & Elliot & Tadmor (3)     | :doc:`pair_style kim <pair_kim>`                   | kim       | KIM        |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`KOKKOS <KOKKOS>`       | Kokkos-enabled styles                | Trott & Edwards (4)                    | :doc:`Section_accelerate <accelerate_kokkos>`      | kokkos    | lib/kokkos |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`KSPACE <KSPACE>`       | long-range Coulombic solvers         | -                                      | :doc:`kspace_style <kspace_style>`                 | peptide   | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`MANYBODY <MANYBODY>`   | many-body potentials                 | -                                      | :doc:`pair_style tersoff <pair_tersoff>`           | shear     | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`MEAM <MEAM>`           | modified EAM potential               | Greg Wagner (Sandia)                   | :doc:`pair_style meam <pair_meam>`                 | meam      | lib/meam   |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`MC <MC>`               | Monte Carlo options                  | -                                      | :doc:`fix gcmc <fix_gcmc>`                         | -         | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`MOLECULE <MOLECULE>`   | molecular system force fields        | -                                      | :ref:`Section_howto 6.3 <howto_3>`                 | peptide   | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`OPT <OPT>`             | optimized pair styles                | Fischer & Richie & Natoli (2)          | :doc:`Section accelerate <accelerate_opt>`         | -         | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`PERI <PERI>`           | Peridynamics models                  | Mike Parks (Sandia)                    | :doc:`pair_style peri <pair_peri>`                 | peri      | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`POEMS <POEMS>`         | coupled rigid body motion            | Rudra Mukherjee (JPL)                  | :doc:`fix poems <fix_poems>`                       | rigid     | lib/poems  |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`PYTHON <PYTHON>`       | embed Python code in an input script | -                                      | :doc:`python <python>`                             | python    | lib/python |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`REAX <REAX>`           | ReaxFF potential                     | Aidan Thompson (Sandia)                | :doc:`pair_style reax <pair_reax>`                 | reax      | lib/reax   |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`REPLICA <REPLICA>`     | multi-replica methods                | -                                      | :ref:`Section_howto 6.5 <howto_5>`                 | tad       | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`RIGID <RIGID>`         | rigid bodies                         | -                                      | :doc:`fix rigid <fix_rigid>`                       | rigid     | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`SHOCK <SHOCK>`         | shock loading methods                | -                                      | :doc:`fix msst <fix_msst>`                         | -         | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`SNAP <SNAP>`           | quantum-fit potential                | Aidan Thompson (Sandia)                | :doc:`pair snap <pair_snap>`                       | snap      | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`SRD <SRD>`             | stochastic rotation dynamics         | -                                      | :doc:`fix srd <fix_srd>`                           | srd       | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`VORONOI <VORONOI>`     | Voronoi tesselations                 | Daniel Schwen (LANL)                   | :doc:`compute voronoi/atom <compute_voronoi_atom>` | -         | Voro++     |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+| :ref:`XTC <XTC>`             | dumps in XTC format                  | -                                      | :doc:`dump <dump>`                                 | -         | -          |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
+|                              |                                      |                                        |                                                    |           |            |
++------------------------------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
 
 The "Authors" column lists a name(s) if a specific person is
 responible for creating and maintaining the package.
-More details on
-multiple authors are give below.
 
 (1) The FLD package was created by Amit Kumar and Michael Bybee from
 Jonathan Higdon's group at UIUC.
@@ -131,9 +134,10 @@ and Ellad Tadmor (U Minn).
 (Sandia).  It uses the Kokkos library which was developed by Carter
 Edwards, Christian, and collaborators at Sandia.
 
-The "Doc page" column links to either a portion of the
+The "Doc page" column links to either a sub-section of the
 :doc:`Section_howto <Section_howto>` of the manual, or an input script
-command implemented as part of the package.
+command implemented as part of the package, or to additional
+documentation provided within the package.
 
 The "Example" column is a sub-directory in the examples directory of
 the distribution which has an input script that uses the package.
@@ -145,80 +149,1164 @@ 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 the src/package/README or src/package/Makefile.lammps file for
-info on where to download the library.  :ref:`Section start <start_3_3>` of the manual also gives details
-on how to build LAMMPS with both kinds of auxiliary libraries.
+See details on all of this below for individual packages.
 
-Except where explained below, all of these packages can be installed,
-and LAMMPS re-built, by issuing these commands from the src dir.
+
+----------
+
+
+.. _ASPHERE:
+
+ASPHERE package
+---------------
+
+Contents: Aspherical particle models for ellipsoids, 2d lines, 3d
+triangles.
+
+To install via make or Make.py:
 
 .. parsed-literal::
 
-   make yes-package
+   make yes-asphere
    make machine
-   or
-   Make.py -p package -a machine
-
-To un-install the package and re-build LAMMPS without it:
 
 .. parsed-literal::
 
-   make no-package
+   Make.py -p asphere -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-asphere
    make machine
-   or
-   Make.py -p ^package -a machine
 
-"Package" is the name of the package in lower-case letters,
-e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or
-serial.
+.. parsed-literal::
+
+   Make.py -p ^asphere -a machine
+
+Supporting info: examples/ASPHERE, examples/ellipse, Section howto
+6.14, pair gayberne
 
 
+----------
 
 
+.. _BODY:
 
-Build instructions for COMPRESS package
------------------------------
+BODY package
+------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Supporting info: examples/body
 
 
-Build instructions for GPU package
-------------------------
+----------
 
 
-Build instructions for KIM package
-------------------------
+.. _CLASS2:
+
+CLASS2 package
+--------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-class2
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p class2 -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-class2
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^class2 -a machine
+
+Supporting info:
 
 
-Build instructions for KOKKOS package
----------------------------
+----------
 
 
-Build instructions for KSPACE package
----------------------------
+.. _COLLOID:
+
+COLLOID package
+---------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-colloid
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p colloid -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-colloid
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^colloid -a machine
+
+Supporting info: examples/colloid, examples/srd
 
 
-Build instructions for MEAM package
--------------------------
+----------
 
 
-Build instructions for POEMS package
---------------------------
+.. _COMPRESS:
+
+COMPRESS package
+----------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-compress
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p compress -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-compress
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^compress -a machine
+
+Supporting info:
 
 
-Build instructions for PYTHON package
----------------------------
+----------
 
 
-Build instructions for REAX package
--------------------------
+.. _CORESHELL:
+
+CORESHELL package
+-----------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-coreshell
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p coreshell -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-coreshell
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^coreshell -a machine
+
+Supporting info: examples/coreshell, Section howto 6.26
 
 
-Build instructions for VORONOI package
-----------------------------
+----------
 
 
-Build instructions for XTC package
-------------------------
+.. _DIPOLE:
 
+DIPOLE package
+--------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-dipole
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p dipole -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-dipole
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^dipole -a machine
+
+Supporting info: examples/dipole
+
+
+----------
+
+
+.. _FLD:
+
+FLD package
+-----------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-fld
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p fld -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-fld
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^fld -a machine
+
+Supporting info:
+
+
+----------
+
+
+.. _GPU:
+
+GPU package
+-----------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-gpu
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p gpu -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-gpu
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^gpu -a machine
+
+Supporting info: examples/accelerate, bench/FERMI, bench/KEPLER
+
+
+----------
+
+
+.. _GRANULAR:
+
+GRANULAR package
+----------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-granular
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p granular -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-granular
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^granular -a machine
+
+Supporting info: examples/pour, bench/in.chute, Section howto 6.6
+
+
+----------
+
+
+.. _KIM:
+
+KIM package
+-----------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-kim
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p kim -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-kim
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^kim -a machine
+
+Supporting info: examples/kim
+
+
+----------
+
+
+.. _KOKKOS:
+
+KOKKOS package
+--------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-kokkow
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p kokkow -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-kokkow
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^kokkow -a machine
+
+Supporting info:
+
+For the KOKKOS package, you have 3 choices when building.  You can
+build with OMP or Cuda or Phi support.  Phi support uses Xeon Phi
+chips in "native" mode.  This can be done by setting the following
+variables in your Makefile.machine:
+
+* for OMP support, set OMP = yes
+* for Cuda support, set OMP = yes and CUDA = yes
+* for Phi support, set OMP = yes and MIC = yes
+
+These can also be set as additional arguments to the make command, e.g.
+
+.. parsed-literal::
+
+   make g++ OMP=yes MIC=yes
+
+Building the KOKKOS package with CUDA support requires a Makefile
+machine that uses the NVIDIA "nvcc" compiler, as well as an
+appropriate "arch" setting appropriate to the GPU hardware and NVIDIA
+software you have on your machine.  See
+src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
+Makefile.
+
+Examples: examples/accelerate, bench/FERMI, bench/KEPLER
+
+
+----------
+
+
+.. _KSPACE:
+
+KSPACE package
+--------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-kspace
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p kspace -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-kspace
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^kspace -a machine
+
+Supporting info:
+
+Examples: examples/peptide, bench/in.rhodo
+
+Doc: Section howto 6.7, Section howto 6.8, Section howto 6.9
+
+
+----------
+
+
+.. _MANYBODY:
+
+MANYBODY package
+----------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-manybody
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p manybody -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-manybody
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^manybody -a machine
+
+Supporting info:
+
+Examples: examples/comb, examples/eim, examples/nb3d, examples/vashishta
+
+
+----------
+
+
+.. _MC:
+
+MC package
+----------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-mc
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p mc -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-mc
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^mc -a machine
+
+Supporting info:
+
+
+----------
+
+
+.. _MEAM:
+
+MEAM package
+------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-meam
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p meam -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-meam
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^meam -a machine
+
+Supporting info: examples/meam
+
+
+----------
+
+
+.. _MISC:
+
+MISC package
+------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-misc
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p misc -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-misc
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^misc -a machine
+
+Supporting info: examples/misc
+
+
+----------
+
+
+.. _MOLECULE:
+
+MOLECULE package
+----------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-molecule
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p molecule -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-molecule
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^molecule -a machine
+
+Supporting info: examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo, Section howto 6.3
+
+
+----------
+
+
+.. _MPIIO:
+
+MPIIO package
+-------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-mpiio
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p mpiio -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-mpiio
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^mpiio -a machine
+
+Supporting info:
+
+
+----------
+
+
+.. _OPT:
+
+OPT package
+-----------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-opt
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p opt -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-opt
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^opt -a machine
+
+Supporting info: examples/accelerate, bench/KEPLER
+
+For the OPT package, your Makefile.machine needs an additional
+settings for CCFLAGS.
+
+* CCFLAGS: add -restrict
+
+
+----------
+
+
+.. _PERI:
+
+PERI package
+------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-peri
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p peri -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-peri
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^peri -a machine
+
+Supporting info: examples/peri
+
+
+----------
+
+
+.. _POEMS:
+
+POEMS package
+-------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-poems
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p poems -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-poems
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^poems -a machine
+
+Supporting info: examples/rigid
+
+
+----------
+
+
+.. _PYTHON:
+
+PYTHON package
+--------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-python
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p python -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-python
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^python -a machine
+
+Supporting info: examples/python
+
+
+----------
+
+
+.. _QEQ:
+
+QEQ package
+-----------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-qeq
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p qeq -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-qeq
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^qeq -a machine
+
+Supporting info: examples/qeq
+
+
+----------
+
+
+.. _REAX:
+
+REAX package
+------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-reax
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p reax -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-reax
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^reax -a machine
+
+Supporting info: examples/reax
+
+
+----------
+
+
+.. _REPLICA:
+
+REPLICA package
+---------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-replica
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p replica -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-replica
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^replica -a machine
+
+Supporting info: examples/neb, examples/prd, examples/tad, Section howto 6.5
+
+
+----------
+
+
+.. _RIGID:
+
+RIGID package
+-------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-rigid
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p rigid -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-rigid
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^rigid -a machine
+
+Supporting info: examples/ASPHERE, examples/rigid
+
+
+----------
+
+
+.. _SHOCK:
+
+SHOCK package
+-------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-shock
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p shock -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-shock
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^shock -a machine
+
+Supporting info: examples/hugoniostat, examples/msst
+
+
+----------
+
+
+.. _SNAP:
+
+SNAP package
+------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-snap
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p snap -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-snap
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^snap -a machine
+
+Supporting info: examples/snap
+
+
+----------
+
+
+.. _SRD:
+
+SRD package
+-----------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-srd
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p srd -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-srd
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^srd -a machine
+
+Supporting info:
+
+
+----------
+
+
+.. _VORONOI:
+
+VORONOI package
+---------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-voronoi
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p voronoi -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-voronoi
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^voronoi -a machine
+
+Supporting info: examples/voronoi
+
+
+----------
+
+
+.. _XTC:
+
+XTC package
+-----------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-xtc
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p xtc -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-xtc
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^xtc -a machine
+
+Supporting info:
 
 
 ----------
@@ -231,63 +1319,65 @@ User packages
 
 The current list of user-contributed packages is as follows:
 
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| Package          | Description                                    | Author(s)                                       | Doc page                                                | Example          | Pic/movie            | Library     |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-ATC         | atom-to-continuum coupling                     | Jones & Templeton & Zimmerman (1)               | :doc:`fix atc <fix_atc>`                                | USER/atc         | `atc <atc_>`_        | lib/atc     |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-AWPMD       | wave-packet MD                                 | Ilya Valuev (JIHT)                              | :doc:`pair_style awpmd/cut <pair_awpmd>`                | USER/awpmd       | -                    | lib/awpmd   |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-CG-CMM      | coarse-graining model                          | Axel Kohlmeyer (Temple U)                       | :doc:`pair_style lj/sdk <pair_sdk>`                     | USER/cg-cmm      | `cg <cg_>`_          | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-COLVARS     | collective variables                           | Fiorin & Henin & Kohlmeyer (2)                  | :doc:`fix colvars <fix_colvars>`                        | USER/colvars     | `colvars <colvars>`_ | lib/colvars |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-CUDA        | NVIDIA GPU styles                              | Christian Trott (U Tech Ilmenau)                | :doc:`Section accelerate <accelerate_cuda>`             | USER/cuda        | -                    | lib/cuda    |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-DIFFRACTION | virutal x-ray and electron diffraction         | Shawn Coleman (ARL)                             | :doc:`compute xrd <compute_xrd>`                        | USER/diffraction | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-DPD         | dissipative particle dynamics (DPD)            | Larentzos & Mattox & Brennan (5)                | src/USER-DPD/README                                     | USER/dpd         | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-DRUDE       | Drude oscillators                              | Dequidt & Devemy & Padua (3)                    | :doc:`tutorial <tutorial_drude>`                        | USER/drude       | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-EFF         | electron force field                           | Andres Jaramillo-Botero (Caltech)               | :doc:`pair_style eff/cut <pair_eff>`                    | USER/eff         | `eff <eff_>`_        | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-FEP         | free energy perturbation                       | Agilio Padua (U Blaise Pascal Clermont-Ferrand) | :doc:`compute fep <compute_fep>`                        | USER/fep         | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-H5MD        | dump output via HDF5                           | Pierre de Buyl (KU Leuven)                      | :doc:`dump h5md <dump_h5md>`                            | -                | -                    | lib/h5md    |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-INTEL       | Vectorized CPU and Intel(R) coprocessor styles | W. Michael Brown (Intel)                        | :doc:`Section accelerate <accelerate_intel>`            | examples/intel   | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-LB          | Lattice Boltzmann fluid                        | Colin Denniston (U Western Ontario)             | :doc:`fix lb/fluid <fix_lb_fluid>`                      | USER/lb          | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-MGPT        | fast MGPT multi-ion potentials                 | Tomas Oppelstrup & John Moriarty (LLNL)         | :doc:`pair_style mgpt <pair_mgpt>`                      | USER/mgpt        | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-MISC        | single-file contributions                      | USER-MISC/README                                | USER-MISC/README                                        | -                | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-MOLFILE     | `VMD <VMD_>`_ molfile plug-ins                 | Axel Kohlmeyer (Temple U)                       | :doc:`dump molfile <dump_molfile>`                      | -                | -                    | VMD-MOLFILE |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-OMP         | OpenMP threaded styles                         | Axel Kohlmeyer (Temple U)                       | :doc:`Section accelerate <accelerate_omp>`              | -                | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-PHONON      | phonon dynamical matrix                        | Ling-Ti Kong (Shanghai Jiao Tong U)             | :doc:`fix phonon <fix_phonon>`                          | USER/phonon      | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-QMMM        | QM/MM coupling                                 | Axel Kohlmeyer (Temple U)                       | :doc:`fix qmmm <fix_qmmm>`                              | USER/qmmm        | -                    | lib/qmmm    |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-QTB         | quantum nuclear effects                        | Yuan Shen (Stanford)                            | :doc:`fix qtb <fix_qtb>` :doc:`fix_qbmsst <fix_qbmsst>` | qtb              | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-QUIP        | QUIP/libatoms interface                        | Albert Bartok-Partay (U Cambridge)              | :doc:`pair_style quip <pair_quip>`                      | USER/quip        | -                    | lib/quip    |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-REAXC       | C version of ReaxFF                            | Metin Aktulga (LBNL)                            | :doc:`pair_style reaxc <pair_reax_c>`                   | reax             | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-SMD         | smoothed Mach dynamics                         | Georg Ganzenmuller (EMI)                        | `userguide.pdf <PDF/SMD_LAMMPS_userguide.pdf>`_         | USER/smd         | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-SMTBQ       | Second Moment Tight Binding - QEq potential    | Salles & Maras & Politano & Tetot (4)           | :doc:`pair_style smtbq <pair_smtbq>`                    | USER/smtbq       | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-SPH         | smoothed particle hydrodynamics                | Georg Ganzenmuller (EMI)                        | `userguide.pdf <PDF/SPH_LAMMPS_userguide.pdf>`_         | USER/sph         | `sph <sph_>`_        | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-| USER-TALLY       | Pairwise tallied computes                      | Axel Kohlmeyer (Temple U)                       | :doc:`compute <...>/tally <compute_tally>`              | USER/tally       | -                    | -           |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
-|                  |                                                |                                                 |                                                         |                  |                      |             |
-+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| Package                                    | Description                                    | Author(s)                                       | Doc page                                                | Example          | Pic/movie            | Library     |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-ATC <USER-ATC>`                 | atom-to-continuum coupling                     | Jones & Templeton & Zimmerman (1)               | :doc:`fix atc <fix_atc>`                                | USER/atc         | `atc <atc_>`_        | lib/atc     |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-AWPMD <USER-AWPMD>`             | wave-packet MD                                 | Ilya Valuev (JIHT)                              | :doc:`pair_style awpmd/cut <pair_awpmd>`                | USER/awpmd       | -                    | lib/awpmd   |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-CG-CMM <USER-CG-CMM>`           | coarse-graining model                          | Axel Kohlmeyer (Temple U)                       | :doc:`pair_style lj/sdk <pair_sdk>`                     | USER/cg-cmm      | `cg <cg_>`_          | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-COLVARS <USER-COLVARS>`         | collective variables                           | Fiorin & Henin & Kohlmeyer (2)                  | :doc:`fix colvars <fix_colvars>`                        | USER/colvars     | `colvars <colvars>`_ | lib/colvars |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-CUDA <USER-CUDA>`               | NVIDIA GPU styles                              | Christian Trott (U Tech Ilmenau)                | :doc:`Section accelerate <accelerate_cuda>`             | USER/cuda        | -                    | lib/cuda    |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-DIFFRACTION <USER-DIFFRACTION>` | virutal x-ray and electron diffraction         | Shawn Coleman (ARL)                             | :doc:`compute xrd <compute_xrd>`                        | USER/diffraction | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-DPD <USER-DPD>`                 | dissipative particle dynamics (DPD)            | Larentzos & Mattox & Brennan (5)                | src/USER-DPD/README                                     | USER/dpd         | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-DRUDE <USER-DRUDE>`             | Drude oscillators                              | Dequidt & Devemy & Padua (3)                    | :doc:`tutorial <tutorial_drude>`                        | USER/drude       | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-EFF <USER-EFF>`                 | electron force field                           | Andres Jaramillo-Botero (Caltech)               | :doc:`pair_style eff/cut <pair_eff>`                    | USER/eff         | `eff <eff_>`_        | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-FEP <USER-FEP>`                 | free energy perturbation                       | Agilio Padua (U Blaise Pascal Clermont-Ferrand) | :doc:`compute fep <compute_fep>`                        | USER/fep         | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-H5MD <USER-H5MD>`               | dump output via HDF5                           | Pierre de Buyl (KU Leuven)                      | :doc:`dump h5md <dump_h5md>`                            | -                | -                    | lib/h5md    |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-INTEL <USER-INTEL>`             | Vectorized CPU and Intel(R) coprocessor styles | W. Michael Brown (Intel)                        | :doc:`Section accelerate <accelerate_intel>`            | examples/intel   | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-LB <USER-LB>`                   | Lattice Boltzmann fluid                        | Colin Denniston (U Western Ontario)             | :doc:`fix lb/fluid <fix_lb_fluid>`                      | USER/lb          | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-MGPT <USER-MGPT>`               | fast MGPT multi-ion potentials                 | Tomas Oppelstrup & John Moriarty (LLNL)         | :doc:`pair_style mgpt <pair_mgpt>`                      | USER/mgpt        | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-MISC <USER-MISC>`               | single-file contributions                      | USER-MISC/README                                | USER-MISC/README                                        | -                | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-MOLFILE <USER-MOLFILE>`         | `VMD <VMD_>`_ molfile plug-ins                 | Axel Kohlmeyer (Temple U)                       | :doc:`dump molfile <dump_molfile>`                      | -                | -                    | VMD-MOLFILE |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-OMP <USER-OMP>`                 | OpenMP threaded styles                         | Axel Kohlmeyer (Temple U)                       | :doc:`Section accelerate <accelerate_omp>`              | -                | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-PHONON <USER-PHONON>`           | phonon dynamical matrix                        | Ling-Ti Kong (Shanghai Jiao Tong U)             | :doc:`fix phonon <fix_phonon>`                          | USER/phonon      | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-QMMM <USER-QMMM>`               | QM/MM coupling                                 | Axel Kohlmeyer (Temple U)                       | :doc:`fix qmmm <fix_qmmm>`                              | USER/qmmm        | -                    | lib/qmmm    |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-QTB <USER-QTB>`                 | quantum nuclear effects                        | Yuan Shen (Stanford)                            | :doc:`fix qtb <fix_qtb>` :doc:`fix_qbmsst <fix_qbmsst>` | qtb              | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-QUIP <USER-QUIP>`               | QUIP/libatoms interface                        | Albert Bartok-Partay (U Cambridge)              | :doc:`pair_style quip <pair_quip>`                      | USER/quip        | -                    | lib/quip    |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-REAXC <USER-REAXC>`             | C version of ReaxFF                            | Metin Aktulga (LBNL)                            | :doc:`pair_style reaxc <pair_reax_c>`                   | reax             | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-SMD <USER-SMD>`                 | smoothed Mach dynamics                         | Georg Ganzenmuller (EMI)                        | `userguide.pdf <PDF/SMD_LAMMPS_userguide.pdf>`_         | USER/smd         | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-SMTBQ <USER-SMTBQ>`             | Second Moment Tight Binding - QEq potential    | Salles & Maras & Politano & Tetot (4)           | :doc:`pair_style smtbq <pair_smtbq>`                    | USER/smtbq       | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-SPH <USER-SPH>`                 | smoothed particle hydrodynamics                | Georg Ganzenmuller (EMI)                        | `userguide.pdf <PDF/SPH_LAMMPS_userguide.pdf>`_         | USER/sph         | `sph <sph_>`_        | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-TALLY <USER-TALLY>`             | Pairwise tallied computes                      | Axel Kohlmeyer (Temple U)                       | :doc:`compute <...>/tally <compute_tally>`              | USER/tally       | -                    | -           |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+| :ref:`USER-VTK <USER-VTK>`                 | VTK-style dumps                                | Berger and Queteschiner (6)                     | :doc:`compute custom/vtk <compute_custom_vtk>`          | -                | -                    | lib/vtk     |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
+|                                            |                                                |                                                 |                                                         |                  |                      |             |
++--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
 
 .. _atc: http://lammps.sandia.gov/pictures.html#atc
 
@@ -326,15 +1416,13 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
 (4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
 Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
 
-(4) The USER-DPD package was created by James Larentzos, Timothy
-Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).
+(5) The USER-DPD package was created by James Larentzos (ARL), Timothy
+Mattox (Engility), and John Brennan (ARL).
 
-If the Library is not listed as lib/package, then it is a third-party
-library not included in the LAMMPS distribution.  See the
-src/package/Makefile.lammps file for info on where to download the
-library from.
+(6) The USER-VTK package was created by Richard Berger (JKU) and
+Daniel Queteschiner (DCS Computing).
 
-The "Doc page" column links to either a portion of the
+The "Doc page" column links to either a sub-section of the
 :doc:`Section_howto <Section_howto>` of the manual, or an input script
 command implemented as part of the package, or to additional
 documentation provided within the package.
@@ -350,41 +1438,25 @@ 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 the src/package/Makefile.lammps file for info on where to download
-the library.  :ref:`Section start <start_3_3>` of the
-manual also gives details on how to build LAMMPS with both kinds of
-auxiliary libraries.
-
-Except where explained below, all of these packages can be installed,
-and LAMMPS re-built, by issuing these commands from the src dir.
-
-.. parsed-literal::
-
-   make yes-user-package
-   make machine
-   or
-   Make.py -p package -a machine
-
-To un-install the package and re-build LAMMPS without it:
-
-.. parsed-literal::
-
-   make no-user-package
-   make machine
-   or
-   Make.py -p ^package -a machine
-
-"Package" is the name of the package (in this case without the user
-prefix) in lower-case letters, e.g. drude or phonon, and "machine" is
-the build target, e.g. mpi or serial.
+See details on all of this below for individual packages.
 
 
+----------
 
 
+.. _USER-ATC:
 
 USER-ATC package
 ----------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package implements a "fix atc" command which can be used in a
 LAMMPS input script.  This fix can be employed to either do concurrent
 coupling of MD with FE-based physics surrogates or on-the-fly
@@ -406,13 +1478,25 @@ sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
 Zimmerman (jzimmer at sandia.gov) at Sandia.  Contact them directly if
 you have questions.
 
+Examples: examples/USER/atc
+
 
 ----------
 
 
+.. _USER-AWPMD:
+
 USER-AWPMD package
 ------------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package contains a LAMMPS implementation of the Antisymmetrized
 Wave Packet Molecular Dynamics (AWPMD) method.
 
@@ -429,13 +1513,43 @@ The person who created this package is Ilya Valuev at the JIHT in
 Russia (valuev at physik.hu-berlin.de).  Contact him directly if you
 have questions.
 
+Examples: examples/USER/awpmd
+
 
 ----------
 
 
+.. _USER-CG-CMM:
+
 USER-CG-CMM package
 -------------------
 
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Supporting info:
+
 This package implements 3 commands which can be used in a LAMMPS input
 script:
 
@@ -473,13 +1587,25 @@ simulation systems.
 The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.
 
+Examples: examples/USER/cg-cmm
+
 
 ----------
 
 
+.. _USER-COLVARS:
+
 USER-COLVARS package
 --------------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package implements the "fix colvars" command which can be
 used in a LAMMPS input script.
 
@@ -510,10 +1636,22 @@ beta quality.
 The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.
 
+Examples: examples/USER/colvars
+
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 
 ----------
 
 
+.. _USER-CUDA:
+
 USER-CUDA package
 -----------------
 
@@ -537,10 +1675,22 @@ The person who created this package is Christian Trott at the
 University of Technology Ilmenau, Germany (christian.trott at
 tu-ilmenau.de).  Contact him directly if you have questions.
 
+Examples: examples/accelerate, bench/FERMI, bench/KEPLER
+
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 
 ----------
 
 
+.. _USER-DIFFRACTION:
+
 USER-DIFFRACTION package
 ------------------------
 
@@ -558,10 +1708,40 @@ The person who created this package is Shawn P. Coleman
 (shawn.p.coleman8.ctr at mail.mil) while at the University of 
 Arkansas.  Contact him directly if you have questions.
 
+Examples: examples/USER/diffraction
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Supporting info:
+
 
 ----------
 
 
+.. _USER-DPD:
+
 USER-DPD package
 ----------------
 
@@ -588,13 +1768,47 @@ The people who created this package are James Larentzos
 engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil).
 Contact them directly if you have questions.
 
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Examples: examples/USER/dpd
+
 
 ----------
 
 
+.. _USER-DRUDE:
+
 USER-DRUDE package
 ------------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package implements methods for simulating polarizable systems
 in LAMMPS using thermalized Drude oscillators.
 
@@ -614,13 +1828,49 @@ Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
 Contact him directly if you have questions. Co-authors: Julien Devemy,
 Agilio Padua.
 
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Examples: examples/USER/drude
+
+Doc: Section howto 6.27
+
 
 ----------
 
 
+.. _USER-EFF:
+
 USER-EFF package
 ----------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package contains a LAMMPS implementation of the electron Force
 Field (eFF) currently under development at Caltech, as described in
 A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
@@ -658,13 +1908,47 @@ The person who created this package is Andres Jaramillo-Botero at
 CalTech (ajaramil at wag.caltech.edu).  Contact him directly if you
 have questions.
 
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Examples: examples/USER/eff
+
 
 ----------
 
 
+.. _USER-FEP:
+
 USER-FEP package
 ----------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package provides methods for performing free energy perturbation
 simulations with soft-core pair potentials in LAMMPS.
 
@@ -678,13 +1962,47 @@ The person who created this package is Agilio Padua at Universite
 Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
 Contact him directly if you have questions.
 
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Examples: examples/USER/fep
+
 
 ----------
 
 
+.. _USER-H5MD:
+
 USER-H5MD package
 -----------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package contains a :doc:`dump h5md <dump_h5md>` command for
 performing a dump of atom properties in HDF5 format.  `HDF5 files <HDF5_>`_ are binary, portable and self-describing and can be
 examined and used by a variety of auxiliary tools.  The output HDF5
@@ -705,9 +2023,19 @@ directly if you have questions.
 ----------
 
 
+.. _USER-INTEL:
+
 USER-INTEL package
 ------------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package provides options for performing neighbor list and
 non-bonded force calculations in single, mixed, or double precision
 and also a capability for accelerating calculations with an
@@ -720,13 +2048,46 @@ See this section of the manual to get started:
 The person who created this package is W. Michael Brown at Intel
 (michael.w.brown at intel.com).  Contact him directly if you have questions.
 
+For the USER-INTEL package, you have 2 choices when building.  You can
+build with CPU or Phi support.  The latter uses Xeon Phi chips in
+"offload" mode.  Each of these modes requires additional settings in
+your Makefile.machine for CCFLAGS and LINKFLAGS.
+
+For CPU mode (if using an Intel compiler):
+
+* CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
+* LINKFLAGS: add -fopenmp
+
+For Phi mode add the following in addition to the CPU mode flags:
+
+* CCFLAGS: add -DLMP_INTEL_OFFLOAD and
+* LINKFLAGS: add -offload
+
+And also add this to CCFLAGS:
+
+.. parsed-literal::
+
+   -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
+
+Examples: examples/accelerate, bench/KEPLER
+
 
 ----------
 
 
+.. _USER-LB:
+
 USER-LB package
 ---------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package contains a LAMMPS implementation of a background
 Lattice-Boltzmann fluid, which can be used to model MD particles
 influenced by hydrodynamic forces.
@@ -739,13 +2100,47 @@ The people who created this package are Frances Mackay (fmackay at
 uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
 Western Ontario.  Contact them directly if you have questions.
 
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Examples: examples/USER/lb
+
 
 ----------
 
 
+.. _USER-MGPT:
+
 USER-MGPT package
 -----------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package contains a fast implementation for LAMMPS of
 quantum-based MGPT multi-ion potentials.  The MGPT or model GPT method
 derives from first-principles DFT-based generalized pseudopotential
@@ -770,13 +2165,47 @@ The persons who created the USER-MGPT package are Tomas Oppelstrup
 (oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov)
 Contact them directly if you have any questions.
 
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Examples: examples/USER/mgpt
+
 
 ----------
 
 
+.. _USER-MISC:
+
 USER-MISC package
 -----------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 The files in this package are a potpourri of (mostly) unrelated
 features contributed to LAMMPS by users.  Each feature is a single
 pair of files (*.cpp and *.h).
@@ -796,13 +2225,47 @@ src/USER-MISC/README file.
 You should contact the author directly if you have specific questions
 about the feature or its coding.
 
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Examples: examples/USER/misc
+
 
 ----------
 
 
+.. _USER-MOLFILE:
+
 USER-MOLFILE package
 --------------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package contains a dump molfile command which uses molfile
 plugins that are bundled with the
 `VMD <http://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
@@ -827,9 +2290,19 @@ The person who created this package is Axel Kohlmeyer at Temple U
 ----------
 
 
+.. _USER-OMP:
+
 USER-OMP package
 ----------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package provides OpenMP multi-threading support and
 other optimizations of various LAMMPS pair styles, dihedral
 styles, and fix styles.
@@ -841,10 +2314,20 @@ See this section of the manual to get started:
 The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.
 
+For the USER-OMP package, your Makefile.machine needs additional
+settings for CCFLAGS and LINKFLAGS.
+
+* CCFLAGS: add -fopenmp and -restrict
+* LINKFLAGS: add -fopenmp
+
+Examples: examples/accelerate, bench/KEPLER
+
 
 ----------
 
 
+.. _USER-PHONON:
+
 USER-PHONON package
 -------------------
 
@@ -860,13 +2343,47 @@ The person who created this package is Ling-Ti Kong (konglt at
 sjtu.edu.cn) at Shanghai Jiao Tong University.  Contact him directly
 if you have questions.
 
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Examples: examples/USER/phonon
+
 
 ----------
 
 
+.. _USER-QMMM:
+
 USER-QMMM package
 -----------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package provides a fix qmmm command which allows LAMMPS to be
 used in a QM/MM simulation, currently only in combination with pw.x
 code from the `Quantum ESPRESSO <espresso_>`_ package.
@@ -894,9 +2411,19 @@ The person who created this package is Axel Kohlmeyer at Temple U
 ----------
 
 
+.. _USER-QTB:
+
 USER-QTB package
 ----------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package provides a self-consistent quantum treatment of the
 vibrational modes in a classical molecular dynamics simulation.  By
 coupling the MD simulation to a colored thermostat, it introduces zero
@@ -920,13 +2447,84 @@ The person who created this package is Yuan Shen (sy0302 at
 stanford.edu) at Stanford University.  Contact him directly if you
 have questions.
 
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Examples: examples/USER/qtb
+
 
 ----------
 
 
+.. _USER-QUIP:
+
+USER-QUIP package
+-----------------
+
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
+Examples: examples/USER/quip
+
+
+----------
+
+
+.. _USER-REAXC:
+
 USER-REAXC package
 ------------------
 
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Supporting info:
+
 This package contains a implementation for LAMMPS of the ReaxFF force
 field.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
@@ -958,13 +2556,25 @@ at lbl.gov), while at Purdue University.  Contact him directly, or
 Aidan Thompson at Sandia (athomps at sandia.gov), if you have
 questions.
 
+Examples: examples/reax
+
 
 ----------
 
 
+.. _USER-SMD:
+
 USER-SMD package
 ----------------
 
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
 This package implements smoothed Mach dynamics (SMD) in
 LAMMPS.  Currently, the package has the following features:
 
@@ -992,13 +2602,43 @@ Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
 Germany (georg.ganzenmueller at emi.fhg.de).  Contact him directly if
 you have questions.
 
+Examples: examples/USER/smd
+
 
 ----------
 
 
+.. _USER-SMTBQ:
+
 USER-SMTBQ package
 ------------------
 
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Supporting info:
+
 This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
 potential for the description of ionocovalent bonds in oxides.
 
@@ -1014,13 +2654,43 @@ Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
 these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr.  Contact
 them directly if you have any questions.
 
+Examples: examples/USER/smtbq
+
 
 ----------
 
 
+.. _USER-SPH:
+
 USER-SPH package
 ----------------
 
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Supporting info:
+
 This package implements smoothed particle hydrodynamics (SPH) in
 LAMMPS.  Currently, the package has the following features:
 
@@ -1046,6 +2716,64 @@ Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
 Germany (georg.ganzenmueller at emi.fhg.de).  Contact him directly if
 you have questions.
 
+Examples: examples/USER/sph
+
+
+----------
+
+
+.. _USER-TALLY:
+
+USER-TALLY package
+------------------
+
+Contents:
+
+To install via make or Make.py:
+
+.. parsed-literal::
+
+   make yes-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p body -a machine
+
+To un-install via make or Make.py:
+
+.. parsed-literal::
+
+   make no-body
+   make machine
+
+.. parsed-literal::
+
+   Make.py -p ^body -a machine
+
+Supporting info:
+
+Examples: examples/USER/tally
+
+
+----------
+
+
+.. _USER-VTK:
+
+USER-VTK package
+----------------
+
+Contents:
+
+To install via make or Make.py:
+
+To un-install via make or Make.py:
+
+Supporting info:
+
+Examples: examples/USER/tally
+
 
 .. _lws: http://lammps.sandia.gov
 .. _ld: Manual.html
diff --git a/doc/improper_distance.html b/doc/improper_distance.html
index 07080408f2..95cb0005fe 100644
--- a/doc/improper_distance.html
+++ b/doc/improper_distance.html
@@ -146,7 +146,7 @@ by the other three atoms.  If the 4 atoms in an improper quadruplet
 (listed in the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
 command) are ordered I,J,K,L then the I-atom is assumed to be the
 central atom.</p>
-<img alt="JPG/improper_distance.jpg" class="align-center" src="JPG/improper_distance.jpg" />
+<img alt="_images/improper_distance.jpg" class="align-center" src="_images/improper_distance.jpg" />
 <p>Note that defining 4 atoms to interact in this way, does not mean that
 bonds necessarily exist between I-J, J-K, or K-L, as they would in a
 linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 3eda7ab04f..0423e42e7c 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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t:[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:[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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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:[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:[6,9,385,392,394],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:9,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,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,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:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,197,200,203,209,210,212,216,217,221,223,230,235,236,239,242,244,246,260,261,262,263,264,265,266,267,268,269,270,273,274,277,279,280,281,282,283,287,296,297,304,306,307,317,320,323,325,326,332,336,340,343,344,345,346,347,348,349,351,352,355,356,357,361,362,364,366,370,371,372,374,375,376,377,378,380,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],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:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,194,196,197,200,209,210,215,217,219,221,223,260,285,293,304,317,343,345,360,361,364,370,371,375,381,400,412,447,449,464,474,477,478,481,483,486,497,502,506],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:[1,12,15,156,376,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,198,208,209,210,212,213,214,215,245,260,290,293,295,307,334,361,369,370,371,378,447,473,476,481,485,487,495,502,504],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:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,194,196,197,198,215,220,222,226,241,244,248,250,256,257,286,293,304,317,319,320,327,331,340,343,359,362,370,374,375,376,378,408,413,426,429,456,471,473,474,476,477,478,480,481,482,486,502],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:[9,337,384,423,424],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:[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:[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],framework:[5,238,377,448],franc:9,fraun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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:[5,7,9,82,83,231,247,251,308,429,471,490],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,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52,153,154,156,157,158,159,160,161,162,163,221,247,250,260,261,265,289,291,304,335,361,362,370,402,423,424,429,444,446,494,502],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:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,5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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:[6,84,148,262,266,270,271,279],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:[6,8,42,68,149,263,267,272,280,381],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:[9,11,12],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:[21,43,177,346,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[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,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:[6,29,395],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:[2,6,8,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309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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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