From 5e6dff36e4e12ff93228009abba034607a6d4734 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 1 Sep 2016 02:01:47 -0400
Subject: [PATCH 01/52] add new commands to lammps.book

---
 doc/lammps.book | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/lammps.book b/doc/lammps.book
index f768cdc7d3..f28bb48b56 100644
--- a/doc/lammps.book
+++ b/doc/lammps.book
@@ -148,6 +148,7 @@ fix_bond_create.html
 fix_bond_swap.html
 fix_box_relax.html
 fix_colvars.html
+fix_controller.html
 fix_deform.html
 fix_deposit.html
 fix_drag.html
@@ -162,6 +163,7 @@ fix_eos_table.html
 fix_eos_table_rx.html
 fix_evaporate.html
 fix_external.html
+fix_flow_gauss.html
 fix_freeze.html
 fix_gcmc.html
 fix_gld.html
-- 
GitLab


From fc093a0aab1760e1edf30c968516f9b95f6720d6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 1 Sep 2016 02:07:16 -0400
Subject: [PATCH 02/52] replace :ule,l and :ole,l with :l<br>:ule and
 :l<br>:ole

---
 doc/src/Manual.txt             | 3 ++-
 doc/src/Section_accelerate.txt | 5 +++--
 doc/src/Section_intro.txt      | 3 ++-
 doc/src/Section_perf.txt       | 3 ++-
 doc/src/dihedral_harmonic.txt  | 3 ++-
 doc/src/dump_image.txt         | 3 ++-
 doc/src/suffix.txt             | 3 ++-
 doc/src/tutorial_drude.txt     | 6 ++++--
 8 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index adf6b5c47e..f4ff4542aa 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -47,7 +47,8 @@ it to be part of every patch. :l
 
 There is also a "Developer.pdf"_Developer.pdf file in the doc
 directory, which describes the internal structure and algorithms of
-LAMMPS.  :ule,l
+LAMMPS.  :l
+:ule
 
 LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
 Simulator.
diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt
index 9977853b43..e002cbb5f9 100644
--- a/doc/src/Section_accelerate.txt
+++ b/doc/src/Section_accelerate.txt
@@ -28,8 +28,9 @@ multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
     5.3.2 "USER-INTEL package"_accelerate_intel.html :l
     5.3.3 "KOKKOS package"_accelerate_kokkos.html :l
     5.3.4 "USER-OMP package"_accelerate_omp.html :l
-    5.3.5 "OPT package"_accelerate_opt.html :l,ule
-5.4 "Comparison of various accelerator packages"_#acc_4 :l,ule
+    5.3.5 "OPT package"_accelerate_opt.html :l
+5.4 "Comparison of various accelerator packages"_#acc_4 :l
+:ule
 
 The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
 web site gives performance results for the various accelerator
diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt
index 99751a13ff..089921d45d 100644
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@@ -460,7 +460,8 @@ Site"_lws.  It might be added to the page.  No promises. :l
 
 Cash.  Small denominations, unmarked bills preferred.  Paper sack OK.
 Leave on desk.  VISA also accepted.  Chocolate chip cookies
-encouraged. :ule,l
+encouraged. :l
+:ule
 
 :line
 
diff --git a/doc/src/Section_perf.txt b/doc/src/Section_perf.txt
index d1cafa0bda..fc59dbe1dc 100644
--- a/doc/src/Section_perf.txt
+++ b/doc/src/Section_perf.txt
@@ -36,7 +36,8 @@ sigma cutoff (7 neighbors per atom), NVE integration :l
 Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force
 field with a 10 Angstrom LJ cutoff (440 neighbors per atom),
 particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT
-integration :ole,l
+integration :l
+:ole
 
 Input files for these 5 problems are provided in the bench directory
 of the LAMMPS distribution.  Each has 32,000 atoms and runs for 100
diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt
index ac124ffd48..1de4370a46 100644
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@@ -45,7 +45,8 @@ in some force fields trans = 0 degrees. :ulb,l
 Some force fields reverse the sign convention on {d}. :l
 
 Some force fields let {n} be positive or negative which corresponds to
-{d} = 1 or -1 for the harmonic style. :ule,l
+{d} = 1 or -1 for the harmonic style. :l
+:ule
 
 :line
 
diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt
index 826c3f992b..2f2ca4809b 100644
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@@ -598,7 +598,8 @@ obviously play movie files directly. Similarly for corresponding tools
 bundled with Linux desktop environments.  However, due to licensing
 issues with some file formats, the formats may require installing
 additional libraries, purchasing a license, or may not be
-supported. :ule,l
+supported. :l
+:ule
 
 :line
 
diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt
index 51aead3f37..7450d27baf 100644
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@@ -59,7 +59,8 @@ multi-threading :l
 OPT = a handful of pair styles, cache-optimized for faster CPU
 performance :l
 
-HYBRID = a combination of two packages can be specified (see below) :ule,l
+HYBRID = a combination of two packages can be specified (see below) :l
+:ule
 
 As an example, all of the packages provide a "pair_style
 lj/cut"_pair_lj.html variant, with style names lj/cut/opt, lj/cut/omp,
diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt
index 3ab8afcae3..a6080fef27 100644
--- a/doc/src/tutorial_drude.txt
+++ b/doc/src/tutorial_drude.txt
@@ -67,7 +67,8 @@ for all Drude particles, and to calculate the force constant for each \
 type of core-Drude bond from equation (1). The timesteps used by these \
 authors are between 0.5 and 2 fs, with the degrees of freedom of the \
 Drude oscillators kept cold at 1 K. :l
-In both these force fields hydrogen atoms are treated as non-polarizable. :ule,l
+In both these force fields hydrogen atoms are treated as non-polarizable. :l
+:ule
 
 
 The motion of of the Drude particles can be calculated by minimizing
@@ -104,7 +105,8 @@ due to the short distances, so an atom may capture the Drude particle \
 (shell) of a neighbor, or the induced dipoles within the same molecule \
 may align too much.  To avoid this, damping at short of the \
 interactions between the point charges composing the induced dipole \
-can be done by "Thole"_#Thole functions. :ole,l
+can be done by "Thole"_#Thole functions. :l
+:ole
 
 
 :line
-- 
GitLab


From ab84acc2cdfc77a9018014d22eb7a632d1afa7f2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 1 Sep 2016 02:26:49 -0400
Subject: [PATCH 03/52] synchronize LAMMPS developer list with webpage and move
 ray to "past"

---
 doc/html/Manual.html | 15 ++++++++++-----
 doc/src/Manual.txt   | 17 ++++++++++++-----
 2 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/doc/html/Manual.html b/doc/html/Manual.html
index 5c7ec2f31d..7c9ef3678f 100644
--- a/doc/html/Manual.html
+++ b/doc/html/Manual.html
@@ -166,11 +166,16 @@ run efficiently on parallel computers.  It was developed at Sandia
 National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
 under the terms of the GNU Public License (GPL).</p>
-<p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
-Thompson, and Paul Crozier who can be contacted at
-sjplimp,athomps,pscrozi at sandia.gov.  The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
-<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
-uses.</p>
+<p>The core group of LAMMPS developers is at Sandia National Labs and Temple University:</p>
+<ul class="simple">
+<li><a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, sjplimp at sandia.gov</li>
+<li>Aidan Thompson, athomps at sandia.gov</li>
+<li>Stan Moore, stamoore at sandia.gov</li>
+<li><a class="reference external" href="http://goo.gl/1wk0">Axel Kohlmeyer</a>, akohlmey at gmail.com</li>
+</ul>
+<p>Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia.
+The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at &#8220;<a class="reference external" href="http://lammps.sandia.gov:_http://lammps.sandia.gov">http://lammps.sandia.gov:_http://lammps.sandia.gov</a>
+has more information about the code and its uses.</p>
 <hr class="docutils" />
 <p>The LAMMPS documentation is organized into the following sections.  If
 you find errors or omissions in this manual or have suggestions for
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index f4ff4542aa..6b6760c3dc 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -59,14 +59,21 @@ National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
 under the terms of the GNU Public License (GPL).
 
-The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan
-Thompson, and Paul Crozier who can be contacted at
-sjplimp,athomps,pscrozi at sandia.gov.  The "LAMMPS WWW Site"_lws at
-http://lammps.sandia.gov has more information about the code and its
-uses.
+The core group of LAMMPS developers is at Sandia National Labs and Temple University:
+
+"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l
+Aidan Thompson, athomps at sandia.gov :l
+Stan Moore, stamoore at sandia.gov :l
+"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
+:ulb
+
+Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia.
+The "LAMMPS WWW Site"_lws at "http://lammps.sandia.gov:_http://lammps.sandia.gov
+has more information about the code and its uses.
 
 :link(bug,http://lammps.sandia.gov/bug.html)
 :link(sjp,http://www.sandia.gov/~sjplimp)
+:link(ako,http://goo.gl/1wk0)
 
 :line
 
-- 
GitLab


From 431d1a6dae03584491ae2194717492400d57f185 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 1 Sep 2016 02:37:55 -0400
Subject: [PATCH 04/52] mention stable releases

---
 doc/html/Manual.html | 6 ++++--
 doc/src/Manual.txt   | 7 +++++--
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/doc/html/Manual.html b/doc/html/Manual.html
index 7c9ef3678f..bcee2c07fd 100644
--- a/doc/html/Manual.html
+++ b/doc/html/Manual.html
@@ -141,7 +141,9 @@
 <h2>Version info:</h2>
 <p>The LAMMPS &#8220;version&#8221; is the date when it was released, such as 1 May
 2010. LAMMPS is updated continuously.  Whenever we fix a bug or add a
-feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>.  Each dated copy of LAMMPS contains all the
+feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>. Every 2-4 months one of the incremental releases
+is subjected to more thorough testing and labeled as a <em>stable</em> version.</p>
+<p>Each dated copy of LAMMPS contains all the
 features and bug-fixes up to and including that version date. The
 version date is printed to the screen and logfile every time you run
 LAMMPS. It is also in the file src/version.h and in the LAMMPS
@@ -174,7 +176,7 @@ under the terms of the GNU Public License (GPL).</p>
 <li><a class="reference external" href="http://goo.gl/1wk0">Axel Kohlmeyer</a>, akohlmey at gmail.com</li>
 </ul>
 <p>Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia.
-The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at &#8220;<a class="reference external" href="http://lammps.sandia.gov:_http://lammps.sandia.gov">http://lammps.sandia.gov:_http://lammps.sandia.gov</a>
+The <strong>LAMMPS home page</strong> at <a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a>
 has more information about the code and its uses.</p>
 <hr class="docutils" />
 <p>The LAMMPS documentation is organized into the following sections.  If
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 6b6760c3dc..e53fddef7d 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -28,7 +28,10 @@ Version info: :h4
 The LAMMPS "version" is the date when it was released, such as 1 May
 2010. LAMMPS is updated continuously.  Whenever we fix a bug or add a
 feature, we release it immediately, and post a notice on "this page of
-the WWW site"_bug.  Each dated copy of LAMMPS contains all the
+the WWW site"_bug. Every 2-4 months one of the incremental releases
+is subjected to more thorough testing and labeled as a {stable} version.
+
+Each dated copy of LAMMPS contains all the
 features and bug-fixes up to and including that version date. The
 version date is printed to the screen and logfile every time you run
 LAMMPS. It is also in the file src/version.h and in the LAMMPS
@@ -68,7 +71,7 @@ Stan Moore, stamoore at sandia.gov :l
 :ulb
 
 Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia.
-The "LAMMPS WWW Site"_lws at "http://lammps.sandia.gov:_http://lammps.sandia.gov
+The [LAMMPS home page] at "http://lammps.sandia.gov"_http://lammps.sandia.gov
 has more information about the code and its uses.
 
 :link(bug,http://lammps.sandia.gov/bug.html)
-- 
GitLab


From 4314299be91001cdce758d041476c9507d7b56b3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Sep 2016 14:50:04 -0400
Subject: [PATCH 05/52] harden fix shear/history against use-after-delete and
 from incorrect use of reverse communication

---
 src/fix_shear_history.cpp | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/src/fix_shear_history.cpp b/src/fix_shear_history.cpp
index 2577c16be8..8e8c1bb53b 100644
--- a/src/fix_shear_history.cpp
+++ b/src/fix_shear_history.cpp
@@ -29,13 +29,13 @@
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
-enum{NPARTNER,PERPARTNER};
+enum{DEFAULT,NPARTNER,PERPARTNER};
 
 /* ---------------------------------------------------------------------- */
 
 FixShearHistory::FixShearHistory(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  npartner(NULL), partner(NULL), shearpartner(NULL), ipage(NULL), dpage(NULL)
+  npartner(NULL), partner(NULL), shearpartner(NULL), pair(NULL), ipage(NULL), dpage(NULL)
 {
   if (narg != 4) error->all(FLERR,"Illegal fix SHEAR_HISTORY commmand");
 
@@ -71,6 +71,7 @@ FixShearHistory::FixShearHistory(LAMMPS *lmp, int narg, char **arg) :
   maxtouch = 0;
 
   nlocal_neigh = nall_neigh = 0;
+  commflag = DEFAULT;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -87,6 +88,14 @@ FixShearHistory::~FixShearHistory()
   memory->destroy(npartner);
   memory->sfree(partner);
   memory->sfree(shearpartner);
+
+  // to better detect use-after-delete errors
+
+  pair = NULL;
+  npartner = NULL;
+  partner = NULL;
+  shearpartner = NULL;
+
   delete [] ipage;
   delete [] dpage;
 }
@@ -609,7 +618,7 @@ int FixShearHistory::pack_reverse_comm(int n, int first, double *buf)
         m += dnum;
       }
     }
-  }
+  } else error->all(FLERR,"Unsupported comm mode in shear history");
 
   return m;
 }
@@ -640,7 +649,7 @@ void FixShearHistory::unpack_reverse_comm(int n, int *list, double *buf)
         m += dnum;
       }
     }
-  }
+  } else error->all(FLERR,"Unsupported comm mode in shear history");
 }
 
 /* ----------------------------------------------------------------------
-- 
GitLab


From fc2d878305382c1760c71422f093cc7f49fdb6d6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Sep 2016 21:20:47 -0400
Subject: [PATCH 06/52] update manual introduction to represent current status.
 correct some markup to better pass through sphinx

---
 doc/html/Manual.html             | 12 ++++---
 doc/html/Section_accelerate.html | 54 +++++++++++---------------------
 doc/html/Section_howto.html      |  2 +-
 doc/src/Manual.txt               | 12 ++++---
 doc/src/Section_accelerate.txt   | 31 +++++++++---------
 doc/src/Section_howto.txt        |  8 +++--
 6 files changed, 55 insertions(+), 64 deletions(-)

diff --git a/doc/html/Manual.html b/doc/html/Manual.html
index 84440161a1..2281f57fbd 100644
--- a/doc/html/Manual.html
+++ b/doc/html/Manual.html
@@ -168,16 +168,20 @@ run efficiently on parallel computers.  It was developed at Sandia
 National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
 under the terms of the GNU Public License (GPL).</p>
-<p>The core group of LAMMPS developers is at Sandia National Labs and Temple University:</p>
+<p>The current core group of LAMMPS developers is at Sandia National
+Labs and Temple University:</p>
 <ul class="simple">
 <li><a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, sjplimp at sandia.gov</li>
 <li>Aidan Thompson, athomps at sandia.gov</li>
 <li>Stan Moore, stamoore at sandia.gov</li>
 <li><a class="reference external" href="http://goo.gl/1wk0">Axel Kohlmeyer</a>, akohlmey at gmail.com</li>
 </ul>
-<p>Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia.
-The <strong>LAMMPS home page</strong> at <a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a>
-has more information about the code and its uses.</p>
+<p>Past core developers include Paul Crozier, Ray Shan and Mark Stevens,
+all at Sandia. The <strong>LAMMPS home page</strong> at
+<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information
+about the code and its uses. Interaction with external LAMMPS developers,
+bug reports and feature requests are mainly coordinated through the
+<a class="reference external" href="https://github.com/lammps/lammps">LAMMPS project on GitHub.</a></p>
 <hr class="docutils" />
 <p>The LAMMPS documentation is organized into the following sections.  If
 you find errors or omissions in this manual or have suggestions for
diff --git a/doc/html/Section_accelerate.html b/doc/html/Section_accelerate.html
index 9fcd094369..331ea71448 100644
--- a/doc/html/Section_accelerate.html
+++ b/doc/html/Section_accelerate.html
@@ -346,8 +346,8 @@ package and are explained in the individual accelerator doc pages,
 listed above:</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="26%" />
-<col width="74%" />
+<col width="65%" />
+<col width="35%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>build the accelerator library</td>
@@ -356,40 +356,24 @@ listed above:</p>
 <tr class="row-even"><td>install the accelerator package</td>
 <td>make yes-opt, make yes-user-intel, etc</td>
 </tr>
-</tbody>
-</table>
-<div class="line-block">
-<div class="line">install the accelerator package             | make yes-opt, make yes-user-intel, etc                                                                                           |</div>
-</div>
-<blockquote>
-<div>only for USER-INTEL, KOKKOS, USER-OMP, OPT packages                                                          |</div></blockquote>
-<table border="1" class="docutils">
-<colgroup>
-<col width="26%" />
-<col width="74%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td>re-build LAMMPS</td>
+<tr class="row-odd"><td>add compile/link flags to Makefile.machine in src/MAKE</td>
+<td>only for USER-INTEL, KOKKOS, USER-OMP, OPT packages</td>
+</tr>
+<tr class="row-even"><td>re-build LAMMPS</td>
 <td>make machine</td>
 </tr>
-</tbody>
-</table>
-<div class="line-block">
-<div class="line">re-build LAMMPS                             | make machine                                                                                                                     |</div>
-</div>
-<blockquote>
-<div>mpirun -np 32 lmp_machine -in in.script                                                          |</div></blockquote>
-<blockquote>
-<div>only for KOKKOS package                                   |</div></blockquote>
-<blockquote>
-<div><a class="reference internal" href="package.html"><span class="doc">package</span></a> command, &lt;br&gt;
-only if defaults need to be changed |</div></blockquote>
-<blockquote>
-<div><a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command                                               |</div></blockquote>
-<table border="1" class="docutils">
-<colgroup>
-</colgroup>
-<tbody valign="top">
+<tr class="row-odd"><td>prepare and test a regular LAMMPS simulation</td>
+<td>lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script</td>
+</tr>
+<tr class="row-even"><td>enable specific accelerator support via &#8216;-k on&#8217; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>,</td>
+<td>only needed for KOKKOS package</td>
+</tr>
+<tr class="row-odd"><td>set any needed options for the package via &#8220;-pk&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> or <a class="reference internal" href="package.html"><span class="doc">package</span></a> command,</td>
+<td>only if defaults need to be changed</td>
+</tr>
+<tr class="row-even"><td>use accelerated styles in your input via &#8220;-sf&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command</td>
+<td>lmp_machine -in in.script -sf gpu</td>
+</tr>
 </tbody>
 </table>
 <p>Note that the first 4 steps can be done as a single command, using the
@@ -528,7 +512,7 @@ full 16 lanes to each of the PCIe 2.0 16x slots.</li>
 <li>The GPU package accelerates only pair force, neighbor list, and PPPM
 calculations.</li>
 <li>The GPU package requires neighbor lists to be built on the CPU when using
-exclusion lists or a triclinic simulation box.</li>
+exclusion lists, hybrid pair styles, or a triclinic simulation box.</li>
 </ul>
 </div>
 </div>
diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html
index d29a4556f4..9ea709012e 100644
--- a/doc/html/Section_howto.html
+++ b/doc/html/Section_howto.html
@@ -933,7 +933,7 @@ vectors of a general parallelepiped, where there is no restriction on
 <strong>A</strong> x <strong>B</strong> . <strong>C</strong> &gt; 0.  The equivalent LAMMPS <strong>a</strong>,<strong>b</strong>,<strong>c</strong> are a linear
 rotation of <strong>A</strong>, <strong>B</strong>, and <strong>C</strong> and can be computed as follows:</p>
 <img alt="_images/transform.jpg" class="align-center" src="_images/transform.jpg" />
-<p>where A = <a href="#id3"><span class="problematic" id="id4">|</span></a><strong>A</strong>| indicates the scalar length of <strong>A</strong>. The ^ hat symbol
+<p>where A = <a href="#id3"><span class="problematic" id="id4">|</span></a><strong>A</strong>| indicates the scalar length of <strong>A</strong>. The hat symbol
 indicates the corresponding unit vector. <em>beta</em> and <em>gamma</em> are angles
 between the vectors described below. Note that by construction,
 <strong>a</strong>, <strong>b</strong>, and <strong>c</strong> have strictly positive x, y, and z components, respectively.
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index afbb824fd7..ab82bb0716 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -62,7 +62,8 @@ National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
 under the terms of the GNU Public License (GPL).
 
-The core group of LAMMPS developers is at Sandia National Labs and Temple University:
+The current core group of LAMMPS developers is at Sandia National
+Labs and Temple University:
 
 "Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l
 Aidan Thompson, athomps at sandia.gov :l
@@ -70,9 +71,12 @@ Stan Moore, stamoore at sandia.gov :l
 "Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
 :ulb
 
-Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia.
-The [LAMMPS home page] at "http://lammps.sandia.gov"_http://lammps.sandia.gov
-has more information about the code and its uses.
+Past core developers include Paul Crozier, Ray Shan and Mark Stevens,
+all at Sandia. The [LAMMPS home page] at
+"http://lammps.sandia.gov"_http://lammps.sandia.gov has more information
+about the code and its uses. Interaction with external LAMMPS developers,
+bug reports and feature requests are mainly coordinated through the
+"LAMMPS project on GitHub."_https://github.com/lammps/lammps
 
 :link(bug,http://lammps.sandia.gov/bug.html)
 :link(sjp,http://www.sandia.gov/~sjplimp)
diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt
index e002cbb5f9..9489dee160 100644
--- a/doc/src/Section_accelerate.txt
+++ b/doc/src/Section_accelerate.txt
@@ -206,24 +206,18 @@ build the accelerator library |
   only for GPU package |
 install the accelerator package |
   make yes-opt, make yes-user-intel, etc |
-add compile/link flags to Makefile.machine |
-  in src/MAKE, <br>
+add compile/link flags to Makefile.machine in src/MAKE |
   only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |
 re-build LAMMPS |
   make machine |
-run a LAMMPS simulation |
-  lmp_machine < in.script <br> 
-  mpirun -np 32 lmp_machine -in in.script |
-enable the accelerator package |
-  via "-c on" and "-k on" "command-line switches"_Section_start.html#start_7, <br>
-  only for KOKKOS package |
-set any needed options for the package |
-  via "-pk" "command-line switch"_Section_start.html#start_7 or
-  "package"_package.html command, <br>
+prepare and test a regular LAMMPS simulation |
+  lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
+enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_7, |
+  only needed for KOKKOS package |
+set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_7 or "package"_package.html command, |
   only if defaults need to be changed |
-use accelerated styles in your input script |
-  via "-sf" "command-line switch"_Section_start.html#start_7 or
-  "suffix"_suffix.html command :tb(c=2,s=|)
+use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_7 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
+:tb(c=2,s=|)
 
 Note that the first 4 steps can be done as a single command, using the
 src/Make.py tool.  This tool is discussed in "Section
@@ -303,7 +297,8 @@ overload the available bandwidth for communication. :l
 
 Styles with an "opt" suffix are part of the OPT package and typically
 speed-up the pairwise calculations of your simulation by 5-25% on a
-CPU. :l,ule
+CPU. :l
+:ule
 
 The individual accelerator package doc pages explain:
 
@@ -369,7 +364,8 @@ and the GPU.  Hence its performance is affected if full 16 PCIe lanes
 are not available for each GPU.  In HPC environments this can be the
 case if S2050/70 servers are used, where two devices generally share
 one PCIe 2.0 16x slot.  Also many multi-GPU mainboards do not provide
-full 16 lanes to each of the PCIe 2.0 16x slots. :l,ule
+full 16 lanes to each of the PCIe 2.0 16x slots. :l
+:ule
 
 [Differences between the two packages:]
 
@@ -377,4 +373,5 @@ The GPU package accelerates only pair force, neighbor list, and PPPM
 calculations. :ulb,l
 
 The GPU package requires neighbor lists to be built on the CPU when using
-exclusion lists or a triclinic simulation box. :l,ule
+exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
+:ule
diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index 13798f8f88..f3283c8360 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -695,7 +695,8 @@ MD with quantum forces calculated by a density functional code :l
 
 lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple
 a kinetic Monte Carlo model for grain growth using MD to calculate
-strain induced across grain boundaries :l,ule
+strain induced across grain boundaries :l
+:ule
 
 :link(quest,http://dft.sandia.gov/Quest)
 :link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
@@ -829,7 +830,7 @@ rotation of [A], [B], and [C] and can be computed as follows:
 
 :c,image(Eqs/transform.jpg)
 
-where A = |[A]| indicates the scalar length of [A]. The ^ hat symbol
+where A = |[A]| indicates the scalar length of [A]. The hat symbol
 indicates the corresponding unit vector. {beta} and {gamma} are angles
 between the vectors described below. Note that by construction, 
 [a], [b], and [c] have strictly positive x, y, and z components, respectively.
@@ -1286,7 +1287,8 @@ print"_fix_print.html for single-line output of
 "variables"_variable.html.  Fix print can also output to the
 screen. :l
 
-"Restart files"_restart.html. :l,ule
+"Restart files"_restart.html. :l
+:ule
 
 A simulation prints one set of thermodynamic output and (optionally)
 restart files.  It can generate any number of dump files and fix
-- 
GitLab


From f56c41eec047868f3f3ddfb20d995ce4f654384a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Sep 2016 21:21:28 -0400
Subject: [PATCH 07/52] update with correct error description. sync with
 manual.

---
 src/SHOCK/fix_append_atoms.h | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/SHOCK/fix_append_atoms.h b/src/SHOCK/fix_append_atoms.h
index 1368d164b6..d9885998be 100644
--- a/src/SHOCK/fix_append_atoms.h
+++ b/src/SHOCK/fix_append_atoms.h
@@ -79,8 +79,7 @@ must be of type m (shrink/minimum).
 
 E: Bad fix ID in fix append/atoms command
 
-The value of the fix_id for keyword spatial must start with the suffix
-f_.
+The value of the fix_id for keyword spatial must start with 'f_'.
 
 E: Invalid basis setting in fix append/atoms command
 
-- 
GitLab


From 77620106a43edce0b41849b0edcb0225b4bfa683 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Sep 2016 21:26:50 -0400
Subject: [PATCH 08/52] update colvars library to version 2016-08-05

(cherry picked from commit 459db2eb6b7b5cb93a6479452ca5959a9a73b112)

# Conflicts:
#	doc/src/PDF/colvars-refman-lammps.pdf
---
 lib/colvars/colvar.cpp               | 65 +++++++++++------------
 lib/colvars/colvarbias_abf.cpp       | 78 ++++++++++++++++++++++++----
 lib/colvars/colvarbias_abf.h         |  2 +
 lib/colvars/colvarbias_histogram.cpp |  7 ++-
 lib/colvars/colvargrid.cpp           |  4 +-
 lib/colvars/colvargrid.h             | 44 ++++++++++++++++
 lib/colvars/colvarmodule.h           |  2 +-
 7 files changed, 152 insertions(+), 50 deletions(-)

diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp
index eec49d1fad..344a9a1301 100644
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@@ -1187,40 +1187,6 @@ cvm::real colvar::update_forces_energy()
       f -= fj;
   }
 
-  if (is_enabled(f_cv_extended_Lagrangian)) {
-
-    cvm::real dt = cvm::dt();
-    cvm::real f_ext;
-
-    // the total force is applied to the fictitious mass, while the
-    // atoms only feel the harmonic force
-    // fr: bias force on extended coordinate (without harmonic spring), for output in trajectory
-    // f_ext: total force on extended coordinate (including harmonic spring)
-    // f: - initially, external biasing force
-    //    - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
-    //      (note: wall potential is added to f after this block)
-    fr    = f;
-    f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
-    f     =     (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
-
-    // leapfrog: starting from x_i, f_i, v_(i-1/2)
-    vr  += (0.5 * dt) * f_ext / ext_mass;
-    // Because of leapfrog, kinetic energy at time i is approximate
-    kinetic_energy = 0.5 * ext_mass * vr * vr;
-    potential_energy = 0.5 * ext_force_k * this->dist2(xr, x);
-    // leap to v_(i+1/2)
-    if (is_enabled(f_cv_Langevin)) {
-      vr -= dt * ext_gamma * vr.real_value;
-      vr += dt * ext_sigma * cvm::rand_gaussian() / ext_mass;
-    }
-    vr  += (0.5 * dt) * f_ext / ext_mass;
-    xr  += dt * vr;
-    xr.apply_constraints();
-    if (this->b_periodic) this->wrap(xr);
-  }
-
-
-  // Adding wall potential to "true" colvar force, whether or not an extended coordinate is in use
   if (is_enabled(f_cv_lower_wall) || is_enabled(f_cv_upper_wall)) {
 
     // Wall force
@@ -1257,6 +1223,37 @@ cvm::real colvar::update_forces_energy()
     }
   }
 
+  if (is_enabled(f_cv_extended_Lagrangian)) {
+
+    cvm::real dt = cvm::dt();
+    cvm::real f_ext;
+
+    // the total force is applied to the fictitious mass, while the
+    // atoms only feel the harmonic force
+    // fr: bias force on extended coordinate (without harmonic spring), for output in trajectory
+    // f_ext: total force on extended coordinate (including harmonic spring)
+    // f: - initially, external biasing force
+    //    - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
+    fr    = f;
+    f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
+    f     =     (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
+
+    // leapfrog: starting from x_i, f_i, v_(i-1/2)
+    vr  += (0.5 * dt) * f_ext / ext_mass;
+    // Because of leapfrog, kinetic energy at time i is approximate
+    kinetic_energy = 0.5 * ext_mass * vr * vr;
+    potential_energy = 0.5 * ext_force_k * this->dist2(xr, x);
+    // leap to v_(i+1/2)
+    if (is_enabled(f_cv_Langevin)) {
+      vr -= dt * ext_gamma * vr.real_value;
+      vr += dt * ext_sigma * cvm::rand_gaussian() / ext_mass;
+    }
+    vr  += (0.5 * dt) * f_ext / ext_mass;
+    xr  += dt * vr;
+    xr.apply_constraints();
+    if (this->b_periodic) this->wrap(xr);
+  }
+
   f_accumulated += f;
 
   if (is_enabled(f_cv_fdiff_velocity)) {
diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp
index 648ef9e721..475e4ecef0 100644
--- a/lib/colvars/colvarbias_abf.cpp
+++ b/lib/colvars/colvarbias_abf.cpp
@@ -12,6 +12,7 @@ colvarbias_abf::colvarbias_abf(char const *key)
     samples(NULL),
     z_gradients(NULL),
     z_samples(NULL),
+    czar_gradients(NULL),
     last_gradients(NULL),
     last_samples(NULL)
 {
@@ -144,6 +145,7 @@ int colvarbias_abf::init(std::string const &conf)
     z_gradients->request_actual_value();
     z_gradients->samples = z_samples;
     z_samples->has_parent_data = true;
+    czar_gradients = new colvar_grid_gradient(colvars);
   }
 
   // For shared ABF, we store a second set of grids.
@@ -178,6 +180,21 @@ colvarbias_abf::~colvarbias_abf()
     gradients = NULL;
   }
 
+  if (z_samples) {
+    delete z_samples;
+    z_samples = NULL;
+  }
+
+  if (z_gradients) {
+    delete z_gradients;
+    z_gradients = NULL;
+  }
+
+  if (czar_gradients) {
+    delete czar_gradients;
+    czar_gradients = NULL;
+  }
+
   // shared ABF
   // We used to only do this if "shared" was defined,
   // but now we can call shared externally
@@ -237,7 +254,11 @@ int colvarbias_abf::update()
         z_bin[i] = z_samples->current_bin_scalar(i);
       }
       if ( z_samples->index_ok(z_bin) ) {
-        // Set increment flag to 0 to only increment
+        for (size_t i=0; i<colvars.size(); i++) {
+          // If we are outside the range of xi, the force has not been obtained above
+          // the function is just an accessor, so cheap to call again anyway
+          force[i] = colvars[i]->system_force();
+        }
         z_gradients->acc_force(z_bin, force);
       }
     }
@@ -404,14 +425,10 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
 {
   std::string  samples_out_name = prefix + ".count";
   std::string  gradients_out_name = prefix + ".grad";
-  std::string  z_gradients_out_name = prefix + ".zgrad";
-  std::string  z_samples_out_name = prefix + ".zcount";
   std::ios::openmode mode = (append ? std::ios::app : std::ios::out);
 
   cvm::ofstream samples_os;
   cvm::ofstream gradients_os;
-  cvm::ofstream z_samples_os;
-  cvm::ofstream z_gradients_os;
 
   if (!append) cvm::backup_file(samples_out_name.c_str());
   samples_os.open(samples_out_name.c_str(), mode);
@@ -442,6 +459,14 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
   }
 
   if (z_gradients) {
+    // Write eABF-related quantities
+    std::string  z_samples_out_name = prefix + ".zcount";
+    std::string  z_gradients_out_name = prefix + ".zgrad";
+    std::string  czar_gradients_out_name = prefix + ".czar";
+    cvm::ofstream z_samples_os;
+    cvm::ofstream z_gradients_os;
+    cvm::ofstream czar_gradients_os;
+
     if (!append) cvm::backup_file(z_samples_out_name.c_str());
     z_samples_os.open(z_samples_out_name.c_str(), mode);
     if (!z_samples_os.is_open()) {
@@ -458,6 +483,24 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
     z_gradients->write_multicol(z_gradients_os);
     z_gradients_os.close();
 
+    // Calculate CZAR estimator of gradients
+    for (std::vector<int> ix = czar_gradients->new_index();
+          czar_gradients->index_ok(ix); czar_gradients->incr(ix)) {
+      for (size_t n = 0; n < czar_gradients->multiplicity(); n++) {
+        czar_gradients->set_value(ix, z_gradients->value_output(ix, n)
+            - cvm::temperature() * cvm::boltzmann() * z_samples->log_gradient_finite_diff(ix, n),
+            n);
+      }
+    }
+
+    if (!append) cvm::backup_file(czar_gradients_out_name.c_str());
+    czar_gradients_os.open(czar_gradients_out_name.c_str(), mode);
+    if (!czar_gradients_os.is_open()) {
+      cvm::error("Error opening CZAR gradient file " + czar_gradients_out_name + " for writing");
+    }
+    czar_gradients->write_multicol(czar_gradients_os);
+    czar_gradients_os.close();
+
     if (colvars.size() == 1) {
       std::string  z_pmf_out_name = prefix + ".zpmf";
       if (!append) cvm::backup_file(z_pmf_out_name.c_str());
@@ -468,6 +511,16 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
       z_gradients->write_1D_integral(z_pmf_os);
       z_pmf_os << std::endl;
       z_pmf_os.close();
+
+      std::string  czar_pmf_out_name = prefix + ".czarpmf";
+      if (!append) cvm::backup_file(czar_pmf_out_name.c_str());
+      cvm::ofstream czar_pmf_os;
+      // Do numerical integration and output a PMF
+      czar_pmf_os.open(czar_pmf_out_name.c_str(), mode);
+      if (!czar_pmf_os.is_open())  cvm::error("Error opening CZAR pmf file " + czar_pmf_out_name + " for writing");
+      czar_gradients->write_1D_integral(czar_pmf_os);
+      czar_pmf_os << std::endl;
+      czar_pmf_os.close();
     }
   }
 
@@ -545,24 +598,27 @@ std::ostream & colvarbias_abf::write_restart(std::ostream& os)
 {
 
   std::ios::fmtflags flags(os.flags());
-  os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format
 
   os << "abf {\n"
      << "  configuration {\n"
      << "    name " << this->name << "\n";
   os << "  }\n";
 
-  os << "samples\n";
+  os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format
+  os << "\nsamples\n";
   samples->write_raw(os, 8);
+  os.flags(flags);
 
   os << "\ngradient\n";
-  gradients->write_raw(os);
+  gradients->write_raw(os, 8);
 
   if (z_gradients) {
-    os << "z_samples\n";
+    os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format
+    os << "\nz_samples\n";
     z_samples->write_raw(os, 8);
+    os.flags(flags);
     os << "\nz_gradient\n";
-    z_gradients->write_raw(os);
+    z_gradients->write_raw(os, 8);
   }
 
   os << "}\n\n";
@@ -638,7 +694,7 @@ std::istream & colvarbias_abf::read_restart(std::istream& is)
   }
 
   if (z_gradients) {
-    if ( !(is >> key)   || !(key == "z_samples")) {
+    if ( !(is >> key) || !(key == "z_samples")) {
       cvm::log("Error: in reading restart configuration for ABF bias \""+
                 this->name+"\" at position "+
                 cvm::to_str(is.tellg())+" in stream.\n");
diff --git a/lib/colvars/colvarbias_abf.h b/lib/colvars/colvarbias_abf.h
index 3527eeb63a..18b9a463b5 100644
--- a/lib/colvars/colvarbias_abf.h
+++ b/lib/colvars/colvarbias_abf.h
@@ -60,6 +60,8 @@ private:
   colvar_grid_gradient  *z_gradients;
   /// n-dim grid of number of samples on "real" coordinate for eABF z-based estimator
   colvar_grid_count     *z_samples;
+  /// n-dim grid contining CZAR estimator of "real" free energy gradients
+  colvar_grid_gradient  *czar_gradients;
 
   // shared ABF
   bool     shared_on;
diff --git a/lib/colvars/colvarbias_histogram.cpp b/lib/colvars/colvarbias_histogram.cpp
index 0d52c18361..542dde2017 100644
--- a/lib/colvars/colvarbias_histogram.cpp
+++ b/lib/colvars/colvarbias_histogram.cpp
@@ -75,13 +75,12 @@ int colvarbias_histogram::init(std::string const &conf)
   }
 
   grid = new colvar_grid_scalar();
+  grid->init_from_colvars(colvars);
 
   {
     std::string grid_conf;
     if (key_lookup(conf, "grid", grid_conf)) {
       grid->parse_params(grid_conf);
-    } else {
-      grid->init_from_colvars(colvars);
     }
   }
 
@@ -256,6 +255,9 @@ std::istream & colvarbias_histogram::read_restart(std::istream& is)
 
 std::ostream & colvarbias_histogram::write_restart(std::ostream& os)
 {
+  std::ios::fmtflags flags(os.flags());
+  os.setf(std::ios::fmtflags(0), std::ios::floatfield);
+
   os << "histogram {\n"
      << "  configuration {\n"
      << "    name " << this->name << "\n";
@@ -266,5 +268,6 @@ std::ostream & colvarbias_histogram::write_restart(std::ostream& os)
 
   os << "}\n\n";
 
+  os.flags(flags);
   return os;
 }
diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp
index 3b07a0b3d5..ca2d935e1c 100644
--- a/lib/colvars/colvargrid.cpp
+++ b/lib/colvars/colvargrid.cpp
@@ -35,13 +35,13 @@ colvar_grid_scalar::colvar_grid_scalar(colvar_grid_scalar const &g)
 }
 
 colvar_grid_scalar::colvar_grid_scalar(std::vector<int> const &nx_i)
-  : colvar_grid<cvm::real>(nx_i, 0.0, 1), samples(NULL)
+  : colvar_grid<cvm::real>(nx_i, 0.0, 1), samples(NULL), grad(NULL)
 {
   grad = new cvm::real[nd];
 }
 
 colvar_grid_scalar::colvar_grid_scalar(std::vector<colvar *> &colvars, bool margin)
-  : colvar_grid<cvm::real>(colvars, 0.0, 1, margin), samples(NULL)
+  : colvar_grid<cvm::real>(colvars, 0.0, 1, margin), samples(NULL), grad(NULL)
 {
   grad = new cvm::real[nd];
 }
diff --git a/lib/colvars/colvargrid.h b/lib/colvars/colvargrid.h
index e00405d278..473348d3e7 100644
--- a/lib/colvars/colvargrid.h
+++ b/lib/colvars/colvargrid.h
@@ -1160,6 +1160,50 @@ public:
     }
     has_data = true;
   }
+
+  /// \brief Return the log-gradient from finite differences
+  /// on the *same* grid for dimension n
+  inline const cvm::real log_gradient_finite_diff( const std::vector<int> &ix0,
+    int n = 0)
+  {
+    cvm::real A0, A1;
+    std::vector<int> ix;
+
+    // factor for mesh width, 2.0 for central finite difference
+    // but only 1.0 on edges for non-PBC coordinates
+    cvm::real factor;
+
+    if (periodic[n]) {
+      factor = 2.;
+      ix = ix0;
+      ix[n]--; wrap(ix);
+      A0 = data[address(ix)];
+      ix = ix0;
+      ix[n]++; wrap(ix);
+      A1 = data[address(ix)];
+    } else {
+      factor = 0.;
+      ix = ix0;
+      if (ix[n] > 0) { // not left edge
+        ix[n]--;
+        factor += 1.;
+      }
+      A0 = data[address(ix)];
+      ix = ix0;
+      if (ix[n]+1 < nx[n]) { // not right edge
+        ix[n]++;
+        factor += 1.;
+      }
+      A1 = data[address(ix)];
+    }
+    if (A0 == 0 || A1 == 0) {
+      // can't handle empty bins
+      return 0.;
+    } else {
+      return (std::log((cvm::real)A1) - std::log((cvm::real)A0))
+        / (widths[n] * factor);
+    }
+  }
 };
 
 
diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h
index e6d21af85b..b8fc01be9e 100644
--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@@ -4,7 +4,7 @@
 #define COLVARMODULE_H
 
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2016-08-01"
+#define COLVARS_VERSION "2016-08-05"
 #endif
 
 #ifndef COLVARS_DEBUG
-- 
GitLab


From ec2a6b9f0de31700481738b7de1af93d8f97d992 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Sep 2016 21:27:41 -0400
Subject: [PATCH 09/52] update colvars to version 2016-08-10

(cherry picked from commit f2ddf828e4855f7626f129a00f30be2191a28f16)
---
 doc/src/PDF/colvars-refman-lammps.pdf | Bin 533229 -> 533480 bytes
 lib/colvars/colvar.cpp                | 178 +++++++++-----------------
 lib/colvars/colvaratoms.cpp           |  12 +-
 lib/colvars/colvarbias.cpp            |   2 +-
 lib/colvars/colvarbias_histogram.cpp  |   4 +-
 lib/colvars/colvarcomp.cpp            |   6 +-
 lib/colvars/colvardeps.cpp            |   8 +-
 lib/colvars/colvardeps.h              |  19 ++-
 lib/colvars/colvarmodule.cpp          |  65 ++++------
 lib/colvars/colvarmodule.h            |  27 ++--
 lib/colvars/colvarparse.cpp           |  99 ++++++++++----
 lib/colvars/colvarparse.h             |   6 +
 lib/colvars/colvarproxy.h             |  10 +-
 lib/colvars/colvarscript.cpp          |  27 ++--
 14 files changed, 222 insertions(+), 241 deletions(-)

diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf
index d1349fd42439be910d3177c5453da5a6e45ca655..0dd82d47947628d5c55c0481499dcc8b79a4598d 100644
GIT binary patch
delta 41952
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diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp
index 344a9a1301..49f0285091 100644
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@@ -43,7 +43,8 @@ colvar::colvar(std::string const &conf)
   kinetic_energy = 0.0;
   potential_energy = 0.0;
 
-  cvm::combine_errors(error_code, init_components(conf));
+  error_code |= init_components(conf);
+  if (error_code != COLVARS_OK) return;
 
   size_t i;
 
@@ -492,110 +493,44 @@ int colvar::init_components(std::string const &conf)
 {
   int error_code = COLVARS_OK;
 
-  cvm::combine_errors(error_code,
-                      init_components_type<distance>(conf,
-                                                     "distance", "distance"));
-  cvm::combine_errors(error_code,
-                      init_components_type<distance_vec>(conf,
-                                                         "distance vector", "distanceVec"));
-  cvm::combine_errors(error_code,
-                      init_components_type<cartesian>(conf,
-                                                      "Cartesian coordinates", "cartesian"));
-  cvm::combine_errors(error_code,
-                      init_components_type<distance_dir>(conf,
-                                                         "distance vector "
-                                                         "direction", "distanceDir"));
-  cvm::combine_errors(error_code,
-                      init_components_type<distance_z>(conf,
-                                                       "distance projection "
-                                                       "on an axis", "distanceZ"));
-  cvm::combine_errors(error_code,
-                      init_components_type<distance_xy>(conf,
-                                                        "distance projection "
-                                                        "on a plane", "distanceXY"));
-  cvm::combine_errors(error_code,
-                      init_components_type<distance_inv>(conf,
-                                                         "average distance "
-                                                         "weighted by inverse power",
-                                                         "distanceInv"));
-  cvm::combine_errors(error_code,
-                      init_components_type<distance_pairs>(conf,
-                                                           "N1xN2-long vector "
-                                                           "of pairwise distances",
-                                                           "distancePairs"));
-
-  cvm::combine_errors(error_code,
-                      init_components_type<coordnum>(conf,
-                                                     "coordination "
-                                                     "number", "coordNum"));
-  cvm::combine_errors(error_code,
-                      init_components_type<selfcoordnum>(conf,
-                                                         "self-coordination "
-                                                         "number", "selfCoordNum"));
-
-  cvm::combine_errors(error_code,
-                      init_components_type<angle>(conf,
-                                                  "angle", "angle"));
-  cvm::combine_errors(error_code,
-                      init_components_type<dipole_angle>(conf,
-                                                         "dipole angle", "dipoleAngle"));
-  cvm::combine_errors(error_code,
-                      init_components_type<dihedral>(conf,
-                                                     "dihedral", "dihedral"));
-
-  cvm::combine_errors(error_code,
-                      init_components_type<h_bond>(conf,
-                                                   "hydrogen bond", "hBond"));
-
-  //    cvm::combine_errors(error_code, init_components_type<alpha_dihedrals>(conf,  "alpha helix", "alphaDihedrals"));
-  cvm::combine_errors(error_code,
-                      init_components_type<alpha_angles>(conf,
-                                                         "alpha helix", "alpha"));
-
-  cvm::combine_errors(error_code,
-                      init_components_type<dihedPC>(conf,
-                                                    "dihedral "
-                                                    "principal component", "dihedralPC"));
-
-  cvm::combine_errors(error_code,
-                      init_components_type<orientation>(conf,
-                                                        "orientation", "orientation"));
-  cvm::combine_errors(error_code,
-                      init_components_type<orientation_angle>(conf,
-                                                              "orientation "
-                                                              "angle", "orientationAngle"));
-  cvm::combine_errors(error_code,
-                      init_components_type<orientation_proj>(conf,
-                                                             "orientation "
-                                                             "projection", "orientationProj"));
-  cvm::combine_errors(error_code,
-                      init_components_type<tilt>(conf,
-                                                 "tilt", "tilt"));
-  cvm::combine_errors(error_code,
-                      init_components_type<spin_angle>(conf,
-                                                       "spin angle", "spinAngle"));
-
-  cvm::combine_errors(error_code,
-                      init_components_type<rmsd>(conf,
-                                                 "RMSD", "rmsd"));
-
-  //  cvm::combine_errors(error_code, init_components_type <logmsd>(conf,"logarithm of MSD", "logmsd"));
-
-  cvm::combine_errors(error_code,
-                      init_components_type<gyration>(conf,
-                                                     "radius of "
-                                                     "gyration", "gyration"));
-  cvm::combine_errors(error_code,
-                      init_components_type<inertia>(conf,
-                                                    "moment of "
-                                                    "inertia", "inertia"));
-  cvm::combine_errors(error_code,
-                      init_components_type<inertia_z>(conf,
-                                                      "moment of inertia around an axis",
-                                                      "inertiaZ"));
-  cvm::combine_errors(error_code,
-                      init_components_type<eigenvector>(conf,
-                                                        "eigenvector", "eigenvector"));
+  error_code |= init_components_type<distance>(conf, "distance", "distance");
+  error_code |= init_components_type<distance_vec>(conf, "distance vector", "distanceVec");
+  error_code |= init_components_type<cartesian>(conf, "Cartesian coordinates", "cartesian");
+  error_code |= init_components_type<distance_dir>(conf, "distance vector "
+    "direction", "distanceDir");
+  error_code |= init_components_type<distance_z>(conf, "distance projection "
+    "on an axis", "distanceZ");
+  error_code |= init_components_type<distance_xy>(conf, "distance projection "
+    "on a plane", "distanceXY");
+  error_code |= init_components_type<distance_inv>(conf, "average distance "
+    "weighted by inverse power", "distanceInv");
+  error_code |= init_components_type<distance_pairs>(conf, "N1xN2-long vector "
+    "of pairwise distances", "distancePairs");
+  error_code |= init_components_type<coordnum>(conf, "coordination "
+    "number", "coordNum");
+  error_code |= init_components_type<selfcoordnum>(conf, "self-coordination "
+    "number", "selfCoordNum");
+  error_code |= init_components_type<angle>(conf, "angle", "angle");
+  error_code |= init_components_type<dipole_angle>(conf, "dipole angle", "dipoleAngle");
+  error_code |= init_components_type<dihedral>(conf, "dihedral", "dihedral");
+  error_code |= init_components_type<h_bond>(conf, "hydrogen bond", "hBond");
+  error_code |= init_components_type<alpha_angles>(conf, "alpha helix", "alpha");
+  error_code |= init_components_type<dihedPC>(conf, "dihedral "
+    "principal component", "dihedralPC");
+  error_code |= init_components_type<orientation>(conf, "orientation", "orientation");
+  error_code |= init_components_type<orientation_angle>(conf, "orientation "
+    "angle", "orientationAngle");
+  error_code |= init_components_type<orientation_proj>(conf, "orientation "
+    "projection", "orientationProj");
+  error_code |= init_components_type<tilt>(conf, "tilt", "tilt");
+  error_code |= init_components_type<spin_angle>(conf, "spin angle", "spinAngle");
+  error_code |= init_components_type<rmsd>(conf, "RMSD", "rmsd");
+  error_code |= init_components_type<gyration>(conf, "radius of "
+    "gyration", "gyration");
+  error_code |= init_components_type<inertia>(conf, "moment of "
+    "inertia", "inertia");
+  error_code |= init_components_type<inertia_z>(conf, "moment of inertia around an axis", "inertiaZ");
+  error_code |= init_components_type<eigenvector>(conf, "eigenvector", "eigenvector");
 
   if (!cvcs.size() || (error_code != COLVARS_OK)) {
     cvm::error("Error: no valid components were provided "
@@ -732,7 +667,7 @@ int colvar::parse_analysis(std::string const &conf)
     } else {
       cvm::log("Unknown type of correlation function, \""+
                         acf_type_str+"\".\n");
-      cvm::set_error_bit(INPUT_ERROR);
+      cvm::set_error_bits(INPUT_ERROR);
     }
 
     get_keyval(conf, "corrFuncOffset", acf_offset, 0);
@@ -803,9 +738,11 @@ int colvar::calc()
   // Note: if anything is added here, it should be added also in the SMP block of calc_colvars()
   int error_code = COLVARS_OK;
   if (is_enabled(f_cv_active)) {
-    cvm::combine_errors(error_code, update_cvc_flags());
-    cvm::combine_errors(error_code, calc_cvcs());
-    cvm::combine_errors(error_code, collect_cvc_data());
+    error_code |= update_cvc_flags();
+    if (error_code != COLVARS_OK) return error_code;
+    error_code |= calc_cvcs();
+    if (error_code != COLVARS_OK) return error_code;
+    error_code |= collect_cvc_data();
   }
   return error_code;
 }
@@ -818,15 +755,15 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
     cvm::log("Calculating colvar \""+this->name+"\", components "+
              cvm::to_str(first_cvc)+" through "+cvm::to_str(first_cvc+num_cvcs)+".\n");
 
-  cvm::combine_errors(error_code, check_cvc_range(first_cvc, num_cvcs));
+  error_code |= check_cvc_range(first_cvc, num_cvcs);
   if (error_code != COLVARS_OK) {
     return error_code;
   }
 
-  cvm::combine_errors(error_code, calc_cvc_values(first_cvc, num_cvcs));
-  cvm::combine_errors(error_code, calc_cvc_gradients(first_cvc, num_cvcs));
-  cvm::combine_errors(error_code, calc_cvc_sys_forces(first_cvc, num_cvcs));
-  cvm::combine_errors(error_code, calc_cvc_Jacobians(first_cvc, num_cvcs));
+  error_code |= calc_cvc_values(first_cvc, num_cvcs);
+  error_code |= calc_cvc_gradients(first_cvc, num_cvcs);
+  error_code |= calc_cvc_sys_forces(first_cvc, num_cvcs);
+  error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);
 
   if (cvm::debug())
     cvm::log("Done calculating colvar \""+this->name+"\".\n");
@@ -842,12 +779,11 @@ int colvar::collect_cvc_data()
 
   int error_code = COLVARS_OK;
 
-  cvm::combine_errors(error_code, collect_cvc_values());
-  cvm::combine_errors(error_code, collect_cvc_gradients());
-  cvm::combine_errors(error_code, collect_cvc_sys_forces());
-  cvm::combine_errors(error_code, collect_cvc_Jacobians());
-
-  cvm::combine_errors(error_code, calc_colvar_properties());
+  error_code |= collect_cvc_values();
+  error_code |= collect_cvc_gradients();
+  error_code |= collect_cvc_sys_forces();
+  error_code |= collect_cvc_Jacobians();
+  error_code |= calc_colvar_properties();
 
   if (cvm::debug())
     cvm::log("Done calculating colvar \""+this->name+"\"'s properties.\n");
@@ -1374,7 +1310,7 @@ bool colvar::periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) c
   if ( (!is_enabled(f_cv_lower_boundary)) || (!is_enabled(f_cv_upper_boundary)) ) {
     cvm::log("Error: checking periodicity for collective variable \""+this->name+"\" "
                     "requires lower and upper boundaries to be defined.\n");
-    cvm::set_error_bit(INPUT_ERROR);
+    cvm::set_error_bits(INPUT_ERROR);
   }
 
   if (period > 0.0) {
diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp
index b77576e896..786a72821f 100644
--- a/lib/colvars/colvaratoms.cpp
+++ b/lib/colvars/colvaratoms.cpp
@@ -297,7 +297,7 @@ int cvm::atom_group::parse(std::string const &conf)
     std::string numbers_conf = "";
     size_t pos = 0;
     while (key_lookup(group_conf, "atomNumbers", numbers_conf, pos)) {
-      cvm::combine_errors(parse_error, add_atom_numbers(numbers_conf));
+      parse_error |= add_atom_numbers(numbers_conf);
       numbers_conf = "";
     }
   }
@@ -306,7 +306,7 @@ int cvm::atom_group::parse(std::string const &conf)
     std::string index_group_name;
     if (get_keyval(group_conf, "indexGroup", index_group_name)) {
       // use an index group from the index file read globally
-      cvm::combine_errors(parse_error, add_index_group(index_group_name));
+      parse_error |= add_index_group(index_group_name);
     }
   }
 
@@ -315,7 +315,7 @@ int cvm::atom_group::parse(std::string const &conf)
     size_t pos = 0;
     while (key_lookup(group_conf, "atomNumbersRange",
                       range_conf, pos)) {
-      cvm::combine_errors(parse_error, add_atom_numbers_range(range_conf));
+      parse_error |= add_atom_numbers_range(range_conf);
       range_conf = "";
     }
   }
@@ -342,8 +342,8 @@ int cvm::atom_group::parse(std::string const &conf)
         cvm::error("Error: more instances of \"atomNameResidueRange\" than "
                    "values of \"psfSegID\".\n", INPUT_ERROR);
       } else {
-        cvm::combine_errors(parse_error, add_atom_name_residue_range(psf_segids.size() ?
-        *psii : std::string(""), range_conf));
+        parse_error |= add_atom_name_residue_range(psf_segids.size() ?
+          *psii : std::string(""), range_conf);
         if (psf_segids.size()) psii++;
       }
       range_conf = "";
@@ -407,7 +407,7 @@ int cvm::atom_group::parse(std::string const &conf)
     index = (cvm::proxy)->init_atom_group(atoms_ids);
   }
 
-  cvm::combine_errors(parse_error, parse_fitting_options(group_conf));
+  parse_error |= parse_fitting_options(group_conf);
 
   // TODO move this to colvarparse object
   check_keywords(group_conf, key.c_str());
diff --git a/lib/colvars/colvarbias.cpp b/lib/colvars/colvarbias.cpp
index 90c552ac0b..073cfc3965 100644
--- a/lib/colvars/colvarbias.cpp
+++ b/lib/colvars/colvarbias.cpp
@@ -203,7 +203,7 @@ cvm::real colvarbias::energy_difference(std::string const &conf)
 }
 
 
-// So far, these are only implemented in colvarsbias_abf
+// So far, these are only implemented in colvarbias_abf
 int colvarbias::bin_num()
 {
   cvm::error("Error: bin_num() not implemented.\n");
diff --git a/lib/colvars/colvarbias_histogram.cpp b/lib/colvars/colvarbias_histogram.cpp
index 542dde2017..15ad5936aa 100644
--- a/lib/colvars/colvarbias_histogram.cpp
+++ b/lib/colvars/colvarbias_histogram.cpp
@@ -104,7 +104,7 @@ int colvarbias_histogram::update()
 {
   int error_code = COLVARS_OK;
   // update base class
-  cvm::combine_errors(error_code, colvarbias::update());
+  error_code |= colvarbias::update();
 
   if (cvm::debug()) {
     cvm::log("Updating histogram bias " + this->name);
@@ -157,7 +157,7 @@ int colvarbias_histogram::update()
     write_output_files();
   }
 
-  cvm::combine_errors(error_code, cvm::get_error());
+  error_code |= cvm::get_error();
   return error_code;
 }
 
diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp
index eec43d0963..89973516be 100644
--- a/lib/colvars/colvarcomp.cpp
+++ b/lib/colvars/colvarcomp.cpp
@@ -43,11 +43,7 @@ colvar::cvc::cvc(std::string const &conf)
 
   // All cvcs implement this
   provide(f_cvc_debug_gradient);
-  {
-    bool b_debug_gradient;
-    get_keyval(conf, "debugGradients", b_debug_gradient, false, parse_silent);
-    if (b_debug_gradient) enable(f_cvc_debug_gradient);
-  }
+  get_keyval(conf, "debugGradients", set_feature(f_cvc_debug_gradient), false, parse_silent);
 
   // Attempt scalable calculations when in parallel? (By default yes, if available)
   get_keyval(conf, "scalable", b_try_scalable, true);
diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp
index eabb67de4c..2801abb191 100644
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@@ -215,7 +215,7 @@ void cvm::deps::init_cvb_requires() {
   // Initialize feature_states for each instance
   feature_states.reserve(f_cvb_ntot);
   for (i = 0; i < f_cvb_ntot; i++) {
-    feature_states.push_back(new feature_state(true, false));
+    feature_states.push_back(new feature_state(this, feature_states.size(), true, false));
     // Most features are available, so we set them so
     // and list exceptions below
   }
@@ -319,7 +319,7 @@ void cvm::deps::init_cv_requires() {
   // Initialize feature_states for each instance
   feature_states.reserve(f_cv_ntot);
   for (i = 0; i < f_cv_ntot; i++) {
-    feature_states.push_back(new feature_state(true, false));
+    feature_states.push_back(new feature_state(this, feature_states.size(), true, false));
     // Most features are available, so we set them so
     // and list exceptions below
    }
@@ -385,7 +385,7 @@ void cvm::deps::init_cvc_requires() {
   // default as unavailable, not enabled
   feature_states.reserve(f_cvc_ntot);
   for (i = 0; i < cvm::deps::f_cvc_ntot; i++) {
-    feature_states.push_back(new feature_state(false, false));
+    feature_states.push_back(new feature_state(this, feature_states.size(), false, false));
   }
 
   // Features that are implemented by all cvcs by default
@@ -429,7 +429,7 @@ void cvm::deps::init_ag_requires() {
   // default as unavailable, not enabled
   feature_states.reserve(f_ag_ntot);
   for (i = 0; i < cvm::deps::f_ag_ntot; i++) {
-    feature_states.push_back(new feature_state(false, false));
+    feature_states.push_back(new feature_state(this, feature_states.size(), false, false));
   }
 
   // Features that are implemented (or not) by all atom groups
diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h
index 8787819b45..2aed77be50 100644
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@@ -27,9 +27,16 @@ public:
   std::string description; // reference to object name (cv, cvc etc.)
 
   /// This contains the current state of each feature for each object
-  struct feature_state {
-    feature_state(bool a, bool e)
-    : available(a), enabled(e) {}
+  class feature_state {
+  private:
+    cvm::deps *const deps_object;
+    int const id;
+    operator int() {} // never cast as int
+  public:
+    inline cvm::deps *object() const { return deps_object; }
+    inline int feature_id() const { return id; }
+    feature_state(cvm::deps *o, int i, bool a, bool e)
+      : deps_object(o), id(i), available(a), enabled(e) {}
 
     /// Available means: supported, subject to dependencies as listed,
     /// MAY BE ENABLED AS A RESULT OF DEPENDENCY SOLVING
@@ -48,6 +55,12 @@ public:
   /// List of the state of all features
   std::vector<feature_state *> feature_states;
 
+  /// Allow setting a feature state while parsing its kewyord
+  inline feature_state * set_feature(int id)
+  {
+    return feature_states[id];
+  }
+
   /// Describes a feature and its dependecies
   /// used in a static array within each subclass
   class feature {
diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp
index 9317c421ed..4537c09509 100644
--- a/lib/colvars/colvarmodule.cpp
+++ b/lib/colvars/colvarmodule.cpp
@@ -340,8 +340,8 @@ int colvarmodule::parse_biases(std::string const &conf)
 int colvarmodule::catch_input_errors(int result)
 {
   if (result != COLVARS_OK || get_error()) {
-    set_error_bit(result);
-    set_error_bit(INPUT_ERROR);
+    set_error_bits(result);
+    set_error_bits(INPUT_ERROR);
     parse->init();
     return get_error();
   }
@@ -493,27 +493,27 @@ int colvarmodule::calc()
              cvm::to_str(cvm::step_absolute())+"\n");
   }
 
-  combine_errors(error_code, calc_colvars());
+  error_code |= calc_colvars();
   // set biasing forces to zero before biases are calculated and summed over
   for (std::vector<colvar *>::iterator cvi = colvars.begin();
        cvi != colvars.end(); cvi++) {
     (*cvi)->reset_bias_force();
   }
-  combine_errors(error_code, calc_biases());
-  combine_errors(error_code, update_colvar_forces());
+  error_code |= calc_biases();
+  error_code |= update_colvar_forces();
 
   if (cvm::b_analysis) {
-    combine_errors(error_code, analyze());
+    error_code |= analyze();
   }
 
   // write trajectory files, if needed
   if (cv_traj_freq && cv_traj_name.size()) {
-    combine_errors(error_code, write_traj_files());
+    error_code |= write_traj_files();
   }
 
   // write restart files, if needed
   if (restart_out_freq && restart_out_name.size()) {
-    combine_errors(error_code, write_restart_files());
+    error_code |= write_restart_files();
   }
 
   return error_code;
@@ -551,7 +551,7 @@ int colvarmodule::calc_colvars()
     for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
 
       if (!(*cvi)->is_enabled()) continue;
-      combine_errors(error_code, (*cvi)->update_cvc_flags());
+      error_code |= (*cvi)->update_cvc_flags();
 
       size_t num_items = (*cvi)->num_active_cvcs();
       colvars_smp.reserve(colvars_smp.size() + num_items);
@@ -566,12 +566,12 @@ int colvarmodule::calc_colvars()
     cvm::decrease_depth();
 
     // calculate colvar components in parallel
-    combine_errors(error_code, proxy->smp_colvars_loop());
+    error_code |= proxy->smp_colvars_loop();
 
     cvm::increase_depth();
     for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
       if (!(*cvi)->is_enabled()) continue;
-      combine_errors(error_code, (*cvi)->collect_cvc_data());
+      error_code |= (*cvi)->collect_cvc_data();
     }
     cvm::decrease_depth();
 
@@ -581,7 +581,7 @@ int colvarmodule::calc_colvars()
     cvm::increase_depth();
     for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
       if (!(*cvi)->is_enabled()) continue;
-      combine_errors(error_code, (*cvi)->calc());
+      error_code |= (*cvi)->calc();
       if (cvm::get_error()) {
         return COLVARS_ERROR;
       }
@@ -589,7 +589,7 @@ int colvarmodule::calc_colvars()
     cvm::decrease_depth();
   }
 
-  combine_errors(error_code, cvm::get_error());
+  error_code |= cvm::get_error();
   return error_code;
 }
 
@@ -609,21 +609,21 @@ int colvarmodule::calc_biases()
 
     if (use_scripted_forces && !scripting_after_biases) {
       // calculate biases and scripted forces in parallel
-      combine_errors(error_code, proxy->smp_biases_script_loop());
+      error_code |= proxy->smp_biases_script_loop();
     } else {
       // calculate biases in parallel
-      combine_errors(error_code, proxy->smp_biases_loop());
+      error_code |= proxy->smp_biases_loop();
     }
 
   } else {
 
     if (use_scripted_forces && !scripting_after_biases) {
-      combine_errors(error_code, calc_scripted_forces());
+      error_code |= calc_scripted_forces();
     }
 
     cvm::increase_depth();
     for (bi = biases.begin(); bi != biases.end(); bi++) {
-      combine_errors(error_code, (*bi)->update());
+      error_code |= (*bi)->update();
       if (cvm::get_error()) {
         return COLVARS_ERROR;
       }
@@ -661,7 +661,7 @@ int colvarmodule::update_colvar_forces()
   cvm::decrease_depth();
 
   if (use_scripted_forces && scripting_after_biases) {
-    combine_errors(error_code, calc_scripted_forces());
+    error_code |= calc_scripted_forces();
   }
 
   cvm::real total_colvar_energy = 0.0;
@@ -913,17 +913,17 @@ int colvarmodule::setup_output()
      std::string(""));
 
   if (cv_traj_freq && cv_traj_name.size()) {
-    combine_errors(error_code, open_traj_file(cv_traj_name));
+    error_code |= open_traj_file(cv_traj_name);
   }
 
   for (std::vector<colvarbias *>::iterator bi = biases.begin();
        bi != biases.end();
        bi++) {
-    combine_errors(error_code, (*bi)->setup_output());
+    error_code |= (*bi)->setup_output();
   }
 
   if (error_code != COLVARS_OK || cvm::get_error()) {
-    set_error_bit(FILE_ERROR);
+    set_error_bits(FILE_ERROR);
   }
 
   return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
@@ -1259,29 +1259,20 @@ size_t & cvm::depth()
 }
 
 
-void colvarmodule::set_error_bit(int code)
+void colvarmodule::set_error_bits(int code)
 {
-  if (code > 0) {
-    cvm::fatal_error("Error: set_error_bit() received positive error code.\n");
+  if (code < 0) {
+    cvm::fatal_error("Error: set_error_bits() received negative error code.\n");
     return;
   }
   proxy->smp_lock();
-  errorCode = -1 * ((-1 * errorCode) | (-1 * code) | (-1 * COLVARS_ERROR));
+  errorCode |= code | COLVARS_ERROR;
   proxy->smp_unlock();
 }
 
 bool colvarmodule::get_error_bit(int code)
 {
-  return bool((-1 * errorCode) & (-1 * code));
-}
-
-void colvarmodule::combine_errors(int &target, int const code)
-{
-  if (code > 0 || target > 0) {
-    cvm::fatal_error("Error: combine_errors() received positive error code.\n");
-    return;
-  }
-  target = -1 * ((-1 * target) | (-1 * code));
+  return bool(errorCode & code);
 }
 
 void colvarmodule::clear_error()
@@ -1294,7 +1285,7 @@ void colvarmodule::clear_error()
 
 void cvm::error(std::string const &message, int code)
 {
-  set_error_bit(code);
+  set_error_bits(code);
   proxy->error(message);
 }
 
@@ -1303,7 +1294,7 @@ void cvm::fatal_error(std::string const &message)
 {
   // TODO once all non-fatal errors have been set to be handled by error(),
   // set DELETE_COLVARS here for VMD to handle it
-  set_error_bit(FATAL_ERROR);
+  set_error_bits(FATAL_ERROR);
   proxy->fatal_error(message);
 }
 
diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h
index b8fc01be9e..516f968769 100644
--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@@ -4,7 +4,7 @@
 #define COLVARMODULE_H
 
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2016-08-05"
+#define COLVARS_VERSION "2016-08-10"
 #endif
 
 #ifndef COLVARS_DEBUG
@@ -23,19 +23,16 @@
 /// shared between all object instances) to be accessed from other
 /// objects.
 
-// Error codes are the negative of powers-of-two
-// as a result, error codes should NOT be bitwise-ORed but only
-// accessed through set_error_bit() and get_error_bit()
 #define COLVARS_OK 0
-#define COLVARS_ERROR   -1
-#define COLVARS_NOT_IMPLEMENTED (-1*(1<<1))
-#define INPUT_ERROR     (-1*(1<<2)) // out of bounds or inconsistent input
-#define BUG_ERROR       (-1*(1<<3)) // Inconsistent state indicating bug
-#define FILE_ERROR      (-1*(1<<4))
-#define MEMORY_ERROR    (-1*(1<<5))
-#define FATAL_ERROR     (-1*(1<<6)) // Should be set, or not, together with other bits
-#define DELETE_COLVARS  (-1*(1<<7)) // Instruct the caller to delete cvm
-#define COLVARS_NO_SUCH_FRAME (-1*(1<<8)) // Cannot load the requested frame
+#define COLVARS_ERROR   1
+#define COLVARS_NOT_IMPLEMENTED (1<<1)
+#define INPUT_ERROR     (1<<2) // out of bounds or inconsistent input
+#define BUG_ERROR       (1<<3) // Inconsistent state indicating bug
+#define FILE_ERROR      (1<<4)
+#define MEMORY_ERROR    (1<<5)
+#define FATAL_ERROR     (1<<6) // Should be set, or not, together with other bits
+#define DELETE_COLVARS  (1<<7) // Instruct the caller to delete cvm
+#define COLVARS_NO_SUCH_FRAME (1<<8) // Cannot load the requested frame
 
 #include <iostream>
 #include <iomanip>
@@ -118,12 +115,10 @@ protected:
 
 public:
 
-  static void set_error_bit(int code);
+  static void set_error_bits(int code);
 
   static bool get_error_bit(int code);
 
-  static void combine_errors(int &target, int const code);
-
   static inline int get_error()
   {
     return errorCode;
diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp
index f6e904c83a..da39f78356 100644
--- a/lib/colvars/colvarparse.cpp
+++ b/lib/colvars/colvarparse.cpp
@@ -354,6 +354,21 @@ bool colvarparse::get_keyval(std::string const &conf,
 }
 
 
+bool colvarparse::get_keyval(std::string const &conf,
+                             char const *key,
+                             cvm::deps::feature_state *value,
+                             bool const &def_value,
+                             Parse_Mode const parse_mode)
+{
+  bool feature_flag = def_value;
+  bool const b_found = get_keyval(conf, key, feature_flag, def_value, parse_mode);
+  if (feature_flag) {
+    value->object()->enable(value->feature_id());
+  }
+  return b_found;
+}
+
+
 // multiple-value keyword parsers
 
 bool colvarparse::get_keyval(std::string const &conf,
@@ -548,6 +563,10 @@ bool colvarparse::key_lookup(std::string const &conf,
                              std::string &data,
                              size_t &save_pos)
 {
+  if (cvm::debug()) {
+    cvm::log("Looking for the keyword \""+std::string(key_in)+"\" and its value.\n");
+  }
+
   // add this keyword to the register (in its camelCase version)
   add_keyword(key_in);
 
@@ -568,11 +587,14 @@ bool colvarparse::key_lookup(std::string const &conf,
   // start from the first occurrence of key
   size_t pos = conf_lower.find(key, save_pos);
 
-  // iterate over all instances until it finds the isolated keyword
+  // iterate over all instances of the substring until it finds it as isolated keyword
   while (true) {
 
     if (pos == std::string::npos) {
       // no valid instance of the keyword has been found
+      if (cvm::debug()) {
+        cvm::log("Keyword \""+std::string(key_in)+"\" not found.\n");
+      }
       return false;
     }
 
@@ -625,25 +647,46 @@ bool colvarparse::key_lookup(std::string const &conf,
   size_t data_begin = (to_lower_cppstr(line)).find(key) + key.size();
   data_begin = line.find_first_not_of(white_space, data_begin+1);
 
-  //   size_t data_begin_absolute = data_begin + line_begin;
-  //   size_t data_end_absolute   = data_begin;
-
   if (data_begin != std::string::npos) {
 
     size_t data_end = line.find_last_not_of(white_space) + 1;
     data_end = (data_end == std::string::npos) ? line.size() : data_end;
-    //     data_end_absolute = data_end + line_begin;
 
-    if (line.find('{', data_begin) != std::string::npos) {
+    size_t brace = line.find('{', data_begin);  // look for an opening brace
+    size_t brace_last = brace;
+
+    if (brace != std::string::npos) {
+
+      // find the matching closing brace
 
-      size_t brace_count = 1;
-      size_t brace = line.find('{', data_begin);  // start from the first opening brace
+      if (cvm::debug()) {
+        cvm::log("Multi-line value, config is now \""+line+"\".\n");
+      }
+
+      int brace_count = 1;
 
       while (brace_count > 0) {
 
-        // find the matching closing brace
-        brace = line.find_first_of("{}", brace+1);
-        while (brace == std::string::npos) {
+        brace = line.find_first_of("{}", brace_last+1);
+        // find all braces within this line
+        while (brace < std::string::npos) {
+          brace_last = brace;
+          if (line[brace] == '{') brace_count++;
+          if (line[brace] == '}') brace_count--;
+          if (brace_count == 0) {
+            data_end = brace+1;
+            break;
+          }
+          brace = line.find_first_of("{}", brace+1);
+        }
+
+        if (brace_count == 0) {
+          data_end = brace+1;
+          break;
+        }
+
+        if (brace == std::string::npos) {
+
           // add a new line
           if (line_end >= conf.size()) {
             cvm::error("Parse error: reached the end while "
@@ -653,7 +696,6 @@ bool colvarparse::key_lookup(std::string const &conf,
             return false;
           }
           size_t const old_end = line.size();
-          //           data_end_absolute += old_end+1;
 
           line_begin = line_end;
           nl = conf.find('\n', line_begin+1);
@@ -663,36 +705,37 @@ bool colvarparse::key_lookup(std::string const &conf,
             line_end = nl;
           line.append(conf, line_begin, (line_end-line_begin));
 
-          brace = line.find_first_of("{}", old_end);
+          if (cvm::debug()) {
+            cvm::log("Added a new line, config is now \""+line+"\".\n");
+          }
         }
 
-        if (line[brace] == '{') brace_count++;
-        if (line[brace] == '}') brace_count--;
+        if (brace_count < 0) {
+          cvm::error("Error: found closing brace without opening brace.\n", INPUT_ERROR);
+        }
       }
 
-      // set data_begin after the opening brace
-      data_begin = line.find_first_of('{', data_begin) + 1;
+      cvm::log("Value so far = "+line.substr(data_begin, (data_end-data_begin))+".\n");
+
+      // strip the leading and trailing braces
+      data_begin = line.find_first_of('{') + 1;
       data_begin = line.find_first_not_of(white_space,
                                           data_begin);
-      // set data_end before the closing brace
-      data_end = brace;
-      data_end = line.find_last_not_of(white_space+"}",
-                                       data_end) + 1;
-      //       data_end_absolute = line_end;
 
-      if (data_end > line.size())
-        data_end = line.size();
+      data_end = line.find_last_of('}', line.size()) - 1;
+      data_end = line.find_last_not_of(white_space,
+                                       data_end) + 1;
     }
 
     data.append(line, data_begin, (data_end-data_begin));
 
+    if (cvm::debug()) {
+      cvm::log("Keyword value = \""+data+"\".\n");
+    }
+
     if (data.size() && save_delimiters) {
       data_begin_pos.push_back(conf.find(data, pos+key.size()));
       data_end_pos.push_back(data_begin_pos.back()+data.size());
-      //       std::cerr << "key = " << key << ", data = \""
-      //                 << data << "\", data_begin, data_end = "
-      //                 << data_begin_pos.back() << ", " << data_end_pos.back()
-      //                 << "\n";
     }
   }
 
diff --git a/lib/colvars/colvarparse.h b/lib/colvars/colvarparse.h
index 9bce5412ed..c091cbc15d 100644
--- a/lib/colvars/colvarparse.h
+++ b/lib/colvars/colvarparse.h
@@ -8,6 +8,7 @@
 
 #include "colvarmodule.h"
 #include "colvarvalue.h"
+#include "colvardeps.h"
 
 
 /// \file colvarparse.h Parsing functions for collective variables
@@ -180,6 +181,11 @@ public:
                   bool &value,
                   bool const &def_value = false,
                   Parse_Mode const parse_mode = parse_normal);
+  bool get_keyval(std::string const &conf,
+                  char const *key,
+                  cvm::deps::feature_state *value,
+                  bool const &def_value = false,
+                  Parse_Mode const parse_mode = parse_normal);
 
   bool get_keyval(std::string const &conf,
                   char const *key,
diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h
index 0d29a7297d..4bba189bb7 100644
--- a/lib/colvars/colvarproxy.h
+++ b/lib/colvars/colvarproxy.h
@@ -69,12 +69,12 @@ public:
   virtual cvm::real rand_gaussian(void) = 0;
 
   /// \brief Get the current frame number
-  // Negative return values indicate error
-  virtual int frame() { return COLVARS_NOT_IMPLEMENTED; }
+  // Returns error code
+  virtual int get_frame(long int&) { return COLVARS_NOT_IMPLEMENTED; }
 
-  /// \brief Set the current frame number
-  // return frame number on success, COLVARS_NO_SUCH_FRAME otherwise
-  virtual int frame(int) { return COLVARS_NOT_IMPLEMENTED; }
+  /// \brief Set the current frame number (as well as colvarmodule::it)
+  // Returns error code
+  virtual int set_frame(long int) { return COLVARS_NOT_IMPLEMENTED; }
 
   /// \brief Prefix to be used for input files (restarts, not
   /// configuration)
diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp
index 091162fc18..374359ccef 100644
--- a/lib/colvars/colvarscript.cpp
+++ b/lib/colvars/colvarscript.cpp
@@ -55,14 +55,14 @@ int colvarscript::run(int argc, char const *argv[]) {
   if (cmd == "delete") {
     // Note: the delete bit may be ignored by some backends
     // it is mostly useful in VMD
-    colvars->set_error_bit(DELETE_COLVARS);
+    colvars->set_error_bits(DELETE_COLVARS);
     return COLVARS_OK;
   }
 
   if (cmd == "update") {
-    cvm::combine_errors(error_code, proxy->update_input());
-    cvm::combine_errors(error_code, colvars->calc());
-    cvm::combine_errors(error_code, proxy->update_output());
+    error_code |= proxy->update_input();
+    error_code |= colvars->calc();
+    error_code |= proxy->update_output();
     if (error_code) {
       result += "Error updating the colvars module.\n";
     }
@@ -142,8 +142,8 @@ int colvarscript::run(int argc, char const *argv[]) {
     }
     proxy->output_prefix_str = argv[2];
     int error = 0;
-    cvm::combine_errors(error, colvars->setup_output());
-    cvm::combine_errors(error, colvars->write_output_files());
+    error |= colvars->setup_output();
+    error |= colvars->write_output_files();
     return error ? COLVARSCRIPT_ERROR : COLVARS_OK;
   }
 
@@ -163,8 +163,9 @@ int colvarscript::run(int argc, char const *argv[]) {
 
   if (cmd == "frame") {
     if (argc == 2) {
-      int f = proxy->frame();
-      if (f >= 0) {
+      long int f;
+      int error = proxy->get_frame(f);
+      if (error == COLVARS_OK) {
         result = cvm::to_str(f);
         return COLVARS_OK;
       } else {
@@ -173,10 +174,9 @@ int colvarscript::run(int argc, char const *argv[]) {
       }
     } else if (argc == 3) {
       // Failure of this function does not trigger an error, but
-      // returns the plain result to let scripts detect available frames
-      long int f = proxy->frame(strtol(argv[2], NULL, 10));
-      colvars->it = proxy->frame();
-      result = cvm::to_str(f);
+      // returns nonzero, to let scripts detect available frames
+      int error = proxy->set_frame(strtol(argv[2], NULL, 10));
+      result = cvm::to_str(error == COLVARS_OK ? 0 : -1);
       return COLVARS_OK;
     } else {
       result = "Wrong arguments to command \"frame\"\n" + help_string();
@@ -414,7 +414,8 @@ Input and output:\n\
   printframe                  -- return a summary of the current frame\n\
   printframelabels            -- return labels to annotate printframe's output\n";
 
-  if (proxy->frame() != COLVARS_NOT_IMPLEMENTED) {
+  long int tmp;
+  if (proxy->get_frame(tmp) != COLVARS_NOT_IMPLEMENTED) {
       buf += "\
   frame                       -- return current frame number\n\
   frame <new_frame>           -- set frame number\n";
-- 
GitLab


From 3d2e5d0a5031a2e1033c3b0d899fe6f8ef5be3c2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 10 Aug 2016 09:12:51 -0400
Subject: [PATCH 10/52] suppress compiler warning

(cherry picked from commit 6f227e194e1f3a13e906b67b6c0a1fa7599a23c7)
---
 lib/colvars/colvardeps.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h
index 2aed77be50..9c86f6028b 100644
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@@ -31,7 +31,7 @@ public:
   private:
     cvm::deps *const deps_object;
     int const id;
-    operator int() {} // never cast as int
+    operator int() { return 0; } // never cast as int
   public:
     inline cvm::deps *object() const { return deps_object; }
     inline int feature_id() const { return id; }
-- 
GitLab


From 1b33d00785b9d9b857cef4954bfc98ab08f9475a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 10 Aug 2016 09:13:08 -0400
Subject: [PATCH 11/52] update colvars makefile dependencies

(cherry picked from commit df99a85930a8e77f6e7741b334c2e61b557c1b28)
---
 lib/colvars/Makefile.fermi         | 66 ++++++++++++++++--------------
 lib/colvars/Makefile.g++           | 62 +++++++++++++++-------------
 lib/colvars/Makefile.mingw32-cross | 66 ++++++++++++++++--------------
 lib/colvars/Makefile.mingw64-cross | 66 ++++++++++++++++--------------
 4 files changed, 138 insertions(+), 122 deletions(-)

diff --git a/lib/colvars/Makefile.fermi b/lib/colvars/Makefile.fermi
index fe8d3ac16c..e17798bbc3 100644
--- a/lib/colvars/Makefile.fermi
+++ b/lib/colvars/Makefile.fermi
@@ -54,58 +54,62 @@ colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
 # ------ DEPENDENCIES ------
 #
 colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarparse.h colvarvalue.h colvaratoms.h
+ colvarvalue.h colvarparse.h colvardeps.h colvaratoms.h
 colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarbias_abf.h \
- colvarbias.h colvargrid.h
+ colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarbias_abf.h colvarbias.h colvargrid.h
 colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarbias_alb.h colvar.h colvarvalue.h colvarparse.h \
- colvarbias_restraint.h colvarbias.h
+ colvarproxy.h colvarvalue.h colvarbias_alb.h colvar.h colvarparse.h \
+ colvardeps.h colvarbias_restraint.h colvarbias.h
 colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarbias.h colvar.h colvarparse.h
+ colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h
 colvarbias_histogram.o: colvarbias_histogram.cpp colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
- colvarbias_histogram.h colvarbias.h colvargrid.h
+ colvardeps.h colvarbias_histogram.h colvarbias.h colvargrid.h
 colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
  colvarbias_meta.h colvarbias.h colvargrid.h
 colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \
- colvarbias.h colvar.h colvarparse.h
+ colvarbias.h colvar.h colvarparse.h colvardeps.h
 colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarcomp.h \
- colvaratoms.h
+ colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarcomp.h colvaratoms.h
 colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarparse.h colvarvalue.h colvaratoms.h \
- colvar.h colvarcomp.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvaratoms.h colvar.h colvarcomp.h
 colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
+ colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarcomp.h \
+ colvaratoms.h
 colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
- colvarcomp.h colvaratoms.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvar.h colvarcomp.h colvaratoms.h
 colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarvalue.h colvarparse.h colvar.h colvarcomp.h \
- colvaratoms.h
-colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
+ colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
  colvarcomp.h colvaratoms.h
+colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvar.h colvarcomp.h colvaratoms.h
 colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
- colvarscript.h colvarbias.h
+ colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
+ colvaratoms.h colvarscript.h colvarbias.h
+colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvardeps.h
 colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
- colvargrid.h
+ colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
+ colvaratoms.h colvargrid.h
 colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarvalue.h colvarparse.h colvar.h colvarbias.h \
- colvarbias_abf.h colvargrid.h colvarbias_alb.h colvarbias_restraint.h \
- colvarbias_histogram.h colvarbias_meta.h colvarscript.h
+ colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
+ colvarbias.h colvarbias_abf.h colvargrid.h colvarbias_alb.h \
+ colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
+ colvarscript.h
 colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h
+ colvarvalue.h colvarparse.h colvardeps.h
 colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
- colvarbias.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
+ colvarparse.h colvardeps.h
 colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarparse.h colvarvalue.h
+ colvarvalue.h colvarparse.h colvardeps.h
 colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h
 
diff --git a/lib/colvars/Makefile.g++ b/lib/colvars/Makefile.g++
index d0fdd1c325..f1fa1734b9 100644
--- a/lib/colvars/Makefile.g++
+++ b/lib/colvars/Makefile.g++
@@ -53,58 +53,62 @@ colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
 # ------ DEPENDENCIES ------
 #
 colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvaratoms.h
+ colvarvalue.h colvarparse.h colvardeps.h colvaratoms.h
 colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvarbias_abf.h \
- colvarbias.h colvargrid.h
+ colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarbias_abf.h colvarbias.h colvargrid.h
 colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
  colvarproxy.h colvarvalue.h colvarbias_alb.h colvar.h colvarparse.h \
- colvarbias_restraint.h colvarbias.h
+ colvardeps.h colvarbias_restraint.h colvarbias.h
 colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarbias.h colvar.h colvarparse.h
+ colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h
 colvarbias_histogram.o: colvarbias_histogram.cpp colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
- colvarbias_histogram.h colvarbias.h colvargrid.h
+ colvardeps.h colvarbias_histogram.h colvarbias.h colvargrid.h
 colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
  colvarbias_meta.h colvarbias.h colvargrid.h
 colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \
- colvarbias.h colvar.h colvarparse.h
+ colvarbias.h colvar.h colvarparse.h colvardeps.h
 colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvarcomp.h \
- colvaratoms.h
+ colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarcomp.h colvaratoms.h
 colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvaratoms.h \
- colvar.h colvarcomp.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvaratoms.h colvar.h colvarcomp.h
 colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
+ colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarcomp.h \
+ colvaratoms.h
 colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
- colvarcomp.h colvaratoms.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvar.h colvarcomp.h colvaratoms.h
 colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarvalue.h colvarparse.h colvar.h colvarcomp.h \
- colvaratoms.h
-colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
+ colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
  colvarcomp.h colvaratoms.h
+colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvar.h colvarcomp.h colvaratoms.h
 colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
- colvarscript.h colvarbias.h
+ colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
+ colvaratoms.h colvarscript.h colvarbias.h
+colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvardeps.h
 colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
- colvargrid.h
+ colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
+ colvaratoms.h colvargrid.h
 colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarvalue.h colvarparse.h colvar.h colvarbias.h \
- colvarbias_abf.h colvargrid.h colvarbias_alb.h colvarbias_restraint.h \
- colvarbias_histogram.h colvarbias_meta.h colvarscript.h
+ colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
+ colvarbias.h colvarbias_abf.h colvargrid.h colvarbias_alb.h \
+ colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
+ colvarscript.h
 colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h
+ colvarvalue.h colvarparse.h colvardeps.h
 colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
- colvarparse.h
+ colvarparse.h colvardeps.h
 colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h
+ colvarvalue.h colvarparse.h colvardeps.h
 colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h
 
diff --git a/lib/colvars/Makefile.mingw32-cross b/lib/colvars/Makefile.mingw32-cross
index 289b006a45..cea3a53c25 100644
--- a/lib/colvars/Makefile.mingw32-cross
+++ b/lib/colvars/Makefile.mingw32-cross
@@ -61,58 +61,62 @@ $(DIR)%.o: %.cpp
 # ------ DEPENDENCIES ------
 #
 $(DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarparse.h colvarvalue.h colvaratoms.h
+ colvarvalue.h colvarparse.h colvardeps.h colvaratoms.h
 $(DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarbias_abf.h \
- colvarbias.h colvargrid.h
+ colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarbias_abf.h colvarbias.h colvargrid.h
 $(DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarbias_alb.h colvar.h colvarvalue.h colvarparse.h \
- colvarbias_restraint.h colvarbias.h
+ colvarproxy.h colvarvalue.h colvarbias_alb.h colvar.h colvarparse.h \
+ colvardeps.h colvarbias_restraint.h colvarbias.h
 $(DIR)colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarbias.h colvar.h colvarparse.h
+ colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h
 $(DIR)colvarbias_histogram.o: colvarbias_histogram.cpp colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
- colvarbias_histogram.h colvarbias.h colvargrid.h
+ colvardeps.h colvarbias_histogram.h colvarbias.h colvargrid.h
 $(DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
  colvarbias_meta.h colvarbias.h colvargrid.h
 $(DIR)colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \
- colvarbias.h colvar.h colvarparse.h
+ colvarbias.h colvar.h colvarparse.h colvardeps.h
 $(DIR)colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarcomp.h \
- colvaratoms.h
+ colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarcomp.h colvaratoms.h
 $(DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarparse.h colvarvalue.h colvaratoms.h \
- colvar.h colvarcomp.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvaratoms.h colvar.h colvarcomp.h
 $(DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
+ colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarcomp.h \
+ colvaratoms.h
 $(DIR)colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
- colvarcomp.h colvaratoms.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvar.h colvarcomp.h colvaratoms.h
 $(DIR)colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarvalue.h colvarparse.h colvar.h colvarcomp.h \
- colvaratoms.h
-$(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
+ colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
  colvarcomp.h colvaratoms.h
+$(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvar.h colvarcomp.h colvaratoms.h
 $(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
- colvarscript.h colvarbias.h
+ colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
+ colvaratoms.h colvarscript.h colvarbias.h
+$(DIR)colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvardeps.h
 $(DIR)colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
- colvargrid.h
+ colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
+ colvaratoms.h colvargrid.h
 $(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarvalue.h colvarparse.h colvar.h colvarbias.h \
- colvarbias_abf.h colvargrid.h colvarbias_alb.h colvarbias_restraint.h \
- colvarbias_histogram.h colvarbias_meta.h colvarscript.h
+ colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
+ colvarbias.h colvarbias_abf.h colvargrid.h colvarbias_alb.h \
+ colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
+ colvarscript.h
 $(DIR)colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h
+ colvarvalue.h colvarparse.h colvardeps.h
 $(DIR)colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
- colvarbias.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
+ colvarparse.h colvardeps.h
 $(DIR)colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarparse.h colvarvalue.h
+ colvarvalue.h colvarparse.h colvardeps.h
 $(DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h
 
diff --git a/lib/colvars/Makefile.mingw64-cross b/lib/colvars/Makefile.mingw64-cross
index a6081273f8..7dd85b48f8 100644
--- a/lib/colvars/Makefile.mingw64-cross
+++ b/lib/colvars/Makefile.mingw64-cross
@@ -61,58 +61,62 @@ $(DIR)%.o: %.cpp
 # ------ DEPENDENCIES ------
 #
 $(DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarparse.h colvarvalue.h colvaratoms.h
+ colvarvalue.h colvarparse.h colvardeps.h colvaratoms.h
 $(DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarbias_abf.h \
- colvarbias.h colvargrid.h
+ colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarbias_abf.h colvarbias.h colvargrid.h
 $(DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarbias_alb.h colvar.h colvarvalue.h colvarparse.h \
- colvarbias_restraint.h colvarbias.h
+ colvarproxy.h colvarvalue.h colvarbias_alb.h colvar.h colvarparse.h \
+ colvardeps.h colvarbias_restraint.h colvarbias.h
 $(DIR)colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarbias.h colvar.h colvarparse.h
+ colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h
 $(DIR)colvarbias_histogram.o: colvarbias_histogram.cpp colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
- colvarbias_histogram.h colvarbias.h colvargrid.h
+ colvardeps.h colvarbias_histogram.h colvarbias.h colvargrid.h
 $(DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
  colvarbias_meta.h colvarbias.h colvargrid.h
 $(DIR)colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \
- colvarbias.h colvar.h colvarparse.h
+ colvarbias.h colvar.h colvarparse.h colvardeps.h
 $(DIR)colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarcomp.h \
- colvaratoms.h
+ colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarcomp.h colvaratoms.h
 $(DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarparse.h colvarvalue.h colvaratoms.h \
- colvar.h colvarcomp.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvaratoms.h colvar.h colvarcomp.h
 $(DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
+ colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarcomp.h \
+ colvaratoms.h
 $(DIR)colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
- colvarcomp.h colvaratoms.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvar.h colvarcomp.h colvaratoms.h
 $(DIR)colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarvalue.h colvarparse.h colvar.h colvarcomp.h \
- colvaratoms.h
-$(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
+ colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
  colvarcomp.h colvaratoms.h
+$(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvar.h colvarcomp.h colvaratoms.h
 $(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
- colvarscript.h colvarbias.h
+ colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
+ colvaratoms.h colvarscript.h colvarbias.h
+$(DIR)colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvardeps.h
 $(DIR)colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
- colvargrid.h
+ colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
+ colvaratoms.h colvargrid.h
 $(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
- colvarproxy.h colvarvalue.h colvarparse.h colvar.h colvarbias.h \
- colvarbias_abf.h colvargrid.h colvarbias_alb.h colvarbias_restraint.h \
- colvarbias_histogram.h colvarbias_meta.h colvarscript.h
+ colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
+ colvarbias.h colvarbias_abf.h colvargrid.h colvarbias_alb.h \
+ colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
+ colvarscript.h
 $(DIR)colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h
+ colvarvalue.h colvarparse.h colvardeps.h
 $(DIR)colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
- colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
- colvarbias.h
+ colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
+ colvarparse.h colvardeps.h
 $(DIR)colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarparse.h colvarvalue.h
+ colvarvalue.h colvarparse.h colvardeps.h
 $(DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h
 
-- 
GitLab


From 977b9e542f5d34f09891f6cce20fd9641475f1e3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 10 Aug 2016 09:35:21 -0400
Subject: [PATCH 12/52] update colvars to another set of changes from the
 upstream repo

(cherry picked from commit cb816f8cba630e27df773b54a584b72741fa20db)
---
 lib/colvars/colvar.cpp       |  2 +-
 lib/colvars/colvar.h         |  2 +-
 lib/colvars/colvaratoms.cpp  |  2 +-
 lib/colvars/colvaratoms.h    |  2 +-
 lib/colvars/colvarbias.cpp   |  2 +-
 lib/colvars/colvarbias.h     |  2 +-
 lib/colvars/colvarcomp.cpp   |  4 ++--
 lib/colvars/colvarcomp.h     |  2 +-
 lib/colvars/colvardeps.cpp   | 34 +++++++++++++++++-----------------
 lib/colvars/colvardeps.h     | 22 +++++++++++-----------
 lib/colvars/colvarmodule.cpp | 10 +++++-----
 lib/colvars/colvarmodule.h   |  3 ---
 lib/colvars/colvarparse.cpp  |  5 +----
 lib/colvars/colvarparse.h    |  2 +-
 14 files changed, 44 insertions(+), 50 deletions(-)

diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp
index 49f0285091..c630154aa3 100644
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@@ -1952,4 +1952,4 @@ void colvar::calc_runave()
 
 // Static members
 
-std::vector<cvm::deps::feature *> colvar::cv_features;
+std::vector<colvardeps::feature *> colvar::cv_features;
diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h
index 5f2fce35e0..05314b78e8 100644
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@@ -38,7 +38,7 @@
 /// \link colvarvalue \endlink type, you should also add its
 /// initialization line in the \link colvar \endlink constructor.
 
-class colvar : public colvarparse, public cvm::deps {
+class colvar : public colvarparse, public colvardeps {
 
 public:
 
diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp
index 786a72821f..5eba67f0f1 100644
--- a/lib/colvars/colvaratoms.cpp
+++ b/lib/colvars/colvaratoms.cpp
@@ -1192,6 +1192,6 @@ void cvm::atom_group::apply_force(cvm::rvector const &force)
 
 // Static members
 
-std::vector<cvm::deps::feature *> cvm::atom_group::ag_features;
+std::vector<colvardeps::feature *> cvm::atom_group::ag_features;
 
 
diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h
index 440afd57cb..4ba70b2855 100644
--- a/lib/colvars/colvaratoms.h
+++ b/lib/colvars/colvaratoms.h
@@ -139,7 +139,7 @@ public:
 /// \brief Group of \link atom \endlink objects, mostly used by a
 /// \link cvc \endlink object to gather all atomic data
 class colvarmodule::atom_group
-  : public colvarparse, public cvm::deps
+  : public colvarparse, public colvardeps
 {
 public:
 
diff --git a/lib/colvars/colvarbias.cpp b/lib/colvars/colvarbias.cpp
index 073cfc3965..76d8489de9 100644
--- a/lib/colvars/colvarbias.cpp
+++ b/lib/colvars/colvarbias.cpp
@@ -246,4 +246,4 @@ std::ostream & colvarbias::write_traj(std::ostream &os)
 
 // Static members
 
-std::vector<cvm::deps::feature *> colvarbias::cvb_features;
+std::vector<colvardeps::feature *> colvarbias::cvb_features;
diff --git a/lib/colvars/colvarbias.h b/lib/colvars/colvarbias.h
index 712dc44ff0..8238f58f40 100644
--- a/lib/colvars/colvarbias.h
+++ b/lib/colvars/colvarbias.h
@@ -9,7 +9,7 @@
 
 
 /// \brief Collective variable bias, base class
-class colvarbias : public colvarparse, public cvm::deps {
+class colvarbias : public colvarparse, public colvardeps {
 public:
 
   /// Name of this bias
diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp
index 89973516be..632e7fabda 100644
--- a/lib/colvars/colvarcomp.cpp
+++ b/lib/colvars/colvarcomp.cpp
@@ -103,7 +103,7 @@ int colvar::cvc::setup()
   description = "cvc " + name;
 
   for (i = 0; i < atom_groups.size(); i++) {
-    add_child((cvm::deps *) atom_groups[i]);
+    add_child((colvardeps *) atom_groups[i]);
   }
 
   return COLVARS_OK;
@@ -272,4 +272,4 @@ void colvar::cvc::debug_gradients(cvm::atom_group *group)
 
 // Static members
 
-std::vector<cvm::deps::feature *> colvar::cvc::cvc_features;
+std::vector<colvardeps::feature *> colvar::cvc::cvc_features;
diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h
index 1ed3c38924..deed1a4721 100644
--- a/lib/colvars/colvarcomp.h
+++ b/lib/colvars/colvarcomp.h
@@ -61,7 +61,7 @@
 /// call to e.g. apply_force().
 
 class colvar::cvc
-  : public colvarparse, public cvm::deps
+  : public colvarparse, public colvardeps
 {
 public:
 
diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp
index 2801abb191..c4915569e2 100644
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@@ -2,7 +2,7 @@
 #include "colvardeps.h"
 
 
-cvm::deps::~deps() {
+colvardeps::~colvardeps() {
   size_t i;
 
   for (i=0; i<feature_states.size(); i++) {
@@ -25,12 +25,12 @@ cvm::deps::~deps() {
 }
 
 
-void cvm::deps::provide(int feature_id) {
+void colvardeps::provide(int feature_id) {
   feature_states[feature_id]->available = true;
 }
 
 
-int cvm::deps::enable(int feature_id,
+int colvardeps::enable(int feature_id,
                       bool dry_run /* default: false */,
                       // dry_run: fail silently, do not enable if available
                       // flag is passed recursively to deps of this feature
@@ -193,7 +193,7 @@ int cvm::deps::enable(int feature_id,
   features()[f]->requires_alt.back()[1] = h;                                           \
   features()[f]->requires_alt.back()[2] = i
 
-void cvm::deps::init_cvb_requires() {
+void colvardeps::init_cvb_requires() {
   int i;
   if (features().size() == 0) {
     for (i = 0; i < f_cvb_ntot; i++) {
@@ -225,7 +225,7 @@ void cvm::deps::init_cvb_requires() {
 }
 
 
-void cvm::deps::init_cv_requires() {
+void colvardeps::init_cv_requires() {
   size_t i;
   if (features().size() == 0) {
     for (i = 0; i < f_cv_ntot; i++) {
@@ -342,11 +342,11 @@ void cvm::deps::init_cv_requires() {
 }
 
 
-void cvm::deps::init_cvc_requires() {
+void colvardeps::init_cvc_requires() {
   size_t i;
   // Initialize static array once and for all
   if (features().size() == 0) {
-    for (i = 0; i < cvm::deps::f_cvc_ntot; i++) {
+    for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
       features().push_back(new feature);
     }
 
@@ -384,7 +384,7 @@ void cvm::deps::init_cvc_requires() {
   // Initialize feature_states for each instance
   // default as unavailable, not enabled
   feature_states.reserve(f_cvc_ntot);
-  for (i = 0; i < cvm::deps::f_cvc_ntot; i++) {
+  for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
     feature_states.push_back(new feature_state(this, feature_states.size(), false, false));
   }
 
@@ -392,12 +392,12 @@ void cvm::deps::init_cvc_requires() {
   // Each cvc specifies what other features are available
   feature_states[f_cvc_active]->available = true;
   feature_states[f_cvc_gradient]->available = true;
-  feature_states[f_cvc_scalable_com]->available = (proxy->scalable_group_coms() == COLVARS_OK);
+  feature_states[f_cvc_scalable_com]->available = (cvm::proxy->scalable_group_coms() == COLVARS_OK);
   feature_states[f_cvc_scalable]->available = feature_states[f_cvc_scalable_com]->available;
 }
 
 
-void cvm::deps::init_ag_requires() {
+void colvardeps::init_ag_requires() {
   size_t i;
   // Initialize static array once and for all
   if (features().size() == 0) {
@@ -428,18 +428,18 @@ void cvm::deps::init_ag_requires() {
   // Initialize feature_states for each instance
   // default as unavailable, not enabled
   feature_states.reserve(f_ag_ntot);
-  for (i = 0; i < cvm::deps::f_ag_ntot; i++) {
+  for (i = 0; i < colvardeps::f_ag_ntot; i++) {
     feature_states.push_back(new feature_state(this, feature_states.size(), false, false));
   }
 
   // Features that are implemented (or not) by all atom groups
   feature_states[f_ag_active]->available = true;
-  feature_states[f_ag_scalable_com]->available = (proxy->scalable_group_coms() == COLVARS_OK);
+  feature_states[f_ag_scalable_com]->available = (cvm::proxy->scalable_group_coms() == COLVARS_OK);
   feature_states[f_ag_scalable]->available = feature_states[f_ag_scalable_com]->available;
 }
 
 
-void cvm::deps::print_state() {
+void colvardeps::print_state() {
   size_t i;
   cvm::log("Enabled features of " + description);
   for (i = 0; i < feature_states.size(); i++) {
@@ -456,13 +456,13 @@ void cvm::deps::print_state() {
 
 
 
-void cvm::deps::add_child(deps *child) {
+void colvardeps::add_child(colvardeps *child) {
   children.push_back(child);
-  child->parents.push_back((deps *)this);
+  child->parents.push_back((colvardeps *)this);
 }
 
 
-void cvm::deps::remove_child(deps *child) {
+void colvardeps::remove_child(colvardeps *child) {
   int i;
   bool found = false;
 
@@ -490,7 +490,7 @@ void cvm::deps::remove_child(deps *child) {
 }
 
 
-void cvm::deps::remove_all_children() {
+void colvardeps::remove_all_children() {
   size_t i;
   int j;
   bool found;
diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h
index 9c86f6028b..7e69865a56 100644
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@@ -16,11 +16,11 @@
 
 // It seems important to have available default to false (for safety) and enabled to false (for efficiency)
 
-class cvm::deps {
+class colvardeps {
 public:
 
-  deps() {}
-  virtual ~deps();
+  colvardeps() {}
+  virtual ~colvardeps();
 
   // Subclasses should initialize the following members:
 
@@ -29,13 +29,13 @@ public:
   /// This contains the current state of each feature for each object
   class feature_state {
   private:
-    cvm::deps *const deps_object;
+    colvardeps *const deps_object;
     int const id;
     operator int() { return 0; } // never cast as int
   public:
-    inline cvm::deps *object() const { return deps_object; }
+    inline colvardeps *object() const { return deps_object; }
     inline int feature_id() const { return id; }
-    feature_state(cvm::deps *o, int i, bool a, bool e)
+    feature_state(colvardeps *o, int i, bool a, bool e)
       : deps_object(o), id(i), available(a), enabled(e) {}
 
     /// Available means: supported, subject to dependencies as listed,
@@ -97,9 +97,9 @@ public:
   // implement this as virtual to allow overriding
   virtual std::vector<feature *>&features() = 0;
 
-  void add_child(deps *child);
+  void add_child(colvardeps *child);
 
-  void remove_child(deps *child);
+  void remove_child(colvardeps *child);
 
   /// Used before deleting an object, if not handled by that object's destructor
   /// (useful for cvcs because their children are member objects)
@@ -111,11 +111,11 @@ private:
   // pointers to objects this object depends on
   // list should be maintained by any code that modifies the object
   // this could be secured by making lists of colvars / cvcs / atom groups private and modified through accessor functions
-  std::vector<deps *> children;
+  std::vector<colvardeps *> children;
 
   // pointers to objects that depend on this object
   // the size of this array is in effect a reference counter
-  std::vector<deps *> parents;
+  std::vector<colvardeps *> parents;
 
 public:
   // disabling a feature f:
@@ -128,7 +128,7 @@ public:
 //
 //   }
 
-  // std::vector<deps *> parents; // Needed to trigger a refresh if capabilities of this object change
+  // std::vector<colvardeps *> parents; // Needed to trigger a refresh if capabilities of this object change
 
   // End of members to be initialized by subclasses
 
diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp
index 4537c09509..6d174be7a2 100644
--- a/lib/colvars/colvarmodule.cpp
+++ b/lib/colvars/colvarmodule.cpp
@@ -302,7 +302,7 @@ int colvarmodule::parse_biases(std::string const &conf)
   size_t i;
 
   for (i = 0; i < biases.size(); i++) {
-    biases[i]->enable(cvm::deps::f_cvb_active);
+    biases[i]->enable(colvardeps::f_cvb_active);
     if (cvm::debug())
       biases[i]->print_state();
   }
@@ -310,8 +310,8 @@ int colvarmodule::parse_biases(std::string const &conf)
   size_t n_hist_dep_biases = 0;
   std::vector<std::string> hist_dep_biases_names;
   for (i = 0; i < biases.size(); i++) {
-    if (biases[i]->is_enabled(cvm::deps::f_cvb_apply_force) &&
-        biases[i]->is_enabled(cvm::deps::f_cvb_history_dependent)) {
+    if (biases[i]->is_enabled(colvardeps::f_cvb_apply_force) &&
+        biases[i]->is_enabled(colvardeps::f_cvb_history_dependent)) {
       n_hist_dep_biases++;
       hist_dep_biases_names.push_back(biases[i]->name);
     }
@@ -531,7 +531,7 @@ int colvarmodule::calc_colvars()
 
   // Determine which colvars are active at this time step
   for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
-    (*cvi)->feature_states[cvm::deps::f_cv_active]->enabled = (step_absolute() % (*cvi)->get_time_step_factor() == 0);
+    (*cvi)->feature_states[colvardeps::f_cv_active]->enabled = (step_absolute() % (*cvi)->get_time_step_factor() == 0);
   }
 
   // if SMP support is available, split up the work
@@ -689,7 +689,7 @@ int colvarmodule::update_colvar_forces()
     cvm::log("Communicating forces from the colvars to the atoms.\n");
   cvm::increase_depth();
   for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
-    if ((*cvi)->is_enabled(cvm::deps::f_cv_gradient)) {
+    if ((*cvi)->is_enabled(colvardeps::f_cv_gradient)) {
       if (!(*cvi)->is_enabled()) continue;
       (*cvi)->communicate_forces();
       if (cvm::get_error()) {
diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h
index 516f968769..f461728de8 100644
--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@@ -74,9 +74,6 @@ private:
 
 public:
 
-  /// Base class to handle mutual dependencies of most objects
-  class deps;
-
   friend class colvarproxy;
   // TODO colvarscript should be unaware of colvarmodule's internals
   friend class colvarscript;
diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp
index da39f78356..47b1970220 100644
--- a/lib/colvars/colvarparse.cpp
+++ b/lib/colvars/colvarparse.cpp
@@ -356,7 +356,7 @@ bool colvarparse::get_keyval(std::string const &conf,
 
 bool colvarparse::get_keyval(std::string const &conf,
                              char const *key,
-                             cvm::deps::feature_state *value,
+                             colvardeps::feature_state *value,
                              bool const &def_value,
                              Parse_Mode const parse_mode)
 {
@@ -695,7 +695,6 @@ bool colvarparse::key_lookup(std::string const &conf,
                        line+"\".\n", INPUT_ERROR);
             return false;
           }
-          size_t const old_end = line.size();
 
           line_begin = line_end;
           nl = conf.find('\n', line_begin+1);
@@ -715,8 +714,6 @@ bool colvarparse::key_lookup(std::string const &conf,
         }
       }
 
-      cvm::log("Value so far = "+line.substr(data_begin, (data_end-data_begin))+".\n");
-
       // strip the leading and trailing braces
       data_begin = line.find_first_of('{') + 1;
       data_begin = line.find_first_not_of(white_space,
diff --git a/lib/colvars/colvarparse.h b/lib/colvars/colvarparse.h
index c091cbc15d..7685b4eeb4 100644
--- a/lib/colvars/colvarparse.h
+++ b/lib/colvars/colvarparse.h
@@ -183,7 +183,7 @@ public:
                   Parse_Mode const parse_mode = parse_normal);
   bool get_keyval(std::string const &conf,
                   char const *key,
-                  cvm::deps::feature_state *value,
+                  colvardeps::feature_state *value,
                   bool const &def_value = false,
                   Parse_Mode const parse_mode = parse_normal);
 
-- 
GitLab


From 3b476d914f5ea387bb074f4f3f2d3d36c7bb92d2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 13 Aug 2016 07:24:26 -0400
Subject: [PATCH 13/52] update colvars to version 2016-08-10

(cherry picked from commit eba3ad9abb37b53fc2f79449bb8eada8f0ec526a)
---
 lib/colvars/colvar.cpp                  | 51 +++++++++++++++----------
 lib/colvars/colvar.h                    | 14 +++----
 lib/colvars/colvaratoms.cpp             | 24 ++++++------
 lib/colvars/colvaratoms.h               | 20 +++++-----
 lib/colvars/colvarbias_abf.cpp          | 44 +++++++++++----------
 lib/colvars/colvarbias_abf.h            |  4 +-
 lib/colvars/colvarcomp.h                | 18 ++++-----
 lib/colvars/colvarcomp_angles.cpp       | 28 +++++++-------
 lib/colvars/colvarcomp_distances.cpp    | 40 +++++++++----------
 lib/colvars/colvardeps.cpp              | 24 ++++++------
 lib/colvars/colvardeps.h                | 16 ++++----
 lib/colvars/colvarmodule.h              |  8 ++--
 lib/colvars/colvarproxy.h               | 25 +++++-------
 lib/colvars/colvarscript.cpp            |  2 +-
 src/USER-COLVARS/colvarproxy_lammps.cpp | 10 +----
 src/USER-COLVARS/colvarproxy_lammps.h   |  6 +--
 src/USER-COLVARS/fix_colvars.cpp        |  2 +-
 17 files changed, 168 insertions(+), 168 deletions(-)

diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp
index c630154aa3..1dd46524ac 100644
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@@ -374,10 +374,19 @@ colvar::colvar(std::string const &conf)
   }
 
   {
-    bool b_output_system_force;
-    get_keyval(conf, "outputSystemForce", b_output_system_force, false);
-    if (b_output_system_force) {
-      enable(f_cv_output_system_force);
+    bool temp;
+    if (get_keyval(conf, "outputSystemForce", temp, false)) {
+      cvm::error("Colvar option outputSystemForce is deprecated.\n"
+        "Please use outputTotalForce, or outputSystemForce within an ABF bias.");
+      return;
+    }
+  }
+
+  {
+    bool b_output_total_force;
+    get_keyval(conf, "outputTotalForce", b_output_total_force, false);
+    if (b_output_total_force) {
+      enable(f_cv_output_total_force);
     }
   }
 
@@ -555,8 +564,8 @@ int colvar::init_components(std::string const &conf)
 int colvar::refresh_deps()
 {
   // If enabled features are changed upstream, the features below should be refreshed
-  if (is_enabled(f_cv_system_force_calc)) {
-    cvm::request_system_force();
+  if (is_enabled(f_cv_total_force_calc)) {
+    cvm::request_total_force();
   }
   if (is_enabled(f_cv_collect_gradient) && atom_ids.size() == 0) {
     build_atom_list();
@@ -972,17 +981,17 @@ int colvar::calc_cvc_sys_forces(int first_cvc, size_t num_cvcs)
   size_t const cvc_max_count = num_cvcs ? num_cvcs : num_active_cvcs();
   size_t i, cvc_count;
 
-  if (is_enabled(f_cv_system_force_calc)) {
+  if (is_enabled(f_cv_total_force_calc)) {
     if (cvm::debug())
-      cvm::log("Calculating system force of colvar \""+this->name+"\".\n");
+      cvm::log("Calculating total force of colvar \""+this->name+"\".\n");
 
     // if (!tasks[task_extended_lagrangian] && (cvm::step_relative() > 0)) {
-   // Disabled check to allow for explicit system force calculation
+   // Disabled check to allow for explicit total force calculation
     // even with extended Lagrangian
 
     if (cvm::step_relative() > 0) {
       cvm::increase_depth();
-      // get from the cvcs the system forces from the PREVIOUS step
+      // get from the cvcs the total forces from the PREVIOUS step
       for (i = first_cvc, cvc_count = 0;
           (i < cvcs.size()) && (cvc_count < cvc_max_count);
           i++) {
@@ -994,7 +1003,7 @@ int colvar::calc_cvc_sys_forces(int first_cvc, size_t num_cvcs)
     }
 
     if (cvm::debug())
-      cvm::log("Done calculating system force of colvar \""+this->name+"\".\n");
+      cvm::log("Done calculating total force of colvar \""+this->name+"\".\n");
   }
 
   return COLVARS_OK;
@@ -1003,20 +1012,20 @@ int colvar::calc_cvc_sys_forces(int first_cvc, size_t num_cvcs)
 
 int colvar::collect_cvc_sys_forces()
 {
-  if (is_enabled(f_cv_system_force_calc)) {
+  if (is_enabled(f_cv_total_force_calc)) {
     ft.reset();
 
     if (cvm::step_relative() > 0) {
-      // get from the cvcs the system forces from the PREVIOUS step
+      // get from the cvcs the total forces from the PREVIOUS step
       for (size_t i = 0; i < cvcs.size();  i++) {
         if (!cvcs[i]->is_enabled()) continue;
         // linear combination is assumed
-        ft += (cvcs[i])->system_force() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
+        ft += (cvcs[i])->total_force() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
       }
     }
 
     if (!is_enabled(f_cv_hide_Jacobian)) {
-      // add the Jacobian force to the system force, and don't apply any silent
+      // add the Jacobian force to the total force, and don't apply any silent
       // correction internally: biases such as colvarbias_abf will handle it
       ft += fj;
     }
@@ -1088,7 +1097,7 @@ int colvar::calc_colvar_properties()
     // report the restraint center as "value"
     x_reported = xr;
     v_reported = vr;
-    // the "system force" with the extended Lagrangian is just the
+    // the "total force" with the extended Lagrangian is just the
     // harmonic term acting on the extended coordinate
     // Note: this is the force for current timestep
     ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
@@ -1117,7 +1126,7 @@ cvm::real colvar::update_forces_energy()
   f += fb;
 
   if (is_enabled(f_cv_Jacobian)) {
-    // the instantaneous Jacobian force was not included in the reported system force;
+    // the instantaneous Jacobian force was not included in the reported total force;
     // instead, it is subtracted from the applied force (silent Jacobian correction)
     if (is_enabled(f_cv_hide_Jacobian))
       f -= fj;
@@ -1482,7 +1491,7 @@ std::istream & colvar::read_traj(std::istream &is)
     }
   }
 
-  if (is_enabled(f_cv_output_system_force)) {
+  if (is_enabled(f_cv_output_total_force)) {
     is >> ft;
     ft_reported = ft;
   }
@@ -1567,8 +1576,8 @@ std::ostream & colvar::write_traj_label(std::ostream & os)
        << cvm::wrap_string(this->name, this_cv_width-3);
   }
 
-  if (is_enabled(f_cv_output_system_force)) {
-    os << " fs_"
+  if (is_enabled(f_cv_output_total_force)) {
+    os << " ft_"
        << cvm::wrap_string(this->name, this_cv_width-3);
   }
 
@@ -1620,7 +1629,7 @@ std::ostream & colvar::write_traj(std::ostream &os)
   }
 
 
-  if (is_enabled(f_cv_output_system_force)) {
+  if (is_enabled(f_cv_output_total_force)) {
     os << " "
        << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
        << ft_reported;
diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h
index 05314b78e8..665b3d6427 100644
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@@ -54,7 +54,7 @@ public:
   /// \brief Current velocity (previously set by calc() or by read_traj())
   colvarvalue const & velocity() const;
 
-  /// \brief Current system force (previously obtained from calc() or
+  /// \brief Current total force (previously obtained from calc() or
   /// read_traj()).  Note: this is calculated using the atomic forces
   /// from the last simulation step.
   ///
@@ -62,7 +62,7 @@ public:
   /// acting on the collective variable is calculated summing those
   /// from all colvar components, the bias and walls forces are
   /// subtracted.
-  colvarvalue const & system_force() const;
+  colvarvalue const & total_force() const;
 
   /// \brief Typical fluctuation amplitude for this collective
   /// variable (e.g. local width of a free energy basin)
@@ -160,7 +160,7 @@ protected:
   /// \brief Jacobian force, when Jacobian_force is enabled
   colvarvalue fj;
 
-  /// Cached reported system force
+  /// Cached reported total force
   colvarvalue ft_reported;
 
 public:
@@ -176,7 +176,7 @@ public:
   colvarvalue f;
 
   /// \brief Total force, as derived from the atomic trajectory;
-  /// should equal the total system force plus \link f \endlink
+  /// should equal the system force plus \link f \endlink
   colvarvalue ft;
 
 
@@ -253,7 +253,7 @@ public:
   int calc_cvc_values(int first, size_t num_cvcs);
   /// \brief Same as \link colvar::calc_cvc_values \endlink but for gradients
   int calc_cvc_gradients(int first, size_t num_cvcs);
-  /// \brief Same as \link colvar::calc_cvc_values \endlink but for system forces
+  /// \brief Same as \link colvar::calc_cvc_values \endlink but for total forces
   int calc_cvc_sys_forces(int first, size_t num_cvcs);
   /// \brief Same as \link colvar::calc_cvc_values \endlink but for Jacobian derivatives/forces
   int calc_cvc_Jacobians(int first, size_t num_cvcs);
@@ -265,7 +265,7 @@ public:
   int collect_cvc_values();
   /// \brief Same as \link colvar::collect_cvc_values \endlink but for gradients
   int collect_cvc_gradients();
-  /// \brief Same as \link colvar::collect_cvc_values \endlink but for system forces
+  /// \brief Same as \link colvar::collect_cvc_values \endlink but for total forces
   int collect_cvc_sys_forces();
   /// \brief Same as \link colvar::collect_cvc_values \endlink but for Jacobian derivatives/forces
   int collect_cvc_Jacobians();
@@ -555,7 +555,7 @@ inline colvarvalue const & colvar::velocity() const
 }
 
 
-inline colvarvalue const & colvar::system_force() const
+inline colvarvalue const & colvar::total_force() const
 {
   return ft_reported;
 }
diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp
index 5eba67f0f1..0d0a339a69 100644
--- a/lib/colvars/colvaratoms.cpp
+++ b/lib/colvars/colvaratoms.cpp
@@ -870,21 +870,21 @@ void cvm::atom_group::read_velocities()
 
 
 // TODO make this a calc function
-void cvm::atom_group::read_system_forces()
+void cvm::atom_group::read_total_forces()
 {
   if (b_dummy) return;
 
   if (b_rotate) {
 
     for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
-      ai->read_system_force();
-      ai->system_force = rot.rotate(ai->system_force);
+      ai->read_total_force();
+      ai->total_force = rot.rotate(ai->total_force);
     }
 
   } else {
 
     for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
-      ai->read_system_force();
+      ai->read_total_force();
     }
   }
 }
@@ -1070,15 +1070,15 @@ std::vector<cvm::rvector> cvm::atom_group::velocities() const
   return v;
 }
 
-std::vector<cvm::rvector> cvm::atom_group::system_forces() const
+std::vector<cvm::rvector> cvm::atom_group::total_forces() const
 {
   if (b_dummy) {
-    cvm::error("Error: system forces are not available "
+    cvm::error("Error: total forces are not available "
                "from a dummy atom group.\n", INPUT_ERROR);
   }
 
   if (is_enabled(f_ag_scalable)) {
-    cvm::error("Error: atomic system forces are not available "
+    cvm::error("Error: atomic total forces are not available "
                "from a scalable atom group.\n", INPUT_ERROR);
   }
 
@@ -1086,27 +1086,27 @@ std::vector<cvm::rvector> cvm::atom_group::system_forces() const
   cvm::atom_const_iter ai = this->begin();
   std::vector<cvm::atom_pos>::iterator fi = f.begin();
   for ( ; ai != this->end(); ++fi, ++ai) {
-    *fi = ai->system_force;
+    *fi = ai->total_force;
   }
   return f;
 }
 
 
 // TODO make this an accessor
-cvm::rvector cvm::atom_group::system_force() const
+cvm::rvector cvm::atom_group::total_force() const
 {
   if (b_dummy) {
-    cvm::error("Error: total system forces are not available "
+    cvm::error("Error: total total forces are not available "
                "from a dummy atom group.\n", INPUT_ERROR);
   }
 
   if (is_enabled(f_ag_scalable)) {
-    return (cvm::proxy)->get_atom_group_system_force(index);
+    return (cvm::proxy)->get_atom_group_total_force(index);
   }
 
   cvm::rvector f(0.0);
   for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) {
-    f += ai->system_force;
+    f += ai->total_force;
   }
   return f;
 }
diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h
index 4ba70b2855..7a4d031daa 100644
--- a/lib/colvars/colvaratoms.h
+++ b/lib/colvars/colvaratoms.h
@@ -45,7 +45,7 @@ public:
 
   /// \brief System force at the previous step (copied from the
   /// program, can be modified if necessary)
-  cvm::rvector    system_force;
+  cvm::rvector    total_force;
 
   /// \brief Gradient of a scalar collective variable with respect
   /// to this atom
@@ -86,7 +86,7 @@ public:
   inline void reset_data()
   {
     pos = cvm::atom_pos(0.0);
-    vel = grad = system_force = cvm::rvector(0.0);
+    vel = grad = total_force = cvm::rvector(0.0);
   }
 
   /// Get the latest value of the mass
@@ -113,10 +113,10 @@ public:
     vel = (cvm::proxy)->get_atom_velocity(index);
   }
 
-  /// Get the system force
-  inline void read_system_force()
+  /// Get the total force
+  inline void read_total_force()
   {
-    system_force = (cvm::proxy)->get_atom_system_force(index);
+    total_force = (cvm::proxy)->get_atom_total_force(index);
   }
 
   /// \brief Apply a force to the atom
@@ -336,10 +336,10 @@ public:
   /// rotation applied to the coordinates will be used
   void read_velocities();
 
-  /// \brief Get the current system_forces; this must be called always
+  /// \brief Get the current total_forces; this must be called always
   /// *after* read_positions(); if b_rotate is defined, the same
   /// rotation applied to the coordinates will be used
-  void read_system_forces();
+  void read_total_forces();
 
   /// Call reset_data() for each atom
   inline void reset_atoms_data()
@@ -410,11 +410,11 @@ public:
     return dip;
   }
 
-  /// \brief Return a copy of the system forces
-  std::vector<cvm::rvector> system_forces() const;
+  /// \brief Return a copy of the total forces
+  std::vector<cvm::rvector> total_forces() const;
 
   /// \brief Return a copy of the aggregated total force on the group
-  cvm::rvector system_force() const;
+  cvm::rvector total_force() const;
 
 
   /// \brief Shorthand: save the specified gradient on each atom,
diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp
index 475e4ecef0..f2659951d4 100644
--- a/lib/colvars/colvarbias_abf.cpp
+++ b/lib/colvars/colvarbias_abf.cpp
@@ -7,7 +7,7 @@
 
 colvarbias_abf::colvarbias_abf(char const *key)
   : colvarbias(key),
-    force(NULL),
+    system_force(NULL),
     gradients(NULL),
     samples(NULL),
     z_gradients(NULL),
@@ -81,8 +81,8 @@ int colvarbias_abf::init(std::string const &conf)
   }
 
   if (update_bias) {
-  // Request calculation of system force (which also checks for availability)
-    if(enable(f_cvb_get_system_force)) return cvm::get_error();
+  // Request calculation of total force (which also checks for availability)
+    if(enable(f_cvb_get_total_force)) return cvm::get_error();
   }
   if (apply_bias) {
     if(enable(f_cvb_apply_force)) return cvm::get_error();
@@ -112,7 +112,7 @@ int colvarbias_abf::init(std::string const &conf)
     if (max_force.size() != colvars.size()) {
       cvm::error("Error: Number of parameters to maxForce does not match number of colvars.");
     }
-    for (size_t i=0; i<colvars.size(); i++) {
+    for (size_t i = 0; i < colvars.size(); i++) {
       if (max_force[i] < 0.0) {
         cvm::error("Error: maxForce should be non-negative.");
       }
@@ -124,7 +124,7 @@ int colvarbias_abf::init(std::string const &conf)
 
   bin.assign(colvars.size(), 0);
   force_bin.assign(colvars.size(), 0);
-  force = new cvm::real [colvars.size()];
+  system_force = new cvm::real [colvars.size()];
 
   // Construct empty grids based on the colvars
   if (cvm::debug()) {
@@ -208,9 +208,9 @@ colvarbias_abf::~colvarbias_abf()
     last_gradients = NULL;
   }
 
-  if (force) {
-    delete [] force;
-    force = NULL;
+  if (system_force) {
+    delete [] system_force;
+    system_force = NULL;
   }
 
   if (cvm::n_abf_biases > 0)
@@ -231,35 +231,39 @@ int colvarbias_abf::update()
     // initialization stuff (file operations relying on n_abf_biases
     // compute current value of colvars
 
-    for (size_t i=0; i<colvars.size(); i++) {
+    for (size_t i = 0; i < colvars.size(); i++) {
       bin[i] = samples->current_bin_scalar(i);
     }
 
   } else {
 
-    for (size_t i=0; i<colvars.size(); i++) {
+    for (size_t i = 0; i < colvars.size(); i++) {
       bin[i] = samples->current_bin_scalar(i);
     }
 
     if ( update_bias && samples->index_ok(force_bin) ) {
       // Only if requested and within bounds of the grid...
 
-      for (size_t i=0; i<colvars.size(); i++) {	  // get forces(lagging by 1 timestep) from colvars
-        force[i] = colvars[i]->system_force();
+      for (size_t i = 0; i < colvars.size(); i++) {
+        // get total forces (lagging by 1 timestep) from colvars
+        // and subtract previous ABF force
+        system_force[i] = colvars[i]->total_force().real_value
+                        - colvar_forces[i].real_value;
       }
-      gradients->acc_force(force_bin, force);
+      gradients->acc_force(force_bin, system_force);
     }
     if ( z_gradients && update_bias ) {
-      for (size_t i=0; i<colvars.size(); i++) {
+      for (size_t i = 0; i < colvars.size(); i++) {
         z_bin[i] = z_samples->current_bin_scalar(i);
       }
       if ( z_samples->index_ok(z_bin) ) {
-        for (size_t i=0; i<colvars.size(); i++) {
+        for (size_t i = 0; i < colvars.size(); i++) {
           // If we are outside the range of xi, the force has not been obtained above
           // the function is just an accessor, so cheap to call again anyway
-          force[i] = colvars[i]->system_force();
+          system_force[i] = colvars[i]->total_force().real_value
+                          - colvar_forces[i].real_value;
         }
-        z_gradients->acc_force(z_bin, force);
+        z_gradients->acc_force(z_bin, system_force);
       }
     }
   }
@@ -268,7 +272,7 @@ int colvarbias_abf::update()
   force_bin = bin;
 
   // Reset biasing forces from previous timestep
-  for (size_t i=0; i<colvars.size(); i++) {
+  for (size_t i = 0; i < colvars.size(); i++) {
     colvar_forces[i].reset();
   }
 
@@ -292,13 +296,13 @@ int colvarbias_abf::update()
         // in other words: boundary condition is that the biasing potential is periodic
         colvar_forces[0].real_value = fact * (grad[0] / cvm::real(count) - gradients->average());
       } else {
-        for (size_t i=0; i<colvars.size(); i++) {
+        for (size_t i = 0; i < colvars.size(); i++) {
           // subtracting the mean force (opposite of the FE gradient) means adding the gradient
           colvar_forces[i].real_value = fact * grad[i] / cvm::real(count);
         }
       }
       if (cap_force) {
-        for (size_t i=0; i<colvars.size(); i++) {
+        for (size_t i = 0; i < colvars.size(); i++) {
           if ( colvar_forces[i].real_value * colvar_forces[i].real_value > max_force[i] * max_force[i] ) {
             colvar_forces[i].real_value = (colvar_forces[i].real_value > 0 ? max_force[i] : -1.0 * max_force[i]);
           }
diff --git a/lib/colvars/colvarbias_abf.h b/lib/colvars/colvarbias_abf.h
index 18b9a463b5..8db0b75632 100644
--- a/lib/colvars/colvarbias_abf.h
+++ b/lib/colvars/colvarbias_abf.h
@@ -27,7 +27,7 @@ public:
 private:
 
   /// Filename prefix for human-readable gradient/sample count output
-  std::string	output_prefix;
+  std::string  output_prefix;
 
   /// Base filename(s) for reading previous gradient data (replaces data from restart file)
   std::vector<std::string> input_prefix;
@@ -50,7 +50,7 @@ private:
   // Internal data and methods
 
   std::vector<int>  bin, force_bin, z_bin;
-  gradient_t	    force;
+  gradient_t    system_force, applied_force;
 
   /// n-dim grid of free energy gradients
   colvar_grid_gradient  *gradients;
diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h
index deed1a4721..f632754ab6 100644
--- a/lib/colvars/colvarcomp.h
+++ b/lib/colvars/colvarcomp.h
@@ -153,8 +153,8 @@ public:
   // /// \brief Return const pointer to the previously calculated value
   // virtual const colvarvalue *p_value() const;
 
-  /// \brief Return the previously calculated system force
-  virtual colvarvalue const & system_force() const;
+  /// \brief Return the previously calculated total force
+  virtual colvarvalue const & total_force() const;
 
   /// \brief Return the previously calculated divergence of the
   /// inverse atomic gradients
@@ -232,7 +232,7 @@ protected:
   /// \brief Value at the previous step
   colvarvalue x_old;
 
-  /// \brief Calculated system force (\b Note: this is calculated from
+  /// \brief Calculated total force (\b Note: this is calculated from
   /// the total atomic forces read from the program, subtracting fromt
   /// the "internal" forces of the system the "external" forces from
   /// the colvar biases)
@@ -256,7 +256,7 @@ inline colvarvalue const & colvar::cvc::value() const
 //   return &x;
 // }
 
-inline colvarvalue const & colvar::cvc::system_force() const
+inline colvarvalue const & colvar::cvc::total_force() const
 {
   return ft;
 }
@@ -306,7 +306,7 @@ protected:
   cvm::rvector     dist_v;
   /// Use absolute positions, ignoring PBCs when present
   bool b_no_PBC;
-  /// Compute system force on first site only to avoid unwanted
+  /// Compute total force on first site only to avoid unwanted
   /// coupling to other colvars (see e.g. Ciccotti et al., 2005)
   bool b_1site_force;
 public:
@@ -388,7 +388,7 @@ protected:
   cvm::atom_group  *ref2;
   /// Use absolute positions, ignoring PBCs when present
   bool b_no_PBC;
-  /// Compute system force on one site only to avoid unwanted
+  /// Compute total force on one site only to avoid unwanted
   /// coupling to other colvars (see e.g. Ciccotti et al., 2005)
   bool b_1site_force;
   /// Vector on which the distance vector is projected
@@ -637,7 +637,7 @@ protected:
   /// Derivatives wrt group centers of mass
   cvm::rvector dxdr1, dxdr3;
 
-  /// Compute system force on first site only to avoid unwanted
+  /// Compute total force on first site only to avoid unwanted
   /// coupling to other colvars (see e.g. Ciccotti et al., 2005)
   /// (or to allow dummy atoms)
   bool b_1site_force;
@@ -683,7 +683,7 @@ protected:
   /// Derivatives wrt group centers of mass
   cvm::rvector dxdr1, dxdr3;
 
-  /// Compute system force on first site only to avoid unwanted
+  /// Compute total force on first site only to avoid unwanted
   /// coupling to other colvars (see e.g. Ciccotti et al., 2005)
   /// (or to allow dummy atoms)
   bool b_1site_force;
@@ -724,7 +724,7 @@ protected:
   /// Inter site vectors
   cvm::rvector r12, r23, r34;
 
-  /// \brief Compute system force on first site only to avoid unwanted
+  /// \brief Compute total force on first site only to avoid unwanted
   /// coupling to other colvars (see e.g. Ciccotti et al., 2005)
   bool b_1site_force;
 
diff --git a/lib/colvars/colvarcomp_angles.cpp b/lib/colvars/colvarcomp_angles.cpp
index a4bf53feb7..b1acb201ae 100644
--- a/lib/colvars/colvarcomp_angles.cpp
+++ b/lib/colvars/colvarcomp_angles.cpp
@@ -19,7 +19,7 @@ colvar::angle::angle(std::string const &conf)
   group2 = parse_group(conf, "group2");
   group3 = parse_group(conf, "group3");
   if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
-    cvm::log("Computing system force on group 1 only");
+    cvm::log("Computing total force on group 1 only");
   }
   x.type(colvarvalue::type_scalar);
 }
@@ -95,15 +95,15 @@ void colvar::angle::calc_force_invgrads()
   // when propagating changes in the angle)
 
   if (b_1site_force) {
-    group1->read_system_forces();
+    group1->read_total_forces();
     cvm::real norm_fact = 1.0 / dxdr1.norm2();
-    ft.real_value = norm_fact * dxdr1 * group1->system_force();
+    ft.real_value = norm_fact * dxdr1 * group1->total_force();
   } else {
-    group1->read_system_forces();
-    group3->read_system_forces();
+    group1->read_total_forces();
+    group3->read_total_forces();
     cvm::real norm_fact = 1.0 / (dxdr1.norm2() + dxdr3.norm2());
-    ft.real_value = norm_fact * ( dxdr1 * group1->system_force()
-                                + dxdr3 * group3->system_force());
+    ft.real_value = norm_fact * ( dxdr1 * group1->total_force()
+                                + dxdr3 * group3->total_force());
   }
   return;
 }
@@ -141,7 +141,7 @@ colvar::dipole_angle::dipole_angle(std::string const &conf)
   group3 = parse_group(conf, "group3");
 
   if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
-    cvm::log("Computing system force on group 1 only");
+    cvm::log("Computing total force on group 1 only");
   }
   x.type(colvarvalue::type_scalar);
 }
@@ -251,7 +251,7 @@ colvar::dihedral::dihedral(std::string const &conf)
   provide(f_cvc_com_based);
 
   if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
-    cvm::log("Computing system force on group 1 only");
+    cvm::log("Computing total force on group 1 only");
   }
   group1 = parse_group(conf, "group1");
   group2 = parse_group(conf, "group2");
@@ -421,15 +421,15 @@ void colvar::dihedral::calc_force_invgrads()
   cvm::real const fact1 = d12 * std::sqrt(1.0 - dot1 * dot1);
   cvm::real const fact4 = d34 * std::sqrt(1.0 - dot4 * dot4);
 
-  group1->read_system_forces();
+  group1->read_total_forces();
   if ( b_1site_force ) {
     // This is only measuring the force on group 1
-    ft.real_value = PI/180.0 * fact1 * (cross1 * group1->system_force());
+    ft.real_value = PI/180.0 * fact1 * (cross1 * group1->total_force());
   } else {
     // Default case: use groups 1 and 4
-    group4->read_system_forces();
-    ft.real_value = PI/180.0 * 0.5 * (fact1 * (cross1 * group1->system_force())
-				      + fact4 * (cross4 * group4->system_force()));
+    group4->read_total_forces();
+    ft.real_value = PI/180.0 * 0.5 * (fact1 * (cross1 * group1->total_force())
+				      + fact4 * (cross4 * group4->total_force()));
   }
 }
 
diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp
index ff6b03e2c5..f7bf2b87f0 100644
--- a/lib/colvars/colvarcomp_distances.cpp
+++ b/lib/colvars/colvarcomp_distances.cpp
@@ -22,7 +22,7 @@ colvar::distance::distance(std::string const &conf)
     cvm::log("Computing distance using absolute positions (not minimal-image)");
   }
   if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
-    cvm::log("Computing system force on group 1 only");
+    cvm::log("Computing total force on group 1 only");
   }
   group1 = parse_group(conf, "group1");
   group2 = parse_group(conf, "group2");
@@ -66,12 +66,12 @@ void colvar::distance::calc_gradients()
 
 void colvar::distance::calc_force_invgrads()
 {
-  group1->read_system_forces();
+  group1->read_total_forces();
   if ( b_1site_force ) {
-    ft.real_value = -1.0 * (group1->system_force() * dist_v.unit());
+    ft.real_value = -1.0 * (group1->total_force() * dist_v.unit());
   } else {
-    group2->read_system_forces();
-    ft.real_value = 0.5 * ((group2->system_force() - group1->system_force()) * dist_v.unit());
+    group2->read_total_forces();
+    ft.real_value = 0.5 * ((group2->total_force() - group1->total_force()) * dist_v.unit());
   }
 }
 
@@ -186,7 +186,7 @@ colvar::distance_z::distance_z(std::string const &conf)
     cvm::log("Computing distance using absolute positions (not minimal-image)");
   }
   if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
-    cvm::log("Computing system force on group \"main\" only");
+    cvm::log("Computing total force on group \"main\" only");
   }
 }
 
@@ -249,13 +249,13 @@ void colvar::distance_z::calc_gradients()
 
 void colvar::distance_z::calc_force_invgrads()
 {
-  main->read_system_forces();
+  main->read_total_forces();
 
   if (fixed_axis && !b_1site_force) {
-    ref1->read_system_forces();
-    ft.real_value = 0.5 * ((main->system_force() - ref1->system_force()) * axis);
+    ref1->read_total_forces();
+    ft.real_value = 0.5 * ((main->total_force() - ref1->total_force()) * axis);
   } else {
-    ft.real_value = main->system_force() * axis;
+    ft.real_value = main->total_force() * axis;
   }
 }
 
@@ -349,13 +349,13 @@ void colvar::distance_xy::calc_gradients()
 
 void colvar::distance_xy::calc_force_invgrads()
 {
-  main->read_system_forces();
+  main->read_total_forces();
 
   if (fixed_axis && !b_1site_force) {
-    ref1->read_system_forces();
-    ft.real_value = 0.5 / x.real_value * ((main->system_force() - ref1->system_force()) * dist_v_ortho);
+    ref1->read_total_forces();
+    ft.real_value = 0.5 / x.real_value * ((main->total_force() - ref1->total_force()) * dist_v_ortho);
   } else {
-    ft.real_value = 1.0 / x.real_value * main->system_force() * dist_v_ortho;
+    ft.real_value = 1.0 / x.real_value * main->total_force() * dist_v_ortho;
   }
 }
 
@@ -655,13 +655,13 @@ void colvar::gyration::calc_gradients()
 
 void colvar::gyration::calc_force_invgrads()
 {
-  atoms->read_system_forces();
+  atoms->read_total_forces();
 
   cvm::real const dxdr = 1.0/x.real_value;
   ft.real_value = 0.0;
 
   for (cvm::atom_iter ai = atoms->begin(); ai != atoms->end(); ai++) {
-    ft.real_value += dxdr * ai->pos * ai->system_force;
+    ft.real_value += dxdr * ai->pos * ai->total_force;
   }
 }
 
@@ -903,13 +903,13 @@ void colvar::rmsd::apply_force(colvarvalue const &force)
 
 void colvar::rmsd::calc_force_invgrads()
 {
-  atoms->read_system_forces();
+  atoms->read_total_forces();
   ft.real_value = 0.0;
 
   // Note: gradient square norm is 1/N_atoms
 
   for (size_t ia = 0; ia < atoms->size(); ia++) {
-    ft.real_value += (*atoms)[ia].grad * (*atoms)[ia].system_force;
+    ft.real_value += (*atoms)[ia].grad * (*atoms)[ia].total_force;
   }
   ft.real_value *= atoms->size();
 }
@@ -1191,12 +1191,12 @@ void colvar::eigenvector::apply_force(colvarvalue const &force)
 
 void colvar::eigenvector::calc_force_invgrads()
 {
-  atoms->read_system_forces();
+  atoms->read_total_forces();
   ft.real_value = 0.0;
 
   for (size_t ia = 0; ia < atoms->size(); ia++) {
     ft.real_value += eigenvec_invnorm2 * (*atoms)[ia].grad *
-      (*atoms)[ia].system_force;
+      (*atoms)[ia].total_force;
   }
 }
 
diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp
index c4915569e2..7d8d05a2be 100644
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@@ -207,8 +207,8 @@ void colvardeps::init_cvb_requires() {
   f_description(f_cvb_apply_force, "apply force");
   f_req_children(f_cvb_apply_force, f_cv_gradient);
 
-  f_description(f_cvb_get_system_force, "obtain system force");
-  f_req_children(f_cvb_get_system_force, f_cv_system_force);
+  f_description(f_cvb_get_total_force, "obtain total force");
+  f_req_children(f_cvb_get_total_force, f_cv_total_force);
 
   f_description(f_cvb_history_dependent, "history-dependent");
 
@@ -247,15 +247,15 @@ void colvardeps::init_cv_requires() {
     f_description(f_cv_fdiff_velocity, "fdiff_velocity");
 
     // System force: either trivial (spring force); through extended Lagrangian, or calculated explicitly
-    f_description(f_cv_system_force, "system force");
-    f_req_alt2(f_cv_system_force, f_cv_extended_Lagrangian, f_cv_system_force_calc);
+    f_description(f_cv_total_force, "total force");
+    f_req_alt2(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc);
 
-    // Deps for explicit system force calculation
-    f_description(f_cv_system_force_calc, "system force calculation");
-    f_req_self(f_cv_system_force_calc, f_cv_scalar);
-    f_req_self(f_cv_system_force_calc, f_cv_linear);
-    f_req_children(f_cv_system_force_calc, f_cvc_inv_gradient);
-    f_req_self(f_cv_system_force_calc, f_cv_Jacobian);
+    // Deps for explicit total force calculation
+    f_description(f_cv_total_force_calc, "total force calculation");
+    f_req_self(f_cv_total_force_calc, f_cv_scalar);
+    f_req_self(f_cv_total_force_calc, f_cv_linear);
+    f_req_children(f_cv_total_force_calc, f_cvc_inv_gradient);
+    f_req_self(f_cv_total_force_calc, f_cv_Jacobian);
 
     f_description(f_cv_Jacobian, "Jacobian derivative");
     f_req_self(f_cv_Jacobian, f_cv_scalar);
@@ -283,8 +283,8 @@ void colvardeps::init_cv_requires() {
 
     f_description(f_cv_output_applied_force, "output applied force");
 
-    f_description(f_cv_output_system_force, "output system force");
-    f_req_self(f_cv_output_system_force, f_cv_system_force);
+    f_description(f_cv_output_total_force, "output total force");
+    f_req_self(f_cv_output_total_force, f_cv_total_force);
 
     f_description(f_cv_lower_boundary, "lower boundary");
     f_req_self(f_cv_lower_boundary, f_cv_scalar);
diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h
index 7e69865a56..a2f6f2d5f9 100644
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@@ -161,7 +161,7 @@ public:
     /// \brief Bias is active
     f_cvb_active,
     f_cvb_apply_force, // will apply forces
-    f_cvb_get_system_force, // requires system forces
+    f_cvb_get_total_force, // requires total forces
     f_cvb_history_dependent, // depends on simulation history
     f_cvb_ntot
   };
@@ -177,14 +177,14 @@ public:
     f_cv_collect_gradient,
     /// \brief Calculate the velocity with finite differences
     f_cv_fdiff_velocity,
-    /// \brief The system force is calculated, projecting the atomic
+    /// \brief The total force is calculated, projecting the atomic
     /// forces on the inverse gradient
-    f_cv_system_force,
-    /// \brief Calculate system force from atomic forces
-    f_cv_system_force_calc,
+    f_cv_total_force,
+    /// \brief Calculate total force from atomic forces
+    f_cv_total_force_calc,
     /// \brief Estimate Jacobian derivative
     f_cv_Jacobian,
-    /// \brief Do not report the Jacobian force as part of the system force
+    /// \brief Do not report the Jacobian force as part of the total force
     /// instead, apply a correction internally to cancel it
     f_cv_hide_Jacobian,
     /// \brief The variable has a harmonic restraint around a moving
@@ -202,8 +202,8 @@ public:
     f_cv_output_velocity,
     /// \brief Output the applied force to the trajectory file
     f_cv_output_applied_force,
-    /// \brief Output the system force to the trajectory file
-    f_cv_output_system_force,
+    /// \brief Output the total force to the trajectory file
+    f_cv_output_total_force,
     /// \brief A lower boundary is defined
     f_cv_lower_boundary,
     /// \brief An upper boundary is defined
diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h
index f461728de8..cb4272f0bd 100644
--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@@ -384,8 +384,8 @@ public:
   /// \brief Time step of MD integrator (fs)
   static real dt();
 
-  /// Request calculation of system force from MD engine
-  static void request_system_force();
+  /// Request calculation of total force from MD engine
+  static void request_total_force();
 
   /// Print a message to the main log
   static void log(std::string const &message);
@@ -634,9 +634,9 @@ inline int cvm::replica_comm_send(char* msg_data, int msg_len, int dest_rep) {
 }
 
 
-inline void cvm::request_system_force()
+inline void cvm::request_total_force()
 {
-  proxy->request_system_force(true);
+  proxy->request_total_force(true);
 }
 
 inline void cvm::select_closest_image(atom_pos &pos,
diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h
index 4bba189bb7..bd5ee3da47 100644
--- a/lib/colvars/colvarproxy.h
+++ b/lib/colvars/colvarproxy.h
@@ -295,11 +295,11 @@ public:
   /// Pass restraint energy value for current timestep to MD engine
   virtual void add_energy(cvm::real energy) = 0;
 
-  /// Tell the proxy whether system forces are needed (may not always be available)
-  virtual void request_system_force(bool yesno)
+  /// Tell the proxy whether total forces are needed (may not always be available)
+  virtual void request_total_force(bool yesno)
   {
     if (yesno == true)
-      cvm::error("Error: system forces are currently not implemented.\n",
+      cvm::error("Error: total forces are currently not implemented.\n",
                  COLVARS_NOT_IMPLEMENTED);
   }
 
@@ -354,8 +354,6 @@ protected:
   std::vector<cvm::rvector> atoms_positions;
   /// \brief Most recent total forces on each atom
   std::vector<cvm::rvector> atoms_total_forces;
-  /// \brief Most recent forces applied by external potentials onto each atom
-  std::vector<cvm::rvector> atoms_applied_forces;
   /// \brief Forces applied from colvars, to be communicated to the MD integrator
   std::vector<cvm::rvector> atoms_new_colvar_forces;
 
@@ -368,7 +366,6 @@ protected:
     atoms_charges.push_back(0.0);
     atoms_positions.push_back(cvm::rvector(0.0, 0.0, 0.0));
     atoms_total_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
-    atoms_applied_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
     atoms_new_colvar_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
     return (atoms_ids.size() - 1);
   }
@@ -439,10 +436,10 @@ public:
     return atoms_positions[index];
   }
 
-  /// Read the current total system force of the given atom
-  inline cvm::rvector get_atom_system_force(int index) const
+  /// Read the current total force of the given atom
+  inline cvm::rvector get_atom_total_force(int index) const
   {
-    return atoms_total_forces[index] - atoms_applied_forces[index];
+    return atoms_total_forces[index];
   }
 
   /// Request that this force is applied to the given atom
@@ -465,7 +462,6 @@ public:
   inline std::vector<cvm::real> *modify_atom_charges() { return &atoms_charges; }
   inline std::vector<cvm::rvector> *modify_atom_positions() { return &atoms_positions; }
   inline std::vector<cvm::rvector> *modify_atom_total_forces() { return &atoms_total_forces; }
-  inline std::vector<cvm::rvector> *modify_atom_applied_forces() { return &atoms_applied_forces; }
   inline std::vector<cvm::rvector> *modify_atom_new_colvar_forces() { return &atoms_new_colvar_forces; }
 
   /// \brief Read atom identifiers from a file \param filename name of
@@ -513,8 +509,6 @@ protected:
   std::vector<cvm::rvector> atom_groups_coms;
   /// \brief Most recently updated total forces on the com of each group
   std::vector<cvm::rvector> atom_groups_total_forces;
-  /// \brief Most recent forces applied by external potentials onto each group
-  std::vector<cvm::rvector> atom_groups_applied_forces;
   /// \brief Forces applied from colvars, to be communicated to the MD integrator
   std::vector<cvm::rvector> atom_groups_new_colvar_forces;
 
@@ -538,7 +532,6 @@ public:
     atom_groups_charges.push_back(0.0);
     atom_groups_coms.push_back(cvm::rvector(0.0, 0.0, 0.0));
     atom_groups_total_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
-    atom_groups_applied_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
     atom_groups_new_colvar_forces.push_back(cvm::rvector(0.0, 0.0, 0.0));
     return (atom_groups_ids.size() - 1);
   }
@@ -592,10 +585,10 @@ public:
     return atom_groups_coms[index];
   }
 
-  /// Read the current total system force of the given atom group
-  inline cvm::rvector get_atom_group_system_force(int index) const
+  /// Read the current total force of the given atom group
+  inline cvm::rvector get_atom_group_total_force(int index) const
   {
-    return atom_groups_total_forces[index] - atom_groups_applied_forces[index];
+    return atom_groups_total_forces[index];
   }
 
   /// Request that this force is applied to the given atom group
diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp
index 374359ccef..069a995135 100644
--- a/lib/colvars/colvarscript.cpp
+++ b/lib/colvars/colvarscript.cpp
@@ -248,7 +248,7 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
   }
 
   if (subcmd == "getsystemforce") {
-    result = (cv->system_force()).to_simple_string();
+    result = (cv->total_force()).to_simple_string();
     return COLVARS_OK;
   }
 
diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp
index 71786f060e..f02fd23951 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.cpp
+++ b/src/USER-COLVARS/colvarproxy_lammps.cpp
@@ -73,7 +73,7 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
   _random = new LAMMPS_NS::RanPark(lmp,seed);
 
   first_timestep=true;
-  system_force_requested=false;
+  total_force_requested=false;
   previous_step=-1;
   t_target=temp;
   do_exit=false;
@@ -154,7 +154,6 @@ void colvarproxy_lammps::init(const char *conf_file)
     log("atoms_ids = "+cvm::to_str(atoms_ids)+"\n");
     log("atoms_ncopies = "+cvm::to_str(atoms_ncopies)+"\n");
     log("atoms_positions = "+cvm::to_str(atoms_positions)+"\n");
-    log("atoms_applied_forces = "+cvm::to_str(atoms_applied_forces)+"\n");
     log(cvm::line_marker);
     log("Info: done initializing the colvars proxy object.\n");
   }
@@ -199,13 +198,8 @@ double colvarproxy_lammps::compute()
              "Updating internal data.\n");
   }
 
-  // backup applied forces if necessary to calculate system forces
-  if (system_force_requested) {
-    atoms_applied_forces = atoms_new_colvar_forces;
-  }
-
   // zero the forces on the atoms, so that they can be accumulated by the colvars
-  for (size_t i = 0; i < atoms_applied_forces.size(); i++) {
+  for (size_t i = 0; i < atoms_new_colvar_forces.size(); i++) {
     atoms_new_colvar_forces[i].reset();
   }
 
diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h
index 0ce7e29a0c..925fefac04 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.h
+++ b/src/USER-COLVARS/colvarproxy_lammps.h
@@ -55,7 +55,7 @@ class colvarproxy_lammps : public colvarproxy {
   int  previous_step;
 
   bool first_timestep;
-  bool system_force_requested;
+  bool total_force_requested;
   bool do_exit;
 
   // std::vector<int>          colvars_atoms;
@@ -86,7 +86,7 @@ class colvarproxy_lammps : public colvarproxy {
   // methods for lammps to move data or trigger actions in the proxy
  public:
   void set_temperature(double t) { t_target = t; };
-  bool need_system_forces() const { return  system_force_requested; };
+  bool need_total_forces() const { return  total_force_requested; };
   bool want_exit() const { return do_exit; };
 
   // perform colvars computation. returns biasing energy
@@ -109,7 +109,7 @@ class colvarproxy_lammps : public colvarproxy {
   inline size_t restart_frequency() { return restart_every; };
 
   void add_energy(cvm::real energy) { bias_energy += energy; };
-  void request_system_force(bool yesno) { system_force_requested = yesno; };
+  void request_total_force(bool yesno) { total_force_requested = yesno; };
 
   void log(std::string const &message);
   void error(std::string const &message);
diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp
index 3e86cd13a4..4f85c882d4 100644
--- a/src/USER-COLVARS/fix_colvars.cpp
+++ b/src/USER-COLVARS/fix_colvars.cpp
@@ -766,7 +766,7 @@ void FixColvars::post_force(int vflag)
   // call our workhorse and retrieve additional information.
   if (me == 0) {
     energy = proxy->compute();
-    store_forces = proxy->need_system_forces();
+    store_forces = proxy->need_total_forces();
   }
   ////////////////////////////////////////////////////////////////////////
 
-- 
GitLab


From 16607a0132d518968f1def738c08041b2be8edb2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 23 Aug 2016 05:53:05 -0400
Subject: [PATCH 14/52] update colvars library to version 2016-08-19

(cherry picked from commit c67326be6d9346d64bf4a0a58acaa132f0c004c8)
---
 doc/src/PDF/colvars-refman-lammps.pdf | Bin 533480 -> 533636 bytes
 lib/colvars/Makefile.fermi            |   8 ++---
 lib/colvars/Makefile.g++              |   8 ++---
 lib/colvars/Makefile.mingw32-cross    |   8 ++---
 lib/colvars/Makefile.mingw64-cross    |   8 ++---
 lib/colvars/colvar.cpp                |  44 ++++++++++++++------------
 lib/colvars/colvar.h                  |   4 +--
 lib/colvars/colvarbias_abf.cpp        |  16 +++++-----
 lib/colvars/colvarbias_abf.h          |   1 -
 lib/colvars/colvarcomp.cpp            |   3 +-
 lib/colvars/colvardeps.cpp            |  29 ++++++++++-------
 lib/colvars/colvardeps.h              |  30 +++++++-----------
 lib/colvars/colvarmodule.h            |   2 +-
 lib/colvars/colvarparse.cpp           |  15 ---------
 lib/colvars/colvarparse.h             |   7 ----
 lib/colvars/colvarscript.cpp          |   5 +++
 16 files changed, 88 insertions(+), 100 deletions(-)

diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf
index 0dd82d47947628d5c55c0481499dcc8b79a4598d..071bdb25b89d87e6b9a7ea20053680408dcf72ee 100644
GIT binary patch
delta 16450
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diff --git a/lib/colvars/Makefile.fermi b/lib/colvars/Makefile.fermi
index e17798bbc3..906675ae12 100644
--- a/lib/colvars/Makefile.fermi
+++ b/lib/colvars/Makefile.fermi
@@ -93,8 +93,8 @@ colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
 colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
  colvaratoms.h colvarscript.h colvarbias.h
-colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvardeps.h
+colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \
+ colvarproxy.h colvarvalue.h colvarparse.h
 colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
  colvaratoms.h colvargrid.h
@@ -104,12 +104,12 @@ colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
  colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
  colvarscript.h
 colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvardeps.h
+ colvarvalue.h colvarparse.h
 colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
  colvarparse.h colvardeps.h
 colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvardeps.h
+ colvarvalue.h colvarparse.h
 colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h
 
diff --git a/lib/colvars/Makefile.g++ b/lib/colvars/Makefile.g++
index f1fa1734b9..c80fa1065e 100644
--- a/lib/colvars/Makefile.g++
+++ b/lib/colvars/Makefile.g++
@@ -92,8 +92,8 @@ colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
 colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
  colvaratoms.h colvarscript.h colvarbias.h
-colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvardeps.h
+colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \
+ colvarproxy.h colvarvalue.h colvarparse.h
 colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
  colvaratoms.h colvargrid.h
@@ -103,12 +103,12 @@ colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
  colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
  colvarscript.h
 colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvardeps.h
+ colvarvalue.h colvarparse.h
 colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
  colvarparse.h colvardeps.h
 colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvardeps.h
+ colvarvalue.h colvarparse.h
 colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h
 
diff --git a/lib/colvars/Makefile.mingw32-cross b/lib/colvars/Makefile.mingw32-cross
index cea3a53c25..eba83c555f 100644
--- a/lib/colvars/Makefile.mingw32-cross
+++ b/lib/colvars/Makefile.mingw32-cross
@@ -100,8 +100,8 @@ $(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
 $(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
  colvaratoms.h colvarscript.h colvarbias.h
-$(DIR)colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvardeps.h
+$(DIR)colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \
+ colvarproxy.h colvarvalue.h colvarparse.h
 $(DIR)colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
  colvaratoms.h colvargrid.h
@@ -111,12 +111,12 @@ $(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
  colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
  colvarscript.h
 $(DIR)colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvardeps.h
+ colvarvalue.h colvarparse.h
 $(DIR)colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
  colvarparse.h colvardeps.h
 $(DIR)colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvardeps.h
+ colvarvalue.h colvarparse.h
 $(DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h
 
diff --git a/lib/colvars/Makefile.mingw64-cross b/lib/colvars/Makefile.mingw64-cross
index 7dd85b48f8..1d83b6a0a8 100644
--- a/lib/colvars/Makefile.mingw64-cross
+++ b/lib/colvars/Makefile.mingw64-cross
@@ -100,8 +100,8 @@ $(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
 $(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
  colvaratoms.h colvarscript.h colvarbias.h
-$(DIR)colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvardeps.h
+$(DIR)colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \
+ colvarproxy.h colvarvalue.h colvarparse.h
 $(DIR)colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
  colvaratoms.h colvargrid.h
@@ -111,12 +111,12 @@ $(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
  colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
  colvarscript.h
 $(DIR)colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvardeps.h
+ colvarvalue.h colvarparse.h
 $(DIR)colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
  colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
  colvarparse.h colvardeps.h
 $(DIR)colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvardeps.h
+ colvarvalue.h colvarparse.h
 $(DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
  colvarvalue.h
 
diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp
index 1dd46524ac..84880808af 100644
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@@ -771,7 +771,7 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
 
   error_code |= calc_cvc_values(first_cvc, num_cvcs);
   error_code |= calc_cvc_gradients(first_cvc, num_cvcs);
-  error_code |= calc_cvc_sys_forces(first_cvc, num_cvcs);
+  error_code |= calc_cvc_total_force(first_cvc, num_cvcs);
   error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);
 
   if (cvm::debug())
@@ -790,7 +790,7 @@ int colvar::collect_cvc_data()
 
   error_code |= collect_cvc_values();
   error_code |= collect_cvc_gradients();
-  error_code |= collect_cvc_sys_forces();
+  error_code |= collect_cvc_total_forces();
   error_code |= collect_cvc_Jacobians();
   error_code |= calc_colvar_properties();
 
@@ -889,21 +889,22 @@ int colvar::calc_cvc_gradients(int first_cvc, size_t num_cvcs)
   size_t const cvc_max_count = num_cvcs ? num_cvcs : num_active_cvcs();
   size_t i, cvc_count;
 
-  if (is_enabled(f_cv_gradient)) {
+  if (cvm::debug())
+    cvm::log("Calculating gradients of colvar \""+this->name+"\".\n");
 
-    if (cvm::debug())
-      cvm::log("Calculating gradients of colvar \""+this->name+"\".\n");
+  // calculate the gradients of each component
+  cvm::increase_depth();
+  for (i = first_cvc, cvc_count = 0;
+      (i < cvcs.size()) && (cvc_count < cvc_max_count);
+      i++) {
+    if (!cvcs[i]->is_enabled()) continue;
+    cvc_count++;
 
-    // calculate the gradients of each component
-    cvm::increase_depth();
-    for (i = first_cvc, cvc_count = 0;
-        (i < cvcs.size()) && (cvc_count < cvc_max_count);
-        i++) {
-      if (!cvcs[i]->is_enabled()) continue;
-      cvc_count++;
+    if ((cvcs[i])->is_enabled(f_cvc_gradient)) {
       (cvcs[i])->calc_gradients();
       // if requested, propagate (via chain rule) the gradients above
       // to the atoms used to define the roto-translation
+      // This could be integrated in the CVC base class
       for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
         if (cvcs[i]->atom_groups[ig]->b_fit_gradients)
           cvcs[i]->atom_groups[ig]->calc_fit_gradients();
@@ -914,6 +915,7 @@ int colvar::calc_cvc_gradients(int first_cvc, size_t num_cvcs)
         }
       }
     }
+
     cvm::decrease_depth();
 
     if (cvm::debug())
@@ -976,7 +978,7 @@ int colvar::collect_cvc_gradients()
 }
 
 
-int colvar::calc_cvc_sys_forces(int first_cvc, size_t num_cvcs)
+int colvar::calc_cvc_total_force(int first_cvc, size_t num_cvcs)
 {
   size_t const cvc_max_count = num_cvcs ? num_cvcs : num_active_cvcs();
   size_t i, cvc_count;
@@ -1010,7 +1012,7 @@ int colvar::calc_cvc_sys_forces(int first_cvc, size_t num_cvcs)
 }
 
 
-int colvar::collect_cvc_sys_forces()
+int colvar::collect_cvc_total_forces()
 {
   if (is_enabled(f_cv_total_force_calc)) {
     ft.reset();
@@ -1097,10 +1099,8 @@ int colvar::calc_colvar_properties()
     // report the restraint center as "value"
     x_reported = xr;
     v_reported = vr;
-    // the "total force" with the extended Lagrangian is just the
-    // harmonic term acting on the extended coordinate
-    // Note: this is the force for current timestep
-    ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
+    // the "total force" with the extended Lagrangian is
+    // calculated in update_forces_energy() below
 
   } else {
 
@@ -1175,14 +1175,18 @@ cvm::real colvar::update_forces_energy()
 
     // the total force is applied to the fictitious mass, while the
     // atoms only feel the harmonic force
-    // fr: bias force on extended coordinate (without harmonic spring), for output in trajectory
-    // f_ext: total force on extended coordinate (including harmonic spring)
+    // fr: bias force on extended variable (without harmonic spring), for output in trajectory
+    // f_ext: total force on extended variable (including harmonic spring)
     // f: - initially, external biasing force
     //    - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
     fr    = f;
     f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
     f     =     (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
 
+    // The total force acting on the extended variable is f_ext
+    // This will be used in the next timestep
+    ft_reported = f_ext;
+
     // leapfrog: starting from x_i, f_i, v_(i-1/2)
     vr  += (0.5 * dt) * f_ext / ext_mass;
     // Because of leapfrog, kinetic energy at time i is approximate
diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h
index 665b3d6427..0058b56a26 100644
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@@ -254,7 +254,7 @@ public:
   /// \brief Same as \link colvar::calc_cvc_values \endlink but for gradients
   int calc_cvc_gradients(int first, size_t num_cvcs);
   /// \brief Same as \link colvar::calc_cvc_values \endlink but for total forces
-  int calc_cvc_sys_forces(int first, size_t num_cvcs);
+  int calc_cvc_total_force(int first, size_t num_cvcs);
   /// \brief Same as \link colvar::calc_cvc_values \endlink but for Jacobian derivatives/forces
   int calc_cvc_Jacobians(int first, size_t num_cvcs);
 
@@ -266,7 +266,7 @@ public:
   /// \brief Same as \link colvar::collect_cvc_values \endlink but for gradients
   int collect_cvc_gradients();
   /// \brief Same as \link colvar::collect_cvc_values \endlink but for total forces
-  int collect_cvc_sys_forces();
+  int collect_cvc_total_forces();
   /// \brief Same as \link colvar::collect_cvc_values \endlink but for Jacobian derivatives/forces
   int collect_cvc_Jacobians();
   /// \brief Calculate the quantities associated to the colvar (but not to the CVCs)
diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp
index f2659951d4..870079a619 100644
--- a/lib/colvars/colvarbias_abf.cpp
+++ b/lib/colvars/colvarbias_abf.cpp
@@ -31,10 +31,8 @@ int colvarbias_abf::init(std::string const &conf)
 
   // ************* parsing general ABF options ***********************
 
-  get_keyval(conf, "applyBias",  apply_bias, true);
-  if (apply_bias) {
-    enable(f_cvb_apply_force);
-  } else {
+  get_keyval_feature((colvarparse *)this, conf, "applyBias",  f_cvb_apply_force, true);
+  if (!is_enabled(f_cvb_apply_force)){
     cvm::log("WARNING: ABF biases will *not* be applied!\n");
   }
 
@@ -84,9 +82,6 @@ int colvarbias_abf::init(std::string const &conf)
   // Request calculation of total force (which also checks for availability)
     if(enable(f_cvb_get_total_force)) return cvm::get_error();
   }
-  if (apply_bias) {
-    if(enable(f_cvb_apply_force)) return cvm::get_error();
-  }
 
   bool b_extended = false;
   for (size_t i = 0; i < colvars.size(); i++) {
@@ -249,6 +244,11 @@ int colvarbias_abf::update()
         // and subtract previous ABF force
         system_force[i] = colvars[i]->total_force().real_value
                         - colvar_forces[i].real_value;
+//         if (cvm::debug())
+//           cvm::log("ABF System force calc: cv " + cvm::to_str(i) +
+//                   " fs " + cvm::to_str(system_force[i]) +
+//                   " = ft " + cvm::to_str(colvars[i]->total_force().real_value) +
+//                   " - fa " + cvm::to_str(colvar_forces[i].real_value));
       }
       gradients->acc_force(force_bin, system_force);
     }
@@ -277,7 +277,7 @@ int colvarbias_abf::update()
   }
 
   // Compute and apply the new bias, if applicable
-  if ( apply_bias && samples->index_ok(bin) ) {
+  if (is_enabled(f_cvb_apply_force) && samples->index_ok(bin)) {
 
     size_t  count = samples->value(bin);
     cvm::real	fact = 1.0;
diff --git a/lib/colvars/colvarbias_abf.h b/lib/colvars/colvarbias_abf.h
index 8db0b75632..93079220ba 100644
--- a/lib/colvars/colvarbias_abf.h
+++ b/lib/colvars/colvarbias_abf.h
@@ -32,7 +32,6 @@ private:
   /// Base filename(s) for reading previous gradient data (replaces data from restart file)
   std::vector<std::string> input_prefix;
 
-  bool		apply_bias;
   bool		update_bias;
   bool		hide_Jacobian;
   size_t	full_samples;
diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp
index 632e7fabda..534a927fda 100644
--- a/lib/colvars/colvarcomp.cpp
+++ b/lib/colvars/colvarcomp.cpp
@@ -43,7 +43,8 @@ colvar::cvc::cvc(std::string const &conf)
 
   // All cvcs implement this
   provide(f_cvc_debug_gradient);
-  get_keyval(conf, "debugGradients", set_feature(f_cvc_debug_gradient), false, parse_silent);
+  get_keyval_feature((colvarparse *)this, conf, "debugGradients",
+                     f_cvc_debug_gradient, false, parse_silent);
 
   // Attempt scalable calculations when in parallel? (By default yes, if available)
   get_keyval(conf, "scalable", b_try_scalable, true);
diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp
index 7d8d05a2be..7dce7e31f6 100644
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@@ -1,4 +1,3 @@
-#include "colvarmodule.h"
 #include "colvardeps.h"
 
 
@@ -30,6 +29,18 @@ void colvardeps::provide(int feature_id) {
 }
 
 
+bool colvardeps::get_keyval_feature(colvarparse *cvp,
+                        std::string const &conf, char const *key,
+                        int feature_id, bool const &def_value,
+                        colvarparse::Parse_Mode const parse_mode)
+{
+  bool value;
+  bool const found = cvp->get_keyval(conf, key, value, def_value, parse_mode);
+  if (value) enable(feature_id);
+  return found;
+}
+
+
 int colvardeps::enable(int feature_id,
                       bool dry_run /* default: false */,
                       // dry_run: fail silently, do not enable if available
@@ -48,7 +59,7 @@ int colvardeps::enable(int feature_id,
   if (cvm::debug()) {
     cvm::log("DEPS: " + description +
       (dry_run ? " testing " : " requiring ") +
-      "\"" + f->description);
+      "\"" + f->description +"\"");
   }
 
   if (fs->enabled) {
@@ -140,11 +151,7 @@ int colvardeps::enable(int feature_id,
   // 4) solve deps in children
   for (i=0; i<f->requires_children.size(); i++) {
     int g = f->requires_children[i];
-    if (cvm::debug())
-      cvm::log("requires children " + features()[g]->description);
-//     cvm::log("children " + cvm::to_str(g));
     for (j=0; j<children.size(); j++) {
-//       cvm::log("child " +  children[j]->description);
       cvm::increase_depth();
       res = children[j]->enable(g, dry_run, false);
       cvm::decrease_depth();
@@ -215,7 +222,7 @@ void colvardeps::init_cvb_requires() {
   // Initialize feature_states for each instance
   feature_states.reserve(f_cvb_ntot);
   for (i = 0; i < f_cvb_ntot; i++) {
-    feature_states.push_back(new feature_state(this, feature_states.size(), true, false));
+    feature_states.push_back(new feature_state(true, false));
     // Most features are available, so we set them so
     // and list exceptions below
   }
@@ -319,7 +326,7 @@ void colvardeps::init_cv_requires() {
   // Initialize feature_states for each instance
   feature_states.reserve(f_cv_ntot);
   for (i = 0; i < f_cv_ntot; i++) {
-    feature_states.push_back(new feature_state(this, feature_states.size(), true, false));
+    feature_states.push_back(new feature_state(true, false));
     // Most features are available, so we set them so
     // and list exceptions below
    }
@@ -364,7 +371,7 @@ void colvardeps::init_cvc_requires() {
     f_description(f_cvc_debug_gradient, "debug gradient");
     f_req_self(f_cvc_debug_gradient, f_cvc_gradient);
 
-    f_description(f_cvc_Jacobian, "Jacobian");
+    f_description(f_cvc_Jacobian, "Jacobian derivative");
     f_req_self(f_cvc_Jacobian, f_cvc_inv_gradient);
 
     f_description(f_cvc_com_based, "depends on group centers of mass");
@@ -385,7 +392,7 @@ void colvardeps::init_cvc_requires() {
   // default as unavailable, not enabled
   feature_states.reserve(f_cvc_ntot);
   for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
-    feature_states.push_back(new feature_state(this, feature_states.size(), false, false));
+    feature_states.push_back(new feature_state(false, false));
   }
 
   // Features that are implemented by all cvcs by default
@@ -429,7 +436,7 @@ void colvardeps::init_ag_requires() {
   // default as unavailable, not enabled
   feature_states.reserve(f_ag_ntot);
   for (i = 0; i < colvardeps::f_ag_ntot; i++) {
-    feature_states.push_back(new feature_state(this, feature_states.size(), false, false));
+    feature_states.push_back(new feature_state(false, false));
   }
 
   // Features that are implemented (or not) by all atom groups
diff --git a/lib/colvars/colvardeps.h b/lib/colvars/colvardeps.h
index a2f6f2d5f9..089461c532 100644
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@@ -1,10 +1,11 @@
 // -*- c++ -*-
 
-#include "colvarmodule.h"
-
 #ifndef COLVARDEPS_H
 #define COLVARDEPS_H
 
+#include "colvarmodule.h"
+#include "colvarparse.h"
+
 /// Parent class for a member object of a bias, cv or cvc etc. containing dependencies
 /// (features) and handling dependency resolution
 
@@ -27,16 +28,9 @@ public:
   std::string description; // reference to object name (cv, cvc etc.)
 
   /// This contains the current state of each feature for each object
-  class feature_state {
-  private:
-    colvardeps *const deps_object;
-    int const id;
-    operator int() { return 0; } // never cast as int
-  public:
-    inline colvardeps *object() const { return deps_object; }
-    inline int feature_id() const { return id; }
-    feature_state(colvardeps *o, int i, bool a, bool e)
-      : deps_object(o), id(i), available(a), enabled(e) {}
+  struct feature_state {
+    feature_state(bool a, bool e)
+    : available(a), enabled(e) {}
 
     /// Available means: supported, subject to dependencies as listed,
     /// MAY BE ENABLED AS A RESULT OF DEPENDENCY SOLVING
@@ -55,12 +49,6 @@ public:
   /// List of the state of all features
   std::vector<feature_state *> feature_states;
 
-  /// Allow setting a feature state while parsing its kewyord
-  inline feature_state * set_feature(int id)
-  {
-    return feature_states[id];
-  }
-
   /// Describes a feature and its dependecies
   /// used in a static array within each subclass
   class feature {
@@ -146,6 +134,12 @@ public:
 
   void provide(int feature_id); // set the feature's flag to available in local object
 
+  /// Parse a keyword and enable a feature accordingly
+  bool get_keyval_feature(colvarparse *cvp,
+                          std::string const &conf, char const *key,
+                          int feature_id, bool const &def_value,
+                          colvarparse::Parse_Mode const parse_mode = colvarparse::parse_normal);
+
   int enable(int f, bool dry_run = false, bool toplevel = true);  // enable a feature and recursively solve its dependencies
   // dry_run is set to true to recursively test if a feature is available, without enabling it
 //     int disable(int f);
diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h
index cb4272f0bd..8c61dcac2d 100644
--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@@ -4,7 +4,7 @@
 #define COLVARMODULE_H
 
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2016-08-10"
+#define COLVARS_VERSION "2016-08-19"
 #endif
 
 #ifndef COLVARS_DEBUG
diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp
index 47b1970220..8699391107 100644
--- a/lib/colvars/colvarparse.cpp
+++ b/lib/colvars/colvarparse.cpp
@@ -354,21 +354,6 @@ bool colvarparse::get_keyval(std::string const &conf,
 }
 
 
-bool colvarparse::get_keyval(std::string const &conf,
-                             char const *key,
-                             colvardeps::feature_state *value,
-                             bool const &def_value,
-                             Parse_Mode const parse_mode)
-{
-  bool feature_flag = def_value;
-  bool const b_found = get_keyval(conf, key, feature_flag, def_value, parse_mode);
-  if (feature_flag) {
-    value->object()->enable(value->feature_id());
-  }
-  return b_found;
-}
-
-
 // multiple-value keyword parsers
 
 bool colvarparse::get_keyval(std::string const &conf,
diff --git a/lib/colvars/colvarparse.h b/lib/colvars/colvarparse.h
index 7685b4eeb4..892f1632e1 100644
--- a/lib/colvars/colvarparse.h
+++ b/lib/colvars/colvarparse.h
@@ -8,7 +8,6 @@
 
 #include "colvarmodule.h"
 #include "colvarvalue.h"
-#include "colvardeps.h"
 
 
 /// \file colvarparse.h Parsing functions for collective variables
@@ -181,12 +180,6 @@ public:
                   bool &value,
                   bool const &def_value = false,
                   Parse_Mode const parse_mode = parse_normal);
-  bool get_keyval(std::string const &conf,
-                  char const *key,
-                  colvardeps::feature_state *value,
-                  bool const &def_value = false,
-                  Parse_Mode const parse_mode = parse_normal);
-
   bool get_keyval(std::string const &conf,
                   char const *key,
                   std::vector<int> &values,
diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp
index 069a995135..dc3619fe5e 100644
--- a/lib/colvars/colvarscript.cpp
+++ b/lib/colvars/colvarscript.cpp
@@ -336,6 +336,11 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
     return COLVARS_OK;
   }
 
+  if (subcmd == "state") {
+    b->print_state();
+    return COLVARS_OK;
+  }
+
   // Subcommands for MW ABF
   if (subcmd == "bin") {
     int r = b->current_bin();
-- 
GitLab


From c8cfd53c1b867d8936c56e56e1bcaa1a16305b2d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Sep 2016 21:28:55 -0400
Subject: [PATCH 15/52] adjust makefiles in lib tree, so they don't return an
 error exit code on "make clean" targets.

(cherry picked from commit 4117218ca3f5d0e726cae55b5d7a38e26c717845)
---
 lib/atc/Makefile.icc                   | 2 +-
 lib/atc/Makefile.mingw32-cross         | 2 +-
 lib/atc/Makefile.mingw32-cross-mpi     | 2 +-
 lib/atc/Makefile.mingw64-cross         | 2 +-
 lib/atc/Makefile.mingw64-cross-mpi     | 2 +-
 lib/atc/Makefile.mpic++                | 2 +-
 lib/atc/Makefile.serial                | 2 +-
 lib/awpmd/Makefile.mingw32-cross       | 2 +-
 lib/awpmd/Makefile.mingw64-cross       | 2 +-
 lib/awpmd/Makefile.mpicc               | 2 +-
 lib/colvars/Makefile.mingw32-cross-mpi | 4 ++--
 lib/colvars/Makefile.mingw64-cross-mpi | 4 ++--
 lib/gpu/Nvidia.makefile                | 6 +++---
 lib/gpu/Opencl.makefile                | 4 ++--
 lib/kokkos/Makefile.kokkos             | 2 +-
 lib/linalg/Makefile.mingw32-cross-mpi  | 4 ++--
 lib/linalg/Makefile.mingw64-cross-mpi  | 4 ++--
 lib/meam/Makefile.mingw32-cross-mpi    | 4 ++--
 lib/meam/Makefile.mingw64-cross-mpi    | 4 ++--
 lib/poems/Makefile.mingw32-cross-mpi   | 4 ++--
 lib/poems/Makefile.mingw64-cross-mpi   | 4 ++--
 lib/qmmm/Makefile.gfortran             | 2 +-
 lib/qmmm/Makefile.ifort                | 2 +-
 23 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/lib/atc/Makefile.icc b/lib/atc/Makefile.icc
index 502f103ba4..59be520b4b 100644
--- a/lib/atc/Makefile.icc
+++ b/lib/atc/Makefile.icc
@@ -48,4 +48,4 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------
 
 clean:
-	rm *.o *.d *~ $(LIB)
+	-rm *.o *.d *~ $(LIB)
diff --git a/lib/atc/Makefile.mingw32-cross b/lib/atc/Makefile.mingw32-cross
index 49795f1fd2..8b33540981 100644
--- a/lib/atc/Makefile.mingw32-cross
+++ b/lib/atc/Makefile.mingw32-cross
@@ -61,7 +61,7 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------
 
 clean:
-	rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
+	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
 
 $(DEPENDS) : $(DIR)
 sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mingw32-cross-mpi b/lib/atc/Makefile.mingw32-cross-mpi
index 522a394dc0..c5feeca81a 100644
--- a/lib/atc/Makefile.mingw32-cross-mpi
+++ b/lib/atc/Makefile.mingw32-cross-mpi
@@ -62,7 +62,7 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------
 
 clean:
-	rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
+	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
 
 $(DEPENDS) : $(DIR)
 sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mingw64-cross b/lib/atc/Makefile.mingw64-cross
index 2dfdf6fe80..fbd3a02610 100644
--- a/lib/atc/Makefile.mingw64-cross
+++ b/lib/atc/Makefile.mingw64-cross
@@ -61,7 +61,7 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------
 
 clean:
-	rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
+	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
 
 $(DEPENDS) : $(DIR)
 sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mingw64-cross-mpi b/lib/atc/Makefile.mingw64-cross-mpi
index 935d86ba25..f8dd64eae3 100644
--- a/lib/atc/Makefile.mingw64-cross-mpi
+++ b/lib/atc/Makefile.mingw64-cross-mpi
@@ -62,7 +62,7 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------
 
 clean:
-	rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
+	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
 
 $(DEPENDS) : $(DIR)
 sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.mpic++ b/lib/atc/Makefile.mpic++
index 982deac5d3..c9dfdb79c9 100644
--- a/lib/atc/Makefile.mpic++
+++ b/lib/atc/Makefile.mpic++
@@ -34,6 +34,6 @@ lib: 	$(OBJ)
 DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------
 clean:
-	@rm *.o *.d *~ $(LIB)
+	-rm *.o *.d *~ $(LIB)
 
 sinclude $(DEPENDS)
diff --git a/lib/atc/Makefile.serial b/lib/atc/Makefile.serial
index 8204430c81..44ce5fd341 100644
--- a/lib/atc/Makefile.serial
+++ b/lib/atc/Makefile.serial
@@ -46,6 +46,6 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------
 
 clean:
-	@rm *.o *.d *~ $(LIB)
+	-rm *.o *.d *~ $(LIB)
 
 sinclude $(DEPENDS)
diff --git a/lib/awpmd/Makefile.mingw32-cross b/lib/awpmd/Makefile.mingw32-cross
index af66187b89..6a93987173 100644
--- a/lib/awpmd/Makefile.mingw32-cross
+++ b/lib/awpmd/Makefile.mingw32-cross
@@ -77,4 +77,4 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------
 
 clean:
-	rm *.d *~ $(OBJ) $(LIB)
+	-rm *.d *~ $(OBJ) $(LIB)
diff --git a/lib/awpmd/Makefile.mingw64-cross b/lib/awpmd/Makefile.mingw64-cross
index f1df999bab..1f3e608129 100644
--- a/lib/awpmd/Makefile.mingw64-cross
+++ b/lib/awpmd/Makefile.mingw64-cross
@@ -76,4 +76,4 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------
 
 clean:
-	rm *.d *~ $(OBJ) $(LIB)
+	-rm *.d *~ $(OBJ) $(LIB)
diff --git a/lib/awpmd/Makefile.mpicc b/lib/awpmd/Makefile.mpicc
index c1a6f3c01d..4c289ad88a 100644
--- a/lib/awpmd/Makefile.mpicc
+++ b/lib/awpmd/Makefile.mpicc
@@ -66,4 +66,4 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------
 
 clean:
-	rm *.d *~ $(OBJ) $(LIB)
+	-rm *.d *~ $(OBJ) $(LIB)
diff --git a/lib/colvars/Makefile.mingw32-cross-mpi b/lib/colvars/Makefile.mingw32-cross-mpi
index cc2a76111a..1e35c5b461 100644
--- a/lib/colvars/Makefile.mingw32-cross-mpi
+++ b/lib/colvars/Makefile.mingw32-cross-mpi
@@ -4,10 +4,10 @@ SHELL=/bin/sh
 
 all:
 	$(MAKE) $(MFLAGS) mingw32-cross
-	rm -f Obj_mingw32-mpi
+	-rm -f Obj_mingw32-mpi
 	ln -s Obj_mingw32 Obj_mingw32-mpi
 
 clean:
 	$(MAKE) $(MFLAGS) clean-mingw32-cross
-	rm -f Obj_mingw32-mpi
+	-rm -f Obj_mingw32-mpi
 
diff --git a/lib/colvars/Makefile.mingw64-cross-mpi b/lib/colvars/Makefile.mingw64-cross-mpi
index 1ec1a0995b..ca6f4a6d43 100644
--- a/lib/colvars/Makefile.mingw64-cross-mpi
+++ b/lib/colvars/Makefile.mingw64-cross-mpi
@@ -4,10 +4,10 @@ SHELL=/bin/sh
 
 all:
 	$(MAKE) $(MFLAGS) mingw64-cross
-	rm -f Obj_mingw64-mpi
+	-rm -f Obj_mingw64-mpi
 	ln -s Obj_mingw64 Obj_mingw64-mpi
 
 clean:
 	$(MAKE) $(MFLAGS) clean-mingw64-cross
-	rm -f Obj_mingw64-mpi
+	-rm -f Obj_mingw64-mpi
 
diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile
index 18efbda55a..e02849cfed 100644
--- a/lib/gpu/Nvidia.makefile
+++ b/lib/gpu/Nvidia.makefile
@@ -789,10 +789,10 @@ $(GPU_LIB): $(OBJS) $(CUDPP)
 	@cp $(EXTRAMAKE) Makefile.lammps
 
 clean:
-	rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CBNS) *.linkinfo
+	-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CBNS) *.linkinfo
 
 veryclean: clean
-	rm -rf *~ *.linkinfo
+	-rm -rf *~ *.linkinfo
 
 cleanlib:
-	rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CBNS) *.linkinfo
+	-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CBNS) *.linkinfo
diff --git a/lib/gpu/Opencl.makefile b/lib/gpu/Opencl.makefile
index b33a392242..7ef1dfba0c 100644
--- a/lib/gpu/Opencl.makefile
+++ b/lib/gpu/Opencl.makefile
@@ -577,8 +577,8 @@ $(OCL_LIB): $(OBJS) $(PTXS)
 opencl: $(OCL_EXECS)
 
 clean:
-	rm -rf $(EXECS) $(OCL_EXECS) $(OCL_LIB) $(OBJS) $(KERS) *.linkinfo
+	-rm -rf $(EXECS) $(OCL_EXECS) $(OCL_LIB) $(OBJS) $(KERS) *.linkinfo
 
 veryclean: clean
-	rm -rf *~ *.linkinfo
+	-rm -rf *~ *.linkinfo
 
diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos
index c01ceaf64d..300a455367 100644
--- a/lib/kokkos/Makefile.kokkos
+++ b/lib/kokkos/Makefile.kokkos
@@ -462,7 +462,7 @@ KOKKOS_OBJ_LINK = $(notdir $(KOKKOS_OBJ))
 include $(KOKKOS_PATH)/Makefile.targets
 
 kokkos-clean:
-	rm -f $(KOKKOS_OBJ_LINK) KokkosCore_config.h KokkosCore_config.tmp libkokkos.a
+	-rm -f $(KOKKOS_OBJ_LINK) KokkosCore_config.h KokkosCore_config.tmp libkokkos.a
 
 libkokkos.a: $(KOKKOS_OBJ_LINK) $(KOKKOS_SRC) $(KOKKOS_HEADERS)
 	ar cr libkokkos.a $(KOKKOS_OBJ_LINK)
diff --git a/lib/linalg/Makefile.mingw32-cross-mpi b/lib/linalg/Makefile.mingw32-cross-mpi
index cc2a76111a..1e35c5b461 100644
--- a/lib/linalg/Makefile.mingw32-cross-mpi
+++ b/lib/linalg/Makefile.mingw32-cross-mpi
@@ -4,10 +4,10 @@ SHELL=/bin/sh
 
 all:
 	$(MAKE) $(MFLAGS) mingw32-cross
-	rm -f Obj_mingw32-mpi
+	-rm -f Obj_mingw32-mpi
 	ln -s Obj_mingw32 Obj_mingw32-mpi
 
 clean:
 	$(MAKE) $(MFLAGS) clean-mingw32-cross
-	rm -f Obj_mingw32-mpi
+	-rm -f Obj_mingw32-mpi
 
diff --git a/lib/linalg/Makefile.mingw64-cross-mpi b/lib/linalg/Makefile.mingw64-cross-mpi
index 1ec1a0995b..ca6f4a6d43 100644
--- a/lib/linalg/Makefile.mingw64-cross-mpi
+++ b/lib/linalg/Makefile.mingw64-cross-mpi
@@ -4,10 +4,10 @@ SHELL=/bin/sh
 
 all:
 	$(MAKE) $(MFLAGS) mingw64-cross
-	rm -f Obj_mingw64-mpi
+	-rm -f Obj_mingw64-mpi
 	ln -s Obj_mingw64 Obj_mingw64-mpi
 
 clean:
 	$(MAKE) $(MFLAGS) clean-mingw64-cross
-	rm -f Obj_mingw64-mpi
+	-rm -f Obj_mingw64-mpi
 
diff --git a/lib/meam/Makefile.mingw32-cross-mpi b/lib/meam/Makefile.mingw32-cross-mpi
index cc2a76111a..1e35c5b461 100644
--- a/lib/meam/Makefile.mingw32-cross-mpi
+++ b/lib/meam/Makefile.mingw32-cross-mpi
@@ -4,10 +4,10 @@ SHELL=/bin/sh
 
 all:
 	$(MAKE) $(MFLAGS) mingw32-cross
-	rm -f Obj_mingw32-mpi
+	-rm -f Obj_mingw32-mpi
 	ln -s Obj_mingw32 Obj_mingw32-mpi
 
 clean:
 	$(MAKE) $(MFLAGS) clean-mingw32-cross
-	rm -f Obj_mingw32-mpi
+	-rm -f Obj_mingw32-mpi
 
diff --git a/lib/meam/Makefile.mingw64-cross-mpi b/lib/meam/Makefile.mingw64-cross-mpi
index 1ec1a0995b..ca6f4a6d43 100644
--- a/lib/meam/Makefile.mingw64-cross-mpi
+++ b/lib/meam/Makefile.mingw64-cross-mpi
@@ -4,10 +4,10 @@ SHELL=/bin/sh
 
 all:
 	$(MAKE) $(MFLAGS) mingw64-cross
-	rm -f Obj_mingw64-mpi
+	-rm -f Obj_mingw64-mpi
 	ln -s Obj_mingw64 Obj_mingw64-mpi
 
 clean:
 	$(MAKE) $(MFLAGS) clean-mingw64-cross
-	rm -f Obj_mingw64-mpi
+	-rm -f Obj_mingw64-mpi
 
diff --git a/lib/poems/Makefile.mingw32-cross-mpi b/lib/poems/Makefile.mingw32-cross-mpi
index cc2a76111a..1e35c5b461 100644
--- a/lib/poems/Makefile.mingw32-cross-mpi
+++ b/lib/poems/Makefile.mingw32-cross-mpi
@@ -4,10 +4,10 @@ SHELL=/bin/sh
 
 all:
 	$(MAKE) $(MFLAGS) mingw32-cross
-	rm -f Obj_mingw32-mpi
+	-rm -f Obj_mingw32-mpi
 	ln -s Obj_mingw32 Obj_mingw32-mpi
 
 clean:
 	$(MAKE) $(MFLAGS) clean-mingw32-cross
-	rm -f Obj_mingw32-mpi
+	-rm -f Obj_mingw32-mpi
 
diff --git a/lib/poems/Makefile.mingw64-cross-mpi b/lib/poems/Makefile.mingw64-cross-mpi
index 1ec1a0995b..ca6f4a6d43 100644
--- a/lib/poems/Makefile.mingw64-cross-mpi
+++ b/lib/poems/Makefile.mingw64-cross-mpi
@@ -4,10 +4,10 @@ SHELL=/bin/sh
 
 all:
 	$(MAKE) $(MFLAGS) mingw64-cross
-	rm -f Obj_mingw64-mpi
+	-rm -f Obj_mingw64-mpi
 	ln -s Obj_mingw64 Obj_mingw64-mpi
 
 clean:
 	$(MAKE) $(MFLAGS) clean-mingw64-cross
-	rm -f Obj_mingw64-mpi
+	-rm -f Obj_mingw64-mpi
 
diff --git a/lib/qmmm/Makefile.gfortran b/lib/qmmm/Makefile.gfortran
index 73fb35cbfd..717922b4b6 100644
--- a/lib/qmmm/Makefile.gfortran
+++ b/lib/qmmm/Makefile.gfortran
@@ -58,7 +58,7 @@ tldeps:
 	$(MAKE) -C ../../src $(MFLAGS) mode=lib $(LAMMPSCFG)
 
 clean :
-	- /bin/rm -f *.x *.o *.a *~ *.F90 *.d *.mod *.i *.L
+	-rm -f *.x *.o *.a *~ *.F90 *.d *.mod *.i *.L
 
 # explicit dependencies
 
diff --git a/lib/qmmm/Makefile.ifort b/lib/qmmm/Makefile.ifort
index fef9653a80..d03e67b8a0 100644
--- a/lib/qmmm/Makefile.ifort
+++ b/lib/qmmm/Makefile.ifort
@@ -58,7 +58,7 @@ tldeps:
 	$(MAKE) -C ../../src $(MFLAGS) mode=lib $(LAMMPSCFG)
 
 clean :
-	- /bin/rm -f *.x *.o *.a *~ *.F90 *.d *.mod *.i *.L
+	-rm -f *.x *.o *.a *~ *.F90 *.d *.mod *.i *.L
 
 # explicit dependencies
 
-- 
GitLab


From 3a74ccffa2ed6bf85625d3ea0b9cf775d4499702 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 5 Sep 2016 20:37:19 -0400
Subject: [PATCH 16/52] update colvars library to version 2016-09-03

(cherry picked from commit 4181f5ac9d7291544e6848f8e8423025857936bc)
---
 lib/colvars/colvarmodule.cpp | 8 ++++++--
 lib/colvars/colvarmodule.h   | 2 +-
 lib/colvars/colvarparse.cpp  | 2 +-
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp
index 6d174be7a2..d7071df0b8 100644
--- a/lib/colvars/colvarmodule.cpp
+++ b/lib/colvars/colvarmodule.cpp
@@ -83,7 +83,9 @@ int colvarmodule::read_config_file(char const  *config_filename)
   std::string conf = "";
   std::string line;
   while (colvarparse::getline_nocomments(config_s, line)) {
-    conf.append(line+"\n");
+    // Delete lines that contain only white space after removing comments
+    if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
+      conf.append(line+"\n");
   }
   config_s.close();
 
@@ -101,7 +103,9 @@ int colvarmodule::read_config_string(std::string const &config_str)
   std::string conf = "";
   std::string line;
   while (colvarparse::getline_nocomments(config_s, line)) {
-    conf.append(line+"\n");
+    // Delete lines that contain only white space after removing comments
+    if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
+      conf.append(line+"\n");
   }
   return parse_config(conf);
 }
diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h
index 8c61dcac2d..deb20c9670 100644
--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@@ -4,7 +4,7 @@
 #define COLVARMODULE_H
 
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2016-08-19"
+#define COLVARS_VERSION "2016-09-03"
 #endif
 
 #ifndef COLVARS_DEBUG
diff --git a/lib/colvars/colvarparse.cpp b/lib/colvars/colvarparse.cpp
index 8699391107..e222fa9ecf 100644
--- a/lib/colvars/colvarparse.cpp
+++ b/lib/colvars/colvarparse.cpp
@@ -524,7 +524,7 @@ int colvarparse::check_keywords(std::string &conf, char const *key)
     }
   }
 
-  init();
+  clear_keyword_registry();
 
   return COLVARS_OK;
 }
-- 
GitLab


From a31c5073706c868ecb67ed9df686f81319468d95 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Sep 2016 22:15:49 -0400
Subject: [PATCH 17/52] correct error message text, sync with source

---
 doc/html/Section_errors.html | 3 +--
 doc/src/Section_errors.txt   | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/doc/html/Section_errors.html b/doc/html/Section_errors.html
index 658dfb8c2d..a8fd33e6b7 100644
--- a/doc/html/Section_errors.html
+++ b/doc/html/Section_errors.html
@@ -486,8 +486,7 @@ be computed.</dd>
 <dt><em>Bad TIP4P bond type for PPPMDisp/TIP4P</em></dt>
 <dd>Specified bond type is not valid.</dd>
 <dt><em>Bad fix ID in fix append/atoms command</em></dt>
-<dd>The value of the fix_id for keyword spatial must start with the suffix
-<a href="#id6"><span class="problematic" id="id7">f_</span></a>.</dd>
+<dd>The value of the fix_id for keyword spatial must start with &#8216;<a href="#id6"><span class="problematic" id="id7">f_</span></a>&#8216;.</dd>
 <dt><em>Bad grid of processors</em></dt>
 <dd>The 3d grid of processors defined by the processors command does not
 match the number of processors LAMMPS is being run on.</dd>
diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt
index 52405f684b..7f5f7857a5 100644
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@@ -535,8 +535,7 @@ Specified bond type is not valid. :dd
 
 {Bad fix ID in fix append/atoms command} :dt
 
-The value of the fix_id for keyword spatial must start with the suffix
-f_. :dd
+The value of the fix_id for keyword spatial must start with 'f_'. :dd
 
 {Bad grid of processors} :dt
 
-- 
GitLab


From 0d491d483c232312a4dfc6449e06cc441751fdfc Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Sep 2016 02:10:49 -0400
Subject: [PATCH 18/52] avoid Inline substitution_reference start-string
 without end-string

---
 doc/src/Section_howto.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index f3283c8360..62550dc0dc 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -830,7 +830,7 @@ rotation of [A], [B], and [C] and can be computed as follows:
 
 :c,image(Eqs/transform.jpg)
 
-where A = |[A]| indicates the scalar length of [A]. The hat symbol
+where A = | [A] | indicates the scalar length of [A]. The hat symbol (^)
 indicates the corresponding unit vector. {beta} and {gamma} are angles
 between the vectors described below. Note that by construction, 
 [a], [b], and [c] have strictly positive x, y, and z components, respectively.
-- 
GitLab


From 55022d126306b49c22e0ea0ec2d06e9762ce43c5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Sep 2016 02:11:59 -0400
Subject: [PATCH 19/52] replace :l,ule and :l,ole with :l :ule or :l :ole

---
 doc/src/Section_howto.txt      |  9 +++++---
 doc/src/Section_intro.txt      |  3 ++-
 doc/src/Section_modify.txt     |  3 ++-
 doc/src/Section_python.txt     |  3 ++-
 doc/src/Section_start.txt      |  6 ++++--
 doc/src/accelerate_gpu.txt     |  6 ++++--
 doc/src/accelerate_intel.txt   | 18 ++++++++++------
 doc/src/accelerate_kokkos.txt  |  3 ++-
 doc/src/accelerate_omp.txt     |  6 ++++--
 doc/src/compute.txt            |  3 ++-
 doc/src/fix.txt                |  3 ++-
 doc/src/fix_adapt_fep.txt      |  3 ++-
 doc/src/fix_addtorque.txt      |  3 ++-
 doc/src/fix_atc.txt            |  3 ++-
 doc/src/fix_ave_correlate.txt  |  6 ++++--
 doc/src/fix_langevin_drude.txt |  3 ++-
 doc/src/fix_rigid.txt          |  3 ++-
 doc/src/fix_temp_berendsen.txt |  3 ++-
 doc/src/fix_temp_csvr.txt      |  3 ++-
 doc/src/fix_temp_rescale.txt   |  3 ++-
 doc/src/neigh_modify.txt       |  3 ++-
 doc/src/pair_bop.txt           | 39 ++++++++++++++++++++++------------
 doc/src/pair_buck_long.txt     |  3 ++-
 doc/src/pair_gran.txt          |  3 ++-
 doc/src/pair_modify.txt        |  3 ++-
 doc/src/pair_table.txt         |  3 ++-
 doc/src/pair_table_rx.txt      |  3 ++-
 doc/src/read_data.txt          |  3 ++-
 doc/src/region.txt             |  3 ++-
 doc/src/rerun.txt              |  3 ++-
 doc/src/tutorial_drude.txt     |  4 ++--
 doc/src/write_dump.txt         |  3 ++-
 32 files changed, 110 insertions(+), 56 deletions(-)

diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index 62550dc0dc..576c80f11f 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -2276,7 +2276,8 @@ molecule diffusion rates. :l
 
 As input to special functions of "equal-style
 variables"_variable.html, like sum() and max().  E.g. to find the
-largest cluster or fastest diffusing molecule. :l,ule
+largest cluster or fastest diffusing molecule. :l
+:ule
 
 Example calculations with chunks :h5
 
@@ -2432,7 +2433,8 @@ package, :ulb,l
 the adiabatic core-shell method, implemented in the
 "CORESHELL"_#howto_26 package, :l
 the thermalized Drude dipole method, implemented in the
-"USER-DRUDE"_#howto_27 package. :l,ule
+"USER-DRUDE"_#howto_27 package. :l
+:ule
 
 The fluctuating charge method calculates instantaneous charges on
 interacting atoms based on the electronegativity equalization
@@ -2739,7 +2741,8 @@ too much. To avoid this, damping at short range can be done by Thole
 functions (for which there are physical grounds). This Thole damping
 is applied to the point charges composing the induced dipole (the
 charge of the Drude particle and the opposite charge on the core, not
-to the total charge of the core atom). :l,ule
+to the total charge of the core atom). :l
+:ule
 
 A detailed tutorial covering the usage of Drude induced dipoles in
 LAMMPS is "available here"_tutorial_drude.html.
diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt
index 089921d45d..1a015a4edf 100644
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@@ -241,7 +241,8 @@ Our group has also written and released a separate toolkit called
 "Pizza.py"_pizza which provides tools for doing setup, analysis,
 plotting, and visualization for LAMMPS simulations.  Pizza.py is
 written in "Python"_python and is available for download from "the
-Pizza.py WWW site"_pizza. :l,ule
+Pizza.py WWW site"_pizza. :l
+:ule
 
 :link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
 :link(python,http://www.python.org)
diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt
index e3447e5df8..a3ac505946 100644
--- a/doc/src/Section_modify.txt
+++ b/doc/src/Section_modify.txt
@@ -130,7 +130,8 @@ If you add something you think is truly useful and doesn't impact
 LAMMPS performance when it isn't used, send an email to the
 "developers"_http://lammps.sandia.gov/authors.html.  We might be
 interested in adding it to the LAMMPS distribution.  See further
-details on this at the bottom of this page. :l,ule
+details on this at the bottom of this page. :l
+:ule
 
 :line
 :line
diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt
index 231a9054fb..ce38053023 100644
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@@ -761,7 +761,8 @@ Add a wrapper method to python/lammps.py for this interface
 function. :l
 
 You should now be able to invoke the new interface function from a
-Python script.  Isn't ctypes amazing? :l,ule
+Python script.  Isn't ctypes amazing? :l
+:ule
 
 :line
 :line
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index 0231fb3357..2705e6fd83 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -1208,7 +1208,8 @@ Move to the directory where you have saved lmp_win_no-mpi.exe
 (e.g. by typing: cd "Documents"). :l
 
 At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
-with the name of your LAMMPS input script. :l,ule
+with the name of your LAMMPS input script. :l
+:ule
 
 For the MPI version, which allows you to run LAMMPS under Windows on 
 multiple processors, follow these steps:
@@ -1237,7 +1238,8 @@ In this mode, output may not immediately show up on the screen, so if
 your input script takes a long time to execute, you may need to be
 patient before the output shows up. :l Alternatively, you can still
 use this executable to run on a single processor by typing something
-like: "lmp_win_mpi -in in.lj". :l,ule
+like: "lmp_win_mpi -in in.lj". :l
+:ule
 
 :line
 
diff --git a/doc/src/accelerate_gpu.txt b/doc/src/accelerate_gpu.txt
index 8e76b85aa2..6b4cddf8be 100644
--- a/doc/src/accelerate_gpu.txt
+++ b/doc/src/accelerate_gpu.txt
@@ -42,7 +42,8 @@ LAMMPS-specific code is in the GPU package.  It makes calls to a
 generic GPU library in the lib/gpu directory.  This library provides
 NVIDIA support as well as more general OpenCL support, so that the
 same functionality can eventually be supported on a variety of GPU
-hardware. :l,ule
+hardware. :l
+:ule
 
 Here is a quick overview of how to enable and use the GPU package:
 
@@ -245,7 +246,8 @@ regardless of asynchronous CPU calculations. :l
 
 The output section "GPU Time Info (average)" reports "Max Mem / Proc".
 This is the maximum memory used at one time on the GPU for data
-storage by a single MPI process. :l,ule
+storage by a single MPI process. :l
+:ule
 
 [Restrictions:]
 
diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt
index c97b19b67d..e1b715e587 100644
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@@ -31,7 +31,8 @@ Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
 Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne, 
 charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
-K-Space Styles: pppm :l,ule
+K-Space Styles: pppm :l
+:ule
 
 [Speed-ups to expect:]
 
@@ -70,7 +71,8 @@ For Intel Xeon CPUs:
 Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
 If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better 
 performance. :l
-"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l,ule
+"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
+:ule
 
 For Intel Xeon Phi CPUs for simulations without {kspace_style 
 pppm} in the input script :
@@ -79,7 +81,8 @@ Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
 Runs should be performed using MCDRAM. :l
 "-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel" 
 should be added to the LAMMPS command-line. Choice for best 
-performance will depend on the simulation. :l,ule
+performance will depend on the simulation. :l
+:ule
 
 For Intel Xeon Phi CPUs for simulations with {kspace_style 
 pppm} in the input script:
@@ -93,13 +96,15 @@ performance. :l
 export KMP_AFFINITY=none :l
 "-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
 -sf intel" added to LAMMPS command-line. Choice for best performance 
-will depend on the simulation. :l,ule
+will depend on the simulation. :l
+:ule
 
 For Intel Xeon Phi coprocessors (Offload): 
 
 Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l
 "-pk intel N omp 1" added to command-line where N is the number of 
-coprocessors per node. :l,ule
+coprocessors per node. :l
+:ule
 
 :line
 
@@ -463,7 +468,8 @@ Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Krake
 
 Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l
 
-Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l,ule
+Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l
+:ule
 
 
 
diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt
index a3d1c9efbd..c33e591712 100644
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@@ -381,7 +381,8 @@ When running large number of atoms per GPU, KOKKOS is typically faster
 than the GPU package. :l
 
 When running on Intel Xeon Phi, KOKKOS is not as fast as
-the USER-INTEL package, which is optimized for that hardware. :l,ule
+the USER-INTEL package, which is optimized for that hardware. :l
+:ule
 
 See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
 LAMMPS web site for performance of the KOKKOS package on different
diff --git a/doc/src/accelerate_omp.txt b/doc/src/accelerate_omp.txt
index 0f969d6de1..f31bbc42a3 100644
--- a/doc/src/accelerate_omp.txt
+++ b/doc/src/accelerate_omp.txt
@@ -163,7 +163,8 @@ sometimes be achived by increasing the length of the Coulombic cutoff
 and thus reducing the work done by the long-range solver.  Using the
 "run_style verlet/split"_run_style.html command, which is compatible
 with the USER-OMP package, is an alternative way to reduce the number
-of MPI tasks assigned to the KSpace calculation. :l,ule
+of MPI tasks assigned to the KSpace calculation. :l
+:ule
 
 Additional performance tips are as follows:
 
@@ -178,7 +179,8 @@ NOTE: By default, several current MPI implementations use a processor
 affinity setting that restricts each MPI task to a single CPU core.
 Using multi-threading in this mode will force all threads to share the
 one core and thus is likely to be counterproductive.  Instead, binding
-MPI tasks to a (multi-core) socket, should solve this issue. :l,ule
+MPI tasks to a (multi-core) socket, should solve this issue. :l
+:ule
 
 [Restrictions:]
 
diff --git a/doc/src/compute.txt b/doc/src/compute.txt
index e680abaa33..8ecfd81af1 100644
--- a/doc/src/compute.txt
+++ b/doc/src/compute.txt
@@ -108,7 +108,8 @@ variable"_variable.html. :l
 Local values can be reduced by the "compute
 reduce"_compute_reduce.html command, or histogrammed by the "fix
 ave/histo"_fix_ave_histo.html command, or output by the "dump
-local"_dump.html command. :l,ule
+local"_dump.html command. :l
+:ule
 
 The results of computes that calculate global quantities can be either
 "intensive" or "extensive" values.  Intensive means the value is
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index 3fbeb013eb..d84ec2aad9 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -130,7 +130,8 @@ variable"_variable.html. :l
 
 Local values can be reduced by the "compute
 reduce"_compute_reduce.html command, or histogrammed by the "fix
-ave/histo"_fix_ave_histo.html command. :l,ule
+ave/histo"_fix_ave_histo.html command. :l
+:ule
 
 See this "howto section"_Section_howto.html#howto_15 for a summary of
 various LAMMPS output options, many of which involve fixes.
diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt
index 3037bc9317..5dd58bc39a 100644
--- a/doc/src/fix_adapt_fep.txt
+++ b/doc/src/fix_adapt_fep.txt
@@ -61,7 +61,8 @@ It is possible to modify the charges of chosen atom types only,
 instead of scaling all the charges in the system. :ulb,l
 
 There is a new option {after} for better compatibility with "fix
-ave/time". :l,ule
+ave/time". :l
+:ule
 
 This version is suited for free energy calculations using
 "compute ti"_compute_ti.html or "compute fep"_compute_fep.html.
diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt
index 25c7855c7d..793ec0e015 100644
--- a/doc/src/fix_addtorque.txt
+++ b/doc/src/fix_addtorque.txt
@@ -32,7 +32,8 @@ the components of the total torque applied on the group (around its
 center of mass) are Tx,Ty,Tz :ulb,l
 
 the group would move as a rigid body in the absence of other
-forces. :l,ule
+forces. :l
+:ule
 
 This command can be used to drive a group of atoms into rotation.
 
diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt
index eddfa52921..0df4e29c0b 100644
--- a/doc/src/fix_atc.txt
+++ b/doc/src/fix_atc.txt
@@ -19,7 +19,8 @@ type = {thermal} or {two_temperature} or {hardy} or {field} :l
  {two_temperature} = electron-phonon coupling with field: temperature and electron_temperature
  {hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) 
  {field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre 
-parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l,ule 
+parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l
+:ule 
 
 [Examples:]
 
diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt
index c4df7671aa..6f97d78219 100644
--- a/doc/src/fix_ave_correlate.txt
+++ b/doc/src/fix_ave_correlate.txt
@@ -232,7 +232,8 @@ so Npair = N*(N+1)/2. :l
 
 If {type} is set to {full} then each input value is correlated with
 itself and every other value.  I.e. Cij = Vi*Vj, for i,j = 1,N so
-Npair = N^2. :l,ule
+Npair = N^2. :l
+:ule
 
 The {ave} keyword determines what happens to the accumulation of
 correlation samples every {Nfreq} timesteps.  If the {ave} setting is
@@ -342,7 +343,8 @@ CNN. :l
 
 For {type} = {full}, the Npair = N^2 columns are ordered: C11, C12,
 ..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1,
-CNN. :l,ule
+CNN. :l
+:ule
 
 The array values calculated by this fix are treated as intensive.  If
 you need to divide them by the number of atoms, you must do this in a
diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt
index 47864e3e2c..4fee37fd31 100644
--- a/doc/src/fix_langevin_drude.txt
+++ b/doc/src/fix_langevin_drude.txt
@@ -229,7 +229,8 @@ computes the global pressure even if its group is {ATOMS}. This is
 what we want. If we thermostated {ATOMS} using {npt}, the pressure
 should be the global one, but the temperature should be only that of
 the cores. That's why the command {fix_modify} should be called in
-that case. :l,ule
+that case. :l
+:ule
 
 
 :line
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index f42c18d387..fb6f0e29cb 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -621,7 +621,8 @@ rigid styles for the rigid bodies. :l
 Use "fix press/berendsen"_fix_press_berendsen.html to compute the
 pressure and change the box dimensions.  Use one of the 4 NVE or 2 NVT
 rigid styles for the rigid bodies.  Use "fix nvt"_fix_nh.thml (or any
-other thermostat) for the non-rigid particles. :l,ule
+other thermostat) for the non-rigid particles. :l
+:ule
 
 In all case, the rigid bodies and non-rigid particles both contribute
 to the global pressure and the box is scaled the same by any of the
diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt
index 202be8921f..dd516d7f08 100644
--- a/doc/src/fix_temp_berendsen.txt
+++ b/doc/src/fix_temp_berendsen.txt
@@ -16,7 +16,8 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l
 temp/berendsen = style name of this fix command :l
 Tstart,Tstop = desired temperature at start/end of run :l
   Tstart can be a variable (see below) :pre
-Tdamp = temperature damping parameter (time units) :l,ule
+Tdamp = temperature damping parameter (time units) :l
+:ule
 
 [Examples:]
 
diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt
index 137654d1ec..7e53926516 100644
--- a/doc/src/fix_temp_csvr.txt
+++ b/doc/src/fix_temp_csvr.txt
@@ -19,7 +19,8 @@ temp/csvr or temp/csld = style name of this fix command :l
 Tstart,Tstop = desired temperature at start/end of run :l
   Tstart can be a variable (see below) :pre
 Tdamp = temperature damping parameter (time units) :l
-seed = random number seed to use for white noise (positive integer) :l,ule
+seed = random number seed to use for white noise (positive integer) :l
+:ule
 
 [Examples:]
 
diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt
index 4f8f216ce4..b5c1ec1b6c 100644
--- a/doc/src/fix_temp_rescale.txt
+++ b/doc/src/fix_temp_rescale.txt
@@ -18,7 +18,8 @@ N = perform rescaling every N steps  :l
 Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
   Tstart can be a variable (see below) :pre
 window = only rescale if temperature is outside this window (temperature units) :l
-fraction = rescale to target temperature by this fraction :l,ule
+fraction = rescale to target temperature by this fraction :l
+:ule
 
 [Examples:]
 
diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt
index b05fcf4d3e..c16b667f7d 100644
--- a/doc/src/neigh_modify.txt
+++ b/doc/src/neigh_modify.txt
@@ -123,7 +123,8 @@ to freeze a wall or portion of a bio-molecule. :l
 
 When one or more rigid bodies are specified, interactions within each
 body can be turned off to save needless computation.  See the "fix
-rigid"_fix_rigid.html command for more details. :l,ule
+rigid"_fix_rigid.html command for more details. :l
+:ule
 
 The {exclude type} option turns off the pairwise interaction if one
 atom is of type M and the other of type N.  M can equal N.  The
diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt
index f08bc5413b..b569750c9c 100644
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@@ -162,7 +162,8 @@ Line 1: nr, nBOt (nr is the number of divisions the radius is broken
 into for function tables and MUST be a factor of 5; nBOt is the number 
 of divisions for the tabulated values of THETA_(S,ij) :ulb,l
 Line 2: delta_1-delta_7 (if all are not used in the particular  :l
-formulation, set unused values to 0.0) :l,ule
+formulation, set unused values to 0.0) :l
+:ule
 
 Following this N lines for e_1-e_N containing p_pi.
 
@@ -176,7 +177,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l
 Line 2: c_sigma, a_sigma, c_pi, a_pi :l
 Line 3: delta_sigma, delta_pi :l
 Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of 
-the previous section but is interaction type dependent) :l,ule
+the previous section but is interaction type dependent) :l
+:ule
 
 The next section contains a line for each three body interaction type 
 e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
@@ -185,7 +187,8 @@ Line 1: g_(sigma0), g_(sigma1), g_(sigma2) (These are coefficients for
 g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. "Ward"_#Ward 
 contains the full expressions for the constants as functions of 
 b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk)) :ulb,l
-Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) :l,ule
+Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) :l
+:ule
 
 The next section contains a block for each interaction type for the 
 phi_ij(r_ij).  Each block has nr entries with 5 entries per line.
@@ -196,7 +199,8 @@ Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues
 until nr) :l
 ... :l
 Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the 
-e_1-e_1 interaction type) :l,ule
+e_1-e_1 interaction type) :l
+:ule
 
 The next section contains a block for each interaction type for the 
 beta_(sigma,ij)(r_ij).  Each block has nr entries with 5 entries per 
@@ -208,7 +212,8 @@ Line 2: beta_sigma(r6), beta_sigma(r7), beta_sigma(r8), beta_sigma(r9),
 beta_sigma(r10) (this continues until nr) :l
 ... :l
 Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), 
-beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) :l,ule
+beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) :l
+:ule
 
 The next section contains a block for each interaction type for 
 beta_(pi,ij)(r_ij).  Each block has nr entries with 5 entries per line.
@@ -219,7 +224,8 @@ Line 2: beta_pi(r6), beta_pi(r7), beta_pi(r8), beta_pi(r9),
 beta_pi(r10) (this continues until nr) :l
 ... :l
 Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), 
-beta_pi(r5) (for the e_1-e_2 interaction type) :l,ule
+beta_pi(r5) (for the e_1-e_2 interaction type) :l
+:ule
 
 The next section contains a block for each interaction type for the 
 THETA_(S,ij)((THETA_(sigma,ij))^(1/2), f_(sigma,ij)).  Each block has 
@@ -231,7 +237,8 @@ Line 2: THETA_(S,ij)(r6), THETA_(S,ij)(r7), THETA_(S,ij)(r8),
 THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt) :l
 ... :l
 Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), 
-THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) :l,ule
+THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) :l
+:ule
 
 The next section contains a block of N lines for e_1-e_N
 
@@ -266,7 +273,8 @@ into for function tables and MUST be a factor of 5; ntheta is the power of the
 power of the spline used to fit the angular function; nBOt is the number 
 of divisions for the tabulated values of THETA_(S,ij) :ulb,l
 Line 2: delta_1-delta_7 (if all are not used in the particular  :l
-formulation, set unused values to 0.0) :l,ule
+formulation, set unused values to 0.0) :l
+:ule
 
 Following this N lines for e_1-e_N containing p_pi.
 
@@ -280,7 +288,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l
 Line 2: c_sigma, a_sigma, c_pi, a_pi :l
 Line 3: delta_sigma, delta_pi :l
 Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of 
-the previous section but is interaction type dependent) :l,ule
+the previous section but is interaction type dependent) :l
+:ule
 
 The next section contains a line for each three body interaction type 
 e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
@@ -292,7 +301,8 @@ can contain up to five constants.  If the spline has more than five
 terms the second line will contain the remaining constants The
 following lines will then contain the constants for the remainaing g0,
 g1, g2... (for e_1-e_1-e_2) and the other three body
-interactions :l,ule
+interactions :l
+:ule
 
 The rest of the table has the same structure as the previous section
 (see above).
@@ -319,7 +329,8 @@ into for function tables and MUST be a factor of 5; ntheta is the number of
 divisions for the tabulated values of the g angular function; nBOt is the number 
 of divisions for the tabulated values of THETA_(S,ij) :ulb,l
 Line 2: delta_1-delta_7 (if all are not used in the particular  :l
-formulation, set unused values to 0.0) :l,ule
+formulation, set unused values to 0.0) :l
+:ule
 
 Following this N lines for e_1-e_N containing p_pi.
 
@@ -333,7 +344,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l
 Line 2: c_sigma, a_sigma, c_pi, a_pi :l
 Line 3: delta_sigma, delta_pi :l
 Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of 
-the previous section but is interaction type dependent) :l,ule
+the previous section but is interaction type dependent) :l
+:ule
 
 The next section contains a line for each three body interaction type 
 e_j-e_i-e_k with i=0->N, j=0->N, k=j->N
@@ -344,7 +356,8 @@ Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues
 until ntheta) :l
 ... :l
 Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the 
-e_1-e_1-e_2 interaction type) :l,ule
+e_1-e_1-e_2 interaction type) :l
+:ule
 
 The rest of the table has the same structure as the previous section (see above).
 
diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt
index aad5bdb0fe..50aee51dd3 100644
--- a/doc/src/pair_buck_long.txt
+++ b/doc/src/pair_buck_long.txt
@@ -20,7 +20,8 @@ flag_coul = {long} or {off} :l
   {long} = use Kspace long-range summation for the Coulombic term 1/r
   {off} = omit the Coulombic term :pre
 cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) :l
-cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule
+cutoff2 = global cutoff for Coulombic (optional) (distance units) :l
+:ule
 
 [Examples:]
 
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index 497d1d553f..baa1154fa5 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -23,7 +23,8 @@ Kt = elastic constant for tangential contact (force/distance units or pressure u
 gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
 gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
 xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
-dampflag = 0 or 1 if tangential damping force is excluded or included :l,ule
+dampflag = 0 or 1 if tangential damping force is excluded or included :l
+:ule
 
 NOTE: Versions of LAMMPS before 9Jan09 had different style names for
 granular force fields.  This is to emphasize the fact that the
diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt
index eb60c6b006..8a4f291583 100644
--- a/doc/src/pair_modify.txt
+++ b/doc/src/pair_modify.txt
@@ -187,7 +187,8 @@ enabled will not be thermodynamically consistent with the truncated
 force-field that was used.  In other words, atoms do not feel any LJ
 pair interactions beyond the cutoff, but the energy and pressure
 reported by the simulation include an estimated contribution from
-those interactions. :l,ule
+those interactions. :l
+:ule
 
 The {compute} keyword allows pairwise computations to be turned off,
 even though a "pair_style"_pair_style.html is defined.  This is not
diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt
index 8a667e40f4..560ff43590 100644
--- a/doc/src/pair_table.txt
+++ b/doc/src/pair_table.txt
@@ -118,7 +118,8 @@ consistent (dE/dr = -F) over the entire range of r values.  LAMMPS
 will warn if this is not the case. :l
 
 Use as large an inner cutoff as possible.  This avoids fitting splines
-to very steep parts of the potential. :l,ule
+to very steep parts of the potential. :l
+:ule
 
 :line
 
diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt
index 6c765d2093..6db0a3fa5c 100644
--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@@ -111,7 +111,8 @@ Make sure that your tabulated forces and tabulated energies are consistent
 (dE/dr = -F) along the entire range of r values. :l
 
 Use as large an inner cutoff as possible.  This avoids fitting splines
-to very steep parts of the potential. :l,ule
+to very steep parts of the potential. :l
+:ule
 
 :line
 
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index d040872e73..bcdc7ac434 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -698,7 +698,8 @@ atoms in such a bond. :l
 If you plan to "dump"_dump.html image flags and perform post-analysis
 that will unwrap atom coordinates, it may be important that a
 continued run (restarted from a data file) begins with image flags
-that are consistent with the previous run. :l,ule
+that are consistent with the previous run. :l
+:ule
 
 NOTE: If your system is an infinite periodic crystal with bonds then
 it is impossible to have fully consistent image flags.  This is because
diff --git a/doc/src/region.txt b/doc/src/region.txt
index 0dc415a8a8..0bc578c07e 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -243,7 +243,8 @@ to yz. :l
 
 For style {sphere}, the lattice spacing in dimensions x,y,z are
 applied to the sphere center x,y,z.  The spacing in dimension x is
-applied to the sphere radius. :l,ule
+applied to the sphere radius. :l
+:ule
 
 :line
 
diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt
index c623d4bebc..da8c8d6895 100644
--- a/doc/src/rerun.txt
+++ b/doc/src/rerun.txt
@@ -60,7 +60,8 @@ Calculate the portion of per-atom forces resulting from a subset of
 the potential.  E.g. compute only Coulombic forces.  This can be done
 by only defining only a Coulombic pair style in the rerun script.
 Doing this in the original script would result in different (bad)
-dynamics.  :l,ule
+dynamics.  :l
+:ule
 
 Conceptually, using the rerun command is like running an input script
 that has a loop in it (see the "next"_next.html and "jump"_jump.html
diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt
index a6080fef27..10de99a80c 100644
--- a/doc/src/tutorial_drude.txt
+++ b/doc/src/tutorial_drude.txt
@@ -332,8 +332,8 @@ For the {thole} pair style the coefficients are
 the atom polarizability in units of cubic length :olb,l
 the screening factor of the Thole function (optional, default value
 specified by the pair_style command) :l
-the cutoff (optional, default value defined by the pair_style command)
-:l,ole
+the cutoff (optional, default value defined by the pair_style command) :l
+:ole
 
 The special neighbors have charge-charge and charge-dipole
 interactions screened by the {coul} factors of the {special_bonds}
diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt
index 8f6e860a48..a4ed7b1664 100644
--- a/doc/src/write_dump.txt
+++ b/doc/src/write_dump.txt
@@ -17,7 +17,8 @@ style = any of the supported "dump styles"_dump.html :l
 file = name of file to write dump info to :l
 dump-args = any additional args needed for a particular "dump style"_dump.html :l
 modify = all args after this keyword are passed to "dump_modify"_dump_modify.html (optional) :l
-dump-modify-args = args for "dump_modify"_dump_modify.html (optional) :l,ule
+dump-modify-args = args for "dump_modify"_dump_modify.html (optional) :l
+:ule
 
 [Examples:]
 
-- 
GitLab


From 3f312244a01d07495bfb18c727da5507684a4339 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 6 Sep 2016 23:31:58 -0400
Subject: [PATCH 20/52] Escape RST special character '*' in final output

(cherry picked from commit 7cb39811d47b1f364286597acea21c3afd010733)
---
 doc/utils/converters/lammpsdoc/txt2rst.py  | 5 +++++
 doc/utils/converters/tests/test_txt2rst.py | 4 ++++
 2 files changed, 9 insertions(+)

diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py
index f9ceb9b7ae..aec1b0d02d 100755
--- a/doc/utils/converters/lammpsdoc/txt2rst.py
+++ b/doc/utils/converters/lammpsdoc/txt2rst.py
@@ -57,10 +57,15 @@ class RSTMarkup(Markup):
         return text
 
     def convert(self, text):
+        text = self.escape_rst_chars(text)
         text = super().convert(text)
         text = self.inline_math(text)
         return text
 
+    def escape_rst_chars(self, text):
+        text = text.replace('*', '\\*')
+        return text
+
     def inline_math(self, text):
         start_pos = text.find("\\(")
         end_pos = text.find("\\)")
diff --git a/doc/utils/converters/tests/test_txt2rst.py b/doc/utils/converters/tests/test_txt2rst.py
index e2c20434be..9403d419a8 100644
--- a/doc/utils/converters/tests/test_txt2rst.py
+++ b/doc/utils/converters/tests/test_txt2rst.py
@@ -77,6 +77,10 @@ class TestMarkup(unittest.TestCase):
         self.assertEqual("**bold** = [bold]\n"
                          "*italic* = {italic}\n", s)
 
+    def test_escape_rst_characters(self):
+        s = self.markup.convert("[*bold] and {italic*}")
+        self.assertEqual("**\*bold** and *italic\**", s)
+
     def test_paragraph_with_italic(self):
         self.assertEqual("A sentence with a *italic* word", self.markup.convert("A sentence with a {italic} word"))
 
-- 
GitLab


From 925f1bfb6fc997c61f42656109208a5336be2c11 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Tue, 6 Sep 2016 23:46:14 -0400
Subject: [PATCH 21/52] Escape RST special character '^' and take care of
 special math cases

(cherry picked from commit 453521c8e682c6563226dfcc57c689052dacd21f)
---
 doc/utils/converters/lammpsdoc/txt2rst.py  |  6 ++++++
 doc/utils/converters/tests/test_txt2rst.py | 17 +++++++++++++++++
 2 files changed, 23 insertions(+)

diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py
index aec1b0d02d..73c5ff91dc 100755
--- a/doc/utils/converters/lammpsdoc/txt2rst.py
+++ b/doc/utils/converters/lammpsdoc/txt2rst.py
@@ -64,6 +64,7 @@ class RSTMarkup(Markup):
 
     def escape_rst_chars(self, text):
         text = text.replace('*', '\\*')
+        text = text.replace('^', '\\^')
         return text
 
     def inline_math(self, text):
@@ -73,6 +74,8 @@ class RSTMarkup(Markup):
         while start_pos >= 0 and end_pos >= 0:
             original = text[start_pos:end_pos+2]
             formula = original[2:-2]
+            formula = formula.replace('\\*', '*')
+            formula = formula.replace('\\^', '^')
             replacement = ":math:`" + formula.replace('\n', ' ').strip() + "`"
             text = text.replace(original, replacement)
 
@@ -300,6 +303,9 @@ class RSTFormatting(Formatting):
                 start = ""
                 body = parts[0]
 
+            body = body.replace('\\*', '*')
+            body = body.replace('\\^', '^')
+
             if len(start) > 0:
                 text += start + "\n"
             text += "\n.. math::\n\n"
diff --git a/doc/utils/converters/tests/test_txt2rst.py b/doc/utils/converters/tests/test_txt2rst.py
index 9403d419a8..a4b059fbf3 100644
--- a/doc/utils/converters/tests/test_txt2rst.py
+++ b/doc/utils/converters/tests/test_txt2rst.py
@@ -81,6 +81,10 @@ class TestMarkup(unittest.TestCase):
         s = self.markup.convert("[*bold] and {italic*}")
         self.assertEqual("**\*bold** and *italic\**", s)
 
+    def test_escape_hat_character(self):
+        s = self.markup.convert("x^2")
+        self.assertEqual("x\^2", s)
+
     def test_paragraph_with_italic(self):
         self.assertEqual("A sentence with a *italic* word", self.markup.convert("A sentence with a {italic} word"))
 
@@ -411,6 +415,16 @@ class TestMathMarkup(unittest.TestCase):
                          "   \\frac{s_{ij} r_{ij} }{2} \\right)\n"
                          "   \\exp \\left( - s_{ij} r_{ij} \\right) \\end{equation}\n\n", s)
 
+    def test_detect_latex_equation_with_mult(self):
+        s = self.txt2rst.convert("\\begin\\{equation\\} a = b * c \\end\\{equation\\}\n")
+        self.assertEqual("\n.. math::\n\n"
+                         "   \\begin{equation} a = b * c \\end{equation}\n\n", s)
+
+    def test_detect_latex_equation_with_pow(self):
+        s = self.txt2rst.convert("\\begin\\{equation\\} a = b^c \\end\\{equation\\}\n")
+        self.assertEqual("\n.. math::\n\n"
+                         "   \\begin{equation} a = b^c \\end{equation}\n\n", s)
+
     def test_detect_inline_latex_equation(self):
         s = self.txt2rst.convert("Masses: \\begin\\{equation\\} M' = M + m \\end\\{equation\\}\n"
                                  "\\begin\\{equation\\} m' = \\frac \\{M\\, m \\} \\{M'\\} \\end\\{equation\\}\n")
@@ -426,6 +440,9 @@ class TestMathMarkup(unittest.TestCase):
     def test_detect_inline_math(self):
         self.assertEqual(":math:`x^2`", self.markup.convert("\\( x^2 \\)"))
 
+    def test_detect_inline_math_mult(self):
+        self.assertEqual(":math:`x * 2`", self.markup.convert("\\( x * 2 \\)"))
+
     def test_detect_multiline_inline_math(self):
         line = "\\(\\sqrt \\{ \\frac \\{2\, k_B \\mathtt\\{Tcom\\}\, m'\\}\n" \
                "\\{\\mathrm dt\\, \\mathtt\\{damp\\_com\\} \\}\n" \
-- 
GitLab


From 9e8256aeb0b7e4f8ffadb97e6a04256018b17138 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 00:52:43 -0400
Subject: [PATCH 22/52] Refactored code and escape RST special character '_'

(cherry picked from commit 4629a464f701f919633fd220860b6610d097c291)
---
 doc/utils/converters/lammpsdoc/txt2rst.py  | 21 ++++++++++++++-------
 doc/utils/converters/tests/test_txt2rst.py |  4 ++++
 2 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py
index 73c5ff91dc..a4196e501b 100755
--- a/doc/utils/converters/lammpsdoc/txt2rst.py
+++ b/doc/utils/converters/lammpsdoc/txt2rst.py
@@ -65,6 +65,13 @@ class RSTMarkup(Markup):
     def escape_rst_chars(self, text):
         text = text.replace('*', '\\*')
         text = text.replace('^', '\\^')
+        text = re.sub(r'([^"])_', r'\1\\_', text)
+        return text
+
+    def unescape_rst_chars(self, text):
+        text = text.replace('\\*', '*')
+        text = text.replace('\\^', '^')
+        text = text.replace('\\_', '_')
         return text
 
     def inline_math(self, text):
@@ -74,8 +81,7 @@ class RSTMarkup(Markup):
         while start_pos >= 0 and end_pos >= 0:
             original = text[start_pos:end_pos+2]
             formula = original[2:-2]
-            formula = formula.replace('\\*', '*')
-            formula = formula.replace('\\^', '^')
+            formula = self.unescape_rst_chars(formula)
             replacement = ":math:`" + formula.replace('\n', ' ').strip() + "`"
             text = text.replace(original, replacement)
 
@@ -88,6 +94,8 @@ class RSTMarkup(Markup):
         content = content.strip()
         content = content.replace('\n', ' ')
 
+        href = self.unescape_rst_chars(href)
+
         anchor_pos = href.find('#')
 
         if anchor_pos >= 0:
@@ -130,11 +138,11 @@ class RSTFormatting(Formatting):
                          link.lower().endswith('.jpeg') or
                          link.lower().endswith('.png') or
                          link.lower().endswith('.gif')):
-            converted = ".. thumbnail:: " + link + "\n"
+            converted = ".. thumbnail:: " + self.markup.unescape_rst_chars(link) + "\n"
         else:
-            converted = ".. image:: " + file + "\n"
+            converted = ".. image:: " + self.markup.unescape_rst_chars(file) + "\n"
             if link:
-                converted += "   :target: " + link + "\n"
+                converted += "   :target: " + self.markup.unescape_rst_chars(link) + "\n"
 
         if "c" in self.current_command_list:
             converted += "   :align: center\n"
@@ -303,8 +311,7 @@ class RSTFormatting(Formatting):
                 start = ""
                 body = parts[0]
 
-            body = body.replace('\\*', '*')
-            body = body.replace('\\^', '^')
+            body = self.markup.unescape_rst_chars(body)
 
             if len(start) > 0:
                 text += start + "\n"
diff --git a/doc/utils/converters/tests/test_txt2rst.py b/doc/utils/converters/tests/test_txt2rst.py
index a4b059fbf3..1602fb61f9 100644
--- a/doc/utils/converters/tests/test_txt2rst.py
+++ b/doc/utils/converters/tests/test_txt2rst.py
@@ -85,6 +85,10 @@ class TestMarkup(unittest.TestCase):
         s = self.markup.convert("x^2")
         self.assertEqual("x\^2", s)
 
+    def test_escape_underscore(self):
+        s = self.markup.convert("x_")
+        self.assertEqual("x\_", s)
+
     def test_paragraph_with_italic(self):
         self.assertEqual("A sentence with a *italic* word", self.markup.convert("A sentence with a {italic} word"))
 
-- 
GitLab


From 4c783ea3b7262ad49f70f010ece79cbc4f43e610 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 01:31:56 -0400
Subject: [PATCH 23/52] Enforce l,ule or l,ole command order for RST

(cherry picked from commit 79e867c213ee022685e5bb8a5089a112099e4f06)
---
 doc/utils/converters/lammpsdoc/txt2html.py | 5 ++++-
 doc/utils/converters/lammpsdoc/txt2rst.py  | 8 ++++++++
 doc/utils/converters/tests/test_txt2rst.py | 8 ++++++++
 3 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/doc/utils/converters/lammpsdoc/txt2html.py b/doc/utils/converters/lammpsdoc/txt2html.py
index ab132a380d..6e559723b4 100755
--- a/doc/utils/converters/lammpsdoc/txt2html.py
+++ b/doc/utils/converters/lammpsdoc/txt2html.py
@@ -518,6 +518,9 @@ class TxtParser(object):
     def last_word(self, text):
         return text.split()[-1]
 
+    def order_commands(self, commands):
+        return list(reversed(commands))
+
     def do_formatting(self, paragraph):
         last_word = self.last_word(paragraph)
         format_str = paragraph[paragraph.rfind(last_word):]
@@ -529,7 +532,7 @@ class TxtParser(object):
 
         commands = [x[0] for x in command_pattern.findall(commands)]
 
-        for command in reversed(commands):
+        for command in self.order_commands(commands):
             paragraph = self.format.convert(command, paragraph, commands)
 
         return paragraph + '\n'
diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py
index a4196e501b..1bc279c0f3 100755
--- a/doc/utils/converters/lammpsdoc/txt2rst.py
+++ b/doc/utils/converters/lammpsdoc/txt2rst.py
@@ -347,6 +347,14 @@ class Txt2Rst(TxtParser):
     def is_raw_textblock_end(self, line):
         return line.startswith('END_RST -->')
 
+    def order_commands(self, commands):
+        if 'ule' in commands and 'l' in commands and commands.index('ule') >  commands.index('l'):
+            return commands
+        elif 'ole' in commands and 'l' in commands and commands.index('ole') > commands.index('l'):
+            return commands
+        return super().order_commands(commands)
+
+
 class Txt2RstConverter(TxtConverter):
     def get_argument_parser(self):
         parser = argparse.ArgumentParser(description='converts a text file with simple formatting & markup into '
diff --git a/doc/utils/converters/tests/test_txt2rst.py b/doc/utils/converters/tests/test_txt2rst.py
index 1602fb61f9..2fa2bd699e 100644
--- a/doc/utils/converters/tests/test_txt2rst.py
+++ b/doc/utils/converters/tests/test_txt2rst.py
@@ -236,6 +236,14 @@ class TestListFormatting(unittest.TestCase):
                          "* two\n"
                          "* three\n\n", s)
 
+    def test_elementwise_unordered_list_reverse(self):
+        s = self.txt2rst.convert("one :ulb,l\n"
+                                 "two :l\n"
+                                 "three :l,ule\n")
+        self.assertEqual("* one\n"
+                         "* two\n"
+                         "* three\n\n", s)
+
     def test_multi_line_unordered_list_elements(self):
         s = self.txt2rst.convert("one :ulb,l\n"
                                  "two\n"
-- 
GitLab


From 348b677148cea0d57eaab992d233f7ab4eca9d19 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Sep 2016 07:41:17 -0400
Subject: [PATCH 24/52] Make formatting and links more consistent and unique

---
 doc/src/Section_packages.txt | 6 +++---
 doc/src/Section_tools.txt    | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index 5282eaa4bb..38afb98de1 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -1160,9 +1160,9 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "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-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "SMD User Guide"_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-SPH"_#USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
 "USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute XXX/tally"_compute_tally.html, USER/tally, -, -
 "USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_dump_custom_vtk.html, -, -, lib/vtk
 :tb(ea=c)
@@ -1336,7 +1336,7 @@ splitting algorithm.  See src/USER-DPD/README for more details.
 Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html
 "compute dpd/atom"_compute_dpd_atom.html
 "fix eos/cv"_fix_eos_table.html "fix eos/table"_fix_eos_table.html
- "fix eos/table/rx"_fix_eos_table_rx.html "fix shardlow"_fix_shardlow.html
+"fix eos/table/rx"_fix_eos_table_rx.html "fix shardlow"_fix_shardlow.html
 "fix rx"_fix_rx.html "pair table/rx"_pair_table_rx.html
 "pair dpd/fdt"_pair_dpd_fdt.html "pair dpd/fdt/energy"_pair_dpd_fdt.html
 "pair exp6/rx"_pair_exp6_rx.html "pair multi/lucy"_pair_multi_lucy.html
diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt
index 6da0690f34..189bc1e35c 100644
--- a/doc/src/Section_tools.txt
+++ b/doc/src/Section_tools.txt
@@ -65,7 +65,7 @@ own sub-directories with their own Makefiles.
 "polymer bonding"_#polybond
 "pymol_asphere"_#pymol
 "python"_#pythontools
-"reax"_#reax
+"reax"_#reax_tool
 "restart2data"_#restart
 "vim"_#vim
 "xmgrace"_#xmgrace
@@ -455,7 +455,7 @@ README for more info on Pizza.py and how to use these scripts.
 
 :line
 
-reax tool :h4,link(reax)
+reax tool :h4,link(reax_tool)
 
 The reax sub-directory contains stand-alond codes that can
 post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
-- 
GitLab


From 70d6718aa31290689f0e7f52af48438e0de43366 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Sep 2016 07:42:06 -0400
Subject: [PATCH 25/52] Update discussion on parallel python packages. There
 seem to be only two left.

---
 doc/src/Section_python.txt | 69 +++++++++++++-------------------------
 1 file changed, 24 insertions(+), 45 deletions(-)

diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt
index ce38053023..b9049d87f7 100644
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@@ -277,35 +277,14 @@ your Python with an interface to MPI.  This also allows you to
 make MPI calls directly from Python in your script, if you desire.
 
 There are several Python packages available that purport to wrap MPI
-as a library and allow MPI functions to be called from Python.
-
-These include
-
-"pyMPI"_http://pympi.sourceforge.net/
-"maroonmpi"_http://code.google.com/p/maroonmpi/
-"mpi4py"_http://code.google.com/p/mpi4py/
-"myMPI"_http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&sid=c997fefc3933bd66204875b436940f16
-"Pypar"_http://code.google.com/p/pypar :ul
-
-All of these except pyMPI work by wrapping the MPI library and
-exposing (some portion of) its interface to your Python script.  This
-means Python cannot be used interactively in parallel, since they do
-not address the issue of interactive input to multiple instances of
-Python running on different processors.  The one exception is pyMPI,
-which alters the Python interpreter to address this issue, and (I
-believe) creates a new alternate executable (in place of "python"
-itself) as a result.
-
-In principle any of these Python/MPI packages should work to invoke
-LAMMPS in parallel and to make MPI calls themselves from a Python
-script which is itself running in parallel.  However, when I
-downloaded and looked at a few of them, their documentation was
-incomplete and I had trouble with their installation.  It's not clear
-if some of the packages are still being actively developed and
-supported.
-
-The packages Pypar and mpi4py have both been successfully tested with
-LAMMPS.  Pypar is simpler and easy to set up and use, but supports
+as a library and allow MPI functions to be called from Python. However,
+development on most of them seems to be halted except on:
+
+"mpi4py"_https://bitbucket.org/mpi4py/mpi4py
+"PyPar"_https://github.com/daleroberts/pypar :ul
+
+Both packages, PyPar and mpi4py have been successfully tested with
+LAMMPS.  PyPar is simpler and easy to set up and use, but supports
 only a subset of MPI.  Mpi4py is more MPI-feature complete, but also a
 bit more complex to use.  As of version 2.0.0, mpi4py is the only
 python MPI wrapper that allows passing a custom MPI communicator to
@@ -314,7 +293,7 @@ LAMMPS instances on subsets of the total MPI ranks.
 
 :line
 
-Pypar requires the ubiquitous "Numpy package"_http://numpy.scipy.org
+PyPar requires the ubiquitous "Numpy package"_http://numpy.scipy.org
 be installed in your Python.  After launching Python, type
 
 import numpy :pre
@@ -329,16 +308,16 @@ sudo python setup.py install :pre
 The "sudo" is only needed if required to copy Numpy files into your
 Python distribution's site-packages directory.
 
-To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it
+To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it
 and from its "source" directory, type
 
 python setup.py build
 sudo python setup.py install :pre
 
-Again, the "sudo" is only needed if required to copy Pypar files into
+Again, the "sudo" is only needed if required to copy PyPar files into
 your Python distribution's site-packages directory.
 
-If you have successully installed Pypar, you should be able to run
+If you have successully installed PyPar, you should be able to run
 Python and type
 
 import pypar :pre
@@ -355,17 +334,17 @@ print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) :pre
 
 and see one line of output for each processor you run on.
 
-NOTE: To use Pypar and LAMMPS in parallel from Python, you must insure
+NOTE: To use PyPar and LAMMPS in parallel from Python, you must insure
 both are using the same version of MPI.  If you only have one MPI
 installed on your system, this is not an issue, but it can be if you
 have multiple MPIs.  Your LAMMPS build is explicit about which MPI it
 is using, since you specify the details in your lo-level
-src/MAKE/Makefile.foo file.  Pypar uses the "mpicc" command to find
+src/MAKE/Makefile.foo file.  PyPar uses the "mpicc" command to find
 information about the MPI it uses to build against.  And it tries to
 load "libmpi.so" from the LD_LIBRARY_PATH.  This may or may not find
 the MPI library that LAMMPS is using.  If you have problems running
-both Pypar and LAMMPS together, this is an issue you may need to
-address, e.g. by moving other MPI installations so that Pypar finds
+both PyPar and LAMMPS together, this is an issue you may need to
+address, e.g. by moving other MPI installations so that PyPar finds
 the right one.
 
 :line
@@ -467,8 +446,8 @@ lmp_g++ -in in.lj :pre
 [Test LAMMPS and Python in parallel:] :h5
 
 To run LAMMPS in parallel, assuming you have installed the
-"Pypar"_Pypar package as discussed above, create a test.py file
-containing these lines:
+"PyPar"_https://github.com/daleroberts/pypar package as discussed
+above, create a test.py file containing these lines:
 
 import pypar
 from lammps import lammps
@@ -478,8 +457,8 @@ print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
 pypar.finalize() :pre
 
 To run LAMMPS in parallel, assuming you have installed the
-"mpi4py"_mpi4py package as discussed above, create a test.py file
-containing these lines:
+"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed
+above, create a test.py file containing these lines:
 
 from mpi4py import MPI
 from lammps import lammps
@@ -498,17 +477,17 @@ and you should see the same output as if you had typed
 
 % mpirun -np 4 lmp_g++ -in in.lj :pre
 
-Note that if you leave out the 3 lines from test.py that specify Pypar
+Note that if you leave out the 3 lines from test.py that specify PyPar
 commands you will instantiate and run LAMMPS independently on each of
 the P processors specified in the mpirun command.  In this case you
 should get 4 sets of output, each showing that a LAMMPS run was made
 on a single processor, instead of one set of output showing that
 LAMMPS ran on 4 processors.  If the 1-processor outputs occur, it
-means that Pypar is not working correctly.
+means that PyPar is not working correctly.
 
-Also note that once you import the PyPar module, Pypar initializes MPI
+Also note that once you import the PyPar module, PyPar initializes MPI
 for you, and you can use MPI calls directly in your Python script, as
-described in the Pypar documentation.  The last line of your Python
+described in the PyPar documentation.  The last line of your Python
 script should be pypar.finalize(), to insure MPI is shut down
 correctly.
 
-- 
GitLab


From 44ce6fac4b911c93bf14eea2b3ac1cd0111f8ab5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Sep 2016 08:29:16 -0400
Subject: [PATCH 26/52] replace backquote with regular quote and `` + '' with
 double quote.

---
 doc/src/Section_errors.txt  |  8 ++++----
 doc/src/Section_start.txt   |  4 ++--
 doc/src/tutorial_github.txt | 10 +++++-----
 src/KIM/pair_kim.h          |  8 ++++----
 4 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt
index 7f5f7857a5..6a18b1bbdb 100644
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@@ -11351,19 +11351,19 @@ have fully consistent image flags, since some bonds will cross
 periodic boundaries and connect two atoms with the same image
 flag. :dd
 
-{KIM Model does not provide `energy'; Potential energy will be zero} :dt
+{KIM Model does not provide 'energy'; Potential energy will be zero} :dt
 
 Self-explanatory. :dd
 
-{KIM Model does not provide `forces'; Forces will be zero} :dt
+{KIM Model does not provide 'forces'; Forces will be zero} :dt
 
 Self-explanatory. :dd
 
-{KIM Model does not provide `particleEnergy'; energy per atom will be zero} :dt
+{KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt
 
 Self-explanatory. :dd
 
-{KIM Model does not provide `particleVirial'; virial per atom will be zero} :dt
+{KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt
 
 Self-explanatory. :dd
 
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index 2705e6fd83..32bd5dae3c 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -1080,12 +1080,12 @@ Here is an example of such errors when the system FFTW or provided
 lib/colvars library have not been built as shared libraries:
 
 /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
-R_X86_64_32 against `.rodata' can not be used when making a shared
+R_X86_64_32 against '.rodata' can not be used when making a shared
 object; recompile with -fPIC
 /usr/local/lib/libfftw3.a: could not read symbols: Bad value :pre
 
 /usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
-relocation R_X86_64_32 against `__pthread_key_create' can not be used
+relocation R_X86_64_32 against '__pthread_key_create' can not be used
 when making a shared object; recompile with -fPIC
 ../../lib/colvars/libcolvars.a: error adding symbols: Bad value :pre
 
diff --git a/doc/src/tutorial_github.txt b/doc/src/tutorial_github.txt
index 06f15df874..f31de522cc 100644
--- a/doc/src/tutorial_github.txt
+++ b/doc/src/tutorial_github.txt
@@ -22,7 +22,7 @@ book"_http://git-scm.com/book/ to reacquaint yourself.
 
 First of all, you need a GitHub account. This is fairly simple, just
 go to "GitHub"_https://github.com and create an account by clicking
-the ``Sign up for GitHub'' button. Once your account is created, you
+the "Sign up for GitHub" button. Once your account is created, you
 can sign in by clicking the button in the top left and filling in your
 username or e-mail address and password.
 
@@ -33,7 +33,7 @@ username or e-mail address and password.
 To get changes into LAMMPS, you need to first fork the repository. At
 the time of writing, LAMMPS-ICMS is the preferred fork. Go to "LAMMPS
 on GitHub"_https://github.com/lammps/lammps and make sure branch is
-set to ``lammps-icms'', see the figure below.
+set to "lammps-icms", see the figure below.
 
 :c,image(JPG/tutorial_branch.png)
 
@@ -58,7 +58,7 @@ will contain these changes, a so-called feature branch.
 
 Since LAMMPS is such a big project and most user contributions come in
 small portions, the most ideal workflow for LAMMPS is the so-called
-``Feature branch'' workflow. It is explained in great detail here:
+"Feature branch" workflow. It is explained in great detail here:
 "feature branch
 workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow.
 
@@ -78,7 +78,7 @@ You can find the proper url to the right of the "HTTPS" block, see figure.
 
 :c,image(JPG/tutorial_https_block.png)
 
-The above command copies (``clones'') the git repository to your local
+The above command copies ("clones") the git repository to your local
 machine. You can use this local clone to make changes and test them
 without interfering with the repository on github. First, however, it
 is recommended to make a new branch for a particular feature you would
@@ -101,7 +101,7 @@ you should switch branches!
 After everything is done, add the files to the branch and commit them:
 
   $ git add src/USER-MANIFOLD examples/USER/manifold/
-  $ git add doc/fix_nv{t,e}_manifold_rattle.txt
+  $ git add doc/fix_nv\{t,e\}_manifold_rattle.txt
   $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt :pre
 
 After the files are added, the change should be comitted:
diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h
index 6e2fd2e342..843fb6db2a 100644
--- a/src/KIM/pair_kim.h
+++ b/src/KIM/pair_kim.h
@@ -197,19 +197,19 @@ E: Unknown unit_style
 
 Self-explanatory. Check the input script or data file.
 
-W: KIM Model does not provide `energy'; Potential energy will be zero
+W: KIM Model does not provide 'energy'; Potential energy will be zero
 
 Self-explanatory.
 
-W: KIM Model does not provide `forces'; Forces will be zero
+W: KIM Model does not provide 'forces'; Forces will be zero
 
 Self-explanatory.
 
-W: KIM Model does not provide `particleEnergy'; energy per atom will be zero
+W: KIM Model does not provide 'particleEnergy'; energy per atom will be zero
 
 Self-explanatory.
 
-W: KIM Model does not provide `particleVirial'; virial per atom will be zero
+W: KIM Model does not provide 'particleVirial'; virial per atom will be zero
 
 Self-explanatory.
 
-- 
GitLab


From 5feedbd8291d2175fd7ee96332a32465a43c0dd0 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Sep 2016 10:09:53 -0400
Subject: [PATCH 27/52] regenerate html pages with new txt2rst tool

---
 doc/html/Section_accelerate.html              |   4 +-
 doc/html/Section_commands.html                |  12 +-
 doc/html/Section_errors.html                  |  10 +-
 doc/html/Section_example.html                 |  20 +-
 doc/html/Section_howto.html                   | 316 +++++++-------
 doc/html/Section_modify.html                  | 102 ++---
 doc/html/Section_packages.html                | 257 ++++++------
 doc/html/Section_python.html                  | 250 ++++++-----
 doc/html/Section_start.html                   | 130 +++---
 doc/html/Section_tools.html                   |  12 +-
 doc/html/accelerate_gpu.html                  |  26 +-
 doc/html/accelerate_intel.html                |  46 +-
 doc/html/accelerate_kokkos.html               | 144 +++----
 doc/html/accelerate_omp.html                  |  16 +-
 doc/html/angle_charmm.html                    |  14 +-
 doc/html/angle_class2.html                    |  18 +-
 doc/html/angle_cosine.html                    |  14 +-
 doc/html/angle_cosine_delta.html              |  14 +-
 doc/html/angle_cosine_periodic.html           |  14 +-
 doc/html/angle_cosine_shift.html              |  14 +-
 doc/html/angle_cosine_shift_exp.html          |  14 +-
 doc/html/angle_cosine_squared.html            |  14 +-
 doc/html/angle_dipole.html                    |  14 +-
 doc/html/angle_fourier.html                   |   6 +-
 doc/html/angle_fourier_simple.html            |   6 +-
 doc/html/angle_harmonic.html                  |  14 +-
 doc/html/angle_quartic.html                   |  14 +-
 doc/html/angle_sdk.html                       |  20 +-
 doc/html/atom_modify.html                     |  16 +-
 doc/html/atom_style.html                      |  24 +-
 doc/html/body.html                            |  20 +-
 doc/html/bond_class2.html                     |  14 +-
 doc/html/bond_fene.html                       |  14 +-
 doc/html/bond_fene_expand.html                |  14 +-
 doc/html/bond_harmonic.html                   |  14 +-
 doc/html/bond_harmonic_shift.html             |  14 +-
 doc/html/bond_harmonic_shift_cut.html         |  14 +-
 doc/html/bond_morse.html                      |  14 +-
 doc/html/bond_nonlinear.html                  |  14 +-
 doc/html/bond_quartic.html                    |  22 +-
 doc/html/change_box.html                      |  56 +--
 doc/html/compute.html                         |  14 +-
 doc/html/compute_bond_local.html              |  10 +-
 doc/html/compute_centro_atom.html             |   2 +-
 doc/html/compute_dipole_chunk.html            |  10 +-
 doc/html/compute_fep.html                     |  10 +-
 doc/html/compute_gyration_chunk.html          |  10 +-
 doc/html/compute_heat_flux.html               |  26 +-
 doc/html/compute_inertia_chunk.html           |  10 +-
 doc/html/compute_ke_atom_eff.html             |  10 +-
 doc/html/compute_ke_eff.html                  |  10 +-
 doc/html/compute_modify.html                  |  14 +-
 doc/html/compute_pe_atom.html                 |  10 +-
 doc/html/compute_pressure.html                |  14 +-
 doc/html/compute_property_atom.html           |  38 +-
 doc/html/compute_property_chunk.html          |  12 +-
 doc/html/compute_reduce.html                  |  62 +--
 doc/html/compute_rigid_local.html             |   8 +-
 doc/html/compute_saed.html                    |  18 +-
 doc/html/compute_sna_atom.html                |  42 +-
 doc/html/compute_stress_atom.html             |  12 +-
 doc/html/compute_temp_cs.html                 |   8 +-
 doc/html/compute_temp_eff.html                |  10 +-
 doc/html/compute_ti.html                      |  10 +-
 doc/html/compute_voronoi_atom.html            |  34 +-
 doc/html/compute_xrd.html                     |  10 +-
 doc/html/create_atoms.html                    |  38 +-
 doc/html/delete_bonds.html                    |  20 +-
 doc/html/dihedral_charmm.html                 |  18 +-
 doc/html/dihedral_class2.html                 |  24 +-
 doc/html/dihedral_cosine_shift_exp.html       |  14 +-
 doc/html/dihedral_fourier.html                |  14 +-
 doc/html/dihedral_harmonic.html               |  14 +-
 doc/html/dihedral_helix.html                  |  14 +-
 doc/html/dihedral_multi_harmonic.html         |  14 +-
 doc/html/dihedral_nharmonic.html              |  14 +-
 doc/html/dihedral_opls.html                   |  18 +-
 doc/html/dihedral_quadratic.html              |  14 +-
 doc/html/dihedral_spherical.html              |  18 +-
 doc/html/dihedral_style.html                  |  16 +-
 doc/html/dihedral_table.html                  |  46 +-
 doc/html/dump.html                            |  62 +--
 doc/html/dump_custom_vtk.html                 |  12 +-
 doc/html/dump_image.html                      |  48 +--
 doc/html/dump_modify.html                     |  70 ++--
 doc/html/fix.html                             |   4 +-
 doc/html/fix_adapt_fep.html                   |  34 +-
 doc/html/fix_addtorque.html                   |  12 +-
 doc/html/fix_atc.html                         | 120 +++---
 doc/html/fix_atom_swap.html                   |  14 +-
 doc/html/fix_ave_atom.html                    |  52 ++-
 doc/html/fix_ave_chunk.html                   |  54 ++-
 doc/html/fix_ave_correlate.html               |  82 ++--
 doc/html/fix_ave_correlate_long.html          |  30 +-
 doc/html/fix_ave_histo.html                   |  54 ++-
 doc/html/fix_ave_time.html                    |  52 ++-
 doc/html/fix_balance.html                     |   4 +-
 doc/html/fix_bond_break.html                  |   4 +-
 doc/html/fix_bond_create.html                 |   6 +-
 doc/html/fix_bond_swap.html                   |   6 +-
 doc/html/fix_box_relax.html                   |  24 +-
 doc/html/fix_colvars.html                     |   4 +-
 doc/html/fix_controller.html                  |  36 +-
 doc/html/fix_deform.html                      |  68 ++-
 doc/html/fix_deposit.html                     |   4 +-
 doc/html/fix_drag.html                        |   4 +-
 doc/html/fix_drude_transform.html             |  36 +-
 doc/html/fix_efield.html                      |  12 +-
 doc/html/fix_ehex.html                        |   4 +-
 doc/html/fix_external.html                    |  22 +-
 doc/html/fix_gcmc.html                        |  32 +-
 doc/html/fix_gld.html                         |   6 +-
 doc/html/fix_gle.html                         |   6 +-
 doc/html/fix_gravity.html                     |  18 +-
 doc/html/fix_heat.html                        |  14 +-
 doc/html/fix_imd.html                         |   4 +-
 doc/html/fix_ipi.html                         |   4 +-
 doc/html/fix_langevin.html                    |   4 +-
 doc/html/fix_langevin_drude.html              |  32 +-
 doc/html/fix_langevin_eff.html                |   4 +-
 doc/html/fix_lb_fluid.html                    |   4 +-
 doc/html/fix_lb_momentum.html                 |   4 +-
 doc/html/fix_lb_pc.html                       |   6 +-
 doc/html/fix_lb_rigid_pc_sphere.html          |   4 +-
 doc/html/fix_lb_viscous.html                  |   4 +-
 doc/html/fix_lineforce.html                   |   4 +-
 doc/html/fix_move.html                        |  38 +-
 doc/html/fix_msst.html                        |  30 +-
 doc/html/fix_neb.html                         |   4 +-
 doc/html/fix_nh.html                          |  26 +-
 doc/html/fix_nh_eff.html                      |  10 +-
 doc/html/fix_nph_asphere.html                 |  12 +-
 doc/html/fix_nph_sphere.html                  |  12 +-
 doc/html/fix_nphug.html                       |  22 +-
 doc/html/fix_npt_asphere.html                 |  12 +-
 doc/html/fix_npt_body.html                    |  12 +-
 doc/html/fix_npt_sphere.html                  |  12 +-
 doc/html/fix_nve_asphere.html                 |   4 +-
 doc/html/fix_nve_asphere_noforce.html         |   4 +-
 doc/html/fix_nve_body.html                    |   4 +-
 doc/html/fix_nve_line.html                    |   4 +-
 doc/html/fix_nve_manifold_rattle.html         |  14 +-
 doc/html/fix_nve_sphere.html                  |   4 +-
 doc/html/fix_nve_tri.html                     |   4 +-
 doc/html/fix_nvt_asphere.html                 |  10 +-
 doc/html/fix_nvt_body.html                    |  10 +-
 doc/html/fix_nvt_sllod.html                   |  10 +-
 doc/html/fix_nvt_sllod_eff.html               |   4 +-
 doc/html/fix_nvt_sphere.html                  |  10 +-
 doc/html/fix_orient.html                      |   4 +-
 doc/html/fix_phonon.html                      |  10 +-
 doc/html/fix_pimd.html                        |  12 +-
 doc/html/fix_pour.html                        |   4 +-
 doc/html/fix_qbmsst.html                      |  32 +-
 doc/html/fix_qeq.html                         |  18 +-
 doc/html/fix_qeq_comb.html                    |   4 +-
 doc/html/fix_qeq_reax.html                    |   4 +-
 doc/html/fix_qmmm.html                        |   4 +-
 doc/html/fix_qtb.html                         |  14 +-
 doc/html/fix_reax_bonds.html                  |   4 +-
 doc/html/fix_reaxc_species.html               |   4 +-
 doc/html/fix_restrain.html                    |  22 +-
 doc/html/fix_rigid.html                       |  34 +-
 doc/html/fix_rx.html                          |  16 +-
 doc/html/fix_saed_vtk.html                    |  60 ++-
 doc/html/fix_shake.html                       |   4 +-
 doc/html/fix_smd.html                         |   4 +-
 doc/html/fix_smd_adjust_dt.html               |  16 +-
 doc/html/fix_smd_integrate_tlsph.html         |  18 +-
 doc/html/fix_smd_integrate_ulsph.html         |  24 +-
 .../fix_smd_move_triangulated_surface.html    |  50 ++-
 doc/html/fix_smd_setvel.html                  |  10 +-
 doc/html/fix_smd_wall_surface.html            |  16 +-
 doc/html/fix_spring.html                      |   4 +-
 doc/html/fix_spring_chunk.html                |   4 +-
 doc/html/fix_spring_rg.html                   |   4 +-
 doc/html/fix_spring_self.html                 |   4 +-
 doc/html/fix_store_state.html                 |  78 ++--
 doc/html/fix_temp_berendsen.html              |  10 +-
 doc/html/fix_temp_csvr.html                   |  10 +-
 doc/html/fix_temp_rescale.html                |  10 +-
 doc/html/fix_temp_rescale_eff.html            |   4 +-
 doc/html/fix_tfmc.html                        |   4 +-
 doc/html/fix_thermal_conductivity.html        |  16 +-
 doc/html/fix_ti_rs.html                       |  10 +-
 doc/html/fix_ti_spring.html                   |  10 +-
 doc/html/fix_ttm.html                         | 116 +++---
 doc/html/fix_viscosity.html                   |   4 +-
 doc/html/fix_viscous.html                     |   4 +-
 doc/html/fix_wall.html                        |  60 ++-
 doc/html/fix_wall_gran.html                   |  16 +-
 doc/html/fix_wall_piston.html                 |   4 +-
 doc/html/fix_wall_reflect.html                |  58 ++-
 doc/html/fix_wall_region.html                 |   4 +-
 doc/html/genindex.html                        | 394 +++++++++---------
 doc/html/group.html                           |  36 +-
 doc/html/if.html                              |  16 +-
 doc/html/improper_class2.html                 |  16 +-
 doc/html/improper_cossq.html                  |  14 +-
 doc/html/improper_cvff.html                   |  14 +-
 doc/html/improper_distance.html               |   8 +-
 doc/html/improper_fourier.html                |  14 +-
 doc/html/improper_harmonic.html               |  14 +-
 doc/html/improper_ring.html                   |  18 +-
 doc/html/improper_umbrella.html               |  14 +-
 doc/html/jump.html                            |  24 +-
 doc/html/kspace_modify.html                   |  14 +-
 doc/html/kspace_style.html                    |  24 +-
 doc/html/lattice.html                         |  54 +--
 doc/html/min_modify.html                      |  12 +-
 doc/html/min_style.html                       |  20 +-
 doc/html/neigh_modify.html                    |  20 +-
 doc/html/next.html                            |  12 +-
 doc/html/package.html                         |  10 +-
 doc/html/pair_adp.html                        |  22 +-
 doc/html/pair_airebo.html                     |  52 +--
 doc/html/pair_beck.html                       |  16 +-
 doc/html/pair_body.html                       |  16 +-
 doc/html/pair_bop.html                        |  26 +-
 doc/html/pair_born.html                       |  56 +--
 doc/html/pair_brownian.html                   |  16 +-
 doc/html/pair_buck.html                       |  58 +--
 doc/html/pair_buck_long.html                  |  20 +-
 doc/html/pair_charmm.html                     |  54 +--
 doc/html/pair_class2.html                     |  42 +-
 doc/html/pair_colloid.html                    |  20 +-
 doc/html/pair_comb.html                       |  32 +-
 doc/html/pair_coul.html                       | 124 +++---
 doc/html/pair_coul_diel.html                  |  14 +-
 doc/html/pair_cs.html                         |  26 +-
 doc/html/pair_dipole.html                     |  52 +--
 doc/html/pair_dpd.html                        |  28 +-
 doc/html/pair_dpd_fdt.html                    |  22 +-
 doc/html/pair_dsmc.html                       |  28 +-
 doc/html/pair_eam.html                        |  64 +--
 doc/html/pair_edip.html                       |  12 +-
 doc/html/pair_eff.html                        |  26 +-
 doc/html/pair_eim.html                        |  24 +-
 doc/html/pair_exp6_rx.html                    |  18 +-
 doc/html/pair_gauss.html                      |  36 +-
 doc/html/pair_gayberne.html                   |  14 +-
 doc/html/pair_gran.html                       |  20 +-
 doc/html/pair_gromacs.html                    |  26 +-
 doc/html/pair_hbond_dreiding.html             |  36 +-
 doc/html/pair_hybrid.html                     | 146 +++----
 doc/html/pair_line_lj.html                    |  18 +-
 doc/html/pair_list.html                       |  24 +-
 doc/html/pair_lj.html                         | 106 ++---
 doc/html/pair_lj96.html                       |  16 +-
 doc/html/pair_lj_cubic.html                   |  14 +-
 doc/html/pair_lj_expand.html                  |  16 +-
 doc/html/pair_lj_long.html                    |  32 +-
 doc/html/pair_lj_sf.html                      |  16 +-
 doc/html/pair_lj_smooth.html                  |  16 +-
 doc/html/pair_lj_smooth_linear.html           |  16 +-
 doc/html/pair_lj_soft.html                    |  88 ++--
 doc/html/pair_lubricate.html                  |  28 +-
 doc/html/pair_lubricateU.html                 |  16 +-
 doc/html/pair_mdf.html                        |  42 +-
 doc/html/pair_meam.html                       |  38 +-
 doc/html/pair_meam_spline.html                |  22 +-
 doc/html/pair_meam_sw_spline.html             |  16 +-
 doc/html/pair_mgpt.html                       |  22 +-
 doc/html/pair_mie.html                        |  18 +-
 doc/html/pair_modify.html                     |  46 +-
 doc/html/pair_morse.html                      |  16 +-
 doc/html/pair_multi_lucy.html                 |  32 +-
 doc/html/pair_multi_lucy_rx.html              |  34 +-
 doc/html/pair_nb3b_harmonic.html              |  20 +-
 doc/html/pair_nm.html                         |  36 +-
 doc/html/pair_peri.html                       |  38 +-
 doc/html/pair_polymorphic.html                |  50 +--
 doc/html/pair_quip.html                       |  16 +-
 doc/html/pair_reax.html                       |  40 +-
 doc/html/pair_reax_c.html                     |  48 +--
 doc/html/pair_resquared.html                  |  14 +-
 doc/html/pair_sdk.html                        |  24 +-
 doc/html/pair_smd_hertz.html                  |   8 +-
 doc/html/pair_smd_triangulated_surface.html   |   8 +-
 doc/html/pair_smtbq.html                      |  22 +-
 doc/html/pair_snap.html                       |  26 +-
 doc/html/pair_soft.html                       |  36 +-
 doc/html/pair_sph_idealgas.html               |  14 +-
 doc/html/pair_sph_taitwater.html              |  14 +-
 doc/html/pair_sph_taitwater_morris.html       |  14 +-
 doc/html/pair_srp.html                        |  36 +-
 doc/html/pair_style.html                      |  26 +-
 doc/html/pair_sw.html                         |  22 +-
 doc/html/pair_table.html                      |  38 +-
 doc/html/pair_table_rx.html                   |  38 +-
 doc/html/pair_tersoff.html                    |  30 +-
 doc/html/pair_tersoff_mod.html                |  20 +-
 doc/html/pair_tersoff_zbl.html                |  20 +-
 doc/html/pair_thole.html                      |  28 +-
 doc/html/pair_tri_lj.html                     |  16 +-
 doc/html/pair_vashishta.html                  |  20 +-
 doc/html/pair_yukawa.html                     |  16 +-
 doc/html/pair_yukawa_colloid.html             |  22 +-
 doc/html/pair_zbl.html                        |  16 +-
 doc/html/prd.html                             |  32 +-
 doc/html/processors.html                      |  20 +-
 doc/html/python.html                          | 106 ++---
 doc/html/read_data.html                       |  32 +-
 doc/html/read_dump.html                       |  30 +-
 doc/html/region.html                          |  34 +-
 doc/html/restart.html                         |  24 +-
 doc/html/run_style.html                       |  60 +--
 doc/html/set.html                             |  24 +-
 doc/html/special_bonds.html                   |  38 +-
 doc/html/tad.html                             |  52 +--
 doc/html/thermo.html                          |   8 +-
 doc/html/thermo_style.html                    |  58 +--
 doc/html/tutorial_drude.html                  | 192 +++++----
 doc/html/tutorial_github.html                 |  16 +-
 doc/html/units.html                           |   2 +-
 doc/html/variable.html                        | 120 +++---
 doc/html/velocity.html                        |  22 +-
 doc/html/write_coeff.html                     |  12 +-
 doc/html/write_dump.html                      |  28 +-
 319 files changed, 4360 insertions(+), 4585 deletions(-)

diff --git a/doc/html/Section_accelerate.html b/doc/html/Section_accelerate.html
index 331ea71448..db8d8af4bd 100644
--- a/doc/html/Section_accelerate.html
+++ b/doc/html/Section_accelerate.html
@@ -346,8 +346,8 @@ package and are explained in the individual accelerator doc pages,
 listed above:</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="65%" />
-<col width="35%" />
+<col width="64%" />
+<col width="36%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>build the accelerator library</td>
diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html
index 88bc54ce5a..69c6609b6c 100644
--- a/doc/html/Section_commands.html
+++ b/doc/html/Section_commands.html
@@ -247,15 +247,15 @@ inside the parenthesis is treated as an &#8220;immediate&#8221; variable and
 evaluated as an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>.  This is a way
 to use numeric formulas in an input script without having to assign
 them to variable names.  For example, these 3 input script lines:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable X equal (xlo+xhi)/2+sqrt(v_area)
+<pre class="literal-block">
+variable X equal (xlo+xhi)/2+sqrt(v_area)
 region 1 block $X 2 INF INF EDGE EDGE
 variable X delete
-</pre></div>
-</div>
+</pre>
 <p>can be replaced by</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
-</pre></div>
-</div>
+<pre class="literal-block">
+region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
+</pre>
 <p>so that you do not have to define (or discard) a temporary variable X.</p>
 <p>Note that neither the curly-bracket or immediate form of variables can
 contain nested $ characters for other variables to substitute for.
diff --git a/doc/html/Section_errors.html b/doc/html/Section_errors.html
index a8fd33e6b7..680f6140be 100644
--- a/doc/html/Section_errors.html
+++ b/doc/html/Section_errors.html
@@ -486,7 +486,7 @@ be computed.</dd>
 <dt><em>Bad TIP4P bond type for PPPMDisp/TIP4P</em></dt>
 <dd>Specified bond type is not valid.</dd>
 <dt><em>Bad fix ID in fix append/atoms command</em></dt>
-<dd>The value of the fix_id for keyword spatial must start with &#8216;<a href="#id6"><span class="problematic" id="id7">f_</span></a>&#8216;.</dd>
+<dd>The value of the fix_id for keyword spatial must start with &#8216;f_&#8217;.</dd>
 <dt><em>Bad grid of processors</em></dt>
 <dd>The 3d grid of processors defined by the processors command does not
 match the number of processors LAMMPS is being run on.</dd>
@@ -6358,13 +6358,13 @@ have an infinite periodic crystal with bonds then it is impossible to
 have fully consistent image flags, since some bonds will cross
 periodic boundaries and connect two atoms with the same image
 flag.</dd>
-<dt><em>KIM Model does not provide `energy&#8217;; Potential energy will be zero</em></dt>
+<dt><em>KIM Model does not provide &#8216;energy&#8217;; Potential energy will be zero</em></dt>
 <dd>Self-explanatory.</dd>
-<dt><em>KIM Model does not provide `forces&#8217;; Forces will be zero</em></dt>
+<dt><em>KIM Model does not provide &#8216;forces&#8217;; Forces will be zero</em></dt>
 <dd>Self-explanatory.</dd>
-<dt><em>KIM Model does not provide `particleEnergy&#8217;; energy per atom will be zero</em></dt>
+<dt><em>KIM Model does not provide &#8216;particleEnergy&#8217;; energy per atom will be zero</em></dt>
 <dd>Self-explanatory.</dd>
-<dt><em>KIM Model does not provide `particleVirial&#8217;; virial per atom will be zero</em></dt>
+<dt><em>KIM Model does not provide &#8216;particleVirial&#8217;; virial per atom will be zero</em></dt>
 <dd>Self-explanatory.</dd>
 <dt><em>Kspace_modify slab param &lt; 2.0 may cause unphysical behavior</em></dt>
 <dd>The kspace_modify slab parameter should be larger to insure periodic
diff --git a/doc/html/Section_example.html b/doc/html/Section_example.html
index 95a590b02f..9c2e1a0c72 100644
--- a/doc/html/Section_example.html
+++ b/doc/html/Section_example.html
@@ -303,11 +303,11 @@ longer times, e.g. to measure a particular quantity.</p>
 </tbody>
 </table>
 <p>Here is how you can run and visualize one of the sample problems:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">indent</span>
-<span class="n">cp</span> <span class="o">../../</span><span class="n">src</span><span class="o">/</span><span class="n">lmp_linux</span> <span class="o">.</span>           <span class="c1"># copy LAMMPS executable to this dir</span>
-<span class="n">lmp_linux</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">indent</span>            <span class="c1"># run the problem</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+cd indent
+cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
+lmp_linux -in in.indent            # run the problem
+</pre>
 <p>Running the simulation produces the files <em>dump.indent</em> and
 <em>log.lammps</em>.  You can visualize the dump file of snapshots with a
 variety of 3rd-party tools highlighted on the
@@ -321,17 +321,17 @@ ImageMagick or QuickTime or various Windows-based tools.  See the
 <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page for more details.  E.g. this
 Imagemagick command would create a GIF file suitable for viewing in a
 browser.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">convert</span> <span class="o">-</span><span class="n">loop</span> <span class="mi">1</span> <span class="o">*.</span><span class="n">jpg</span> <span class="n">foo</span><span class="o">.</span><span class="n">gif</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+% convert -loop 1 *.jpg foo.gif
+</pre>
 </div>
 <hr class="docutils" />
 <div class="section" id="uppercase-directories">
 <h2>7.2. Uppercase directories</h2>
 <table border="1" class="docutils">
 <colgroup>
-<col width="10%" />
-<col width="90%" />
+<col width="11%" />
+<col width="89%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>ASPHERE</td>
diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html
index 9ea709012e..feb6e5e5c9 100644
--- a/doc/html/Section_howto.html
+++ b/doc/html/Section_howto.html
@@ -252,13 +252,13 @@ scripts are based on.  If that script had the line</p>
 and tmp.restart.100) as it ran.</p>
 <p>This script could be used to read the 1st restart file and re-run the
 last 50 timesteps:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_restart</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="mi">50</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neighbor</span>     <span class="mf">0.4</span> <span class="nb">bin</span>
-<span class="n">neigh_modify</span> <span class="n">every</span> <span class="mi">1</span> <span class="n">delay</span> <span class="mi">1</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+read_restart        tmp.restart.50
+</pre>
+<pre class="literal-block">
+neighbor     0.4 bin
+neigh_modify        every 1 delay 1
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span>          <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span>
 <span class="n">fix</span>          <span class="mi">2</span> <span class="nb">all</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mi">904297</span>
 </pre></div>
@@ -281,25 +281,25 @@ notice that the thermodynamic data match at step 50 (if you also put a
 uses random numbers in a way that does not allow for perfect restarts.</p>
 <p>As an alternate approach, the restart file could be converted to a data
 file as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">r</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="mi">50</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="n">data</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_g++ -r tmp.restart.50 tmp.restart.data
+</pre>
 <p>Then, this script could be used to re-run the last 50 steps:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">units</span>                <span class="n">lj</span>
-<span class="n">atom_style</span>   <span class="n">bond</span>
-<span class="n">pair_style</span>   <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.12</span>
-<span class="n">pair_modify</span>  <span class="n">shift</span> <span class="n">yes</span>
-<span class="n">bond_style</span>   <span class="n">fene</span>
-<span class="n">special_bonds</span>   <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_data</span>    <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="n">data</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neighbor</span>     <span class="mf">0.4</span> <span class="nb">bin</span>
-<span class="n">neigh_modify</span> <span class="n">every</span> <span class="mi">1</span> <span class="n">delay</span> <span class="mi">1</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+units                lj
+atom_style  bond
+pair_style  lj/cut 1.12
+pair_modify shift yes
+bond_style  fene
+special_bonds   0.0 1.0 1.0
+</pre>
+<pre class="literal-block">
+read_data   tmp.restart.data
+</pre>
+<pre class="literal-block">
+neighbor     0.4 bin
+neigh_modify        every 1 delay 1
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span>          <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span>
 <span class="n">fix</span>          <span class="mi">2</span> <span class="nb">all</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mi">904297</span>
 </pre></div>
@@ -307,10 +307,10 @@ file as follows:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">timestep</span>     <span class="mf">0.012</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">reset_timestep</span>       <span class="mi">50</span>
-<span class="n">run</span>          <span class="mi">50</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+reset_timestep      50
+run          50
+</pre>
 <p>Note that nearly all the settings specified in the original <em>in.chain</em>
 script must be repeated, except the <em>pair_coeff</em> and <em>bond_coeff</em>
 commands since the new data file lists the force field coefficients.
@@ -420,39 +420,40 @@ individual commands for more details on how these examples work.</p>
 <p>If &#8220;multiple simulations&#8221; means continue a previous simulation for
 more timesteps, then you simply use the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command
 multiple times.  For example, this script</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">units</span> <span class="n">lj</span>
-<span class="n">atom_style</span> <span class="n">atomic</span>
-<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">lj</span>
-<span class="n">run</span> <span class="mi">10000</span>
-<span class="n">run</span> <span class="mi">10000</span>
-<span class="n">run</span> <span class="mi">10000</span>
-<span class="n">run</span> <span class="mi">10000</span>
-<span class="n">run</span> <span class="mi">10000</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+units lj
+atom_style atomic
+read_data data.lj
+run 10000
+run 10000
+run 10000
+run 10000
+run 10000
+</pre>
 <p>would run 5 successive simulations of the same system for a total of
 50,000 timesteps.</p>
 <p>If you wish to run totally different simulations, one after the other,
 the <a class="reference internal" href="clear.html"><span class="doc">clear</span></a> command can be used in between them to
 re-initialize LAMMPS.  For example, this script</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">units</span> <span class="n">lj</span>
-<span class="n">atom_style</span> <span class="n">atomic</span>
-<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">lj</span>
-<span class="n">run</span> <span class="mi">10000</span>
-<span class="n">clear</span>
-<span class="n">units</span> <span class="n">lj</span>
-<span class="n">atom_style</span> <span class="n">atomic</span>
-<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">lj</span><span class="o">.</span><span class="n">new</span>
-<span class="n">run</span> <span class="mi">10000</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+units lj
+atom_style atomic
+read_data data.lj
+run 10000
+clear
+units lj
+atom_style atomic
+read_data data.lj.new
+run 10000
+</pre>
 <p>would run 2 independent simulations, one after the other.</p>
 <p>For large numbers of independent simulations, you can use
 <a class="reference internal" href="variable.html"><span class="doc">variables</span></a> and the <a class="reference internal" href="next.html"><span class="doc">next</span></a> and
 <a class="reference internal" href="jump.html"><span class="doc">jump</span></a> commands to loop over the same input script
 multiple times with different settings.  For example, this
 script, named in.polymer</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable d index run1 run2 run3 run4 run5 run6 run7 run8
+<pre class="literal-block">
+variable d index run1 run2 run3 run4 run5 run6 run7 run8
 shell cd $d
 read_data data.polymer
 run 10000
@@ -460,8 +461,7 @@ shell cd ..
 clear
 next d
 jump in.polymer
-</pre></div>
-</div>
+</pre>
 <p>would run 8 simulations in different directories, using a data.polymer
 file in each directory.  The same concept could be used to run the
 same system at 8 different temperatures, using a temperature variable
@@ -528,10 +528,10 @@ replica.  The processors assigned to each replica are determined at
 run-time by using the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-partition command-line switch</span></a> to launch LAMMPS on multiple
 partitions, which in this context are the same as replicas.  E.g.
 these commands:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_linux</span> <span class="o">-</span><span class="n">partition</span> <span class="mi">8</span><span class="n">x2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">temper</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">8</span> <span class="n">lmp_linux</span> <span class="o">-</span><span class="n">partition</span> <span class="mi">8</span><span class="n">x1</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">neb</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
+mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
+</pre>
 <p>would each run 8 replicas, on either 16 or 8 processors.  Note the use
 of the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-in command-line switch</span></a> to specify
 the input script which is required when running in multi-replica mode.</p>
@@ -933,7 +933,7 @@ vectors of a general parallelepiped, where there is no restriction on
 <strong>A</strong> x <strong>B</strong> . <strong>C</strong> &gt; 0.  The equivalent LAMMPS <strong>a</strong>,<strong>b</strong>,<strong>c</strong> are a linear
 rotation of <strong>A</strong>, <strong>B</strong>, and <strong>C</strong> and can be computed as follows:</p>
 <img alt="_images/transform.jpg" class="align-center" src="_images/transform.jpg" />
-<p>where A = <a href="#id3"><span class="problematic" id="id4">|</span></a><strong>A</strong>| indicates the scalar length of <strong>A</strong>. The hat symbol
+<p>where A = | <strong>A</strong> | indicates the scalar length of <strong>A</strong>. The hat symbol (^)
 indicates the corresponding unit vector. <em>beta</em> and <em>gamma</em> are angles
 between the vectors described below. Note that by construction,
 <strong>a</strong>, <strong>b</strong>, and <strong>c</strong> have strictly positive x, y, and z components, respectively.
@@ -1037,23 +1037,23 @@ BOUNDS for a snapshot is written to a dump file for a triclinic box,
 an orthogonal bounding box which encloses the triclinic simulation box
 is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
 box, formatted as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ITEM</span><span class="p">:</span> <span class="n">BOX</span> <span class="n">BOUNDS</span> <span class="n">xy</span> <span class="n">xz</span> <span class="n">yz</span>
-<span class="n">xlo_bound</span> <span class="n">xhi_bound</span> <span class="n">xy</span>
-<span class="n">ylo_bound</span> <span class="n">yhi_bound</span> <span class="n">xz</span>
-<span class="n">zlo_bound</span> <span class="n">zhi_bound</span> <span class="n">yz</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+ITEM: BOX BOUNDS xy xz yz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz
+</pre>
 <p>This bounding box is convenient for many visualization programs and is
 calculated from the 9 triclinic box parameters
 (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">xlo_bound</span> <span class="o">=</span> <span class="n">xlo</span> <span class="o">+</span> <span class="n">MIN</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">xy</span><span class="p">,</span><span class="n">xz</span><span class="p">,</span><span class="n">xy</span><span class="o">+</span><span class="n">xz</span><span class="p">)</span>
-<span class="n">xhi_bound</span> <span class="o">=</span> <span class="n">xhi</span> <span class="o">+</span> <span class="n">MAX</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">xy</span><span class="p">,</span><span class="n">xz</span><span class="p">,</span><span class="n">xy</span><span class="o">+</span><span class="n">xz</span><span class="p">)</span>
-<span class="n">ylo_bound</span> <span class="o">=</span> <span class="n">ylo</span> <span class="o">+</span> <span class="n">MIN</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">yz</span><span class="p">)</span>
-<span class="n">yhi_bound</span> <span class="o">=</span> <span class="n">yhi</span> <span class="o">+</span> <span class="n">MAX</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">yz</span><span class="p">)</span>
-<span class="n">zlo_bound</span> <span class="o">=</span> <span class="n">zlo</span>
-<span class="n">zhi_bound</span> <span class="o">=</span> <span class="n">zhi</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
+xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
+ylo_bound = ylo + MIN(0.0,yz)
+yhi_bound = yhi + MAX(0.0,yz)
+zlo_bound = zlo
+zhi_bound = zhi
+</pre>
 <p>These formulas can be inverted if you need to convert the bounding box
 back into the triclinic box parameters, e.g. xlo = xlo_bound -
 MIN(0.0,xy,xz,xy+xz).</p>
@@ -1136,9 +1136,9 @@ of individual particles, after then are created.</p>
 <p>The dipole style does not actually define finite-size particles, but
 is often used in conjunction with spherical particles, via a command
 like</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">sphere</span> <span class="n">dipole</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+atom_style hybrid sphere dipole
+</pre>
 <p>This is because when dipoles interact with each other, they induce
 torques, and a particle must be finite-size (i.e. have a moment of
 inertia) in order to respond and rotate.  See the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dipole</span></a> command for details.  The &#8220;set&#8221; command can be
@@ -1372,11 +1372,11 @@ per-atom vector.</p>
 <p>When a quantity is accessed, as in many of the output commands
 discussed below, it can be referenced via the following bracket
 notation, where ID in this case is the ID of a compute.  The leading
-&#8220;<a href="#id74"><span class="problematic" id="id75">c_</span></a>&#8221; would be replaced by &#8220;<a href="#id76"><span class="problematic" id="id77">f_</span></a>&#8221; for a fix, or &#8220;<a href="#id78"><span class="problematic" id="id79">v_</span></a>&#8221; for a variable:</p>
+&#8220;c_&#8221; would be replaced by &#8220;f_&#8221; for a fix, or &#8220;v_&#8221; for a variable:</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="21%" />
-<col width="79%" />
+<col width="23%" />
+<col width="77%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>c_ID</td>
@@ -1911,13 +1911,13 @@ internal LAMMPS operations.  Note that LAMMPS classes are defined
 within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
 application.</p>
 <p>Library.cpp contains these 5 basic functions:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">void</span> <span class="n">lammps_open</span><span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">char</span> <span class="o">**</span><span class="p">,</span> <span class="n">MPI_Comm</span><span class="p">,</span> <span class="n">void</span> <span class="o">**</span><span class="p">)</span>
-<span class="n">void</span> <span class="n">lammps_close</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">)</span>
-<span class="nb">int</span> <span class="n">lammps_version</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">)</span>
-<span class="n">void</span> <span class="n">lammps_file</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
-<span class="n">char</span> <span class="o">*</span><span class="n">lammps_command</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+void lammps_open(int, char **, MPI_Comm, void **)
+void lammps_close(void *)
+int lammps_version(void *)
+void lammps_file(void *, char *)
+char *lammps_command(void *, char *)
+</pre>
 <p>The lammps_open() function is used to initialize LAMMPS, passing in a
 list of strings as if they were <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line arguments</span></a> when LAMMPS is run in
 stand-alone mode from the command line, and a MPI communicator for
@@ -1951,17 +1951,17 @@ interleaving the lammps_command() calls with other calls to extract
 information from LAMMPS, perform its own operations, or call another
 code&#8217;s library.</p>
 <p>Other useful functions are also included in library.cpp.  For example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
-<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_atom</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
-<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_compute</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span>
-<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_fix</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span>
-<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_variable</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
-<span class="nb">int</span> <span class="n">lammps_set_variable</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
-<span class="nb">int</span> <span class="n">lammps_get_natoms</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">)</span>
-<span class="n">void</span> <span class="n">lammps_get_coords</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">double</span> <span class="o">*</span><span class="p">)</span>
-<span class="n">void</span> <span class="n">lammps_put_coords</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">double</span> <span class="o">*</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+void *lammps_extract_global(void *, char *)
+void *lammps_extract_atom(void *, char *)
+void *lammps_extract_compute(void *, char *, int, int)
+void *lammps_extract_fix(void *, char *, int, int, int, int)
+void *lammps_extract_variable(void *, char *, char *)
+int lammps_set_variable(void *, char *, char *)
+int lammps_get_natoms(void *)
+void lammps_get_coords(void *, double *)
+void lammps_put_coords(void *, double *)
+</pre>
 <p>These can extract various global or per-atom quantities from LAMMPS as
 well as values calculated by a compute, fix, or variable.  The
 &#8220;set_variable&#8221; function can set an existing string-style variable to a
@@ -2087,29 +2087,30 @@ liquid Ar via the GK formalism:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Sample LAMMPS input script for viscosity of liquid Ar</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>units       real
+<pre class="literal-block">
+units       real
 variable    T equal 86.4956
 variable    V equal vol
 variable    dt equal 4.0
 variable    p equal 400     # correlation length
 variable    s equal 5       # sample interval
 variable    d equal $p*$s   # dump interval
-</pre></div>
-</div>
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># convert from LAMMPS real units to SI</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable    kB equal 1.3806504e-23    # [J/K/** Boltzmann
+<pre class="literal-block">
+variable    kB equal 1.3806504e-23    # [J/K/** Boltzmann
 variable    atm2Pa equal 101325.0
 variable    A2m equal 1.0e-10
 variable    fs2s equal 1.0e-15
 variable    convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}
-</pre></div>
-</div>
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>dimension    3
+<pre class="literal-block">
+dimension    3
 boundary     p p p
 lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
 region       box block 0 4 0 4 0 4
@@ -2120,8 +2121,7 @@ pair_style   lj/cut 13.0
 pair_coeff   * * 0.2381 3.405
 timestep     ${dt}
 thermo            $d
-</pre></div>
-</div>
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span>
 </pre></div>
 </div>
@@ -2137,7 +2137,8 @@ run          8000
 <span class="c1">#fix         NVE all nve</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>reset_timestep 0
+<pre class="literal-block">
+reset_timestep 0
 variable     pxy equal pxy
 variable     pxz equal pxz
 variable     pyz equal pyz
@@ -2151,9 +2152,8 @@ thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
 run          100000
 variable     v equal (v_v11+v_v22+v_v33)/3.0
 variable     ndens equal count(all)/vol
-print        &quot;average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3&quot;
-</pre></div>
-</div>
+print        &quot;average viscosity: $v [Pa.s/** &#64; $T K, ${ndens} /A^3&quot;
+</pre>
 <p>The fifth method is related to the above Green-Kubo method,
 but uses the Einstein formulation, analogous to the Einstein
 mean-square-displacement formulation for self-diffusivity. The
@@ -2274,7 +2274,7 @@ fix produces a global array as output with one row of values per
 chunk.</p>
 </div>
 <div class="section" id="compute-chunk-commands">
-<h3>6.23.3. Compute <a href="#id71"><span class="problematic" id="id72">*</span></a>/chunk commands:</h3>
+<h3>6.23.3. Compute */chunk commands:</h3>
 <p>Currently the following computes operate on chunks of atoms to produce
 per-chunk values.</p>
 <ul class="simple">
@@ -2331,31 +2331,31 @@ velocity:</p>
 <ol class="arabic simple" start="3">
 <li>Center of mass of each molecule:</li>
 </ol>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute cc1 all chunk/atom molecule
+compute myChunk all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+</pre>
 <ol class="arabic simple" start="4">
 <li>Total force on each molecule and ave/max across all molecules:</li>
 </ol>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">1000</span> <span class="mi">1</span> <span class="mi">1000</span> <span class="n">cc1</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span>
-<span class="n">variable</span> <span class="n">xave</span> <span class="n">equal</span> <span class="n">ave</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
-<span class="n">variable</span> <span class="n">xmax</span> <span class="n">equal</span> <span class="nb">max</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
-<span class="n">thermo</span> <span class="mi">1000</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">v_xave</span> <span class="n">v_xmax</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute cc1 all chunk/atom molecule
+fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
+variable xave equal ave(f_1[2])
+variable xmax equal max(f_1[2])
+thermo 1000
+thermo_style custom step temp v_xave v_xmax
+</pre>
 <ol class="arabic simple" start="5">
 <li>Histogram of cluster sizes:</li>
 </ol>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cluster</span> <span class="nb">all</span> <span class="n">cluster</span><span class="o">/</span><span class="n">atom</span> <span class="mf">1.0</span>
-<span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">c_cluster</span> <span class="n">compress</span> <span class="n">yes</span>
-<span class="n">compute</span> <span class="n">size</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span> <span class="n">count</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">0</span> <span class="mi">20</span> <span class="mi">20</span> <span class="n">c_size</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">ave</span> <span class="n">running</span> <span class="n">beyond</span> <span class="n">ignore</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">histo</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute cluster all cluster/atom 1.0
+compute cc1 all chunk/atom c_cluster compress yes
+compute size all property/chunk cc1 count
+fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
+</pre>
 <hr class="docutils" />
 </div>
 </div>
@@ -2607,18 +2607,18 @@ by the <a class="reference internal" href="kspace_style.html"><span class="doc">
 Ewald solvers can be used.</p>
 <p>For the NaCL example problem, these pair style and bond style settings
 are used:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span>      <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">20.0</span> <span class="mf">20.0</span>
-<span class="n">pair_coeff</span>      <span class="o">*</span> <span class="o">*</span>      <span class="mf">0.0</span> <span class="mf">1.000</span>   <span class="mf">0.00</span>  <span class="mf">0.00</span>   <span class="mf">0.00</span>
-<span class="n">pair_coeff</span>      <span class="mi">3</span> <span class="mi">3</span>    <span class="mf">487.0</span> <span class="mf">0.23768</span> <span class="mf">0.00</span>  <span class="mf">1.05</span>   <span class="mf">0.50</span> <span class="c1">#Na-Na</span>
-<span class="n">pair_coeff</span>      <span class="mi">3</span> <span class="mi">4</span> <span class="mf">145134.0</span> <span class="mf">0.23768</span> <span class="mf">0.00</span>  <span class="mf">6.99</span>   <span class="mf">8.70</span> <span class="c1">#Na-Cl</span>
-<span class="n">pair_coeff</span>      <span class="mi">4</span> <span class="mi">4</span> <span class="mf">405774.0</span> <span class="mf">0.23768</span> <span class="mf">0.00</span> <span class="mf">72.40</span> <span class="mf">145.40</span> <span class="c1">#Cl-Cl</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span>      <span class="n">harmonic</span>
-<span class="n">bond_coeff</span>      <span class="mi">1</span> <span class="mf">63.014</span> <span class="mf">0.0</span>
-<span class="n">bond_coeff</span>      <span class="mi">2</span> <span class="mf">25.724</span> <span class="mf">0.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style      born/coul/long/cs 20.0 20.0
+pair_coeff      * *      0.0 1.000   0.00  0.00   0.00
+pair_coeff      3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+pair_coeff      3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+pair_coeff      4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+</pre>
+<pre class="literal-block">
+bond_style      harmonic
+bond_coeff      1 63.014 0.0
+bond_coeff      2 25.724 0.0
+</pre>
 <p>When running dynamics with the adiabatic core/shell model, the
 following issues should be considered.  Since the relative motion of
 the core and shell particles corresponds to the polarization, typical
@@ -2645,15 +2645,15 @@ used to assign the compute to the thermostat fix.  Likewise the
 <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify temp</span></a> command can be used to make
 this temperature be output for the overall system.</p>
 <p>For the NaCl example, this can be done as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">group</span> <span class="n">cores</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span>
-<span class="n">group</span> <span class="n">shells</span> <span class="nb">type</span> <span class="mi">3</span> <span class="mi">4</span>
-<span class="n">compute</span> <span class="n">CSequ</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">cores</span> <span class="n">shells</span>
-<span class="n">fix</span> <span class="n">thermoberendsen</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">berendsen</span> <span class="mi">1427</span> <span class="mi">1427</span> <span class="mf">0.4</span>    <span class="c1"># thermostat for the true physical system</span>
-<span class="n">fix</span> <span class="n">thermostatequ</span> <span class="nb">all</span> <span class="n">nve</span>                               <span class="c1"># integrator as needed for the berendsen thermostat</span>
-<span class="n">fix_modify</span> <span class="n">thermoberendsen</span> <span class="n">temp</span> <span class="n">CSequ</span>
-<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">CSequ</span>                                <span class="c1"># output of center-of-mass derived temperature</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+group cores type 1 2
+group shells type 3 4
+compute CSequ all temp/cs cores shells
+fix thermoberendsen all temp/berendsen 1427 1427 0.4    # thermostat for the true physical system
+fix thermostatequ all nve                               # integrator as needed for the berendsen thermostat
+fix_modify thermoberendsen temp CSequ
+thermo_modify temp CSequ                                # output of center-of-mass derived temperature
+</pre>
 <p>If <a class="reference internal" href="compute_temp_cs.html"><span class="doc">compute temp/cs</span></a> is used, the decoupled
 relative motion of the core and the shell should in theory be
 stable.  However numerical fluctuation can introduce a small
@@ -2702,14 +2702,14 @@ accessed by the <a class="reference internal" href="compute_property_atom.html">
 command, to use as input to the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command to define the core/shell
 pairs as chunks.</p>
 <p>For example,</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">csinfo</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">i_CSID</span>                       <span class="c1"># property/atom command</span>
-<span class="n">read_data</span> <span class="n">NaCl_CS_x0</span><span class="o">.</span><span class="mi">1</span><span class="n">_prop</span><span class="o">.</span><span class="n">data</span> <span class="n">fix</span> <span class="n">csinfo</span> <span class="n">NULL</span> <span class="n">CS</span><span class="o">-</span><span class="n">Info</span>  <span class="c1"># atom property added in the data-file</span>
-<span class="n">compute</span> <span class="n">prop</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">i_CSID</span>
-<span class="n">compute</span> <span class="n">cs_chunk</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">c_prop</span>
-<span class="n">compute</span> <span class="n">cstherm</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cs_chunk</span> <span class="n">temp</span> <span class="n">internal</span> <span class="n">com</span> <span class="n">yes</span> <span class="n">cdof</span> <span class="mf">3.0</span>     <span class="c1"># note the chosen degrees of freedom for the core/shell pairs</span>
-<span class="n">fix</span> <span class="n">ave_chunk</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">10</span> <span class="mi">1</span> <span class="mi">10</span> <span class="n">c_cstherm</span> <span class="n">file</span> <span class="n">chunk</span><span class="o">.</span><span class="n">dump</span> <span class="n">mode</span> <span class="n">vector</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix csinfo all property/atom i_CSID                       # property/atom command
+read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info  # atom property added in the data-file
+compute prop all property/atom i_CSID
+compute cs_chunk all chunk/atom c_prop
+compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
+fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
+</pre>
 <p>The additional section in the date file would be formatted like this:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">CS</span><span class="o">-</span><span class="n">Info</span>         <span class="c1"># header of additional section</span>
 </pre></div>
diff --git a/doc/html/Section_modify.html b/doc/html/Section_modify.html
index 1ddbd8f04a..41c466042e 100644
--- a/doc/html/Section_modify.html
+++ b/doc/html/Section_modify.html
@@ -193,8 +193,8 @@ C-style data structures (vectors and arrays).</p>
 <p>Most of the new features described in this section require you to
 write a new C++ derived class (except for exceptions described below,
 where you can make small edits to existing files).  Creating a new
-class requires 2 files, a source code file (<em>.cpp) and a header file
-(</em>.h).  The derived class must provide certain methods to work as a
+class requires 2 files, a source code file (*.cpp) and a header file
+(*.h).  The derived class must provide certain methods to work as a
 new option.  Depending on how different your new feature is compared
 to existing features, you can either derive from the base class
 itself, or from a derived class that already exists.  Enabling LAMMPS
@@ -209,19 +209,19 @@ and pair_foo.h that define a new class PairFoo that computes pairwise
 potentials described in the classic 1997 <a class="reference internal" href="#foo"><span class="std std-ref">paper</span></a> by Foo, et al.
 If you wish to invoke those potentials in a LAMMPS input script with a
 command like</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">foo</span> <span class="mf">0.1</span> <span class="mf">3.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style foo 0.1 3.5
+</pre>
 <p>then your pair_foo.h file should be structured as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1">#ifdef PAIR_CLASS</span>
-<span class="n">PairStyle</span><span class="p">(</span><span class="n">foo</span><span class="p">,</span><span class="n">PairFoo</span><span class="p">)</span>
-<span class="c1">#else</span>
-<span class="o">...</span>
-<span class="p">(</span><span class="k">class</span> <span class="nc">definition</span> <span class="k">for</span> <span class="n">PairFoo</span><span class="p">)</span>
-<span class="o">...</span>
-<span class="c1">#endif</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+#ifdef PAIR_CLASS
+PairStyle(foo,PairFoo)
+#else
+...
+(class definition for PairFoo)
+...
+#endif
+</pre>
 <p>where &#8220;foo&#8221; is the style keyword in the pair_style command, and
 PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h
 files.</p>
@@ -275,8 +275,8 @@ atoms.</p>
 class.  See atom_vec.h for details.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="22%" />
-<col width="78%" />
+<col width="24%" />
+<col width="76%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>init</td>
@@ -393,18 +393,18 @@ output the custom values.</p>
 The code for these classes can use the per-atom properties defined by
 fix property/atom.  The Atom class has a find_custom() method that is
 useful in this context:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">int</span> <span class="n">index</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-&gt;</span><span class="n">find_custom</span><span class="p">(</span><span class="n">char</span> <span class="o">*</span><span class="n">name</span><span class="p">,</span> <span class="nb">int</span> <span class="o">&amp;</span><span class="n">flag</span><span class="p">);</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+int index = atom-&gt;find_custom(char *name, int &amp;flag);
+</pre>
 <p>The &#8220;name&#8221; of a custom attribute, as specified in the <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command, is checked to verify
 that it exists and its index is returned.  The method also sets flag =
 0/1 depending on whether it is an integer or floating-point attribute.
 The vector of values associated with the attribute can then be
 accessed using the returned index as</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">int</span> <span class="o">*</span><span class="n">ivector</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-&gt;</span><span class="n">ivector</span><span class="p">[</span><span class="n">index</span><span class="p">];</span>
-<span class="n">double</span> <span class="o">*</span><span class="n">dvector</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-&gt;</span><span class="n">dvector</span><span class="p">[</span><span class="n">index</span><span class="p">];</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+int *ivector = atom-&gt;ivector[index];
+double *dvector = atom-&gt;dvector[index];
+</pre>
 <p>Ivector or dvector are vectors of length Nlocal = # of owned atoms,
 which store the attributes of individual atoms.</p>
 <hr class="docutils" />
@@ -474,8 +474,8 @@ per-atom kinetic energy.</p>
 class.  See compute.h for details.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="24%" />
-<col width="76%" />
+<col width="26%" />
+<col width="74%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>init</td>
@@ -551,8 +551,8 @@ DumpCustom class contained in the dump_custom.cpp file.</p>
 class.  See dump.h for details.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="22%" />
-<col width="78%" />
+<col width="23%" />
+<col width="77%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>write_header</td>
@@ -597,8 +597,8 @@ implement.</p>
 derived class.  See fix.h for details.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="22%" />
-<col width="78%" />
+<col width="23%" />
+<col width="77%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>setmask</td>
@@ -823,8 +823,8 @@ styles can be created to add new K-space options to LAMMPS.</p>
 class.  See kspace.h for details.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="23%" />
-<col width="77%" />
+<col width="25%" />
+<col width="75%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>init</td>
@@ -853,8 +853,8 @@ LAMMPS.</p>
 class.  See min.h for details.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="25%" />
-<col width="75%" />
+<col width="26%" />
+<col width="74%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>init</td>
@@ -882,8 +882,8 @@ includes some optional methods to enable its use with rRESPA.</p>
 <p>Here is a brief description of the class methods in pair.h:</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="32%" />
-<col width="68%" />
+<col width="33%" />
+<col width="67%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>compute</td>
@@ -929,8 +929,8 @@ styles can be created to add new region shapes to LAMMPS.</p>
 class.  See region.h for details.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="21%" />
-<col width="79%" />
+<col width="22%" />
+<col width="78%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>inside</td>
@@ -965,8 +965,8 @@ a rigid body containing N sub-particles.</p>
 class.  See body.h for details.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="25%" />
-<col width="75%" />
+<col width="27%" />
+<col width="73%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>data_body</td>
@@ -1030,14 +1030,14 @@ via the <a class="reference internal" href="print.html"><span class="doc">print<
 <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> commands.  Variables of style
 &#8220;equal&#8221; can compute complex equations that involve the following types
 of arguments:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo</span> <span class="n">keywords</span> <span class="o">=</span> <span class="n">ke</span><span class="p">,</span> <span class="n">vol</span><span class="p">,</span> <span class="n">atoms</span><span class="p">,</span> <span class="o">...</span>
-<span class="n">other</span> <span class="n">variables</span> <span class="o">=</span> <span class="n">v_a</span><span class="p">,</span> <span class="n">v_myvar</span><span class="p">,</span> <span class="o">...</span>
-<span class="n">math</span> <span class="n">functions</span> <span class="o">=</span> <span class="n">div</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span> <span class="n">mult</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span> <span class="n">add</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span> <span class="o">...</span>
-<span class="n">group</span> <span class="n">functions</span> <span class="o">=</span> <span class="n">mass</span><span class="p">(</span><span class="n">group</span><span class="p">),</span> <span class="n">xcm</span><span class="p">(</span><span class="n">group</span><span class="p">,</span><span class="n">x</span><span class="p">),</span> <span class="o">...</span>
-<span class="n">atom</span> <span class="n">values</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">123</span><span class="p">],</span> <span class="n">y</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">vx</span><span class="p">[</span><span class="mi">34</span><span class="p">],</span> <span class="o">...</span>
-<span class="n">compute</span> <span class="n">values</span> <span class="o">=</span> <span class="n">c_mytemp</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+thermo keywords = ke, vol, atoms, ...
+other variables = v_a, v_myvar, ...
+math functions = div(x,y), mult(x,y), add(x,y), ...
+group functions = mass(group), xcm(group,x), ...
+atom values = x[123], y[3], vx[34], ...
+compute values = c_mytemp[0], c_thermo_press[3], ...
+</pre>
 <p>Adding keywords for the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command
 (which can then be accessed by variables) was discussed
 <a class="reference internal" href="Section_howto.html#thermo"><span class="std std-ref">here</span></a> on this page.</p>
@@ -1157,7 +1157,7 @@ structures, performs its operations, and is formatted similar to other
 LAMMPS source files, including the use of the error class for error
 and warning messages.</li>
 <li>If you want your contribution to be added as a user-contributed
-feature, and it&#8217;s a single file (actually a <a href="#id8"><span class="problematic" id="id9">*</span></a>.cpp and <a href="#id10"><span class="problematic" id="id11">*</span></a>.h file) it can
+feature, and it&#8217;s a single file (actually a *.cpp and *.h file) it can
 rapidly be added to the USER-MISC directory.  Send us the one-line
 entry to add to the USER-MISC/README file in that dir, along with the
 2 source files.  You can do this multiple times if you wish to
@@ -1192,12 +1192,12 @@ to HTML and PDF. The tools for this conversion are included in the
 source distribution, and the translation can be as simple as doing
 &#8220;make html pdf&#8221; in the doc folder.
 Thus the documentation source files must be in the same format and
-style as other <em>.txt files in the lammps/doc/src directory for similar
+style as other *.txt files in the lammps/doc/src directory for similar
 commands and styles; use one or more of them as a starting point.
 A description of the markup can also be found in
 lammps/doc/utils/txt2html/README.html
 As appropriate, the text files can include links to equations
-(see doc/Eqs/</em>.tex for examples, we auto-create the associated JPG
+(see doc/Eqs/*.tex for examples, we auto-create the associated JPG
 files), or figures (see doc/JPG for examples), or even additional PDF
 files with further details (see doc/PDF for examples).  The doc page
 should also include literature citations as appropriate; see the
@@ -1220,7 +1220,7 @@ These example inputs are also required for validating memory accesses
 and testing for memory leaks with valgrind</li>
 <li>If there is a paper of yours describing your feature (either the
 algorithm/science behind the feature itself, or its initial usage, or
-its implementation in LAMMPS), you can add the citation to the <a href="#id12"><span class="problematic" id="id13">*</span></a>.cpp
+its implementation in LAMMPS), you can add the citation to the *.cpp
 source file.  See src/USER-EFF/atom_vec_electron.cpp for an example.
 A LaTeX citation is stored in a variable at the top of the file and a
 single line of code that references the variable is added to the
diff --git a/doc/html/Section_packages.html b/doc/html/Section_packages.html
index fedd3cc1ae..2565c51206 100644
--- a/doc/html/Section_packages.html
+++ b/doc/html/Section_packages.html
@@ -630,9 +630,9 @@ for aspherical particle models: ellipsoids, 2d lines, 3d triangles.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">asphere</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^asphere -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-14"><span class="std std-ref">Section howto 6.14</span></a>,
 <a class="reference internal" href="pair_gayberne.html"><span class="doc">pair_style gayberne</span></a>, <a class="reference internal" href="pair_resquared.html"><span class="doc">pair_style resquared</span></a>,
 <a class="reference external" href="PDF/pair_gayberne_extra.pdf">doc/PDF/pair_gayberne_extra.pdf</a>,
@@ -658,9 +658,9 @@ themselves.  See the <a class="reference internal" href="body.html"><span class=
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">body</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^body -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a>, <a class="reference internal" href="body.html"><span class="doc">body</span></a>,
 <a class="reference internal" href="pair_body.html"><span class="doc">pair_style body</span></a>, examples/body</p>
 <hr class="docutils" />
@@ -682,9 +682,9 @@ COMPASS CLASS2 molecular force field.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">class2</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^class2 -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="bond_class2.html"><span class="doc">bond_style class2</span></a>, <a class="reference internal" href="angle_class2.html"><span class="doc">angle_style class2</span></a>, <a class="reference internal" href="dihedral_class2.html"><span class="doc">dihedral_style class2</span></a>, <a class="reference internal" href="improper_class2.html"><span class="doc">improper_style class2</span></a>, <a class="reference internal" href="pair_class2.html"><span class="doc">pair_style lj/class2</span></a></p>
 <hr class="docutils" />
 </div>
@@ -708,9 +708,9 @@ approximation to Stokesian dynamics.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">colloid</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^colloid -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="fix_wall.html"><span class="doc">fix wall/colloid</span></a>, <a class="reference internal" href="pair_colloid.html"><span class="doc">pair_style colloid</span></a>, <a class="reference internal" href="pair_yukawa_colloid.html"><span class="doc">pair_style yukawa/colloid</span></a>, <a class="reference internal" href="pair_brownian.html"><span class="doc">pair_style brownian</span></a>, <a class="reference internal" href="pair_lubricate.html"><span class="doc">pair_style lubricate</span></a>, <a class="reference internal" href="pair_lubricateU.html"><span class="doc">pair_style lubricateU</span></a>, examples/colloid, examples/srd</p>
 <hr class="docutils" />
 </div>
@@ -737,9 +737,9 @@ zlib info it specifies.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">compress</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^compress -a machine
+</pre>
 <p>Supporting info: src/COMPRESS/README, lib/compress/README, <a class="reference internal" href="dump.html"><span class="doc">dump atom/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump cfg/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump custom/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump xyz/gz</span></a></p>
 <hr class="docutils" />
 </div>
@@ -764,9 +764,9 @@ package.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">coreshell</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^coreshell -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-26"><span class="std std-ref">Section howto 6.26</span></a>, <a class="reference internal" href="compute_temp_cs.html"><span class="doc">compute temp/cs</span></a>,
 <a class="reference internal" href="pair_cs.html"><span class="doc">pair_style born/coul/long/cs</span></a>, <a class="reference internal" href="pair_cs.html"><span class="doc">pair_style buck/coul/long/cs</span></a>, pair_style
 lj/cut/coul/long/cs&#8221;_pair_lj.html, examples/coreshell</p>
@@ -789,9 +789,9 @@ dipole models with short-range or long-range interactions.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">dipole</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^dipole -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dipole</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/cut/dipole/cut</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/cut/dipole/long</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/long/dipole/long</span></a>, examples/dipole</p>
 <hr class="docutils" />
 </div>
@@ -841,9 +841,9 @@ one step, with Type &#8220;python src/Make.py -h -gpu&#8221; to see the details.
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">gpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^gpu -a machine
+</pre>
 <p>Supporting info: src/GPU/README, lib/gpu/README, <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_gpu.html"><span class="doc">Section accelerate gpu</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed with a (g),
 <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>, <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a>,
 examples/accelerate, bench/FERMI, bench/KEPLER</p>
@@ -867,9 +867,9 @@ frictional and dissipative potentials.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">granular</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^granular -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-6"><span class="std std-ref">Section howto 6.6</span></a>, <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>, <a class="reference internal" href="fix_wall_gran.html"><span class="doc">fix wall/gran</span></a>, <a class="reference internal" href="pair_gran.html"><span class="doc">pair_style gran/hooke</span></a>, <a class="reference internal" href="pair_gran.html"><span class="doc">pair_style gran/hertz/history</span></a>, examples/pour, bench/in.chute</p>
 <hr class="docutils" />
 </div>
@@ -896,9 +896,9 @@ process.  You should not need to edit this file.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">kim</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^kim -a machine
+</pre>
 <p>Supporting info: src/KIM/README, lib/kim/README, <a class="reference internal" href="pair_kim.html"><span class="doc">pair_style kim</span></a>, examples/kim</p>
 <hr class="docutils" />
 </div>
@@ -928,12 +928,12 @@ choose which hardware to build for.  Type &#8220;python src/Make.py -h
 system, you will need to read the <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">Section accelerate kokkos</span></a> doc page for details of what
 Makefile.machine settings are needed.</p>
 <p>To install via make or Make.py for each of 3 hardware options:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
-<span class="n">make</span> <span class="n">kokkos_omp</span>    <span class="c1"># for CPUs with OpenMP</span>
-<span class="n">make</span> <span class="n">kokkos_cuda</span>   <span class="c1"># for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda</span>
-<span class="n">make</span> <span class="n">kokkos_phi</span>    <span class="c1"># for Xeon Phis</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+make yes-kokkos
+make kokkos_omp    # for CPUs with OpenMP
+make kokkos_cuda   # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda
+make kokkos_phi    # for Xeon Phis
+</pre>
 <p>Make.py -p kokkos -kokkos omp -a machine           # for CPUs with OpenMP
 Make.py -p kokkos -kokkos cuda arch=35 -a machine  # for GPUs of style arch
 Make.py -p kokkos -kokkos phi -a machine           # for Xeon Phis</p>
@@ -942,9 +942,9 @@ Make.py -p kokkos -kokkos phi -a machine           # for Xeon Phis</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">kokkos</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^kokkos -a machine
+</pre>
 <p>Supporting info: src/KOKKOS/README, lib/kokkos/README, <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">Section accelerate kokkos</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed
 with a (k), <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a>,
 examples/accelerate, bench/FERMI, bench/KEPLER</p>
@@ -977,9 +977,9 @@ see the details.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">kspace</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^kspace -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>,
 <a class="reference external" href="PDF/kspace.pdf">doc/PDF/kspace.pdf</a>, <a class="reference internal" href="Section_howto.html#howto-7"><span class="std std-ref">Section howto 6.7</span></a>, <a class="reference internal" href="Section_howto.html#howto-8"><span class="std std-ref">Section howto 6.8</span></a>, <a class="reference internal" href="Section_howto.html#howto-9"><span class="std std-ref">Section howto 6.9</span></a>, <a class="reference internal" href="pair_coul.html"><span class="doc">pair_style coul</span></a>,
 other pair style command doc pages which have &#8220;long&#8221; or &#8220;msm&#8221; in their
@@ -1005,9 +1005,9 @@ the full list.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">manybody</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^manybody -a machine
+</pre>
 <p>Supporting info:</p>
 <p>Examples: Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a>, examples/comb, examples/eim,
 examples/nb3d, examples/vashishta</p>
@@ -1032,9 +1032,9 @@ in conjuction with dynamics.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">mc</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^mc -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="fix_atom_swap.html"><span class="doc">fix atom/swap</span></a>, <a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</span></a>, <a class="reference internal" href="fix_bond_create.html"><span class="doc">fix bond/create</span></a>, <a class="reference internal" href="fix_bond_swap.html"><span class="doc">fix bond/swap</span></a>,
 <a class="reference internal" href="fix_gcmc.html"><span class="doc">fix gcmc</span></a>, <a class="reference internal" href="pair_dsmc.html"><span class="doc">pair_style dsmc</span></a></p>
 <hr class="docutils" />
@@ -1079,9 +1079,9 @@ Intel Fortran compiler, rather than the GNU Fortran compiler.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">meam</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^meam -a machine
+</pre>
 <p>Supporting info: lib/meam/README, <a class="reference internal" href="pair_meam.html"><span class="doc">pair_style meam</span></a>,
 examples/meam</p>
 <hr class="docutils" />
@@ -1104,9 +1104,9 @@ listing, &#8220;ls src/MISC&#8221;, to see the list of commands.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">misc</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^misc -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="compute_ti.html"><span class="doc">compute ti</span></a>, <a class="reference internal" href="fix_evaporate.html"><span class="doc">fix evaporate</span></a>, <a class="reference internal" href="fix_ttm.html"><span class="doc">fix tmm</span></a>, <a class="reference internal" href="fix_viscosity.html"><span class="doc">fix viscosity</span></a>, examples/misc</p>
 <hr class="docutils" />
 </div>
@@ -1129,9 +1129,9 @@ covalent bonds.  The pair styles include terms for the Dreiding
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">molecule</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^molecule -a machine
+</pre>
 <p>Supporting info:<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>,
 <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>, <a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a>,
 <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a>,
@@ -1159,9 +1159,9 @@ are also written and read in parallel.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">mpiio</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^mpiio -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="restart.html"><span class="doc">restart</span></a>,
 <a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a></p>
 <hr class="docutils" />
@@ -1192,9 +1192,9 @@ creates and uses.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">opt</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^opt -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_opt.html"><span class="doc">Section accelerate opt</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed
 with an (o), examples/accelerate, bench/KEPLER</p>
 <hr class="docutils" />
@@ -1218,9 +1218,9 @@ styles which implement different materials models.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">peri</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^peri -a machine
+</pre>
 <p>Supporting info:
 <a class="reference external" href="PDF/PDLammps_overview.pdf">doc/PDF/PDLammps_overview.pdf</a>,
 <a class="reference external" href="PDF/PDLammps_EPS.pdf">doc/PDF/PDLammps_EPS.pdf</a>,
@@ -1261,9 +1261,9 @@ one step.  Type &#8220;python src/Make.py -h -poems&#8221; to see the details.</
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">meam</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^meam -a machine
+</pre>
 <p>Supporting info: src/POEMS/README, lib/poems/README,
 <a class="reference internal" href="fix_poems.html"><span class="doc">fix poems</span></a>, examples/rigid</p>
 <hr class="docutils" />
@@ -1296,9 +1296,9 @@ in one step.  Type &#8220;python src/Make.py -h -python&#8221; to see the detail
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">python</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^python -a machine
+</pre>
 <p>Supporting info: examples/python</p>
 <hr class="docutils" />
 </div>
@@ -1320,9 +1320,9 @@ that use QEq as part of their formulation.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">qeq</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^qeq -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="fix_qeq.html"><span class="doc">fix qeq/*</span></a>, examples/qeq</p>
 <hr class="docutils" />
 </div>
@@ -1362,9 +1362,9 @@ one step.  Type &#8220;python src/Make.py -h -reax&#8221; to see the details.</p
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">reax</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^reax -a machine
+</pre>
 <p>Supporting info: lib/reax/README, <a class="reference internal" href="pair_reax.html"><span class="doc">pair_style reax</span></a>,
 <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a>, examples/reax</p>
 <hr class="docutils" />
@@ -1394,9 +1394,9 @@ field calcalation on another set.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">replica</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^replica -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-5"><span class="std std-ref">Section howto 6.5</span></a>,
 <a class="reference internal" href="neb.html"><span class="doc">neb</span></a>, <a class="reference internal" href="prd.html"><span class="doc">prd</span></a>, <a class="reference internal" href="tad.html"><span class="doc">tad</span></a>, <a class="reference internal" href="temper.html"><span class="doc">temper</span></a>,
 <a class="reference internal" href="run_style.html"><span class="doc">run_style verlet/split</span></a>, examples/neb, examples/prd,
@@ -1422,9 +1422,9 @@ few large bodies or many small bodies.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">rigid</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^rigid -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="compute_erotate_rigid.html"><span class="doc">compute erotate/rigid</span></a>,
 <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>, <a class="reference internal" href="fix_shake.html"><span class="doc">fix rattle</span></a>, <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/*</span></a>, examples/ASPHERE, examples/rigid</p>
 <hr class="docutils" />
@@ -1446,9 +1446,9 @@ simulations where a shock-wave passes through a material.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">shock</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^shock -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="fix_append_atoms.html"><span class="doc">fix append/atoms</span></a>, <a class="reference internal" href="fix_msst.html"><span class="doc">fix msst</span></a>, <a class="reference internal" href="fix_nphug.html"><span class="doc">fix nphug</span></a>, <a class="reference internal" href="fix_wall_piston.html"><span class="doc">fix wall/piston</span></a>, examples/hugoniostat, examples/msst</p>
 <hr class="docutils" />
 </div>
@@ -1471,9 +1471,9 @@ properties of the potential are also included.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">snap</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^snap -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="pair_snap.html"><span class="doc">pair snap</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snad/atom</span></a>,
 <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snav/atom</span></a>, examples/snap</p>
 <hr class="docutils" />
@@ -1496,9 +1496,9 @@ colloidal-scale particles.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">srd</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^srd -a machine
+</pre>
 <p>Supporting info: <a class="reference internal" href="fix_srd.html"><span class="doc">fix srd</span></a>, <a class="reference internal" href="fix_wall_srd.html"><span class="doc">fix wall/srd</span></a>, examples/srd, examples/ASPHERE</p>
 <hr class="docutils" />
 </div>
@@ -1541,9 +1541,9 @@ src/Make.py -h -voronoi&#8221; to see the details.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">voronoi</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^voronoi -a machine
+</pre>
 <p>Supporting info: src/VORONOI/README, lib/voronoi/README, <a class="reference internal" href="compute_voronoi_atom.html"><span class="doc">compute voronoi/atom</span></a>, examples/voronoi</p>
 <hr class="docutils" />
 </div>
@@ -1860,7 +1860,7 @@ src/Make.py -h -voronoi&#8221; to see the details.</p>
 <tr class="row-even"><td><a class="reference internal" href="#user-smd"><span class="std std-ref">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>
+<td><a class="reference external" href="PDF/SMD_LAMMPS_userguide.pdf">SMD User Guide</a></td>
 <td>USER/smd</td>
 <td><ul class="first last simple">
 <li></li>
@@ -1888,7 +1888,7 @@ src/Make.py -h -voronoi&#8221; to see the details.</p>
 <tr class="row-even"><td><a class="reference internal" href="#user-sph"><span class="std std-ref">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>
+<td><a class="reference external" href="PDF/SPH_LAMMPS_userguide.pdf">SPH User Guide</a></td>
 <td>USER/sph</td>
 <td><a class="reference external" href="http://lammps.sandia.gov/movies.html#sph">sph</a></td>
 <td><ul class="first last simple">
@@ -1986,9 +1986,9 @@ more details.</p>
 <span class="n">make</span> <span class="n">machine</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">atc</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -p ^atc -a machine
+</pre>
 <p>Supporting <a class="reference external" href="info:src/USER-ATC/README">info:src/USER-ATC/README</a>, <a class="reference internal" href="fix_atc.html"><span class="doc">fix atc</span></a>,
 examples/USER/atc</p>
 <p>Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl
@@ -2064,10 +2064,9 @@ equations of motion are integrated efficiently through the Shardlow
 splitting algorithm.  See src/USER-DPD/README for more details.</p>
 <p>Supporting info: /src/USER-DPD/README, <a class="reference internal" href="compute_dpd.html"><span class="doc">compute dpd</span></a>
 <a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a>
-<a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/cv</span></a> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/table</span></a></p>
-<blockquote>
-<div><a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a></div></blockquote>
-<p><a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> <a class="reference internal" href="pair_table_rx.html"><span class="doc">pair table/rx</span></a>
+<a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/cv</span></a> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/table</span></a>
+<a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>
+<a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> <a class="reference internal" href="pair_table_rx.html"><span class="doc">pair table/rx</span></a>
 <a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt</span></a> <a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt/energy</span></a>
 <a class="reference internal" href="pair_exp6_rx.html"><span class="doc">pair exp6/rx</span></a> <a class="reference internal" href="pair_multi_lucy.html"><span class="doc">pair multi/lucy</span></a>
 <a class="reference internal" href="pair_multi_lucy_rx.html"><span class="doc">pair multi/lucy/rx</span></a>, examples/USER/dpd</p>
@@ -2213,7 +2212,7 @@ Contact them directly if you have any questions.</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>
+pair of files (*.cpp and *.h).</p>
 <p>More information about each feature can be found by reading its doc
 page in the LAMMPS doc directory.  The doc page which lists all LAMMPS
 input script commands is as follows:</p>
@@ -2382,18 +2381,18 @@ questions.</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">
-<li>Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</li>
-<li>Also solves solids mechanics problems via a state of the art
-stabilized meshless method with hourglass control.</li>
-<li>Can specify hydrostatic interactions independently from material
-strength models, i.e. pressure and deviatoric stresses are separated.</li>
-<li>Many material models available (Johnson-Cook, plasticity with
-hardening, Mie-Grueneisen, Polynomial EOS).  Easy to add new
-material models.</li>
-<li>Rigid boundary conditions (walls) can be loaded as surface geometries
-from <a href="#id8"><span class="problematic" id="id9">*</span></a>.STL files.</li>
-</ul>
+<p>* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</p>
+<dl class="docutils">
+<dt>* Also solves solids mechanics problems via a state of the art</dt>
+<dd>stabilized meshless method with hourglass control.</dd>
+<dt>* Can specify hydrostatic interactions independently from material</dt>
+<dd>strength models, i.e. pressure and deviatoric stresses are separated.</dd>
+<dt>* Many material models available (Johnson-Cook, plasticity with</dt>
+<dd>hardening, Mie-Grueneisen, Polynomial EOS).  Easy to add new
+material models.</dd>
+<dt>* Rigid boundary conditions (walls) can be loaded as surface geometries</dt>
+<dd>from *.STL files.</dd>
+</dl>
 <p>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.</p>
 <p>There are example scripts for using this package in examples/USER/smd.</p>
 <p>The person who created this package is Georg Ganzenmuller at the
@@ -2424,16 +2423,18 @@ them directly if you have any questions.</p>
 <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">
-<li>Tait, ideal gas, Lennard-Jones equation of states, full support for
-complete (i.e. internal-energy dependent) equations of state</li>
-<li>Plain or Monaghans XSPH integration of the equations of motion</li>
-<li>Density continuity or density summation to propagate the density field</li>
-<li>Commands to set internal energy and density of particles from the
-input script</li>
-<li>Output commands to access internal energy and density for dumping and
-thermo output</li>
-</ul>
+<dl class="docutils">
+<dt>* Tait, ideal gas, Lennard-Jones equation of states, full support for</dt>
+<dd>complete (i.e. internal-energy dependent) equations of state</dd>
+</dl>
+<p>* Plain or Monaghans XSPH integration of the equations of motion</p>
+<p>* Density continuity or density summation to propagate the density field</p>
+<dl class="docutils">
+<dt>* Commands to set internal energy and density of particles from the</dt>
+<dd>input script</dd>
+<dt>* Output commands to access internal energy and density for dumping and</dt>
+<dd>thermo output</dd>
+</dl>
 <p>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.</p>
 <p>There are example scripts for using this package in examples/USER/sph.</p>
 <p>The person who created this package is Georg Ganzenmuller at the
diff --git a/doc/html/Section_python.html b/doc/html/Section_python.html
index 8b4dc1cffb..971aeb58dc 100644
--- a/doc/html/Section_python.html
+++ b/doc/html/Section_python.html
@@ -343,10 +343,10 @@ described above.</p>
 <p>If you set the paths to these files as environment variables, you only
 have to do it once.  For the csh or tcsh shells, add something like
 this to your ~/.cshrc file, one line for each of the two files:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
+<pre class="literal-block">
+setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
 setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
-</pre></div>
-</div>
+</pre>
 <p>If you use the python/install.py script, you need to invoke it every
 time you rebuild LAMMPS (as a shared library) or make changes to the
 python/lammps.py file.</p>
@@ -393,39 +393,21 @@ environment variable as described above.</p>
 your Python with an interface to MPI.  This also allows you to
 make MPI calls directly from Python in your script, if you desire.</p>
 <p>There are several Python packages available that purport to wrap MPI
-as a library and allow MPI functions to be called from Python.</p>
-<p>These include</p>
+as a library and allow MPI functions to be called from Python. However,
+development on most of them seems to be halted except on:</p>
 <ul class="simple">
-<li><a class="reference external" href="http://pympi.sourceforge.net/">pyMPI</a></li>
-<li><a class="reference external" href="http://code.google.com/p/maroonmpi/">maroonmpi</a></li>
-<li><a class="reference external" href="http://code.google.com/p/mpi4py/">mpi4py</a></li>
-<li><a class="reference external" href="http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&amp;sid=c997fefc3933bd66204875b436940f16">myMPI</a></li>
-<li><a class="reference external" href="http://code.google.com/p/pypar">Pypar</a></li>
+<li><a class="reference external" href="https://bitbucket.org/mpi4py/mpi4py">mpi4py</a></li>
+<li><a class="reference external" href="https://github.com/daleroberts/pypar">PyPar</a></li>
 </ul>
-<p>All of these except pyMPI work by wrapping the MPI library and
-exposing (some portion of) its interface to your Python script.  This
-means Python cannot be used interactively in parallel, since they do
-not address the issue of interactive input to multiple instances of
-Python running on different processors.  The one exception is pyMPI,
-which alters the Python interpreter to address this issue, and (I
-believe) creates a new alternate executable (in place of &#8220;python&#8221;
-itself) as a result.</p>
-<p>In principle any of these Python/MPI packages should work to invoke
-LAMMPS in parallel and to make MPI calls themselves from a Python
-script which is itself running in parallel.  However, when I
-downloaded and looked at a few of them, their documentation was
-incomplete and I had trouble with their installation.  It&#8217;s not clear
-if some of the packages are still being actively developed and
-supported.</p>
-<p>The packages Pypar and mpi4py have both been successfully tested with
-LAMMPS.  Pypar is simpler and easy to set up and use, but supports
+<p>Both packages, PyPar and mpi4py have been successfully tested with
+LAMMPS.  PyPar is simpler and easy to set up and use, but supports
 only a subset of MPI.  Mpi4py is more MPI-feature complete, but also a
 bit more complex to use.  As of version 2.0.0, mpi4py is the only
 python MPI wrapper that allows passing a custom MPI communicator to
 the LAMMPS constructor, which means one can easily run one or more
 LAMMPS instances on subsets of the total MPI ranks.</p>
 <hr class="docutils" />
-<p>Pypar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a>
+<p>PyPar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a>
 be installed in your Python.  After launching Python, type</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span>
 </pre></div>
@@ -439,15 +421,15 @@ top-level directory, type</p>
 </div>
 <p>The &#8220;sudo&#8221; is only needed if required to copy Numpy files into your
 Python distribution&#8217;s site-packages directory.</p>
-<p>To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it
+<p>To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it
 and from its &#8220;source&#8221; directory, type</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span>
 <span class="n">sudo</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
 </pre></div>
 </div>
-<p>Again, the &#8220;sudo&#8221; is only needed if required to copy Pypar files into
+<p>Again, the &#8220;sudo&#8221; is only needed if required to copy PyPar files into
 your Python distribution&#8217;s site-packages directory.</p>
-<p>If you have successully installed Pypar, you should be able to run
+<p>If you have successully installed PyPar, you should be able to run
 Python and type</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pypar</span>
 </pre></div>
@@ -465,17 +447,17 @@ on a simple test script</p>
 <p>and see one line of output for each processor you run on.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">To use Pypar and LAMMPS in parallel from Python, you must insure
+<p class="last">To use PyPar and LAMMPS in parallel from Python, you must insure
 both are using the same version of MPI.  If you only have one MPI
 installed on your system, this is not an issue, but it can be if you
 have multiple MPIs.  Your LAMMPS build is explicit about which MPI it
 is using, since you specify the details in your lo-level
-src/MAKE/Makefile.foo file.  Pypar uses the &#8220;mpicc&#8221; command to find
+src/MAKE/Makefile.foo file.  PyPar uses the &#8220;mpicc&#8221; command to find
 information about the MPI it uses to build against.  And it tries to
 load &#8220;libmpi.so&#8221; from the LD_LIBRARY_PATH.  This may or may not find
 the MPI library that LAMMPS is using.  If you have problems running
-both Pypar and LAMMPS together, this is an issue you may need to
-address, e.g. by moving other MPI installations so that Pypar finds
+both PyPar and LAMMPS together, this is an issue you may need to
+address, e.g. by moving other MPI installations so that PyPar finds
 the right one.</p>
 </div>
 <hr class="docutils" />
@@ -502,11 +484,11 @@ on a simple test script</p>
 </pre></div>
 </div>
 <p>where test.py contains the lines</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="k">import</span> <span class="n">MPI</span>
-<span class="n">comm</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span>
-<span class="nb">print</span> <span class="s2">&quot;Proc </span><span class="si">%d</span><span class="s2"> out of </span><span class="si">%d</span><span class="s2"> procs&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">comm</span><span class="o">.</span><span class="n">Get_rank</span><span class="p">(),</span><span class="n">comm</span><span class="o">.</span><span class="n">Get_size</span><span class="p">())</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+from mpi4py import MPI
+comm = MPI.COMM_WORLD
+print &quot;Proc %d out of %d procs&quot; % (comm.Get_rank(),comm.Get_size())
+</pre>
 <p>and see one line of output for each processor you run on.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
@@ -568,15 +550,15 @@ interactively from the bench directory:</p>
 <p>Either way, you should see the results of running the in.lj benchmark
 on a single processor appear on the screen, the same as if you had
 typed something like:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_g++ -in in.lj
+</pre>
 </div>
 <div class="section" id="test-lammps-and-python-in-parallel">
 <h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></h3>
 <p>To run LAMMPS in parallel, assuming you have installed the
-<a class="reference external" href="Pypar">Pypar</a> package as discussed above, create a test.py file
-containing these lines:</p>
+<a class="reference external" href="https://github.com/daleroberts/pypar">PyPar</a> package as discussed
+above, create a test.py file containing these lines:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pypar</span>
 <span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
 <span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>
@@ -586,36 +568,36 @@ containing these lines:</p>
 </pre></div>
 </div>
 <p>To run LAMMPS in parallel, assuming you have installed the
-<a class="reference external" href="mpi4py">mpi4py</a> package as discussed above, create a test.py file
-containing these lines:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="k">import</span> <span class="n">MPI</span>
-<span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
-<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>
-<span class="n">lmp</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="s2">&quot;in.lj&quot;</span><span class="p">)</span>
-<span class="n">me</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span><span class="o">.</span><span class="n">Get_rank</span><span class="p">()</span>
-<span class="n">nprocs</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span><span class="o">.</span><span class="n">Get_size</span><span class="p">()</span>
-<span class="nb">print</span> <span class="s2">&quot;Proc </span><span class="si">%d</span><span class="s2"> out of </span><span class="si">%d</span><span class="s2"> procs has&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">me</span><span class="p">,</span><span class="n">nprocs</span><span class="p">),</span><span class="n">lmp</span>
-<span class="n">MPI</span><span class="o">.</span><span class="n">Finalize</span><span class="p">()</span>
-</pre></div>
-</div>
+<a class="reference external" href="https://bitbucket.org/mpi4py/mpi4py">mpi4py</a> package as discussed
+above, create a test.py file containing these lines:</p>
+<pre class="literal-block">
+from mpi4py import MPI
+from lammps import lammps
+lmp = lammps()
+lmp.file(&quot;in.lj&quot;)
+me = MPI.COMM_WORLD.Get_rank()
+nprocs = MPI.COMM_WORLD.Get_size()
+print &quot;Proc %d out of %d procs has&quot; % (me,nprocs),lmp
+MPI.Finalize()
+</pre>
 <p>You can either script in parallel as:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">python</span> <span class="n">test</span><span class="o">.</span><span class="n">py</span>
 </pre></div>
 </div>
 <p>and you should see the same output as if you had typed</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>
-</pre></div>
-</div>
-<p>Note that if you leave out the 3 lines from test.py that specify Pypar
+<pre class="literal-block">
+% mpirun -np 4 lmp_g++ -in in.lj
+</pre>
+<p>Note that if you leave out the 3 lines from test.py that specify PyPar
 commands you will instantiate and run LAMMPS independently on each of
 the P processors specified in the mpirun command.  In this case you
 should get 4 sets of output, each showing that a LAMMPS run was made
 on a single processor, instead of one set of output showing that
 LAMMPS ran on 4 processors.  If the 1-processor outputs occur, it
-means that Pypar is not working correctly.</p>
-<p>Also note that once you import the PyPar module, Pypar initializes MPI
+means that PyPar is not working correctly.</p>
+<p>Also note that once you import the PyPar module, PyPar initializes MPI
 for you, and you can use MPI calls directly in your Python script, as
-described in the Pypar documentation.  The last line of your Python
+described in the PyPar documentation.  The last line of your Python
 script should be pypar.finalize(), to insure MPI is shut down
 correctly.</p>
 </div>
@@ -661,14 +643,14 @@ Python script, as follows:</p>
 the files src/library.cpp and src/library.h you will see that they
 correspond one-to-one with calls you can make to the LAMMPS library
 from a C++ or C or Fortran program.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>           <span class="c1"># create a LAMMPS object using the default liblammps.so library</span>
-                         <span class="mi">4</span> <span class="n">optional</span> <span class="n">args</span> <span class="n">are</span> <span class="n">allowed</span><span class="p">:</span> <span class="n">name</span><span class="p">,</span> <span class="n">cmdargs</span><span class="p">,</span> <span class="n">ptr</span><span class="p">,</span> <span class="n">comm</span>
-<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">ptr</span><span class="o">=</span><span class="n">lmpptr</span><span class="p">)</span> <span class="c1"># use lmpptr as previously created LAMMPS object</span>
-<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">comm</span><span class="o">=</span><span class="n">split</span><span class="p">)</span> <span class="c1"># create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later</span>
-<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;g++&quot;</span><span class="p">)</span>   <span class="c1"># create a LAMMPS object using the liblammps_g++.so library</span>
-<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;g++&quot;</span><span class="p">,</span><span class="n">cmdargs</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span>    <span class="c1"># add LAMMPS command-line args, e.g. list = [&quot;-echo&quot;,&quot;screen&quot;]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
+                         4 optional args are allowed: name, cmdargs, ptr, comm
+lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
+lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
+lmp = lammps(name=&quot;g++&quot;)   # create a LAMMPS object using the liblammps_g++.so library
+lmp = lammps(name=&quot;g++&quot;,cmdargs=list)    # add LAMMPS command-line args, e.g. list = [&quot;-echo&quot;,&quot;screen&quot;]
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>              <span class="c1"># destroy a LAMMPS object</span>
 </pre></div>
 </div>
@@ -677,49 +659,49 @@ from a C++ or C or Fortran program.</p>
 <span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="n">cmd</span><span class="p">)</span>         <span class="c1"># invoke a single LAMMPS command, cmd = &quot;run 100&quot;</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">xlo</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_global</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span>  <span class="c1"># extract a global quantity</span>
-                                     <span class="c1"># name = &quot;boxxlo&quot;, &quot;nlocal&quot;, etc</span>
-                                  <span class="c1"># type = 0 = int</span>
-                                  <span class="c1">#        1 = double</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">coords</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_atom</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span>      <span class="c1"># extract a per-atom quantity</span>
-                                          <span class="c1"># name = &quot;x&quot;, &quot;type&quot;, etc</span>
-                                       <span class="c1"># type = 0 = vector of ints</span>
-                                       <span class="c1">#        1 = array of ints</span>
-                                       <span class="c1">#        2 = vector of doubles</span>
-                                       <span class="c1">#        3 = array of doubles</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">eng</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_compute</span><span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">style</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span>  <span class="c1"># extract value(s) from a compute</span>
-<span class="n">v3</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_fix</span><span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">style</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">)</span>   <span class="c1"># extract value(s) from a fix</span>
-                                          <span class="c1"># id = ID of compute or fix</span>
-                                       <span class="c1"># style = 0 = global data</span>
-                                       <span class="c1">#         1 = per-atom data</span>
-                                       <span class="c1">#         2 = local data</span>
-                                       <span class="c1"># type = 0 = scalar</span>
-                                       <span class="c1">#        1 = vector</span>
-                                       <span class="c1">#        2 = array</span>
-                                       <span class="c1"># i,j = indices of value in global vector or array</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">var</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_variable</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="n">group</span><span class="p">,</span><span class="n">flag</span><span class="p">)</span>  <span class="c1"># extract value(s) from a variable</span>
-                                          <span class="c1"># name = name of variable</span>
-                                          <span class="c1"># group = group ID (ignored for equal-style variables)</span>
-                                          <span class="c1"># flag = 0 = equal-style variable</span>
-                                          <span class="c1">#        1 = atom-style variable</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">flag</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="n">value</span><span class="p">)</span>       <span class="c1"># set existing named string-style variable to value, flag = 0 if successful</span>
-<span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span>                 <span class="c1"># total # of atoms as int</span>
-<span class="n">data</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">gather_atoms</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">)</span>  <span class="c1"># return atom attribute of all atoms gathered into data, ordered by atom ID</span>
-                                          <span class="c1"># name = &quot;x&quot;, &quot;charge&quot;, &quot;type&quot;, etc</span>
-                                          <span class="c1"># count = # of per-atom values, 1 or 3, etc</span>
-<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_atoms</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">,</span><span class="n">data</span><span class="p">)</span>   <span class="c1"># scatter atom attribute of all atoms from data, ordered by atom ID</span>
-                                          <span class="c1"># name = &quot;x&quot;, &quot;charge&quot;, &quot;type&quot;, etc</span>
-                                          <span class="c1"># count = # of per-atom values, 1 or 3, etc</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+xlo = lmp.extract_global(name,type)  # extract a global quantity
+                                     # name = &quot;boxxlo&quot;, &quot;nlocal&quot;, etc
+                                  # type = 0 = int
+                                  #        1 = double
+</pre>
+<pre class="literal-block">
+coords = lmp.extract_atom(name,type)      # extract a per-atom quantity
+                                          # name = &quot;x&quot;, &quot;type&quot;, etc
+                                       # type = 0 = vector of ints
+                                       #        1 = array of ints
+                                       #        2 = vector of doubles
+                                       #        3 = array of doubles
+</pre>
+<pre class="literal-block">
+eng = lmp.extract_compute(id,style,type)  # extract value(s) from a compute
+v3 = lmp.extract_fix(id,style,type,i,j)   # extract value(s) from a fix
+                                          # id = ID of compute or fix
+                                       # style = 0 = global data
+                                       #         1 = per-atom data
+                                       #         2 = local data
+                                       # type = 0 = scalar
+                                       #        1 = vector
+                                       #        2 = array
+                                       # i,j = indices of value in global vector or array
+</pre>
+<pre class="literal-block">
+var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
+                                          # name = name of variable
+                                          # group = group ID (ignored for equal-style variables)
+                                          # flag = 0 = equal-style variable
+                                          #        1 = atom-style variable
+</pre>
+<pre class="literal-block">
+flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
+natoms = lmp.get_natoms()                 # total # of atoms as int
+data = lmp.gather_atoms(name,type,count)  # return atom attribute of all atoms gathered into data, ordered by atom ID
+                                          # name = &quot;x&quot;, &quot;charge&quot;, &quot;type&quot;, etc
+                                          # count = # of per-atom values, 1 or 3, etc
+lmp.scatter_atoms(name,type,count,data)   # scatter atom attribute of all atoms from data, ordered by atom ID
+                                          # name = &quot;x&quot;, &quot;charge&quot;, &quot;type&quot;, etc
+                                          # count = # of per-atom values, 1 or 3, etc
+</pre>
 <hr class="docutils" />
 <p>The lines</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
@@ -767,8 +749,8 @@ argument.</p>
 returned, which you can use via normal Python subscripting.  See the
 extract() method in the src/atom.cpp file for a list of valid names.
 Again, new names could easily be added.  A pointer to a vector of
-doubles or integers, or a pointer to an array of doubles (double <a href="#id3"><span class="problematic" id="id4">**</span></a>)
-or integers (int <a href="#id5"><span class="problematic" id="id6">**</span></a>) is returned.  You need to specify the appropriate
+doubles or integers, or a pointer to an array of doubles (double **)
+or integers (int **) is returned.  You need to specify the appropriate
 data type via the type argument.</p>
 <p>For extract_compute() and extract_fix(), the global, per-atom, or
 local data calulated by the compute or fix can be accessed.  What is
@@ -824,19 +806,19 @@ consecutively ordered, no coordinates are reset.</p>
 <p>The array of coordinates passed to scatter_atoms() must be a ctypes
 vector of ints or doubles, allocated and initialized something like
 this:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ctypes</span> <span class="k">import</span> <span class="o">*</span>
-<span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span>
-<span class="n">n3</span> <span class="o">=</span> <span class="mi">3</span><span class="o">*</span><span class="n">natoms</span>
-<span class="n">x</span> <span class="o">=</span> <span class="p">(</span><span class="n">n3</span><span class="o">*</span><span class="n">c_double</span><span class="p">)()</span>
-<span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
-<span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">y</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
-<span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
-<span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">2</span>
-<span class="o">...</span>
-<span class="n">x</span><span class="p">[</span><span class="n">n3</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="n">natoms</span>
-<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_coords</span><span class="p">(</span><span class="s2">&quot;x&quot;</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="n">x</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+from ctypes import *
+natoms = lmp.get_natoms()
+n3 = 3*natoms
+x = (n3*c_double)()
+x[0] = x coord of atom with ID 1
+x[1] = y coord of atom with ID 1
+x[2] = z coord of atom with ID 1
+x[3] = x coord of atom with ID 2
+...
+x[n3-1] = z coord of atom with ID natoms
+lmp.scatter_coords(&quot;x&quot;,1,3,x)
+</pre>
 <p>Alternatively, you can just change values in the vector returned by
 gather_atoms(&#8220;x&#8221;,1,3), since it is a ctypes vector of doubles.</p>
 <hr class="docutils" />
@@ -915,10 +897,10 @@ capability needed by these Python scripts.</p>
 open-source version of PyMol in your Python, so that you can import it
 from a Python script.  See the PyMol WWW pages <a class="reference external" href="http://www.pymol.org">here</a> or
 <a class="reference external" href="http://sourceforge.net/scm/?type=svn&amp;group_id=4546">here</a> for more details:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>http://www.pymol.org
-http://sourceforge.net/scm/?type=svn&amp;group_id=4546
-</pre></div>
-</div>
+<pre class="literal-block">
+<a class="reference external" href="http://www.pymol.org">http://www.pymol.org</a>
+<a class="reference external" href="http://sourceforge.net/scm/?type=svn&amp;group_id=4546">http://sourceforge.net/scm/?type=svn&amp;group_id=4546</a>
+</pre>
 <p>The latter link is to the open-source version.</p>
 <p>Note that for VMD, you need a fairly current version (1.8.7 works for
 me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
diff --git a/doc/html/Section_start.html b/doc/html/Section_start.html
index 4d422cdc2a..b3ebfd3dca 100644
--- a/doc/html/Section_start.html
+++ b/doc/html/Section_start.html
@@ -173,10 +173,10 @@ experienced users.</p>
 <p>When you download a LAMMPS tarball you will need to unzip and untar
 the downloaded file with the following commands, after placing the
 tarball in an appropriate directory.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">gunzip</span> <span class="n">lammps</span><span class="o">*.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
-<span class="n">tar</span> <span class="n">xvf</span> <span class="n">lammps</span><span class="o">*.</span><span class="n">tar</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+gunzip lammps*.tar.gz
+tar xvf lammps*.tar
+</pre>
 <p>This will create a LAMMPS directory containing two files and several
 sub-directories:</p>
 <table border="1" class="docutils">
@@ -315,13 +315,13 @@ it will be never be touched by any LAMMPS updates.</p>
 a list of available choices from src/MAKE and all of its
 sub-directories.  If one of those has the options you want or is the
 machine you want, you can type a command like:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">mpi</span>
-<span class="ow">or</span>
-<span class="n">make</span> <span class="n">serial_icc</span>
-<span class="ow">or</span>
-<span class="n">gmake</span> <span class="n">mac</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+make mpi
+or
+make serial_icc
+or
+gmake mac
+</pre>
 <p>Note that the corresponding Makefile.machine can exist in src/MAKE or
 any of its sub-directories.  If a file with the same name appears in
 multiple places (not a good idea), the order they are used is as
@@ -362,13 +362,13 @@ then you should list them as part of the LIB variable.  You should
 not need to do this if you use mpicxx.</p>
 <p>The DEPFLAGS setting is what triggers the C++ compiler to create a
 dependency list for a source file.  This speeds re-compilation when
-source (<em>.cpp) or header (</em>.h) files are edited.  Some compilers do
+source (*.cpp) or header (*.h) files are edited.  Some compilers do
 not support dependency file creation, or may use a different switch
 than -D.  GNU g++ and Intel icc works with -D.  If your compiler can&#8217;t
 create dependency files, then you&#8217;ll need to create a Makefile.foo
 patterned after Makefile.storm, which uses different rules that do not
 involve dependency files.  Note that when you build LAMMPS for the
-first time on a new platform, a long list of <a href="#id5"><span class="problematic" id="id6">*</span></a>.d files will be printed
+first time on a new platform, a long list of *.d files will be printed
 out rapidly.  This is not an error; it is the Makefile doing its
 normal creation of dependencies.</p>
 <p><strong>Step 4</strong></p>
@@ -598,7 +598,7 @@ faster, depending on how many cores your compilation machine has.  N
 is the number of cores the build runs on.</p>
 <p>You should get the executable lmp_foo when the build is complete.</p>
 <hr class="docutils" />
-<p id="start-2-3"><a href="#id7"><span class="problematic" id="id8">**</span></a><em>Errors that can occur when making LAMMPS:</em>**</p>
+<p id="start-2-3"><a href="#id5"><span class="problematic" id="id6">**</span></a><em>Errors that can occur when making LAMMPS:</em>**</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">If an error occurs when building LAMMPS, the compiler or linker
@@ -632,17 +632,17 @@ is undefined&#8217;, then your machine does not support &#8220;long long&#8221;
 integers.  Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
 above in Step 4.</p>
 <hr class="docutils" />
-<p id="start-2-4"><a href="#id9"><span class="problematic" id="id10">**</span></a><em>Additional build tips:</em>**</p>
+<p id="start-2-4"><a href="#id7"><span class="problematic" id="id8">**</span></a><em>Additional build tips:</em>**</p>
 <ol class="arabic simple">
 <li>Building LAMMPS for multiple platforms.</li>
 </ol>
 <p>You can make LAMMPS for multiple platforms from the same src
 directory.  Each target creates its own object sub-directory called
-Obj_target where it stores the system-specific <a href="#id11"><span class="problematic" id="id12">*</span></a>.o files.</p>
+Obj_target where it stores the system-specific *.o files.</p>
 <ol class="arabic simple" start="2">
 <li>Cleaning up.</li>
 </ol>
-<p>Typing &#8220;make clean-all&#8221; or &#8220;make clean-machine&#8221; will delete <a href="#id13"><span class="problematic" id="id14">*</span></a>.o object
+<p>Typing &#8220;make clean-all&#8221; or &#8220;make clean-machine&#8221; will delete *.o object
 files created when LAMMPS is built, for either all builds or for a
 particular machine.</p>
 <p>(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
@@ -686,11 +686,11 @@ basis is limited by 4-byte integer storage to 2^31 atoms per processor
 a problem would have a huge per-processor memory footprint due to
 neighbor lists and would run very slowly in terms of CPU secs/timestep.</p>
 <hr class="docutils" />
-<p id="start-2-5"><a href="#id15"><span class="problematic" id="id16">**</span></a><em>Building for a Mac:</em>**</p>
+<p id="start-2-5"><a href="#id9"><span class="problematic" id="id10">**</span></a><em>Building for a Mac:</em>**</p>
 <p>OS X is BSD Unix, so it should just work.  See the
 src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.</p>
 <hr class="docutils" />
-<p id="start-2-6"><a href="#id17"><span class="problematic" id="id18">**</span></a><em>Building for Windows:</em>**</p>
+<p id="start-2-6"><a href="#id11"><span class="problematic" id="id12">**</span></a><em>Building for Windows:</em>**</p>
 <p>The LAMMPS download page has an option to download both a serial and
 parallel pre-built Windows executable.  See the <a class="reference internal" href="#start-6"><span class="std std-ref">Running LAMMPS</span></a> section for instructions on running these executables
 on a Windows box.</p>
@@ -725,7 +725,7 @@ tool which can be used to install/un-install packages and build the
 auxiliary libraries which some of them use.  It can also auto-edit a
 Makefile.machine to add settings needed by some packages.</p>
 <hr class="docutils" />
-<p id="start-3-1"><a href="#id19"><span class="problematic" id="id20">**</span></a><em>Package basics:</em>**</p>
+<p id="start-3-1"><a href="#id13"><span class="problematic" id="id14">**</span></a><em>Package basics:</em>**</p>
 <p>The source code for LAMMPS is structured as a set of core files which
 are always included, plus optional packages.  Packages are groups of
 files that enable a specific set of features.  For example, force
@@ -742,9 +742,9 @@ package, you must have built LAMMPS with that package, else you will
 get an error that the style is invalid or the command is unknown.
 Every command&#8217;s doc page specfies if it is part of a package.  You can
 also type</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">h</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_machine -h
+</pre>
 <p>to run your executable with the optional <a class="reference internal" href="#start-7"><span class="std std-ref">-h command-line switch</span></a> for &#8220;help&#8221;, which will simply list the styles and
 commands known to your executable, and immediately exit.</p>
 <p>There are two kinds of packages in LAMMPS, standard and user packages.
@@ -768,7 +768,7 @@ Information on how to submit additions you make to LAMMPS as single
 files or either a standard or user-contributed package are given in
 <a class="reference internal" href="Section_modify.html#mod-15"><span class="std std-ref">this section</span></a> of the documentation.</p>
 <hr class="docutils" />
-<p id="start-3-2"><a href="#id21"><span class="problematic" id="id22">**</span></a><em>Including/excluding packages:</em>**</p>
+<p id="start-3-2"><a href="#id15"><span class="problematic" id="id16">**</span></a><em>Including/excluding packages:</em>**</p>
 <p>To use (or not use) a package you must include it (or exclude it)
 before building LAMMPS.  From the src directory, this is typically as
 simple as:</p>
@@ -837,7 +837,7 @@ sub-directory.  Typing &#8220;make package-diff&#8221; lists all differences
 between these files.  Again, type &#8220;make package&#8221; to see all of the
 package-related make options.</p>
 <hr class="docutils" />
-<p id="start-3-3"><a href="#id23"><span class="problematic" id="id24">**</span></a><em>Packages that require extra libraries:</em>**</p>
+<p id="start-3-3"><a href="#id17"><span class="problematic" id="id18">**</span></a><em>Packages that require extra libraries:</em>**</p>
 <p>A few of the standard and user packages require additional auxiliary
 libraries.  Many of them are provided with LAMMPS, in which case they
 must be compiled first, before LAMMPS is built, if you wish to include
@@ -908,7 +908,7 @@ needed soft links.  Type &#8220;python install.py&#8221; for further instruction
 or settings in the lib/package/Makefile.lammps files are not correct,
 the LAMMPS build will typically fail.</p>
 <hr class="docutils" />
-<p id="start-3-4"><a href="#id25"><span class="problematic" id="id26">**</span></a><em>Packages that require Makefile.machine settings</em>**</p>
+<p id="start-3-4"><a href="#id19"><span class="problematic" id="id20">**</span></a><em>Packages that require Makefile.machine settings</em>**</p>
 <p>A few packages require specific settings in Makefile.machine, to
 either build or use the package effectively.  These are the
 USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
@@ -1081,7 +1081,7 @@ LAMMPS to other codes.  See <a class="reference internal" href="Section_python.h
 more info on wrapping and running LAMMPS from Python.</p>
 <div class="section" id="static-library">
 <h3>2.5.1. <strong>Static library:</strong></h3>
-<p>To build LAMMPS as a static library (<a href="#id27"><span class="problematic" id="id28">*</span></a>.a file on Linux), type</p>
+<p>To build LAMMPS as a static library (*.a file on Linux), type</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">foo</span> <span class="n">mode</span><span class="o">=</span><span class="n">lib</span>
 </pre></div>
 </div>
@@ -1095,7 +1095,7 @@ point to the most recently built static library.</p>
 </div>
 <div class="section" id="shared-library">
 <h3>2.5.2. <strong>Shared library:</strong></h3>
-<p>To build LAMMPS as a shared library (<a href="#id29"><span class="problematic" id="id30">*</span></a>.so file on Linux), which can be
+<p>To build LAMMPS as a shared library (*.so file on Linux), which can be
 dynamically loaded, e.g. from Python, type</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">foo</span> <span class="n">mode</span><span class="o">=</span><span class="n">shlib</span>
 </pre></div>
@@ -1122,18 +1122,18 @@ of the auxiliary library.  The build instructions for the library
 should tell you how to do this.</p>
 <p>Here is an example of such errors when the system FFTW or provided
 lib/colvars library have not been built as shared libraries:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
-R_X86_64_32 against `.rodata&#39; can not be used when making a shared
+<pre class="literal-block">
+/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
+R_X86_64_32 against '.rodata' can not be used when making a shared
 object; recompile with -fPIC
 /usr/local/lib/libfftw3.a: could not read symbols: Bad value
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
-relocation R_X86_64_32 against `__pthread_key_create&#39; can not be used
+</pre>
+<pre class="literal-block">
+/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
+relocation R_X86_64_32 against '__pthread_key_create' can not be used
 when making a shared object; recompile with -fPIC
 ../../lib/colvars/libcolvars.a: error adding symbols: Bad value
-</pre></div>
-</div>
+</pre>
 <p>As an example, here is how to build and install the <a class="reference external" href="http://www-unix.mcs.anl.gov/mpi">MPICH library</a>, a popular open-source version of MPI, distributed by
 Argonne National Labs, as a shared library in the default
 /usr/local/lib location:</p>
@@ -1157,9 +1157,9 @@ current version of the shared library is always available to programs
 that use it.</p>
 <p>For the csh or tcsh shells, you would add something like this to your
 ~/.cshrc file:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
-</pre></div>
-</div>
+<pre class="literal-block">
+setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
+</pre>
 </div>
 <div class="section" id="calling-the-lammps-library">
 <h3>2.5.4. <strong>Calling the LAMMPS library:</strong></h3>
@@ -1188,20 +1188,20 @@ interface and how to extend it for your needs.</p>
 <span id="start-6"></span><h2>2.6. Running LAMMPS</h2>
 <p>By default, LAMMPS runs by reading commands from standard input.  Thus
 if you run the LAMMPS executable by itself, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_linux</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_linux
+</pre>
 <p>it will simply wait, expecting commands from the keyboard.  Typically
 you should put commands in an input script and use I/O redirection,
 e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_linux</span> <span class="o">&lt;</span> <span class="ow">in</span><span class="o">.</span><span class="n">file</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_linux &lt; in.file
+</pre>
 <p>For parallel environments this should also work.  If it does not, use
 the &#8216;-in&#8217; command-line switch, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_linux</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">file</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_linux -in in.file
+</pre>
 <p><a class="reference internal" href="Section_commands.html"><span class="doc">This section</span></a> describes how input scripts are
 structured and what commands they contain.</p>
 <p>You can test LAMMPS on any of the sample inputs provided in the
@@ -1210,13 +1210,13 @@ outputs are named log.*.name.P where name is a machine and P is the
 number of processors it was run on.</p>
 <p>Here is how you might run a standard Lennard-Jones benchmark on a
 Linux box, using mpirun to launch a parallel job:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">src</span>
-<span class="n">make</span> <span class="n">linux</span>
-<span class="n">cp</span> <span class="n">lmp_linux</span> <span class="o">../</span><span class="n">bench</span>
-<span class="n">cd</span> <span class="o">../</span><span class="n">bench</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_linux</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+cd src
+make linux
+cp lmp_linux ../bench
+cd ../bench
+mpirun -np 4 lmp_linux -in in.lj
+</pre>
 <p>See <a class="reference external" href="http://lammps.sandia.gov/bench.html">this page</a> for timings for this and the other benchmarks on
 various platforms.  Note that some of the example scripts require
 LAMMPS to be built with one or more of its optional packages.</p>
@@ -1256,7 +1256,7 @@ in.lj&#8221;, replacing in.lj with the name of your LAMMPS input script.</li>
 matter what you type).</li>
 <li>In this mode, output may not immediately show up on the screen, so if
 your input script takes a long time to execute, you may need to be
-patient before the output shows up. :l Alternatively, you can still
+patient before the output shows up.  Alternatively, you can still
 use this executable to run on a single processor by typing something
 like: &#8220;lmp_win_mpi -in in.lj&#8221;.</li>
 </ul>
@@ -1309,10 +1309,10 @@ letter abbreviation can be used:</p>
 <li>-v or -var</li>
 </ul>
 <p>For example, lmp_ibm might be launched as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_ibm</span> <span class="o">-</span><span class="n">v</span> <span class="n">f</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="o">-</span><span class="n">l</span> <span class="n">my</span><span class="o">.</span><span class="n">log</span> <span class="o">-</span><span class="n">sc</span> <span class="n">none</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">alloy</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_ibm</span> <span class="o">-</span><span class="n">var</span> <span class="n">f</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="o">-</span><span class="n">log</span> <span class="n">my</span><span class="o">.</span><span class="n">log</span> <span class="o">-</span><span class="n">screen</span> <span class="n">none</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">alloy</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
+mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy
+</pre>
 <p>Here are the details on the options:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">-</span><span class="n">echo</span> <span class="n">style</span>
 </pre></div>
@@ -1395,11 +1395,11 @@ are intended for computational work like running LAMMPS.  By default
 Ng = 1 and Ns is not set.</p>
 <p>Depending on which flavor of MPI you are running, LAMMPS will look for
 one of these 3 environment variables</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">SLURM_LOCALID</span> <span class="p">(</span><span class="n">various</span> <span class="n">MPI</span> <span class="n">variants</span> <span class="n">compiled</span> <span class="k">with</span> <span class="n">SLURM</span> <span class="n">support</span><span class="p">)</span>
-<span class="n">MV2_COMM_WORLD_LOCAL_RANK</span> <span class="p">(</span><span class="n">Mvapich</span><span class="p">)</span>
-<span class="n">OMPI_COMM_WORLD_LOCAL_RANK</span> <span class="p">(</span><span class="n">OpenMPI</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+SLURM_LOCALID (various MPI variants compiled with SLURM support)
+MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
+OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
+</pre>
 <p>which are initialized by the &#8220;srun&#8221;, &#8220;mpirun&#8221; or &#8220;mpiexec&#8221; commands.
 The environment variable setting for each MPI rank is used to assign a
 unique GPU ID to the MPI task.</p>
diff --git a/doc/html/Section_tools.html b/doc/html/Section_tools.html
index 285debd48d..0e3948b6a0 100644
--- a/doc/html/Section_tools.html
+++ b/doc/html/Section_tools.html
@@ -218,7 +218,7 @@ own sub-directories with their own Makefiles.</p>
 <li><a class="reference internal" href="#polybond"><span class="std std-ref">polymer bonding</span></a></li>
 <li><span class="xref std std-ref">pymol_asphere</span></li>
 <li><a class="reference internal" href="#pythontools"><span class="std std-ref">python</span></a></li>
-<li><a class="reference internal" href="#reax"><span class="std std-ref">reax</span></a></li>
+<li><a class="reference internal" href="#reax-tool"><span class="std std-ref">reax</span></a></li>
 <li><a class="reference internal" href="#restart"><span class="std std-ref">restart2data</span></a></li>
 <li><a class="reference internal" href="#vim"><span class="std std-ref">vim</span></a></li>
 <li><a class="reference internal" href="#xmgrace"><span class="std std-ref">xmgrace</span></a></li>
@@ -289,9 +289,9 @@ at: <a class="reference external" href="https://github.com/colvars/colvars/issue
 <p>abf_integrate:</p>
 <p>MC-based integration of multidimensional free energy gradient
 Version 20110511</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Syntax</span><span class="p">:</span> <span class="o">./</span><span class="n">abf_integrate</span> <span class="o">&lt;</span> <span class="n">filename</span> <span class="o">&gt;</span> <span class="p">[</span><span class="o">-</span><span class="n">n</span> <span class="o">&lt;</span> <span class="n">nsteps</span> <span class="o">&gt;</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">t</span> <span class="o">&lt;</span> <span class="n">temp</span> <span class="o">&gt;</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">m</span> <span class="p">[</span><span class="mi">0</span><span class="o">|</span><span class="mi">1</span><span class="p">]</span> <span class="p">(</span><span class="n">metadynamics</span><span class="p">)]</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span> <span class="o">&lt;</span> <span class="n">hill_height</span> <span class="o">&gt;</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">f</span> <span class="o">&lt;</span> <span class="n">variable_hill_factor</span> <span class="o">&gt;</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Syntax: ./abf_integrate &lt; filename &gt; [-n &lt; nsteps &gt;] [-t &lt; temp &gt;] [-m [0|1] (metadynamics)] [-h &lt; hill_height &gt;] [-f &lt; variable_hill_factor &gt;]
+</pre>
 <p>The LAMMPS interface to the colvars collective variable library, as
 well as these tools, were created by Axel Kohlmeyer (akohlmey at
 gmail.com) at ICTP, Italy.</p>
@@ -419,7 +419,7 @@ Greathouse at Sandia (jagreat at sandia.gov).</p>
 <div class="section" id="lmp2cfg-tool">
 <span id="cfg"></span><h2>9.17. lmp2cfg tool</h2>
 <p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
-files into a series of <a href="#id1"><span class="problematic" id="id2">*</span></a>.cfg files which can be read into the
+files into a series of *.cfg files which can be read into the
 <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer.  See
 the README file for more information.</p>
 <p>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).</p>
@@ -538,7 +538,7 @@ README for more info on Pizza.py and how to use these scripts.</p>
 <hr class="docutils" />
 </div>
 <div class="section" id="reax-tool">
-<span id="reax"></span><h2>9.27. reax tool</h2>
+<span id="id4"></span><h2>9.27. reax tool</h2>
 <p>The reax sub-directory contains stand-alond codes that can
 post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a>
 command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><span class="doc">ReaxFF</span></a>.  See
diff --git a/doc/html/accelerate_gpu.html b/doc/html/accelerate_gpu.html
index b4fc73c25e..33e9cc6d76 100644
--- a/doc/html/accelerate_gpu.html
+++ b/doc/html/accelerate_gpu.html
@@ -202,11 +202,11 @@ attention to 3 settings in this makefile.</p>
 <p>See lib/gpu/Makefile.linux.double for examples of the ARCH settings
 for different GPU choices, e.g. Fermi vs Kepler.  It also lists the
 possible precision settings:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_SINGLE_SINGLE</span>  <span class="c1"># single precision for all calculations</span>
-<span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_DOUBLE_DOUBLE</span>  <span class="c1"># double precision for all calculations</span>
-<span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_SINGLE_DOUBLE</span>  <span class="c1"># accumulation of forces, etc, in double</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+CUDA_PREC = -D_SINGLE_SINGLE  # single precision for all calculations
+CUDA_PREC = -D_DOUBLE_DOUBLE  # double precision for all calculations
+CUDA_PREC = -D_SINGLE_DOUBLE  # accumulation of forces, etc, in double
+</pre>
 <p>The last setting is the mixed mode referred to above.  Note that your
 GPU must support double precision to use either the 2nd or 3rd of
 these settings.</p>
@@ -253,11 +253,11 @@ shared by 4 MPI tasks.</p>
 which will automatically append &#8220;gpu&#8221; to styles that support it.  Use
 the &#8220;-pk gpu Ng&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> to
 set Ng = # of GPUs/node to use.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">1</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>                         <span class="c1"># 1 MPI task uses 1 GPU</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">12</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>           <span class="c1"># 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">48</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">12</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>   <span class="c1"># ditto on 4 16-core nodes</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_machine -sf gpu -pk gpu 1 -in in.script                         # 1 MPI task uses 1 GPU
+mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script           # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
+mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script   # ditto on 4 16-core nodes
+</pre>
 <p>Note that if the &#8220;-sf gpu&#8221; switch is used, it also issues a default
 <a class="reference internal" href="package.html"><span class="doc">package gpu 1</span></a> command, which sets the number of
 GPUs/node to 1.</p>
@@ -276,9 +276,9 @@ GPU package pair styles.</p>
 and use of multiple MPI tasks/GPU is the same.</p>
 <p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix gpu</span></a> command, or you can explicitly add an
 &#8220;gpu&#8221; suffix to individual styles in your input script, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">gpu</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut/gpu 2.5
+</pre>
 <p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a> command to enable the
 GPU package, unless the &#8220;-sf gpu&#8221; or &#8220;-pk gpu&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switches</span></a> were used.  It specifies the
 number of GPUs/node to use, as well as other options.</p>
diff --git a/doc/html/accelerate_intel.html b/doc/html/accelerate_intel.html
index ad8f8560d4..cc1a7a68b6 100644
--- a/doc/html/accelerate_intel.html
+++ b/doc/html/accelerate_intel.html
@@ -268,30 +268,30 @@ this information can normally be obtained with:</p>
 </div>
 <p>Several example Makefiles for building with the Intel compiler are
 included with LAMMPS in the src/MAKE/OPTIONS/ directory:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Makefile</span><span class="o">.</span><span class="n">intel_cpu_intelmpi</span> <span class="c1"># Intel Compiler, Intel MPI, No Offload</span>
-<span class="n">Makefile</span><span class="o">.</span><span class="n">knl</span>                <span class="c1"># Intel Compiler, Intel MPI, No Offload</span>
-<span class="n">Makefile</span><span class="o">.</span><span class="n">intel_cpu_mpich</span>    <span class="c1"># Intel Compiler, MPICH, No Offload</span>
-<span class="n">Makefile</span><span class="o">.</span><span class="n">intel_cpu_openpmi</span>  <span class="c1"># Intel Compiler, OpenMPI, No Offload</span>
-<span class="n">Makefile</span><span class="o">.</span><span class="n">intel_coprocessor</span>  <span class="c1"># Intel Compiler, Intel MPI, Offload</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
+Makefile.knl                # Intel Compiler, Intel MPI, No Offload
+Makefile.intel_cpu_mpich    # Intel Compiler, MPICH, No Offload
+Makefile.intel_cpu_openpmi  # Intel Compiler, OpenMPI, No Offload
+Makefile.intel_coprocessor  # Intel Compiler, Intel MPI, Offload
+</pre>
 <p>Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that
 it explicitly specifies that vectorization should be for Intel
 Xeon Phi x200 processors making it easier to cross-compile. For
 users with recent installations of Intel Parallel Studio, the
 process can be as simple as:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">user</span><span class="o">-</span><span class="n">intel</span>
-<span class="n">source</span> <span class="o">/</span><span class="n">opt</span><span class="o">/</span><span class="n">intel</span><span class="o">/</span><span class="n">parallel_studio_xe_2016</span><span class="o">.</span><span class="mf">3.067</span><span class="o">/</span><span class="n">psxevars</span><span class="o">.</span><span class="n">sh</span>
-<span class="c1"># or psxevars.csh for C-shell</span>
-<span class="n">make</span> <span class="n">intel_cpu_intelmpi</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+make yes-user-intel
+source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
+# or psxevars.csh for C-shell
+make intel_cpu_intelmpi
+</pre>
 <p>Alternatively, the build can be accomplished with the src/Make.py
 script, described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the
 manual. Type &#8220;Make.py -h&#8221; for help. For an example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">intel</span> <span class="n">omp</span> <span class="o">-</span><span class="n">intel</span> <span class="n">cpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">intel_cpu_intelmpi</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi
+</pre>
 <p>Note that if you build with support for a Phi coprocessor, the same
 binary can be used on nodes with or without coprocessors installed.
 However, if you do not have coprocessors on your system, building
@@ -385,10 +385,10 @@ set the number of OpenMP threads via the OMP_NUM_THREADS environment
 variable if desired.</p>
 <p>Examples (see documentation for your MPI/Machine for differences in
 launching MPI applications):</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">72</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">36</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">intel</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>                                 <span class="c1"># 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">72</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">36</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">intel</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="o">-</span><span class="n">pk</span> <span class="n">intel</span> <span class="mi">0</span> <span class="n">omp</span> <span class="mi">2</span> <span class="n">mode</span> <span class="n">double</span>   <span class="c1"># Don&#39;t use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script                                 # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
+mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double   # Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision
+</pre>
 <p><strong>Or run with the USER-INTEL package by editing an input script:</strong></p>
 <p>As an alternative to adding command-line arguments, the input script
 can be edited to enable the USER-INTEL package. This requires adding
@@ -399,9 +399,9 @@ script. For the second example above, this would be:</p>
 </div>
 <p>To enable the USER-INTEL package only for individual styles, you can
 add an &#8220;intel&#8221; suffix to the individual style, e.g.:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">intel</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut/intel 2.5
+</pre>
 <p>Alternatively, the <a class="reference internal" href="suffix.html"><span class="doc">suffix intel</span></a> command can be added to
 the input script to enable USER-INTEL styles for the commands that
 follow in the input script.</p>
diff --git a/doc/html/accelerate_kokkos.html b/doc/html/accelerate_kokkos.html
index e517e0e2c5..c592745bea 100644
--- a/doc/html/accelerate_kokkos.html
+++ b/doc/html/accelerate_kokkos.html
@@ -166,19 +166,19 @@ produce an executable compatible with specific hardware.</p>
 <p>Here is a quick overview of how to use the KOKKOS package
 for CPU acceleration, assuming one or more 16-core nodes.
 More details follow.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span>
-<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
-<span class="n">make</span> <span class="n">mpi</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span>                 <span class="c1"># build with the KOKKOS package</span>
-<span class="n">make</span> <span class="n">kokkos_omp</span>                                <span class="c1"># or Makefile.kokkos_omp already has variable set</span>
-<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">omp</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span>   <span class="c1"># or one-line build via Make.py</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>              <span class="c1"># 1 node, 16 MPI tasks/node, no threads</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">1</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">16</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>   <span class="c1"># 2 nodes, 1 MPI task/node, 16 threads/task</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>           <span class="c1"># 1 node, 2 MPI tasks/node, 8 threads/task</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">4</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>   <span class="c1"># 8 nodes, 4 MPI tasks/node, 4 threads/task</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+use a C++11 compatible compiler
+make yes-kokkos
+make mpi KOKKOS_DEVICES=OpenMP                 # build with the KOKKOS package
+make kokkos_omp                                # or Makefile.kokkos_omp already has variable set
+Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi   # or one-line build via Make.py
+</pre>
+<pre class="literal-block">
+mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
+mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
+mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj           # 1 node, 2 MPI tasks/node, 8 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj   # 8 nodes, 4 MPI tasks/node, 4 threads/task
+</pre>
 <ul class="simple">
 <li>specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support</li>
 <li>include the KOKKOS package and build LAMMPS</li>
@@ -188,39 +188,39 @@ More details follow.</p>
 assuming one or more nodes, each with 16 cores and a GPU.  More
 details follow.</p>
 <p>discuss use of NVCC, which Makefiles to examine</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span>
-<span class="n">KOKKOS_DEVICES</span> <span class="o">=</span> <span class="n">Cuda</span><span class="p">,</span> <span class="n">OpenMP</span>
-<span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">Kepler35</span>
-<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
-<span class="n">make</span> <span class="n">machine</span>
-<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">cuda</span> <span class="n">arch</span><span class="o">=</span><span class="mi">31</span> <span class="o">-</span><span class="n">o</span> <span class="n">kokkos_cuda</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">kokkos_cuda</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">1</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">6</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>          <span class="c1"># one MPI task, 6 threads on CPU</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">1</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">6</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>   <span class="c1"># ditto on 4 nodes</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="n">g</span> <span class="mi">2</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>           <span class="c1"># two MPI tasks, 8 threads per CPU</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">2</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="n">g</span> <span class="mi">2</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>   <span class="c1"># ditto on 16 nodes</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+use a C++11 compatible compiler
+KOKKOS_DEVICES = Cuda, OpenMP
+KOKKOS_ARCH = Kepler35
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
+</pre>
+<pre class="literal-block">
+mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj          # one MPI task, 6 threads on CPU
+mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj   # ditto on 4 nodes
+</pre>
+<pre class="literal-block">
+mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj           # two MPI tasks, 8 threads per CPU
+mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj   # ditto on 16 nodes
+</pre>
 <p>Here is a quick overview of how to use the KOKKOS package
 for the Intel Phi:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span>
-<span class="n">KOKKOS_DEVICES</span> <span class="o">=</span> <span class="n">OpenMP</span>
-<span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">KNC</span>
-<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
-<span class="n">make</span> <span class="n">machine</span>
-<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">phi</span> <span class="o">-</span><span class="n">o</span> <span class="n">kokkos_phi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">host</span><span class="o">=</span><span class="n">MIC</span><span class="p">,</span> <span class="n">Intel</span> <span class="n">Phi</span> <span class="k">with</span> <span class="mi">61</span> <span class="n">cores</span> <span class="p">(</span><span class="mi">240</span> <span class="n">threads</span><span class="o">/</span><span class="n">phi</span> <span class="n">via</span> <span class="mi">4</span><span class="n">x</span> <span class="n">hardware</span> <span class="n">threading</span><span class="p">):</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">1</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">240</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>           <span class="c1"># 1 MPI task on 1 Phi, 1*240 = 240</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">30</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>            <span class="c1"># 30 MPI tasks on 1 Phi, 30*8 = 240</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">12</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">20</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>           <span class="c1"># 12 MPI tasks on 1 Phi, 12*20 = 240</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">96</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">12</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">20</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>   <span class="c1"># ditto on 8 Phis</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+use a C++11 compatible compiler
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = KNC
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
+</pre>
+<pre class="literal-block">
+host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
+mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj           # 1 MPI task on 1 Phi, 1*240 = 240
+mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj            # 30 MPI tasks on 1 Phi, 30*8 = 240
+mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj           # 12 MPI tasks on 1 Phi, 12*20 = 240
+mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis
+</pre>
 <p><strong>Required hardware/software:</strong></p>
 <p>Kokkos support within LAMMPS must be built with a C++11 compatible
 compiler.  If using gcc, version 4.8.1 or later is required.</p>
@@ -257,40 +257,40 @@ respectively.  Or the effect of the &#8220;-pk&#8221; or &#8220;-sf&#8221; switc
 duplicated by adding the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> commands respectively to your input script.</p>
 <p>Or you can follow these steps:</p>
 <p>CPU-only (run all-MPI or with OpenMP threading):</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
-<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
-<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+cd lammps/src
+make yes-kokkos
+make g++ KOKKOS_DEVICES=OpenMP
+</pre>
 <p>Intel Xeon Phi:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
-<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
-<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span> <span class="n">KOKKOS_ARCH</span><span class="o">=</span><span class="n">KNC</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+cd lammps/src
+make yes-kokkos
+make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC
+</pre>
 <p>CPUs and GPUs:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
-<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
-<span class="n">make</span> <span class="n">cuda</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">Cuda</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+cd lammps/src
+make yes-kokkos
+make cuda KOKKOS_DEVICES=Cuda
+</pre>
 <p>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
 make command line which requires a GNU-compatible make command.  Try
 &#8220;gmake&#8221; if your system&#8217;s standard make complains.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">If you build using make line variables and re-build LAMMPS twice
-with different KOKKOS options and the <em>same</em> target, e.g. g++ in the
-first two examples above, then you <em>must</em> perform a &#8220;make clean-all&#8221;
+with different KOKKOS options and the *same* target, e.g. g++ in the
+first two examples above, then you *must* perform a &#8220;make clean-all&#8221;
 or &#8220;make clean-machine&#8221; before each build.  This is to force all the
 KOKKOS-dependent files to be re-compiled with the new options.</p>
 </div>
 <p>You can also hardwire these make variables in the specified machine
 makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
 with a line like:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">KNC</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+KOKKOS_ARCH = KNC
+</pre>
 <p>Note that if you build LAMMPS multiple times in this manner, using
 different KOKKOS options (defined in different machine makefiles), you
 do not have to worry about doing a &#8220;clean&#8221; in between.  This is
@@ -342,7 +342,7 @@ with compute capability 3.x.  For the LINK setting, &#8220;nvcc&#8221; should no
 be used; instead use g++ or another compiler suitable for linking C++
 applications.  Often you will want to use your MPI compiler wrapper
 for this setting (i.e. mpicxx).  Finally, the lo-level Makefile must
-also have a &#8220;Compilation rule&#8221; for creating <a href="#id1"><span class="problematic" id="id2">*</span></a>.o files from <a href="#id3"><span class="problematic" id="id4">*</span></a>.cu files.
+also have a &#8220;Compilation rule&#8221; for creating *.o files from *.cu files.
 See src/Makefile.cuda for an example of a lo-level Makefile with all
 of these settings.</p>
 <p>KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
@@ -430,9 +430,9 @@ specify its additional arguments for hardware options appopriate to
 your system, as documented above.</p>
 <p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> command, or you can explicitly add a
 &#8220;kk&#8221; suffix to individual styles in your input script, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">kk</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut/kk 2.5
+</pre>
 <p>You only need to use the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> command if you
 wish to change any of its option defaults, as set by the &#8220;-k on&#8221;
 <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>.</p>
@@ -483,10 +483,10 @@ performance to bind both MPI tasks to physical cores, and threads to
 physical cores, so they do not migrate during a simulation.</p>
 <p>If you are not certain MPI tasks are being bound (check the defaults
 for your MPI installation), binding can be forced with these flags:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">OpenMPI</span> <span class="mf">1.8</span><span class="p">:</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">bind</span><span class="o">-</span><span class="n">to</span> <span class="n">socket</span> <span class="o">-</span><span class="nb">map</span><span class="o">-</span><span class="n">by</span> <span class="n">socket</span> <span class="o">./</span><span class="n">lmp_openmpi</span> <span class="o">...</span>
-<span class="n">Mvapich2</span> <span class="mf">2.0</span><span class="p">:</span> <span class="n">mpiexec</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">bind</span><span class="o">-</span><span class="n">to</span> <span class="n">socket</span> <span class="o">-</span><span class="nb">map</span><span class="o">-</span><span class="n">by</span> <span class="n">socket</span> <span class="o">./</span><span class="n">lmp_mvapich</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
+Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ...
+</pre>
 <p>For binding threads with the KOKKOS OMP option, use thread affinity
 environment variables to force binding.  With OpenMP 3.1 (gcc 4.7 or
 later, intel 12 or later) setting the environment variable
diff --git a/doc/html/accelerate_omp.html b/doc/html/accelerate_omp.html
index b77f59e8cd..8409d38821 100644
--- a/doc/html/accelerate_omp.html
+++ b/doc/html/accelerate_omp.html
@@ -141,11 +141,11 @@ one or more 16-core nodes.  More details follow.</p>
 <span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">omp</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span>       <span class="c1"># or one-line build via Make.py</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">16</span> <span class="o">&lt;</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>                         <span class="c1"># 1 MPI task, 16 threads</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">4</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>           <span class="c1"># 4 MPI tasks, 4 threads/task</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">4</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>   <span class="c1"># 8 nodes, 4 MPI tasks/node, 4 threads/task</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_mpi -sf omp -pk omp 16 &lt; in.script                         # 1 MPI task, 16 threads
+mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task
+</pre>
 <p><strong>Required hardware/software:</strong></p>
 <p>Your compiler must support the OpenMP interface.  You should have one
 or more multi-core CPUs so that multiple threads can be launched by
@@ -184,9 +184,9 @@ threads via the OMP_NUM_THREADS environment variable.</p>
 and threads/MPI task is the same.</p>
 <p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix omp</span></a> command, or you can explicitly add an
 &#8220;omp&#8221; suffix to individual styles in your input script, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">omp</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut/omp 2.5
+</pre>
 <p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package omp</span></a> command to enable the
 USER-OMP package.  When you do this you also specify how many threads
 per MPI task to use.  The command doc page explains other options and
diff --git a/doc/html/angle_charmm.html b/doc/html/angle_charmm.html
index df9e20c662..3d6bb4e8cd 100644
--- a/doc/html/angle_charmm.html
+++ b/doc/html/angle_charmm.html
@@ -137,16 +137,16 @@
 <h1>angle_style charmm/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style charmm
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span>
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span> <span class="mf">50.0</span> <span class="mf">3.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style charmm
+angle_coeff 1 300.0 107.0 50.0 3.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_class2.html b/doc/html/angle_class2.html
index 1977415a6d..1b800d6c0d 100644
--- a/doc/html/angle_class2.html
+++ b/doc/html/angle_class2.html
@@ -131,18 +131,18 @@
 <h1>angle_style class2/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style class2
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span>
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span>
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="n">bb</span> <span class="mf">10.5872</span> <span class="mf">1.0119</span> <span class="mf">1.5228</span>
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="n">ba</span> <span class="mf">3.6551</span> <span class="mf">24.895</span> <span class="mf">1.0119</span> <span class="mf">1.5228</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style class2
+angle_coeff * 75.0
+angle_coeff 1 bb 10.5872 1.0119 1.5228
+angle_coeff * ba 3.6551 24.895 1.0119 1.5228
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_cosine.html b/doc/html/angle_cosine.html
index ef3eba806d..6876620bb5 100644
--- a/doc/html/angle_cosine.html
+++ b/doc/html/angle_cosine.html
@@ -131,16 +131,16 @@
 <h1>angle_style cosine/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span>
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine
+angle_coeff * 75.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_cosine_delta.html b/doc/html/angle_cosine_delta.html
index e3dedd0a2b..fda0b0a0a5 100644
--- a/doc/html/angle_cosine_delta.html
+++ b/doc/html/angle_cosine_delta.html
@@ -131,16 +131,16 @@
 <h1>angle_style cosine/delta/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine/delta
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span>
-<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">75.0</span> <span class="mf">100.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine/delta
+angle_coeff 2*4 75.0 100.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_cosine_periodic.html b/doc/html/angle_cosine_periodic.html
index 8a358d76d2..9851cea9d4 100644
--- a/doc/html/angle_cosine_periodic.html
+++ b/doc/html/angle_cosine_periodic.html
@@ -131,16 +131,16 @@
 <h1>angle_style cosine/periodic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">periodic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine/periodic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">periodic</span>
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span> <span class="mi">1</span> <span class="mi">6</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine/periodic
+angle_coeff * 75.0 1 6
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_cosine_shift.html b/doc/html/angle_cosine_shift.html
index d9c19717bc..76d4b6dcb4 100644
--- a/doc/html/angle_cosine_shift.html
+++ b/doc/html/angle_cosine_shift.html
@@ -131,16 +131,16 @@
 <h1>angle_style cosine/shift/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine/shift
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span>
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine/shift
+angle_coeff * 10.0 45.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_cosine_shift_exp.html b/doc/html/angle_cosine_shift_exp.html
index 60dcbf1a2d..2bb957b561 100644
--- a/doc/html/angle_cosine_shift_exp.html
+++ b/doc/html/angle_cosine_shift_exp.html
@@ -131,16 +131,16 @@
 <h1>angle_style cosine/shift/exp/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine/shift/exp
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span> <span class="mf">2.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine/shift/exp
+angle_coeff * 10.0 45.0 2.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_cosine_squared.html b/doc/html/angle_cosine_squared.html
index 2797e23fda..e7f0d49193 100644
--- a/doc/html/angle_cosine_squared.html
+++ b/doc/html/angle_cosine_squared.html
@@ -131,16 +131,16 @@
 <h1>angle_style cosine/squared/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">squared</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine/squared
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">squared</span>
-<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">75.0</span> <span class="mf">100.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style cosine/squared
+angle_coeff 2*4 75.0 100.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_dipole.html b/doc/html/angle_dipole.html
index 92fec1da89..13f560db0e 100644
--- a/doc/html/angle_dipole.html
+++ b/doc/html/angle_dipole.html
@@ -131,16 +131,16 @@
 <h1>angle_style dipole/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style dipole
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span>
-<span class="n">angle_coeff</span> <span class="mi">6</span> <span class="mf">2.1</span> <span class="mf">180.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style dipole
+angle_coeff 6 2.1 180.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_fourier.html b/doc/html/angle_fourier.html
index ea480d563e..c49686daf1 100644
--- a/doc/html/angle_fourier.html
+++ b/doc/html/angle_fourier.html
@@ -131,9 +131,9 @@
 <h1>angle_style fourier/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style fourier
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
diff --git a/doc/html/angle_fourier_simple.html b/doc/html/angle_fourier_simple.html
index fb8db727a9..91c3ac4eeb 100644
--- a/doc/html/angle_fourier_simple.html
+++ b/doc/html/angle_fourier_simple.html
@@ -131,9 +131,9 @@
 <h1>angle_style fourier/simple/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span><span class="o">/</span><span class="n">simple</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style fourier/simple
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
diff --git a/doc/html/angle_harmonic.html b/doc/html/angle_harmonic.html
index 8a15d8a8d6..403ca622ca 100644
--- a/doc/html/angle_harmonic.html
+++ b/doc/html/angle_harmonic.html
@@ -137,16 +137,16 @@
 <h1>angle_style harmonic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style harmonic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style harmonic
+angle_coeff 1 300.0 107.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_quartic.html b/doc/html/angle_quartic.html
index 3cd4e9b3ca..4134601496 100644
--- a/doc/html/angle_quartic.html
+++ b/doc/html/angle_quartic.html
@@ -131,16 +131,16 @@
 <h1>angle_style quartic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style quartic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span>
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">129.1948</span> <span class="mf">56.8726</span> <span class="o">-</span><span class="mf">25.9442</span> <span class="o">-</span><span class="mf">14.2221</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style quartic
+angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/angle_sdk.html b/doc/html/angle_sdk.html
index ef4126c1f5..d94d31ccf8 100644
--- a/doc/html/angle_sdk.html
+++ b/doc/html/angle_sdk.html
@@ -128,19 +128,19 @@
 <span id="index-0"></span><h1>angle_style sdk command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span><span class="o">/</span><span class="n">omp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style sdk
+</pre>
+<pre class="literal-block">
+angle_style sdk/omp
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span>
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+angle_style sdk
+angle_coeff 1 300.0 107.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/atom_modify.html b/doc/html/atom_modify.html
index b2e3f8585d..0922591416 100644
--- a/doc/html/atom_modify.html
+++ b/doc/html/atom_modify.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>atom_modify command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+atom_modify keyword values ...
+</pre>
 <ul class="simple">
 <li>one or more keyword/value pairs may be appended</li>
 <li>keyword = <em>id</em> or <em>map</em> or <em>first</em> or <em>sort</em></li>
@@ -146,11 +146,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="nb">map</span> <span class="nb">hash</span>
-<span class="n">atom_modify</span> <span class="nb">map</span> <span class="n">array</span> <span class="n">sort</span> <span class="mi">10000</span> <span class="mf">2.0</span>
-<span class="n">atom_modify</span> <span class="n">first</span> <span class="n">colloid</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+atom_modify map hash
+atom_modify map array sort 10000 2.0
+atom_modify first colloid
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/atom_style.html b/doc/html/atom_style.html
index 2ed9ccbab0..a2cbd22a72 100644
--- a/doc/html/atom_style.html
+++ b/doc/html/atom_style.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>atom_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+atom_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or         <em>dpd</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or        <em>molecular</em> or <em>peri</em> or <em>smd</em> or <em>sphere</em> or <em>tri</em> or         <em>template</em> or <em>hybrid</em></li>
 </ul>
@@ -150,15 +150,15 @@ args = none for any style except the following
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">atomic</span>
-<span class="n">atom_style</span> <span class="n">bond</span>
-<span class="n">atom_style</span> <span class="n">full</span>
-<span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">10</span>
-<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">bond</span>
-<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">5</span>
-<span class="n">atom_style</span> <span class="n">template</span> <span class="n">myMols</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+atom_style atomic
+atom_style bond
+atom_style full
+atom_style body nparticle 2 10
+atom_style hybrid charge bond
+atom_style hybrid charge body nparticle 2 5
+atom_style template myMols
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/body.html b/doc/html/body.html
index 6a2be8aff8..5aaa8ec563 100644
--- a/doc/html/body.html
+++ b/doc/html/body.html
@@ -247,11 +247,11 @@ mentioned above, the <a class="reference internal" href="fix_rigid.html"><span c
 duplicates its functionality.</p>
 <p>The atom_style body command for this body style takes two additional
 arguments:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
-<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of sub-particles in any body in the system</span>
-<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of sub-particles in any body in the system</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+atom_style body nparticle Nmin Nmax
+Nmin = minimum # of sub-particles in any body in the system
+Nmax = maximum # of sub-particles in any body in the system
+</pre>
 <p>The Nmin and Nmax arguments are used to bound the size of data
 structures used internally by each particle.</p>
 <p>When the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command reads a data file for this
@@ -313,11 +313,11 @@ used for 2d models.  One example use of this body style is for 2d
 discrete element models, as described in <a class="reference internal" href="#fraige"><span class="std std-ref">Fraige</span></a>.  Similar to
 body style <em>nparticle</em>, the atom_style body command for this body
 style takes two additional arguments:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">rounded</span><span class="o">/</span><span class="n">polygon</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
-<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of vertices in any body in the system</span>
-<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of vertices in any body in the system</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+atom_style body rounded/polygon Nmin Nmax
+Nmin = minimum # of vertices in any body in the system
+Nmax = maximum # of vertices in any body in the system
+</pre>
 <p>The Nmin and Nmax arguments are used to bound the size of data
 structures used internally by each particle.</p>
 <p>When the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command reads a data file for this
diff --git a/doc/html/bond_class2.html b/doc/html/bond_class2.html
index 7e3e5100ec..dad9e1dba9 100644
--- a/doc/html/bond_class2.html
+++ b/doc/html/bond_class2.html
@@ -131,16 +131,16 @@
 <h1>bond_style class2/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style class2
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span>
-<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">100.0</span> <span class="mf">80.0</span> <span class="mf">80.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style class2
+bond_coeff 1 1.0 100.0 80.0 80.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/bond_fene.html b/doc/html/bond_fene.html
index 7a74e3c9ef..d836487156 100644
--- a/doc/html/bond_fene.html
+++ b/doc/html/bond_fene.html
@@ -137,16 +137,16 @@
 <h1>bond_style fene/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style fene
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span>
-<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/bond_fene_expand.html b/doc/html/bond_fene_expand.html
index e2b5ed6ad5..577a4cde04 100644
--- a/doc/html/bond_fene_expand.html
+++ b/doc/html/bond_fene_expand.html
@@ -131,16 +131,16 @@
 <h1>bond_style fene/expand/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span><span class="o">/</span><span class="n">expand</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style fene/expand
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span><span class="o">/</span><span class="n">expand</span>
-<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style fene/expand
+bond_coeff 1 30.0 1.5 1.0 1.0 0.5
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/bond_harmonic.html b/doc/html/bond_harmonic.html
index f1594a77d6..fc22160d18 100644
--- a/doc/html/bond_harmonic.html
+++ b/doc/html/bond_harmonic.html
@@ -137,16 +137,16 @@
 <h1>bond_style harmonic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style harmonic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
-<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">80.0</span> <span class="mf">1.2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style harmonic
+bond_coeff 5 80.0 1.2
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/bond_harmonic_shift.html b/doc/html/bond_harmonic_shift.html
index 91a6674537..4ab86dc316 100644
--- a/doc/html/bond_harmonic_shift.html
+++ b/doc/html/bond_harmonic_shift.html
@@ -131,16 +131,16 @@
 <h1>bond_style harmonic/shift/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style harmonic/shift
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span>
-<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">10.0</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style harmonic/shift
+bond_coeff 5 10.0 0.5 1.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/bond_harmonic_shift_cut.html b/doc/html/bond_harmonic_shift_cut.html
index c53ad2cc14..121eda2221 100644
--- a/doc/html/bond_harmonic_shift_cut.html
+++ b/doc/html/bond_harmonic_shift_cut.html
@@ -131,16 +131,16 @@
 <h1>bond_style harmonic/shift/cut/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">cut</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style harmonic/shift/cut
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">cut</span>
-<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">10.0</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style harmonic/shift/cut
+bond_coeff 5 10.0 0.5 1.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/bond_morse.html b/doc/html/bond_morse.html
index facb9a0c9c..42794978e3 100644
--- a/doc/html/bond_morse.html
+++ b/doc/html/bond_morse.html
@@ -131,16 +131,16 @@
 <h1>bond_style morse/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style morse
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span>
-<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">1.0</span> <span class="mf">2.0</span> <span class="mf">1.2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style morse
+bond_coeff 5 1.0 2.0 1.2
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/bond_nonlinear.html b/doc/html/bond_nonlinear.html
index 02540da242..ad8a574f82 100644
--- a/doc/html/bond_nonlinear.html
+++ b/doc/html/bond_nonlinear.html
@@ -131,16 +131,16 @@
 <h1>bond_style nonlinear/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">nonlinear</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style nonlinear
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">nonlinear</span>
-<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mf">100.0</span> <span class="mf">1.1</span> <span class="mf">1.4</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style nonlinear
+bond_coeff 2 100.0 1.1 1.4
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/bond_quartic.html b/doc/html/bond_quartic.html
index d2b57516a1..290a9f8055 100644
--- a/doc/html/bond_quartic.html
+++ b/doc/html/bond_quartic.html
@@ -131,16 +131,16 @@
 <h1>bond_style quartic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style quartic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span>
-<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mi">1200</span> <span class="o">-</span><span class="mf">0.55</span> <span class="mf">0.25</span> <span class="mf">1.3</span> <span class="mf">34.6878</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+bond_style quartic
+bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -184,10 +184,10 @@ to 1,1,1, as indicated as a restriction below.</p>
 <p>Note that when bonds are dumped to a file via the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command, bonds with type 0 are not included.  The
 <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command can also be used to query the
 status of broken bonds or permanently delete them, e.g.:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span>
-<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">bond</span> <span class="mi">0</span> <span class="n">remove</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+delete_bonds all stats
+delete_bonds all bond 0 remove
+</pre>
 <hr class="docutils" />
 <p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
 functionally the same as the corresponding style without the suffix.
diff --git a/doc/html/change_box.html b/doc/html/change_box.html
index fc034cbe2f..5fd817925f 100644
--- a/doc/html/change_box.html
+++ b/doc/html/change_box.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>change_box command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">parameter</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+change_box group-ID parameter args ... keyword args ...
+</pre>
 <ul class="simple">
 <li>group-ID = ID of group of atoms to (optionally) displace</li>
 <li>one or more parameter/arg pairs may be appended</li>
@@ -175,10 +175,10 @@ parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</em>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">xy</span> <span class="n">final</span> <span class="o">-</span><span class="mf">2.0</span> <span class="n">z</span> <span class="n">final</span> <span class="mf">0.0</span> <span class="mf">5.0</span> <span class="n">boundary</span> <span class="n">p</span> <span class="n">p</span> <span class="n">f</span> <span class="n">remap</span> <span class="n">units</span> <span class="n">box</span>
-<span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">remap</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
+change_box all x scale 1.1 y volume z volume remap
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -223,15 +223,15 @@ will be re-shrink-wrapped before the change_box command completes.
 Instead you could do something like this, assuming the simulation box
 is non-periodic and atoms extend from 0 to 20 in all dimensions:</p>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span>
-<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span>   <span class="c1"># this will fail to insert an atom</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span> <span class="n">boundary</span> <span class="n">f</span> <span class="n">s</span> <span class="n">s</span>
-<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span>
-<span class="n">change_box</span> <span class="n">boundary</span> <span class="n">s</span> <span class="n">s</span> <span class="n">s</span>      <span class="c1"># this will work</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+change_box all x final -10 20
+create_atoms 1 single -5 5 5   # this will fail to insert an atom
+</pre>
+<pre class="literal-block">
+change_box all x final -10 20 boundary f s s
+create_atoms 1 single -5 5 5
+change_box boundary s s s      # this will work
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">Unlike the earlier &#8220;displace_box&#8221; version of this command, atom
@@ -295,30 +295,30 @@ used following a keyword that changed the volume, which is any of the
 <em>x</em>, <em>y</em>, <em>z</em> keywords.  If the preceding keyword &#8220;key&#8221; had a <em>volume</em>
 style, then both it and the current keyword apply to the keyword
 preceding &#8220;key&#8221;.  I.e. this sequence of keywords is allowed:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+change_box all x scale 1.1 y volume z volume
+</pre>
 <p>The <em>volume</em> style changes the associated dimension so that the
 overall box volume is unchanged relative to its value before the
 preceding keyword was invoked.</p>
 <p>If the following command is used, then the z box length will shrink by
 the same 1.1 factor the x box length was increased by:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+change_box all x scale 1.1 z volume
+</pre>
 <p>If the following command is used, then the y,z box lengths will each
 shrink by sqrt(1.1) to keep the volume constant.  In this case, the
 y,z box lengths shrink so as to keep their relative aspect ratio
 constant:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span><span class="s2">&quot;x scale 1.1 y volume z volume</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+change_box all&quot;x scale 1.1 y volume z volume
+</pre>
 <p>If the following command is used, then the final box will be a factor
 of 10% larger in x and y, and a factor of 21% smaller in z, so as to
 keep the volume constant:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">y</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+change_box all x scale 1.1 z volume y scale 1.1 z volume
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">For solids or liquids, when one dimension of the box is
diff --git a/doc/html/compute.html b/doc/html/compute.html
index b4f0375d18..ec28819bbb 100644
--- a/doc/html/compute.html
+++ b/doc/html/compute.html
@@ -186,8 +186,8 @@ discussed below, it can be referenced via the following bracket
 notation, where ID is the ID of the compute:</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="21%" />
-<col width="79%" />
+<col width="23%" />
+<col width="77%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>c_ID</td>
@@ -245,11 +245,11 @@ computes for further info.</p>
 Three computes are always created, named &#8220;thermo_temp&#8221;,
 &#8220;thermo_press&#8221;, and &#8220;thermo_pe&#8221;, as if these commands had been invoked
 in the input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_temp</span> <span class="nb">all</span> <span class="n">temp</span>
-<span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
-<span class="n">compute</span> <span class="n">thermo_pe</span> <span class="nb">all</span> <span class="n">pe</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute thermo_temp all temp
+compute thermo_press all pressure thermo_temp
+compute thermo_pe all pe
+</pre>
 <p>Additional computes for other quantities are created if the thermo
 style requires it.  See the documentation for the
 <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command.</p>
diff --git a/doc/html/compute_bond_local.html b/doc/html/compute_bond_local.html
index 5bde75437f..79f34ad60f 100644
--- a/doc/html/compute_bond_local.html
+++ b/doc/html/compute_bond_local.html
@@ -177,11 +177,11 @@ For example, bond output from the <a class="reference internal" href="compute_pr
 with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
 command in a consistent way.</p>
 <p>Here is an example of how to do this:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">btype</span> <span class="n">batom1</span> <span class="n">batom2</span>
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span>
-<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all property/local btype batom1 batom2
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a local vector or local array depending on the
 number of keywords.  The length of the vector or number of rows in the
diff --git a/doc/html/compute_centro_atom.html b/doc/html/compute_centro_atom.html
index 743a69e651..5b1779546e 100644
--- a/doc/html/compute_centro_atom.html
+++ b/doc/html/compute_centro_atom.html
@@ -234,7 +234,7 @@ simulation into gold (FCC).  These were provided by Jon Zimmerman
 <span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">23.0</span>
 </pre></div>
 </div>
-<p>These values are <em>not</em> normalized by the square of the lattice
+<p>These values are *not* normalized by the square of the lattice
 parameter.  If they were, normalized values would be:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span>
 <span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">0.06</span> <span class="p">(</span><span class="mf">0.03</span> <span class="n">to</span> <span class="mf">0.075</span><span class="p">)</span>
diff --git a/doc/html/compute_dipole_chunk.html b/doc/html/compute_dipole_chunk.html
index 55452e3a0f..efedfa0512 100644
--- a/doc/html/compute_dipole_chunk.html
+++ b/doc/html/compute_dipole_chunk.html
@@ -181,11 +181,11 @@ and how they are set for each atom.  You can reset the image flags
 <p>The simplest way to output the results of the compute com/chunk
 calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
 command, for example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">dipole</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute cc1 all chunk/atom molecule
+compute myChunk all dipole/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =
diff --git a/doc/html/compute_fep.html b/doc/html/compute_fep.html
index 5a7910465c..0824a98ae4 100644
--- a/doc/html/compute_fep.html
+++ b/doc/html/compute_fep.html
@@ -164,10 +164,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">fep</span> <span class="mi">298</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">epsilon</span> <span class="mi">1</span> <span class="o">*</span> <span class="n">v_delta</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">sigma</span> <span class="mi">1</span> <span class="o">*</span> <span class="n">v_delta</span> <span class="n">volume</span> <span class="n">yes</span>
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">fep</span> <span class="mi">300</span> <span class="n">atom</span> <span class="n">charge</span> <span class="mi">2</span> <span class="n">v_delta</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
+compute 1 all fep 300 atom charge 2 v_delta
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -307,7 +307,7 @@ each, as in the 1st example above.  I &lt;= J is required.  LAMMPS sets
 the coefficients for the symmetric J,I interaction to the same
 values. A wild-card asterisk can be used in place of or in conjunction
 with the I,J arguments to set the coefficients for multiple pairs of
-atom types.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N =
+atom types.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N =
 the number of atom types, then an asterisk with no numeric values
 means all types from 1 to N.  A leading asterisk means all types from
 1 to n (inclusive).  A trailing asterisk means all types from n to N
diff --git a/doc/html/compute_gyration_chunk.html b/doc/html/compute_gyration_chunk.html
index 388ee64c04..3ec0dca379 100644
--- a/doc/html/compute_gyration_chunk.html
+++ b/doc/html/compute_gyration_chunk.html
@@ -193,11 +193,11 @@ using the <a class="reference internal" href="set.html"><span class="doc">set im
 <p>The simplest way to output the results of the compute gyration/chunk
 calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
 command, for example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute cc1 all chunk/atom molecule
+compute myChunk all gyration/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global vector if the <em>tensor</em> keyword is not
 specified and a global array if it is.  The length of the vector or
diff --git a/doc/html/compute_heat_flux.html b/doc/html/compute_heat_flux.html
index 1ef755717d..1595174920 100644
--- a/doc/html/compute_heat_flux.html
+++ b/doc/html/compute_heat_flux.html
@@ -237,29 +237,30 @@ energy/area/time <a class="reference internal" href="units.html"><span class="do
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Sample LAMMPS input script for thermal conductivity of solid Ar</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>units       real
+<pre class="literal-block">
+units       real
 variable    T equal 70
 variable    V equal vol
 variable    dt equal 4.0
 variable    p equal 200     # correlation length
 variable    s equal 10      # sample interval
 variable    d equal $p*$s   # dump interval
-</pre></div>
-</div>
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># convert from LAMMPS real units to SI</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable    kB equal 1.3806504e-23    # [J/K] Boltzmann
+<pre class="literal-block">
+variable    kB equal 1.3806504e-23    # [J/K] Boltzmann
 variable    kCal2J equal 4186.0/6.02214e23
 variable    A2m equal 1.0e-10
 variable    fs2s equal 1.0e-15
 variable    convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
-</pre></div>
-</div>
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>dimension    3
+<pre class="literal-block">
+dimension    3
 boundary     p p p
 lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
 region       box block 0 4 0 4 0 4
@@ -270,8 +271,7 @@ pair_style   lj/cut 13.0
 pair_coeff   * * 0.2381 3.405
 timestep     ${dt}
 thermo            $d
-</pre></div>
-</div>
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span>
 </pre></div>
 </div>
@@ -287,7 +287,8 @@ run          8000
 <span class="c1">#fix         NVE all nve</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>reset_timestep 0
+<pre class="literal-block">
+reset_timestep 0
 compute      myKE all ke/atom
 compute      myPE all pe/atom
 compute      myStress all stress/atom NULL virial
@@ -305,9 +306,8 @@ thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
 run          100000
 variable     k equal (v_k11+v_k22+v_k33)/3.0
 variable     ndens equal count(all)/vol
-print        &quot;average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3&quot;
-</pre></div>
-</div>
+print        &quot;average conductivity: $k[W/mK] &#64; $T K, ${ndens} /A^3&quot;
+</pre>
 </div>
 </div>
 
diff --git a/doc/html/compute_inertia_chunk.html b/doc/html/compute_inertia_chunk.html
index b93575cfc5..d718f90f47 100644
--- a/doc/html/compute_inertia_chunk.html
+++ b/doc/html/compute_inertia_chunk.html
@@ -177,11 +177,11 @@ how they are set for each atom.  You can reset the image flags
 <p>The simplest way to output the results of the compute inertia/chunk
 calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
 command, for example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">inertia</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute cc1 all chunk/atom molecule
+compute myChunk all inertia/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =
diff --git a/doc/html/compute_ke_atom_eff.html b/doc/html/compute_ke_atom_eff.html
index 00b22b9256..6a017dc79b 100644
--- a/doc/html/compute_ke_atom_eff.html
+++ b/doc/html/compute_ke_atom_eff.html
@@ -168,11 +168,11 @@ eFF.</p>
 thermodynamic output by using the <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>
 command, as shown in the following example:</p>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>         <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
-<span class="n">thermo_style</span>    <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
-<span class="n">thermo_modify</span>   <span class="n">temp</span> <span class="n">effTemp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute         effTemp all temp/eff
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+</pre>
 <p>The value of the kinetic energy will be 0.0 for atoms (nuclei or
 electrons) not in the specified compute group.</p>
 <p><strong>Output info:</strong></p>
diff --git a/doc/html/compute_ke_eff.html b/doc/html/compute_ke_eff.html
index b614a9d25b..ff0e0b4e68 100644
--- a/doc/html/compute_ke_eff.html
+++ b/doc/html/compute_ke_eff.html
@@ -169,11 +169,11 @@ the <a class="reference internal" href="compute_temp_eff.html"><span class="doc"
 printed with thermodynamic output by using the
 <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
 example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>         <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
-<span class="n">thermo_style</span>    <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
-<span class="n">thermo_modify</span>   <span class="n">temp</span> <span class="n">effTemp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute         effTemp all temp/eff
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+</pre>
 <p>See <a class="reference internal" href="compute_temp_eff.html"><span class="doc">compute temp/eff</span></a>.</p>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global scalar (the KE).  This value can be
diff --git a/doc/html/compute_modify.html b/doc/html/compute_modify.html
index 8c31af05b2..6556686bb9 100644
--- a/doc/html/compute_modify.html
+++ b/doc/html/compute_modify.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>compute_modify command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">compute</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute_modify compute-ID keyword value ...
+</pre>
 <ul class="simple">
 <li>compute-ID = ID of the compute to modify</li>
 <li>one or more keyword/value pairs may be listed</li>
@@ -145,10 +145,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">myTemp</span> <span class="n">extra</span> <span class="mi">0</span>
-<span class="n">compute_modify</span> <span class="n">newtemp</span> <span class="n">dynamic</span> <span class="n">yes</span> <span class="n">extra</span> <span class="mi">600</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute_modify myTemp extra 0
+compute_modify newtemp dynamic yes extra 600
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/compute_pe_atom.html b/doc/html/compute_pe_atom.html
index fafebf006b..b5de90dfdb 100644
--- a/doc/html/compute_pe_atom.html
+++ b/doc/html/compute_pe_atom.html
@@ -185,11 +185,11 @@ command.</p>
 <p>As an example of per-atom potential energy compared to total potential
 energy, these lines in an input script should yield the same result
 in the last 2 columns of thermo output:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>              <span class="n">peratom</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span>
-<span class="n">compute</span>              <span class="n">pe</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">pe</span> <span class="n">c_pe</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute              peratom all pe/atom
+compute              pe all reduce sum c_peratom
+thermo_style        custom step temp etotal press pe c_pe
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The per-atom energy does not any Lennard-Jones tail corrections
diff --git a/doc/html/compute_pressure.html b/doc/html/compute_pressure.html
index eb4ac742f3..1d117a4f5e 100644
--- a/doc/html/compute_pressure.html
+++ b/doc/html/compute_pressure.html
@@ -141,10 +141,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">NULL</span> <span class="n">pair</span> <span class="n">bond</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all pressure thermo_temp
+compute 1 all pressure NULL pair bond
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -196,9 +196,9 @@ degrees-of-freedom divided by d = dimensionality, where the DOF value
 is calcluated by the temperature compute.  See the various <a class="reference internal" href="compute.html"><span class="doc">compute temperature</span></a> styles for details.</p>
 <p>A compute of this style with the ID of &#8220;thermo_press&#8221; is created when
 LAMMPS starts up, as if this command were in the input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute thermo_press all pressure thermo_temp
+</pre>
 <p>where &#8220;thermo_temp&#8221; is the ID of a similarly defined compute of style
 &#8220;temp&#8221;.  See the &#8220;thermo_style&#8221; command for more details.</p>
 <hr class="docutils" />
diff --git a/doc/html/compute_property_atom.html b/doc/html/compute_property_atom.html
index 9fdc98e352..f91b814e33 100644
--- a/doc/html/compute_property_atom.html
+++ b/doc/html/compute_property_atom.html
@@ -136,25 +136,25 @@
 <li>property/atom = style name of this compute command</li>
 <li>input = one or more atom attributes</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">possible</span> <span class="n">attributes</span> <span class="o">=</span> <span class="nb">id</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">proc</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span>
-                   <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">xs</span><span class="p">,</span> <span class="n">ys</span><span class="p">,</span> <span class="n">zs</span><span class="p">,</span> <span class="n">xu</span><span class="p">,</span> <span class="n">yu</span><span class="p">,</span> <span class="n">zu</span><span class="p">,</span> <span class="n">ix</span><span class="p">,</span> <span class="n">iy</span><span class="p">,</span> <span class="n">iz</span><span class="p">,</span>
-                   <span class="n">vx</span><span class="p">,</span> <span class="n">vy</span><span class="p">,</span> <span class="n">vz</span><span class="p">,</span> <span class="n">fx</span><span class="p">,</span> <span class="n">fy</span><span class="p">,</span> <span class="n">fz</span><span class="p">,</span>
-                      <span class="n">q</span><span class="p">,</span> <span class="n">mux</span><span class="p">,</span> <span class="n">muy</span><span class="p">,</span> <span class="n">muz</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span>
-                      <span class="n">radius</span><span class="p">,</span> <span class="n">diameter</span><span class="p">,</span> <span class="n">omegax</span><span class="p">,</span> <span class="n">omegay</span><span class="p">,</span> <span class="n">omegaz</span><span class="p">,</span>
-                   <span class="n">angmomx</span><span class="p">,</span> <span class="n">angmomy</span><span class="p">,</span> <span class="n">angmomz</span><span class="p">,</span>
-                   <span class="n">shapex</span><span class="p">,</span><span class="n">shapey</span><span class="p">,</span> <span class="n">shapez</span><span class="p">,</span>
-                   <span class="n">quatw</span><span class="p">,</span> <span class="n">quati</span><span class="p">,</span> <span class="n">quatj</span><span class="p">,</span> <span class="n">quatk</span><span class="p">,</span> <span class="n">tqx</span><span class="p">,</span> <span class="n">tqy</span><span class="p">,</span> <span class="n">tqz</span><span class="p">,</span>
-                   <span class="n">end1x</span><span class="p">,</span> <span class="n">end1y</span><span class="p">,</span> <span class="n">end1z</span><span class="p">,</span> <span class="n">end2x</span><span class="p">,</span> <span class="n">end2y</span><span class="p">,</span> <span class="n">end2z</span><span class="p">,</span>
-                   <span class="n">corner1x</span><span class="p">,</span> <span class="n">corner1y</span><span class="p">,</span> <span class="n">corner1z</span><span class="p">,</span>
-                   <span class="n">corner2x</span><span class="p">,</span> <span class="n">corner2y</span><span class="p">,</span> <span class="n">corner2z</span><span class="p">,</span>
-                   <span class="n">corner3x</span><span class="p">,</span> <span class="n">corner3y</span><span class="p">,</span> <span class="n">corner3z</span><span class="p">,</span>
-                   <span class="n">nbonds</span><span class="p">,</span>
-                      <span class="n">vfrac</span><span class="p">,</span> <span class="n">s0</span><span class="p">,</span>
-                   <span class="n">spin</span><span class="p">,</span> <span class="n">eradius</span><span class="p">,</span> <span class="n">ervel</span><span class="p">,</span> <span class="n">erforce</span><span class="p">,</span>
-                      <span class="n">rho</span><span class="p">,</span> <span class="n">drho</span><span class="p">,</span> <span class="n">e</span><span class="p">,</span> <span class="n">de</span><span class="p">,</span> <span class="n">cv</span><span class="p">,</span>
-                      <span class="n">i_name</span><span class="p">,</span> <span class="n">d_name</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+possible attributes = id, mol, proc, type, mass,
+                   x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+                   vx, vy, vz, fx, fy, fz,
+                      q, mux, muy, muz, mu,
+                      radius, diameter, omegax, omegay, omegaz,
+                   angmomx, angmomy, angmomz,
+                   shapex,shapey, shapez,
+                   quatw, quati, quatj, quatk, tqx, tqy, tqz,
+                   end1x, end1y, end1z, end2x, end2y, end2z,
+                   corner1x, corner1y, corner1z,
+                   corner2x, corner2y, corner2z,
+                   corner3x, corner3y, corner3z,
+                   nbonds,
+                      vfrac, s0,
+                   spin, eradius, ervel, erforce,
+                      rho, drho, e, de, cv,
+                      i_name, d_name
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">id</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span>
 <span class="n">mol</span> <span class="o">=</span> <span class="n">molecule</span> <span class="n">ID</span>
 <span class="n">proc</span> <span class="o">=</span> <span class="n">ID</span> <span class="n">of</span> <span class="n">processor</span> <span class="n">that</span> <span class="n">owns</span> <span class="n">atom</span>
diff --git a/doc/html/compute_property_chunk.html b/doc/html/compute_property_chunk.html
index 2012335a47..7cf73b649d 100644
--- a/doc/html/compute_property_chunk.html
+++ b/doc/html/compute_property_chunk.html
@@ -192,12 +192,12 @@ will be in unitless reduced units (0-1).</p>
 <p>The simplest way to output the results of the compute property/chunk
 calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
 command, for example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
-<span class="n">compute</span> <span class="n">myChunk1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span> <span class="n">count</span>
-<span class="n">compute</span> <span class="n">myChunk2</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk1</span> <span class="n">c_myChunk2</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute cc1 all chunk/atom molecule
+compute myChunk1 all property/chunk cc1 count
+compute myChunk2 all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global vector or global array depending on
 the number of input values.  The length of the vector or number of
diff --git a/doc/html/compute_reduce.html b/doc/html/compute_reduce.html
index 519bc9ff3c..56a155c53a 100644
--- a/doc/html/compute_reduce.html
+++ b/doc/html/compute_reduce.html
@@ -148,14 +148,14 @@
 <li>one or more inputs can be listed</li>
 <li>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
-<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+c_ID = per-atom or local vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = per-atom or local vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
+v_name = per-atom vector calculated by an atom-style variable with name
+</pre>
 <ul class="simple">
 <li>zero or more keyword/args pairs may be appended</li>
 <li>keyword = <em>replace</em></li>
@@ -168,13 +168,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_force</span>
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">reduce</span><span class="o">/</span><span class="n">region</span> <span class="n">subbox</span> <span class="nb">sum</span> <span class="n">c_force</span>
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">c_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">f_ave</span> <span class="n">v_myKE</span>
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">c_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">f_ave</span> <span class="n">v_myKE</span>
-<span class="n">compute</span> <span class="mi">3</span> <span class="n">fluid</span> <span class="n">reduce</span> <span class="nb">max</span> <span class="n">c_index</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_index</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_dist</span> <span class="n">replace</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">replace</span> <span class="mi">2</span> <span class="mi">3</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all reduce sum c_force
+compute 1 all reduce/region subbox sum c_force
+compute 2 all reduce min c_press[2] f_ave v_myKE
+compute 2 all reduce min c_press[*] f_ave v_myKE
+compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -211,7 +211,7 @@ component) or can be the result of a <a class="reference internal" href="compute
 <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.</p>
 <p>Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
+specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
 &#8220;m*n&#8221;.  If N = the size of the vector (for <em>mode</em> = scalar) or the
 number of columns in the array (for <em>mode</em> = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -222,18 +222,18 @@ means all indices from m to n (inclusive).</p>
 had been listed one by one.  E.g. these 2 compute reduce commands are
 equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
 command creates a per-atom array with 6 columns:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
-                         <span class="n">myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute myPress all stress/atom NULL
+compute 2 all reduce min myPress[*]
+compute 2 all reduce min myPress[1] myPress[2] myPress[3] &amp;
+                         myPress[4] myPress[5] myPress[6]
+</pre>
 <hr class="docutils" />
 <p>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
 self-explanatory.  Note that other atom attributes can be used as
 inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
 an input value from that compute.</p>
-<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
+<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
 previously defined in the input script.  Computes can generate
 per-atom or local quantities.  See the individual
 <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> doc page for details.  If no bracketed integer
@@ -243,7 +243,7 @@ by the compute is used.  Users can also write code for their own
 compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.  See the
 discussion above for how I can be specified with a wildcard asterisk
 to effectively specify multiple values.</p>
-<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
+<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
 previously defined in the input script.  Fixes can generate per-atom
 or local quantities.  See the individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> doc page for
 details.  Note that some fixes only produce their values on certain
@@ -254,7 +254,7 @@ integer is appended, the Ith column of the array calculated by the fix
 is used.  Users can also write code for their own fix style and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.  See the discussion above for how
 I can be specified with a wildcard asterisk to effectively specify
 multiple values.</p>
-<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
+<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
 been previously defined in the input script.  It must be an
 <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>.  Atom-style variables can
 reference thermodynamic keywords and various per-atom attributes, or
@@ -271,12 +271,12 @@ Then, instead of performing a min/max on the <em>vec1</em> input vector, the
 stored index is used to select the Nth element of the <em>vec1</em> vector.</p>
 <p>Thus, for example, if you wish to use this compute to find the bond
 with maximum stretch, you can do it as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span>
-<span class="n">compute</span>      <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span>
-<span class="n">compute</span>      <span class="mi">3</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">max</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_2</span> <span class="n">replace</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">replace</span> <span class="mi">2</span> <span class="mi">3</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all property/local batom1 batom2
+compute      2 all bond/local dist
+compute      3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
+thermo_style custom step temp c_3[1] c_3[2] c_3[3]
+</pre>
 <p>The first two input values in the compute reduce command are vectors
 with the IDs of the 2 atoms in each bond, using the <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a> command.  The last input
 value is bond distance, using the <a class="reference internal" href="compute_bond_local.html"><span class="doc">compute bond/local</span></a> command.  Instead of taking the
diff --git a/doc/html/compute_rigid_local.html b/doc/html/compute_rigid_local.html
index 154d01a909..7f7d5630fa 100644
--- a/doc/html/compute_rigid_local.html
+++ b/doc/html/compute_rigid_local.html
@@ -202,10 +202,10 @@ there will be no consistent ordering of the entries within the local
 vector or array from one timestep to the next.</p>
 <p>Here is an example of how to use this compute to dump rigid body info
 to a file:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rigid</span><span class="o">/</span><span class="n">local</span> <span class="n">myRigid</span> <span class="n">mol</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span>
-<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all rigid/local myRigid mol x y z fx fy fz
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]
+</pre>
 <hr class="docutils" />
 <p>This section explains the rigid body attributes that can be specified.</p>
 <p>The <em>id</em> attribute is the atomID of the atom which owns the rigid body, which is
diff --git a/doc/html/compute_saed.html b/doc/html/compute_saed.html
index 5a40350a0d..bc78dd1378 100644
--- a/doc/html/compute_saed.html
+++ b/doc/html/compute_saed.html
@@ -157,14 +157,14 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="n">dR_Ewald</span> <span class="mf">0.01</span> <span class="n">c</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">0.5</span>
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Ni</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="n">c</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="n">manual</span> <span class="n">echo</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_1</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
-<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_2</span> <span class="n">file</span> <span class="n">Ni_000</span><span class="o">.</span><span class="n">saed</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
+</pre>
+<pre class="literal-block">
+fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+fix saed/vtk 1 1 1 c_2 file Ni_000.saed
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -193,7 +193,7 @@ shown in the 2D diagram below.</p>
                      height="auto"
                      alt=""/>
                 </a><p>For a mesh defined by the simulation domain, a rectilinear grid is
-constructed with spacing <em>c</em><a href="#id1"><span class="problematic" id="id2">*</span></a>inv(A) along each reciprocal lattice
+constructed with spacing <em>c</em>*inv(A) along each reciprocal lattice
 axis. Where A are the vectors corresponding to the edges of the
 simulation cell. If one or two directions has non-periodic boundary
 conditions, then the spacing in these directions is defined from the
diff --git a/doc/html/compute_sna_atom.html b/doc/html/compute_sna_atom.html
index e61705f25a..930f66a12e 100644
--- a/doc/html/compute_sna_atom.html
+++ b/doc/html/compute_sna_atom.html
@@ -134,11 +134,11 @@
 <h1>compute snav/atom command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">sna</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-<span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">snad</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-<span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">snav</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
 <li>sna/atom = style name of this compute command</li>
@@ -276,22 +276,22 @@ corresponding to a particular bispectrum component.  The total number
 of columns and the identities of the bispectrum component contained in
 each column depend on the values of <em>twojmax</em> and <em>diagonal</em>, as
 described by the following piece of python code:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">j1</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">twojmax</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
-    <span class="k">if</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">2</span><span class="p">):</span>
-        <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span>
-    <span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">1</span><span class="p">):</span>
-        <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="mi">2</span><span class="o">*</span><span class="n">j1</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
-            <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
-    <span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">0</span><span class="p">):</span>
-        <span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
-            <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
-                <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
-    <span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">3</span><span class="p">):</span>
-        <span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
-            <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
-                <span class="k">if</span> <span class="p">(</span><span class="n">j</span><span class="o">&gt;=</span><span class="n">j1</span><span class="p">):</span> <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+for j1 in range(0,twojmax+1):
+    if(diagonal==2):
+        print j1/2.,j1/2.,j1/2.
+    elif(diagonal==1):
+        for j in range(0,min(twojmax,2*j1)+1,2):
+            print j1/2.,j1/2.,j/2.
+    elif(diagonal==0):
+        for j2 in range(0,j1+1):
+            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
+                print j1/2.,j2/2.,j/2.
+    elif(diagonal==3):
+        for j2 in range(0,j1+1):
+            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
+                if (j&gt;=j1): print j1/2.,j2/2.,j/2.
+</pre>
 <p>Compute <em>snad/atom</em> evaluates a per-atom array. The columns are
 arranged into <em>ntypes</em> blocks, listed in order of atom type <em>I</em>.  Each
 block contains three sub-blocks corresponding to the <em>x</em>, <em>y</em>, and <em>z</em>
diff --git a/doc/html/compute_stress_atom.html b/doc/html/compute_stress_atom.html
index e99ece1705..c4704bbbbd 100644
--- a/doc/html/compute_stress_atom.html
+++ b/doc/html/compute_stress_atom.html
@@ -234,12 +234,12 @@ d = dimension and V is the volume of the system, the result should be
 -P, where P is the total pressure of the system.</p>
 <p>These lines in an input script for a 3d system should yield that
 result.  I.e. the last 2 columns of thermo output will be the same:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>              <span class="n">peratom</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
-<span class="n">compute</span>              <span class="n">p</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
-<span class="n">variable</span>     <span class="n">press</span> <span class="n">equal</span> <span class="o">-</span><span class="p">(</span><span class="n">c_p</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">c_p</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">+</span><span class="n">c_p</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span><span class="o">/</span><span class="p">(</span><span class="mi">3</span><span class="o">*</span><span class="n">vol</span><span class="p">)</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">v_press</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute              peratom all stress/atom NULL
+compute              p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
+variable     press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
+thermo_style        custom step temp etotal press v_press
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a per-atom array with 6 columns, which can be
 accessed by indices 1-6 by any command that uses per-atom values from
diff --git a/doc/html/compute_temp_cs.html b/doc/html/compute_temp_cs.html
index 4751726a56..81927952be 100644
--- a/doc/html/compute_temp_cs.html
+++ b/doc/html/compute_temp_cs.html
@@ -140,10 +140,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">oxygen_c</span><span class="o">-</span><span class="n">s</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">O_core</span> <span class="n">O_shell</span>
-<span class="n">compute</span> <span class="n">core_shells</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">cores</span> <span class="n">shells</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute oxygen_c-s all temp/cs O_core O_shell
+compute core_shells all temp/cs cores shells
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/compute_temp_eff.html b/doc/html/compute_temp_eff.html
index 4dadf7de39..d11ad256a8 100644
--- a/doc/html/compute_temp_eff.html
+++ b/doc/html/compute_temp_eff.html
@@ -170,11 +170,11 @@ reported by LAMMPS in the thermodynamic quantities reported via the
 <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
 example:</p>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>         <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
-<span class="n">thermo_style</span>    <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
-<span class="n">thermo_modify</span>   <span class="n">temp</span> <span class="n">effTemp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute         effTemp all temp/eff
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+</pre>
 <p>A 6-component kinetic energy tensor is also calculated by this compute
 for use in the computation of a pressure tensor.  The formula for the
 components of the tensor is the same as the above formula, except that
diff --git a/doc/html/compute_ti.html b/doc/html/compute_ti.html
index 5701aeee75..8d6198637d 100644
--- a/doc/html/compute_ti.html
+++ b/doc/html/compute_ti.html
@@ -154,10 +154,10 @@ pair style args = atype v_name1 v_name2
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ti</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span> <span class="n">v_lj</span> <span class="n">v_dlj</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mi">2</span> <span class="n">v_c</span> <span class="n">v_dc</span> <span class="n">kspace</span> <span class="mi">1</span> <span class="n">v_ks</span> <span class="n">v_dks</span>
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ti</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">v_lj</span> <span class="n">v_dlj</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="o">*</span> <span class="n">v_c</span> <span class="n">v_dc</span> <span class="n">kspace</span> <span class="o">*</span> <span class="n">v_ks</span> <span class="n">v_dks</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
+compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -192,7 +192,7 @@ with respect to <em>lambda</em>.</p>
 numeric values can be used, as in the 1st example above.  Or a
 wildcard asterisk can be used in place of or in conjunction with the
 <em>atype</em> argument to select multiple atom types.  This takes the form
-&#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the number of atom types, then
+&#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the number of atom types, then
 an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
 asterisk means all types from n to N (inclusive).  A middle asterisk
diff --git a/doc/html/compute_voronoi_atom.html b/doc/html/compute_voronoi_atom.html
index 630ee3bac6..ed4cd612a1 100644
--- a/doc/html/compute_voronoi_atom.html
+++ b/doc/html/compute_voronoi_atom.html
@@ -158,14 +158,14 @@ or <em>face_threshold</em> or <em>neighbors</em> or <em>peratom</em></li>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span>
-<span class="n">compute</span> <span class="mi">2</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">surface</span> <span class="n">matrix</span>
-<span class="n">compute</span> <span class="mi">3</span><span class="n">b</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span> <span class="n">v_r</span>
-<span class="n">compute</span> <span class="mi">4</span> <span class="n">solute</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">only_group</span>
-<span class="n">compute</span> <span class="mi">5</span> <span class="n">defects</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">occupation</span>
-<span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all voronoi/atom
+compute 2 precipitate voronoi/atom surface matrix
+compute 3b precipitate voronoi/atom radius v_r
+compute 4 solute voronoi/atom only_group
+compute 5 defects voronoi/atom occupation
+compute 6 all voronoi/atom neighbors yes
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -199,11 +199,11 @@ can be obtained by running a &#8220;reduce sum&#8221; compute on c_2[3]</p>
 <p>If the <em>radius</em> keyword is specified with an atom style variable as
 the argument, a poly-disperse Voronoi tessellation is
 performed. Examples for radius variables are</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">r1</span> <span class="n">atom</span> <span class="p">(</span><span class="nb">type</span><span class="o">==</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="mf">0.1</span><span class="o">+</span><span class="p">(</span><span class="nb">type</span><span class="o">==</span><span class="mi">2</span><span class="p">)</span><span class="o">*</span><span class="mf">0.4</span>
-<span class="n">compute</span> <span class="n">radius</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span>
-<span class="n">variable</span> <span class="n">r2</span> <span class="n">atom</span> <span class="n">c_radius</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable r1 atom (type==1)*0.1+(type==2)*0.4
+compute radius all property/atom radius
+variable r2 atom c_radius
+</pre>
 <p>Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms
 and 0.4 units for type 2 atoms, and v_r2 accesses the radius property
 present in atom_style sphere for granular models.</p>
@@ -247,10 +247,10 @@ uses local values from a compute as input.  See <a class="reference internal" hr
 options. More specifically, the array can be accessed by a
 <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command to write a file containing
 all the Voronoi neighbors in a system:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
-<span class="n">dump</span> <span class="n">d2</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1</span> <span class="n">dump</span><span class="o">.</span><span class="n">neighbors</span> <span class="n">index</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 6 all voronoi/atom neighbors yes
+dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
+</pre>
 <p>If the <em>face_threshold</em> keyword is used, then only faces
 with areas greater than the threshold are stored.</p>
 <hr class="docutils" />
diff --git a/doc/html/compute_xrd.html b/doc/html/compute_xrd.html
index b16569ab91..caeec6cf77 100644
--- a/doc/html/compute_xrd.html
+++ b/doc/html/compute_xrd.html
@@ -159,10 +159,10 @@
 <span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">xrd</span> <span class="mf">1.541838</span> <span class="n">Al</span> <span class="n">O</span> <span class="mi">2</span><span class="n">Theta</span> <span class="mi">10</span> <span class="mi">100</span> <span class="n">c</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="n">LP</span> <span class="mi">1</span> <span class="n">manual</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span><span class="o">/</span><span class="n">weight</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.087</span> <span class="mf">0.87</span> <span class="mi">250</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">file</span> <span class="n">Rad2Theta</span><span class="o">.</span><span class="n">xrd</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span><span class="o">/</span><span class="n">weight</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">250</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">file</span> <span class="n">Deg2Theta</span><span class="o">.</span><span class="n">xrd</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
+fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -196,7 +196,7 @@ shown in the 2D diagram below.</p>
                      height="auto"
                      alt=""/>
                 </a><p>For a mesh defined by the simulation domain, a rectilinear grid is
-constructed with spacing <em>c</em><a href="#id1"><span class="problematic" id="id2">*</span></a>inv(A) along each reciprocal lattice
+constructed with spacing <em>c</em>*inv(A) along each reciprocal lattice
 axis. Where A are the vectors corresponding to the edges of the
 simulation cell. If one or two directions has non-periodic boundary
 conditions, then the spacing in these directions is defined from the
diff --git a/doc/html/create_atoms.html b/doc/html/create_atoms.html
index 03785a73f4..3786038236 100644
--- a/doc/html/create_atoms.html
+++ b/doc/html/create_atoms.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>create_atoms command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_atoms</span> <span class="nb">type</span> <span class="n">style</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+create_atoms type style args keyword values ...
+</pre>
 <ul class="simple">
 <li>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</li>
 <li>style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></li>
@@ -172,12 +172,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span>
-<span class="n">create_atoms</span> <span class="mi">3</span> <span class="n">region</span> <span class="n">regsphere</span> <span class="n">basis</span> <span class="mi">2</span> <span class="mi">3</span>
-<span class="n">create_atoms</span> <span class="mi">3</span> <span class="n">single</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">5</span>
-<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">var</span> <span class="n">v</span> <span class="nb">set</span> <span class="n">x</span> <span class="n">xpos</span> <span class="nb">set</span> <span class="n">y</span> <span class="n">ypos</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+create_atoms 1 box
+create_atoms 3 region regsphere basis 2 3
+create_atoms 3 single 0 0 5
+create_atoms 1 box var v set x xpos set y ypos
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -328,19 +328,19 @@ the sinusoid would appear to be &#8220;smoother&#8221;.  Also note the use of th
 &#8220;xlat&#8221; and &#8220;ylat&#8221; <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> keywords which
 converts lattice spacings to distance.  Click on the image for a
 larger version.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable        x equal 100
+<pre class="literal-block">
+variable        x equal 100
 variable        y equal 25
 lattice              hex 0.8442
 region               box block 0 $x 0 $y -0.5 0.5
-create_box   1 box
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span>        <span class="n">xx</span> <span class="n">equal</span> <span class="mf">0.0</span>
-<span class="n">variable</span>        <span class="n">yy</span> <span class="n">equal</span> <span class="mf">0.0</span>
-<span class="n">variable</span>        <span class="n">v</span> <span class="n">equal</span> <span class="s2">&quot;(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) &gt; 0.0&quot;</span>
-<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">var</span> <span class="n">v</span> <span class="nb">set</span> <span class="n">x</span> <span class="n">xx</span> <span class="nb">set</span> <span class="n">y</span> <span class="n">yy</span>
-</pre></div>
-</div>
+create_box  1 box
+</pre>
+<pre class="literal-block">
+variable        xx equal 0.0
+variable        yy equal 0.0
+variable        v equal &quot;(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) &gt; 0.0&quot;
+create_atoms        1 box var v set x xx set y yy
+</pre>
 <a class=""
                data-lightbox="group-default"
                href="_images/sinusoid.jpg"
diff --git a/doc/html/delete_bonds.html b/doc/html/delete_bonds.html
index 18e52920f4..b10ff2515d 100644
--- a/doc/html/delete_bonds.html
+++ b/doc/html/delete_bonds.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>delete_bonds command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">arg</span> <span class="n">keyword</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+delete_bonds group-ID style arg keyword ...
+</pre>
 <ul>
 <li><p class="first">group-ID = group ID</p>
 </li>
@@ -157,12 +157,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="n">frozen</span> <span class="n">multi</span> <span class="n">remove</span>
-<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">4</span> <span class="n">special</span>
-<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">bond</span> <span class="mi">0</span><span class="o">*</span><span class="mi">3</span> <span class="n">special</span>
-<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+delete_bonds frozen multi remove
+delete_bonds all atom 4 special
+delete_bonds all bond 0*3 special
+delete_bonds all stats
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -183,7 +183,7 @@ be an integer from 0 to N, where N is the number of relevant types
 (atom types, bond types, etc).  A value of 0 is only relevant for
 style <em>bond</em>; see details below.  In all cases, a wildcard asterisk
 can be used in place of or in conjunction with the <em>type</em> argument to
-specify a range of types.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
+specify a range of types.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
 &#8220;m*n&#8221;.  If N = the number of types, then an asterisk with no numeric
 values means all types from 0 to N.  A leading asterisk means all
 types from 0 to n (inclusive).  A trailing asterisk means all types
diff --git a/doc/html/dihedral_charmm.html b/doc/html/dihedral_charmm.html
index 80c9b47043..9794ca050e 100644
--- a/doc/html/dihedral_charmm.html
+++ b/doc/html/dihedral_charmm.html
@@ -137,18 +137,18 @@
 <h1>dihedral_style charmm/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">charmm</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style charmm
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">charmm</span>
-<span class="n">dihedral_coeff</span>  <span class="mi">1</span> <span class="mf">0.2</span> <span class="mi">1</span> <span class="mi">180</span> <span class="mf">1.0</span>
-<span class="n">dihedral_coeff</span>  <span class="mi">2</span> <span class="mf">1.8</span> <span class="mi">1</span>   <span class="mi">0</span> <span class="mf">1.0</span>
-<span class="n">dihedral_coeff</span>  <span class="mi">1</span> <span class="mf">3.1</span> <span class="mi">2</span> <span class="mi">180</span> <span class="mf">0.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style charmm
+dihedral_coeff  1 0.2 1 180 1.0
+dihedral_coeff  2 1.8 1   0 1.0
+dihedral_coeff  1 3.1 2 180 0.5
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_class2.html b/doc/html/dihedral_class2.html
index 40f10f1e74..e9556733e2 100644
--- a/doc/html/dihedral_class2.html
+++ b/doc/html/dihedral_class2.html
@@ -131,21 +131,21 @@
 <h1>dihedral_style class2/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">class2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style class2
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">class2</span>
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">75</span> <span class="mi">100</span> <span class="mi">70</span> <span class="mi">80</span> <span class="mi">60</span>
-<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">mbt</span> <span class="mf">3.5945</span> <span class="mf">0.1704</span> <span class="o">-</span><span class="mf">0.5490</span> <span class="mf">1.5228</span>
-<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">ebt</span> <span class="mf">0.3417</span> <span class="mf">0.3264</span> <span class="o">-</span><span class="mf">0.9036</span> <span class="mf">0.1368</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.8080</span> <span class="mf">1.0119</span> <span class="mf">1.1010</span>
-<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="n">at</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.1850</span> <span class="o">-</span><span class="mf">0.7963</span> <span class="o">-</span><span class="mf">2.0220</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.3991</span> <span class="mf">110.2453</span> <span class="mf">105.1270</span>
-<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">aat</span> <span class="o">-</span><span class="mf">13.5271</span> <span class="mf">110.2453</span> <span class="mf">105.1270</span>
-<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">bb13</span> <span class="mf">0.0</span> <span class="mf">1.0119</span> <span class="mf">1.1010</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style class2
+dihedral_coeff 1 100 75 100 70 80 60
+dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
+dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
+dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
+dihedral_coeff * aat -13.5271 110.2453 105.1270
+dihedral_coeff * bb13 0.0 1.0119 1.1010
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_cosine_shift_exp.html b/doc/html/dihedral_cosine_shift_exp.html
index b6e718bce8..1cc73331be 100644
--- a/doc/html/dihedral_cosine_shift_exp.html
+++ b/doc/html/dihedral_cosine_shift_exp.html
@@ -131,16 +131,16 @@
 <h1>dihedral_style cosine/shift/exp/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style cosine/shift/exp
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">10.0</span> <span class="mf">45.0</span> <span class="mf">2.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style cosine/shift/exp
+dihedral_coeff 1 10.0 45.0 2.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_fourier.html b/doc/html/dihedral_fourier.html
index 0feb09036b..1470ba7346 100644
--- a/doc/html/dihedral_fourier.html
+++ b/doc/html/dihedral_fourier.html
@@ -131,16 +131,16 @@
 <h1>dihedral_style fourier/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">fourier</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style fourier
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">fourier</span>
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">3</span> <span class="o">-</span><span class="mf">0.846200</span> <span class="mi">3</span> <span class="mf">0.0</span> <span class="mf">7.578800</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mf">0.138000</span> <span class="mi">2</span> <span class="o">-</span><span class="mf">180.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style fourier
+dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_harmonic.html b/doc/html/dihedral_harmonic.html
index 0c37cf26cc..2a8ed8a6f7 100644
--- a/doc/html/dihedral_harmonic.html
+++ b/doc/html/dihedral_harmonic.html
@@ -134,16 +134,16 @@
 <h1>dihedral_style harmonic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">harmonic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style harmonic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">harmonic</span>
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="mi">1</span> <span class="mi">2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style harmonic
+dihedral_coeff 1 80.0 1 2
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_helix.html b/doc/html/dihedral_helix.html
index 14a06fac03..b8d5653099 100644
--- a/doc/html/dihedral_helix.html
+++ b/doc/html/dihedral_helix.html
@@ -131,16 +131,16 @@
 <h1>dihedral_style helix/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">helix</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style helix
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">helix</span>
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="mf">100.0</span> <span class="mf">40.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style helix
+dihedral_coeff 1 80.0 100.0 40.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_multi_harmonic.html b/doc/html/dihedral_multi_harmonic.html
index c8f3b7b886..ec192b670e 100644
--- a/doc/html/dihedral_multi_harmonic.html
+++ b/doc/html/dihedral_multi_harmonic.html
@@ -131,16 +131,16 @@
 <h1>dihedral_style multi/harmonic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style multi/harmonic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span>
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style multi/harmonic
+dihedral_coeff 1 20 20 20 20 20
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_nharmonic.html b/doc/html/dihedral_nharmonic.html
index eb35a50a58..eb59b45627 100644
--- a/doc/html/dihedral_nharmonic.html
+++ b/doc/html/dihedral_nharmonic.html
@@ -131,16 +131,16 @@
 <h1>dihedral_style nharmonic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">nharmonic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style nharmonic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">nharmonic</span>
-<span class="n">dihedral_coeff</span> <span class="mi">3</span> <span class="mf">10.0</span> <span class="mf">20.0</span> <span class="mf">30.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style nharmonic
+dihedral_coeff 3 10.0 20.0 30.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_opls.html b/doc/html/dihedral_opls.html
index 2f73119b58..fd7c9f1e4f 100644
--- a/doc/html/dihedral_opls.html
+++ b/doc/html/dihedral_opls.html
@@ -137,18 +137,18 @@
 <h1>dihedral_style opls/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">opls</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style opls
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">opls</span>
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">1.740</span> <span class="o">-</span><span class="mf">0.157</span> <span class="mf">0.279</span> <span class="mf">0.00</span>   <span class="c1"># CT-CT-CT-CT</span>
-<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="mf">0.000</span> <span class="mf">0.000</span> <span class="mf">0.366</span> <span class="mf">0.000</span>   <span class="c1"># CT-CT-CT-HC</span>
-<span class="n">dihedral_coeff</span> <span class="mi">3</span> <span class="mf">0.000</span> <span class="mf">0.000</span> <span class="mf">0.318</span> <span class="mf">0.000</span>   <span class="c1"># HC-CT-CT-HC</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style opls
+dihedral_coeff 1 1.740 -0.157 0.279 0.00   # CT-CT-CT-CT
+dihedral_coeff 2 0.000 0.000 0.366 0.000   # CT-CT-CT-HC
+dihedral_coeff 3 0.000 0.000 0.318 0.000   # HC-CT-CT-HC
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_quadratic.html b/doc/html/dihedral_quadratic.html
index 3cc35b63dd..3b490ae5d6 100644
--- a/doc/html/dihedral_quadratic.html
+++ b/doc/html/dihedral_quadratic.html
@@ -131,16 +131,16 @@
 <h1>dihedral_style quadratic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">quadratic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style quadratic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">quadratic</span>
-<span class="n">dihedral_coeff</span> <span class="mf">100.0</span> <span class="mf">80.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style quadratic
+dihedral_coeff 100.0 80.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_spherical.html b/doc/html/dihedral_spherical.html
index 1d9a9f7402..3e38d2d8ca 100644
--- a/doc/html/dihedral_spherical.html
+++ b/doc/html/dihedral_spherical.html
@@ -128,18 +128,18 @@
 <span id="index-0"></span><h1>dihedral_style spherical command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">spherical</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style spherical
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">1</span>  <span class="mf">286.1</span>  <span class="mi">1</span> <span class="mi">124</span> <span class="mi">1</span>   <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span>   <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span>
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">3</span>  <span class="mf">286.1</span>  <span class="mi">1</span> <span class="mi">114</span> <span class="mi">1</span>   <span class="mi">1</span> <span class="mi">90</span>  <span class="mi">0</span>    <span class="mi">1</span> <span class="mf">90.0</span>  <span class="mi">0</span>  <span class="o">&amp;</span>
-                    <span class="mf">17.3</span>   <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span>   <span class="mi">1</span> <span class="mi">158</span> <span class="mi">1</span>    <span class="mi">0</span> <span class="mf">0.0</span>   <span class="mi">0</span>  <span class="o">&amp;</span>
-                    <span class="mf">15.1</span>   <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span>   <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span>    <span class="mi">1</span> <span class="mf">167.3</span> <span class="mi">1</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_coeff 1 1  286.1  1 124 1   1 90.0 0   1 90.0 0
+dihedral_coeff 1 3  286.1  1 114 1   1 90  0    1 90.0  0  &amp;
+                    17.3   0 0.0 0   1 158 1    0 0.0   0  &amp;
+                    15.1   0 0.0 0   0 0.0 0    1 167.3 1
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_style.html b/doc/html/dihedral_style.html
index 9b21cd4640..c19d4a1a2e 100644
--- a/doc/html/dihedral_style.html
+++ b/doc/html/dihedral_style.html
@@ -128,20 +128,20 @@
 <span id="index-0"></span><h1>dihedral_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">style</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style style
+</pre>
 <ul class="simple">
 <li>style = <em>none</em> or <em>hybrid</em> or <em>charmm</em> or <em>class2</em> or <em>harmonic</em> or <em>helix</em> or         <em>multi/harmonic</em> or <em>opls</em></li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">harmonic</span>
-<span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span>
-<span class="n">dihedral_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">charmm</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style harmonic
+dihedral_style multi/harmonic
+dihedral_style hybrid harmonic charmm
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/dihedral_table.html b/doc/html/dihedral_table.html
index d967731158..fe30f6ab11 100644
--- a/doc/html/dihedral_table.html
+++ b/doc/html/dihedral_table.html
@@ -131,9 +131,9 @@
 <h1>dihedral_style table/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">Ntable</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style table style Ntable
+</pre>
 <ul class="simple">
 <li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
 <li>Ntable = size of the internal lookup table</li>
@@ -141,12 +141,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">spline</span> <span class="mi">400</span>
-<span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">DIH_TABLE1</span>
-<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">DIH_TABLE2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dihedral_style table spline 400
+dihedral_style table linear 1000
+dihedral_coeff 1 file.table DIH_TABLE1
+dihedral_coeff 2 file.table DIH_TABLE2
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -185,23 +185,23 @@ or blank lines.</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Table of the potential and its negative derivative</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DIH_TABLE1</span>                   <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">the</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
-<span class="n">N</span> <span class="mi">30</span> <span class="n">DEGREES</span>                 <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">NOF</span><span class="p">,</span> <span class="n">DEGREES</span><span class="p">,</span> <span class="n">RADIANS</span><span class="p">,</span> <span class="n">CHECKU</span><span class="o">/</span><span class="n">F</span><span class="p">)</span>
-                             <span class="p">(</span><span class="n">blank</span> <span class="n">line</span><span class="p">)</span>
-<span class="mi">1</span> <span class="o">-</span><span class="mf">168.0</span> <span class="o">-</span><span class="mf">1.40351172223</span> <span class="mf">0.0423346818422</span>
-<span class="mi">2</span> <span class="o">-</span><span class="mf">156.0</span> <span class="o">-</span><span class="mf">1.70447981034</span> <span class="mf">0.00811786522531</span>
-<span class="mi">3</span> <span class="o">-</span><span class="mf">144.0</span> <span class="o">-</span><span class="mf">1.62956100432</span> <span class="o">-</span><span class="mf">0.0184129719987</span>
-<span class="o">...</span>
-<span class="mi">30</span> <span class="mf">180.0</span> <span class="o">-</span><span class="mf">0.707106781187</span> <span class="mf">0.0719306095245</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+DIH_TABLE1                   (keyword is the first text on line)
+N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
+                             (blank line)
+1 -168.0 -1.40351172223 0.0423346818422
+2 -156.0 -1.70447981034 0.00811786522531
+3 -144.0 -1.62956100432 -0.0184129719987
+...
+30 180.0 -0.707106781187 0.0719306095245
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Example 2: table of the potential. Forces omitted</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DIH_TABLE2</span>
-<span class="n">N</span> <span class="mi">30</span> <span class="n">NOF</span> <span class="n">CHECKU</span> <span class="n">testU</span><span class="o">.</span><span class="n">dat</span> <span class="n">CHECKF</span> <span class="n">testF</span><span class="o">.</span><span class="n">dat</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+DIH_TABLE2
+N 30 NOF CHECKU testU.dat CHECKF testF.dat
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="o">-</span><span class="mf">168.0</span> <span class="o">-</span><span class="mf">1.40351172223</span>
 <span class="mi">2</span> <span class="o">-</span><span class="mf">156.0</span> <span class="o">-</span><span class="mf">1.70447981034</span>
 <span class="mi">3</span> <span class="o">-</span><span class="mf">144.0</span> <span class="o">-</span><span class="mf">1.62956100432</span>
diff --git a/doc/html/dump.html b/doc/html/dump.html
index b47465bc33..d76697dbba 100644
--- a/doc/html/dump.html
+++ b/doc/html/dump.html
@@ -239,19 +239,19 @@ i_name = per-atom integer vector with name, managed by fix property/atom
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span>
-<span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">mpiio</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span><span class="o">.</span><span class="n">mpiio</span>
-<span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">gz</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span><span class="o">.</span><span class="n">gz</span>
-<span class="n">dump</span> <span class="mi">2</span> <span class="n">subgroup</span> <span class="n">atom</span> <span class="mi">50</span> <span class="n">dump</span><span class="o">.</span><span class="n">run</span><span class="o">.</span><span class="n">bin</span>
-<span class="n">dump</span> <span class="mi">2</span> <span class="n">subgroup</span> <span class="n">atom</span> <span class="mi">50</span> <span class="n">dump</span><span class="o">.</span><span class="n">run</span><span class="o">.</span><span class="n">mpiio</span><span class="o">.</span><span class="n">bin</span>
-<span class="n">dump</span> <span class="mi">4</span><span class="n">a</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">myforce</span><span class="o">.*</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">x</span> <span class="n">y</span> <span class="n">vx</span> <span class="n">fx</span>
-<span class="n">dump</span> <span class="mi">4</span><span class="n">b</span> <span class="n">flow</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.%.</span><span class="n">myforce</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myF</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">v_ke</span>
-<span class="n">dump</span> <span class="mi">4</span><span class="n">b</span> <span class="n">flow</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.%.</span><span class="n">myforce</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myF</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">v_ke</span>
-<span class="n">dump</span> <span class="mi">2</span> <span class="n">inner</span> <span class="n">cfg</span> <span class="mi">10</span> <span class="n">dump</span><span class="o">.</span><span class="n">snap</span><span class="o">.*.</span><span class="n">cfg</span> <span class="n">mass</span> <span class="nb">type</span> <span class="n">xs</span> <span class="n">ys</span> <span class="n">zs</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span>
-<span class="n">dump</span> <span class="n">snap</span> <span class="nb">all</span> <span class="n">cfg</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">config</span><span class="o">.*.</span><span class="n">cfg</span> <span class="n">mass</span> <span class="nb">type</span> <span class="n">xs</span> <span class="n">ys</span> <span class="n">zs</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_Stress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">xtc</span> <span class="mi">1000</span> <span class="n">file</span><span class="o">.</span><span class="n">xtc</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dump myDump all atom 100 dump.atom
+dump myDump all atom/mpiio 100 dump.atom.mpiio
+dump myDump all atom/gz 100 dump.atom.gz
+dump 2 subgroup atom 50 dump.run.bin
+dump 2 subgroup atom 50 dump.run.mpiio.bin
+dump 4a all custom 100 dump.myforce.* id type x y vx fx
+dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
+dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
+dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
+dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
+dump 1 all xtc 1000 file.xtc
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -347,12 +347,12 @@ or m = shrink wrapped with a minimum value.  See the
 bounding box which encloses the triclinic simulation box is output,
 along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
 formatted as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ITEM</span><span class="p">:</span> <span class="n">BOX</span> <span class="n">BOUNDS</span> <span class="n">xy</span> <span class="n">xz</span> <span class="n">yz</span> <span class="n">xx</span> <span class="n">yy</span> <span class="n">zz</span>
-<span class="n">xlo_bound</span> <span class="n">xhi_bound</span> <span class="n">xy</span>
-<span class="n">ylo_bound</span> <span class="n">yhi_bound</span> <span class="n">xz</span>
-<span class="n">zlo_bound</span> <span class="n">zhi_bound</span> <span class="n">yz</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+ITEM: BOX BOUNDS xy xz yz xx yy zz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz
+</pre>
 <p>The presence of the text &#8220;xy xz yz&#8221; in the ITEM line indicates that
 the 3 tilt factors will be included on each of the 3 following lines.
 This bounding box is convenient for many visualization programs.  The
@@ -541,7 +541,7 @@ styles.</p>
 reference values from a compute or fix, like the <em>custom</em>, <em>cfg</em>, or
 <em>local</em> styles, the bracketed index I can be specified using a
 wildcard asterisk with the index to effectively specify multiple
-values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the
+values.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the
 size of the vector (for <em>mode</em> = scalar) or the number of columns in
 the array (for <em>mode</em> = vector), then an asterisk with no numeric
 values means all indices from 1 to N.  A leading asterisk means all
@@ -552,12 +552,12 @@ from m to n (inclusive).</p>
 had been listed one by one.  E.g. these 2 dump commands are
 equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
 command creates a per-atom array with 6 columns:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
-<span class="n">dump</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="nb">id</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
-<span class="n">dump</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="nb">id</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
-                                  <span class="n">myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute myPress all stress/atom NULL
+dump 2 all custom 100 tmp.dump id myPress[*]
+dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &amp;
+                                  myPress[4] myPress[5] myPress[6]
+</pre>
 <hr class="docutils" />
 <p>This section explains the local attributes that can be specified as
 part of the <em>local</em> style.</p>
@@ -598,11 +598,11 @@ be specified with a wildcard asterisk to effectively specify multiple
 values.</p>
 <p>Here is an example of how to dump bond info for a system, including
 the distance and energy of each bond:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span> <span class="n">btype</span>
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span>
-<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all property/local batom1 batom2 btype
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
+</pre>
 <hr class="docutils" />
 <p>This section explains the atom attributes that can be specified as
 part of the <em>custom</em> and <em>cfg</em> styles.</p>
diff --git a/doc/html/dump_custom_vtk.html b/doc/html/dump_custom_vtk.html
index 8bd838f671..b77890476a 100644
--- a/doc/html/dump_custom_vtk.html
+++ b/doc/html/dump_custom_vtk.html
@@ -182,15 +182,15 @@ v_name = per-atom vector calculated by an atom-style variable with name
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">dmpvtk</span> <span class="nb">all</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.</span><span class="n">myforce</span><span class="o">.</span><span class="n">vtk</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">vx</span> <span class="n">fx</span>
-<span class="n">dump</span> <span class="n">dmpvtp</span> <span class="n">flow</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.%.</span><span class="n">displace</span><span class="o">.</span><span class="n">vtp</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">v_ke</span>
-<span class="n">dump</span> <span class="n">e_data</span> <span class="nb">all</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.</span><span class="n">vtu</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">spin</span> <span class="n">eradius</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">eforce</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
+dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
+dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
+</pre>
 <p>The style <em>custom/vtk</em> is similar to the <a class="reference internal" href="dump.html"><span class="doc">custom</span></a> style but
 uses the VTK library to write data to VTK simple legacy or XML format
 depending on the filename extension specified. This can be either
-<a href="#id1"><span class="problematic" id="id2">**</span></a>.vtk* for the legacy format or <a href="#id3"><span class="problematic" id="id4">**</span></a>.vtp* and <a href="#id5"><span class="problematic" id="id6">**</span></a>.vtu*, respectively,
+<em>*.vtk</em> for the legacy format or <em>*.vtp</em> and <em>*.vtu</em>, respectively,
 for the XML format; see the <a class="reference external" href="http://www.vtk.org/VTK/img/file-formats.pdf">VTK homepage</a> for a detailed
 description of these formats.  Since this naming convention conflicts
 with the way binary output is usually specified (see below),
diff --git a/doc/html/dump_image.html b/doc/html/dump_image.html
index 2df937c169..356893b5d4 100644
--- a/doc/html/dump_image.html
+++ b/doc/html/dump_image.html
@@ -206,14 +206,14 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">d0</span> <span class="nb">all</span> <span class="n">image</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.*.</span><span class="n">jpg</span> <span class="nb">type</span> <span class="nb">type</span>
-<span class="n">dump</span> <span class="n">d1</span> <span class="n">mobile</span> <span class="n">image</span> <span class="mi">500</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">png</span> <span class="n">element</span> <span class="n">element</span> <span class="n">ssao</span> <span class="n">yes</span> <span class="mi">4539</span> <span class="mf">0.6</span>
-<span class="n">dump</span> <span class="n">d2</span> <span class="nb">all</span> <span class="n">image</span> <span class="mi">200</span> <span class="n">img</span><span class="o">-*.</span><span class="n">ppm</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">zoom</span> <span class="mf">2.5</span> <span class="n">adiam</span> <span class="mf">1.5</span> <span class="n">size</span> <span class="mi">1280</span> <span class="mi">720</span>
-<span class="n">dump</span> <span class="n">m0</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">1000</span> <span class="n">movie</span><span class="o">.</span><span class="n">mpg</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">size</span> <span class="mi">640</span> <span class="mi">480</span>
-<span class="n">dump</span> <span class="n">m1</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">1000</span> <span class="n">movie</span><span class="o">.</span><span class="n">avi</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">size</span> <span class="mi">640</span> <span class="mi">480</span>
-<span class="n">dump</span> <span class="n">m2</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">100</span> <span class="n">movie</span><span class="o">.</span><span class="n">m4v</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">zoom</span> <span class="mf">1.8</span> <span class="n">adiam</span> <span class="n">v_value</span> <span class="n">size</span> <span class="mi">1280</span> <span class="mi">720</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dump d0 all image 100 dump.*.jpg type type
+dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
+dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
+dump m0 all movie 1000 movie.mpg type type size 640 480
+dump m1 all movie 1000 movie.avi type type size 640 480
+dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -310,7 +310,7 @@ atoms rendered in the image.  They can be any atom attribute defined
 for the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command, including <em>type</em> and
 <em>element</em>.  This includes per-atom quantities calculated by a
 <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix.html"><span class="doc">fix</span></a>, or <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>,
-which are prefixed by &#8220;<a href="#id9"><span class="problematic" id="id10">c_</span></a>&#8221;, &#8220;<a href="#id11"><span class="problematic" id="id12">f_</span></a>&#8221;, or &#8220;<a href="#id13"><span class="problematic" id="id14">v_</span></a>&#8221; respectively.  Note that the
+which are prefixed by &#8220;c_&#8221;, &#8220;f_&#8221;, or &#8220;v_&#8221; respectively.  Note that the
 <em>diameter</em> setting can be overridden with a numeric value applied to
 all atoms by the optional <em>adiam</em> keyword.</p>
 <p>If <em>type</em> is specified for the <em>color</em> setting, then the color of each
@@ -545,9 +545,9 @@ plane perpendicular to the view vector implied by the <em>theta</em> and
 <em>pni</em> values, and which is also in the plane defined by the view
 vector and user-specified up vector.  Thus this internal vector is
 computed from the user-specified <em>up</em> vector as</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">up_internal</span> <span class="o">=</span> <span class="n">view</span> <span class="n">cross</span> <span class="p">(</span><span class="n">up</span> <span class="n">cross</span> <span class="n">view</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+up_internal = view cross (up cross view)
+</pre>
 <p>This means the only restriction on the specified <em>up</em> vector is that
 it cannot be parallel to the <em>view</em> vector, implied by the <em>theta</em> and
 <em>phi</em> values.</p>
@@ -619,10 +619,10 @@ MPEG or other movie file you can use:</p>
 </ol>
 </li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">convert</span> <span class="o">*.</span><span class="n">jpg</span> <span class="n">foo</span><span class="o">.</span><span class="n">gif</span>
-<span class="o">%</span> <span class="n">convert</span> <span class="o">-</span><span class="n">loop</span> <span class="mi">1</span> <span class="o">*.</span><span class="n">ppm</span> <span class="n">foo</span><span class="o">.</span><span class="n">mpg</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+% convert *.jpg foo.gif
+% convert -loop 1 *.ppm foo.mpg
+</pre>
 <p>Animated GIF files from ImageMagick are unoptimized. You can use a
 program like gifsicle to optimize and massively shrink them.
 MPEG files created by ImageMagick are in MPEG-1 format with rather
@@ -635,7 +635,7 @@ inefficient compression and low quality.</p>
 </ul>
 <p>Select &#8220;Open Image Sequence&#8221; under the File menu Load the images into
 QuickTime to animate them Select &#8220;Export&#8221; under the File menu Save the
-movie as a QuickTime movie (<a href="#id7"><span class="problematic" id="id8">*</span></a>.mov) or in another format.  QuickTime
+movie as a QuickTime movie (*.mov) or in another format.  QuickTime
 can generate very high quality and efficiently compressed movie
 files. Some of the supported formats require to buy a license and some
 are not readable on all platforms until specific runtime libraries are
@@ -648,10 +648,10 @@ installed.</p>
 </ul>
 <p>FFmpeg is a command line tool that is available on many platforms and
 allows extremely flexible encoding and decoding of movies.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cat</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">jpg</span> <span class="o">|</span> <span class="n">ffmpeg</span> <span class="o">-</span><span class="n">y</span> <span class="o">-</span><span class="n">f</span> <span class="n">image2pipe</span> <span class="o">-</span><span class="n">c</span><span class="p">:</span><span class="n">v</span> <span class="n">mjpeg</span> <span class="o">-</span><span class="n">i</span> <span class="o">-</span> <span class="o">-</span><span class="n">b</span><span class="p">:</span><span class="n">v</span> <span class="mi">2000</span><span class="n">k</span> <span class="n">movie</span><span class="o">.</span><span class="n">m4v</span>
-<span class="n">cat</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">ppm</span> <span class="o">|</span> <span class="n">ffmpeg</span> <span class="o">-</span><span class="n">y</span> <span class="o">-</span><span class="n">f</span> <span class="n">image2pipe</span> <span class="o">-</span><span class="n">c</span><span class="p">:</span><span class="n">v</span> <span class="n">ppm</span> <span class="o">-</span><span class="n">i</span> <span class="o">-</span> <span class="o">-</span><span class="n">b</span><span class="p">:</span><span class="n">v</span> <span class="mi">2400</span><span class="n">k</span> <span class="n">movie</span><span class="o">.</span><span class="n">avi</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
+cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
+</pre>
 <p>Frontends for FFmpeg exist for multiple platforms. For more
 information see the <a class="reference external" href="http://www.ffmpeg.org/">FFmpeg homepage</a></p>
 <hr class="docutils" />
@@ -678,9 +678,9 @@ variety of file formats and decoders.</li>
 <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza/doc/animate.html">animate tool</a>,
 which works directly on a series of image files.</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">a</span> <span class="o">=</span> <span class="n">animate</span><span class="p">(</span><span class="s2">&quot;foo*.jpg&quot;</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+a = animate(&quot;foo*.jpg&quot;)
+</pre>
 <ul class="simple">
 <li>d) QuickTime and other Windows- or MacOS-based media players can
 obviously play movie files directly. Similarly for corresponding tools
diff --git a/doc/html/dump_modify.html b/doc/html/dump_modify.html
index 492ef0a5f5..08afa5c7c6 100644
--- a/doc/html/dump_modify.html
+++ b/doc/html/dump_modify.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>dump_modify command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump_modify</span> <span class="n">dump</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dump_modify dump-ID keyword values ...
+</pre>
 <ul class="simple">
 <li>dump-ID = ID of dump to modify</li>
 <li>one or more keyword/value pairs may be appended</li>
@@ -228,16 +228,16 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="n">line</span> <span class="s2">&quot;</span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%20.15g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2">&quot;</span> <span class="n">scale</span> <span class="n">yes</span>
-<span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="nb">float</span> <span class="o">%</span><span class="mf">20.15</span><span class="n">g</span> <span class="n">scale</span> <span class="n">yes</span>
-<span class="n">dump_modify</span> <span class="n">myDump</span> <span class="n">image</span> <span class="n">yes</span> <span class="n">scale</span> <span class="n">no</span> <span class="n">flush</span> <span class="n">yes</span>
-<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">region</span> <span class="n">mySphere</span> <span class="n">thresh</span> <span class="n">x</span> <span class="o">&lt;</span> <span class="mf">0.0</span> <span class="n">thresh</span> <span class="n">epair</span> <span class="o">&gt;=</span> <span class="mf">3.2</span>
-<span class="n">dump_modify</span> <span class="n">xtcdump</span> <span class="n">precision</span> <span class="mi">10000</span> <span class="n">sfactor</span> <span class="mf">0.1</span>
-<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="mi">1000</span> <span class="n">nfile</span> <span class="mi">20</span>
-<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_myVar</span>
-<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">amap</span> <span class="nb">min</span> <span class="nb">max</span> <span class="n">cf</span> <span class="mf">0.0</span> <span class="mi">3</span> <span class="nb">min</span> <span class="n">green</span> <span class="mf">0.5</span> <span class="n">yellow</span> <span class="nb">max</span> <span class="n">blue</span> <span class="n">boxcolor</span> <span class="n">red</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dump_modify 1 format line &quot;%d %d %20.15g %g %g&quot; scale yes
+dump_modify 1 format float %20.15g scale yes
+dump_modify myDump image yes scale no flush yes
+dump_modify 1 region mySphere thresh x &lt; 0.0 thresh epair &gt;= 3.2
+dump_modify xtcdump precision 10000 sfactor 0.1
+dump_modify 1 every 1000 nfile 20
+dump_modify 1 every v_myVar
+dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -318,19 +318,19 @@ to the dump file.  The <em>every</em> keyword cannot be used with the dump
 <em>dcd</em> style.</p>
 <p>For example, the following commands will
 write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span>     <span class="n">s</span> <span class="n">equal</span> <span class="n">logfreq</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
-<span class="n">dump</span>         <span class="mi">1</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span>
-<span class="n">dump_modify</span>  <span class="mi">1</span> <span class="n">every</span> <span class="n">v_s</span> <span class="n">first</span> <span class="n">yes</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable     s equal logfreq(10,3,10)
+dump         1 all atom 100 tmp.dump
+dump_modify 1 every v_s first yes
+</pre>
 <p>The following commands would write snapshots at the timesteps listed
 in file tmp.times:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span>        <span class="n">f</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">times</span>
-<span class="n">variable</span>     <span class="n">s</span> <span class="n">equal</span> <span class="nb">next</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-<span class="n">dump</span>         <span class="mi">1</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span>
-<span class="n">dump_modify</span>  <span class="mi">1</span> <span class="n">every</span> <span class="n">v_s</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable        f file tmp.times
+variable     s equal next(f)
+dump         1 all atom 100 tmp.dump
+dump_modify 1 every v_s
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">When using a file-style variable with the <em>every</em> keyword, the
@@ -406,11 +406,11 @@ an integer and you wish it to appear in the text dump file as a
 (large) integer, then you need to use an appropriate format.  For
 example, these commands:</p>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>     <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span>
-<span class="n">dump</span>        <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">bonds</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-<span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="s2">&quot;</span><span class="si">%d</span><span class="s2"> </span><span class="si">%0.0f</span><span class="s2"> </span><span class="si">%0.0f</span><span class="s2">&quot;</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute     1 all property/local batom1 batom2
+dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
+dump_modify 1 format &quot;%d %0.0f %0.0f&quot;
+</pre>
 <p>will output the two atom IDs for atoms in each bond as integers.  If
 the dump_modify command were omitted, they would appear as
 floating-point values, assuming they were large integers (more than 6
@@ -566,7 +566,7 @@ atoms of each type will be drawn in the image.</p>
 <p>The specified <em>type</em> should be an integer from 1 to Ntypes = the
 number of atom types.  A wildcard asterisk can be used in place of or
 in conjunction with the <em>type</em> argument to specify a range of atom
-types.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the
+types.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the
 number of atom types, then an asterisk with no numeric values means
 all types from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A trailing asterisk means all types from n to N
@@ -689,15 +689,15 @@ color map without having to specify where all the bin boundaries are.</p>
 atoms in individual molecules with a different color.  See the
 examples/pour/in.pour.2d.molecule input script for an example of how
 this is used.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable        colors string &amp;
+<pre class="literal-block">
+variable        colors string &amp;
                 &quot;red green blue yellow white &amp;
                 purple pink orange lime gray&quot;
 variable     mol atom mol%10
 dump         1 all image 250 image.*.jpg v_mol type &amp;
              zoom 1.6 adiam 1.5
-dump_modify  1 pad 5 amap 0 10 sa 1 10 ${colors}
-</pre></div>
-</div>
+dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
+</pre>
 <p>In this case, 10 colors are defined, and molecule IDs are
 mapped to one of the colors, even if there are 1000s of molecules.</p>
 <hr class="docutils" />
@@ -711,7 +711,7 @@ set the color that bonds of each type will be drawn in the image.</p>
 <p>The specified <em>type</em> should be an integer from 1 to Nbondtypes = the
 number of bond types.  A wildcard asterisk can be used in place of or
 in conjunction with the <em>type</em> argument to specify a range of bond
-types.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the
+types.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the
 number of bond types, then an asterisk with no numeric values means
 all types from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A trailing asterisk means all types from n to N
diff --git a/doc/html/fix.html b/doc/html/fix.html
index 885ad1653b..cc8435af47 100644
--- a/doc/html/fix.html
+++ b/doc/html/fix.html
@@ -210,8 +210,8 @@ discussed below, it can be referenced via the following bracket
 notation, where ID is the ID of the fix:</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="21%" />
-<col width="79%" />
+<col width="23%" />
+<col width="77%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>f_ID</td>
diff --git a/doc/html/fix_adapt_fep.html b/doc/html/fix_adapt_fep.html
index 51d29b8b76..908ef5b395 100644
--- a/doc/html/fix_adapt_fep.html
+++ b/doc/html/fix_adapt_fep.html
@@ -170,12 +170,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">v_prefactor</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="mi">2</span><span class="o">*</span> <span class="mi">3</span> <span class="n">v_prefactor</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">epsilon</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_scale1</span> <span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="n">scale</span> <span class="mi">3</span> <span class="mi">3</span> <span class="n">v_scale2</span> <span class="n">scale</span> <span class="n">yes</span> <span class="n">reset</span> <span class="n">yes</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">10</span> <span class="n">atom</span> <span class="n">diameter</span> <span class="mi">1</span> <span class="n">v_size</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor
+fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor
+fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
+fix 1 all adapt/fep 10 atom diameter 1 v_size
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -307,7 +307,7 @@ each, as in the 1st example above.  I &lt;= J is required.  LAMMPS sets
 the coefficients for the symmetric J,I interaction to the same values.</p>
 <p>A wild-card asterisk can be used in place of or in conjunction with
 the I,J arguments to set the coefficients for multiple pairs of atom
-types.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the
+types.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the
 number of atom types, then an asterisk with no numeric values means
 all types from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A trailing asterisk means all types from n to N
@@ -333,10 +333,10 @@ details.</p>
 <p>For example, these commands would change the prefactor coefficient of
 the <a class="reference internal" href="pair_soft.html"><span class="doc">pair_style soft</span></a> potential from 10.0 to 30.0 in a
 linear fashion over the course of a simulation:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">prefactor</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mi">30</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_prefactor</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable prefactor equal ramp(10,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+</pre>
 <hr class="docutils" />
 <p>The <em>kspace</em> keyword used the specified variable as a scale factor on
 the energy, forces, virial calculated by whatever K-Space solver is
@@ -369,16 +369,14 @@ constant).</p>
 <p>For example, these commands would shrink the diameter of all granular
 particles in the &#8220;center&#8221; group from 1.0 to 0.1 in a linear fashion
 over the course of a 1000-step simulation:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">size</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span><span class="mf">0.1</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">center</span> <span class="n">adapt</span> <span class="mi">10</span> <span class="n">atom</span> <span class="n">diameter</span> <span class="o">*</span> <span class="n">v_size</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable size equal ramp(1.0,0.1)
+fix 1 center adapt 10 atom diameter * v_size
+</pre>
 <p>For <a class="reference internal" href="run_style.html"><span class="doc">rRESPA time integration</span></a>, this fix changes
 parameters on the outermost rRESPA level.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_addtorque.html b/doc/html/fix_addtorque.html
index 8926210c55..2cc2a8b678 100644
--- a/doc/html/fix_addtorque.html
+++ b/doc/html/fix_addtorque.html
@@ -140,10 +140,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">kick</span> <span class="n">bead</span> <span class="n">addtorque</span> <span class="mf">2.0</span> <span class="mf">3.0</span> <span class="mf">5.0</span>
-<span class="n">fix</span> <span class="n">kick</span> <span class="n">bead</span> <span class="n">addtorque</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">v_oscillate</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix kick bead addtorque 2.0 3.0 5.0
+fix kick bead addtorque 0.0 0.0 v_oscillate
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -166,10 +166,8 @@ torque component.</p>
 functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
 keywords for the simulation box parameters and timestep and elapsed
 time.  Thus it is easy to specify a time-dependent torque.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the potential &#8220;energy&#8221; inferred by the added forces to the
diff --git a/doc/html/fix_atc.html b/doc/html/fix_atc.html
index 2714ede1fe..d295f3cc18 100644
--- a/doc/html/fix_atc.html
+++ b/doc/html/fix_atc.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix atc command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="o">&lt;</span><span class="n">fixID</span><span class="o">&gt;</span> <span class="o">&lt;</span><span class="n">group</span><span class="o">&gt;</span> <span class="n">atc</span> <span class="o">&lt;</span><span class="nb">type</span><span class="o">&gt;</span> <span class="o">&lt;</span><span class="n">parameter_file</span><span class="o">&gt;</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix &lt;fixID&gt; &lt;group&gt; atc &lt;type&gt; &lt;parameter_file&gt;
+</pre>
 <ul class="simple">
 <li>fixID = name of fix</li>
 <li>group = name of group fix is to be applied</li>
@@ -148,12 +148,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">thermal</span> <span class="n">Ar_thermal</span><span class="o">.</span><span class="n">dat</span>
-<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">two_temperature</span> <span class="n">Ar_ttm</span><span class="o">.</span><span class="n">mat</span>
-<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">hardy</span>
-<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">field</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix AtC internal atc thermal Ar_thermal.dat
+fix AtC internal atc two_temperature Ar_ttm.mat
+fix AtC internal atc hardy
+fix AtC internal atc field
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -163,31 +163,31 @@
  <span class="c1"># ... commands to create and initialize the MD system</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># initial fix to designate coupling type and group to apply it to</span>
-<span class="c1"># tag group physics material_file</span>
-<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">thermal</span> <span class="n">Ar_thermal</span><span class="o">.</span><span class="n">mat</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create a uniform 12 x 2 x 2 mesh that covers region contain the group</span>
-<span class="c1"># nx ny nz region periodicity</span>
-<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">mesh</span> <span class="n">create</span> <span class="mi">12</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">mdRegion</span> <span class="n">f</span> <span class="n">p</span> <span class="n">p</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># specify the control method for the type of coupling</span>
-<span class="c1"># physics control_type</span>
-<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">thermal</span> <span class="n">control</span> <span class="n">flux</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># specify the initial values for the empirical field &quot;temperature&quot;</span>
-<span class="c1"># field node_group value</span>
-<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">initial</span> <span class="n">temperature</span> <span class="nb">all</span> <span class="mi">30</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create an output stream for nodal fields</span>
-<span class="c1"># filename output_frequency</span>
-<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">output</span> <span class="n">atc_fe_output</span> <span class="mi">100</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+# initial fix to designate coupling type and group to apply it to
+# tag group physics material_file
+fix AtC internal atc thermal Ar_thermal.mat
+</pre>
+<pre class="literal-block">
+# create a uniform 12 x 2 x 2 mesh that covers region contain the group
+# nx ny nz region periodicity
+fix_modify AtC mesh create 12 2 2 mdRegion f p p
+</pre>
+<pre class="literal-block">
+# specify the control method for the type of coupling
+# physics control_type
+fix_modify AtC thermal control flux
+</pre>
+<pre class="literal-block">
+# specify the initial values for the empirical field &quot;temperature&quot;
+# field node_group value
+fix_modify AtC initial temperature all 30
+</pre>
+<pre class="literal-block">
+# create an output stream for nodal fields
+# filename output_frequency
+fix_modify AtC output atc_fe_output 100
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span>
 </pre></div>
 </div>
@@ -200,30 +200,30 @@
 <span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">hardy</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># for hardy fix, specific kernel function (function type and range) to # be used as a localization function</span>
-<span class="n">fix</span> <span class="n">AtC</span> <span class="n">kernel</span> <span class="n">quartic_sphere</span> <span class="mf">10.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create a uniform 1 x 1 x 1 mesh that covers region contain the group</span>
-<span class="c1"># with periodicity this effectively creats a system average</span>
-<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">mesh</span> <span class="n">create</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">p</span> <span class="n">p</span> <span class="n">p</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># change from default lagrangian map to eulerian</span>
-<span class="c1"># refreshed every 100 steps</span>
-<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">atom_element_map</span> <span class="n">eulerian</span> <span class="mi">100</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># start with no field defined</span>
-<span class="c1"># add mass density, potential energy density, stress and temperature</span>
-<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">fields</span> <span class="n">add</span> <span class="n">density</span> <span class="n">energy</span> <span class="n">stress</span> <span class="n">temperature</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create an output stream for nodal fields</span>
-<span class="c1"># filename output_frequency</span>
-<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">output</span> <span class="n">nvtFE</span> <span class="mi">100</span> <span class="n">text</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+# for hardy fix, specific kernel function (function type and range) to # be used as a localization function
+fix AtC kernel quartic_sphere 10.0
+</pre>
+<pre class="literal-block">
+# create a uniform 1 x 1 x 1 mesh that covers region contain the group
+# with periodicity this effectively creats a system average
+fix_modify AtC mesh create 1 1 1 box p p p
+</pre>
+<pre class="literal-block">
+# change from default lagrangian map to eulerian
+# refreshed every 100 steps
+fix_modify AtC atom_element_map eulerian 100
+</pre>
+<pre class="literal-block">
+# start with no field defined
+# add mass density, potential energy density, stress and temperature
+fix_modify AtC fields add density energy stress temperature
+</pre>
+<pre class="literal-block">
+# create an output stream for nodal fields
+# filename output_frequency
+fix_modify AtC output nvtFE 100 text
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span>
 </pre></div>
 </div>
@@ -235,10 +235,8 @@
 <p>fix_modify AtC mesh create 1 1 1 box p p p</p>
 <p>...</p>
 <p>Note coupling and post-processing can be combined in the same simulations using separate fixes.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options relevant to this fix are listed below.  No global scalar or vector or per-atom quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.  This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
diff --git a/doc/html/fix_atom_swap.html b/doc/html/fix_atom_swap.html
index 862d6932af..a56f3b4f8b 100644
--- a/doc/html/fix_atom_swap.html
+++ b/doc/html/fix_atom_swap.html
@@ -156,11 +156,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">29494</span> <span class="mf">300.0</span> <span class="n">ke</span> <span class="n">no</span> <span class="n">types</span> <span class="mi">1</span> <span class="mi">2</span>
-<span class="n">fix</span> <span class="n">myFix</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">12345</span> <span class="mf">298.0</span> <span class="n">region</span> <span class="n">my_swap_region</span> <span class="n">types</span> <span class="mi">5</span> <span class="mi">6</span>
-<span class="n">fix</span> <span class="n">SGMC</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">345</span> <span class="mf">1.0</span> <span class="n">semi</span><span class="o">-</span><span class="n">grand</span> <span class="n">yes</span> <span class="n">types</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="n">mu</span> <span class="mf">0.0</span> <span class="mf">4.3</span> <span class="o">-</span><span class="mf">5.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
+fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
+fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -250,9 +250,7 @@ system (the quantity used when performing GCMC moves),
 you MUST enable the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option for
 that fix.  The doc pages for individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> commands
 specify if this should be done.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  This includes information about the random
 number generator seed, the next timestep for MC exchanges, etc.  See
 the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to
diff --git a/doc/html/fix_ave_atom.html b/doc/html/fix_ave_atom.html
index b8459a1d96..72641a5006 100644
--- a/doc/html/fix_ave_atom.html
+++ b/doc/html/fix_ave_atom.html
@@ -140,22 +140,22 @@
 one or more input values can be listed</li>
 <li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
-<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+v_name = per-atom vector calculated by an atom-style variable with name
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">100</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all ave/atom 1 100 100 vx vy vz
+fix 1 all ave/atom 10 20 1000 c_my_stress[1]
+fix 1 all ave/atom 10 20 1000 c_my_stress[*]
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -181,7 +181,7 @@ are the only ones that can be used with this fix since they produce
 per-atom vectors.</p>
 <p>Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
+specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
 &#8220;m*n&#8221;.  If N = the size of the vector (for <em>mode</em> = scalar) or the
 number of columns in the array (for <em>mode</em> = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -192,13 +192,13 @@ means all indices from m to n (inclusive).</p>
 had been listed one by one.  E.g. these 2 fix ave/atom commands are
 equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
 command creates a per-atom array with 6 columns:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">my_stress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">&amp;</span>
-                              <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="o">&amp;</span>
-                              <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute my_stress all stress/atom NULL
+fix 1 all ave/atom 10 20 1000 c_my_stress[*]
+fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &amp;
+                              c_my_stress[3] c_my_stress[4] &amp;
+                              c_my_stress[5] c_my_stress[6]
+</pre>
 <hr class="docutils" />
 <p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
 timesteps the input values will be used in order to contribute to the
@@ -228,7 +228,7 @@ this is not what you want, consider averaging unwrapped coordinates,
 which can be provided by the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command via its xu,yu,zu
 attributes.</p>
 </div>
-<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
+<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
 previously defined in the input script.  If no bracketed term is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed term containing an index I is appended, the Ith column of
@@ -236,7 +236,7 @@ the per-atom array calculated by the compute is used.  Users can also
 write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.  See the discussion above for how I can
 be specified with a wildcard asterisk to effectively specify multiple
 values.</p>
-<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
+<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
 previously defined in the input script.  If no bracketed term is
 appended, the per-atom vector calculated by the fix is used.  If a
 bracketed term containing an index I is appended, the Ith column of
@@ -246,15 +246,13 @@ compatible with <em>Nevery</em>, else an error will result.  Users can also
 write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.  See the discussion above for how I can
 be specified with a wildcard asterisk to effectively specify multiple
 values.</p>
-<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
+<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
 been previously defined in the input script as an <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a> Variables of style <em>atom</em> can reference
 thermodynamic keywords, or invoke other computes, fixes, or variables
 when they are evaluated, so this is a very general means of generating
 per-atom quantities to time average.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global scalar or vector quantities are
 stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.</p>
diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html
index 564b91e3ef..a6293fb62e 100644
--- a/doc/html/fix_ave_chunk.html
+++ b/doc/html/fix_ave_chunk.html
@@ -141,16 +141,16 @@
 <li>one or more input values can be listed</li>
 <li>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
-<span class="n">density</span><span class="o">/</span><span class="n">number</span><span class="p">,</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="o">=</span> <span class="n">number</span> <span class="ow">or</span> <span class="n">mass</span> <span class="n">density</span>
-<span class="n">temp</span> <span class="o">=</span> <span class="n">temperature</span>
-<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
+density/number, density/mass = number or mass density
+temp = temperature
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+v_name = per-atom vector calculated by an atom-style variable with name
+</pre>
 <ul class="simple">
 <li>zero or more keyword/arg pairs may be appended</li>
 <li>keyword = <em>norm</em> or <em>ave</em> or <em>bias</em> or <em>adof</em> or <em>cdof</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@@ -185,12 +185,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">10000</span> <span class="mi">1</span> <span class="mi">10000</span> <span class="n">binchunk</span> <span class="n">c_myCentro</span> <span class="n">title1</span> <span class="s2">&quot;My output values&quot;</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">molchunk</span> <span class="n">vx</span> <span class="n">vz</span> <span class="n">norm</span> <span class="n">sample</span> <span class="n">file</span> <span class="n">vel</span><span class="o">.</span><span class="n">profile</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">binchunk</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="n">ave</span> <span class="n">running</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">binchunk</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="n">ave</span> <span class="n">running</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 &quot;My output values&quot;
+fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
+fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
+fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
+</pre>
 <p><strong>NOTE:</strong></p>
 <p>If you are trying to replace a deprectated fix ave/spatial command
 with the newer, more flexible fix ave/chunk and <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> commands, you simply need to split
@@ -242,7 +242,7 @@ ones that can be used with this fix since all other styles of variable
 produce global quantities.</p>
 <p>Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
+specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
 &#8220;m*n&#8221;.  If N = the size of the vector (for <em>mode</em> = scalar) or the
 number of columns in the array (for <em>mode</em> = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -253,11 +253,11 @@ means all indices from m to n (inclusive).</p>
 had been listed one by one.  E.g. these 2 fix ave/chunk commands are
 equivalent, since the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command creates, in this
 case, a per-atom array with 3 columns:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myAng</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">angmomx</span> <span class="n">angmomy</span> <span class="n">angmomz</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">cc1</span> <span class="n">c_myAng</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">angmom</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">cc1</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">angmom</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute myAng all property/atom angmomx angmomy angmomz
+fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
+fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">This fix works by creating an array of size <em>Nchunk</em> by Nvalues
@@ -349,7 +349,7 @@ in the chunk on different timesteps were collected together as one set
 of atoms to calculate their temperature.  The compute allows the
 center-of-mass velocity of each chunk to be subtracted before
 calculating the temperature; this fix does not.</p>
-<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
+<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
 previously defined in the input script.  If no bracketed integer is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
@@ -357,7 +357,7 @@ calculated by the compute is used.  Users can also write code for
 their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.
 See the discussion above for how I can be specified with a wildcard
 asterisk to effectively specify multiple values.</p>
-<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
+<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
 previously defined in the input script.  If no bracketed integer is
 appended, the per-atom vector calculated by the fix is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
@@ -367,7 +367,7 @@ their values on certain timesteps, which must be compatible with
 own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.  See the
 discussion above for how I can be specified with a wildcard asterisk
 to effectively specify multiple values.</p>
-<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
+<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
 been previously defined in the input script.  Variables of style
 <em>atom</em> can reference thermodynamic keywords and various per-atom
 attributes, or invoke other computes, fixes, or variables when they
@@ -502,10 +502,8 @@ value of the <em>units</em> keyword is <em>reduced</em>, the coordinate values w
 be in unitless reduced units (0-1).  This is not true for the Coord1 value
 of style <em>bin/sphere</em> or <em>bin/cylinder</em> which both represent radial
 dimensions.  Those values are always in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix computes a global array of values which can be accessed by
diff --git a/doc/html/fix_ave_correlate.html b/doc/html/fix_ave_correlate.html
index 5386d0dd57..c191ecefa1 100644
--- a/doc/html/fix_ave_correlate.html
+++ b/doc/html/fix_ave_correlate.html
@@ -140,14 +140,14 @@
 <li>one or more input values can be listed</li>
 <li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">v_name</span> <span class="o">=</span> <span class="k">global</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-<span class="n">v_name</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="n">a</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+c_ID = global scalar calculated by a compute with ID
+c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
+v_name = global value calculated by an equal-style variable with name
+v_name[I] = Ith component of a vector-style variable with name
+</pre>
 <ul class="simple">
 <li>zero or more keyword/arg pairs may be appended</li>
 <li>keyword = <em>type</em> or <em>ave</em> or <em>start</em> or <em>prefactor</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@@ -180,12 +180,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span> <span class="mi">5</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">c_myTemp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">correlate</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span> <span class="mi">1</span> <span class="mi">50</span> <span class="mi">10000</span> <span class="o">&amp;</span>
-          <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
-       <span class="nb">type</span> <span class="n">upper</span> <span class="n">ave</span> <span class="n">running</span> <span class="n">title1</span> <span class="s2">&quot;My correlation data&quot;</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
+fix 1 all ave/correlate 1 50 10000 &amp;
+          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &amp;
+       type upper ave running title1 &quot;My correlation data&quot;
+</pre>
 <p>fix 1 all ave/correlate 1 50 10000 c_thermo_press[*]</p>
 </div>
 <div class="section" id="description">
@@ -221,7 +221,7 @@ ones that can be used with this fix.  Variables of style <em>atom</em> cannot
 be used, since they produce per-atom values.</p>
 <p>Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
+specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
 &#8220;m*n&#8221;.  If N = the size of the vector (for <em>mode</em> = scalar) or the
 number of columns in the array (for <em>mode</em> = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -232,13 +232,13 @@ means all indices from m to n (inclusive).</p>
 vector had been listed one by one.  E.g. these 2 fix ave/correlate
 commands are equivalent, since the <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> command creates a global vector with 6
 values.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">NULL</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span> <span class="mi">1</span> <span class="mi">50</span> <span class="mi">10000</span> <span class="n">c_myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span> <span class="mi">1</span> <span class="mi">50</span> <span class="mi">10000</span> <span class="o">&amp;</span>
-          <span class="n">c_myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
-          <span class="n">c_myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute myPress all pressure NULL
+fix 1 all ave/correlate 1 50 10000 c_myPress[*]
+fix 1 all ave/correlate 1 50 10000 &amp;
+          c_myPress[1] c_myPress[2] c_myPress[3] &amp;
+          c_myPress[4] c_myPress[5] c_myPress[6]
+</pre>
 <hr class="docutils" />
 <p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
 timesteps the input values will be used to calculate correlation data.
@@ -249,9 +249,9 @@ initial time up to an output timestep.  The initial time could be the
 beginning of the simulation or the last output time; see the <em>ave</em>
 keyword for options.  For the set of samples, the correlation value
 Cij is calculated as:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Cij</span><span class="p">(</span><span class="n">delta</span><span class="p">)</span> <span class="o">=</span> <span class="n">ave</span><span class="p">(</span><span class="n">Vi</span><span class="p">(</span><span class="n">t</span><span class="p">)</span><span class="o">*</span><span class="n">Vj</span><span class="p">(</span><span class="n">t</span><span class="o">+</span><span class="n">delta</span><span class="p">))</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Cij(delta) = ave(Vi(t)*Vj(t+delta))
+</pre>
 <p>which is the correlation value between input values Vi and Vj,
 separated by time delta.  Note that the second value Vj in the pair is
 always the one sampled at the later time.  The ave() represents an
@@ -259,9 +259,9 @@ average over every pair of samples in the set that are separated by
 time delta.  The maximum delta used is of size (<em>Nrepeat</em>-1)*<em>Nevery</em>.
 Thus the correlation between a pair of input values yields <em>Nrepeat</em>
 correlation datums:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Cij</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="n">Nevery</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">Nevery</span><span class="p">),</span> <span class="o">...</span><span class="p">,</span> <span class="n">Cij</span><span class="p">((</span><span class="n">Nrepeat</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="n">Nevery</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery)
+</pre>
 <p>For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
 timesteps 0,5,10,15,...,100 will be used to compute the final averages
 on timestep 100.  Six averages will be computed: Cij(0), Cij(5),
@@ -272,7 +272,7 @@ Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100).</p>
 non-zero.  Also, if the <em>ave</em> keyword is set to <em>one</em> which is the
 default, then <em>Nfreq</em> &gt;= (<em>Nrepeat</em>-1)*<em>Nevery</em> is required.</p>
 <hr class="docutils" />
-<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">c_</span></a>&#8221;, a compute ID must follow which has been
+<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
 previously defined in the input script.  If no bracketed term is
 appended, the global scalar calculated by the compute is used.  If a
 bracketed term is appended, the Ith element of the global vector
@@ -286,7 +286,7 @@ defined not in your input script, but by <a class="reference internal" href="the
 or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>.  See the doc pages for
 these commands which give the IDs of these computes.  Users can also
 write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">f_</span></a>&#8221;, a fix ID must follow which has been
+<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
 previously defined in the input script.  If no bracketed term is
 appended, the global scalar calculated by the fix is used.  If a
 bracketed term is appended, the Ith element of the global vector
@@ -296,7 +296,7 @@ values.</p>
 <p>Note that some fixes only produce their values on certain timesteps,
 which must be compatible with <em>Nevery</em>, else an error will result.
 Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with &#8220;<a href="#id7"><span class="problematic" id="id8">v_</span></a>&#8221;, a variable name must follow which has
+<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
 been previously defined in the input script.  Only equal-style or
 vector-style variables can be referenced; the latter requires a
 bracketed term to specify the Ith element of the vector calculated by
@@ -366,11 +366,11 @@ the strings that will be printed as the first 3 lines of the output
 file, assuming the <em>file</em> keyword was used.  LAMMPS uses default
 values for each of these, so they do not need to be specified.</p>
 <p>By default, these header lines are as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Time-correlated data for fix ID</span>
-<span class="c1"># TimeStep Number-of-time-windows</span>
-<span class="c1"># Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+# Time-correlated data for fix ID
+# TimeStep Number-of-time-windows
+# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...
+</pre>
 <p>In the first line, ID is replaced with the fix-ID.  The second line
 describes the two values that are printed at the first of each section
 of output.  In the third line the value pairs are replaced with the
@@ -378,9 +378,9 @@ appropriate fields from the fix ave/correlate command.</p>
 <hr class="docutils" />
 <p>Let Sij = a set of time correlation data for input values I and J,
 namely the <em>Nrepeat</em> values:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Sij</span> <span class="o">=</span> <span class="n">Cij</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="n">Nevery</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">Nevery</span><span class="p">),</span> <span class="o">...</span><span class="p">,</span> <span class="n">Cij</span><span class="p">(</span><span class="o">*</span><span class="n">Nrepeat</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="n">Nevery</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery)
+</pre>
 <p>As explained below, these datums are output as one column of a global
 array, which is effectively the correlation matrix.</p>
 <p>The <em>trap</em> function defined for <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a>
@@ -389,10 +389,8 @@ using a trapezoidal rule.  This is useful for calculating various
 quantities which can be derived from time correlation data.  If a
 normalization factor is needed for the time integration, it can be
 included in the variable formula or via the <em>prefactor</em> keyword.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix computes a global array of values which can be accessed by
diff --git a/doc/html/fix_ave_correlate_long.html b/doc/html/fix_ave_correlate_long.html
index ccd754dbaf..a673143beb 100644
--- a/doc/html/fix_ave_correlate_long.html
+++ b/doc/html/fix_ave_correlate_long.html
@@ -139,13 +139,13 @@
 <li>one or more input values can be listed</li>
 <li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">v_name</span> <span class="o">=</span> <span class="k">global</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+c_ID = global scalar calculated by a compute with ID
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = global value calculated by an equal-style variable with name
+</pre>
 <ul class="simple">
 <li>zero or more keyword/arg pairs may be appended</li>
 <li>keyword = <em>type</em> or <em>start</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>ncorr</em> or <em>p</em> or <em>m</em></li>
@@ -177,12 +177,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span><span class="o">/</span><span class="n">long</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_myTemp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">correlate</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span><span class="o">/</span><span class="n">long</span> <span class="mi">1</span> <span class="mi">10000</span> <span class="o">&amp;</span>
-          <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
-       <span class="nb">type</span> <span class="n">upper</span> <span class="n">title1</span> <span class="s2">&quot;My correlation data&quot;</span> <span class="n">nlen</span> <span class="mi">15</span> <span class="n">ncount</span> <span class="mi">3</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
+fix 1 all ave/correlate/long 1 10000 &amp;
+          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &amp;
+       type upper title1 &quot;My correlation data&quot; nlen 15 ncount 3
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -221,9 +221,7 @@ steps can be calculated.</p>
 4*ncorr*nlen*8 bytes. With the default values of the parameters, this
 corresponds to about 10 KB.</p>
 <p>For the meaning of the additional optional keywords, see the <a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a> doc page.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>Since this fix in intended for the calculation of time correlation
 functions over very long MD simulations, the information about this
 fix is written automatically to binary restart files, so that the time
diff --git a/doc/html/fix_ave_histo.html b/doc/html/fix_ave_histo.html
index e8291ddeb4..bb07687b4a 100644
--- a/doc/html/fix_ave_histo.html
+++ b/doc/html/fix_ave_histo.html
@@ -145,15 +145,15 @@
 <li>one or more input values can be listed</li>
 <li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
-<span class="n">c_ID</span> <span class="o">=</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">f_ID</span> <span class="o">=</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-<span class="n">v_name</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+c_ID = scalar or vector calculated by a compute with ID
+c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = scalar or vector calculated by a fix with ID
+f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
+v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
+v_name[I] = value calculated by a vector-style variable with name
+</pre>
 <ul class="simple">
 <li>zero or more keyword/arg pairs may be appended</li>
 <li>keyword = <em>mode</em> or <em>file</em> or <em>ave</em> or <em>start</em> or <em>beyond</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@@ -185,13 +185,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="mf">0.5</span> <span class="mf">1.5</span> <span class="mi">50</span> <span class="n">c_myTemp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">histo</span> <span class="n">ave</span> <span class="n">running</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">100</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">title1</span> <span class="s2">&quot;My output values&quot;</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">100</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="o">-</span><span class="mf">2.0</span> <span class="mf">2.0</span> <span class="mi">18</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">ave</span> <span class="n">running</span> <span class="n">beyond</span> <span class="n">extra</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span><span class="o">/</span><span class="n">weight</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">2000</span> <span class="n">c_XRD</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_XRD</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
+fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 &quot;My output values&quot;
+fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[*]
+fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
+fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -232,7 +232,7 @@ with a bracketed term appended, indicating the Ith column of the array
 is used.</p>
 <p>Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
+specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
 &#8220;m*n&#8221;.  If N = the size of the vector (for <em>mode</em> = scalar) or the
 number of columns in the array (for <em>mode</em> = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -243,11 +243,11 @@ means all indices from m to n (inclusive).</p>
 vector or columns of the array had been listed one by one.  E.g. these
 2 fix ave/histo commands are equivalent, since the <a class="reference internal" href="compute_com_chunk.html"><span class="doc">compute com/chunk</span></a> command creates a global array with
 3 columns:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myCOM</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp1</span><span class="o">.</span><span class="n">com</span> <span class="n">mode</span> <span class="n">vector</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp2</span><span class="o">.</span><span class="n">com</span> <span class="n">mode</span> <span class="n">vector</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute myCOM all com/chunk
+fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
+fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
+</pre>
 <p>If the fix ave/histo/weight command is used, exactly two values must
 be specified.  If the values are vectors, they must be the same
 length.  The first value (a scalar or vector) is what is histogrammed
@@ -278,7 +278,7 @@ simply generated on timesteps 100,200,etc.</p>
 self-explanatory.  Note that other atom attributes can be used as
 inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
 an input value from that compute.</p>
-<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
+<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
 previously defined in the input script.  If <em>mode</em> = scalar, then if
 no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
@@ -295,7 +295,7 @@ can thus be accessed by fix ave/histo.  Or it can be a compute defined
 not in your input script, but by <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> or other fixes such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>.  See
 the doc pages for these commands which give the IDs of these computes.
 Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
+<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
 previously defined in the input script.  If <em>mode</em> = scalar, then if
 no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
@@ -309,7 +309,7 @@ values.</p>
 <p>Note that some fixes only produce their values on certain timesteps,
 which must be compatible with <em>Nevery</em>, else an error will result.
 Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
+<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
 been previously defined in the input script.  If <em>mode</em> = scalar, then
 only equal-style or vector-style variables can be used, which both
 produce global values.  In this mode, a vector-style variable requires
@@ -399,10 +399,8 @@ values for each of these, so they do not need to be specified.</p>
 describes the six values that are printed at the first of each section
 of output.  The third describes the 4 values printed for each bin in
 the histogram.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix produces a global vector and global array which can be
diff --git a/doc/html/fix_ave_time.html b/doc/html/fix_ave_time.html
index 6c6744c5e6..2d41fdc0dc 100644
--- a/doc/html/fix_ave_time.html
+++ b/doc/html/fix_ave_time.html
@@ -140,14 +140,14 @@
 <li>one or more input values can be listed</li>
 <li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="k">global</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="k">global</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
-<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-<span class="n">v_name</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+c_ID = global scalar or vector calculated by a compute with ID
+c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = global scalar or vector calculated by a fix with ID
+f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
+v_name = value(s) calculated by an equal-style or vector-style variable with name
+v_name[I] = value calculated by a vector-style variable with name
+</pre>
 <ul class="simple">
 <li>zero or more keyword/arg pairs may be appended</li>
 <li>keyword = <em>mode</em> or <em>file</em> or <em>ave</em> or <em>start</em> or <em>off</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@@ -179,13 +179,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_myTemp</span> <span class="n">c_thermo_temp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">profile</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">ave</span> <span class="n">window</span> <span class="mi">20</span> <span class="o">&amp;</span>
-                              <span class="n">title1</span> <span class="s2">&quot;My output values&quot;</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">f_indent</span> <span class="n">f_indent</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">indent</span> <span class="n">off</span> <span class="mi">1</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
+fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &amp;
+                              title1 &quot;My output values&quot;
+fix 1 all ave/time 100 5 1000 c_thermo_press[*]
+fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -228,7 +228,7 @@ is used.  All vectors must be the same length, which is the length of
 the vector or number of rows in the array.</p>
 <p>Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
+specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
 &#8220;m*n&#8221;.  If N = the size of the vector (for <em>mode</em> = scalar) or the
 number of columns in the array (for <em>mode</em> = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -239,11 +239,11 @@ means all indices from m to n (inclusive).</p>
 vector or columns of the array had been listed one by one.  E.g. these
 2 fix ave/time commands are equivalent, since the <a class="reference internal" href="compute_rdf.html"><span class="doc">compute rdf</span></a> command creates, in this case, a global array
 with 3 columns, each of length 50:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myRDF</span> <span class="nb">all</span> <span class="n">rdf</span> <span class="mi">50</span> <span class="mi">1</span> <span class="mi">2</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp1</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp2</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute myRDF all rdf 50 1 2
+fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
+fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
+</pre>
 <hr class="docutils" />
 <p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
 timesteps the input values will be used in order to contribute to the
@@ -261,7 +261,7 @@ timestep 200, etc.  If Nrepeat=1 and Nfreq = 100, then no time
 averaging is done; values are simply generated on timesteps
 100,200,etc.</p>
 <hr class="docutils" />
-<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
+<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
 previously defined in the input script.  If <em>mode</em> = scalar, then if
 no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
@@ -277,7 +277,7 @@ can thus be accessed by fix ave/time.  Or it can be a compute defined
 not in your input script, but by <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> or other fixes such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>.  See
 the doc pages for these commands which give the IDs of these computes.
 Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
+<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
 previously defined in the input script.  If <em>mode</em> = scalar, then if
 no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
@@ -290,7 +290,7 @@ specify multiple values.</p>
 <p>Note that some fixes only produce their values on certain timesteps,
 which must be compatible with <em>Nevery</em>, else an error will result.
 Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
+<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
 been previously defined in the input script.  If <em>mode</em> = scalar, then
 only equal-style or vector-style variables can be used, which both
 produce global values.  In this mode, a vector-style variable requires
@@ -383,10 +383,8 @@ so the <em>title3</em> setting is ignored when <em>mode</em> = scalar.</p>
 describes the two values that are printed at the first of each section
 of output.  In the third line the values are replaced with the
 appropriate fields from the fix ave/time command.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix produces a global scalar or global vector or global array
diff --git a/doc/html/fix_balance.html b/doc/html/fix_balance.html
index 0415a0054b..56beb5da2b 100644
--- a/doc/html/fix_balance.html
+++ b/doc/html/fix_balance.html
@@ -432,10 +432,8 @@ will be duplicate nodes in the list.</p>
 rectangle for each processor (1 to 4).</p>
 <p>For a 3d problem, the syntax is similar with 8 vertices listed for
 each processor, instead of 4, and &#8220;SQUARES&#8221; replaced by &#8220;CUBES&#8221;.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix computes a global scalar which is the imbalance factor
diff --git a/doc/html/fix_bond_break.html b/doc/html/fix_bond_break.html
index 9be191ab77..ef0c90e2a9 100644
--- a/doc/html/fix_bond_break.html
+++ b/doc/html/fix_bond_break.html
@@ -224,10 +224,8 @@ dramatically released when the bond is broken.  More generally, you
 may need to thermostat your system to compensate for energy changes
 resulting from broken bonds (and angles, dihedrals, impropers).</p>
 </div>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix computes two statistics which it stores in a global vector of
diff --git a/doc/html/fix_bond_create.html b/doc/html/fix_bond_create.html
index 8ab79a00a5..8854f57578 100644
--- a/doc/html/fix_bond_create.html
+++ b/doc/html/fix_bond_create.html
@@ -265,7 +265,7 @@ percolation simulation.</p>
 1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
 the system) for use in weighting pairwise interactions for bonded
 atoms.  Note that adding a single bond always adds a new 1st neighbor
-but may also induce <em>many</em> new 2nd and 3rd neighbors, depending on the
+but may also induce *many* new 2nd and 3rd neighbors, depending on the
 molecular topology of your system.  The &#8220;extra special per atom&#8221;
 parameter must typically be set to allow for the new maximum total
 size (1st + 2nd + 3rd neighbors) of this per-atom list.  There are 3
@@ -320,10 +320,8 @@ dramatically when the bond is formed.  More generally, you may need to
 thermostat your system to compensate for energy changes resulting from
 created bonds (and angles, dihedrals, impropers).</p>
 </div>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix computes two statistics which it stores in a global vector of
diff --git a/doc/html/fix_bond_swap.html b/doc/html/fix_bond_swap.html
index 27a56cba19..a3ae59400a 100644
--- a/doc/html/fix_bond_swap.html
+++ b/doc/html/fix_bond_swap.html
@@ -229,9 +229,9 @@ quantities or the printing of unwrapped coordinates to a dump file.</p>
 <p>This fix computes a temperature each time it is invoked for use by the
 Boltzmann criterion.  To do this, the fix creates its own compute of
 style <em>temp</em>, as if this command had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp all temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details.  Note
 that the ID of the new compute is the fix-ID with underscore + &#8220;temp&#8221;
 appended and the group for the new compute is &#8220;all&#8221;, so that the
diff --git a/doc/html/fix_box_relax.html b/doc/html/fix_box_relax.html
index ea16211584..e81bc87098 100644
--- a/doc/html/fix_box_relax.html
+++ b/doc/html/fix_box_relax.html
@@ -371,10 +371,10 @@ temperature is used to compute the kinetic contribution to the
 pressure, even though this is subsequently ignored by default.  To do
 this, the fix creates its own computes of style &#8220;temp&#8221; and &#8220;pressure&#8221;,
 as if these commands had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">virial</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp virial
+</pre>
 <p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
 + underscore + &#8220;press&#8221;, and the group for the new computes is the same
@@ -388,10 +388,8 @@ fix&#8217;s temperature or pressure via the
 or pressure during thermodynamic output via the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command using the appropriate compute-ID.
 It also means that changing attributes of <em>thermo_temp</em> or
 <em>thermo_press</em> will have no effect on this fix.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> and <em>press</em> options are
 supported by this fix.  You can use them to assign a
@@ -425,12 +423,12 @@ potential energy. This fix does not support the
 because that would result in double-counting of the fix energy in the
 minimization energy. Instead, the fix energy can be explicitly
 added to the potential energy using one of these two variants:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">emin</span> <span class="n">equal</span> <span class="n">pe</span><span class="o">+</span><span class="n">f_1</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">emin</span> <span class="n">equal</span> <span class="n">pe</span><span class="o">+</span><span class="n">f_1</span><span class="o">/</span><span class="n">atoms</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable emin equal pe+f_1
+</pre>
+<pre class="literal-block">
+variable emin equal pe+f_1/atoms
+</pre>
 <p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
 the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
 <p>This fix is invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>, but
diff --git a/doc/html/fix_colvars.html b/doc/html/fix_colvars.html
index 8ac1624b80..367d9b091c 100644
--- a/doc/html/fix_colvars.html
+++ b/doc/html/fix_colvars.html
@@ -200,9 +200,7 @@ wrapped back into the simulation cell at each re-neighboring instead.</p>
 fix that thermostats all atoms in the fix colvars group. This will be
 used to provide the colvars module with the current thermostat target
 temperature.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the current status of the colvars module into
 <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This is in addition to the text
 mode status file that is written by the colvars module itself and the
diff --git a/doc/html/fix_controller.html b/doc/html/fix_controller.html
index e6608bc009..e9e662670c 100644
--- a/doc/html/fix_controller.html
+++ b/doc/html/fix_controller.html
@@ -141,13 +141,13 @@
 <li>Kd = derivative gain in PID equation (unitless)</li>
 <li>pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or v_name</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+c_ID = global scalar calculated by a compute with ID
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = value calculated by an equal-style variable with name
+</pre>
 <ul class="simple">
 <li>setpoint = desired value of process variable (same units as process variable)</li>
 <li>cvar = name of control variable</li>
@@ -155,11 +155,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">controller</span> <span class="mi">100</span> <span class="mf">1.0</span> <span class="mf">0.5</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">c_thermo_temp</span> <span class="mf">1.5</span> <span class="n">tcontrol</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">controller</span> <span class="mi">100</span> <span class="mf">0.2</span> <span class="mf">0.5</span> <span class="mi">0</span> <span class="mf">100.0</span> <span class="n">v_pxxwall</span> <span class="mf">1.01325</span> <span class="n">xwall</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">controller</span> <span class="mi">10000</span> <span class="mf">0.2</span> <span class="mf">0.5</span> <span class="mi">0</span> <span class="mi">2000</span> <span class="n">v_avpe</span> <span class="o">-</span><span class="mf">3.785</span> <span class="n">tcontrol</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
+fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
+fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -269,14 +269,14 @@ because the value of <em>e_n-1</em> is not yet defined.</p>
 <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> or <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> or the evaluation of a
 <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.  In each case, the compute, fix, or variable
 must produce a global quantity, not a per-atom or local quantity.</p>
-<p>If <em>pvar</em> begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
+<p>If <em>pvar</em> begins with &#8220;c_&#8221;, a compute ID must follow which has been
 previously defined in the input script and which generates a global
 scalar or vector.  See the individual <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> doc page
 for details.  If no bracketed integer is appended, the scalar
 calculated by the compute is used.  If a bracketed integer is
 appended, the Ith value of the vector calculated by the compute is
 used.  Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If <em>pvar</em> begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
+<p>If <em>pvar</em> begins with &#8220;f_&#8221;, a fix ID must follow which has been
 previously defined in the input script and which generates a global
 scalar or vector.  See the individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> doc page for
 details.  Note that some fixes only produce their values on certain
@@ -285,7 +285,7 @@ references the values, or else an error results.  If no bracketed integer
 is appended, the scalar calculated by the fix is used.  If a bracketed
 integer is appended, the Ith value of the vector calculated by the fix
 is used.  Users can also write code for their own fix style and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If <em>pvar</em> begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has been
+<p>If <em>pvar</em> begins with &#8220;v_&#8221;, a variable name must follow which has been
 previously defined in the input script.  Only equal-style variables
 can be referenced.  See the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command for
 details.  Note that variables of style <em>equal</em> define a formula which
@@ -296,14 +296,12 @@ variable.</p>
 <p>The target value <em>setpoint</em> for the process variable must be a numeric
 value, in whatever units <em>pvar</em> is defined for.</p>
 <p>The control variable <em>cvar</em> must be the name of an <a class="reference internal" href="variable.html"><span class="doc">internal-style variable</span></a> previously defined in the input script.  Note
-that it is not specified with a &#8220;<a href="#id7"><span class="problematic" id="id8">v_</span></a>&#8221; prefix, just the name of the
+that it is not specified with a &#8220;v_&#8221; prefix, just the name of the
 variable.  It must be an internal-style variable, because this fix
 updates its value directly.  Note that other commands can use an
 equal-style versus internal-style variable interchangeably.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>Currenlty, no information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix produces a global vector with 3 values which can be accessed
diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html
index e8ad31ffb0..d23425a85b 100644
--- a/doc/html/fix_deform.html
+++ b/doc/html/fix_deform.html
@@ -272,9 +272,9 @@ e.g. picoseconds for &#8220;metal&#8221; units).  Tensile strain is unitless and
 is defined as delta/L0, where L0 is the original box length and delta
 is the change relative to the original length.  The box length L as a
 function of time will change as</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">L</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">L0</span> <span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">erate</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+L(t) = L0 (1 + erate*dt)
+</pre>
 <p>where dt is the elapsed time (in time units).  Thus if <em>erate</em> R is
 specified as 0.1 and time units are picoseconds, this means the box
 length will increase by 10% of its original length every picosecond.
@@ -295,9 +295,9 @@ e.g. picoseconds for &#8220;metal&#8221; units).  Tensile strain is unitless and
 is defined as delta/L0, where L0 is the original box length and delta
 is the change relative to the original length.</p>
 <p>The box length L as a function of time will change as</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">L</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">L0</span> <span class="n">exp</span><span class="p">(</span><span class="n">trate</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+L(t) = L0 exp(trate*dt)
+</pre>
 <p>where dt is the elapsed time (in time units).  Thus if <em>trate</em> R is
 specified as ln(1.1) and time units are picoseconds, this means the
 box length will increase by 10% of its current (not original) length
@@ -341,9 +341,9 @@ dimensions, so that they respond to the tensile strain dynamically.</p>
 <p>The <em>wiggle</em> style oscillates the specified box length dimension
 sinusoidally with the specified amplitude and period.  I.e. the box
 length L as a function of time is given by</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">L</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">L0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">pi</span> <span class="n">t</span><span class="o">/</span><span class="n">Tp</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+L(t) = L0 + A sin(2*pi t/Tp)
+</pre>
 <p>where L0 is its initial length.  If the amplitude A is a positive
 number the box initially expands, then contracts, etc.  If A is
 negative then the box initially contracts, then expands, etc.  The
@@ -370,13 +370,13 @@ arbitrary variable.</p>
 <p>Here is an example of using the <em>variable</em> style to perform the same
 box deformation as the <em>wiggle</em> style formula listed above, where we
 assume that the current timestep = 0.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">A</span> <span class="n">equal</span> <span class="mf">5.0</span>
-<span class="n">variable</span> <span class="n">Tp</span> <span class="n">equal</span> <span class="mf">10.0</span>
-<span class="n">variable</span> <span class="n">displace</span> <span class="n">equal</span> <span class="s2">&quot;v_A * sin(2*PI * step*dt/v_Tp)&quot;</span>
-<span class="n">variable</span> <span class="n">rate</span> <span class="n">equal</span> <span class="s2">&quot;2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)&quot;</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">deform</span> <span class="mi">1</span> <span class="n">x</span> <span class="n">variable</span> <span class="n">v_displace</span> <span class="n">v_rate</span> <span class="n">remap</span> <span class="n">v</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable A equal 5.0
+variable Tp equal 10.0
+variable displace equal &quot;v_A * sin(2*PI * step*dt/v_Tp)&quot;
+variable rate equal &quot;2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)&quot;
+fix 2 all deform 1 x variable v_displace v_rate remap v
+</pre>
 <p>For the <em>scale</em>, <em>vel</em>, <em>erate</em>, <em>trate</em>, <em>volume</em>, <em>wiggle</em>, and
 <em>variable</em> styles, the box length is expanded or compressed around its
 mid point.</p>
@@ -413,9 +413,9 @@ to the shear direction (e.g. y box length for xy deformation) and
 offset is the displacement distance in the shear direction (e.g. x
 direction for xy deformation) from the unstrained orientation.</p>
 <p>The tilt factor T as a function of time will change as</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">T</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">T0</span> <span class="o">+</span> <span class="n">L0</span><span class="o">*</span><span class="n">erate</span><span class="o">*</span><span class="n">dt</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+T(t) = T0 + L0*erate*dt
+</pre>
 <p>where T0 is the initial tilt factor, L0 is the original length of the
 box perpendicular to the shear direction (e.g. y box length for xy
 deformation), and dt is the elapsed time (in time units).  Thus if
@@ -441,9 +441,9 @@ where length is the box length perpendicular to the shear direction
 distance in the shear direction (e.g. x direction for xy deformation)
 from the unstrained orientation.</p>
 <p>The tilt factor T as a function of time will change as</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">T</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">T0</span> <span class="n">exp</span><span class="p">(</span><span class="n">trate</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+T(t) = T0 exp(trate*dt)
+</pre>
 <p>where T0 is the initial tilt factor and dt is the elapsed time (in
 time units).  Thus if <em>trate</em> R is specified as ln(1.1) and time units
 are picoseconds, this means the shear strain or tilt factor will
@@ -464,9 +464,9 @@ parameter), then this effect on the shear strain is ignored.</p>
 <p>The <em>wiggle</em> style oscillates the specified tilt factor sinusoidally
 with the specified amplitude and period.  I.e. the tilt factor T as a
 function of time is given by</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">T</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">T0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">pi</span> <span class="n">t</span><span class="o">/</span><span class="n">Tp</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+T(t) = T0 + A sin(2*pi t/Tp)
+</pre>
 <p>where T0 is its initial value.  If the amplitude A is a positive
 number the tilt factor initially becomes more positive, then more
 negative, etc.  If A is negative then the tilt factor initially
@@ -492,13 +492,13 @@ arbitrary variable.</p>
 <p>Here is an example of using the <em>variable</em> style to perform the same
 box deformation as the <em>wiggle</em> style formula listed above, where we
 assume that the current timestep = 0.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">A</span> <span class="n">equal</span> <span class="mf">5.0</span>
-<span class="n">variable</span> <span class="n">Tp</span> <span class="n">equal</span> <span class="mf">10.0</span>
-<span class="n">variable</span> <span class="n">displace</span> <span class="n">equal</span> <span class="s2">&quot;v_A * sin(2*PI * step*dt/v_Tp)&quot;</span>
-<span class="n">variable</span> <span class="n">rate</span> <span class="n">equal</span> <span class="s2">&quot;2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)&quot;</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">deform</span> <span class="mi">1</span> <span class="n">xy</span> <span class="n">variable</span> <span class="n">v_displace</span> <span class="n">v_rate</span> <span class="n">remap</span> <span class="n">v</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable A equal 5.0
+variable Tp equal 10.0
+variable displace equal &quot;v_A * sin(2*PI * step*dt/v_Tp)&quot;
+variable rate equal &quot;2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)&quot;
+fix 2 all deform 1 xy variable v_displace v_rate remap v
+</pre>
 <hr class="docutils" />
 <p>All of the tilt styles change the xy, xz, yz tilt factors during a
 simulation.  In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes
@@ -633,9 +633,7 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.</p>
diff --git a/doc/html/fix_deposit.html b/doc/html/fix_deposit.html
index 6e7e0be54f..566b353255 100644
--- a/doc/html/fix_deposit.html
+++ b/doc/html/fix_deposit.html
@@ -355,9 +355,7 @@ count is changing due to adding particles, you typically should use
 the <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify dynamic yes</span></a> command for the
 temperature compute you are using.</p>
 </div>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the deposition to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  This includes information about how many
 particles have been depositied, the random number generator seed, the
 next timestep for deposition, etc.  See the
diff --git a/doc/html/fix_drag.html b/doc/html/fix_drag.html
index c464c735a2..5864fe2ce5 100644
--- a/doc/html/fix_drag.html
+++ b/doc/html/fix_drag.html
@@ -156,9 +156,7 @@ include that dimension in the distance calculation or force
 application.</p>
 <p>This command can be used to steer one or more atoms to a new location
 in the simulation.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
 fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
diff --git a/doc/html/fix_drude_transform.html b/doc/html/fix_drude_transform.html
index 7134e2dbf5..6a078677dc 100644
--- a/doc/html/fix_drude_transform.html
+++ b/doc/html/fix_drude_transform.html
@@ -219,14 +219,14 @@ Nose-Hoover thermostating fixes.  The <em>fix drude/transform/inverse</em>
 command must appear after any Nose-Hoover thermostating fixes.</p>
 </div>
 <p>Example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">fDIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
-<span class="n">fix</span> <span class="n">fNVT</span> <span class="n">gCORES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mi">100</span>
-<span class="n">fix</span> <span class="n">fNVT</span> <span class="n">gDRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">100</span>
-<span class="n">fix</span> <span class="n">fINVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
-<span class="n">compute</span> <span class="n">TDRUDE</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">drude</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">cpu</span> <span class="n">etotal</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">ebond</span> <span class="n">ecoul</span> <span class="n">elong</span> <span class="n">press</span> <span class="n">vol</span> <span class="n">temp</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix fDIRECT all drude/transform/direct
+fix fNVT gCORES nvt temp 300.0 300.0 100
+fix fNVT gDRUDES nvt temp 1.0 1.0 100
+fix fINVERSE all drude/transform/inverse
+compute TDRUDE all temp/drude
+thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
+</pre>
 <p>In this example, <em>gCORES</em> is the group of the atom cores and <em>gDRUDES</em>
 is the group of the Drude particles (electrons). The centers of mass
 of the Drude oscillators will be thermostated at 300.0 and the
@@ -240,14 +240,14 @@ the other one should be <em>nvt</em>. You must add a <em>compute temp/com</em> a
 that of its group (the Drude cores) but the pressure be the overall
 pressure <em>thermo_press</em>.</p>
 <p>Example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cTEMP_CORE</span> <span class="n">gCORES</span> <span class="n">temp</span><span class="o">/</span><span class="n">com</span>
-<span class="n">fix</span> <span class="n">fDIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
-<span class="n">fix</span> <span class="n">fNPT</span> <span class="n">gCORES</span> <span class="n">npt</span> <span class="n">temp</span> <span class="mf">298.0</span> <span class="mf">298.0</span> <span class="mi">100</span> <span class="n">iso</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">500</span>
-<span class="n">fix_modify</span> <span class="n">fNPT</span> <span class="n">temp</span> <span class="n">cTEMP_CORE</span> <span class="n">press</span> <span class="n">thermo_press</span>
-<span class="n">fix</span> <span class="n">fNVT</span> <span class="n">gDRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">5.0</span> <span class="mf">5.0</span> <span class="mi">100</span>
-<span class="n">fix</span> <span class="n">fINVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute cTEMP_CORE gCORES temp/com
+fix fDIRECT all drude/transform/direct
+fix fNPT gCORES npt temp 298.0 298.0 100 iso 1.0 1.0 500
+fix_modify fNPT temp cTEMP_CORE press thermo_press
+fix fNVT gDRUDES nvt temp 5.0 5.0 100
+fix fINVERSE all drude/transform/inverse
+</pre>
 <p>In this example, <em>gCORES</em> is the group of the atom cores and <em>gDRUDES</em>
 is the group of the Drude particles. The centers of mass of the Drude
 oscillators will be thermostated at 298.0 and the internal degrees of
@@ -259,10 +259,8 @@ to add a <em>fix momentum</em> command:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">fMOMENTUM</span> <span class="nb">all</span> <span class="n">momentum</span> <span class="mi">100</span> <span class="n">linear</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span>
 </pre></div>
 </div>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 </div>
 <div class="section" id="restrictions">
diff --git a/doc/html/fix_efield.html b/doc/html/fix_efield.html
index c724217123..6ddd5f9067 100644
--- a/doc/html/fix_efield.html
+++ b/doc/html/fix_efield.html
@@ -148,10 +148,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">kick</span> <span class="n">external</span><span class="o">-</span><span class="n">field</span> <span class="n">efield</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
-<span class="n">fix</span> <span class="n">kick</span> <span class="n">external</span><span class="o">-</span><span class="n">field</span> <span class="n">efield</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">v_oscillate</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix kick external-field efield 1.0 0.0 0.0
+fix kick external-field efield 0.0 0.0 v_oscillate
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -218,10 +218,8 @@ variable formulas, i.e. that -Grad(E) = F.  For example, if the force
 due to the electric field were a spring-like F = kx, then the energy
 formula should be E = -0.5kx^2.  If you don&#8217;t do this correctly, the
 minimization will not converge properly.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the potential &#8220;energy&#8221; inferred by the added force due to
diff --git a/doc/html/fix_ehex.html b/doc/html/fix_ehex.html
index f1cc66f404..a753adb554 100644
--- a/doc/html/fix_ehex.html
+++ b/doc/html/fix_ehex.html
@@ -262,10 +262,8 @@ be on the order of <span class="math">\(10^{-7}\)</span> for relatively large
 temperature gradients.  A higher precision can be achieved by
 decreasing the timestep.</p>
 </div>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
diff --git a/doc/html/fix_external.html b/doc/html/fix_external.html
index d2a176da50..264a4cf9ba 100644
--- a/doc/html/fix_external.html
+++ b/doc/html/fix_external.html
@@ -167,9 +167,9 @@ in the group, once every <em>Napply</em> steps, similar to the way the <a class=
 <em>Napply</em>, the force values produced by one callback will persist, and
 be used multiple times to update atom forces.</p>
 <p>The callback function &#8220;foo&#8221; is invoked by the fix as:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">foo</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="n">ptr</span><span class="p">,</span> <span class="n">bigint</span> <span class="n">timestep</span><span class="p">,</span> <span class="nb">int</span> <span class="n">nlocal</span><span class="p">,</span> <span class="nb">int</span> <span class="o">*</span><span class="n">ids</span><span class="p">,</span> <span class="n">double</span> <span class="o">**</span><span class="n">x</span><span class="p">,</span> <span class="n">double</span> <span class="o">**</span><span class="n">fexternal</span><span class="p">);</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
+</pre>
 <p>The arguments are as follows:</p>
 <ul class="simple">
 <li>ptr = pointer provided by and simply passed back to external driver</li>
@@ -194,9 +194,9 @@ array.  The fix adds these forces to each atom in the group, once
 every <em>Napply</em> steps, similar to the way the <a class="reference internal" href="fix_addforce.html"><span class="doc">fix addforce</span></a> command works.</p>
 <p>The name of the public force array provided by the FixExternal
 class is</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">double</span> <span class="o">**</span><span class="n">fexternal</span><span class="p">;</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+double **fexternal;
+</pre>
 <p>It is allocated by the FixExternal class as an (N,3) array where N is
 the number of atoms owned by a processor.  The 3 corresponds to the
 fx, fy, fz components of force.</p>
@@ -212,18 +212,16 @@ to the added forces must also be set so as to be consistent with the
 added forces.  Otherwise the minimization will not converge correctly.</p>
 <p>This can be done from the external driver by calling this public
 method of the FixExternal class:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">void</span> <span class="n">set_energy</span><span class="p">(</span><span class="n">double</span> <span class="n">eng</span><span class="p">);</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+void set_energy(double eng);
+</pre>
 <p>where eng is the potential energy.  Eng is an extensive quantity,
 meaning it should be the sum over per-atom energies of all affected
 atoms.  It should also be provided in <a class="reference internal" href="units.html"><span class="doc">energy units</span></a>
 consistent with the simulation.  See the details below for how to
 insure this energy setting is used appropriately in a minimization.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the potential &#8220;energy&#8221; set by the external driver to the
diff --git a/doc/html/fix_gcmc.html b/doc/html/fix_gcmc.html
index 02f1da98e6..2210a5c5c4 100644
--- a/doc/html/fix_gcmc.html
+++ b/doc/html/fix_gcmc.html
@@ -168,11 +168,11 @@ keyword = <em>mol</em>, <em>region</em>, <em>maxangle</em>, <em>pressure</em>, <
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">2</span> <span class="n">gas</span> <span class="n">gcmc</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="mi">1000</span> <span class="mi">2</span> <span class="mi">29494</span> <span class="mf">298.0</span> <span class="o">-</span><span class="mf">0.5</span> <span class="mf">0.01</span>
-<span class="n">fix</span> <span class="mi">3</span> <span class="n">water</span> <span class="n">gcmc</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">100</span> <span class="mi">0</span> <span class="mi">3456543</span> <span class="mf">3.0</span> <span class="o">-</span><span class="mf">2.5</span> <span class="mf">0.1</span> <span class="n">mol</span> <span class="n">my_one_water</span> <span class="n">maxangle</span> <span class="mi">180</span> <span class="n">full_energy</span>
-<span class="n">fix</span> <span class="mi">4</span> <span class="n">my_gas</span> <span class="n">gcmc</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">10</span> <span class="mi">1</span> <span class="mi">123456543</span> <span class="mf">300.0</span> <span class="o">-</span><span class="mf">12.5</span> <span class="mf">1.0</span> <span class="n">region</span> <span class="n">disk</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
+fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
+fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -239,12 +239,12 @@ used in fix nvt. Otherwise, the imaginary reservoir
 will not be in thermal equilibrium with the simulation cell. Also,
 it is important that the temperature used by fix nvt be dynamic,
 which can be achieved as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">mdtemp</span> <span class="n">mdatoms</span> <span class="n">temp</span>
-<span class="n">compute_modify</span> <span class="n">mdtemp</span> <span class="n">dynamic</span> <span class="n">yes</span>
-<span class="n">fix</span> <span class="n">mdnvt</span> <span class="n">mdatoms</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">10.0</span>
-<span class="n">fix_modify</span> <span class="n">mdnvt</span> <span class="n">temp</span> <span class="n">mdtemp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute mdtemp mdatoms temp
+compute_modify mdtemp dynamic yes
+fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
+fix_modify mdnvt temp mdtemp
+</pre>
 <p>Note that neighbor lists are re-built every timestep that this fix is
 invoked, so you should not set N to be too small.  However, periodic
 rebuilds are necessary in order to avoid dangerous rebuilds and missed
@@ -363,9 +363,9 @@ therefore, you will want to use the
 <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command to insure that the
 current number of atoms is used as a normalizing factor each time
 temperature is computed.  Here is the necessary command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">thermo_temp</span> <span class="n">dynamic</span> <span class="n">yes</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute_modify thermo_temp dynamic yes
+</pre>
 <p>If LJ units are used, note that a value of 0.18292026 is used by this
 fix as the reduced value for Planck&#8217;s constant.  This value was
 derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
@@ -375,9 +375,7 @@ mass = 39.948 amu.</p>
 of the group-ID value. The <em>grouptype</em> keyword assigns all
 inserted atoms of the specified type to the <a class="reference internal" href="group.html"><span class="doc">group</span></a>
 of the group-ID value.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  This includes information about the random
 number generator seed, the next timestep for MC exchanges, etc.  See
 the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to
diff --git a/doc/html/fix_gld.html b/doc/html/fix_gld.html
index aba80b6a9d..96beaab03f 100644
--- a/doc/html/fix_gld.html
+++ b/doc/html/fix_gld.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix gld command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">gld</span> <span class="n">Tstart</span> <span class="n">Tstop</span> <span class="n">N_k</span> <span class="n">seed</span> <span class="n">series</span> <span class="n">c_1</span> <span class="n">tau_1</span> <span class="o">...</span> <span class="n">c_N_k</span> <span class="n">tau_N_k</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ...
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>gld = style name of this fix command</li>
diff --git a/doc/html/fix_gle.html b/doc/html/fix_gle.html
index 9f9296aea3..e51ed41bf3 100644
--- a/doc/html/fix_gle.html
+++ b/doc/html/fix_gle.html
@@ -145,7 +145,7 @@
 <dd><p class="first"><em>noneq</em> Cmatrix  = file to read the non-equilibrium covariance matrix from
 <em>every</em> stride   = apply the GLE once every time steps. Reduces the accuracy</p>
 <blockquote class="last">
-<div>of the integration of the GLE, but has <em>no effect</em> on the accuracy of equilibrium
+<div>of the integration of the GLE, but has *no effect* on the accuracy of equilibrium
 sampling. It might change sampling properties when used together with <em>noneq</em>.</div></blockquote>
 </dd>
 </dl>
@@ -207,9 +207,7 @@ Prony series form of the memory kernel used by GLD into an appropriate
 input matrix for <a class="reference internal" href="#"><span class="doc">fix gle</span></a>. While the GLE scheme is more
 general, the form used by <a class="reference internal" href="fix_gld.html"><span class="doc">fix gld</span></a> can be more directly
 related to the representation of an implicit solvent environment.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>The instantaneous values of the extended variables are written to
 <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  Because the state of the random
 number generator is not saved in restart files, this means you cannot
diff --git a/doc/html/fix_gravity.html b/doc/html/fix_gravity.html
index e770f8e7fe..f10e0f3416 100644
--- a/doc/html/fix_gravity.html
+++ b/doc/html/fix_gravity.html
@@ -156,13 +156,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">1.0</span> <span class="n">chute</span> <span class="mf">24.0</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="n">v_increase</span> <span class="n">chute</span> <span class="mf">24.0</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">1.0</span> <span class="n">spherical</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">180.0</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">10.0</span> <span class="n">spherical</span> <span class="n">v_phi</span> <span class="n">v_theta</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">100.0</span> <span class="n">vector</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all gravity 1.0 chute 24.0
+fix 1 all gravity v_increase chute 24.0
+fix 1 all gravity 1.0 spherical 0.0 -180.0
+fix 1 all gravity 10.0 spherical v_phi v_theta
+fix 1 all gravity 100.0 vector 1 1 0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -220,10 +220,8 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the gravitational potential energy of the system to the
diff --git a/doc/html/fix_heat.html b/doc/html/fix_heat.html
index fb5b0f55e7..2e88845d31 100644
--- a/doc/html/fix_heat.html
+++ b/doc/html/fix_heat.html
@@ -147,11 +147,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">3</span> <span class="n">qin</span> <span class="n">heat</span> <span class="mi">1</span> <span class="mf">1.0</span>
-<span class="n">fix</span> <span class="mi">3</span> <span class="n">qin</span> <span class="n">heat</span> <span class="mi">10</span> <span class="n">v_flux</span>
-<span class="n">fix</span> <span class="mi">4</span> <span class="n">qout</span> <span class="n">heat</span> <span class="mi">1</span> <span class="o">-</span><span class="mf">1.0</span> <span class="n">region</span> <span class="n">top</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 3 qin heat 1 1.0
+fix 3 qin heat 10 v_flux
+fix 4 qout heat 1 -1.0 region top
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -219,9 +219,7 @@ their velocities.  Thus you must still use an integration fix
 (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) on the affected atoms.  This fix should
 not normally be used on atoms that have their temperature controlled
 by another fix - e.g. <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> fix.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_imd.html b/doc/html/fix_imd.html
index 5c92083e88..3245c8523d 100644
--- a/doc/html/fix_imd.html
+++ b/doc/html/fix_imd.html
@@ -237,9 +237,7 @@ they were real objects. See the <a class="reference external" href="http://www.k
 <p>If IMD control messages are received, a line of text describing the
 message and its effect will be printed to the LAMMPS output screen, if
 screen output is active.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global scalar or vector or per-atom
 quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_ipi.html b/doc/html/fix_ipi.html
index 615515d668..40917601b7 100644
--- a/doc/html/fix_ipi.html
+++ b/doc/html/fix_ipi.html
@@ -173,9 +173,7 @@ configurations make sense. It is assumed that the species in the i-PI
 input are listed in the same order as in the data file of LAMMPS. The
 initial configuration is ignored, as it will be substituted with the
 coordinates received from i-PI before forces are ever evaluated.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>There is no restart information associated with this fix, since all
 the dynamical parameters are dealt with by i-PI.</p>
 </div>
diff --git a/doc/html/fix_langevin.html b/doc/html/fix_langevin.html
index 40cfbcd9cc..bf67a0e983 100644
--- a/doc/html/fix_langevin.html
+++ b/doc/html/fix_langevin.html
@@ -375,10 +375,8 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  Because the state of the random number generator
 is not saved in restart files, this means you cannot do &#8220;exact&#8221;
 restarts with this fix, where the simulation continues on the same as
diff --git a/doc/html/fix_langevin_drude.html b/doc/html/fix_langevin_drude.html
index f01d0bd451..ea9f9510a0 100644
--- a/doc/html/fix_langevin_drude.html
+++ b/doc/html/fix_langevin_drude.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix langevin/drude command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="n">Tcom</span> <span class="n">damp_com</span> <span class="n">seed_com</span> <span class="n">Tdrude</span> <span class="n">damp_drude</span> <span class="n">seed_drude</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ...
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>langevin/drude = style name of this fix command</li>
@@ -236,9 +236,9 @@ partner (electron).</p>
 correctly.  You must use the <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify</span></a> command to
 enable this, e.g.</p>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+comm_modify vel yes
+</pre>
 <hr class="docutils" />
 <p><em>Tcom</em> is the target temperature of the centers of mass, which would
 be used to thermostate the non-polarizable atoms.  <em>Tdrude</em> is the
@@ -299,14 +299,14 @@ calculated using the <a class="reference internal" href="compute_temp_drude.html
 command.</p>
 <hr class="docutils" />
 <p>Usage example for rigid bodies in the NPT ensemble:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
-<span class="n">fix</span> <span class="n">TEMP</span> <span class="nb">all</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="mf">300.</span> <span class="mf">100.</span> <span class="mi">1256</span> <span class="mf">1.</span> <span class="mf">20.</span> <span class="mi">13977</span> <span class="n">zero</span> <span class="n">yes</span>
-<span class="n">fix</span> <span class="n">NPH</span> <span class="n">ATOMS</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nph</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">iso</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mf">500.</span>
-<span class="n">fix</span> <span class="n">NVE</span> <span class="n">DRUDES</span> <span class="n">nve</span>
-<span class="n">compute</span> <span class="n">TDRUDE</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">drude</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">cpu</span> <span class="n">etotal</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">ebond</span> <span class="n">ecoul</span> <span class="n">elong</span> <span class="n">press</span> <span class="n">vol</span> <span class="n">temp</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+comm_modify vel yes
+fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes
+fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500.
+fix NVE DRUDES nve
+compute TDRUDE all temp/drude
+thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
+</pre>
 <p>Comments:</p>
 <ul class="simple">
 <li>Drude particles should not be in the rigid group, otherwise the Drude
@@ -332,10 +332,8 @@ should be the global one, but the temperature should be only that of
 the cores. That&#8217;s why the command <em>fix_modify</em> should be called in
 that case.</li>
 </ul>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  Because the state of the random number generator
 is not saved in restart files, this means you cannot do &#8220;exact&#8221;
 restarts with this fix, where the simulation continues on the same as
diff --git a/doc/html/fix_langevin_eff.html b/doc/html/fix_langevin_eff.html
index 506e61e35c..dea014ff7b 100644
--- a/doc/html/fix_langevin_eff.html
+++ b/doc/html/fix_langevin_eff.html
@@ -178,9 +178,7 @@ interactions (<a class="reference internal" href="pair_style.html"><span class="
 <p>The operation of this fix is exactly like that described by the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> command, except that the thermostatting
 is also applied to the radial electron velocity for electron
 particles.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  Because the state of the random number generator
 is not saved in restart files, this means you cannot do &#8220;exact&#8221;
 restarts with this fix, where the simulation continues on the same as
diff --git a/doc/html/fix_lb_fluid.html b/doc/html/fix_lb_fluid.html
index 51eefacda2..fadee5ceb3 100644
--- a/doc/html/fix_lb_fluid.html
+++ b/doc/html/fix_lb_fluid.html
@@ -374,10 +374,8 @@ screen every N timesteps.</p>
 test runs, see <a class="reference internal" href="#fluid-mackay"><span class="std std-ref">Mackay et al.</span></a>.  Please include a citation to
 this paper if the lb_fluid fix is used in work contributing to
 published research.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>Due to the large size of the fluid data, this fix writes it&#8217;s own
 binary restart files, if requested, independent of the main LAMMPS
 <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>; no information about <em>lb_fluid</em>
diff --git a/doc/html/fix_lb_momentum.html b/doc/html/fix_lb_momentum.html
index aefe19517d..5ca4e990b6 100644
--- a/doc/html/fix_lb_momentum.html
+++ b/doc/html/fix_lb_momentum.html
@@ -167,9 +167,7 @@ and the fluid velocities at each lattice site.</p>
 be changed by specifying the keyword <em>linear</em>, along with a set of
 three flags set to 0/1 in order to exclude/ include the corresponding
 dimension.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can be
diff --git a/doc/html/fix_lb_pc.html b/doc/html/fix_lb_pc.html
index 4fe4f72ced..8d27f6cd24 100644
--- a/doc/html/fix_lb_pc.html
+++ b/doc/html/fix_lb_pc.html
@@ -146,12 +146,10 @@
 <h2>Description</h2>
 <p>Update the positions and velocities of the individual particles
 described by <em>group-ID</em>, experiencing velocity-dependent hydrodynamic
-forces, using the integration algorithm described in <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a>.  This integration algorithm should only be used if a
+forces, using the integration algorithm described in <a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>.  This integration algorithm should only be used if a
 user-specified value for the force-coupling constant used in <a class="reference internal" href="fix_lb_fluid.html"><span class="doc">fix lb/fluid</span></a> has been set; do not use this integration
 algorithm if the force coupling constant has been set by default.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can be
diff --git a/doc/html/fix_lb_rigid_pc_sphere.html b/doc/html/fix_lb_rigid_pc_sphere.html
index ca3adc0748..8bda0b4a82 100644
--- a/doc/html/fix_lb_rigid_pc_sphere.html
+++ b/doc/html/fix_lb_rigid_pc_sphere.html
@@ -202,9 +202,7 @@ central atoms interact with one another.</p>
 the rigid fix (although it includes fewer optional arguments, and
 assumes the constituent atoms are point particles); see
 <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> for a complete documentation.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about the <em>rigid</em> and <em>rigid/nve</em> fixes are written to
 <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>Similar to the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> command: The rigid
diff --git a/doc/html/fix_lb_viscous.html b/doc/html/fix_lb_viscous.html
index efc00565c9..876c9eb1f0 100644
--- a/doc/html/fix_lb_viscous.html
+++ b/doc/html/fix_lb_viscous.html
@@ -164,10 +164,8 @@ hydrodynamic forces to the particles.</p>
 test runs, see <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a>.  Please include a citation to
 this paper if this fix is used in work contributing to published
 research.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>As described in the <a class="reference internal" href="fix_viscous.html"><span class="doc">fix viscous</span></a> documentation:</p>
 <p>&#8220;No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
diff --git a/doc/html/fix_lineforce.html b/doc/html/fix_lineforce.html
index 5ca8460a42..2734d0ff4e 100644
--- a/doc/html/fix_lineforce.html
+++ b/doc/html/fix_lineforce.html
@@ -151,9 +151,7 @@ remains.  This is done by subtracting out components of force in the
 plane perpendicular to the line.</p>
 <p>If the initial velocity of the atom is 0.0 (or along the line), then
 it should continue to move along the line thereafter.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_move.html b/doc/html/fix_move.html
index 66cf61d80e..ad7177b2bd 100644
--- a/doc/html/fix_move.html
+++ b/doc/html/fix_move.html
@@ -160,11 +160,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">boundary</span> <span class="n">move</span> <span class="n">wiggle</span> <span class="mf">3.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="n">units</span> <span class="n">box</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="n">boundary</span> <span class="n">move</span> <span class="n">rotate</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">5.0</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="n">boundary</span> <span class="n">move</span> <span class="n">variable</span> <span class="n">v_myx</span> <span class="n">v_myy</span> <span class="n">NULL</span> <span class="n">v_VX</span> <span class="n">v_VY</span> <span class="n">NULL</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
+fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
+fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -202,9 +202,9 @@ command.</p>
 <p>The <em>linear</em> style moves atoms at a constant velocity, so that their
 position <em>X</em> = (x,y,z) as a function of time is given in vector
 notation as</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">X</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">X0</span> <span class="o">+</span> <span class="n">V</span> <span class="o">*</span> <span class="n">delta</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+X(t) = X0 + V * delta
+</pre>
 <p>where <em>X0</em> = (x0,y0,z0) is their position at the time the fix is
 specified, <em>V</em> is the specified velocity vector with components
 (Vx,Vy,Vz), and <em>delta</em> is the time elapsed since the fix was
@@ -216,17 +216,17 @@ the corresponding force component on the atom.</p>
 <p>Note that the <em>linear</em> style is identical to using the <em>variable</em>
 style with an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> that uses the
 vdisplace() function.  E.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable V equal 10.0
+<pre class="literal-block">
+variable V equal 10.0
 variable x equal vdisplace(0.0,$V)
 fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
-</pre></div>
-</div>
+</pre>
 <p>The <em>wiggle</em> style moves atoms in an oscillatory fashion, so that
 their position <em>X</em> = (x,y,z) as a function of time is given in vector
 notation as</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">X</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">X0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+X(t) = X0 + A sin(omega*delta)
+</pre>
 <p>where <em>X0</em> = (x0,y0,z0) is their position at the time the fix is
 specified, <em>A</em> is the specified amplitude vector with components
 (Ax,Ay,Az), <em>omega</em> is 2 PI / <em>period</em>, and <em>delta</em> is the time
@@ -239,14 +239,14 @@ corresponding force component on the atom.</p>
 <p>Note that the <em>wiggle</em> style is identical to using the <em>variable</em>
 style with <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a> that use the
 swiggle() and cwiggle() functions.  E.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable A equal 10.0
+<pre class="literal-block">
+variable A equal 10.0
 variable T equal 5.0
 variable omega equal 2.0*PI/$T
 variable x equal swiggle(0.0,$A,$T)
 variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
-</pre></div>
-</div>
+</pre>
 <p>The <em>rotate</em> style rotates atoms around a rotation axis <em>R</em> =
 (Rx,Ry,Rz) that goes thru a point <em>P</em> = (Px,Py,Pz).  The <em>period</em> of
 the rotation is also specified.  The direction of rotation for the
@@ -302,10 +302,8 @@ are in lattice spacings.  The <a class="reference internal" href="lattice.html">
 been previously used to define the lattice spacing.  Each of these 3
 quantities may be dependent on the x,y,z dimension, since the lattice
 spacings can be different in x,y,z.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the original coordinates of moving atoms to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, as well as the initial timestep, so that
 the motion can be continuous in a restarted simulation.  See the
 <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_msst.html b/doc/html/fix_msst.html
index f5a8d09ba8..c54106e01e 100644
--- a/doc/html/fix_msst.html
+++ b/doc/html/fix_msst.html
@@ -197,16 +197,14 @@ LAMMPS, but are not implemented for MSST.</p>
 <p>This fix computes a temperature and pressure each timestep. To do
 this, the fix creates its own computes of style &#8220;temp&#8221; and &#8220;pressure&#8221;,
 as if these commands had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
 + underscore + &#8220;press&#8221;.  The group for the new computes is &#8220;all&#8221;.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of all internal variables to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command
 for info on how to re-specify a fix in an input script that reads a
 restart file, so that the operation of the fix continues in an
@@ -230,15 +228,15 @@ equations. See also <a class="reference internal" href="thermo_style.html"><span
 </ol>
 <p>To print these quantities to the log file with descriptive column
 headers, the following LAMMPS commands are suggested:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span>           <span class="n">msst</span> <span class="nb">all</span> <span class="n">msst</span> <span class="n">z</span>
-<span class="n">fix_modify</span>       <span class="n">msst</span> <span class="n">energy</span> <span class="n">yes</span>
-<span class="n">variable</span> <span class="n">dhug</span>    <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-<span class="n">variable</span> <span class="n">dray</span>    <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-<span class="n">variable</span> <span class="n">lgr_vel</span> <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
-<span class="n">variable</span> <span class="n">lgr_pos</span> <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
-<span class="n">thermo_style</span>     <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">lz</span> <span class="n">pzz</span> <span class="n">etotal</span> <span class="n">v_dhug</span> <span class="n">v_dray</span> <span class="n">v_lgr_vel</span> <span class="n">v_lgr_pos</span> <span class="n">f_msst</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix           msst all msst z
+fix_modify       msst energy yes
+variable dhug    equal f_msst[1]
+variable dray    equal f_msst[2]
+variable lgr_vel equal f_msst[3]
+variable lgr_pos equal f_msst[4]
+thermo_style     custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
+</pre>
 <p>These fixes compute a global scalar and a global vector of 4
 quantities, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar values calculated
 by this fix are &#8220;extensive&#8221;; the vector values are &#8220;intensive&#8221;.</p>
diff --git a/doc/html/fix_neb.html b/doc/html/fix_neb.html
index 4b5777e1e2..1e50f393e0 100644
--- a/doc/html/fix_neb.html
+++ b/doc/html/fix_neb.html
@@ -190,9 +190,7 @@ forces on atoms in this replica are described in the
 </div>
 <p>The inter-replica forces for the other replicas are unchanged from the
 first equation.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html
index ff55e4e302..8cbee0b46f 100644
--- a/doc/html/fix_nh.html
+++ b/doc/html/fix_nh.html
@@ -158,9 +158,9 @@
 <h1>fix nph/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style_name</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID style_name keyword value ...
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>style_name = <em>nvt</em> or <em>npt</em> or <em>nph</em></li>
@@ -508,14 +508,14 @@ thermostatting and barostatting.</p>
 <p>These fixes compute a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style &#8220;temp&#8221; and &#8220;pressure&#8221;,
 as if one of these two sets of commands had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+</pre>
+<pre class="literal-block">
+compute fix-ID_temp all temp
+compute fix-ID_press all pressure fix-ID_temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
 + underscore + &#8220;press&#8221;.  For fix nvt, the group for the new computes
@@ -606,10 +606,8 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>These fixes writes the state of all the thermostat and barostat
 variables to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the
 <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_nh_eff.html b/doc/html/fix_nh_eff.html
index 5e8d66853c..d11bbb105e 100644
--- a/doc/html/fix_nh_eff.html
+++ b/doc/html/fix_nh_eff.html
@@ -134,9 +134,9 @@
 <h1>fix nph/eff command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style_name</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID style_name keyword value ...
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>style_name = <em>nvt/eff</em> or <em>npt/eff</em> or <em>nph/eff</em></li>
@@ -223,9 +223,7 @@ degrees of freedom with the <a class="reference internal" href="velocity.html"><
 the user must allow for these degrees of freedom to equilibrate
 (i.e. equi-partitioning of energy) through time integration.</p>
 </div>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>See the doc page for the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt, npt, and nph</span></a> commands
 for details.</p>
 </div>
diff --git a/doc/html/fix_nph_asphere.html b/doc/html/fix_nph_asphere.html
index d7c91846db..2c2d1a4d0a 100644
--- a/doc/html/fix_nph_asphere.html
+++ b/doc/html/fix_nph_asphere.html
@@ -175,10 +175,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
 <p>This fix computes a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style &#8220;temp/asphere&#8221; and
 &#8220;pressure&#8221;, as if these commands had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp all temp/asphere
+compute fix-ID_press all pressure fix-ID_temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
 + underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
@@ -207,9 +207,7 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the Nose/Hoover barostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nph_sphere.html b/doc/html/fix_nph_sphere.html
index 0529dba9db..ec7a15a0cd 100644
--- a/doc/html/fix_nph_sphere.html
+++ b/doc/html/fix_nph_sphere.html
@@ -175,10 +175,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
 <p>This fix computes a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style &#8220;temp/sphere&#8221; and
 &#8220;pressure&#8221;, as if these commands had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">sphere</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp all temp/sphere
+compute fix-ID_press all pressure fix-ID_temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
 + underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
@@ -207,9 +207,7 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the Nose/Hoover barostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nphug.html b/doc/html/fix_nphug.html
index da32f6307b..85dd234fe3 100644
--- a/doc/html/fix_nphug.html
+++ b/doc/html/fix_nphug.html
@@ -229,14 +229,14 @@ controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.h
 <p>This fix computes a temperature and pressure at each timestep.  To do
 this, the fix creates its own computes of style &#8220;temp&#8221; and &#8220;pressure&#8221;,
 as if one of these two sets of commands had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+</pre>
+<pre class="literal-block">
+compute fix-ID_temp all temp
+compute fix-ID_press all pressure fix-ID_temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
 + underscore + &#8220;press&#8221;.  The group for
@@ -266,10 +266,8 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the values of E0, V0, and P0, as well as the
 state of all the thermostat and barostat
 variables to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the
@@ -293,7 +291,7 @@ compute temperature on a subset of atoms.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by these
 fixes to add the energy change induced by Nose/Hoover thermostatting
 and barostatting to the system&#8217;s potential energy as part of
-<a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>. Either way, this energy is <em>not</em>
+<a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>. Either way, this energy is *not*
 included in the definition of internal energy E when calculating the value
 of Delta in the above equation.</p>
 <p>These fixes compute a global scalar and a global vector of quantities,
diff --git a/doc/html/fix_npt_asphere.html b/doc/html/fix_npt_asphere.html
index 203bb248e0..2216a34678 100644
--- a/doc/html/fix_npt_asphere.html
+++ b/doc/html/fix_npt_asphere.html
@@ -182,10 +182,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
 <p>This fix computes a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style &#8220;temp/asphere&#8221; and
 &#8220;pressure&#8221;, as if these commands had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp all temp/asphere
+compute fix-ID_press all pressure fix-ID_temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
 + underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
@@ -227,9 +227,7 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the Nose/Hoover thermostat and barostat
 to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the
 <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_npt_body.html b/doc/html/fix_npt_body.html
index 7a21169513..b037898463 100644
--- a/doc/html/fix_npt_body.html
+++ b/doc/html/fix_npt_body.html
@@ -179,10 +179,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
 <p>This fix computes a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style &#8220;temp/body&#8221; and
 &#8220;pressure&#8221;, as if these commands had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">body</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp all temp/body
+compute fix-ID_press all pressure fix-ID_temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp_body.html"><span class="doc">compute temp/body</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
 + underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
@@ -224,9 +224,7 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the Nose/Hoover thermostat and barostat
 to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the
 <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_npt_sphere.html b/doc/html/fix_npt_sphere.html
index 1d5d6ed867..f05e786221 100644
--- a/doc/html/fix_npt_sphere.html
+++ b/doc/html/fix_npt_sphere.html
@@ -181,10 +181,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
 <p>This fix computes a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style &#8220;temp/sphere&#8221; and
 &#8220;pressure&#8221;, as if these commands had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">sphere</span>
-<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp all temp/sphere
+compute fix-ID_press all pressure fix-ID_temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
 + underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
@@ -226,9 +226,7 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the Nose/Hoover thermostat and barostat
 to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the
 <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_nve_asphere.html b/doc/html/fix_nve_asphere.html
index 435fea89b4..88dbabd521 100644
--- a/doc/html/fix_nve_asphere.html
+++ b/doc/html/fix_nve_asphere.html
@@ -153,9 +153,7 @@ group each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.</p>
 <p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
 assumes point particles and only updates their position and velocity.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_nve_asphere_noforce.html b/doc/html/fix_nve_asphere_noforce.html
index 75760b0c6a..dd98e2ce40 100644
--- a/doc/html/fix_nve_asphere_noforce.html
+++ b/doc/html/fix_nve_asphere_noforce.html
@@ -150,10 +150,8 @@ angularm momenta are used to update their positions and orientation.</p>
 <p>This is useful as an implicit time integrator for Fast Lubrication
 Dynamics, since the velocity and angular momentum are updated by the
 <a class="reference external" href="pair_lubricateU.txt">pair_style lubricuteU</a> command.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_nve_body.html b/doc/html/fix_nve_body.html
index cd459a4379..45816df757 100644
--- a/doc/html/fix_nve_body.html
+++ b/doc/html/fix_nve_body.html
@@ -151,9 +151,7 @@ consistent with the microcanonical ensemble.  See <a class="reference internal"
 doc page for more details on using body particles.</p>
 <p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
 assumes point particles and only updates their position and velocity.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_nve_line.html b/doc/html/fix_nve_line.html
index 5168b08db0..5b6a9bb8ab 100644
--- a/doc/html/fix_nve_line.html
+++ b/doc/html/fix_nve_line.html
@@ -152,9 +152,7 @@ trajectory consistent with the microcanonical ensemble.  See
 using line segment particles.</p>
 <p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
 assumes point particles and only updates their position and velocity.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html
index 06d68cd6ae..149e6de046 100644
--- a/doc/html/fix_nve_manifold_rattle.html
+++ b/doc/html/fix_nve_manifold_rattle.html
@@ -159,7 +159,7 @@ keyword = <em>every</em>
 atoms constrained to a curved surface (manifold) in the group each
 timestep. The constraint is handled by RATTLE <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a>
 written out for the special case of single-particle constraints as
-explained in <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a>.  V is volume; E is energy. This way,
+explained in <a class="reference internal" href="#paquay"><span class="std std-ref">(Paquay)</span></a>.  V is volume; E is energy. This way,
 the dynamics of particles constrained to curved surfaces can be
 studied. If combined with <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this
 generates Brownian motion of particles constrained to a curved
@@ -172,20 +172,18 @@ manifolds this can be achieved with <em>region</em> and <em>create_atoms</em>
 commands, but for more complex surfaces it might be more useful to
 write a script.</p>
 <p>The manifold args may be equal-style variables, like so:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">R</span> <span class="n">equal</span> <span class="s2">&quot;ramp(5.0,3.0)&quot;</span>
-<span class="n">fix</span> <span class="n">shrink_sphere</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">manifold</span><span class="o">/</span><span class="n">rattle</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">4</span> <span class="mi">10</span> <span class="n">sphere</span> <span class="n">v_R</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable R equal &quot;ramp(5.0,3.0)&quot;
+fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R
+</pre>
 <p>In this case, the manifold parameter will change in time according to
 the variable.  This is not a problem for the time integrator as long
 as the change of the manifold is slow with respect to the dynamics of
 the particles.  Note that if the manifold has to exert work on the
 particles because of these changes, the total energy might not be
 conserved.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_nve_sphere.html b/doc/html/fix_nve_sphere.html
index e0e8bf5189..2a70998598 100644
--- a/doc/html/fix_nve_sphere.html
+++ b/doc/html/fix_nve_sphere.html
@@ -189,10 +189,8 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_nve_tri.html b/doc/html/fix_nve_tri.html
index e707401c30..1462555ef2 100644
--- a/doc/html/fix_nve_tri.html
+++ b/doc/html/fix_nve_tri.html
@@ -152,9 +152,7 @@ trajectory consistent with the microcanonical ensemble.  See
 using triangular particles.</p>
 <p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
 assumes point particles and only updates their position and velocity.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_nvt_asphere.html b/doc/html/fix_nvt_asphere.html
index 08a1bea12b..473db13d7f 100644
--- a/doc/html/fix_nvt_asphere.html
+++ b/doc/html/fix_nvt_asphere.html
@@ -169,9 +169,9 @@ keywords.</p>
 <p>This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style &#8220;temp/asphere&#8221;, as if this command
 had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp/asphere
+</pre>
 <p>See the <a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a> command for
 details.  Note that the ID of the new compute is the fix-ID +
 underscore + &#8220;temp&#8221;, and the group for the new compute is the same as
@@ -213,9 +213,7 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_body.html b/doc/html/fix_nvt_body.html
index 9fecb55fc4..57ba66659d 100644
--- a/doc/html/fix_nvt_body.html
+++ b/doc/html/fix_nvt_body.html
@@ -166,9 +166,9 @@ keywords.</p>
 <p>This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style &#8220;temp/body&#8221;, as if this command
 had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">body</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp/body
+</pre>
 <p>See the <a class="reference internal" href="compute_temp_body.html"><span class="doc">compute temp/body</span></a> command for
 details.  Note that the ID of the new compute is the fix-ID +
 underscore + &#8220;temp&#8221;, and the group for the new compute is the same as
@@ -210,9 +210,7 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_sllod.html b/doc/html/fix_nvt_sllod.html
index a2592ab7e7..09875bceb8 100644
--- a/doc/html/fix_nvt_sllod.html
+++ b/doc/html/fix_nvt_sllod.html
@@ -194,9 +194,9 @@ keywords.</p>
 <p>This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style &#8220;temp/deform&#8221;, as if this command had
 been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">deform</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp/deform
+</pre>
 <p>See the <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a> command for
 details.  Note that the ID of the new compute is the fix-ID +
 underscore + &#8220;temp&#8221;, and the group for the new compute is the same as
@@ -238,9 +238,7 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_sllod_eff.html b/doc/html/fix_nvt_sllod_eff.html
index 8492983e42..c175a68bdc 100644
--- a/doc/html/fix_nvt_sllod_eff.html
+++ b/doc/html/fix_nvt_sllod_eff.html
@@ -157,9 +157,7 @@ creates (as discussed in the <a class="reference internal" href="fix_nh.html"><s
 page), is performed with a <a class="reference internal" href="compute_temp_deform_eff.html"><span class="doc">compute temp/deform/eff</span></a> commmand that includes
 the eFF contribution to the temperature from the electron radial
 velocity.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_sphere.html b/doc/html/fix_nvt_sphere.html
index fc5b3ddab1..6a27b967ed 100644
--- a/doc/html/fix_nvt_sphere.html
+++ b/doc/html/fix_nvt_sphere.html
@@ -169,9 +169,9 @@ keywords.</p>
 <p>This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style &#8220;temp/sphere&#8221;, as if this command
 had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">sphere</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp/sphere
+</pre>
 <p>See the <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></a> command for
 details.  Note that the ID of the new compute is the fix-ID +
 underscore + &#8220;temp&#8221;, and the group for the new compute is the same as
@@ -213,9 +213,7 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_orient.html b/doc/html/fix_orient.html
index 74dd4d3477..9b01605d28 100644
--- a/doc/html/fix_orient.html
+++ b/doc/html/fix_orient.html
@@ -232,9 +232,7 @@ symmetry, so the list must include one from each pair of
 equal-and-opposite neighbors.  A pair of orientation files for a
 Sigma=5 tilt boundary are shown below. A tutorial that can help for
 writing the orientation files is given in <a class="reference internal" href="#wicaksono2"><span class="std std-ref">(Wicaksono2)</span></a></p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the potential energy of atom interactions with the grain
diff --git a/doc/html/fix_phonon.html b/doc/html/fix_phonon.html
index 40d369afee..3094e830ae 100644
--- a/doc/html/fix_phonon.html
+++ b/doc/html/fix_phonon.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix phonon command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">phonon</span> <span class="n">N</span> <span class="n">Noutput</span> <span class="n">Nwait</span> <span class="n">map_file</span> <span class="n">prefix</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ...
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>phonon = style name of this fix command</li>
@@ -239,9 +239,7 @@ even degrade the performance of lammps in case the unit cell is too large.</p>
 <a class="reference internal" href="units.html"><span class="doc">energy/distance^2/mass</span></a> units.  The coordinates for <em>q</em>
 points in the log file is in the units of the basis vectors of the
 corresponding reciprocal lattice.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
 fix. You can use it to change the temperature compute from thermo_temp
diff --git a/doc/html/fix_pimd.html b/doc/html/fix_pimd.html
index 57ee90e294..545be26b57 100644
--- a/doc/html/fix_pimd.html
+++ b/doc/html/fix_pimd.html
@@ -232,9 +232,9 @@ ring.</p>
 <p>To run a PIMD simulation with M quasi-beads in each ring polymer using
 N MPI tasks for each partition&#8217;s domain-decomposition, you would use P
 = MxN processors (cores) and run the simulation as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="n">P</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">partition</span> <span class="n">MxN</span> <span class="o">-</span><span class="ow">in</span> <span class="n">script</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+mpirun -np P lmp_mpi -partition MxN -in script
+</pre>
 <p>Note that in the LAMMPS input script for a multi-partition simulation,
 it is often very useful to define a <a class="reference internal" href="variable.html"><span class="doc">uloop-style variable</span></a> such as</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ibead</span> <span class="n">uloop</span> <span class="n">M</span> <span class="n">pad</span>
@@ -243,11 +243,11 @@ it is often very useful to define a <a class="reference internal" href="variable
 <p>where M is the number of quasi-beads (partitions) used in the
 calculation.  The uloop variable can then be used to manage I/O
 related tasks for each of the partitions, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>dump dcd all dcd 10 system_${ibead}.dcd
+<pre class="literal-block">
+dump dcd all dcd 10 system_${ibead}.dcd
 restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
 read_restart system_${ibead}.restart2
-</pre></div>
-</div>
+</pre>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/fix_pour.html b/doc/html/fix_pour.html
index ca471ec2c3..ee3f050be4 100644
--- a/doc/html/fix_pour.html
+++ b/doc/html/fix_pour.html
@@ -316,10 +316,8 @@ can prevent particles from being inserted.  The <em>ignore</em> keyword
 causes the overlap check to skip any line or triangle particles.
 Obviously you should only use it if there is in fact no overlap of the
 line or triangle particles with the insertion region.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  This means you must be careful when restarting a
 pouring simulation, when the restart file was written in the middle of
 the pouring operation.  Specifically, you should use a new fix pour
diff --git a/doc/html/fix_qbmsst.html b/doc/html/fix_qbmsst.html
index 1fb67f4518..f3dca0ee47 100644
--- a/doc/html/fix_qbmsst.html
+++ b/doc/html/fix_qbmsst.html
@@ -157,10 +157,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qbmsst</span> <span class="n">z</span> <span class="mf">0.122</span> <span class="n">q</span> <span class="mi">25</span> <span class="n">mu</span> <span class="mf">0.9</span> <span class="n">tscale</span> <span class="mf">0.01</span> <span class="n">damp</span> <span class="mi">200</span> <span class="n">seed</span> <span class="mi">35082</span> <span class="n">f_max</span> <span class="mf">0.3</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="n">eta</span> <span class="mi">1</span> <span class="n">beta</span> <span class="mi">400</span> <span class="n">T_init</span> <span class="mi">110</span> <span class="p">(</span><span class="n">liquid</span> <span class="n">methane</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">REAX</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">real</span> <span class="n">units</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">qbmsst</span> <span class="n">z</span> <span class="mi">72</span> <span class="n">q</span> <span class="mi">40</span> <span class="n">tscale</span> <span class="mf">0.05</span> <span class="n">damp</span> <span class="mi">1</span> <span class="n">seed</span> <span class="mi">47508</span> <span class="n">f_max</span> <span class="mf">120.0</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="n">eta</span> <span class="mf">1.0</span> <span class="n">beta</span> <span class="mi">500</span> <span class="n">T_init</span> <span class="mi">300</span> <span class="p">(</span><span class="n">quartz</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">BKS</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">metal</span> <span class="n">units</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
+fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units)
+</pre>
 <p>Two example input scripts are given, including shocked alpha quartz
 and shocked liquid methane. The input script first equilibrate an
 initial state with the quantum thermal bath at the target temperature
@@ -242,10 +242,8 @@ thermal bath and the system before shock loading.</p>
 <p>For all pressure styles, the simulation box stays orthorhombic in
 shape. Parrinello-Rahman boundary conditions (tilted box) are
 supported by LAMMPS, but are not implemented for QBMSST.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>Because the state of the random number generator is not written to
 <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, this fix cannot be restarted
 &#8220;exactly&#8221; in an uninterrupted fashion. However, in a statistical
@@ -271,16 +269,16 @@ headers, the following LAMMPS commands are suggested. Here the
 <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> energy command is also enabled to allow
 the thermo keyword <em>etotal</em> to print the quantity &lt;i&gt;etot&lt;/i&gt;.  See
 also the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span>          <span class="n">fix_id</span> <span class="nb">all</span> <span class="n">msst</span> <span class="n">z</span>
-<span class="n">fix_modify</span>   <span class="n">fix_id</span> <span class="n">energy</span> <span class="n">yes</span>
-<span class="n">variable</span>     <span class="n">dhug</span>    <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-<span class="n">variable</span>     <span class="n">dray</span>    <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-<span class="n">variable</span>     <span class="n">lgr_vel</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
-<span class="n">variable</span>     <span class="n">lgr_pos</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
-<span class="n">variable</span>     <span class="n">T_qm</span>    <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span>
-<span class="n">thermo_style</span> <span class="n">custom</span>  <span class="n">step</span> <span class="n">temp</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">lz</span> <span class="n">pzz</span> <span class="n">etotal</span> <span class="n">v_dhug</span> <span class="n">v_dray</span> <span class="n">v_lgr_vel</span> <span class="n">v_lgr_pos</span> <span class="n">v_T_qm</span> <span class="n">f_fix_id</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix          fix_id all msst z
+fix_modify  fix_id energy yes
+variable     dhug    equal f_fix_id[1]
+variable     dray    equal f_fix_id[2]
+variable     lgr_vel        equal f_fix_id[3]
+variable     lgr_pos        equal f_fix_id[4]
+variable     T_qm   equal f_fix_id[5]
+thermo_style        custom  step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id
+</pre>
 <p>The global scalar under the entry f_fix_id is the quantity of thermo
 energy as an extra part of &lt;i&gt;etot&lt;/i&gt;. This global scalar and the
 vector of 5 quantities can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. It is worth noting that the
diff --git a/doc/html/fix_qeq.html b/doc/html/fix_qeq.html
index addd4b9ecf..05e428f671 100644
--- a/doc/html/fix_qeq.html
+++ b/doc/html/fix_qeq.html
@@ -162,13 +162,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">point</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mf">1.0e-6</span> <span class="mi">200</span> <span class="n">param</span><span class="o">.</span><span class="n">qeq1</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">qeq</span> <span class="n">qeq</span><span class="o">/</span><span class="n">shielded</span> <span class="mi">1</span> <span class="mi">8</span> <span class="mf">1.0e-6</span> <span class="mi">100</span> <span class="n">param</span><span class="o">.</span><span class="n">qeq2</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">slater</span> <span class="mi">5</span> <span class="mi">10</span> <span class="mf">1.0e-6</span> <span class="mi">100</span> <span class="n">params</span> <span class="n">alpha</span> <span class="mf">0.2</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">qeq</span> <span class="n">qeq</span><span class="o">/</span><span class="n">dynamic</span> <span class="mi">1</span> <span class="mi">12</span> <span class="mf">1.0e-3</span> <span class="mi">100</span> <span class="n">my_qeq</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">fire</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mf">1.0e-3</span> <span class="mi">100</span> <span class="n">my_qeq</span> <span class="n">qdamp</span> <span class="mf">0.2</span> <span class="n">qstep</span> <span class="mf">0.1</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
+fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
+fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
+fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
+fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -292,9 +292,7 @@ non-trivial.  Charges on atoms are not guaranteed to equilibrate with
 arbitrary choices of these parameters.  We do not develop these QEq
 paramters.  See the examples/qeq directory for some examples.</p>
 </div>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about these fixes is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  No global scalar or vector or per-atom
 quantities are stored by these fixes for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of these fixes
 can be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a>
diff --git a/doc/html/fix_qeq_comb.html b/doc/html/fix_qeq_comb.html
index c7382d021d..3bf7a12a5c 100644
--- a/doc/html/fix_qeq_comb.html
+++ b/doc/html/fix_qeq_comb.html
@@ -195,10 +195,8 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
 fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
diff --git a/doc/html/fix_qeq_reax.html b/doc/html/fix_qeq_reax.html
index cc02c2516a..665de2e845 100644
--- a/doc/html/fix_qeq_reax.html
+++ b/doc/html/fix_qeq_reax.html
@@ -180,9 +180,7 @@ exponent.  Note that these 3 quantities are also in the ReaxFF
 potential file, except that eta is defined here as twice the eta value
 in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
 of this fix are hard-coded to be A, eV, and electronic charge.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  No global scalar or vector or per-atom
 quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
 be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
diff --git a/doc/html/fix_qmmm.html b/doc/html/fix_qmmm.html
index 1adbcf6567..fa8cf47576 100644
--- a/doc/html/fix_qmmm.html
+++ b/doc/html/fix_qmmm.html
@@ -156,9 +156,7 @@ other QM codes.  This will allow the LAMMPS side of the implementation
 to be adapted if necessary before being finalized.</p>
 <p>Details about how to use this fix are currently documented in the
 description of the QM/MM interface code itself in lib/qmmm/README.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global scalar or vector or per-atom
 quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_qtb.html b/doc/html/fix_qtb.html
index 2f8934ddd0..cffd9b2764 100644
--- a/doc/html/fix_qtb.html
+++ b/doc/html/fix_qtb.html
@@ -147,12 +147,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qtb</span> <span class="n">temp</span> <span class="mi">110</span> <span class="n">damp</span> <span class="mi">200</span> <span class="n">seed</span> <span class="mi">35082</span> <span class="n">f_max</span> <span class="mf">0.3</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="p">(</span><span class="n">liquid</span> <span class="n">methane</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">REAX</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">real</span> <span class="n">units</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">nph</span> <span class="n">iso</span> <span class="mf">1.01325</span> <span class="mf">1.01325</span> <span class="mi">1</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">qtb</span> <span class="n">temp</span> <span class="mi">300</span> <span class="n">damp</span> <span class="mi">1</span> <span class="n">seed</span> <span class="mi">47508</span> <span class="n">f_max</span> <span class="mf">120.0</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="p">(</span><span class="n">quartz</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">BKS</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">metal</span> <span class="n">units</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all nve
+fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
+fix 2 all nph iso 1.01325 1.01325 1
+fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -219,7 +219,7 @@ runs on different numbers of processors.</p>
 vibrational modes with frequencies higher than <em>f_max</em> will not be
 modulated. If we denote &amp;Delta;&lt;i&gt;t&lt;/i&gt; as the time interval for the
 MD integration, <em>f_max</em> is always reset by the code to make
-&lt;i&gt;&amp;alpha;&lt;/i&gt; = (int)(2<em>f_max</em>&amp;Delta;&lt;i&gt;t&lt;/i&gt;)&lt;sup&gt;&lt;i&gt;-1&lt;/i&gt;&lt;/sup&gt; a
+&lt;i&gt;&amp;alpha;&lt;/i&gt; = (int)(2*f_max*&amp;Delta;&lt;i&gt;t&lt;/i&gt;)&lt;sup&gt;&lt;i&gt;-1&lt;/i&gt;&lt;/sup&gt; a
 positive integer and print out relative information. An appropriate
 value for the cutoff frequency <em>f_max</em> would be around 2~3
 &lt;i&gt;f&lt;/i&gt;&lt;sub&gt;D&lt;/sub&gt;, where &lt;i&gt;f&lt;/i&gt;&lt;sub&gt;D&lt;/sub&gt; is the Debye
diff --git a/doc/html/fix_reax_bonds.html b/doc/html/fix_reax_bonds.html
index 0275b0ad0e..e8c6d12136 100644
--- a/doc/html/fix_reax_bonds.html
+++ b/doc/html/fix_reax_bonds.html
@@ -157,10 +157,8 @@ written to <em>filename</em> on timesteps that are multiples of <em>Nevery</em>,
 including timestep 0.  For time-averaged chemical species analysis,
 please see the <a class="reference internal" href="fix_reaxc_species.html"><span class="doc">fix reaxc/c/species</span></a> command.</p>
 <p>The format of the output file should be self-explantory.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_reaxc_species.html b/doc/html/fix_reaxc_species.html
index d4f4f182bd..fb72dd69c4 100644
--- a/doc/html/fix_reaxc_species.html
+++ b/doc/html/fix_reaxc_species.html
@@ -215,10 +215,8 @@ i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
 <p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
 values on timesteps 90,92,94,96,98,100 will be used to compute the
 average bond-order for the species analysis output on timestep 100.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix computes both a global vector of length 2 and a per-atom
diff --git a/doc/html/fix_restrain.html b/doc/html/fix_restrain.html
index 34228509c9..ef8c9949c2 100644
--- a/doc/html/fix_restrain.html
+++ b/doc/html/fix_restrain.html
@@ -154,12 +154,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">holdem</span> <span class="nb">all</span> <span class="n">restrain</span> <span class="n">bond</span> <span class="mi">45</span> <span class="mi">48</span> <span class="mf">2000.0</span> <span class="mf">2000.0</span> <span class="mf">2.75</span>
-<span class="n">fix</span> <span class="n">holdem</span> <span class="nb">all</span> <span class="n">restrain</span> <span class="n">dihedral</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mf">2000.0</span> <span class="mf">2000.0</span> <span class="mf">120.0</span>
-<span class="n">fix</span> <span class="n">holdem</span> <span class="nb">all</span> <span class="n">restrain</span> <span class="n">bond</span> <span class="mi">45</span> <span class="mi">48</span> <span class="mf">2000.0</span> <span class="mf">2000.0</span> <span class="mf">2.75</span> <span class="n">dihedral</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mf">2000.0</span> <span class="mf">2000.0</span> <span class="mf">120.0</span>
-<span class="n">fix</span> <span class="n">texas_holdem</span> <span class="nb">all</span> <span class="n">restrain</span> <span class="n">dihedral</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mf">0.0</span> <span class="mf">2000.0</span> <span class="mf">120.0</span> <span class="n">dihedral</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">5</span> <span class="mf">0.0</span> <span class="mf">2000.0</span> <span class="o">-</span><span class="mf">120.0</span> <span class="n">dihedral</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">6</span> <span class="mf">0.0</span> <span class="mf">2000.0</span> <span class="mf">0.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
+fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
+fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
+fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -202,7 +202,8 @@ works best for a given application.</p>
 molecule with particular restratins (e.g. for fitting forcefield
 parameters or constructing a potential energy surface), commands such
 as the following may be useful:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span># minimize molecule energy with restraints
+<pre class="literal-block">
+# minimize molecule energy with restraints
 velocity all create 600.0 8675309 mom yes rot yes dist gaussian
 fix NVE all nve
 fix TFIX all langevin 600.0 0.0 100 24601
@@ -218,8 +219,7 @@ minimize 1e-6 1e-9 1000 100000
 # report unrestrained energies
 unfix REST
 run 0
-</pre></div>
-</div>
+</pre>
 <hr class="docutils" />
 <p>The <em>bond</em> keyword applies a bond restraint to the specified atoms
 using the same functional form used by the <a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_style harmonic</span></a> command.  The potential associated with
@@ -259,10 +259,8 @@ associated with the restraint is</p>
 <p>K and phi0 are specified with the fix.  Note that the value of n is
 hard-wired to 1.  Also note that the energy will be a minimum when the
 current dihedral angle phi is equal to phi0.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the potential energy associated with this fix to the
diff --git a/doc/html/fix_rigid.html b/doc/html/fix_rigid.html
index 8b0eef3e3a..3dc4ef9053 100644
--- a/doc/html/fix_rigid.html
+++ b/doc/html/fix_rigid.html
@@ -211,19 +211,19 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">clump</span> <span class="n">rigid</span> <span class="n">single</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">clump</span> <span class="n">rigid</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">clump</span> <span class="n">rigid</span> <span class="n">single</span> <span class="n">force</span> <span class="mi">1</span> <span class="n">off</span> <span class="n">off</span> <span class="n">on</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">428984</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">polychains</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nvt</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">5.0</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">polychains</span> <span class="n">rigid</span> <span class="n">molecule</span> <span class="n">force</span> <span class="mi">1</span><span class="o">*</span><span class="mi">5</span> <span class="n">off</span> <span class="n">off</span> <span class="n">off</span> <span class="n">force</span> <span class="mi">6</span><span class="o">*</span><span class="mi">10</span> <span class="n">off</span> <span class="n">off</span> <span class="n">on</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">polychains</span> <span class="n">rigid</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">428984</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="n">fluid</span> <span class="n">rigid</span> <span class="n">group</span> <span class="mi">3</span> <span class="n">clump1</span> <span class="n">clump2</span> <span class="n">clump3</span> <span class="n">torque</span> <span class="o">*</span> <span class="n">off</span> <span class="n">off</span> <span class="n">off</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">rods</span> <span class="n">rigid</span><span class="o">/</span><span class="n">npt</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">iso</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">10.0</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">particles</span> <span class="n">rigid</span><span class="o">/</span><span class="n">npt</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">5.0</span> <span class="n">x</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">1.0</span> <span class="n">z</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">1.0</span> <span class="n">couple</span> <span class="n">xz</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">water</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nph</span> <span class="n">molecule</span> <span class="n">iso</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="n">particles</span> <span class="n">rigid</span><span class="o">/</span><span class="n">npt</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="n">iso</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 clump rigid single
+fix 1 clump rigid/small molecule
+fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
+fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
+fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
+fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
+fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
+fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
+fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
+fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
+fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -385,8 +385,8 @@ apply to is determined by the first argument of the <em>force</em> and
 <em>torque</em> keywords.  It can be an integer M from 1 to Nbody, where
 Nbody is the number of rigid bodies defined.  A wild-card asterisk can
 be used in place of, or in conjunction with, the M argument to set the
-flags for multiple rigid bodies.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or
-&#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the number of rigid bodies, then an asterisk
+flags for multiple rigid bodies.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or
+&#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the number of rigid bodies, then an asterisk
 with no numeric values means all bodies from 1 to N.  A leading
 asterisk means all bodies from 1 to n (inclusive).  A trailing
 asterisk means all bodies from n to N (inclusive).  A middle asterisk
@@ -745,10 +745,8 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about the 4 NVE rigid styles is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  The exception is if the <em>infile</em> or
 <em>mol</em> keyword is used, in which case an auxiliary file is written out
 with rigid body information each time a restart file is written, as
diff --git a/doc/html/fix_rx.html b/doc/html/fix_rx.html
index b39fe17f46..6d337133f8 100644
--- a/doc/html/fix_rx.html
+++ b/doc/html/fix_rx.html
@@ -147,13 +147,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rx</span> <span class="n">kinetics</span><span class="o">.</span><span class="n">rx</span> <span class="n">none</span> <span class="n">dense</span> <span class="n">lammps_rk4</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rx</span> <span class="n">kinetics</span><span class="o">.</span><span class="n">rx</span> <span class="n">none</span> <span class="n">sparse</span> <span class="n">lammps_rk4</span> <span class="mi">1</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rx</span> <span class="n">kinetics</span><span class="o">.</span><span class="n">rx</span> <span class="n">lucy</span> <span class="n">sparse</span> <span class="n">lammps_rk4</span> <span class="mi">10</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rx</span> <span class="n">kinetics</span><span class="o">.</span><span class="n">rx</span> <span class="n">none</span> <span class="n">dense</span> <span class="n">rkf45</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">6</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">8</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rx</span> <span class="n">kinetics</span><span class="o">.</span><span class="n">rx</span> <span class="n">none</span> <span class="n">dense</span> <span class="n">rkf45</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">6</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">8</span> <span class="o">-</span><span class="mi">1</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all rx kinetics.rx none dense lammps_rk4
+fix 1 all rx kinetics.rx none sparse lammps_rk4 1
+fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10
+fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8
+fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -271,7 +271,7 @@ temperature exponent <em>n</em>, and the activation energy <em>Ea</em>.</p>
 are used by the <a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> command to
 define the thermodynamic properties of each species.  Furthermore, the
 number of species molecules (i.e., concentration) can be specified
-either with the <a class="reference internal" href="set.html"><span class="doc">set</span></a> command using the &#8220;<a href="#id3"><span class="problematic" id="id4">d_</span></a>&#8221; prefix or by
+either with the <a class="reference internal" href="set.html"><span class="doc">set</span></a> command using the &#8220;d_&#8221; prefix or by
 reading directly the concentrations from a data file.  For the latter
 case, the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command with the fix keyword
 should be specified, where the fix-ID will be the &#8220;fix rx`ID with a &lt;SPECIES&#8221;&gt;`_ suffix, e.g.</p>
diff --git a/doc/html/fix_saed_vtk.html b/doc/html/fix_saed_vtk.html
index 29f7570dc9..08de66a8eb 100644
--- a/doc/html/fix_saed_vtk.html
+++ b/doc/html/fix_saed_vtk.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix saed/vtk command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="n">Nevery</span> <span class="n">Nrepeat</span> <span class="n">Nfreak</span> <span class="n">c_ID</span> <span class="n">attribute</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>saed/vtk = style name of this fix command</li>
@@ -154,14 +154,14 @@ keyword = <em>file</em> or <em>ave</em> or <em>start</em> or <em>file</em> or <e
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="n">dR_Ewald</span> <span class="mf">0.01</span> <span class="n">c</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">0.5</span>
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Ni</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="n">c</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="n">manual</span> <span class="n">echo</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_1</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
-<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_2</span> <span class="n">file</span> <span class="n">Ni_000</span><span class="o">.</span><span class="n">saed</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
+</pre>
+<pre class="literal-block">
+fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+fix saed/vtk 1 1 1 c_2 file Ni_000.saed
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -182,10 +182,10 @@ specified values may represent calculations performed by saed computes
 which store their own &#8220;group&#8221; definitions.</p>
 <p>Fix saed/vtk is designed to work only with <a class="reference internal" href="compute_saed.html"><span class="doc">compute saed</span></a>
 values, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">3</span> <span class="n">top</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span>
-<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_3</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 3 top saed 0.0251 Al O
+fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
+</pre>
 <hr class="docutils" />
 <p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
 timesteps the input values will be used in order to contribute to the
@@ -209,19 +209,19 @@ vtk image data formatting.  The filename assigned by the <em>file</em> keyword i
 appended with _N.vtk where N is an index (0,1,2...) to account for multiple
 diffraction intensity outputs.</p>
 <p>By default the header contains the following information (with example data):</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># vtk DataFile Version 3.0 c_SAED</span>
-<span class="n">Image</span> <span class="n">data</span> <span class="nb">set</span>
-<span class="n">ASCII</span>
-<span class="n">DATASET</span> <span class="n">STRUCTURED_POINTS</span>
-<span class="n">DIMENSIONS</span> <span class="mi">337</span> <span class="mi">219</span> <span class="mi">209</span>
-<span class="n">ASPECT_RATIO</span> <span class="mf">0.00507953</span> <span class="mf">0.00785161</span> <span class="mf">0.00821458</span>
-<span class="n">ORIGIN</span> <span class="o">-</span><span class="mf">0.853361</span> <span class="o">-</span><span class="mf">0.855826</span> <span class="o">-</span><span class="mf">0.854316</span>
-<span class="n">POINT_DATA</span> <span class="mi">15424827</span>
-<span class="n">SCALARS</span> <span class="n">intensity</span> <span class="nb">float</span>
-<span class="n">LOOKUP_TABLE</span> <span class="n">default</span>
-<span class="o">...</span><span class="n">data</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+# vtk DataFile Version 3.0 c_SAED
+Image data set
+ASCII
+DATASET STRUCTURED_POINTS
+DIMENSIONS 337 219 209
+ASPECT_RATIO 0.00507953 0.00785161 0.00821458
+ORIGIN -0.853361 -0.855826 -0.854316
+POINT_DATA 15424827
+SCALARS intensity float
+LOOKUP_TABLE default
+...data
+</pre>
 <p>In this example, kspace is sampled across a 337 x 219 x 209 point mesh
 where the mesh spacing is approximately 0.005, 0.007, and 0.008
 inv(length) units in the k1, k2, and k3 directions, respectively.
@@ -264,9 +264,7 @@ intensity outputs.</p>
 <p>The <em>overwrite</em> keyword will continuously overwrite the output file
 with the latest output, so that it only contains one timestep worth of
 output.  This option can only be used with the <em>ave running</em> setting.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
diff --git a/doc/html/fix_shake.html b/doc/html/fix_shake.html
index 7cfb03e019..6c279062d0 100644
--- a/doc/html/fix_shake.html
+++ b/doc/html/fix_shake.html
@@ -289,10 +289,8 @@ the RATTLE constraints.  You can check whether the constraints work
 correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp
 to 1 and recompiling LAMMPS.</p>
 </div>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about these fixes is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to these fixes.  No global or per-atom quantities are
 stored by these fixes for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of these fixes
diff --git a/doc/html/fix_smd.html b/doc/html/fix_smd.html
index 5be23f5d7b..0c2d9bc519 100644
--- a/doc/html/fix_smd.html
+++ b/doc/html/fix_smd.html
@@ -212,9 +212,7 @@ over the pulling force in direction of the spring is recorded and
 can then later be used to compute the potential of mean force (PMF)
 by averaging over multiple independent trajectories along the same
 pulling path.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>The fix stores the direction of the spring, current pulling target
 distance and the running PMF to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.
 See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to
diff --git a/doc/html/fix_smd_adjust_dt.html b/doc/html/fix_smd_adjust_dt.html
index ebf49b94ca..734c433f36 100644
--- a/doc/html/fix_smd_adjust_dt.html
+++ b/doc/html/fix_smd_adjust_dt.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix smd/adjust_dt command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">adjust_dt</span> <span class="n">arg</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID smd/adjust_dt arg
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>smd/adjust_dt = style name of this fix command</li>
@@ -142,9 +142,9 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">adjust_dt</span> <span class="mf">0.1</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all smd/adjust_dt 0.1
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -157,9 +157,7 @@ stable maximum time step.</p>
 <p>This fix inquires the minimum stable time increment across all particles contained in the group for which this
 fix is defined. An additional safety factor <em>s_fact</em> is applied to the time increment.</p>
 <p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>Currently, no part of USER-SMD supports restarting nor minimization.</p>
 </div>
 <div class="section" id="restrictions">
diff --git a/doc/html/fix_smd_integrate_tlsph.html b/doc/html/fix_smd_integrate_tlsph.html
index 194f99be37..04c9db062a 100644
--- a/doc/html/fix_smd_integrate_tlsph.html
+++ b/doc/html/fix_smd_integrate_tlsph.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix smd/integrate_tlsph command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_tlsph</span> <span class="n">keyword</span> <span class="n">values</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID smd/integrate_tlsph keyword values
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>smd/integrate_tlsph = style name of this fix command</li>
@@ -144,10 +144,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_tlsph</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_tlsph</span> <span class="n">limit_velocity</span> <span class="mi">1000</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all smd/integrate_tlsph
+fix 1 all smd/integrate_tlsph limit_velocity 1000
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -155,9 +155,7 @@
 <p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
 <p>The <em>limit_velocity</em> keyword will control the velocity, scaling the norm of
 the velocity vector to max_vel in case it exceeds this velocity limit.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
 </div>
 <div class="section" id="restrictions">
diff --git a/doc/html/fix_smd_integrate_ulsph.html b/doc/html/fix_smd_integrate_ulsph.html
index e45d7d3f31..58bd9fda2c 100644
--- a/doc/html/fix_smd_integrate_ulsph.html
+++ b/doc/html/fix_smd_integrate_ulsph.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix smd/integrate_ulsph command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_ulsph</span> <span class="n">keyword</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID smd/integrate_ulsph keyword
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>smd/integrate_ulsph = style name of this fix command</li>
@@ -148,12 +148,12 @@ max_nn = maximum number of neighbors</dd>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_ulsph</span> <span class="n">adjust_radius</span> <span class="mf">1.02</span> <span class="mi">25</span> <span class="mi">50</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_ulsph</span> <span class="n">limit_velocity</span> <span class="mi">1000</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
+</pre>
+<pre class="literal-block">
+fix 1 all smd/integrate_ulsph limit_velocity 1000
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -161,12 +161,10 @@ max_nn = maximum number of neighbors</dd>
 See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
 <p>The <em>adjust_radius</em> keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
 within the interval <em>min_nn</em> to <em>max_nn</em>. The parameter <em>adjust_radius_factor</em> determines the amount of adjustment per timestep. Typical values are
-<em>adjust_radius_factor</em>=1.02, <em>min_nn</em>=15, and <em>max_nn</em>=20.</p>
+<a href="#id1"><span class="problematic" id="id2">*</span></a>adjust_radius_factor*=1.02, <a href="#id3"><span class="problematic" id="id4">*</span></a>min_nn*=15, and <a href="#id5"><span class="problematic" id="id6">*</span></a>max_nn*=20.</p>
 <p>The <em>limit_velocity</em> keyword will control the velocity, scaling the norm of
 the velocity vector to max_vel in case it exceeds this velocity limit.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
 </div>
 <div class="section" id="restrictions">
diff --git a/doc/html/fix_smd_move_triangulated_surface.html b/doc/html/fix_smd_move_triangulated_surface.html
index 689017806f..e3c04397e7 100644
--- a/doc/html/fix_smd_move_triangulated_surface.html
+++ b/doc/html/fix_smd_move_triangulated_surface.html
@@ -128,55 +128,53 @@
 <span id="index-0"></span><h1>fix smd/move_tri_surf command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="n">keyword</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID smd/move_tri_surf keyword
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>smd/move_tri_surf keyword = style name of this fix command</li>
-<li>keyword = <a href="#id1"><span class="problematic" id="id2">**</span></a>LINEAR* or <a href="#id3"><span class="problematic" id="id4">**</span></a>WIGGLE* or <a href="#id5"><span class="problematic" id="id6">**</span></a>ROTATE*</li>
+<li>keyword = <em>*LINEAR</em> or <em>*WIGGLE</em> or <em>*ROTATE</em></li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">**</span><span class="n">LINEAR</span><span class="o">*</span> <span class="n">args</span> <span class="o">=</span> <span class="n">Vx</span> <span class="n">Vy</span> <span class="n">Vz</span>
-   <span class="n">Vx</span><span class="p">,</span><span class="n">Vy</span><span class="p">,</span><span class="n">Vz</span> <span class="o">=</span> <span class="n">components</span> <span class="n">of</span> <span class="n">velocity</span> <span class="n">vector</span> <span class="p">(</span><span class="n">velocity</span> <span class="n">units</span><span class="p">),</span> <span class="nb">any</span> <span class="n">component</span> <span class="n">can</span> <span class="n">be</span> <span class="n">specified</span> <span class="k">as</span> <span class="n">NULL</span>
-<span class="o">**</span><span class="n">WIGGLE</span><span class="o">*</span> <span class="n">args</span> <span class="o">=</span> <span class="n">Vx</span> <span class="n">Vy</span> <span class="n">Vz</span> <span class="n">max_travel</span>
-   <span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span> <span class="o">=</span> <span class="n">components</span> <span class="n">of</span> <span class="n">velocity</span> <span class="n">vector</span> <span class="p">(</span><span class="n">velocity</span> <span class="n">units</span><span class="p">),</span> <span class="nb">any</span> <span class="n">component</span> <span class="n">can</span> <span class="n">be</span> <span class="n">specified</span> <span class="k">as</span> <span class="n">NULL</span>
-   <span class="n">max_travel</span> <span class="o">=</span> <span class="n">wiggle</span> <span class="n">amplitude</span>
-<span class="o">**</span><span class="n">ROTATE</span><span class="o">*</span> <span class="n">args</span> <span class="o">=</span> <span class="n">Px</span> <span class="n">Py</span> <span class="n">Pz</span> <span class="n">Rx</span> <span class="n">Ry</span> <span class="n">Rz</span> <span class="n">period</span>
-   <span class="n">Px</span><span class="p">,</span><span class="n">Py</span><span class="p">,</span><span class="n">Pz</span> <span class="o">=</span> <span class="n">origin</span> <span class="n">point</span> <span class="n">of</span> <span class="n">axis</span> <span class="n">of</span> <span class="n">rotation</span> <span class="p">(</span><span class="n">distance</span> <span class="n">units</span><span class="p">)</span>
-   <span class="n">Rx</span><span class="p">,</span><span class="n">Ry</span><span class="p">,</span><span class="n">Rz</span> <span class="o">=</span> <span class="n">axis</span> <span class="n">of</span> <span class="n">rotation</span> <span class="n">vector</span>
-   <span class="n">period</span> <span class="o">=</span> <span class="n">period</span> <span class="n">of</span> <span class="n">rotation</span> <span class="p">(</span><span class="n">time</span> <span class="n">units</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+<em>*LINEAR</em> args = Vx Vy Vz
+   Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+<em>*WIGGLE</em> args = Vx Vy Vz max_travel
+   vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
+   max_travel = wiggle amplitude
+<em>*ROTATE</em> args = Px Py Pz Rx Ry Rz period
+   Px,Py,Pz = origin point of axis of rotation (distance units)
+   Rx,Ry,Rz = axis of rotation vector
+   period = period of rotation (time units)
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">tool</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="o">*</span><span class="n">LINEAR</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">10</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="n">tool</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="o">*</span><span class="n">WIGGLE</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">10</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="n">tool</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="o">*</span><span class="n">ROTATE</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">5</span> <span class="mi">2</span> <span class="mi">1</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
+fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
+fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
 <p>This fix applies only to rigid surfaces read from .STL files via fix <a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">smd/wall_surface</span></a> .
 It updates position and velocity for the particles in the group each timestep without regard to forces on the particles.
 The rigid surfaces can thus be moved along simple trajectories during the simulation.</p>
-<p>The <a href="#id19"><span class="problematic" id="id20">**</span></a>LINEAR* style moves particles with the specified constant velocity
+<p>The <em>*LINEAR</em> style moves particles with the specified constant velocity
 vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle
 to V = (Vx,Vy,Vz).</p>
-<p>The <a href="#id21"><span class="problematic" id="id22">**</span></a>WIGGLE* style moves particles in an oscillatory fashion.
+<p>The <em>*WIGGLE</em> style moves particles in an oscillatory fashion.
 Particles are moved along (vx, vy, vz) with constant velocity until a
 displacement of max_travel is reached. Then, the velocity vector is
 reversed. This process is repeated.</p>
-<p>The <a href="#id23"><span class="problematic" id="id24">**</span></a>ROTATE* style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
+<p>The <em>*ROTATE</em> style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
 goes through a point P = (Px,Py,Pz). The period of the rotation is also
 specified. This style also sets the velocity of each particle to (omega cross
 Rperp) where omega is its angular velocity around the rotation axis and
 Rperp is a perpendicular vector from the rotation axis to the particle.</p>
 <p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
 </div>
 <div class="section" id="restrictions">
diff --git a/doc/html/fix_smd_setvel.html b/doc/html/fix_smd_setvel.html
index cb8449f1c0..16fc5abc50 100644
--- a/doc/html/fix_smd_setvel.html
+++ b/doc/html/fix_smd_setvel.html
@@ -146,9 +146,9 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">top_velocity</span> <span class="n">top_group</span> <span class="n">setvel</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix top_velocity top_group setvel 1.0 0.0 0.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -174,10 +174,8 @@ coordinates.  Thus it is easy to specify a spatially-dependent velocity
 field with optional time-dependence as well.</p>
 <p>If the <em>region</em> keyword is used, the particle must also be in the
 specified geometric <a class="reference internal" href="region.html"><span class="doc">region</span></a> in order to have its velocity set by this command.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>Currently, no part of USER-SMD supports restarting nor minimization
 None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
diff --git a/doc/html/fix_smd_wall_surface.html b/doc/html/fix_smd_wall_surface.html
index 92d197d542..f51d51f6a6 100644
--- a/doc/html/fix_smd_wall_surface.html
+++ b/doc/html/fix_smd_wall_surface.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix smd/wall_surface command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">wall_surface</span> <span class="n">arg</span> <span class="nb">type</span> <span class="n">mol</span><span class="o">-</span><span class="n">ID</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID smd/wall_surface arg type mol-ID
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>smd/wall_surface = style name of this fix command</li>
@@ -146,9 +146,9 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">stl_surf</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">wall_surface</span> <span class="n">tool</span><span class="o">.</span><span class="n">stl</span> <span class="mi">2</span> <span class="mi">65535</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix stl_surf all smd/wall_surface tool.stl 2 65535
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -160,9 +160,7 @@ It is possible to move the triangulated surface via the <a class="reference inte
 <p>Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles
 in the system. See the &#8220;funnel_flow&#8221; example in the USER-SMD examples directory.</p>
 <p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
 </div>
 <div class="section" id="restrictions">
diff --git a/doc/html/fix_spring.html b/doc/html/fix_spring.html
index a1d40fbf68..413066a788 100644
--- a/doc/html/fix_spring.html
+++ b/doc/html/fix_spring.html
@@ -215,9 +215,7 @@ spring command, if the rigid body will cross a periodic boundary.
 This is because image flags for rigid bodies are used in a different
 way, as explained on the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> doc page.</p>
 </div>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the energy stored in the spring to the system&#8217;s potential
diff --git a/doc/html/fix_spring_chunk.html b/doc/html/fix_spring_chunk.html
index 7373fd8e56..5ea20d8a43 100644
--- a/doc/html/fix_spring_chunk.html
+++ b/doc/html/fix_spring_chunk.html
@@ -166,9 +166,7 @@ the mass of the atom, and Mm is the total mass of all atoms in the
 chunk.  Note that <em>K</em> thus represents the spring constant for the
 total force on each chunk of atoms, not for a spring applied to each
 atom.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the energy stored in all the springs to the system&#8217;s potential
diff --git a/doc/html/fix_spring_rg.html b/doc/html/fix_spring_rg.html
index aeaa3bece4..8cb641326c 100644
--- a/doc/html/fix_spring_rg.html
+++ b/doc/html/fix_spring_rg.html
@@ -166,9 +166,7 @@ the mass of the entire group.  Note that K is thus a force constant
 for the aggregate force on the group of atoms, not a per-atom force.</p>
 <p>If RG0 is specified as NULL, then the RG of the group is computed at
 the time the fix is specified, and that value is used as the target.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_spring_self.html b/doc/html/fix_spring_self.html
index dbc542e600..28e33fc5ed 100644
--- a/doc/html/fix_spring_self.html
+++ b/doc/html/fix_spring_self.html
@@ -160,9 +160,7 @@ spring force is applied. By default, the restraint is applied in all
 directions, but it can be limited to the xy-, xz-, yz-plane and the
 x-, y-, or z-direction, thus restraining the atoms to a line or a
 plane, respectively.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the original coordinates of tethered atoms to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that the spring effect will be the
 same in a restarted simulation.  See the
 <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_store_state.html b/doc/html/fix_store_state.html
index 9d236aa13f..0a885ed683 100644
--- a/doc/html/fix_store_state.html
+++ b/doc/html/fix_store_state.html
@@ -137,43 +137,43 @@
 <li>N = store atom attributes every N steps, N = 0 for initial store only</li>
 <li>input = one or more atom attributes</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">possible</span> <span class="n">attributes</span> <span class="o">=</span> <span class="nb">id</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span>
-                   <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">xs</span><span class="p">,</span> <span class="n">ys</span><span class="p">,</span> <span class="n">zs</span><span class="p">,</span> <span class="n">xu</span><span class="p">,</span> <span class="n">yu</span><span class="p">,</span> <span class="n">zu</span><span class="p">,</span> <span class="n">xsu</span><span class="p">,</span> <span class="n">ysu</span><span class="p">,</span> <span class="n">zsu</span><span class="p">,</span> <span class="n">ix</span><span class="p">,</span> <span class="n">iy</span><span class="p">,</span> <span class="n">iz</span><span class="p">,</span>
-                   <span class="n">vx</span><span class="p">,</span> <span class="n">vy</span><span class="p">,</span> <span class="n">vz</span><span class="p">,</span> <span class="n">fx</span><span class="p">,</span> <span class="n">fy</span><span class="p">,</span> <span class="n">fz</span><span class="p">,</span>
-                      <span class="n">q</span><span class="p">,</span> <span class="n">mux</span><span class="p">,</span> <span class="n">muy</span><span class="p">,</span> <span class="n">muz</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span>
-                      <span class="n">radius</span><span class="p">,</span> <span class="n">diameter</span><span class="p">,</span> <span class="n">omegax</span><span class="p">,</span> <span class="n">omegay</span><span class="p">,</span> <span class="n">omegaz</span><span class="p">,</span>
-                      <span class="n">angmomx</span><span class="p">,</span> <span class="n">angmomy</span><span class="p">,</span> <span class="n">angmomz</span><span class="p">,</span> <span class="n">tqx</span><span class="p">,</span> <span class="n">tqy</span><span class="p">,</span> <span class="n">tqz</span><span class="p">,</span>
-                      <span class="n">c_ID</span><span class="p">,</span> <span class="n">c_ID</span><span class="p">[</span><span class="n">N</span><span class="p">],</span> <span class="n">f_ID</span><span class="p">,</span> <span class="n">f_ID</span><span class="p">[</span><span class="n">N</span><span class="p">],</span> <span class="n">v_name</span><span class="p">,</span>
-                      <span class="n">d_name</span><span class="p">,</span> <span class="n">i_name</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">id</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span>
-<span class="n">mol</span> <span class="o">=</span> <span class="n">molecule</span> <span class="n">ID</span>
-<span class="nb">type</span> <span class="o">=</span> <span class="n">atom</span> <span class="nb">type</span>
-<span class="n">mass</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">mass</span>
-<span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span> <span class="o">=</span> <span class="n">unscaled</span> <span class="n">atom</span> <span class="n">coordinates</span>
-<span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="p">,</span><span class="n">zs</span> <span class="o">=</span> <span class="n">scaled</span> <span class="n">atom</span> <span class="n">coordinates</span>
-<span class="n">xu</span><span class="p">,</span><span class="n">yu</span><span class="p">,</span><span class="n">zu</span> <span class="o">=</span> <span class="n">unwrapped</span> <span class="n">atom</span> <span class="n">coordinates</span>
-<span class="n">xsu</span><span class="p">,</span><span class="n">ysu</span><span class="p">,</span><span class="n">zsu</span> <span class="o">=</span> <span class="n">scaled</span> <span class="n">unwrapped</span> <span class="n">atom</span> <span class="n">coordinates</span>
-<span class="n">ix</span><span class="p">,</span><span class="n">iy</span><span class="p">,</span><span class="n">iz</span> <span class="o">=</span> <span class="n">box</span> <span class="n">image</span> <span class="n">that</span> <span class="n">the</span> <span class="n">atom</span> <span class="ow">is</span> <span class="ow">in</span>
-<span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">velocities</span>
-<span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">forces</span> <span class="n">on</span> <span class="n">atoms</span>
-<span class="n">q</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">charge</span>
-<span class="n">mux</span><span class="p">,</span><span class="n">muy</span><span class="p">,</span><span class="n">muz</span> <span class="o">=</span> <span class="n">orientation</span> <span class="n">of</span> <span class="n">dipolar</span> <span class="n">atom</span>
-<span class="n">mu</span> <span class="o">=</span> <span class="n">magnitued</span> <span class="n">of</span> <span class="n">dipole</span> <span class="n">moment</span> <span class="n">of</span> <span class="n">atom</span>
-<span class="n">radius</span><span class="p">,</span><span class="n">diameter</span> <span class="o">=</span> <span class="n">radius</span><span class="o">.</span><span class="n">diameter</span> <span class="n">of</span> <span class="n">spherical</span> <span class="n">particle</span>
-<span class="n">omegax</span><span class="p">,</span><span class="n">omegay</span><span class="p">,</span><span class="n">omegaz</span> <span class="o">=</span> <span class="n">angular</span> <span class="n">velocity</span> <span class="n">of</span> <span class="n">spherical</span> <span class="n">particle</span>
-<span class="n">angmomx</span><span class="p">,</span><span class="n">angmomy</span><span class="p">,</span><span class="n">angmomz</span> <span class="o">=</span> <span class="n">angular</span> <span class="n">momentum</span> <span class="n">of</span> <span class="n">aspherical</span> <span class="n">particle</span>
-<span class="n">tqx</span><span class="p">,</span><span class="n">tqy</span><span class="p">,</span><span class="n">tqz</span> <span class="o">=</span> <span class="n">torque</span> <span class="n">on</span> <span class="n">finite</span><span class="o">-</span><span class="n">size</span> <span class="n">particles</span>
-<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
-<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
-<span class="n">d_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">floating</span> <span class="n">point</span> <span class="n">vector</span> <span class="n">name</span><span class="p">,</span> <span class="n">managed</span> <span class="n">by</span> <span class="n">fix</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span>
-<span class="n">i_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">integer</span> <span class="n">vector</span> <span class="n">name</span><span class="p">,</span> <span class="n">managed</span> <span class="n">by</span> <span class="n">fix</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+possible attributes = id, mol, type, mass,
+                   x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
+                   vx, vy, vz, fx, fy, fz,
+                      q, mux, muy, muz, mu,
+                      radius, diameter, omegax, omegay, omegaz,
+                      angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                      c_ID, c_ID[N], f_ID, f_ID[N], v_name,
+                      d_name, i_name
+</pre>
+<pre class="literal-block">
+id = atom ID
+mol = molecule ID
+type = atom type
+mass = atom mass
+x,y,z = unscaled atom coordinates
+xs,ys,zs = scaled atom coordinates
+xu,yu,zu = unwrapped atom coordinates
+xsu,ysu,zsu = scaled unwrapped atom coordinates
+ix,iy,iz = box image that the atom is in
+vx,vy,vz = atom velocities
+fx,fy,fz = forces on atoms
+q = atom charge
+mux,muy,muz = orientation of dipolar atom
+mu = magnitued of dipole moment of atom
+radius,diameter = radius.diameter of spherical particle
+omegax,omegay,omegaz = angular velocity of spherical particle
+angmomx,angmomy,angmomz = angular momentum of aspherical particle
+tqx,tqy,tqz = torque on finite-size particles
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
+d_name = per-atom floating point vector name, managed by fix property/atom
+i_name = per-atom integer vector name, managed by fix property/atom
+</pre>
 <ul class="simple">
 <li>zero or more keyword/value pairs may be appended</li>
 <li>keyword = <em>com</em></li>
@@ -217,9 +217,7 @@ of the group of atoms, instead of storing the absolute position.</p>
 <p>The requested values are stored in a per-atom vector or array as
 discussed below.  Zeroes are stored for atoms not in the specified
 group.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the per-atom values it stores to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that the values can be restored when a
 simulation is restarted.  See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
 command for info on how to re-specify a fix in an input script that
diff --git a/doc/html/fix_temp_berendsen.html b/doc/html/fix_temp_berendsen.html
index d628854ba7..56ae7e3339 100644
--- a/doc/html/fix_temp_berendsen.html
+++ b/doc/html/fix_temp_berendsen.html
@@ -192,9 +192,9 @@ thermostatting.</p>
 <p>This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style &#8220;temp&#8221;, as if this command had been
 issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details.  Note
 that the ID of the new compute is the fix-ID + underscore + &#8220;temp&#8221;,
 and the group for the new compute is the same as the fix group.</p>
@@ -219,10 +219,8 @@ this case, the thermostat works in the following manner: the current
 temperature is calculated taking the bias into account, bias is
 removed from each atom, thermostatting is performed on the remaining
 thermal degrees of freedom, and the bias is added back in.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
 fix.  You can use it to assign a temperature <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>
diff --git a/doc/html/fix_temp_csvr.html b/doc/html/fix_temp_csvr.html
index 0d3874ecdd..1a1b23cc0d 100644
--- a/doc/html/fix_temp_csvr.html
+++ b/doc/html/fix_temp_csvr.html
@@ -210,9 +210,9 @@ thermostatting.</p>
 <p>These fixes compute a temperature each timestep.  To do this, the fix
 creates its own compute of style &#8220;temp&#8221;, as if this command had been
 issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details.  Note
 that the ID of the new compute is the fix-ID + underscore + &#8220;temp&#8221;,
 and the group for the new compute is the same as the fix group.</p>
@@ -237,10 +237,8 @@ this case, the thermostat works in the following manner: the current
 temperature is calculated taking the bias into account, bias is
 removed from each atom, thermostatting is performed on the remaining
 thermal degrees of freedom, and the bias is added back in.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about these fixes are written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by these
 fixes.  You can use it to assign a temperature <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>
diff --git a/doc/html/fix_temp_rescale.html b/doc/html/fix_temp_rescale.html
index bfa398c38e..2b96f60e2e 100644
--- a/doc/html/fix_temp_rescale.html
+++ b/doc/html/fix_temp_rescale.html
@@ -198,9 +198,9 @@ thermostatting.</p>
 <p>This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style &#8220;temp&#8221;, as if one of this command had
 been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute fix-ID_temp group-ID temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> for details.  Note that the
 ID of the new compute is the fix-ID + underscore + &#8220;temp&#8221;, and the
 group for the new compute is the same as the fix group.</p>
@@ -225,10 +225,8 @@ this case, the thermostat works in the following manner: the current
 temperature is calculated taking the bias into account, bias is
 removed from each atom, thermostatting is performed on the remaining
 thermal degrees of freedom, and the bias is added back in.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
 fix.  You can use it to assign a temperature <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>
diff --git a/doc/html/fix_temp_rescale_eff.html b/doc/html/fix_temp_rescale_eff.html
index 826fcfb6f4..4a5b09b42a 100644
--- a/doc/html/fix_temp_rescale_eff.html
+++ b/doc/html/fix_temp_rescale_eff.html
@@ -154,9 +154,7 @@ their velocities.</p>
 <p>The operation of this fix is exactly like that described by the <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> command, except that the rescaling
 is also applied to the radial electron velocity for electron
 particles.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
 fix.  You can use it to assign a temperature <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>
diff --git a/doc/html/fix_tfmc.html b/doc/html/fix_tfmc.html
index 1fa84393e7..32b9de3cbb 100644
--- a/doc/html/fix_tfmc.html
+++ b/doc/html/fix_tfmc.html
@@ -228,10 +228,8 @@ translations or rotations of the fix group could be induced by these
 external forces, and removing them will lead to a violation of
 detailed balance.</p>
 </div>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options are relevant to this
 fix.</p>
diff --git a/doc/html/fix_thermal_conductivity.html b/doc/html/fix_thermal_conductivity.html
index 97325bd91e..05f63ab2de 100644
--- a/doc/html/fix_thermal_conductivity.html
+++ b/doc/html/fix_thermal_conductivity.html
@@ -180,12 +180,12 @@ of the 2 atoms is performed, to conserve kinetic energy.  Over time,
 this induces a temperature gradient in the system which can be
 measured using commands such as the following, which writes the
 temperature profile (assuming z = edim) to the file tmp.profile:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>   <span class="n">ke</span> <span class="nb">all</span> <span class="n">ke</span><span class="o">/</span><span class="n">atom</span>
-<span class="n">variable</span>  <span class="n">temp</span> <span class="n">atom</span> <span class="n">c_ke</span><span class="o">/</span><span class="mf">1.5</span>
-<span class="n">compute</span>   <span class="n">layers</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="mi">1</span><span class="n">d</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.05</span> <span class="n">units</span> <span class="n">reduced</span>
-<span class="n">fix</span>       <span class="mi">3</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">layers</span> <span class="n">v_temp</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">profile</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute   ke all ke/atom
+variable  temp atom c_ke/1.5
+compute   layers all chunk/atom bin/1d z lower 0.05 units reduced
+fix       3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile
+</pre>
 <p>Note that by default, Nswap = 1, though this can be changed by the
 optional <em>swap</em> keyword.  Setting this parameter appropriately, in
 conjunction with the swap rate N, allows the heat flux to be adjusted
@@ -221,9 +221,7 @@ not in a regime of linear response.  In this case you cannot
 accurately infer a thermal conductivity and should try increasing the
 Nevery parameter.</p>
 </div>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_ti_rs.html b/doc/html/fix_ti_rs.html
index 311cabb702..f298fc952d 100644
--- a/doc/html/fix_ti_rs.html
+++ b/doc/html/fix_ti_rs.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix ti/rs command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ti</span><span class="o">/</span><span class="n">rs</span> <span class="n">lambda_initial</span> <span class="n">lambda_final</span> <span class="n">t_switch</span> <span class="n">t_equil</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ...
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>ti/rs = style name of this fix command</li>
@@ -198,9 +198,7 @@ scaling is faster at temperatures closer to the initial temperature of
 the procedure.</p>
 <p>An example script using this command is provided in the
 examples/USER/misc/ti directory.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>This fix computes a global vector quantitie which can be accessed by
 various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The vector has
diff --git a/doc/html/fix_ti_spring.html b/doc/html/fix_ti_spring.html
index a0a3a6db23..e7d63d947a 100644
--- a/doc/html/fix_ti_spring.html
+++ b/doc/html/fix_ti_spring.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix ti/spring command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ti</span><span class="o">/</span><span class="n">spring</span> <span class="n">K</span> <span class="n">t_switch</span> <span class="n">t_equil</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID ti/spring K t_switch t_equil keyword value ...
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>ti/spring = style name of this fix command</li>
@@ -205,9 +205,7 @@ issues with the canonical sampling of harmonic degrees of freedom
 (notice that the <em>chain</em> option will NOT solve this problem). The
 Langevin thermostat (<a class="reference external" href="fix_langevin.html&quot;">fix langevin</a>) works fine.</p>
 </div>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the original coordinates of tethered atoms to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that the spring effect will be the
 same in a restarted simulation. See the <a class="reference internal" href="read_restart.html"><span class="doc">read restart</span></a> command for info on how to re-specify a fix
 in an input script that reads a restart file, so that the operation of
diff --git a/doc/html/fix_ttm.html b/doc/html/fix_ttm.html
index af630d2964..1b12323895 100644
--- a/doc/html/fix_ttm.html
+++ b/doc/html/fix_ttm.html
@@ -131,50 +131,50 @@
 <h1>fix ttm/mod command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ttm</span> <span class="n">seed</span> <span class="n">C_e</span> <span class="n">rho_e</span> <span class="n">kappa_e</span> <span class="n">gamma_p</span> <span class="n">gamma_s</span> <span class="n">v_0</span> <span class="n">Nx</span> <span class="n">Ny</span> <span class="n">Nz</span> <span class="n">T_infile</span> <span class="n">N</span> <span class="n">T_outfile</span>
-<span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ttm</span><span class="o">/</span><span class="n">mod</span> <span class="n">seed</span> <span class="n">init_file</span> <span class="n">Nx</span> <span class="n">Ny</span> <span class="n">Nz</span> <span class="n">T_infile</span> <span class="n">N</span> <span class="n">T_outfile</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile
+fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>style = <em>ttm</em> or <em>ttm_mod</em></li>
 <li>seed = random number seed to use for white noise (positive integer)</li>
 <li>remaining arguments for fix ttm:</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">C_e</span>  <span class="o">=</span> <span class="n">electronic</span> <span class="n">specific</span> <span class="n">heat</span> <span class="p">(</span><span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">electron</span><span class="o">*</span><span class="n">temperature</span><span class="p">)</span> <span class="n">units</span><span class="p">)</span>
-<span class="n">rho_e</span> <span class="o">=</span> <span class="n">electronic</span> <span class="n">density</span> <span class="p">(</span><span class="n">electrons</span><span class="o">/</span><span class="n">volume</span> <span class="n">units</span><span class="p">)</span>
-<span class="n">kappa_e</span> <span class="o">=</span> <span class="n">electronic</span> <span class="n">thermal</span> <span class="n">conductivity</span> <span class="p">(</span><span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">time</span><span class="o">*</span><span class="n">distance</span><span class="o">*</span><span class="n">temperature</span><span class="p">)</span> <span class="n">units</span><span class="p">)</span>
-<span class="n">gamma_p</span> <span class="o">=</span> <span class="n">friction</span> <span class="n">coefficient</span> <span class="n">due</span> <span class="n">to</span> <span class="n">electron</span><span class="o">-</span><span class="n">ion</span> <span class="n">interactions</span> <span class="p">(</span><span class="n">mass</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span><span class="p">)</span>
-<span class="n">gamma_s</span> <span class="o">=</span> <span class="n">friction</span> <span class="n">coefficient</span> <span class="n">due</span> <span class="n">to</span> <span class="n">electronic</span> <span class="n">stopping</span> <span class="p">(</span><span class="n">mass</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span><span class="p">)</span>
-<span class="n">v_0</span> <span class="o">=</span> <span class="n">electronic</span> <span class="n">stopping</span> <span class="n">critical</span> <span class="n">velocity</span> <span class="p">(</span><span class="n">velocity</span> <span class="n">units</span><span class="p">)</span>
-<span class="n">Nx</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">x</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
-<span class="n">Ny</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">y</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
-<span class="n">Nz</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">z</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
-<span class="n">T_infile</span> <span class="o">=</span> <span class="n">filename</span> <span class="n">to</span> <span class="n">read</span> <span class="n">initial</span> <span class="n">electronic</span> <span class="n">temperature</span> <span class="kn">from</span>
-<span class="nn">N</span> <span class="o">=</span> <span class="n">dump</span> <span class="n">TTM</span> <span class="n">temperatures</span> <span class="n">every</span> <span class="n">this</span> <span class="n">many</span> <span class="n">timesteps</span><span class="p">,</span> <span class="mi">0</span> <span class="o">=</span> <span class="n">no</span> <span class="n">dump</span>
-<span class="n">T_outfile</span> <span class="o">=</span> <span class="n">filename</span> <span class="n">to</span> <span class="n">write</span> <span class="n">TTM</span> <span class="n">temperatures</span> <span class="n">to</span> <span class="p">(</span><span class="n">only</span> <span class="n">needed</span> <span class="k">if</span> <span class="n">N</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+C_e  = electronic specific heat (energy/(electron*temperature) units)
+rho_e = electronic density (electrons/volume units)
+kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
+gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
+gamma_s = friction coefficient due to electronic stopping (mass/time units)
+v_0 = electronic stopping critical velocity (velocity units)
+Nx = number of thermal solve grid points in the x-direction (positive integer)
+Ny = number of thermal solve grid points in the y-direction (positive integer)
+Nz = number of thermal solve grid points in the z-direction (positive integer)
+T_infile = filename to read initial electronic temperature from
+N = dump TTM temperatures every this many timesteps, 0 = no dump
+T_outfile = filename to write TTM temperatures to (only needed if N &gt; 0)
+</pre>
 <ul class="simple">
 <li>remaining arguments for fix ttm/mod:</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">init_file</span> <span class="o">=</span> <span class="n">file</span> <span class="k">with</span> <span class="n">the</span> <span class="n">parameters</span> <span class="n">to</span> <span class="n">TTM</span>
-<span class="n">Nx</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">x</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
-<span class="n">Ny</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">y</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
-<span class="n">Nz</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">z</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
-<span class="n">T_infile</span> <span class="o">=</span> <span class="n">filename</span> <span class="n">to</span> <span class="n">read</span> <span class="n">initial</span> <span class="n">electronic</span> <span class="n">temperature</span> <span class="kn">from</span>
-<span class="nn">N</span> <span class="o">=</span> <span class="n">dump</span> <span class="n">TTM</span> <span class="n">temperatures</span> <span class="n">every</span> <span class="n">this</span> <span class="n">many</span> <span class="n">timesteps</span><span class="p">,</span> <span class="mi">0</span> <span class="o">=</span> <span class="n">no</span> <span class="n">dump</span>
-<span class="n">T_outfile</span> <span class="o">=</span> <span class="n">filename</span> <span class="n">to</span> <span class="n">write</span> <span class="n">TTM</span> <span class="n">temperatures</span> <span class="n">to</span> <span class="p">(</span><span class="n">only</span> <span class="n">needed</span> <span class="k">if</span> <span class="n">N</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+init_file = file with the parameters to TTM
+Nx = number of thermal solve grid points in the x-direction (positive integer)
+Ny = number of thermal solve grid points in the y-direction (positive integer)
+Nz = number of thermal solve grid points in the z-direction (positive integer)
+T_infile = filename to read initial electronic temperature from
+N = dump TTM temperatures every this many timesteps, 0 = no dump
+T_outfile = filename to write TTM temperatures to (only needed if N &gt; 0)
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ttm</span> <span class="mi">699489</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">10</span> <span class="mf">0.1</span> <span class="mf">0.0</span> <span class="mf">2.0</span> <span class="mi">1</span> <span class="mi">12</span> <span class="mi">1</span> <span class="n">initialTs</span> <span class="mi">1000</span> <span class="n">T</span><span class="o">.</span><span class="n">out</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ttm</span> <span class="mi">123456</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">5.0</span> <span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span> <span class="n">Te</span><span class="o">.</span><span class="ow">in</span> <span class="mi">1</span> <span class="n">Te</span><span class="o">.</span><span class="n">out</span>
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ttm</span><span class="o">/</span><span class="n">mod</span> <span class="mi">34277</span> <span class="n">parameters</span><span class="o">.</span><span class="n">txt</span> <span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span> <span class="n">T_init</span> <span class="mi">10</span> <span class="n">T_out</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out
+fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out
+fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -330,34 +330,32 @@ is calculated as</p>
 <p>The fix ttm/mod parameter file <em>init_file</em> has the following syntax/
 Every line with the odd number is considered as a comment and
 ignored. The lines with the even numbers are treated as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">a_0</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
-<span class="n">a_1</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">^</span><span class="mi">2</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
-<span class="n">a_2</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">^</span><span class="mi">3</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
-<span class="n">a_3</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">^</span><span class="mi">4</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
-<span class="n">a_4</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">^</span><span class="mi">5</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
-<span class="n">C_0</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
-<span class="n">A</span><span class="p">,</span> <span class="mi">1</span><span class="o">/</span><span class="n">temperature</span> <span class="n">units</span>
-<span class="n">rho_e</span><span class="p">,</span> <span class="n">electrons</span><span class="o">/</span><span class="n">volume</span> <span class="n">units</span>
-<span class="n">D_e</span><span class="p">,</span> <span class="n">length</span><span class="o">^</span><span class="mi">2</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span>
-<span class="n">gamma_p</span><span class="p">,</span> <span class="n">mass</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span>
-<span class="n">gamma_s</span><span class="p">,</span> <span class="n">mass</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span>
-<span class="n">v_0</span><span class="p">,</span> <span class="n">length</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span>
-<span class="n">I_0</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">time</span><span class="o">*</span><span class="n">length</span><span class="o">^</span><span class="mi">2</span><span class="p">)</span> <span class="n">units</span>
-<span class="n">lsurface</span><span class="p">,</span> <span class="n">electron</span> <span class="n">grid</span> <span class="n">units</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
-<span class="n">rsurface</span><span class="p">,</span> <span class="n">electron</span> <span class="n">grid</span> <span class="n">units</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
-<span class="n">l_skin</span><span class="p">,</span> <span class="n">length</span> <span class="n">units</span>
-<span class="n">tau</span><span class="p">,</span> <span class="n">time</span> <span class="n">units</span>
-<span class="n">B</span><span class="p">,</span> <span class="n">dimensionless</span>
-<span class="k">lambda</span><span class="p">,</span> <span class="n">length</span> <span class="n">units</span>
-<span class="n">n_ion</span><span class="p">,</span> <span class="n">ions</span><span class="o">/</span><span class="n">volume</span> <span class="n">units</span>
-<span class="n">surface_movement</span><span class="p">:</span> <span class="mi">0</span> <span class="n">to</span> <span class="n">disable</span> <span class="n">tracking</span> <span class="n">of</span> <span class="n">surface</span> <span class="n">motion</span><span class="p">,</span> <span class="mi">1</span> <span class="n">to</span> <span class="n">enable</span>
-<span class="n">T_e_min</span><span class="p">,</span> <span class="n">temperature</span> <span class="n">units</span>
-</pre></div>
-</div>
-</div>
+<pre class="literal-block">
+a_0, energy/(temperature*electron) units
+a_1, energy/(temperature^2*electron) units
+a_2, energy/(temperature^3*electron) units
+a_3, energy/(temperature^4*electron) units
+a_4, energy/(temperature^5*electron) units
+C_0, energy/(temperature*electron) units
+A, 1/temperature units
+rho_e, electrons/volume units
+D_e, length^2/time units
+gamma_p, mass/time units
+gamma_s, mass/time units
+v_0, length/time units
+I_0, energy/(time*length^2) units
+lsurface, electron grid units (positive integer)
+rsurface, electron grid units (positive integer)
+l_skin, length units
+tau, time units
+B, dimensionless
+lambda, length units
+n_ion, ions/volume units
+surface_movement: 0 to disable tracking of surface motion, 1 to enable
+T_e_min, temperature units
+</pre>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>These fixes write the state of the electronic subsystem and the energy
 exchange between the subsystems to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command
 for info on how to re-specify a fix in an input script that reads a
diff --git a/doc/html/fix_viscosity.html b/doc/html/fix_viscosity.html
index 03773104e4..16fa977a8f 100644
--- a/doc/html/fix_viscosity.html
+++ b/doc/html/fix_viscosity.html
@@ -226,9 +226,7 @@ deform the simmulation box via the <a class="reference internal" href="fix_defor
 command.  Thus they cannot be run on a charged system using a <a class="reference internal" href="kspace_style.html"><span class="doc">PPPM solver</span></a> since PPPM does not currently support
 non-orthogonal boxes.  Using fix viscosity keeps the box orthogonal;
 thus it does not suffer from this limitation.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.</p>
 <p>This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_viscous.html b/doc/html/fix_viscous.html
index 5bf3e54e0a..e63286eaeb 100644
--- a/doc/html/fix_viscous.html
+++ b/doc/html/fix_viscous.html
@@ -194,10 +194,8 @@ performing the same operation as fix viscous.  Also note that the
 gamma of fix viscous is related to the damping parameter of <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, however the former is specified in units
 of force/velocity and the latter in units of time, so that it can more
 easily be used as a thermostat.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_wall.html b/doc/html/fix_wall.html
index 8f3ac46551..0a1d123b92 100644
--- a/doc/html/fix_wall.html
+++ b/doc/html/fix_wall.html
@@ -179,12 +179,12 @@ args = coord epsilon sigma cutoff
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj93</span> <span class="n">xlo</span> <span class="o">-</span><span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="n">units</span> <span class="n">box</span>
-<span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj93</span> <span class="n">xhi</span> <span class="n">EDGE</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
-<span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj126</span> <span class="n">v_wiggle</span> <span class="mf">23.2</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
-<span class="n">fix</span> <span class="n">zwalls</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">colloid</span> <span class="n">zlo</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.858</span> <span class="n">zhi</span> <span class="mf">40.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.858</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
+fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
+fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
+fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -321,22 +321,22 @@ want.</p>
 in a time-dependent fashion using equal-style
 <a class="reference internal" href="variable.html"><span class="doc">variables</span></a>.  The wall interaction parameters (epsilon,
 sigma) could be varied with additional variable definitions.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ramp</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_ramp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">linear</span> <span class="n">equal</span> <span class="n">vdisplace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_linear</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">swiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_wiggle</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">cwiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_wiggle</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable ramp equal ramp(0,10)
+fix 1 all wall xlo v_ramp 1.0 1.0 2.5
+</pre>
+<pre class="literal-block">
+variable linear equal vdisplace(0,20)
+fix 1 all wall xlo v_linear 1.0 1.0 2.5
+</pre>
+<pre class="literal-block">
+variable wiggle equal swiggle(0.0,5.0,3.0)
+fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
+</pre>
+<pre class="literal-block">
+variable wiggle equal cwiggle(0.0,5.0,3.0)
+fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
+</pre>
 <p>The ramp(lo,hi) function adjusts the wall position linearly from lo to
 hi over the course of a run.  The vdisplace(c0,velocity) function does
 something similar using the equation position = c0 + velocity*delta,
@@ -344,20 +344,18 @@ where delta is the elapsed time.</p>
 <p>The swiggle(c0,A,period) function causes the wall position to
 oscillate sinusoidally according to this equation, where omega = 2 PI
 / period:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+position = c0 + A sin(omega*delta)
+</pre>
 <p>The cwiggle(c0,A,period) function causes the wall position to
 oscillate sinusoidally according to this equation, which will have an
 initial wall velocity of 0.0, and thus may impose a gentler
 perturbation on the particles:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">))</span>
-</pre></div>
-</div>
-</div>
+<pre class="literal-block">
+position = c0 + A (1 - cos(omega*delta))
+</pre>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the energy of interaction between atoms and each wall to
diff --git a/doc/html/fix_wall_gran.html b/doc/html/fix_wall_gran.html
index 08178f888a..b6360f4ffb 100644
--- a/doc/html/fix_wall_gran.html
+++ b/doc/html/fix_wall_gran.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>fix wall/gran command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">wall</span><span class="o">/</span><span class="n">gran</span> <span class="n">Kn</span> <span class="n">Kt</span> <span class="n">fstyle</span> <span class="n">gamma_n</span> <span class="n">gamma_t</span> <span class="n">xmu</span> <span class="n">dampflag</span> <span class="n">wallstyle</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix ID group-ID wall/gran Kn Kt fstyle gamma_n gamma_t xmu dampflag wallstyle args keyword values ...
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
 <li>wall/gran = style name of this fix command</li>
@@ -241,9 +241,9 @@ is perpendicular to the wall, it is more of a shaking motion.  A
 <em>zcylinder</em> wall can only be wiggled in the z dimension.</p>
 <p>Each timestep, the position of a wiggled wall in the appropriate <em>dim</em>
 is set according to this equation:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">coord</span> <span class="o">+</span> <span class="n">A</span> <span class="o">-</span> <span class="n">A</span> <span class="n">cos</span> <span class="p">(</span><span class="n">omega</span> <span class="o">*</span> <span class="n">delta</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+position = coord + A - A cos (omega * delta)
+</pre>
 <p>where <em>coord</em> is the specified initial position of the wall, <em>A</em> is
 the <em>amplitude</em>, <em>omega</em> is 2 PI / <em>period</em>, and <em>delta</em> is the time
 elapsed since the fix was specified.  The velocity of the wall is set
@@ -257,9 +257,7 @@ cylinder is moving in the z-direction along it&#8217;s axis.  A dimension of
 the clockwise direction for <em>vshear</em> &gt; 0 or counter-clockwise for
 <em>vshear</em> &lt; 0.  In this case, <em>vshear</em> is the tangential velocity of
 the wall at whatever <em>radius</em> has been defined.</p>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>This fix writes the shear friction state of atoms interacting with the
 wall to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that a simulation can
 continue correctly if granular potentials with shear &#8220;history&#8221; effects
diff --git a/doc/html/fix_wall_piston.html b/doc/html/fix_wall_piston.html
index ade80b4497..baed71d961 100644
--- a/doc/html/fix_wall_piston.html
+++ b/doc/html/fix_wall_piston.html
@@ -199,10 +199,8 @@ to define a wall position, but only when a numeric constant is used.</p>
 A <em>lattice</em> value means the distance units are in lattice spacings.
 The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
 define the lattice spacings.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html
index 4c6467cd42..9df5dfe8ef 100644
--- a/doc/html/fix_wall_reflect.html
+++ b/doc/html/fix_wall_reflect.html
@@ -162,11 +162,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">xwalls</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">EDGE</span> <span class="n">xhi</span> <span class="n">EDGE</span>
-<span class="n">fix</span> <span class="n">walls</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="mf">0.0</span> <span class="n">ylo</span> <span class="mf">10.0</span> <span class="n">units</span> <span class="n">box</span>
-<span class="n">fix</span> <span class="n">top</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">zhi</span> <span class="n">v_pressdown</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix xwalls all wall/reflect xlo EDGE xhi EDGE
+fix walls all wall/reflect xlo 0.0 ylo 10.0 units box
+fix top all wall/reflect zhi v_pressdown
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -215,22 +215,22 @@ define the lattice spacings.</p>
 <p>Here are examples of variable definitions that move the wall position
 in a time-dependent fashion using equal-style
 <a class="reference internal" href="variable.html"><span class="doc">variables</span></a>.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ramp</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_ramp</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">linear</span> <span class="n">equal</span> <span class="n">vdisplace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_linear</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">swiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_wiggle</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">cwiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_wiggle</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable ramp equal ramp(0,10)
+fix 1 all wall/reflect xlo v_ramp
+</pre>
+<pre class="literal-block">
+variable linear equal vdisplace(0,20)
+fix 1 all wall/reflect xlo v_linear
+</pre>
+<pre class="literal-block">
+variable wiggle equal swiggle(0.0,5.0,3.0)
+fix 1 all wall/reflect xlo v_wiggle
+</pre>
+<pre class="literal-block">
+variable wiggle equal cwiggle(0.0,5.0,3.0)
+fix 1 all wall/reflect xlo v_wiggle
+</pre>
 <p>The ramp(lo,hi) function adjusts the wall position linearly from lo to
 hi over the course of a run.  The vdisplace(c0,velocity) function does
 something similar using the equation position = c0 + velocity*delta,
@@ -238,16 +238,16 @@ where delta is the elapsed time.</p>
 <p>The swiggle(c0,A,period) function causes the wall position to
 oscillate sinusoidally according to this equation, where omega = 2 PI
 / period:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+position = c0 + A sin(omega*delta)
+</pre>
 <p>The cwiggle(c0,A,period) function causes the wall position to
 oscillate sinusoidally according to this equation, which will have an
 initial wall velocity of 0.0, and thus may impose a gentler
 perturbation on the particles:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">))</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+position = c0 + A (1 - cos(omega*delta))
+</pre>
 <hr class="docutils" />
 <p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
 functionally the same as the corresponding style without the suffix.
@@ -264,10 +264,8 @@ by including their suffix, or you can use the <a class="reference internal" href
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
 <p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
 more instructions on how to use the accelerated styles effectively.</p>
-</div>
 <hr class="docutils" />
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
diff --git a/doc/html/fix_wall_region.html b/doc/html/fix_wall_region.html
index 4f24bee99a..ba645d66ef 100644
--- a/doc/html/fix_wall_region.html
+++ b/doc/html/fix_wall_region.html
@@ -280,9 +280,7 @@ and does not blow up as r -&gt; 0, but you must use a large enough
 <em>epsilon</em> that particles always reamin on the correct side of the
 region surface (r &gt; 0).</p>
 </div>
-</div>
-<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
-<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
+<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
 <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the energy of interaction between atoms and the wall to the
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index b30e351edf..b40e27bf00 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -156,93 +156,93 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="angle_coeff.html#index-0">angle_coeff</a>
+  <dt><a href="angle_coeff.html#index-0">angle\_coeff</a>
   </dt>
 
       
-  <dt><a href="angle_style.html#index-0">angle_style</a>
+  <dt><a href="angle_style.html#index-0">angle\_style</a>
   </dt>
 
       
-  <dt><a href="angle_charmm.html#index-0">angle_style charmm</a>
+  <dt><a href="angle_charmm.html#index-0">angle\_style charmm</a>
   </dt>
 
       
-  <dt><a href="angle_class2.html#index-0">angle_style class2</a>
+  <dt><a href="angle_class2.html#index-0">angle\_style class2</a>
   </dt>
 
       
-  <dt><a href="angle_cosine.html#index-0">angle_style cosine</a>
+  <dt><a href="angle_cosine.html#index-0">angle\_style cosine</a>
   </dt>
 
       
-  <dt><a href="angle_cosine_delta.html#index-0">angle_style cosine/delta</a>
+  <dt><a href="angle_cosine_delta.html#index-0">angle\_style cosine/delta</a>
   </dt>
 
       
-  <dt><a href="angle_cosine_periodic.html#index-0">angle_style cosine/periodic</a>
+  <dt><a href="angle_cosine_periodic.html#index-0">angle\_style cosine/periodic</a>
   </dt>
 
       
-  <dt><a href="angle_cosine_shift.html#index-0">angle_style cosine/shift</a>
+  <dt><a href="angle_cosine_shift.html#index-0">angle\_style cosine/shift</a>
   </dt>
 
       
-  <dt><a href="angle_cosine_shift_exp.html#index-0">angle_style cosine/shift/exp</a>
+  <dt><a href="angle_cosine_shift_exp.html#index-0">angle\_style cosine/shift/exp</a>
   </dt>
 
       
-  <dt><a href="angle_cosine_squared.html#index-0">angle_style cosine/squared</a>
+  <dt><a href="angle_cosine_squared.html#index-0">angle\_style cosine/squared</a>
   </dt>
 
       
-  <dt><a href="angle_dipole.html#index-0">angle_style dipole</a>
+  <dt><a href="angle_dipole.html#index-0">angle\_style dipole</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="angle_fourier.html#index-0">angle_style fourier</a>
+  <dt><a href="angle_fourier.html#index-0">angle\_style fourier</a>
   </dt>
 
       
-  <dt><a href="angle_fourier_simple.html#index-0">angle_style fourier/simple</a>
+  <dt><a href="angle_fourier_simple.html#index-0">angle\_style fourier/simple</a>
   </dt>
 
       
-  <dt><a href="angle_harmonic.html#index-0">angle_style harmonic</a>
+  <dt><a href="angle_harmonic.html#index-0">angle\_style harmonic</a>
   </dt>
 
       
-  <dt><a href="angle_hybrid.html#index-0">angle_style hybrid</a>
+  <dt><a href="angle_hybrid.html#index-0">angle\_style hybrid</a>
   </dt>
 
       
-  <dt><a href="angle_none.html#index-0">angle_style none</a>
+  <dt><a href="angle_none.html#index-0">angle\_style none</a>
   </dt>
 
       
-  <dt><a href="angle_quartic.html#index-0">angle_style quartic</a>
+  <dt><a href="angle_quartic.html#index-0">angle\_style quartic</a>
   </dt>
 
       
-  <dt><a href="angle_sdk.html#index-0">angle_style sdk</a>
+  <dt><a href="angle_sdk.html#index-0">angle\_style sdk</a>
   </dt>
 
       
-  <dt><a href="angle_table.html#index-0">angle_style table</a>
+  <dt><a href="angle_table.html#index-0">angle\_style table</a>
   </dt>
 
       
-  <dt><a href="angle_zero.html#index-0">angle_style zero</a>
+  <dt><a href="angle_zero.html#index-0">angle\_style zero</a>
   </dt>
 
       
-  <dt><a href="atom_modify.html#index-0">atom_modify</a>
+  <dt><a href="atom_modify.html#index-0">atom\_modify</a>
   </dt>
 
       
-  <dt><a href="atom_style.html#index-0">atom_style</a>
+  <dt><a href="atom_style.html#index-0">atom\_style</a>
   </dt>
 
   </dl></td>
@@ -256,69 +256,69 @@
   </dt>
 
       
-  <dt><a href="bond_coeff.html#index-0">bond_coeff</a>
+  <dt><a href="bond_coeff.html#index-0">bond\_coeff</a>
   </dt>
 
       
-  <dt><a href="bond_style.html#index-0">bond_style</a>
+  <dt><a href="bond_style.html#index-0">bond\_style</a>
   </dt>
 
       
-  <dt><a href="bond_class2.html#index-0">bond_style class2</a>
+  <dt><a href="bond_class2.html#index-0">bond\_style class2</a>
   </dt>
 
       
-  <dt><a href="bond_fene.html#index-0">bond_style fene</a>
+  <dt><a href="bond_fene.html#index-0">bond\_style fene</a>
   </dt>
 
       
-  <dt><a href="bond_fene_expand.html#index-0">bond_style fene/expand</a>
+  <dt><a href="bond_fene_expand.html#index-0">bond\_style fene/expand</a>
   </dt>
 
       
-  <dt><a href="bond_harmonic.html#index-0">bond_style harmonic</a>
+  <dt><a href="bond_harmonic.html#index-0">bond\_style harmonic</a>
   </dt>
 
       
-  <dt><a href="bond_harmonic_shift.html#index-0">bond_style harmonic/shift</a>
+  <dt><a href="bond_harmonic_shift.html#index-0">bond\_style harmonic/shift</a>
   </dt>
 
       
-  <dt><a href="bond_harmonic_shift_cut.html#index-0">bond_style harmonic/shift/cut</a>
+  <dt><a href="bond_harmonic_shift_cut.html#index-0">bond\_style harmonic/shift/cut</a>
   </dt>
 
       
-  <dt><a href="bond_hybrid.html#index-0">bond_style hybrid</a>
+  <dt><a href="bond_hybrid.html#index-0">bond\_style hybrid</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="bond_morse.html#index-0">bond_style morse</a>
+  <dt><a href="bond_morse.html#index-0">bond\_style morse</a>
   </dt>
 
       
-  <dt><a href="bond_none.html#index-0">bond_style none</a>
+  <dt><a href="bond_none.html#index-0">bond\_style none</a>
   </dt>
 
       
-  <dt><a href="bond_nonlinear.html#index-0">bond_style nonlinear</a>
+  <dt><a href="bond_nonlinear.html#index-0">bond\_style nonlinear</a>
   </dt>
 
       
-  <dt><a href="bond_quartic.html#index-0">bond_style quartic</a>
+  <dt><a href="bond_quartic.html#index-0">bond\_style quartic</a>
   </dt>
 
       
-  <dt><a href="bond_table.html#index-0">bond_style table</a>
+  <dt><a href="bond_table.html#index-0">bond\_style table</a>
   </dt>
 
       
-  <dt><a href="bond_zero.html#index-0">bond_style zero</a>
+  <dt><a href="bond_zero.html#index-0">bond\_style zero</a>
   </dt>
 
       
-  <dt><a href="bond_write.html#index-0">bond_write</a>
+  <dt><a href="bond_write.html#index-0">bond\_write</a>
   </dt>
 
       
@@ -336,7 +336,7 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="change_box.html#index-0">change_box</a>
+  <dt><a href="change_box.html#index-0">change\_box</a>
   </dt>
 
       
@@ -344,11 +344,11 @@
   </dt>
 
       
-  <dt><a href="comm_modify.html#index-0">comm_modify</a>
+  <dt><a href="comm_modify.html#index-0">comm\_modify</a>
   </dt>
 
       
-  <dt><a href="comm_style.html#index-0">comm_style</a>
+  <dt><a href="comm_style.html#index-0">comm\_style</a>
   </dt>
 
       
@@ -798,19 +798,19 @@
   </dt>
 
       
-  <dt><a href="compute_modify.html#index-0">compute_modify</a>
+  <dt><a href="compute_modify.html#index-0">compute\_modify</a>
   </dt>
 
       
-  <dt><a href="create_atoms.html#index-0">create_atoms</a>
+  <dt><a href="create_atoms.html#index-0">create\_atoms</a>
   </dt>
 
       
-  <dt><a href="create_bonds.html#index-0">create_bonds</a>
+  <dt><a href="create_bonds.html#index-0">create\_bonds</a>
   </dt>
 
       
-  <dt><a href="create_box.html#index-0">create_box</a>
+  <dt><a href="create_box.html#index-0">create\_box</a>
   </dt>
 
   </dl></td>
@@ -820,11 +820,11 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="delete_atoms.html#index-0">delete_atoms</a>
+  <dt><a href="delete_atoms.html#index-0">delete\_atoms</a>
   </dt>
 
       
-  <dt><a href="delete_bonds.html#index-0">delete_bonds</a>
+  <dt><a href="delete_bonds.html#index-0">delete\_bonds</a>
   </dt>
 
       
@@ -832,73 +832,73 @@
   </dt>
 
       
-  <dt><a href="dihedral_coeff.html#index-0">dihedral_coeff</a>
+  <dt><a href="dihedral_coeff.html#index-0">dihedral\_coeff</a>
   </dt>
 
       
-  <dt><a href="dihedral_style.html#index-0">dihedral_style</a>
+  <dt><a href="dihedral_style.html#index-0">dihedral\_style</a>
   </dt>
 
       
-  <dt><a href="dihedral_charmm.html#index-0">dihedral_style charmm</a>
+  <dt><a href="dihedral_charmm.html#index-0">dihedral\_style charmm</a>
   </dt>
 
       
-  <dt><a href="dihedral_class2.html#index-0">dihedral_style class2</a>
+  <dt><a href="dihedral_class2.html#index-0">dihedral\_style class2</a>
   </dt>
 
       
-  <dt><a href="dihedral_cosine_shift_exp.html#index-0">dihedral_style cosine/shift/exp</a>
+  <dt><a href="dihedral_cosine_shift_exp.html#index-0">dihedral\_style cosine/shift/exp</a>
   </dt>
 
       
-  <dt><a href="dihedral_fourier.html#index-0">dihedral_style fourier</a>
+  <dt><a href="dihedral_fourier.html#index-0">dihedral\_style fourier</a>
   </dt>
 
       
-  <dt><a href="dihedral_harmonic.html#index-0">dihedral_style harmonic</a>
+  <dt><a href="dihedral_harmonic.html#index-0">dihedral\_style harmonic</a>
   </dt>
 
       
-  <dt><a href="dihedral_helix.html#index-0">dihedral_style helix</a>
+  <dt><a href="dihedral_helix.html#index-0">dihedral\_style helix</a>
   </dt>
 
       
-  <dt><a href="dihedral_hybrid.html#index-0">dihedral_style hybrid</a>
+  <dt><a href="dihedral_hybrid.html#index-0">dihedral\_style hybrid</a>
   </dt>
 
       
-  <dt><a href="dihedral_multi_harmonic.html#index-0">dihedral_style multi/harmonic</a>
+  <dt><a href="dihedral_multi_harmonic.html#index-0">dihedral\_style multi/harmonic</a>
   </dt>
 
       
-  <dt><a href="dihedral_nharmonic.html#index-0">dihedral_style nharmonic</a>
+  <dt><a href="dihedral_nharmonic.html#index-0">dihedral\_style nharmonic</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="dihedral_none.html#index-0">dihedral_style none</a>
+  <dt><a href="dihedral_none.html#index-0">dihedral\_style none</a>
   </dt>
 
       
-  <dt><a href="dihedral_opls.html#index-0">dihedral_style opls</a>
+  <dt><a href="dihedral_opls.html#index-0">dihedral\_style opls</a>
   </dt>
 
       
-  <dt><a href="dihedral_quadratic.html#index-0">dihedral_style quadratic</a>
+  <dt><a href="dihedral_quadratic.html#index-0">dihedral\_style quadratic</a>
   </dt>
 
       
-  <dt><a href="dihedral_spherical.html#index-0">dihedral_style spherical</a>
+  <dt><a href="dihedral_spherical.html#index-0">dihedral\_style spherical</a>
   </dt>
 
       
-  <dt><a href="dihedral_table.html#index-0">dihedral_style table</a>
+  <dt><a href="dihedral_table.html#index-0">dihedral\_style table</a>
   </dt>
 
       
-  <dt><a href="dihedral_zero.html#index-0">dihedral_style zero</a>
+  <dt><a href="dihedral_zero.html#index-0">dihedral\_style zero</a>
   </dt>
 
       
@@ -906,7 +906,7 @@
   </dt>
 
       
-  <dt><a href="displace_atoms.html#index-0">displace_atoms</a>
+  <dt><a href="displace_atoms.html#index-0">displace\_atoms</a>
   </dt>
 
       
@@ -930,7 +930,7 @@
   </dt>
 
       
-  <dt><a href="dump_modify.html#index-0">dump_modify</a>
+  <dt><a href="dump_modify.html#index-0">dump\_modify</a>
   </dt>
 
   </dl></td>
@@ -1408,19 +1408,19 @@
   </dt>
 
       
-  <dt><a href="fix_smd_adjust_dt.html#index-0">fix smd/adjust_dt</a>
+  <dt><a href="fix_smd_adjust_dt.html#index-0">fix smd/adjust\_dt</a>
   </dt>
 
       
-  <dt><a href="fix_smd_integrate_tlsph.html#index-0">fix smd/integrate_tlsph</a>
+  <dt><a href="fix_smd_integrate_tlsph.html#index-0">fix smd/integrate\_tlsph</a>
   </dt>
 
       
-  <dt><a href="fix_smd_integrate_ulsph.html#index-0">fix smd/integrate_ulsph</a>
+  <dt><a href="fix_smd_integrate_ulsph.html#index-0">fix smd/integrate\_ulsph</a>
   </dt>
 
       
-  <dt><a href="fix_smd_move_triangulated_surface.html#index-0">fix smd/move_tri_surf</a>
+  <dt><a href="fix_smd_move_triangulated_surface.html#index-0">fix smd/move\_tri\_surf</a>
   </dt>
 
       
@@ -1428,7 +1428,7 @@
   </dt>
 
       
-  <dt><a href="fix_smd_wall_surface.html#index-0">fix smd/wall_surface</a>
+  <dt><a href="fix_smd_wall_surface.html#index-0">fix smd/wall\_surface</a>
   </dt>
 
       
@@ -1540,7 +1540,7 @@
   </dt>
 
       
-  <dt><a href="fix_modify.html#index-0">fix_modify</a>
+  <dt><a href="fix_modify.html#index-0">fix\_modify</a>
   </dt>
 
   </dl></td>
@@ -1570,57 +1570,57 @@
   </dt>
 
       
-  <dt><a href="improper_coeff.html#index-0">improper_coeff</a>
+  <dt><a href="improper_coeff.html#index-0">improper\_coeff</a>
   </dt>
 
       
-  <dt><a href="improper_style.html#index-0">improper_style</a>
+  <dt><a href="improper_style.html#index-0">improper\_style</a>
   </dt>
 
       
-  <dt><a href="improper_class2.html#index-0">improper_style class2</a>
+  <dt><a href="improper_class2.html#index-0">improper\_style class2</a>
   </dt>
 
       
-  <dt><a href="improper_cossq.html#index-0">improper_style cossq</a>
+  <dt><a href="improper_cossq.html#index-0">improper\_style cossq</a>
   </dt>
 
       
-  <dt><a href="improper_cvff.html#index-0">improper_style cvff</a>
+  <dt><a href="improper_cvff.html#index-0">improper\_style cvff</a>
   </dt>
 
       
-  <dt><a href="improper_distance.html#index-0">improper_style distance</a>
+  <dt><a href="improper_distance.html#index-0">improper\_style distance</a>
   </dt>
 
       
-  <dt><a href="improper_fourier.html#index-0">improper_style fourier</a>
+  <dt><a href="improper_fourier.html#index-0">improper\_style fourier</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="improper_harmonic.html#index-0">improper_style harmonic</a>
+  <dt><a href="improper_harmonic.html#index-0">improper\_style harmonic</a>
   </dt>
 
       
-  <dt><a href="improper_hybrid.html#index-0">improper_style hybrid</a>
+  <dt><a href="improper_hybrid.html#index-0">improper\_style hybrid</a>
   </dt>
 
       
-  <dt><a href="improper_none.html#index-0">improper_style none</a>
+  <dt><a href="improper_none.html#index-0">improper\_style none</a>
   </dt>
 
       
-  <dt><a href="improper_ring.html#index-0">improper_style ring</a>
+  <dt><a href="improper_ring.html#index-0">improper\_style ring</a>
   </dt>
 
       
-  <dt><a href="improper_umbrella.html#index-0">improper_style umbrella</a>
+  <dt><a href="improper_umbrella.html#index-0">improper\_style umbrella</a>
   </dt>
 
       
-  <dt><a href="improper_zero.html#index-0">improper_style zero</a>
+  <dt><a href="improper_zero.html#index-0">improper\_style zero</a>
   </dt>
 
       
@@ -1648,13 +1648,13 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="kspace_modify.html#index-0">kspace_modify</a>
+  <dt><a href="kspace_modify.html#index-0">kspace\_modify</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="kspace_style.html#index-0">kspace_style</a>
+  <dt><a href="kspace_style.html#index-0">kspace\_style</a>
   </dt>
 
   </dl></td>
@@ -1688,11 +1688,11 @@
   </dt>
 
       
-  <dt><a href="min_modify.html#index-0">min_modify</a>
+  <dt><a href="min_modify.html#index-0">min\_modify</a>
   </dt>
 
       
-  <dt><a href="min_style.html#index-0">min_style</a>
+  <dt><a href="min_style.html#index-0">min\_style</a>
   </dt>
 
   </dl></td>
@@ -1716,7 +1716,7 @@
   </dt>
 
       
-  <dt><a href="neigh_modify.html#index-0">neigh_modify</a>
+  <dt><a href="neigh_modify.html#index-0">neigh\_modify</a>
   </dt>
 
       
@@ -1744,385 +1744,385 @@
   </dt>
 
       
-  <dt><a href="pair_coeff.html#index-0">pair_coeff</a>
+  <dt><a href="pair_coeff.html#index-0">pair\_coeff</a>
   </dt>
 
       
-  <dt><a href="pair_modify.html#index-0">pair_modify</a>
+  <dt><a href="pair_modify.html#index-0">pair\_modify</a>
   </dt>
 
       
-  <dt><a href="pair_style.html#index-0">pair_style</a>
+  <dt><a href="pair_style.html#index-0">pair\_style</a>
   </dt>
 
       
-  <dt><a href="pair_adp.html#index-0">pair_style adp</a>
+  <dt><a href="pair_adp.html#index-0">pair\_style adp</a>
   </dt>
 
       
-  <dt><a href="pair_airebo.html#index-0">pair_style airebo</a>
+  <dt><a href="pair_airebo.html#index-0">pair\_style airebo</a>
   </dt>
 
       
-  <dt><a href="pair_awpmd.html#index-0">pair_style awpmd/cut</a>
+  <dt><a href="pair_awpmd.html#index-0">pair\_style awpmd/cut</a>
   </dt>
 
       
-  <dt><a href="pair_beck.html#index-0">pair_style beck</a>
+  <dt><a href="pair_beck.html#index-0">pair\_style beck</a>
   </dt>
 
       
-  <dt><a href="pair_body.html#index-0">pair_style body</a>
+  <dt><a href="pair_body.html#index-0">pair\_style body</a>
   </dt>
 
       
-  <dt><a href="pair_bop.html#index-0">pair_style bop</a>
+  <dt><a href="pair_bop.html#index-0">pair\_style bop</a>
   </dt>
 
       
-  <dt><a href="pair_born.html#index-0">pair_style born</a>
+  <dt><a href="pair_born.html#index-0">pair\_style born</a>
   </dt>
 
       
-  <dt><a href="pair_cs.html#index-0">pair_style born/coul/long/cs</a>
+  <dt><a href="pair_cs.html#index-0">pair\_style born/coul/long/cs</a>
   </dt>
 
       
-  <dt><a href="pair_brownian.html#index-0">pair_style brownian</a>
+  <dt><a href="pair_brownian.html#index-0">pair\_style brownian</a>
   </dt>
 
       
-  <dt><a href="pair_buck.html#index-0">pair_style buck</a>
+  <dt><a href="pair_buck.html#index-0">pair\_style buck</a>
   </dt>
 
       
-  <dt><a href="pair_buck_long.html#index-0">pair_style buck/long/coul/long</a>
+  <dt><a href="pair_buck_long.html#index-0">pair\_style buck/long/coul/long</a>
   </dt>
 
       
-  <dt><a href="pair_colloid.html#index-0">pair_style colloid</a>
+  <dt><a href="pair_colloid.html#index-0">pair\_style colloid</a>
   </dt>
 
       
-  <dt><a href="pair_comb.html#index-0">pair_style comb</a>
+  <dt><a href="pair_comb.html#index-0">pair\_style comb</a>
   </dt>
 
       
-  <dt><a href="pair_coul.html#index-0">pair_style coul/cut</a>
+  <dt><a href="pair_coul.html#index-0">pair\_style coul/cut</a>
   </dt>
 
       
-  <dt><a href="pair_coul_diel.html#index-0">pair_style coul/diel</a>
+  <dt><a href="pair_coul_diel.html#index-0">pair\_style coul/diel</a>
   </dt>
 
       
-  <dt><a href="pair_dpd.html#index-0">pair_style dpd</a>
+  <dt><a href="pair_dpd.html#index-0">pair\_style dpd</a>
   </dt>
 
       
-  <dt><a href="pair_dpd_fdt.html#index-0">pair_style dpd/fdt</a>
+  <dt><a href="pair_dpd_fdt.html#index-0">pair\_style dpd/fdt</a>
   </dt>
 
       
-  <dt><a href="pair_dsmc.html#index-0">pair_style dsmc</a>
+  <dt><a href="pair_dsmc.html#index-0">pair\_style dsmc</a>
   </dt>
 
       
-  <dt><a href="pair_eam.html#index-0">pair_style eam</a>
+  <dt><a href="pair_eam.html#index-0">pair\_style eam</a>
   </dt>
 
       
-  <dt><a href="pair_edip.html#index-0">pair_style edip</a>
+  <dt><a href="pair_edip.html#index-0">pair\_style edip</a>
   </dt>
 
       
-  <dt><a href="pair_eff.html#index-0">pair_style eff/cut</a>
+  <dt><a href="pair_eff.html#index-0">pair\_style eff/cut</a>
   </dt>
 
       
-  <dt><a href="pair_eim.html#index-0">pair_style eim</a>
+  <dt><a href="pair_eim.html#index-0">pair\_style eim</a>
   </dt>
 
       
-  <dt><a href="pair_exp6_rx.html#index-0">pair_style exp6/rx</a>
+  <dt><a href="pair_exp6_rx.html#index-0">pair\_style exp6/rx</a>
   </dt>
 
       
-  <dt><a href="pair_gauss.html#index-0">pair_style gauss</a>
+  <dt><a href="pair_gauss.html#index-0">pair\_style gauss</a>
   </dt>
 
       
-  <dt><a href="pair_gayberne.html#index-0">pair_style gayberne</a>
+  <dt><a href="pair_gayberne.html#index-0">pair\_style gayberne</a>
   </dt>
 
       
-  <dt><a href="pair_gran.html#index-0">pair_style gran/hooke</a>
+  <dt><a href="pair_gran.html#index-0">pair\_style gran/hooke</a>
   </dt>
 
       
-  <dt><a href="pair_hbond_dreiding.html#index-0">pair_style hbond/dreiding/lj</a>
+  <dt><a href="pair_hbond_dreiding.html#index-0">pair\_style hbond/dreiding/lj</a>
   </dt>
 
       
-  <dt><a href="pair_hybrid.html#index-0">pair_style hybrid</a>
+  <dt><a href="pair_hybrid.html#index-0">pair\_style hybrid</a>
   </dt>
 
       
-  <dt><a href="pair_kim.html#index-0">pair_style kim</a>
+  <dt><a href="pair_kim.html#index-0">pair\_style kim</a>
   </dt>
 
       
-  <dt><a href="pair_lcbop.html#index-0">pair_style lcbop</a>
+  <dt><a href="pair_lcbop.html#index-0">pair\_style lcbop</a>
   </dt>
 
       
-  <dt><a href="pair_line_lj.html#index-0">pair_style line/lj</a>
+  <dt><a href="pair_line_lj.html#index-0">pair\_style line/lj</a>
   </dt>
 
       
-  <dt><a href="pair_list.html#index-0">pair_style list</a>
+  <dt><a href="pair_list.html#index-0">pair\_style list</a>
   </dt>
 
       
-  <dt><a href="pair_charmm.html#index-0">pair_style lj/charmm/coul/charmm</a>
+  <dt><a href="pair_charmm.html#index-0">pair\_style lj/charmm/coul/charmm</a>
   </dt>
 
       
-  <dt><a href="pair_class2.html#index-0">pair_style lj/class2</a>
+  <dt><a href="pair_class2.html#index-0">pair\_style lj/class2</a>
   </dt>
 
       
-  <dt><a href="pair_lj_cubic.html#index-0">pair_style lj/cubic</a>
+  <dt><a href="pair_lj_cubic.html#index-0">pair\_style lj/cubic</a>
   </dt>
 
       
-  <dt><a href="pair_lj.html#index-0">pair_style lj/cut</a>
+  <dt><a href="pair_lj.html#index-0">pair\_style lj/cut</a>
   </dt>
 
       
-  <dt><a href="pair_dipole.html#index-0">pair_style lj/cut/dipole/cut</a>
+  <dt><a href="pair_dipole.html#index-0">pair\_style lj/cut/dipole/cut</a>
   </dt>
 
       
-  <dt><a href="pair_lj_soft.html#index-0">pair_style lj/cut/soft</a>
+  <dt><a href="pair_lj_soft.html#index-0">pair\_style lj/cut/soft</a>
   </dt>
 
       
-  <dt><a href="pair_lj_expand.html#index-0">pair_style lj/expand</a>
+  <dt><a href="pair_lj_expand.html#index-0">pair\_style lj/expand</a>
   </dt>
 
       
-  <dt><a href="pair_gromacs.html#index-0">pair_style lj/gromacs</a>
+  <dt><a href="pair_gromacs.html#index-0">pair\_style lj/gromacs</a>
   </dt>
 
       
-  <dt><a href="pair_lj_long.html#index-0">pair_style lj/long/coul/long</a>
+  <dt><a href="pair_lj_long.html#index-0">pair\_style lj/long/coul/long</a>
   </dt>
 
       
-  <dt><a href="pair_mdf.html#index-0">pair_style lj/mdf</a>
+  <dt><a href="pair_mdf.html#index-0">pair\_style lj/mdf</a>
   </dt>
 
       
-  <dt><a href="pair_sdk.html#index-0">pair_style lj/sdk</a>
+  <dt><a href="pair_sdk.html#index-0">pair\_style lj/sdk</a>
   </dt>
 
       
-  <dt><a href="pair_lj_sf.html#index-0">pair_style lj/sf</a>
+  <dt><a href="pair_lj_sf.html#index-0">pair\_style lj/sf</a>
   </dt>
 
       
-  <dt><a href="pair_lj_smooth.html#index-0">pair_style lj/smooth</a>
+  <dt><a href="pair_lj_smooth.html#index-0">pair\_style lj/smooth</a>
   </dt>
 
       
-  <dt><a href="pair_lj_smooth_linear.html#index-0">pair_style lj/smooth/linear</a>
+  <dt><a href="pair_lj_smooth_linear.html#index-0">pair\_style lj/smooth/linear</a>
   </dt>
 
       
-  <dt><a href="pair_lj96.html#index-0">pair_style lj96/cut</a>
+  <dt><a href="pair_lj96.html#index-0">pair\_style lj96/cut</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="pair_lubricate.html#index-0">pair_style lubricate</a>
+  <dt><a href="pair_lubricate.html#index-0">pair\_style lubricate</a>
   </dt>
 
       
-  <dt><a href="pair_lubricateU.html#index-0">pair_style lubricateU</a>
+  <dt><a href="pair_lubricateU.html#index-0">pair\_style lubricateU</a>
   </dt>
 
       
-  <dt><a href="pair_meam.html#index-0">pair_style meam</a>
+  <dt><a href="pair_meam.html#index-0">pair\_style meam</a>
   </dt>
 
       
-  <dt><a href="pair_mgpt.html#index-0">pair_style mgpt</a>
+  <dt><a href="pair_mgpt.html#index-0">pair\_style mgpt</a>
   </dt>
 
       
-  <dt><a href="pair_mie.html#index-0">pair_style mie/cut</a>
+  <dt><a href="pair_mie.html#index-0">pair\_style mie/cut</a>
   </dt>
 
       
-  <dt><a href="pair_morse.html#index-0">pair_style morse</a>
+  <dt><a href="pair_morse.html#index-0">pair\_style morse</a>
   </dt>
 
       
-  <dt><a href="pair_multi_lucy.html#index-0">pair_style multi/lucy</a>
+  <dt><a href="pair_multi_lucy.html#index-0">pair\_style multi/lucy</a>
   </dt>
 
       
-  <dt><a href="pair_multi_lucy_rx.html#index-0">pair_style multi/lucy/rx</a>
+  <dt><a href="pair_multi_lucy_rx.html#index-0">pair\_style multi/lucy/rx</a>
   </dt>
 
       
-  <dt><a href="pair_nb3b_harmonic.html#index-0">pair_style nb3b/harmonic</a>
+  <dt><a href="pair_nb3b_harmonic.html#index-0">pair\_style nb3b/harmonic</a>
   </dt>
 
       
-  <dt><a href="pair_nm.html#index-0">pair_style nm/cut</a>
+  <dt><a href="pair_nm.html#index-0">pair\_style nm/cut</a>
   </dt>
 
       
-  <dt><a href="pair_none.html#index-0">pair_style none</a>
+  <dt><a href="pair_none.html#index-0">pair\_style none</a>
   </dt>
 
       
-  <dt><a href="pair_peri.html#index-0">pair_style peri/pmb</a>
+  <dt><a href="pair_peri.html#index-0">pair\_style peri/pmb</a>
   </dt>
 
       
-  <dt><a href="pair_polymorphic.html#index-0">pair_style polymorphic</a>
+  <dt><a href="pair_polymorphic.html#index-0">pair\_style polymorphic</a>
   </dt>
 
       
-  <dt><a href="pair_quip.html#index-0">pair_style quip</a>
+  <dt><a href="pair_quip.html#index-0">pair\_style quip</a>
   </dt>
 
       
-  <dt><a href="pair_reax.html#index-0">pair_style reax</a>
+  <dt><a href="pair_reax.html#index-0">pair\_style reax</a>
   </dt>
 
       
-  <dt><a href="pair_reax_c.html#index-0">pair_style reax/c</a>
+  <dt><a href="pair_reax_c.html#index-0">pair\_style reax/c</a>
   </dt>
 
       
-  <dt><a href="pair_resquared.html#index-0">pair_style resquared</a>
+  <dt><a href="pair_resquared.html#index-0">pair\_style resquared</a>
   </dt>
 
       
-  <dt><a href="pair_smd_hertz.html#index-0">pair_style smd/hertz</a>
+  <dt><a href="pair_smd_hertz.html#index-0">pair\_style smd/hertz</a>
   </dt>
 
       
-  <dt><a href="pair_smd_tlsph.html#index-0">pair_style smd/tlsph</a>
+  <dt><a href="pair_smd_tlsph.html#index-0">pair\_style smd/tlsph</a>
   </dt>
 
       
-  <dt><a href="pair_smd_triangulated_surface.html#index-0">pair_style smd/tri_surface</a>
+  <dt><a href="pair_smd_triangulated_surface.html#index-0">pair\_style smd/tri\_surface</a>
   </dt>
 
       
-  <dt><a href="pair_smd_ulsph.html#index-0">pair_style smd/ulsph</a>
+  <dt><a href="pair_smd_ulsph.html#index-0">pair\_style smd/ulsph</a>
   </dt>
 
       
-  <dt><a href="pair_smtbq.html#index-0">pair_style smtbq</a>
+  <dt><a href="pair_smtbq.html#index-0">pair\_style smtbq</a>
   </dt>
 
       
-  <dt><a href="pair_snap.html#index-0">pair_style snap</a>
+  <dt><a href="pair_snap.html#index-0">pair\_style snap</a>
   </dt>
 
       
-  <dt><a href="pair_soft.html#index-0">pair_style soft</a>
+  <dt><a href="pair_soft.html#index-0">pair\_style soft</a>
   </dt>
 
       
-  <dt><a href="pair_sph_heatconduction.html#index-0">pair_style sph/heatconduction</a>
+  <dt><a href="pair_sph_heatconduction.html#index-0">pair\_style sph/heatconduction</a>
   </dt>
 
       
-  <dt><a href="pair_sph_idealgas.html#index-0">pair_style sph/idealgas</a>
+  <dt><a href="pair_sph_idealgas.html#index-0">pair\_style sph/idealgas</a>
   </dt>
 
       
-  <dt><a href="pair_sph_lj.html#index-0">pair_style sph/lj</a>
+  <dt><a href="pair_sph_lj.html#index-0">pair\_style sph/lj</a>
   </dt>
 
       
-  <dt><a href="pair_sph_rhosum.html#index-0">pair_style sph/rhosum</a>
+  <dt><a href="pair_sph_rhosum.html#index-0">pair\_style sph/rhosum</a>
   </dt>
 
       
-  <dt><a href="pair_sph_taitwater.html#index-0">pair_style sph/taitwater</a>
+  <dt><a href="pair_sph_taitwater.html#index-0">pair\_style sph/taitwater</a>
   </dt>
 
       
-  <dt><a href="pair_sph_taitwater_morris.html#index-0">pair_style sph/taitwater/morris</a>
+  <dt><a href="pair_sph_taitwater_morris.html#index-0">pair\_style sph/taitwater/morris</a>
   </dt>
 
       
-  <dt><a href="pair_srp.html#index-0">pair_style srp</a>
+  <dt><a href="pair_srp.html#index-0">pair\_style srp</a>
   </dt>
 
       
-  <dt><a href="pair_sw.html#index-0">pair_style sw</a>
+  <dt><a href="pair_sw.html#index-0">pair\_style sw</a>
   </dt>
 
       
-  <dt><a href="pair_table.html#index-0">pair_style table</a>
+  <dt><a href="pair_table.html#index-0">pair\_style table</a>
   </dt>
 
       
-  <dt><a href="pair_table_rx.html#index-0">pair_style table/rx</a>
+  <dt><a href="pair_table_rx.html#index-0">pair\_style table/rx</a>
   </dt>
 
       
-  <dt><a href="pair_tersoff.html#index-0">pair_style tersoff</a>
+  <dt><a href="pair_tersoff.html#index-0">pair\_style tersoff</a>
   </dt>
 
       
-  <dt><a href="pair_tersoff_mod.html#index-0">pair_style tersoff/mod</a>
+  <dt><a href="pair_tersoff_mod.html#index-0">pair\_style tersoff/mod</a>
   </dt>
 
       
-  <dt><a href="pair_tersoff_zbl.html#index-0">pair_style tersoff/zbl</a>
+  <dt><a href="pair_tersoff_zbl.html#index-0">pair\_style tersoff/zbl</a>
   </dt>
 
       
-  <dt><a href="pair_thole.html#index-0">pair_style thole</a>
+  <dt><a href="pair_thole.html#index-0">pair\_style thole</a>
   </dt>
 
       
-  <dt><a href="pair_tri_lj.html#index-0">pair_style tri/lj</a>
+  <dt><a href="pair_tri_lj.html#index-0">pair\_style tri/lj</a>
   </dt>
 
       
-  <dt><a href="pair_vashishta.html#index-0">pair_style vashishta</a>
+  <dt><a href="pair_vashishta.html#index-0">pair\_style vashishta</a>
   </dt>
 
       
-  <dt><a href="pair_yukawa.html#index-0">pair_style yukawa</a>
+  <dt><a href="pair_yukawa.html#index-0">pair\_style yukawa</a>
   </dt>
 
       
-  <dt><a href="pair_yukawa_colloid.html#index-0">pair_style yukawa/colloid</a>
+  <dt><a href="pair_yukawa_colloid.html#index-0">pair\_style yukawa/colloid</a>
   </dt>
 
       
-  <dt><a href="pair_zbl.html#index-0">pair_style zbl</a>
+  <dt><a href="pair_zbl.html#index-0">pair\_style zbl</a>
   </dt>
 
       
-  <dt><a href="pair_zero.html#index-0">pair_style zero</a>
+  <dt><a href="pair_zero.html#index-0">pair\_style zero</a>
   </dt>
 
       
-  <dt><a href="pair_write.html#index-0">pair_write</a>
+  <dt><a href="pair_write.html#index-0">pair\_write</a>
   </dt>
 
       
@@ -2162,15 +2162,15 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="read_data.html#index-0">read_data</a>
+  <dt><a href="read_data.html#index-0">read\_data</a>
   </dt>
 
       
-  <dt><a href="read_dump.html#index-0">read_dump</a>
+  <dt><a href="read_dump.html#index-0">read\_dump</a>
   </dt>
 
       
-  <dt><a href="read_restart.html#index-0">read_restart</a>
+  <dt><a href="read_restart.html#index-0">read\_restart</a>
   </dt>
 
       
@@ -2188,7 +2188,7 @@
   </dt>
 
       
-  <dt><a href="reset_timestep.html#index-0">reset_timestep</a>
+  <dt><a href="reset_timestep.html#index-0">reset\_timestep</a>
   </dt>
 
       
@@ -2200,7 +2200,7 @@
   </dt>
 
       
-  <dt><a href="run_style.html#index-0">run_style</a>
+  <dt><a href="run_style.html#index-0">run\_style</a>
   </dt>
 
   </dl></td>
@@ -2220,7 +2220,7 @@
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="special_bonds.html#index-0">special_bonds</a>
+  <dt><a href="special_bonds.html#index-0">special\_bonds</a>
   </dt>
 
       
@@ -2246,13 +2246,13 @@
   </dt>
 
       
-  <dt><a href="thermo_modify.html#index-0">thermo_modify</a>
+  <dt><a href="thermo_modify.html#index-0">thermo\_modify</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="thermo_style.html#index-0">thermo_style</a>
+  <dt><a href="thermo_style.html#index-0">thermo\_style</a>
   </dt>
 
       
@@ -2310,21 +2310,21 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="write_coeff.html#index-0">write_coeff</a>
+  <dt><a href="write_coeff.html#index-0">write\_coeff</a>
   </dt>
 
       
-  <dt><a href="write_data.html#index-0">write_data</a>
+  <dt><a href="write_data.html#index-0">write\_data</a>
   </dt>
 
   </dl></td>
   <td style="width: 33%" valign="top"><dl>
       
-  <dt><a href="write_dump.html#index-0">write_dump</a>
+  <dt><a href="write_dump.html#index-0">write\_dump</a>
   </dt>
 
       
-  <dt><a href="write_restart.html#index-0">write_restart</a>
+  <dt><a href="write_restart.html#index-0">write\_restart</a>
   </dt>
 
   </dl></td>
diff --git a/doc/html/group.html b/doc/html/group.html
index d21faf214a..009ce0deea 100644
--- a/doc/html/group.html
+++ b/doc/html/group.html
@@ -257,22 +257,22 @@ or exclude from a group.</p>
 <p>For example, these lines define a variable &#8220;eatom&#8221; that calculates the
 potential energy of each atom and includes it in the group if its
 potential energy is above the threshhold value -3.0.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>         <span class="mi">1</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span>
-<span class="n">compute</span>         <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_1</span>
-<span class="n">thermo_style</span>    <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">pe</span> <span class="n">c_2</span>
-<span class="n">run</span>             <span class="mi">0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span>        <span class="n">eatom</span> <span class="n">atom</span> <span class="s2">&quot;c_1 &gt; -3.0&quot;</span>
-<span class="n">group</span>           <span class="n">hienergy</span> <span class="n">variable</span> <span class="n">eatom</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute         1 all pe/atom
+compute         2 all reduce sum c_1
+thermo_style    custom step temp pe c_2
+run             0
+</pre>
+<pre class="literal-block">
+variable        eatom atom &quot;c_1 &gt; -3.0&quot;
+group           hienergy variable eatom
+</pre>
 <p>Note that these lines</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>         <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_1</span>
-<span class="n">thermo_style</span>    <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">pe</span> <span class="n">c_2</span>
-<span class="n">run</span>             <span class="mi">0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute         2 all reduce sum c_1
+thermo_style    custom step temp pe c_2
+run             0
+</pre>
 <p>are necessary to insure that the &#8220;eatom&#8221; variable is current when the
 group command invokes it.  Because the eatom variable computes the
 per-atom energy via the pe/atom compute, it will only be current if a
@@ -353,7 +353,8 @@ being integrated by using a spherical region with a variable radius
 used to model a quench of the system, freezing atoms outside the
 shrinking sphere, then converting the remaining atoms to a static
 group and running further.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable        nsteps equal 5000
+<pre class="literal-block">
+variable        nsteps equal 5000
 variable        rad equal 18-(step/v_nsteps)*(18-5)
 region          ss sphere 20 20 0 v_rad
 group           mobile dynamic all region ss
@@ -361,8 +362,7 @@ fix             1 mobile nve
 run             ${nsteps}
 group           mobile static
 run          ${nsteps}
-</pre></div>
-</div>
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">All fixes and computes take a group ID as an argument, but they
diff --git a/doc/html/if.html b/doc/html/if.html
index f2ba9d34e7..fe0350f9d5 100644
--- a/doc/html/if.html
+++ b/doc/html/if.html
@@ -143,7 +143,8 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span>if &quot;${steps} &gt; 1000&quot; then quit
+<pre class="literal-block">
+if &quot;${steps} &gt; 1000&quot; then quit
 if &quot;${myString} == a10&quot; then quit
 if &quot;$x &lt;= $y&quot; then &quot;print X is smaller = $x&quot; else &quot;print Y is smaller = $y&quot;
 if &quot;(${eng} &gt; 0.0) || ($n &lt; 1000)&quot; then &amp;
@@ -152,10 +153,9 @@ elif $n&lt;10000 &amp;
   &quot;timestep 0.01&quot; &amp;
 else &amp;
   &quot;timestep 0.02&quot; &amp;
-  &quot;print &#39;Max step reached&#39;&quot;
+  &quot;print 'Max step reached'&quot;
 if &quot;${eng} &gt; ${eng_previous}&quot; then &quot;jump file1&quot; else &quot;jump file2&quot;
-</pre></div>
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -249,10 +249,10 @@ clarity, you must enclose the entire expression in quotes.</p>
 <p>An expression is built out of numbers (which start with a digit or
 period or minus sign) or strings (which start with a letter and can
 contain alphanumeric characters or underscores):</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mf">0.2</span><span class="p">,</span> <span class="mi">100</span><span class="p">,</span> <span class="mf">1.0e20</span><span class="p">,</span> <span class="o">-</span><span class="mf">15.4</span><span class="p">,</span> <span class="n">etc</span>
-<span class="n">InP</span><span class="p">,</span> <span class="n">myString</span><span class="p">,</span> <span class="n">a123</span><span class="p">,</span> <span class="n">ab_23_cd</span><span class="p">,</span> <span class="n">etc</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+0.2, 100, 1.0e20, -15.4, etc
+InP, myString, a123, ab_23_cd, etc
+</pre>
 <p>and Boolean operators:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span>A == B, A != B, A &lt; B, A &lt;= B, A &gt; B, A &gt;= B, A &amp;&amp; B, A || B, !A
 </pre></div>
diff --git a/doc/html/improper_class2.html b/doc/html/improper_class2.html
index c6758cff97..0d39e5935a 100644
--- a/doc/html/improper_class2.html
+++ b/doc/html/improper_class2.html
@@ -131,17 +131,17 @@
 <h1>improper_style class2/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">class2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style class2
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">class2</span>
-<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mi">0</span>
-<span class="n">improper_coeff</span> <span class="o">*</span> <span class="n">aa</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">115.06</span> <span class="mf">130.01</span> <span class="mf">115.06</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style class2
+improper_coeff 1 100.0 0
+improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/improper_cossq.html b/doc/html/improper_cossq.html
index 9a7aa85c8d..28c2370f09 100644
--- a/doc/html/improper_cossq.html
+++ b/doc/html/improper_cossq.html
@@ -131,16 +131,16 @@
 <h1>improper_style cossq/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">cossq</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style cossq
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">cossq</span>
-<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">4.0</span> <span class="mf">0.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style cossq
+improper_coeff 1 4.0 0.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/improper_cvff.html b/doc/html/improper_cvff.html
index 186c5aa3e1..461f02eeab 100644
--- a/doc/html/improper_cvff.html
+++ b/doc/html/improper_cvff.html
@@ -134,16 +134,16 @@
 <h1>improper_style cvff/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">cvff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style cvff
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">cvff</span>
-<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="o">-</span><span class="mi">1</span> <span class="mi">4</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style cvff
+improper_coeff 1 80.0 -1 4
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/improper_distance.html b/doc/html/improper_distance.html
index 69718ece9a..3f42cef8d0 100644
--- a/doc/html/improper_distance.html
+++ b/doc/html/improper_distance.html
@@ -132,10 +132,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">distance</span>
-<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="mf">100.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style distance
+improper_coeff 1 80.0 100.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/improper_fourier.html b/doc/html/improper_fourier.html
index 545282aa2a..be22144ccf 100644
--- a/doc/html/improper_fourier.html
+++ b/doc/html/improper_fourier.html
@@ -131,16 +131,16 @@
 <h1>improper_style fourier/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">fourier</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style fourier
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">fourier</span>
-<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">180.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style fourier
+improper_coeff 1 100.0 180.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/improper_harmonic.html b/doc/html/improper_harmonic.html
index d268c62014..11553c0187 100644
--- a/doc/html/improper_harmonic.html
+++ b/doc/html/improper_harmonic.html
@@ -137,16 +137,16 @@
 <h1>improper_style harmonic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">harmonic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style harmonic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">harmonic</span>
-<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mi">0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style harmonic
+improper_coeff 1 100.0 0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/improper_ring.html b/doc/html/improper_ring.html
index aa3b557a57..0e7e4330b0 100644
--- a/doc/html/improper_ring.html
+++ b/doc/html/improper_ring.html
@@ -131,16 +131,16 @@
 <h1>improper_style ring/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">ring</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style ring
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">ring</span>
-<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mi">8000</span> <span class="mf">70.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style ring
+improper_coeff 1 8000 70.5
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -150,8 +150,8 @@
 specified by (i,j,k,l) indices and theta0 its equilibrium value.</p>
 <p>If the 4 atoms in an improper quadruplet (listed in the data file read
 by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command) are ordered i,j,k,l then
-<a href="#id1"><span class="problematic" id="id2">theta_</span></a><em>ijl</em> is the angle between atoms i,j and l, <a href="#id3"><span class="problematic" id="id4">theta_</span></a><em>ijk</em> is the
-angle between atoms i,j and k, <a href="#id5"><span class="problematic" id="id6">theta_</span></a><em>kjl</em> is the angle between atoms
+theta_<em>ijl</em> is the angle between atoms i,j and l, theta_<em>ijk</em> is the
+angle between atoms i,j and k, theta_<em>kjl</em> is the angle between atoms
 j,k, and l.</p>
 <p>The &#8220;ring&#8221; improper style implements the improper potential introduced
 by Destree et al., in Equation (9) of <a class="reference internal" href="#destree"><span class="std std-ref">(Destree)</span></a>.  This
diff --git a/doc/html/improper_umbrella.html b/doc/html/improper_umbrella.html
index f1fb943d5e..de79db67ef 100644
--- a/doc/html/improper_umbrella.html
+++ b/doc/html/improper_umbrella.html
@@ -131,16 +131,16 @@
 <h1>improper_style umbrella/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">umbrella</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style umbrella
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">umbrella</span>
-<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">180.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+improper_style umbrella
+improper_coeff 1 100.0 180.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/jump.html b/doc/html/jump.html
index a87db9100d..8b2f4578a4 100644
--- a/doc/html/jump.html
+++ b/doc/html/jump.html
@@ -158,22 +158,22 @@ script is re-opened and read again.</p>
 <p class="last">The SELF option is not guaranteed to work when the current input
 script is being read through stdin (standard input), e.g.</p>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">&lt;</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_g++ &lt; in.script
+</pre>
 <p>since the SELF option invokes the C-library rewind() call, which may
 not be supported for stdin on some systems or by some MPI
 implementations.  This can be worked around by using the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-in command-line argument</span></a>, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_g++ -in in.script
+</pre>
 <p>or by using the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-var command-line argument</span></a> to pass the script name as a
 variable to the input script.  In the latter case, a
 <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> called &#8220;fname&#8221; could be used in place of
 SELF, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">var</span> <span class="n">fname</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="o">&lt;</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+lmp_g++ -var fname in.script &lt; in.script
+</pre>
 <p>The 2nd argument to the jump command is optional.  If specified, it is
 treated as a label and the new file is scanned (without executing
 commands) until the label is found, and commands are executed from
@@ -198,9 +198,9 @@ scripts.  In this example, LAMMPS is run on 40 processors, with 4
 partitions of 10 procs each.  An in.file containing the example
 variable and jump command will cause each partition to run a different
 simulation.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">40</span> <span class="n">lmp_ibm</span> <span class="o">-</span><span class="n">partition</span> <span class="mi">4</span><span class="n">x10</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">file</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+mpirun -np 40 lmp_ibm -partition 4x10 -in in.file
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span>variable f world script.1 script.2 script.3 script.4
 jump $f
 </pre></div>
diff --git a/doc/html/kspace_modify.html b/doc/html/kspace_modify.html
index 961ea342d6..2019d48cff 100644
--- a/doc/html/kspace_modify.html
+++ b/doc/html/kspace_modify.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>kspace_modify command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">kspace_modify</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+kspace_modify keyword value ...
+</pre>
 <ul class="simple">
 <li>one or more keyword/value pairs may be listed</li>
 </ul>
@@ -174,10 +174,10 @@ keyword = <em>mesh</em> or <em>order</em> or <em>order/disp</em> or <em>mix/disp
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">kspace_modify</span> <span class="n">mesh</span> <span class="mi">24</span> <span class="mi">24</span> <span class="mi">30</span> <span class="n">order</span> <span class="mi">6</span>
-<span class="n">kspace_modify</span> <span class="n">slab</span> <span class="mf">3.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+kspace_modify mesh 24 24 30 order 6
+kspace_modify slab 3.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/kspace_style.html b/doc/html/kspace_style.html
index 53a0c22ce2..5cecc5b41d 100644
--- a/doc/html/kspace_style.html
+++ b/doc/html/kspace_style.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>kspace_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">kspace_style</span> <span class="n">style</span> <span class="n">value</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+kspace_style style value
+</pre>
 <ul class="simple">
 <li>style = <em>none</em> or <em>ewald</em> or <em>ewald/disp</em> or <em>ewald/omp</em> or <em>pppm</em> or <em>pppm/cg</em> or <em>pppm/disp</em> or <em>pppm/tip4p</em> or <em>pppm/stagger</em> or <em>pppm/disp/tip4p</em> or <em>pppm/gpu</em> or <em>pppm/kk</em> or <em>pppm/omp</em> or <em>pppm/cg/omp</em> or <em>pppm/tip4p/omp</em> or <em>msm</em> or <em>msm/cg</em> or <em>msm/omp</em> or <em>msm/cg/omp</em></li>
 </ul>
@@ -179,12 +179,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">kspace_style</span> <span class="n">pppm</span> <span class="mf">1.0e-4</span>
-<span class="n">kspace_style</span> <span class="n">pppm</span><span class="o">/</span><span class="n">cg</span> <span class="mf">1.0e-5</span> <span class="mf">1.0e-6</span>
-<span class="n">kspace</span> <span class="n">style</span> <span class="n">msm</span> <span class="mf">1.0e-4</span>
-<span class="n">kspace_style</span> <span class="n">none</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+kspace_style pppm 1.0e-4
+kspace_style pppm/cg 1.0e-5 1.0e-6
+kspace style msm 1.0e-4
+kspace_style none
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -422,9 +422,9 @@ must be periodic and the z dimension must be non-periodic.</p>
 </div>
 <div class="section" id="default">
 <h2>Default</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">kspace_style</span> <span class="n">none</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+kspace_style none
+</pre>
 <hr class="docutils" />
 <p id="darden"><strong>(Darden)</strong> Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).</p>
 <p id="deserno"><strong>(Deserno)</strong> Deserno and Holm, J Chem Phys, 109, 7694 (1998).</p>
diff --git a/doc/html/lattice.html b/doc/html/lattice.html
index 636cba7437..07d659915c 100644
--- a/doc/html/lattice.html
+++ b/doc/html/lattice.html
@@ -135,10 +135,10 @@
 <li>style = <em>none</em> or <em>sc</em> or <em>bcc</em> or <em>fcc</em> or <em>hcp</em> or <em>diamond</em> or         <em>sq</em> or <em>sq2</em> or <em>hex</em> or <em>custom</em></li>
 <li>scale = scale factor between lattice and simulation box</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">scale</span> <span class="o">=</span> <span class="n">reduced</span> <span class="n">density</span> <span class="n">rho</span><span class="o">*</span> <span class="p">(</span><span class="k">for</span> <span class="n">LJ</span> <span class="n">units</span><span class="p">)</span>
-<span class="n">scale</span> <span class="o">=</span> <span class="n">lattice</span> <span class="n">constant</span> <span class="ow">in</span> <span class="n">distance</span> <span class="n">units</span> <span class="p">(</span><span class="k">for</span> <span class="nb">all</span> <span class="n">other</span> <span class="n">units</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+scale = reduced density rho* (for LJ units)
+scale = lattice constant in distance units (for all other units)
+</pre>
 <ul class="simple">
 <li>zero or more keyword/value pairs may be appended</li>
 <li>keyword = <em>origin</em> or <em>orient</em> or <em>spacing</em> or <em>a1</em> or <em>a2</em> or <em>a3</em> or <em>basis</em></li>
@@ -349,20 +349,21 @@ in commands that use the spacings should be decipherable.</p>
 <hr class="docutils" />
 <p>Example commands for generating a Wurtzite crystal (courtesy
 of Aidan Thompson), with its 8 atom unit cell.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable a equal  4.340330
+<pre class="literal-block">
+variable a equal  4.340330
 variable b equal  $a*sqrt(3.0)
 variable c equal  $a*sqrt(8.0/3.0)
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="mi">1</span><span class="n">_3</span> <span class="n">equal</span> <span class="mf">1.0</span><span class="o">/</span><span class="mf">3.0</span>
-<span class="n">variable</span> <span class="mi">2</span><span class="n">_3</span> <span class="n">equal</span> <span class="mf">2.0</span><span class="o">/</span><span class="mf">3.0</span>
-<span class="n">variable</span> <span class="mi">1</span><span class="n">_6</span> <span class="n">equal</span> <span class="mf">1.0</span><span class="o">/</span><span class="mf">6.0</span>
-<span class="n">variable</span> <span class="mi">5</span><span class="n">_6</span> <span class="n">equal</span> <span class="mf">5.0</span><span class="o">/</span><span class="mf">6.0</span>
-<span class="n">variable</span> <span class="mi">1</span><span class="n">_12</span> <span class="n">equal</span> <span class="mf">1.0</span><span class="o">/</span><span class="mf">12.0</span>
-<span class="n">variable</span> <span class="mi">5</span><span class="n">_12</span> <span class="n">equal</span> <span class="mf">5.0</span><span class="o">/</span><span class="mf">12.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>lattice custom    1.0     &amp;
+</pre>
+<pre class="literal-block">
+variable 1_3 equal 1.0/3.0
+variable 2_3 equal 2.0/3.0
+variable 1_6 equal 1.0/6.0
+variable 5_6 equal 5.0/6.0
+variable 1_12 equal 1.0/12.0
+variable 5_12 equal 5.0/12.0
+</pre>
+<pre class="literal-block">
+lattice custom    1.0     &amp;
         a1      $a      0.0     0.0     &amp;
         a2      0.0     $b      0.0     &amp;
         a3      0.0     0.0     $c      &amp;
@@ -374,17 +375,16 @@ variable c equal  $a*sqrt(8.0/3.0)
         basis   0.5     0.5     0.625   &amp;
         basis   ${1_3}  0.0     0.125   &amp;
         basis   ${5_6}  0.5     0.125
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">region</span> <span class="n">myreg</span> <span class="n">block</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mi">1</span>
-<span class="n">create_box</span>      <span class="mi">2</span> <span class="n">myreg</span>
-<span class="n">create_atoms</span>    <span class="mi">1</span> <span class="n">box</span>      <span class="o">&amp;</span>
-        <span class="n">basis</span>   <span class="mi">5</span>       <span class="mi">2</span>       <span class="o">&amp;</span>
-        <span class="n">basis</span>   <span class="mi">6</span>       <span class="mi">2</span>       <span class="o">&amp;</span>
-        <span class="n">basis</span>   <span class="mi">7</span>       <span class="mi">2</span>       <span class="o">&amp;</span>
-        <span class="n">basis</span>   <span class="mi">8</span>       <span class="mi">2</span>
-</pre></div>
-</div>
+</pre>
+<pre class="literal-block">
+region myreg block 0 1 0 1 0 1
+create_box      2 myreg
+create_atoms    1 box      &amp;
+        basis   5       2       &amp;
+        basis   6       2       &amp;
+        basis   7       2       &amp;
+        basis   8       2
+</pre>
 </div>
 <hr class="docutils" />
 <div class="section" id="restrictions">
diff --git a/doc/html/min_modify.html b/doc/html/min_modify.html
index 5434586014..bd9a1f285f 100644
--- a/doc/html/min_modify.html
+++ b/doc/html/min_modify.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>min_modify command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">min_modify</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+min_modify keyword values ...
+</pre>
 <ul class="simple">
 <li>one or more keyword/value pairs may be listed</li>
 </ul>
@@ -144,9 +144,9 @@ keyword = <em>dmax</em> or <em>line</em>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">min_modify</span> <span class="n">dmax</span> <span class="mf">0.2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+min_modify dmax 0.2
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/min_style.html b/doc/html/min_style.html
index 158cf94d45..c2c66e37b9 100644
--- a/doc/html/min_style.html
+++ b/doc/html/min_style.html
@@ -128,19 +128,19 @@
 <span id="index-0"></span><h1>min_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">min_style</span> <span class="n">style</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+min_style style
+</pre>
 <ul class="simple">
 <li>style = <em>cg</em> or <em>hftn</em> or <em>sd</em> or <em>quickmin</em> or <em>fire</em></li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">min_style</span> <span class="n">cg</span>
-<span class="n">min_style</span> <span class="n">fire</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+min_style cg
+min_style fire
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -206,9 +206,9 @@ involving the electron radius in <a class="reference internal" href="pair_eff.ht
 </div>
 <div class="section" id="default">
 <h2>Default</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">min_style</span> <span class="n">cg</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+min_style cg
+</pre>
 <hr class="docutils" />
 <p id="sheppard"><strong>(Sheppard)</strong> Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106
 (2008).  See ref 1 in this paper for original reference to Qmin in
diff --git a/doc/html/neigh_modify.html b/doc/html/neigh_modify.html
index cdad858eee..991e8aaf9b 100644
--- a/doc/html/neigh_modify.html
+++ b/doc/html/neigh_modify.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>neigh_modify command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neigh_modify</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+neigh_modify keyword values ...
+</pre>
 <ul class="simple">
 <li>one or more keyword/value pairs may be listed</li>
 </ul>
@@ -170,13 +170,13 @@ keyword = <em>delay</em> or <em>every</em> or <em>check</em> or <em>once</em> or
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neigh_modify</span> <span class="n">every</span> <span class="mi">2</span> <span class="n">delay</span> <span class="mi">10</span> <span class="n">check</span> <span class="n">yes</span> <span class="n">page</span> <span class="mi">100000</span>
-<span class="n">neigh_modify</span> <span class="n">exclude</span> <span class="nb">type</span> <span class="mi">2</span> <span class="mi">3</span>
-<span class="n">neigh_modify</span> <span class="n">exclude</span> <span class="n">group</span> <span class="n">frozen</span> <span class="n">frozen</span> <span class="n">check</span> <span class="n">no</span>
-<span class="n">neigh_modify</span> <span class="n">exclude</span> <span class="n">group</span> <span class="n">residue1</span> <span class="n">chain3</span>
-<span class="n">neigh_modify</span> <span class="n">exclude</span> <span class="n">molecule</span> <span class="n">rigid</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+neigh_modify every 2 delay 10 check yes page 100000
+neigh_modify exclude type 2 3
+neigh_modify exclude group frozen frozen check no
+neigh_modify exclude group residue1 chain3
+neigh_modify exclude molecule rigid
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/next.html b/doc/html/next.html
index 91a180f677..e8b2338450 100644
--- a/doc/html/next.html
+++ b/doc/html/next.html
@@ -196,7 +196,8 @@ see in your directory during and after such a LAMMPS run.</p>
 command with an <em>index</em>-style variable.  If this input script is named
 in.polymer, 8 simulations would be run using data files from
 directories run1 thru run8.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable d index run1 run2 run3 run4 run5 run6 run7 run8
+<pre class="literal-block">
+variable d index run1 run2 run3 run4 run5 run6 run7 run8
 shell cd $d
 read_data data.polymer
 run 10000
@@ -204,8 +205,7 @@ shell cd ..
 clear
 next d
 jump in.polymer
-</pre></div>
-</div>
+</pre>
 <p>If the variable &#8220;d&#8221; were of style <em>universe</em>, and the same in.polymer
 input script were run on 3 partitions of processors, then the first 3
 simulations would begin, one on each set of processors.  Whichever
@@ -214,7 +214,8 @@ and run another simulation, and so forth until all 8 simulations were
 finished.</p>
 <p>Jump and next commands can also be nested to enable multi-level loops.
 For example, this script will run 15 simulations in a double loop.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable i loop 3
+<pre class="literal-block">
+variable i loop 3
   variable j loop 5
   clear
   ...
@@ -225,8 +226,7 @@ For example, this script will run 15 simulations in a double loop.</p>
   jump in.script
 next i
 jump in.script
-</pre></div>
-</div>
+</pre>
 <p>Here is an example of a double loop which uses the <a class="reference internal" href="if.html"><span class="doc">if</span></a> and
 <a class="reference internal" href="jump.html"><span class="doc">jump</span></a> commands to break out of the inner loop when a
 condition is met, then continues iterating thru the outer loop.</p>
diff --git a/doc/html/package.html b/doc/html/package.html
index 90477fc5ec..7146faef4d 100644
--- a/doc/html/package.html
+++ b/doc/html/package.html
@@ -572,11 +572,11 @@ compilers is to use one thread for each available CPU core when
 performance.</p>
 <p>Here are examples of how to set the environment variable when
 launching LAMMPS:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">env</span> <span class="n">OMP_NUM_THREADS</span><span class="o">=</span><span class="mi">4</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
-<span class="n">env</span> <span class="n">OMP_NUM_THREADS</span><span class="o">=</span><span class="mi">2</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">x</span> <span class="n">OMP_NUM_THREADS</span><span class="o">=</span><span class="mi">2</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
+env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
+mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script
+</pre>
 <p>or you can set it permanently in your shell&#8217;s start-up script.
 All three of these examples use a total of 4 CPU cores.</p>
 <p>Note that different MPI implementations have different ways of passing
diff --git a/doc/html/pair_adp.html b/doc/html/pair_adp.html
index c38bbab6b5..5bc88ab7d0 100644
--- a/doc/html/pair_adp.html
+++ b/doc/html/pair_adp.html
@@ -131,17 +131,17 @@
 <h1>pair_style adp/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">adp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style adp
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">adp</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ta</span><span class="o">.</span><span class="n">adp</span> <span class="n">Ta</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">AlCu</span><span class="o">.</span><span class="n">adp</span> <span class="n">Al</span> <span class="n">Al</span> <span class="n">Cu</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style adp
+pair_coeff * * Ta.adp Ta
+pair_coeff * * ../potentials/AlCu.adp Al Al Cu
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -188,9 +188,9 @@ file which has tabulated ADP values for w elements and their alloy
 interactions: Cu and Al.  If your LAMMPS simulation has 4 atoms types
 and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
 the following pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">AlCu</span><span class="o">.</span><span class="n">adp</span> <span class="n">Al</span> <span class="n">Al</span> <span class="n">Al</span> <span class="n">Cu</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * AlCu.adp Al Al Al Cu
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Al arguments map LAMMPS atom types 1,2,3 to the Al
 element in the extended <em>setfl</em> file.  The final Cu argument maps
diff --git a/doc/html/pair_airebo.html b/doc/html/pair_airebo.html
index 503da5ef6a..6827568073 100644
--- a/doc/html/pair_airebo.html
+++ b/doc/html/pair_airebo.html
@@ -143,9 +143,9 @@
 <h1>pair_style rebo/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">cutoff</span> <span class="n">LJ_flag</span> <span class="n">TORSION_flag</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style cutoff LJ_flag TORSION_flag
+</pre>
 <ul class="simple">
 <li>style = <em>airebo</em> or <em>airebo/morse</em> or <em>rebo</em></li>
 <li>cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only)</li>
@@ -155,19 +155,19 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">airebo</span> <span class="mf">3.0</span>
-<span class="n">pair_style</span> <span class="n">airebo</span> <span class="mf">2.5</span> <span class="mi">1</span> <span class="mi">0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">H</span> <span class="n">C</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">airebo</span><span class="o">/</span><span class="n">morse</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span><span class="o">-</span><span class="n">m</span> <span class="n">H</span> <span class="n">C</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">rebo</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">H</span> <span class="n">C</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style airebo 3.0
+pair_style airebo 2.5 1 0
+pair_coeff * * ../potentials/CH.airebo H C
+</pre>
+<pre class="literal-block">
+pair_style airebo/morse 3.0
+pair_coeff * * ../potentials/CH.airebo-m H C
+</pre>
+<pre class="literal-block">
+pair_style rebo
+pair_coeff * * ../potentials/CH.airebo H C
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -242,9 +242,9 @@ to specify the path for the potential file.</p>
 <p>As an example, if your LAMMPS simulation has 4 atom types and you want
 the 1st 3 to be C, and the 4th to be H, you would use the following
 pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">C</span> <span class="n">C</span> <span class="n">C</span> <span class="n">H</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * CH.airebo C C C H
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three C arguments map LAMMPS atom types 1,2,3 to the C
 element in the AIREBO file.  The final H argument maps LAMMPS atom
@@ -273,13 +273,13 @@ The 3 values correspond to the following sub-categories:</p>
 </ol>
 <p>To print these quantities to the log file (with descriptive column
 headings) the following commands could be included in an input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">0</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">airebo</span>
-<span class="n">variable</span> <span class="n">REBO</span>     <span class="n">equal</span> <span class="n">c_0</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-<span class="n">variable</span> <span class="n">LJ</span>       <span class="n">equal</span> <span class="n">c_0</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-<span class="n">variable</span> <span class="n">TORSION</span>  <span class="n">equal</span> <span class="n">c_0</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_REBO</span> <span class="n">v_LJ</span> <span class="n">v_TORSION</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute 0 all pair airebo
+variable REBO     equal c_0[1]
+variable LJ       equal c_0[2]
+variable TORSION  equal c_0[3]
+thermo_style custom step temp epair v_REBO v_LJ v_TORSION
+</pre>
 <hr class="docutils" />
 <p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
 functionally the same as the corresponding style without the suffix.
diff --git a/doc/html/pair_beck.html b/doc/html/pair_beck.html
index 10325668e8..baf69eecfa 100644
--- a/doc/html/pair_beck.html
+++ b/doc/html/pair_beck.html
@@ -134,20 +134,20 @@
 <h1>pair_style beck/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">beck</span> <span class="n">Rc</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style beck Rc
+</pre>
 <ul class="simple">
 <li>Rc = cutoff for interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">beck</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">399.671876712</span> <span class="mf">0.0000867636112694</span> <span class="mf">0.675</span> <span class="mf">4.390</span> <span class="mf">0.0003746</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">399.671876712</span> <span class="mf">0.0000867636112694</span> <span class="mf">0.675</span> <span class="mf">4.390</span> <span class="mf">0.0003746</span> <span class="mf">6.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style beck 8.0
+pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746
+pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_body.html b/doc/html/pair_body.html
index 5f4df83aa4..5f623fb0b7 100644
--- a/doc/html/pair_body.html
+++ b/doc/html/pair_body.html
@@ -128,18 +128,18 @@
 <span id="index-0"></span><h1>pair_style body command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">body</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style body cutoff
+</pre>
 <p>cutoff = global cutoff for interactions (distance units)</p>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">body</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.5</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style body 3.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_bop.html b/doc/html/pair_bop.html
index 1c1d5e2ce7..f3b0785cd0 100644
--- a/doc/html/pair_bop.html
+++ b/doc/html/pair_bop.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_style bop command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">bop</span> <span class="n">keyword</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style bop keyword ...
+</pre>
 <ul class="simple">
 <li>zero or more keywords may be appended</li>
 <li>keyword = <em>save</em></li>
@@ -141,13 +141,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">bop</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CdTe_bop</span> <span class="n">Cd</span> <span class="n">Te</span>
-<span class="n">pair_style</span> <span class="n">bop</span> <span class="n">save</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CdTe</span><span class="o">.</span><span class="n">bop</span><span class="o">.</span><span class="n">table</span> <span class="n">Cd</span> <span class="n">Te</span> <span class="n">Te</span>
-<span class="n">comm_modify</span> <span class="n">cutoff</span> <span class="mf">14.70</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style bop
+pair_coeff * * ../potentials/CdTe_bop Cd Te
+pair_style bop save
+pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te
+comm_modify cutoff 14.70
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -238,9 +238,9 @@ where N is the number of LAMMPS atom types:</p>
 and Te.  If your LAMMPS simulation has 4 atoms types and you want the
 1st 3 to be Cd, and the 4th to be Te, you would use the following
 pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">CdTe</span> <span class="n">Cd</span> <span class="n">Cd</span> <span class="n">Cd</span> <span class="n">Te</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * CdTe Cd Cd Cd Te
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd
 element in the BOP file.  The final Te argument maps LAMMPS atom type
diff --git a/doc/html/pair_born.html b/doc/html/pair_born.html
index 3740bb4699..c73ca9761f 100644
--- a/doc/html/pair_born.html
+++ b/doc/html/pair_born.html
@@ -161,9 +161,9 @@
 <h1>pair_style born/coul/wolf/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>born</em> or <em>born/coul/long</em> or <em>born/coul/long/cs</em> or <em>born/coul/msm</em> or <em>born/coul/wolf</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -185,31 +185,31 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">wolf</span> <span class="mf">0.25</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">wolf</span> <span class="mf">0.25</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style born 10.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+</pre>
+<pre class="literal-block">
+pair_style born/coul/long 10.0
+pair_style born/coul/long/cs 10.0
+pair_style born/coul/long 10.0 8.0
+pair_style born/coul/long/cs 10.0 8.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+</pre>
+<pre class="literal-block">
+pair_style born/coul/msm 10.0
+pair_style born/coul/msm 10.0 8.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+</pre>
+<pre class="literal-block">
+pair_style born/coul/wolf 0.25 10.0
+pair_style born/coul/wolf 0.25 10.0 9.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_brownian.html b/doc/html/pair_brownian.html
index eaf0a723c3..777cb46f10 100644
--- a/doc/html/pair_brownian.html
+++ b/doc/html/pair_brownian.html
@@ -137,9 +137,9 @@
 <h1>pair_style brownian/poly/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">mu</span> <span class="n">flaglog</span> <span class="n">flagfld</span> <span class="n">cutinner</span> <span class="n">cutoff</span> <span class="n">t_target</span> <span class="n">seed</span> <span class="n">flagHI</span> <span class="n">flagVF</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
+</pre>
 <ul class="simple">
 <li>style = <em>brownian</em> or <em>brownian/poly</em></li>
 <li>mu = dynamic viscosity (dynamic viscosity units)</li>
@@ -155,11 +155,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">brownian</span> <span class="mf">1.5</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">2.01</span> <span class="mf">2.5</span> <span class="mf">2.0</span> <span class="mi">5878567</span> <span class="p">(</span><span class="n">assuming</span> <span class="n">radius</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">2.05</span> <span class="mf">2.8</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
+pair_coeff 1 1 2.05 2.8
+pair_coeff * *
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_buck.html b/doc/html/pair_buck.html
index 58eccb8ce8..fa537931bf 100644
--- a/doc/html/pair_buck.html
+++ b/doc/html/pair_buck.html
@@ -179,9 +179,9 @@
 <h1>pair_style buck/coul/msm/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>buck</em> or <em>buck/coul/cut</em> or <em>buck/coul/long</em> or <em>buck/coul/long/cs</em> or <em>buck/coul/msm</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -202,32 +202,32 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">3.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">9.0</span> <span class="mf">8.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style buck 2.5
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff * * 100.0 1.5 200.0 3.0
+</pre>
+<pre class="literal-block">
+pair_style buck/coul/cut 10.0
+pair_style buck/coul/cut 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0
+</pre>
+<pre class="literal-block">
+pair_style buck/coul/long 10.0
+pair_style buck/coul/long/cs 10.0
+pair_style buck/coul/long 10.0 8.0
+pair_style buck/coul/long/cs 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+</pre>
+<pre class="literal-block">
+pair_style buck/coul/msm 10.0
+pair_style buck/coul/msm 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_buck_long.html b/doc/html/pair_buck_long.html
index a9e6b7e670..82fc5d5641 100644
--- a/doc/html/pair_buck_long.html
+++ b/doc/html/pair_buck_long.html
@@ -131,9 +131,9 @@
 <h1>pair_style buck/long/coul/long/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">flag_buck</span> <span class="n">flag_coul</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2)
+</pre>
 <ul class="simple">
 <li>flag_buck = <em>long</em> or <em>cut</em></li>
 </ul>
@@ -155,13 +155,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">cut</span> <span class="n">off</span> <span class="mf">2.5</span>
-<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">cut</span> <span class="n">long</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
-<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">long</span> <span class="n">long</span> <span class="mf">4.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">1</span> <span class="mi">1</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mi">4</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style buck/long/coul/long cut off 2.5
+pair_style buck/long/coul/long cut long 2.5 4.0
+pair_style buck/long/coul/long long long 4.0
+pair_coeff * * 1 1
+pair_coeff 1 1 1 3 4
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_charmm.html b/doc/html/pair_charmm.html
index 75994eddd2..93e44709ce 100644
--- a/doc/html/pair_charmm.html
+++ b/doc/html/pair_charmm.html
@@ -158,9 +158,9 @@
 <h1>pair_style lj/charmm/coul/msm/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>lj/charmm/coul/charmm</em> or <em>lj/charmm/coul/charmm/implicit</em> or <em>lj/charmm/coul/long</em> or <em>lj/charmm/coul/msm</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -182,30 +182,30 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">7.0</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">implicit</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">implicit</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">7.0</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/charmm/coul/charmm 8.0 10.0
+pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+</pre>
+<pre class="literal-block">
+pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
+pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+</pre>
+<pre class="literal-block">
+pair_style lj/charmm/coul/long 8.0 10.0
+pair_style lj/charmm/coul/long 8.0 10.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+</pre>
+<pre class="literal-block">
+pair_style lj/charmm/coul/msm 8.0 10.0
+pair_style lj/charmm/coul/msm 8.0 10.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_class2.html b/doc/html/pair_class2.html
index 5e62dd99ef..a2dee8a442 100644
--- a/doc/html/pair_class2.html
+++ b/doc/html/pair_class2.html
@@ -158,9 +158,9 @@
 <h1>pair_style lj/class2/coul/long/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>lj/class2</em> or <em>lj/class2/coul/cut</em> or <em>lj/class2/coul/long</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -178,24 +178,24 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">class2</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span><span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.5</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">class2</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">class2</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">class2</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">class2</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/class2 10.0
+pair_coeff * * 100.0 2.5
+pair_coeff 1 2* 100.0 2.5 9.0
+</pre>
+<pre class="literal-block">
+pair_style lj/class2/coul/cut 10.0
+pair_style lj/class2/coul/cut 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+pair_coeff 1 1 100.0 3.5 9.0 9.0
+</pre>
+<pre class="literal-block">
+pair_style lj/class2/coul/long 10.0
+pair_style lj/class2/coul/long 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_colloid.html b/doc/html/pair_colloid.html
index c4254f1606..a1520bc730 100644
--- a/doc/html/pair_colloid.html
+++ b/doc/html/pair_colloid.html
@@ -134,22 +134,22 @@
 <h1>pair_style colloid/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">colloid</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style colloid cutoff
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for colloidal interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">colloid</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>  <span class="mi">25</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">144</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span>  <span class="mf">75.398</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span>  <span class="mf">39.478</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mf">10.0</span> <span class="mf">25.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style colloid 10.0
+pair_coeff * *  25 1.0 10.0 10.0
+pair_coeff 1 1 144 1.0 0.0 0.0 3.0
+pair_coeff 1 2  75.398 1.0 0.0 10.0 9.0
+pair_coeff 2 2  39.478 1.0 10.0 10.0 25.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_comb.html b/doc/html/pair_comb.html
index d7ca86f242..c0768ee36a 100644
--- a/doc/html/pair_comb.html
+++ b/doc/html/pair_comb.html
@@ -134,10 +134,10 @@
 <h1>pair_style comb3 command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">comb</span>
-<span class="n">pair_style</span> <span class="n">comb3</span> <span class="n">keyword</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style comb
+pair_style comb3 keyword
+</pre>
 <pre class="literal-block">
 keyword = <em>polar</em>
   <em>polar</em> value = <em>polar_on</em> or <em>polar_off</em> = whether or not to include atomic polarization
@@ -145,15 +145,15 @@ keyword = <em>polar</em>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">comb</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb</span> <span class="n">Si</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb</span> <span class="n">Hf</span> <span class="n">Si</span> <span class="n">O</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">comb3</span> <span class="n">polar_off</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb3</span> <span class="n">O</span> <span class="n">Cu</span> <span class="n">N</span> <span class="n">C</span> <span class="n">O</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style comb
+pair_coeff * * ../potentials/ffield.comb Si
+pair_coeff * * ../potentials/ffield.comb Hf Si O
+</pre>
+<pre class="literal-block">
+pair_style comb3 polar_off
+pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -191,9 +191,9 @@ command, where N is the number of LAMMPS atom types.</p>
 HfO&lt;sub&gt;2&lt;/sub&gt; interface has 4 atom types, and you want the 1st and
 last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
 use the following pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb</span> <span class="n">Si</span> <span class="n">Hf</span> <span class="n">O</span> <span class="n">Si</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * ../potentials/ffield.comb Si Hf O Si
+</pre>
 <p>The first two arguments must be * * so as to span all LAMMPS atom
 types.  The first and last Si arguments map LAMMPS atom types 1 and 4
 to the Si element in the <em>ffield.comb</em> file.  The second Hf argument
diff --git a/doc/html/pair_coul.html b/doc/html/pair_coul.html
index 1df9e6791a..98cba31724 100644
--- a/doc/html/pair_coul.html
+++ b/doc/html/pair_coul.html
@@ -206,18 +206,18 @@
 <h1>pair_style tip4p/long/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span>
-<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">debye</span> <span class="n">kappa</span> <span class="n">cutoff</span>
-<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">dsf</span> <span class="n">alpha</span> <span class="n">cutoff</span>
-<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">cutoff</span>
-<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="n">cutoff</span>
-<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">gpu</span> <span class="n">cutoff</span>
-<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">wolf</span> <span class="n">alpha</span> <span class="n">cutoff</span>
-<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="n">cutoff</span> <span class="n">keyword</span> <span class="n">alpha</span>
-<span class="n">pair_style</span> <span class="n">tip4p</span><span class="o">/</span><span class="n">cut</span> <span class="n">otype</span> <span class="n">htype</span> <span class="n">btype</span> <span class="n">atype</span> <span class="n">qdist</span> <span class="n">cutoff</span>
-<span class="n">pair_style</span> <span class="n">tip4p</span><span class="o">/</span><span class="n">long</span> <span class="n">otype</span> <span class="n">htype</span> <span class="n">btype</span> <span class="n">atype</span> <span class="n">qdist</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style coul/cut cutoff
+pair_style coul/debye kappa cutoff
+pair_style coul/dsf alpha cutoff
+pair_style coul/long cutoff
+pair_style coul/long/cs cutoff
+pair_style coul/long/gpu cutoff
+pair_style coul/wolf alpha cutoff
+pair_style coul/streitz cutoff keyword alpha
+pair_style tip4p/cut otype htype btype atype qdist cutoff
+pair_style tip4p/long otype htype btype atype qdist cutoff
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for Coulombic interactions</li>
 <li>kappa = Debye length (inverse distance units)</li>
@@ -226,46 +226,46 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">3.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">debye</span> <span class="mf">1.4</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">3.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">dsf</span> <span class="mf">0.05</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">wolf</span> <span class="mf">0.2</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="mf">12.0</span> <span class="n">ewald</span>
-<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="mf">12.0</span> <span class="n">wolf</span> <span class="mf">0.30</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">AlO</span><span class="o">.</span><span class="n">streitz</span> <span class="n">Al</span> <span class="n">O</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tip4p</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">12.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tip4p</span><span class="o">/</span><span class="n">long</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style coul/cut 2.5
+pair_coeff * *
+pair_coeff 2 2 3.5
+</pre>
+<pre class="literal-block">
+pair_style coul/debye 1.4 3.0
+pair_coeff * *
+pair_coeff 2 2 3.5
+</pre>
+<pre class="literal-block">
+pair_style coul/dsf 0.05 10.0
+pair_coeff * *
+</pre>
+<pre class="literal-block">
+pair_style coul/long 10.0
+pair_style coul/long/cs 10.0
+pair_coeff * *
+</pre>
+<pre class="literal-block">
+pair_style coul/msm 10.0
+pair_coeff * *
+</pre>
+<pre class="literal-block">
+pair_style coul/wolf 0.2 9.0
+pair_coeff * *
+</pre>
+<pre class="literal-block">
+pair_style coul/streitz 12.0 ewald
+pair_style coul/streitz 12.0 wolf 0.30
+pair_coeff * * AlO.streitz Al O
+</pre>
+<pre class="literal-block">
+pair_style tip4p/cut 1 2 7 8 0.15 12.0
+pair_coeff * *
+</pre>
+<pre class="literal-block">
+pair_style tip4p/long 1 2 7 8 0.15 10.0
+pair_coeff * *
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -317,21 +317,21 @@ used with <a class="reference internal" href="pair_eam.html"><span class="doc">p
 short-range potential that has been parameterized appropriately) via
 the <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid/overlay</span></a> command.  Likewise,
 charge equilibration must be performed via the <a class="reference internal" href="fix_qeq.html"><span class="doc">fix qeq/slater</span></a> command. For example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="mf">12.0</span> <span class="n">wolf</span> <span class="mf">0.31</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="n">AlO</span><span class="o">.</span><span class="n">streitz</span> <span class="n">Al</span> <span class="n">O</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span> <span class="n">AlO</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">alloy</span> <span class="n">Al</span> <span class="n">O</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">slater</span> <span class="mi">1</span> <span class="mf">12.0</span> <span class="mf">1.0e-6</span> <span class="mi">100</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
+pair_coeff * * coul/streitz AlO.streitz Al O
+pair_coeff * * eam/alloy AlO.eam.alloy Al O
+fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
+</pre>
 <p>The keyword <em>wolf</em> in the coul/streitz command denotes computing
 Coulombic interactions via Wolf summation.  An additional damping
 parameter is required for the Wolf summation, as described for the
 coul/wolf potential above.  Alternatively, Coulombic interactions can
 be computed via an Ewald summation.  For example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="mf">12.0</span> <span class="n">ewald</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span>
-<span class="n">kspace_style</span> <span class="n">ewald</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">6</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
+kspace_style ewald 1e-6
+</pre>
 <p>Keyword <em>ewald</em> does not need a damping parameter, but a
 <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> must be defined, which can be style
 <em>ewald</em> or <em>pppm</em>.  The Ewald method was used in Streitz and
diff --git a/doc/html/pair_coul_diel.html b/doc/html/pair_coul_diel.html
index 1f7d3e04af..88e078dfd5 100644
--- a/doc/html/pair_coul_diel.html
+++ b/doc/html/pair_coul_diel.html
@@ -131,17 +131,17 @@
 <h1>pair_style coul/diel/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">diel</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style coul/diel cutoff
+</pre>
 <p>cutoff = global cutoff (distance units)</p>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">diel</span> <span class="mf">3.5</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mf">78.</span> <span class="mf">1.375</span> <span class="mf">0.112</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style coul/diel 3.5
+pair_coeff 1 4 78. 1.375 0.112
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_cs.html b/doc/html/pair_cs.html
index 75b462f741..12d0c515ef 100644
--- a/doc/html/pair_cs.html
+++ b/doc/html/pair_cs.html
@@ -131,9 +131,9 @@
 <h1>pair_style buck/coul/long/cs command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>born/coul/long/cs</em> or <em>buck/coul/long/cs</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -149,16 +149,16 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style born/coul/long/cs 10.0 8.0
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+</pre>
+<pre class="literal-block">
+pair_style buck/coul/long/cs 10.0
+pair_style buck/coul/long/cs 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_dipole.html b/doc/html/pair_dipole.html
index a8b5437180..25e82fc6e3 100644
--- a/doc/html/pair_dipole.html
+++ b/doc/html/pair_dipole.html
@@ -149,12 +149,12 @@
 <h1>pair_style lj/long/dipole/long command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sf</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">sf</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">flag_lj</span> <span class="n">flag_coul</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut/dipole/cut cutoff (cutoff2)
+pair_style lj/sf/dipole/sf cutoff (cutoff2)
+pair_style lj/cut/dipole/long cutoff (cutoff2)
+pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2)
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units)</li>
 <li>cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units)</li>
@@ -175,26 +175,26 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sf</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">sf</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">long</span> <span class="n">long</span> <span class="mf">3.5</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut/dipole/cut 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+</pre>
+<pre class="literal-block">
+pair_style lj/sf/dipole/sf 9.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/dipole/long 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+</pre>
+<pre class="literal-block">
+pair_style lj/long/dipole/long long long 3.5 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_dpd.html b/doc/html/pair_dpd.html
index f605baaa87..1275469c41 100644
--- a/doc/html/pair_dpd.html
+++ b/doc/html/pair_dpd.html
@@ -143,10 +143,10 @@
 <h1>pair_style dpd/tstat/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span> <span class="n">T</span> <span class="n">cutoff</span> <span class="n">seed</span>
-<span class="n">pair_style</span> <span class="n">dpd</span><span class="o">/</span><span class="n">tstat</span> <span class="n">Tstart</span> <span class="n">Tstop</span> <span class="n">cutoff</span> <span class="n">seed</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style dpd T cutoff seed
+pair_style dpd/tstat Tstart Tstop cutoff seed
+</pre>
 <ul class="simple">
 <li>T = temperature (temperature units)</li>
 <li>Tstart,Tstop = desired temperature at start/end of run (temperature units)</li>
@@ -156,16 +156,16 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mi">34387</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">3.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">3.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span><span class="o">/</span><span class="n">tstat</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mi">34387</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style dpd 1.0 2.5 34387
+pair_coeff * * 3.0 1.0
+pair_coeff 1 1 3.0 1.0 1.0
+</pre>
+<pre class="literal-block">
+pair_style dpd/tstat 1.0 1.0 2.5 34387
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0 1.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_dpd_fdt.html b/doc/html/pair_dpd_fdt.html
index cd8033694c..e6132b19d2 100644
--- a/doc/html/pair_dpd_fdt.html
+++ b/doc/html/pair_dpd_fdt.html
@@ -131,9 +131,9 @@
 <h1>pair_style dpd/fdt/energy command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>dpd/fdt</em> or <em>dpd/fdt/energy</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -150,14 +150,14 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span><span class="o">/</span><span class="n">fdt</span> <span class="mf">300.0</span> <span class="mf">2.5</span> <span class="mi">34387</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">3.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span><span class="o">/</span><span class="n">fdt</span><span class="o">/</span><span class="n">energy</span> <span class="mf">2.5</span> <span class="mi">34387</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">3.0</span> <span class="mf">1.0</span> <span class="mf">0.1</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style dpd/fdt 300.0 2.5 34387
+pair_coeff * * 3.0 1.0 2.5
+</pre>
+<pre class="literal-block">
+pair_style dpd/fdt/energy 2.5 34387
+pair_coeff * * 3.0 1.0 0.1 2.5
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_dsmc.html b/doc/html/pair_dsmc.html
index 5f8ddd5600..4c971f1dd1 100644
--- a/doc/html/pair_dsmc.html
+++ b/doc/html/pair_dsmc.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_style dsmc command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dsmc</span> <span class="n">max_cell_size</span> <span class="n">seed</span> <span class="n">weighting</span> <span class="n">Tref</span> <span class="n">Nrecompute</span> <span class="n">Nsample</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
+</pre>
 <ul class="simple">
 <li>max_cell_size = global maximum cell size for DSMC interactions (distance units)</li>
 <li>seed = random # seed (positive integer)</li>
@@ -142,11 +142,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dsmc</span> <span class="mf">2.5</span> <span class="mi">34387</span> <span class="mi">10</span> <span class="mf">1.0</span> <span class="mi">100</span> <span class="mi">20</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style dsmc 2.5 34387 10 1.0 100 20
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -191,12 +191,12 @@ neighboring processors every timestep as they move.  This makes it
 possible to perform all collisions between pairs of particles that are
 on the same processor.  To ensure this occurs, you should use
 these commands:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neighbor</span> <span class="mf">0.0</span> <span class="nb">bin</span>
-<span class="n">neigh_modify</span> <span class="n">every</span> <span class="mi">1</span> <span class="n">delay</span> <span class="mi">0</span> <span class="n">check</span> <span class="n">no</span>
-<span class="n">atom_modify</span> <span class="n">sort</span> <span class="mi">0</span> <span class="mf">0.0</span>
-<span class="n">communicate</span> <span class="n">single</span> <span class="n">cutoff</span> <span class="mf">0.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+neighbor 0.0 bin
+neigh_modify every 1 delay 0 check no
+atom_modify sort 0 0.0
+communicate single cutoff 0.0
+</pre>
 <p>These commands ensure that LAMMPS communicates particles to
 neighboring processors every timestep and that no ghost atoms are
 created.  The output statistics for a simulation run should indicate
diff --git a/doc/html/pair_eam.html b/doc/html/pair_eam.html
index 81abf57a5a..62a0305a0c 100644
--- a/doc/html/pair_eam.html
+++ b/doc/html/pair_eam.html
@@ -176,32 +176,32 @@
 <h1>pair_style eam/fs/opt command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style
+</pre>
 <ul class="simple">
 <li>style = <em>eam</em> or <em>eam/alloy</em> or <em>eam/cd</em> or <em>eam/fs</em></li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">cuu3</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">niu3</span><span class="o">.</span><span class="n">eam</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">alloy</span> <span class="n">Ni</span> <span class="n">Al</span> <span class="n">Ni</span> <span class="n">Ni</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">cd</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">FeCr</span><span class="o">.</span><span class="n">cdeam</span> <span class="n">Fe</span> <span class="n">Cr</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">fs</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">fs</span> <span class="n">Ni</span> <span class="n">Al</span> <span class="n">Ni</span> <span class="n">Ni</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style eam
+pair_coeff * * cuu3
+pair_coeff 1*3 1*3 niu3.eam
+</pre>
+<pre class="literal-block">
+pair_style eam/alloy
+pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
+</pre>
+<pre class="literal-block">
+pair_style eam/cd
+pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
+</pre>
+<pre class="literal-block">
+pair_style eam/fs
+pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -270,9 +270,9 @@ single argument:</p>
 <li>filename</li>
 </ul>
 <p>Thus the following command</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span><span class="mi">2</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="n">cuu3</span><span class="o">.</span><span class="n">eam</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff *2 1*2 cuu3.eam
+</pre>
 <p>will read the cuu3 potential file and use the tabulated Cu values for
 F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
 1,2 and 2,1 are ignored).  See the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> doc
@@ -315,9 +315,9 @@ density).  The units for the effective charge Z are &#8220;atomic charge&#8221;
 sqrt(Hartree * Bohr-radii).  For two interacting atoms i,j this is used
 by LAMMPS to compute the pair potential term in the EAM energy
 expression as r*phi, in units of eV-Angstroms, via the formula</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">r</span><span class="o">*</span><span class="n">phi</span> <span class="o">=</span> <span class="mf">27.2</span> <span class="o">*</span> <span class="mf">0.529</span> <span class="o">*</span> <span class="n">Zi</span> <span class="o">*</span> <span class="n">Zj</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+r*phi = 27.2 * 0.529 * Zi * Zj
+</pre>
 <p>where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.</p>
 <hr class="docutils" />
 <p>Style <em>eam/alloy</em> computes pairwise interactions using the same
@@ -350,9 +350,9 @@ page for alternate ways to specify the path for the potential file.
 If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to
 be Ni, and the 4th to be Al, you would use the following pair_coeff
 command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">alloy</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Al</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
 element in the <em>setfl</em> file.  The final Al argument maps LAMMPS atom
@@ -446,9 +446,9 @@ require that; the user can tabulate any functional form desired in the
 FS potential files.</p>
 <p>For style <em>eam/fs</em>, the form of the pair_coeff command is exactly the
 same as for style <em>eam/alloy</em>, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">fs</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Al</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
+</pre>
 <p>where there are N additional arguments after the filename, where N is
 the number of LAMMPS atom types.  See the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>
 doc page for alternate ways to specify the path for the potential
diff --git a/doc/html/pair_edip.html b/doc/html/pair_edip.html
index 8c9d9ccdee..54a690dde1 100644
--- a/doc/html/pair_edip.html
+++ b/doc/html/pair_edip.html
@@ -128,12 +128,12 @@
 <span id="index-0"></span><h1>pair_style edip command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">edip</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">edip</span><span class="o">/</span><span class="n">omp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style edip
+</pre>
+<pre class="literal-block">
+pair_style edip/omp
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
diff --git a/doc/html/pair_eff.html b/doc/html/pair_eff.html
index 6bcd28cef2..939cdbbf5c 100644
--- a/doc/html/pair_eff.html
+++ b/doc/html/pair_eff.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_style eff/cut command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style eff/cut cutoff keyword args ...
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for Coulombic interactions</li>
 <li>zero or more keyword/value pairs may be appended</li>
@@ -146,16 +146,16 @@ keyword = <em>limit/eradius</em> or <em>pressure/evirials</em> or <em>ecp</em>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">39.7</span>
-<span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">40.0</span> <span class="n">limit</span><span class="o">/</span><span class="n">eradius</span>
-<span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">40.0</span> <span class="n">limit</span><span class="o">/</span><span class="n">eradius</span> <span class="n">pressure</span><span class="o">/</span><span class="n">evirials</span>
-<span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">40.0</span> <span class="n">ecp</span> <span class="mi">1</span> <span class="n">Si</span> <span class="mi">3</span> <span class="n">C</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">20.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="n">s</span> <span class="mf">0.320852</span> <span class="mf">2.283269</span> <span class="mf">0.814857</span>
-<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="n">p</span> <span class="mf">22.721015</span> <span class="mf">0.728733</span> <span class="mf">1.103199</span> <span class="mf">17.695345</span> <span class="mf">6.693621</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style eff/cut 39.7
+pair_style eff/cut 40.0 limit/eradius
+pair_style eff/cut 40.0 limit/eradius pressure/evirials
+pair_style eff/cut 40.0 ecp 1 Si 3 C
+pair_coeff * *
+pair_coeff 2 2 20.0
+pair_coeff 1 s 0.320852 2.283269 0.814857
+pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_eim.html b/doc/html/pair_eim.html
index 62c5a4a918..831c9f00dc 100644
--- a/doc/html/pair_eim.html
+++ b/doc/html/pair_eim.html
@@ -131,21 +131,21 @@
 <h1>pair_style eim/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style
+</pre>
 <ul class="simple">
 <li>style = <em>eim</em></li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eim</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Na</span> <span class="n">Cl</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="n">ffield</span><span class="o">.</span><span class="n">eim</span>  <span class="n">Na</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Cl</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Cl</span> <span class="n">NULL</span> <span class="n">Na</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style eim
+pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
+pair_coeff * * Na Cl ffield.eim  Na Na Na Cl
+pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -207,9 +207,9 @@ to specify the path for the potential file.</p>
 system with Na and Cl atoms.  If your LAMMPS simulation has 4 atoms
 types and you want the 1st 3 to be Na, and the 4th to be Cl, you would
 use the following pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Cl</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * Na Cl ffield.eim Na Na Na Cl
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The filename is the EIM potential file.  The Na and Cl arguments
 (before the file name) are the two elements for which info will be
diff --git a/doc/html/pair_exp6_rx.html b/doc/html/pair_exp6_rx.html
index 6bd4ae6865..79f0a9b4ae 100644
--- a/doc/html/pair_exp6_rx.html
+++ b/doc/html/pair_exp6_rx.html
@@ -128,21 +128,21 @@
 <span id="index-0"></span><h1>pair_style exp6/rx command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">exp6</span><span class="o">/</span><span class="n">rx</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style exp6/rx cutoff
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for DPD interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">exp6</span><span class="o">/</span><span class="n">rx</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="n">h2o</span> <span class="n">h2o</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="n">h2o</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style exp6/rx 10.0
+pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0
+pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0
+pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_gauss.html b/doc/html/pair_gauss.html
index 2f167476f8..d90d449b83 100644
--- a/doc/html/pair_gauss.html
+++ b/doc/html/pair_gauss.html
@@ -140,25 +140,25 @@
 <h1>pair_style gauss/cut/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gauss</span> <span class="n">cutoff</span>
-<span class="n">pair_style</span> <span class="n">gauss</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style gauss cutoff
+pair_style gauss/cut cutoff
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for Gauss interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gauss</span> <span class="mf">12.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">0.9</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mf">1.0</span> <span class="mf">0.9</span> <span class="mf">10.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gauss</span><span class="o">/</span><span class="n">cut</span> <span class="mf">3.5</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mf">0.2805</span> <span class="mf">1.45</span> <span class="mf">0.112</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style gauss 12.0
+pair_coeff * * 1.0 0.9
+pair_coeff 1 4 1.0 0.9 10.0
+</pre>
+<pre class="literal-block">
+pair_style gauss/cut 3.5
+pair_coeff 1 4 0.2805 1.45 0.112
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -239,11 +239,11 @@ sites have an atom within the distance at which the force is a maximum
 = sqrt(0.5/b).  This quantity can be accessed via the <a class="reference internal" href="compute_pair.html"><span class="doc">compute pair</span></a> command as a vector of values of length 1.</p>
 <p>To print this quantity to the log file (with a descriptive column
 heading) the following commands could be included in an input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">gauss</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">gauss</span>
-<span class="n">variable</span> <span class="n">occ</span> <span class="n">equal</span> <span class="n">c_gauss</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_occ</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute gauss all pair gauss
+variable occ equal c_gauss[1]
+thermo_style custom step temp epair v_occ
+</pre>
 </div>
 <hr class="docutils" />
 <div class="section" id="restrictions">
diff --git a/doc/html/pair_gayberne.html b/doc/html/pair_gayberne.html
index 0b02a49a51..68e46bd2d8 100644
--- a/doc/html/pair_gayberne.html
+++ b/doc/html/pair_gayberne.html
@@ -137,9 +137,9 @@
 <h1>pair_style gayberne/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gayberne</span> <span class="n">gamma</span> <span class="n">upsilon</span> <span class="n">mu</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style gayberne gamma upsilon mu cutoff
+</pre>
 <ul class="simple">
 <li>gamma = shift for potential minimum (typically 1)</li>
 <li>upsilon = exponent for eta orientation-dependent energy function</li>
@@ -149,10 +149,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gayberne</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.7</span> <span class="mf">1.7</span> <span class="mf">3.4</span> <span class="mf">3.4</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style gayberne 1.0 1.0 1.0 10.0
+pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_gran.html b/doc/html/pair_gran.html
index a1fb53f824..37946c96aa 100644
--- a/doc/html/pair_gran.html
+++ b/doc/html/pair_gran.html
@@ -143,9 +143,9 @@
 <h1>pair_style gran/hertz/history/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">Kn</span> <span class="n">Kt</span> <span class="n">gamma_n</span> <span class="n">gamma_t</span> <span class="n">xmu</span> <span class="n">dampflag</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style Kn Kt gamma_n gamma_t xmu dampflag
+</pre>
 <ul class="simple">
 <li>style = <em>gran/hooke</em> or <em>gran/hooke/history</em> or <em>gran/hertz/history</em></li>
 <li>Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)</li>
@@ -169,10 +169,10 @@ for details.</p>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gran</span><span class="o">/</span><span class="n">hooke</span><span class="o">/</span><span class="n">history</span> <span class="mf">200000.0</span> <span class="n">NULL</span> <span class="mf">50.0</span> <span class="n">NULL</span> <span class="mf">0.5</span> <span class="mi">1</span>
-<span class="n">pair_style</span> <span class="n">gran</span><span class="o">/</span><span class="n">hooke</span> <span class="mf">200000.0</span> <span class="mf">70000.0</span> <span class="mf">50.0</span> <span class="mf">30.0</span> <span class="mf">0.5</span> <span class="mi">0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
+pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -287,9 +287,9 @@ each pair of atom types via the <a class="reference internal" href="pair_coeff.h
 All settings are global and are made via the pair_style command.
 However you must still use the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> for all
 pairs of granular atom types.  For example the command</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * *
+</pre>
 <p>should be used if all atoms in the simulation interact via a granular
 potential (i.e. one of the pair styles above is used).  If a granular
 potential is used as a sub-style of <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid</span></a>, then specific atom types can be used in the
diff --git a/doc/html/pair_gromacs.html b/doc/html/pair_gromacs.html
index 7cc3aee2ce..a58a10912a 100644
--- a/doc/html/pair_gromacs.html
+++ b/doc/html/pair_gromacs.html
@@ -140,9 +140,9 @@
 <h1>pair_style lj/gromacs/coul/gromacs/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>lj/gromacs</em> or <em>lj/gromacs/coul/gromacs</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -157,16 +157,16 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">gromacs</span> <span class="mf">9.0</span> <span class="mf">12.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">gromacs</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">gromacs</span> <span class="mf">9.0</span> <span class="mf">12.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">gromacs</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">gromacs</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">7.0</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/gromacs 9.0 12.0
+pair_coeff * * 100.0 2.0
+pair_coeff 2 2 100.0 2.0 8.0 10.0
+</pre>
+<pre class="literal-block">
+pair_style lj/gromacs/coul/gromacs 9.0 12.0
+pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
+pair_coeff * * 100.0 2.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_hbond_dreiding.html b/doc/html/pair_hbond_dreiding.html
index 659f637dec..e639ba34e8 100644
--- a/doc/html/pair_hbond_dreiding.html
+++ b/doc/html/pair_hbond_dreiding.html
@@ -137,9 +137,9 @@
 <h1>pair_style hbond/dreiding/morse/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">N</span> <span class="n">inner_distance_cutoff</span> <span class="n">outer_distance_cutoff</span> <span class="n">angle_cutof</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
+</pre>
 <ul class="simple">
 <li>style = <em>hbond/dreiding/lj</em> or <em>hbond/dreiding/morse</em></li>
 <li>n = cosine angle periodicity</li>
@@ -151,14 +151,14 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">lj</span> <span class="mi">4</span> <span class="mf">9.0</span> <span class="mf">11.0</span> <span class="mi">90</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">lj</span> <span class="mi">3</span> <span class="n">i</span> <span class="mf">9.5</span> <span class="mf">2.75</span> <span class="mi">4</span> <span class="mf">9.0</span> <span class="mf">11.0</span> <span class="mf">90.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">morse</span> <span class="mi">2</span> <span class="mf">9.0</span> <span class="mf">11.0</span> <span class="mi">90</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">morse</span> <span class="mi">3</span> <span class="n">i</span> <span class="mf">3.88</span> <span class="mf">1.7241379</span> <span class="mf">2.9</span> <span class="mi">2</span> <span class="mi">9</span> <span class="mi">11</span> <span class="mi">90</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
+pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
+</pre>
+<pre class="literal-block">
+pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
+pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -265,7 +265,7 @@ follows:</p>
 <p>A single hydrogen atom type K can be specified, or a wild-card
 asterisk can be used in place of or in conjunction with the K
 arguments to select multiple types as hydrogens.  This takes the form
-&#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  See the <a class="reference external" href="pair_coeff">pair_coeff</a> command
+&#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  See the <a class="reference external" href="pair_coeff">pair_coeff</a> command
 doc page for details.</p>
 <p>If the donor flag is <em>i</em>, then the atom of type I in the pair_coeff
 command is treated as the donor, and J is the acceptor.  If the donor
@@ -321,12 +321,12 @@ quantities can be accessed via the <a class="reference internal" href="compute_p
 command as a vector of values of length 2.</p>
 <p>To print these quantities to the log file (with a descriptive column
 heading) the following commands could be included in an input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">hb</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">lj</span>
-<span class="n">variable</span> <span class="n">n_hbond</span> <span class="n">equal</span> <span class="n">c_hb</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="c1">#number hbonds</span>
-<span class="n">variable</span> <span class="n">E_hbond</span> <span class="n">equal</span> <span class="n">c_hb</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="c1">#hbond energy</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_E_hbond</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute hb all pair hbond/dreiding/lj
+variable n_hbond equal c_hb[1] #number hbonds
+variable E_hbond equal c_hb[2] #hbond energy
+thermo_style custom step temp epair v_E_hbond
+</pre>
 </div>
 <hr class="docutils" />
 <div class="section" id="restrictions">
diff --git a/doc/html/pair_hybrid.html b/doc/html/pair_hybrid.html
index afe0cebcd6..60044d0faf 100644
--- a/doc/html/pair_hybrid.html
+++ b/doc/html/pair_hybrid.html
@@ -137,27 +137,27 @@
 <h1>pair_style hybrid/overlay/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">style1</span> <span class="n">args</span> <span class="n">style2</span> <span class="n">args</span> <span class="o">...</span>
-<span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">style1</span> <span class="n">args</span> <span class="n">style2</span> <span class="n">args</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid style1 args style2 args ...
+pair_style hybrid/overlay style1 args style2 args ...
+</pre>
 <ul class="simple">
 <li>style1,style2 = list of one or more pair styles and their arguments</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="n">eam</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">5.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="n">eam</span> <span class="n">niu3</span>
-<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">0.5</span> <span class="mf">1.2</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">2.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
+pair_coeff 1*2 1*2 eam niu3
+pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
+pair_coeff 1*2 3 lj/cut 0.5 1.2
+</pre>
+<pre class="literal-block">
+pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * coul/long
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -218,22 +218,22 @@ these coefficients apply to.</p>
 <p>For example, consider a simulation with 3 atom types: types 1 and 2
 are Ni atoms, type 3 are LJ atoms with charges.  The following
 commands would set up a hybrid simulation:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span> <span class="n">nialhjea</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">NULL</span>
-<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">0.8</span> <span class="mf">1.3</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
+pair_coeff * * eam/alloy nialhjea Ni Ni NULL
+pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
+pair_coeff 1*2 3 lj/cut 0.8 1.3
+</pre>
 <p>As an example of using the same pair style multiple times, consider a
 simulation with 2 atom types.  Type 1 is Si, type 2 is C.  The
 following commands would model the Si atoms with Tersoff, the C atoms
 with Tersoff, and the cross-interactions with Lennard-Jones:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span> <span class="n">tersoff</span> <span class="n">tersoff</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">tersoff</span> <span class="mi">1</span> <span class="n">Si</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span> <span class="n">NULL</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">tersoff</span> <span class="mi">2</span> <span class="n">C</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">NULL</span> <span class="n">C</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid lj/cut 2.5 tersoff tersoff
+pair_coeff * * tersoff 1 Si.tersoff Si NULL
+pair_coeff * * tersoff 2 C.tersoff NULL C
+pair_coeff 1 2 lj/cut 1.0 1.5
+</pre>
 <p>If pair coefficients are specified in the data file read via the
 <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command, then the same rule applies.
 E.g. &#8220;eam/alloy&#8221; or &#8220;lj/cut&#8221; must be added after the atom type, for
@@ -266,16 +266,16 @@ sub-style that has already been defined for that pair of atoms, then
 the new pair coefficients simply override the previous ones, as in the
 normal usage of the pair_coeff command.  E.g. these two sets of
 commands are the same:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">1.5</span> <span class="mf">0.8</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.5</span> <span class="mf">0.8</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 2 2 1.5 0.8
+</pre>
+<pre class="literal-block">
+pair_style hybrid/overlay lj/cut 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 2 2 lj/cut 1.5 0.8
+</pre>
 <p>Coefficients must be defined for each pair of atoms types via the
 <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as described above, or in the
 data file or restart files read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or
@@ -293,9 +293,9 @@ command.  You can assign it to some sub-style and set the coefficients
 so that there is effectively no interaction (e.g. epsilon = 0.0 in a
 LJ potential).  Or, for <em>hybrid</em> and <em>hybrid/overlay</em> simulations, you
 can use this form of the pair_coeff command in your input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span>   <span class="mi">2</span> <span class="mi">3</span> <span class="n">none</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff  2 3 none
+</pre>
 <p>or this form in the &#8220;Pair Coeffs&#8221; section of the data file:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">3</span> <span class="n">none</span>
 </pre></div>
@@ -321,29 +321,29 @@ described by the different force fields do not mix.</p>
 <p>Here is an example for mixing CHARMM and AMBER: The global <em>amber</em>
 setting sets the 1-4 interactions to non-zero scaling factors and
 then overrides them with 0.0 only for CHARMM:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">amber</span>
-<span class="n">pair_hybrid</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
-<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">special</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+special_bonds amber
+pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+</pre>
 <p>The this input achieves the same effect:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.1</span>
-<span class="n">pair_hybrid</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
-<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">special</span> <span class="n">lj</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.5</span>
-<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">special</span> <span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.83333333</span>
-<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">special</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+special_bonds 0.0 0.0 0.1
+pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
+pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
+pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+</pre>
 <p>Here is an example for mixing Tersoff with OPLS/AA based on
 a data file that defines bonds for all atoms where for the
 Tersoff part of the system the force constants for the bonded
 interactions have been set to 0. Note the global settings are
 effectively <em>lj/coul 0.0 0.0 0.5</em> as required for OPLS/AA:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">20</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">20</span> <span class="mf">0.5</span>
-<span class="n">pair_hybrid</span> <span class="n">tersoff</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">12.0</span>
-<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">tersoff</span> <span class="n">special</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+special_bonds lj/coul 1e-20 1e-20 0.5
+pair_hybrid tersoff lj/cut/coul/long 12.0
+pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
+</pre>
 <p>See the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> doc page for details on
 the specific syntax, requirements and restrictions.</p>
 <hr class="docutils" />
@@ -358,7 +358,7 @@ ReaxFF, etc.  The way to think about using these potentials in a
 hybrid setting is as follows.</p>
 </div>
 <p>A subset of atom types is assigned to the many-body potential with a
-single <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command, using &#8220;* <a href="#id1"><span class="problematic" id="id2">*</span></a>&#8221; to include
+single <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command, using &#8220;* *&#8221; to include
 all types and the NULL keywords described above to exclude specific
 types not assigned to that potential.  If types 1,3,4 were assigned in
 that way (but not type 2), this means that all many-body interactions
@@ -388,16 +388,16 @@ atoms in one surface, and type 2 for atoms in the other, and you wish
 to use a Tersoff potential to compute interactions within each
 surface, but not between surfaces.  Then either of these two command
 sequences would implement that model:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">tersoff</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">tersoff</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">C</span> <span class="n">C</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">none</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">C</span> <span class="n">C</span>
-<span class="n">neigh_modify</span> <span class="n">exclude</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid tersoff
+pair_coeff * * tersoff SiC.tersoff C C
+pair_coeff 1 2 none
+</pre>
+<pre class="literal-block">
+pair_style tersoff
+pair_coeff * * SiC.tersoff C C
+neigh_modify exclude type 1 2
+</pre>
 <p>Either way, only neighbor lists with 1-1 or 2-2 interactions would be
 passed to the Tersoff potential, which means it would compute no
 3-body interactions containing both type 1 and 2 atoms.</p>
@@ -406,11 +406,11 @@ potentials together, in an overlapping manner.  Imagine you have CNT
 (C atoms) on a Si surface.  You want to use Tersoff for Si/Si and Si/C
 interactions, and AIREBO for C/C interactions.  Si atoms are type 1; C
 atoms are type 2.  Something like this will work:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">tersoff</span> <span class="n">airebo</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">tersoff</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span><span class="o">.</span><span class="n">custom</span> <span class="n">Si</span> <span class="n">C</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">airebo</span> <span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">NULL</span> <span class="n">C</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid/overlay tersoff airebo 3.0
+pair_coeff * * tersoff SiC.tersoff.custom Si C
+pair_coeff * * airebo CH.airebo NULL C
+</pre>
 <p>Note that to prevent the Tersoff potential from computing C/C
 interactions, you would need to modify the SiC.tersoff file to turn
 off C/C interaction, i.e. by setting the appropriate coefficients to
diff --git a/doc/html/pair_line_lj.html b/doc/html/pair_line_lj.html
index f36f573822..c79f73301e 100644
--- a/doc/html/pair_line_lj.html
+++ b/doc/html/pair_line_lj.html
@@ -128,19 +128,19 @@
 <span id="index-0"></span><h1>pair_style line/lj command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">line</span><span class="o">/</span><span class="n">lj</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style line/lj cutoff
+</pre>
 <p>cutoff = global cutoff for interactions (distance units)</p>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">line</span><span class="o">/</span><span class="n">lj</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.8</span> <span class="mf">1.12</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mf">1.0</span> <span class="mf">2.0</span> <span class="mf">1.0</span> <span class="mf">1.5</span> <span class="mf">1.12</span> <span class="mf">5.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style line/lj 3.0
+pair_coeff * * 1.0 1.0 1.0 0.8 1.12
+pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
+pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_list.html b/doc/html/pair_list.html
index f7d59aba21..2897df868b 100644
--- a/doc/html/pair_list.html
+++ b/doc/html/pair_list.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_style list command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="nb">list</span> <span class="n">listfile</span> <span class="n">cutoff</span> <span class="n">keyword</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style list listfile cutoff keyword
+</pre>
 <ul class="simple">
 <li>listfile = name of file with list of pairwise interactions</li>
 <li>cutoff = global cutoff (distance units)</li>
@@ -139,15 +139,15 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="nb">list</span> <span class="n">restraints</span><span class="o">.</span><span class="n">txt</span> <span class="mf">200.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.1225</span> <span class="nb">list</span> <span class="n">pair_list</span><span class="o">.</span><span class="n">txt</span> <span class="mf">300.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">3</span><span class="o">*</span> <span class="mi">3</span><span class="o">*</span> <span class="nb">list</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style list restraints.txt 200.0
+pair_coeff * *
+</pre>
+<pre class="literal-block">
+pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 3* 3* list
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lj.html b/doc/html/pair_lj.html
index fd46ab5d3b..73f9948c27 100644
--- a/doc/html/pair_lj.html
+++ b/doc/html/pair_lj.html
@@ -218,9 +218,9 @@
 <h1>pair_style lj/cut/tip4p/long/opt command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>lj/cut</em> or <em>lj/cut/coul/cut</em> or <em>lj/cut/coul/debye</em> or <em>lj/cut/coul/dsf</em> or <em>lj/cut/coul/long</em> or <em>lj/cut/coul/long/cs</em> or <em>lj/cut/coul/msm</em> or <em>lj/cut/tip4p/long</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -261,56 +261,56 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">1</span> <span class="mi">1</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.1</span> <span class="mf">2.8</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">debye</span> <span class="mf">1.5</span> <span class="mf">3.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">debye</span> <span class="mf">1.5</span> <span class="mf">2.5</span> <span class="mf">5.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.5</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.5</span> <span class="mf">2.5</span> <span class="mf">5.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">dsf</span> <span class="mf">0.05</span> <span class="mf">2.5</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">tip4p</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">12.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">tip4p</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">12.0</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">tip4p</span><span class="o">/</span><span class="n">long</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">12.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">tip4p</span><span class="o">/</span><span class="n">long</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">12.0</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut 2.5
+pair_coeff * * 1 1
+pair_coeff 1 1 1 1.1 2.8
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/coul/cut 10.0
+pair_style lj/cut/coul/cut 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+pair_coeff 1 1 100.0 3.5 9.0 9.0
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/coul/debye 1.5 3.0
+pair_style lj/cut/coul/debye 1.5 2.5 5.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+pair_coeff 1 1 1.0 1.5 2.5 5.0
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/coul/dsf 0.05 2.5 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.0 2.5
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/coul/long 10.0
+pair_style lj/cut/coul/long/cs 10.0
+pair_style lj/cut/coul/long 10.0 8.0
+pair_style lj/cut/coul/long/cs 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/coul/msm 10.0
+pair_style lj/cut/coul/msm 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
+pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
+pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lj96.html b/doc/html/pair_lj96.html
index 25b68df4b4..3f7e8fdd9b 100644
--- a/doc/html/pair_lj96.html
+++ b/doc/html/pair_lj96.html
@@ -134,20 +134,20 @@
 <h1>pair_style lj96/cut/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj96</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj96/cut cutoff
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for lj96/cut interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj96</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">4.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj96/cut 2.5
+pair_coeff * * 1.0 1.0 4.0
+pair_coeff 1 1 1.0 1.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lj_cubic.html b/doc/html/pair_lj_cubic.html
index 6032650397..6dad5de332 100644
--- a/doc/html/pair_lj_cubic.html
+++ b/doc/html/pair_lj_cubic.html
@@ -134,16 +134,16 @@
 <h1>pair_style lj/cubic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cubic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cubic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cubic</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">0.8908987</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cubic
+pair_coeff * * 1.0 0.8908987
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lj_expand.html b/doc/html/pair_lj_expand.html
index fef3f21c46..69fc39c046 100644
--- a/doc/html/pair_lj_expand.html
+++ b/doc/html/pair_lj_expand.html
@@ -134,20 +134,20 @@
 <h1>pair_style lj/expand/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">expand</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/expand cutoff
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for lj/expand interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">expand</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.5</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="o">-</span><span class="mf">0.2</span> <span class="mf">2.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/expand 2.5
+pair_coeff * * 1.0 1.0 0.5
+pair_coeff 1 1 1.0 1.0 -0.2 2.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lj_long.html b/doc/html/pair_lj_long.html
index fd2fa29241..2256d2d48e 100644
--- a/doc/html/pair_lj_long.html
+++ b/doc/html/pair_lj_long.html
@@ -137,9 +137,9 @@
 <h1>pair_style lj/long/tip4p/long command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>lj/long/coul/long</em> or <em>lj/long/tip4p/long</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -171,19 +171,19 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">cut</span> <span class="n">off</span> <span class="mf">2.5</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">cut</span> <span class="n">long</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">long</span> <span class="n">long</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">1</span> <span class="mi">1</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mi">4</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">tip4p</span><span class="o">/</span><span class="n">long</span> <span class="n">long</span> <span class="n">long</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">12.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">tip4p</span><span class="o">/</span><span class="n">long</span> <span class="n">long</span> <span class="n">long</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">12.0</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/long/coul/long cut off 2.5
+pair_style lj/long/coul/long cut long 2.5 4.0
+pair_style lj/long/coul/long long long 2.5 4.0
+pair_coeff * * 1 1
+pair_coeff 1 1 1 3 4
+</pre>
+<pre class="literal-block">
+pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0
+pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lj_sf.html b/doc/html/pair_lj_sf.html
index 8505d91cf5..b09ff7e036 100644
--- a/doc/html/pair_lj_sf.html
+++ b/doc/html/pair_lj_sf.html
@@ -131,20 +131,20 @@
 <h1>pair_style lj/sf/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sf</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/sf cutoff
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for Lennard-Jones interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sf</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">3.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/sf 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.0 3.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lj_smooth.html b/doc/html/pair_lj_smooth.html
index 22565da2d7..0973d95ff9 100644
--- a/doc/html/pair_lj_smooth.html
+++ b/doc/html/pair_lj_smooth.html
@@ -131,9 +131,9 @@
 <h1>pair_style lj/smooth/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">smooth</span> <span class="n">Rin</span> <span class="n">Rc</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/smooth Rin Rc
+</pre>
 <ul class="simple">
 <li>Rin = inner cutoff beyond which force smoothing will be applied (distance units)</li>
 <li>Rc = outer cutoff for lj/smooth interactions (distance units)</li>
@@ -141,11 +141,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">smooth</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">1.5</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">20.0</span> <span class="mf">1.3</span> <span class="mf">7.0</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/smooth 8.0 10.0
+pair_coeff * * 10.0 1.5
+pair_coeff 1 1 20.0 1.3 7.0 9.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lj_smooth_linear.html b/doc/html/pair_lj_smooth_linear.html
index f19e28551e..edd6d68386 100644
--- a/doc/html/pair_lj_smooth_linear.html
+++ b/doc/html/pair_lj_smooth_linear.html
@@ -131,20 +131,20 @@
 <h1>pair_style lj/smooth/linear/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">smooth</span><span class="o">/</span><span class="n">linear</span> <span class="n">Rc</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/smooth/linear Rc
+</pre>
 <ul class="simple">
 <li>Rc = cutoff for lj/smooth/linear interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">smooth</span><span class="o">/</span><span class="n">linear</span> <span class="mf">5.456108274435118</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.7242785984051078</span> <span class="mf">2.598146797350056</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">20.0</span> <span class="mf">1.3</span> <span class="mf">9.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/smooth/linear 5.456108274435118
+pair_coeff * * 0.7242785984051078 2.598146797350056
+pair_coeff 1 1 20.0 1.3 9.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lj_soft.html b/doc/html/pair_lj_soft.html
index e253536083..f67e200935 100644
--- a/doc/html/pair_lj_soft.html
+++ b/doc/html/pair_lj_soft.html
@@ -173,9 +173,9 @@
 <h1>pair_style tip4p/long/soft/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>lj/cut/soft</em> or <em>lj/cut/coul/cut/soft</em> or <em>lj/cut/coul/long/soft</em> or <em>lj/cut/tip4p/long/soft</em> or <em>lj/charmm/coul/long/soft</em> or <em>coul/cut/soft</em> or <em>coul/long/soft</em> or <em>tip4p/long/soft</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -219,47 +219,47 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">soft</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">9.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.28</span> <span class="mf">3.1</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.28</span> <span class="mf">3.1</span> <span class="mf">1.0</span> <span class="mf">9.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">soft</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">10.0</span> <span class="mf">9.5</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">soft</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">10.0</span> <span class="mf">9.5</span> <span class="mf">9.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.28</span> <span class="mf">3.1</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.28</span> <span class="mf">3.1</span> <span class="mf">0.5</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.28</span> <span class="mf">3.1</span> <span class="mf">0.5</span> <span class="mf">10.0</span> <span class="mf">9.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">soft</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">10.0</span> <span class="mf">9.5</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">soft</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">10.0</span> <span class="mf">9.5</span> <span class="mf">9.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.28</span> <span class="mf">3.1</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.28</span> <span class="mf">3.1</span> <span class="mf">0.0</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.28</span> <span class="mf">3.1</span> <span class="mf">0.0</span> <span class="mf">10.0</span> <span class="mf">9.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">tip4p</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">soft</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">10.0</span> <span class="mf">9.8</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">tip4p</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">soft</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">10.0</span> <span class="mf">9.8</span> <span class="mf">9.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.155</span> <span class="mf">3.1536</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.155</span> <span class="mf">3.1536</span> <span class="mf">1.0</span> <span class="mf">9.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">10.0</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">10.0</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.28</span> <span class="mf">3.1</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.28</span> <span class="mf">3.1</span> <span class="mf">1.0</span> <span class="mf">0.14</span> <span class="mf">3.1</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">soft</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mf">9.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">9.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tip4p</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">soft</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">10.0</span> <span class="mf">9.8</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">9.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut/soft 2.0 0.5 9.5
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 1.0 9.5
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5
+pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 0.5 10.0
+pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5
+pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 0.0 10.0
+pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
+pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
+pair_coeff * * 0.155 3.1536 1.0
+pair_coeff 1 1 0.155 3.1536 1.0 9.5
+</pre>
+<pre class="literal-block">
+pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
+pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1
+</pre>
+<pre class="literal-block">
+pair_style coul/long/soft 1.0 10.0 9.5
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0 9.5
+</pre>
+<pre class="literal-block">
+pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0 9.5
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lubricate.html b/doc/html/pair_lubricate.html
index 2cae3906c3..b415ee6c3a 100644
--- a/doc/html/pair_lubricate.html
+++ b/doc/html/pair_lubricate.html
@@ -137,9 +137,9 @@
 <h1>pair_style lubricate/poly/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">mu</span> <span class="n">flaglog</span> <span class="n">flagfld</span> <span class="n">cutinner</span> <span class="n">cutoff</span> <span class="n">flagHI</span> <span class="n">flagVF</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF
+</pre>
 <ul class="simple">
 <li>style = <em>lubricate</em> or <em>lubricate/poly</em></li>
 <li>mu = dynamic viscosity (dynamic viscosity units)</li>
@@ -151,17 +151,17 @@
 <li>flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms</li>
 </ul>
 <p><strong>Examples:</strong> (all assume radius = 1)</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lubricate</span> <span class="mf">1.5</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">2.01</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">2.05</span> <span class="mf">2.8</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lubricate</span> <span class="mf">1.5</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">2.01</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-<span class="n">variable</span> <span class="n">mu</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">lubricate</span> <span class="n">mu</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_mu</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lubricate 1.5 1 1 2.01 2.5
+pair_coeff 1 1 2.05 2.8
+pair_coeff * *
+</pre>
+<pre class="literal-block">
+pair_style lubricate 1.5 1 1 2.01 2.5
+pair_coeff * *
+variable mu equal ramp(1,2)
+fix 1 all adapt 1 pair lubricate mu * * v_mu
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_lubricateU.html b/doc/html/pair_lubricateU.html
index 4d518c72e8..deca70058e 100644
--- a/doc/html/pair_lubricateU.html
+++ b/doc/html/pair_lubricateU.html
@@ -131,9 +131,9 @@
 <h1>pair_style lubricateU/poly command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">mu</span> <span class="n">flaglog</span> <span class="n">cutinner</span> <span class="n">cutoff</span> <span class="n">gdot</span> <span class="n">flagHI</span> <span class="n">flagVF</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF
+</pre>
 <ul class="simple">
 <li>style = <em>lubricateU</em> or <em>lubricateU/poly</em></li>
 <li>mu = dynamic viscosity (dynamic viscosity units)</li>
@@ -145,11 +145,11 @@
 <li>flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms</li>
 </ul>
 <p><strong>Examples:</strong> (all assume radius = 1)</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lubricateU</span> <span class="mf">1.5</span> <span class="mi">1</span> <span class="mf">2.01</span> <span class="mf">2.5</span> <span class="mf">0.01</span> <span class="mi">1</span> <span class="mi">1</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">2.05</span> <span class="mf">2.8</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1
+pair_coeff 1 1 2.05 2.8
+pair_coeff * *
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_mdf.html b/doc/html/pair_mdf.html
index 9f78149009..477829e523 100644
--- a/doc/html/pair_mdf.html
+++ b/doc/html/pair_mdf.html
@@ -134,9 +134,9 @@
 <h1>pair_style lennard/mdf command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>lj/mdf</em> or <em>buck/mdf</em> or <em>lennard/mdf</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -155,21 +155,21 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">mdf</span> <span class="mf">2.5</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">1</span> <span class="mi">1</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.1</span> <span class="mf">2.8</span> <span class="mf">3.0</span> <span class="mf">3.2</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span> <span class="mf">2.5</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">3.0</span> <span class="mf">3.5</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lennard</span><span class="o">/</span><span class="n">mdf</span> <span class="mf">2.5</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">1</span> <span class="mi">1</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.1</span> <span class="mf">2.8</span> <span class="mf">3.0</span> <span class="mf">3.2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/mdf 2.5 3.0
+pair_coeff * * 1 1
+pair_coeff 1 1 1 1.1 2.8 3.0 3.2
+</pre>
+<pre class="literal-block">
+pair_style buck 2.5 3.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff * * 100.0 1.5 200.0 3.0 3.5
+</pre>
+<pre class="literal-block">
+pair_style lennard/mdf 2.5 3.0
+pair_coeff * * 1 1
+pair_coeff 1 1 1 1.1 2.8 3.0 3.2
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -198,7 +198,7 @@ below:</p>
 <li>epsilon (energy units)</li>
 <li>sigma (distance units)</li>
 <li>r_m (distance units)</li>
-<li><a href="#id1"><span class="problematic" id="id2">r_</span></a><em>cut</em> (distance units)</li>
+<li>r_<em>cut</em> (distance units)</li>
 </ul>
 <hr class="docutils" />
 <p>For the <em>buck/mdf</em> pair_style, the potential energy, <em>E(r)</em>, is the
@@ -209,7 +209,7 @@ standard Buckingham potential:</p>
 <li>rho (distance units)</li>
 <li>C (energy-distance^6 units)</li>
 <li>r_m (distance units)</li>
-<li><a href="#id3"><span class="problematic" id="id4">r_</span></a><em>cut</em>$ (distance units)</li>
+<li>r_<em>cut</em>$ (distance units)</li>
 </ul>
 <hr class="docutils" />
 <p>For the <em>lennard/mdf</em> pair_style, the potential energy, <em>E(r)</em>, is the
@@ -223,7 +223,7 @@ commands, or by mixing as described below:</p>
 <li>A (energy-distance^12 units)</li>
 <li>B (energy-distance^6 units)</li>
 <li>r_m (distance units)</li>
-<li><a href="#id5"><span class="problematic" id="id6">r_</span></a><em>cut</em> (distance units)</li>
+<li>r_<em>cut</em> (distance units)</li>
 </ul>
 <hr class="docutils" />
 <p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
diff --git a/doc/html/pair_meam.html b/doc/html/pair_meam.html
index 4c704bc583..e9ec4ac13b 100644
--- a/doc/html/pair_meam.html
+++ b/doc/html/pair_meam.html
@@ -128,17 +128,17 @@
 <span id="index-0"></span><h1>pair_style meam command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style meam
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">library</span><span class="o">.</span><span class="n">meam</span> <span class="n">Si</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">si</span><span class="o">.</span><span class="n">meam</span> <span class="n">Si</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">library</span><span class="o">.</span><span class="n">meam</span> <span class="n">Ni</span> <span class="n">Al</span> <span class="n">NULL</span> <span class="n">Ni</span> <span class="n">Al</span> <span class="n">Ni</span> <span class="n">Ni</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style meam
+pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
+pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -194,9 +194,9 @@ settings for a variety of elements.  The potentials/sic.meam file has
 specific parameter settings for a Si and C alloy system.  If your
 LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
 and the 4th to be C, you would use the following pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">library</span><span class="o">.</span><span class="n">meam</span> <span class="n">Si</span> <span class="n">C</span> <span class="n">sic</span><span class="o">.</span><span class="n">meam</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * library.meam Si C sic.meam Si Si Si C
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The two filenames are for the library and parameter file respectively.
 The Si and C arguments (between the file names) are the two elements
@@ -390,14 +390,14 @@ parameter erose_form, can be used to modify the Rose energy function
 used to compute the pair potential.  This function gives the energy of
 the reference state as a function of interatomic spacing.  The form of
 this function is:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">astar</span> <span class="o">=</span> <span class="n">alpha</span> <span class="o">*</span> <span class="p">(</span><span class="n">r</span><span class="o">/</span><span class="n">re</span> <span class="o">-</span> <span class="mf">1.</span><span class="n">d0</span><span class="p">)</span>
-<span class="k">if</span> <span class="n">erose_form</span> <span class="o">=</span> <span class="mi">0</span><span class="p">:</span> <span class="n">erose</span> <span class="o">=</span> <span class="o">-</span><span class="n">Ec</span><span class="o">*</span><span class="p">(</span><span class="mi">1</span><span class="o">+</span><span class="n">astar</span><span class="o">+</span><span class="n">a3</span><span class="o">*</span><span class="p">(</span><span class="n">astar</span><span class="o">**</span><span class="mi">3</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="n">r</span><span class="o">/</span><span class="n">re</span><span class="p">))</span><span class="o">*</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">astar</span><span class="p">)</span>
-<span class="k">if</span> <span class="n">erose_form</span> <span class="o">=</span> <span class="mi">1</span><span class="p">:</span> <span class="n">erose</span> <span class="o">=</span> <span class="o">-</span><span class="n">Ec</span><span class="o">*</span><span class="p">(</span><span class="mi">1</span><span class="o">+</span><span class="n">astar</span><span class="o">+</span><span class="p">(</span><span class="o">-</span><span class="n">attrac</span><span class="o">+</span><span class="n">repuls</span><span class="o">/</span><span class="n">r</span><span class="p">)</span><span class="o">*</span><span class="p">(</span><span class="n">astar</span><span class="o">**</span><span class="mi">3</span><span class="p">))</span><span class="o">*</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">astar</span><span class="p">)</span>
-<span class="k">if</span> <span class="n">erose_form</span> <span class="o">=</span> <span class="mi">2</span><span class="p">:</span> <span class="n">erose</span> <span class="o">=</span> <span class="o">-</span><span class="n">Ec</span><span class="o">*</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span><span class="n">astar</span> <span class="o">+</span> <span class="n">a3</span><span class="o">*</span><span class="p">(</span><span class="n">astar</span><span class="o">**</span><span class="mi">3</span><span class="p">))</span><span class="o">*</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">astar</span><span class="p">)</span>
-<span class="n">a3</span> <span class="o">=</span> <span class="n">repuls</span><span class="p">,</span> <span class="n">astar</span> <span class="o">&lt;</span> <span class="mi">0</span>
-<span class="n">a3</span> <span class="o">=</span> <span class="n">attrac</span><span class="p">,</span> <span class="n">astar</span> <span class="o">&gt;=</span> <span class="mi">0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+astar = alpha * (r/re - 1.d0)
+if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar)
+if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
+if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
+a3 = repuls, astar &lt; 0
+a3 = attrac, astar &gt;= 0
+</pre>
 <p>Most published MEAM parameter sets use the default values attrac=repulse=0.
 Setting repuls=attrac=delta corresponds to the form used in several
 recent published MEAM parameter sets, such as <a class="reference internal" href="#valone"><span class="std std-ref">(Valone)</span></a></p>
diff --git a/doc/html/pair_meam_spline.html b/doc/html/pair_meam_spline.html
index 04957d08ca..d0f57e43cb 100644
--- a/doc/html/pair_meam_spline.html
+++ b/doc/html/pair_meam_spline.html
@@ -131,17 +131,17 @@
 <h1>pair_style meam/spline/omp</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span><span class="o">/</span><span class="n">spline</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style meam/spline
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span><span class="o">/</span><span class="n">spline</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ti</span><span class="o">.</span><span class="n">meam</span><span class="o">.</span><span class="n">spline</span> <span class="n">Ti</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ti</span><span class="o">.</span><span class="n">meam</span><span class="o">.</span><span class="n">spline</span> <span class="n">Ti</span> <span class="n">Ti</span> <span class="n">Ti</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style meam/spline
+pair_coeff * * Ti.meam.spline Ti
+pair_coeff * * Ti.meam.spline Ti Ti Ti
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -180,9 +180,9 @@ to specify the path for the potential file.</p>
 your LAMMPS simulation has 3 atoms types and they are all to be
 treated with this potentials, you would use the following pair_coeff
 command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ti</span><span class="o">.</span><span class="n">meam</span><span class="o">.</span><span class="n">spline</span> <span class="n">Ti</span> <span class="n">Ti</span> <span class="n">Ti</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * Ti.meam.spline Ti Ti Ti
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element
 in the potential file.  If a mapping value is specified as NULL, the
diff --git a/doc/html/pair_meam_sw_spline.html b/doc/html/pair_meam_sw_spline.html
index 2608d4c901..f3b221fef6 100644
--- a/doc/html/pair_meam_sw_spline.html
+++ b/doc/html/pair_meam_sw_spline.html
@@ -131,17 +131,17 @@
 <h1>pair_style meam/sw/spline/omp</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span><span class="o">/</span><span class="n">sw</span><span class="o">/</span><span class="n">spline</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style meam/sw/spline
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">meam</span><span class="o">/</span><span class="n">sw</span><span class="o">/</span><span class="n">spline</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ti</span><span class="o">.</span><span class="n">meam</span><span class="o">.</span><span class="n">sw</span><span class="o">.</span><span class="n">spline</span> <span class="n">Ti</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ti</span><span class="o">.</span><span class="n">meam</span><span class="o">.</span><span class="n">sw</span><span class="o">.</span><span class="n">spline</span> <span class="n">Ti</span> <span class="n">Ti</span> <span class="n">Ti</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style meam/sw/spline
+pair_coeff * * Ti.meam.sw.spline Ti
+pair_coeff * * Ti.meam.sw.spline Ti Ti Ti
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_mgpt.html b/doc/html/pair_mgpt.html
index b014cdeb42..9ac4b2224d 100644
--- a/doc/html/pair_mgpt.html
+++ b/doc/html/pair_mgpt.html
@@ -128,20 +128,20 @@
 <span id="index-0"></span><h1>pair_style mgpt command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">mgpt</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style mgpt
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">mgpt</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">parmin</span> <span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">potin</span> <span class="n">Omega</span>
-<span class="n">cp</span> <span class="o">~/</span><span class="n">lammps</span><span class="o">/</span><span class="n">potentials</span><span class="o">/</span><span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">parmin</span> <span class="n">parmin</span>
-<span class="n">cp</span> <span class="o">~/</span><span class="n">lammps</span><span class="o">/</span><span class="n">potentials</span><span class="o">/</span><span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">potin</span> <span class="n">potin</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">parmin</span> <span class="n">potin</span> <span class="n">Omega</span> <span class="n">volpress</span> <span class="n">yes</span> <span class="n">nbody</span> <span class="mi">1234</span> <span class="n">precision</span> <span class="n">double</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">parmin</span> <span class="n">potin</span> <span class="n">Omega</span> <span class="n">volpress</span> <span class="n">yes</span> <span class="n">nbody</span> <span class="mi">12</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style mgpt
+pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
+cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
+cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
+pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
+pair_coeff * * parmin potin Omega volpress yes nbody 12
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_mie.html b/doc/html/pair_mie.html
index cdab3eaf53..517b4bbec6 100644
--- a/doc/html/pair_mie.html
+++ b/doc/html/pair_mie.html
@@ -131,21 +131,21 @@
 <h1>pair_style mie/cut/gpu command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">mie</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style mie/cut cutoff
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for mie/cut interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">mie</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.72</span> <span class="mf">3.40</span> <span class="mf">23.00</span> <span class="mf">6.66</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">0.30</span> <span class="mf">3.55</span> <span class="mf">12.65</span> <span class="mf">6.00</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mf">0.46</span> <span class="mf">3.32</span> <span class="mf">16.90</span> <span class="mf">6.31</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style mie/cut 10.0
+pair_coeff 1 1 0.72 3.40 23.00 6.66
+pair_coeff 2 2 0.30 3.55 12.65 6.00
+pair_coeff 1 2 0.46 3.32 16.90 6.31
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_modify.html b/doc/html/pair_modify.html
index 3dbe93a18c..2dfeb618aa 100644
--- a/doc/html/pair_modify.html
+++ b/doc/html/pair_modify.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_modify command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_modify</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_modify keyword values ...
+</pre>
 <ul class="simple">
 <li>one or more keyword/value pairs may be listed</li>
 <li>keyword = <em>pair</em> or <em>shift</em> or <em>mix</em> or <em>table</em> or <em>table/disp</em> or <em>tabinner</em> or <em>tabinner/disp</em> or <em>tail</em> or <em>compute</em></li>
@@ -158,13 +158,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_modify</span> <span class="n">shift</span> <span class="n">yes</span> <span class="n">mix</span> <span class="n">geometric</span>
-<span class="n">pair_modify</span> <span class="n">tail</span> <span class="n">yes</span>
-<span class="n">pair_modify</span> <span class="n">table</span> <span class="mi">12</span>
-<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">compute</span> <span class="n">no</span>
-<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mi">1</span> <span class="n">special</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_modify shift yes mix geometric
+pair_modify tail yes
+pair_modify table 12
+pair_modify pair lj/cut compute no
+pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -201,21 +201,21 @@ individual pair styles for those restrictions.  Note also that the
 coefficients for a specific I != J pairing, in which case no mixing is
 performed.</p>
 <p>mix <em>geometric</em></p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">epsilon_ij</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">epsilon_i</span> <span class="o">*</span> <span class="n">epsilon_j</span><span class="p">)</span>
-<span class="n">sigma_ij</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">sigma_i</span> <span class="o">*</span> <span class="n">sigma_j</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+epsilon_ij = sqrt(epsilon_i * epsilon_j)
+sigma_ij = sqrt(sigma_i * sigma_j)
+</pre>
 <p>mix <em>arithmetic</em></p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">epsilon_ij</span> <span class="o">=</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">epsilon_i</span> <span class="o">*</span> <span class="n">epsilon_j</span><span class="p">)</span>
-<span class="n">sigma_ij</span> <span class="o">=</span> <span class="p">(</span><span class="n">sigma_i</span> <span class="o">+</span> <span class="n">sigma_j</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+epsilon_ij = sqrt(epsilon_i * epsilon_j)
+sigma_ij = (sigma_i + sigma_j) / 2
+</pre>
 <p>mix <em>sixthpower</em></p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">epsilon_ij</span> <span class="o">=</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">sqrt</span><span class="p">(</span><span class="n">epsilon_i</span><span class="o">*</span><span class="n">epsilon_j</span><span class="p">)</span> <span class="o">*</span> <span class="n">sigma_i</span><span class="o">^</span><span class="mi">3</span> <span class="o">*</span> <span class="n">sigma_j</span><span class="o">^</span><span class="mi">3</span><span class="p">)</span> <span class="o">/</span>
-             <span class="p">(</span><span class="n">sigma_i</span><span class="o">^</span><span class="mi">6</span> <span class="o">+</span> <span class="n">sigma_j</span><span class="o">^</span><span class="mi">6</span><span class="p">)</span>
-<span class="n">sigma_ij</span> <span class="o">=</span> <span class="p">((</span><span class="n">sigma_i</span><span class="o">**</span><span class="mi">6</span> <span class="o">+</span> <span class="n">sigma_j</span><span class="o">**</span><span class="mi">6</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)</span> <span class="o">^</span> <span class="p">(</span><span class="mi">1</span><span class="o">/</span><span class="mi">6</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
+             (sigma_i^6 + sigma_j^6)
+sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
+</pre>
 <p>The <em>shift</em> keyword determines whether a Lennard-Jones potential is
 shifted at its cutoff to 0.0.  If so, this adds an energy term to each
 pairwise interaction which will be included in the thermodynamic
diff --git a/doc/html/pair_morse.html b/doc/html/pair_morse.html
index bac9a4aa44..bcf7271af0 100644
--- a/doc/html/pair_morse.html
+++ b/doc/html/pair_morse.html
@@ -146,9 +146,9 @@
 <h1>pair_style morse/soft command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>morse</em> or <em>morse/smooth/linear</em> or <em>morse/soft</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -170,11 +170,11 @@
 pair_style morse/smooth/linear 2.5
 pair_coeff * * 100.0 2.0 1.5
 pair_coeff 1 1 100.0 2.0 1.5 3.0</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">morse</span><span class="o">/</span><span class="n">soft</span> <span class="mi">4</span> <span class="mf">0.9</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">3.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style morse/soft 4 0.9 10.0
+pair_coeff * * 100.0 2.0 1.5 1.0
+pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_multi_lucy.html b/doc/html/pair_multi_lucy.html
index 6835ef752e..4a16b32697 100644
--- a/doc/html/pair_multi_lucy.html
+++ b/doc/html/pair_multi_lucy.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_style multi/lucy command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">lucy</span> <span class="n">style</span> <span class="n">N</span> <span class="n">keyword</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style multi/lucy style N keyword ...
+</pre>
 <ul class="simple">
 <li>style = <em>lookup</em> or <em>linear</em> = method of interpolation</li>
 <li>N = use N values in <em>lookup</em>, <em>linear</em> tables</li>
@@ -138,10 +138,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">lucy</span> <span class="n">linear</span> <span class="mi">1000</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">multibody</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="mf">7.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style multi/lucy linear 1000
+pair_coeff * * multibody.table ENTRY1 7.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -196,15 +196,15 @@ defined as follows (without the parenthesized comments):</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Density-dependent function (one or more comment or blank lines)</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DD</span><span class="o">-</span><span class="n">FUNCTION</span>                <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
-<span class="n">N</span> <span class="mi">500</span> <span class="n">R</span> <span class="mf">1.0</span> <span class="mf">10.0</span>           <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">R</span><span class="p">,</span> <span class="n">RSQ</span> <span class="n">parameters</span><span class="p">)</span>
-                           <span class="p">(</span><span class="n">blank</span><span class="p">)</span>
-<span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">25.5</span> <span class="mf">102.34</span>          <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">density</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="n">r</span><span class="o">^</span><span class="mi">4</span><span class="p">,</span> <span class="n">force</span><span class="p">)</span>
-<span class="mi">2</span> <span class="mf">1.02</span> <span class="mf">23.4</span> <span class="mf">98.5</span>
-<span class="o">...</span>
-<span class="mi">500</span> <span class="mf">10.0</span> <span class="mf">0.001</span> <span class="mf">0.003</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+DD-FUNCTION                (keyword is first text on line)
+N 500 R 1.0 10.0           (N, R, RSQ parameters)
+                           (blank)
+1 1.0 25.5 102.34          (index, density, energy/r^4, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+</pre>
 <p>A section begins with a non-blank line whose 1st character is not a
 &#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
 between sections.  The first line begins with a keyword which
diff --git a/doc/html/pair_multi_lucy_rx.html b/doc/html/pair_multi_lucy_rx.html
index 380cdc22fa..ca4b859cdd 100644
--- a/doc/html/pair_multi_lucy_rx.html
+++ b/doc/html/pair_multi_lucy_rx.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_style multi/lucy/rx command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">lucy</span><span class="o">/</span><span class="n">rx</span> <span class="n">style</span> <span class="n">N</span> <span class="n">keyword</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style multi/lucy/rx style N keyword ...
+</pre>
 <ul class="simple">
 <li>style = <em>lookup</em> or <em>linear</em> = method of interpolation</li>
 <li>N = use N values in <em>lookup</em>, <em>linear</em> tables</li>
@@ -138,11 +138,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">lucy</span><span class="o">/</span><span class="n">rx</span> <span class="n">linear</span> <span class="mi">1000</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">multibody</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="n">h2o</span> <span class="n">h2o</span> <span class="mf">7.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">multibody</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="n">h2o</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">7.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style multi/lucy/rx linear 1000
+pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0
+pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -215,15 +215,15 @@ defined as follows (without the parenthesized comments):</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Density-dependent function (one or more comment or blank lines)</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DD</span><span class="o">-</span><span class="n">FUNCTION</span>                <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
-<span class="n">N</span> <span class="mi">500</span> <span class="n">R</span> <span class="mf">1.0</span> <span class="mf">10.0</span>           <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">R</span><span class="p">,</span> <span class="n">RSQ</span> <span class="n">parameters</span><span class="p">)</span>
-                           <span class="p">(</span><span class="n">blank</span><span class="p">)</span>
-<span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">25.5</span> <span class="mf">102.34</span>          <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">density</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="n">r</span><span class="o">^</span><span class="mi">4</span><span class="p">,</span> <span class="n">force</span><span class="p">)</span>
-<span class="mi">2</span> <span class="mf">1.02</span> <span class="mf">23.4</span> <span class="mf">98.5</span>
-<span class="o">...</span>
-<span class="mi">500</span> <span class="mf">10.0</span> <span class="mf">0.001</span> <span class="mf">0.003</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+DD-FUNCTION                (keyword is first text on line)
+N 500 R 1.0 10.0           (N, R, RSQ parameters)
+                           (blank)
+1 1.0 25.5 102.34          (index, density, energy/r^4, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+</pre>
 <p>A section begins with a non-blank line whose 1st character is not a
 &#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
 between sections.  The first line begins with a keyword which
diff --git a/doc/html/pair_nb3b_harmonic.html b/doc/html/pair_nb3b_harmonic.html
index 59fe5effb2..a24bb092e7 100644
--- a/doc/html/pair_nb3b_harmonic.html
+++ b/doc/html/pair_nb3b_harmonic.html
@@ -131,16 +131,16 @@
 <h1>pair_style nb3b/harmonic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">nb3b</span><span class="o">/</span><span class="n">harmonic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style nb3b/harmonic
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">nb3b</span><span class="o">/</span><span class="n">harmonic</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">MgOH</span><span class="o">.</span><span class="n">nb3bharmonic</span> <span class="n">Mg</span> <span class="n">O</span> <span class="n">H</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style nb3b/harmonic
+pair_coeff * * MgOH.nb3bharmonic Mg O H
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -166,9 +166,9 @@ to specify the path for the potential file.</p>
 for Si and C.  If your LAMMPS simulation has 4 atoms types and you
 want the 1st 3 to be Si, and the 4th to be C, you would use the
 following pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">nb3b</span><span class="o">.</span><span class="n">harmonic</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * SiC.nb3b.harmonic Si Si Si C
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
 element in the potential file.  The final C argument maps LAMMPS atom
diff --git a/doc/html/pair_nm.html b/doc/html/pair_nm.html
index 10052c9d20..c7759721cf 100644
--- a/doc/html/pair_nm.html
+++ b/doc/html/pair_nm.html
@@ -143,9 +143,9 @@
 <h1>pair_style nm/cut/coul/long/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>nm/cut</em> or <em>nm/cut/coul/cut</em> or <em>nm/cut/coul/long</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -163,21 +163,21 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">nm</span><span class="o">/</span><span class="n">cut</span> <span class="mf">12.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.01</span> <span class="mf">5.4</span> <span class="mf">8.0</span> <span class="mf">7.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.01</span> <span class="mf">4.4</span> <span class="mf">7.0</span> <span class="mf">6.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">nm</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">12.0</span> <span class="mf">15.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.01</span> <span class="mf">5.4</span> <span class="mf">8.0</span> <span class="mf">7.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.01</span> <span class="mf">4.4</span> <span class="mf">7.0</span> <span class="mf">6.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">nm</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">12.0</span> <span class="mf">15.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.01</span> <span class="mf">5.4</span> <span class="mf">8.0</span> <span class="mf">7.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.01</span> <span class="mf">4.4</span> <span class="mf">7.0</span> <span class="mf">6.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style nm/cut 12.0
+pair_coeff * * 0.01 5.4 8.0 7.0
+pair_coeff 1 1 0.01 4.4 7.0 6.0
+</pre>
+<pre class="literal-block">
+pair_style nm/cut/coul/cut 12.0 15.0
+pair_coeff * * 0.01 5.4 8.0 7.0
+pair_coeff 1 1 0.01 4.4 7.0 6.0
+</pre>
+<pre class="literal-block">
+pair_style nm/cut/coul/long 12.0 15.0
+pair_coeff * * 0.01 5.4 8.0 7.0
+pair_coeff 1 1 0.01 4.4 7.0 6.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_peri.html b/doc/html/pair_peri.html
index a57e98bbb1..c2fa31cce8 100644
--- a/doc/html/pair_peri.html
+++ b/doc/html/pair_peri.html
@@ -143,31 +143,31 @@
 <h1>pair_style peri/eps command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style
+</pre>
 <ul class="simple">
 <li>style = <em>peri/pmb</em> or <em>peri/lps</em> or <em>peri/ves</em> or <em>peri/eps</em></li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">peri</span><span class="o">/</span><span class="n">pmb</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.6863e22</span> <span class="mf">0.0015001</span> <span class="mf">0.0005</span> <span class="mf">0.25</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">peri</span><span class="o">/</span><span class="n">lps</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">14.9e9</span> <span class="mf">14.9e9</span> <span class="mf">0.0015001</span> <span class="mf">0.0005</span> <span class="mf">0.25</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">peri</span><span class="o">/</span><span class="n">ves</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">14.9e9</span> <span class="mf">14.9e9</span> <span class="mf">0.0015001</span> <span class="mf">0.0005</span> <span class="mf">0.25</span> <span class="mf">0.5</span> <span class="mf">0.001</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">peri</span><span class="o">/</span><span class="n">eps</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">14.9e9</span> <span class="mf">14.9e9</span> <span class="mf">0.0015001</span> <span class="mf">0.0005</span> <span class="mf">0.25</span> <span class="mf">118.43</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style peri/pmb
+pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
+</pre>
+<pre class="literal-block">
+pair_style peri/lps
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
+</pre>
+<pre class="literal-block">
+pair_style peri/ves
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
+</pre>
+<pre class="literal-block">
+pair_style peri/eps
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_polymorphic.html b/doc/html/pair_polymorphic.html
index 550805f4da..017a5148d0 100644
--- a/doc/html/pair_polymorphic.html
+++ b/doc/html/pair_polymorphic.html
@@ -128,20 +128,20 @@
 <span id="index-0"></span><h1>pair_style polymorphic command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">polymorphic</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style polymorphic
+</pre>
 <p>style = <em>polymorphic</em></p>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">polymorphic</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">TlBr_msw</span><span class="o">.</span><span class="n">polymorphic</span> <span class="n">Tl</span> <span class="n">Br</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">AlCu_eam</span><span class="o">.</span><span class="n">polymorphic</span> <span class="n">Al</span> <span class="n">Cu</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">GaN_tersoff</span><span class="o">.</span><span class="n">polymorphic</span> <span class="n">Ga</span> <span class="n">N</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">GaN_sw</span><span class="o">.</span><span class="n">polymorphic</span> <span class="n">GaN</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style polymorphic
+pair_coeff * * TlBr_msw.polymorphic Tl Br
+pair_coeff * * AlCu_eam.polymorphic Al Cu
+pair_coeff * * GaN_tersoff.polymorphic Ga N
+pair_coeff * * GaN_sw.polymorphic GaN
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -210,9 +210,9 @@ included in the potentials dir of the LAMMPS distro.  They have a
 functions for Si-C tersoff potential. If your LAMMPS simulation has 4
 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you
 would use the following pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC_tersoff</span><span class="o">.</span><span class="n">polymorphic</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * SiC_tersoff.polymorphic Si Si Si C
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom
 types. The first three Si arguments map LAMMPS atom types 1,2,3 to the
 Si element in the polymorphic file. The final C argument maps LAMMPS
@@ -235,19 +235,19 @@ eta_ij defined in the potential functions above is set to 1 -
 delta_ij, otherwise eta_ij is set to delta_ij. The next ntypes lines
 each lists two numbers and a character string representing atomic
 number, atomic mass, and name of the species of the ntypes elements:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atomic_number</span> <span class="n">atomic</span><span class="o">-</span><span class="n">mass</span> <span class="n">element</span> <span class="p">(</span><span class="mi">1</span><span class="p">)</span>
-<span class="n">atomic_number</span> <span class="n">atomic</span><span class="o">-</span><span class="n">mass</span> <span class="n">element</span> <span class="p">(</span><span class="mi">2</span><span class="p">)</span>
-<span class="o">...</span>
-<span class="n">atomic_number</span> <span class="n">atomic</span><span class="o">-</span><span class="n">mass</span> <span class="n">element</span> <span class="p">(</span><span class="n">ntypes</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+atomic_number atomic-mass element (1)
+atomic_number atomic-mass element (2)
+...
+atomic_number atomic-mass element (ntypes)
+</pre>
 <p>The next ntypes*(ntypes+1)/2 lines contain two numbers:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cut</span> <span class="n">xi</span> <span class="p">(</span><span class="mi">1</span><span class="p">)</span>
-<span class="n">cut</span> <span class="n">xi</span> <span class="p">(</span><span class="mi">2</span><span class="p">)</span>
-<span class="o">...</span>
-<span class="n">cut</span> <span class="n">xi</span> <span class="p">(</span><span class="n">ntypes</span><span class="o">*</span><span class="p">(</span><span class="n">ntypes</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span><span class="o">/</span><span class="mi">2</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+cut xi (1)
+cut xi (2)
+...
+cut xi (ntypes*(ntypes+1)/2)
+</pre>
 <p>Here cut means the cutoff distance of the pair functions, xi is the
 same as defined in the potential functions above. The
 ntypes*(ntypes+1)/2 lines are related to the pairs according to the
diff --git a/doc/html/pair_quip.html b/doc/html/pair_quip.html
index e2bae6d90b..91f1131efb 100644
--- a/doc/html/pair_quip.html
+++ b/doc/html/pair_quip.html
@@ -128,17 +128,17 @@
 <span id="index-0"></span><h1>pair_style quip command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">quip</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style quip
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span>      <span class="n">quip</span>
-<span class="n">pair_coeff</span>      <span class="o">*</span> <span class="o">*</span> <span class="n">gap_example</span><span class="o">.</span><span class="n">xml</span> <span class="s2">&quot;Potential xml_label=GAP_2014_5_8_60_17_10_38_466&quot;</span> <span class="mi">14</span>
-<span class="n">pair_coeff</span>      <span class="o">*</span> <span class="o">*</span> <span class="n">sw_example</span><span class="o">.</span><span class="n">xml</span> <span class="s2">&quot;IP SW&quot;</span> <span class="mi">14</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style      quip
+pair_coeff      * * gap_example.xml &quot;Potential xml_label=GAP_2014_5_8_60_17_10_38_466&quot; 14
+pair_coeff      * * sw_example.xml &quot;IP SW&quot; 14
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_reax.html b/doc/html/pair_reax.html
index 3093a0b62b..3929a8cd0d 100644
--- a/doc/html/pair_reax.html
+++ b/doc/html/pair_reax.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_style reax command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span> <span class="n">hbcut</span> <span class="n">hbnewflag</span> <span class="n">tripflag</span> <span class="n">precision</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style reax hbcut hbnewflag tripflag precision
+</pre>
 <ul class="simple">
 <li>hbcut = hydrogen-bond cutoff (optional) (distance units)</li>
 <li>hbnewflag = use old or new hbond function style (0 or 1) (optional)</li>
@@ -140,12 +140,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span>
-<span class="n">pair_style</span> <span class="n">reax</span> <span class="mf">10.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">1.0e-5</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="mi">3</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">2</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="mi">3</span> <span class="n">NULL</span> <span class="n">NULL</span> <span class="mi">3</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style reax
+pair_style reax 10.0 0 1 1.0e-5
+pair_coeff * * ffield.reax 3 1 2 2
+pair_coeff * * ffield.reax 3 NULL NULL 3
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -238,14 +238,14 @@ names in italics match those used in the ReaxFF FORTRAN library):</p>
 </ol>
 <p>To print these quantities to the log file (with descriptive column
 headings) the following commands could be included in an input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">reax</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">reax</span>
-<span class="n">variable</span> <span class="n">eb</span>           <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-<span class="n">variable</span> <span class="n">ea</span>           <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-<span class="o">...</span>
-<span class="n">variable</span> <span class="n">eqeq</span>         <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">14</span><span class="p">]</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_eb</span> <span class="n">v_ea</span> <span class="o">...</span> <span class="n">v_eqeq</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute reax all pair reax
+variable eb           equal c_reax[1]
+variable ea           equal c_reax[2]
+...
+variable eqeq         equal c_reax[14]
+thermo_style custom step temp epair v_eb v_ea ... v_eqeq
+</pre>
 <p>Only a single pair_coeff command is used with the <em>reax</em> style which
 specifies a ReaxFF potential file with parameters for all needed
 elements.  These are mapped to LAMMPS atom types by specifying N
@@ -286,9 +286,9 @@ enable this.</p>
 elements are ordered as C, H, O, N in the <em>ffield</em> file.  If you want
 the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
 H, you would use the following pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mi">2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * ffield.reax 1 1 4 2
+</pre>
 <hr class="docutils" />
 <p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
 <p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>
diff --git a/doc/html/pair_reax_c.html b/doc/html/pair_reax_c.html
index bd96471c6b..38e27022b9 100644
--- a/doc/html/pair_reax_c.html
+++ b/doc/html/pair_reax_c.html
@@ -131,9 +131,9 @@
 <h1>pair_style reax/c/kk command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">cfile</span> <span class="n">keyword</span> <span class="n">value</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style reax/c cfile keyword value
+</pre>
 <ul class="simple">
 <li>cfile = NULL or name of a control file</li>
 <li>zero or more keyword/value pairs may be appended</li>
@@ -148,13 +148,13 @@ keyword = <em>checkqeq</em> or <em>lgvdw</em> or <em>safezone</em> or <em>mincap
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">NULL</span>
-<span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">controlfile</span> <span class="n">checkqeq</span> <span class="n">no</span>
-<span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">NULL</span> <span class="n">lgvdw</span> <span class="n">yes</span>
-<span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">NULL</span> <span class="n">safezone</span> <span class="mf">1.6</span> <span class="n">mincap</span> <span class="mi">100</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="n">C</span> <span class="n">H</span> <span class="n">O</span> <span class="n">N</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style reax/c NULL
+pair_style reax/c controlfile checkqeq no
+pair_style reax/c NULL lgvdw yes
+pair_style reax/c NULL safezone 1.6 mincap 100
+pair_coeff * * ffield.reax C H O N
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -276,14 +276,14 @@ names in italics match those used in the original FORTRAN ReaxFF code):</p>
 </ol>
 <p>To print these quantities to the log file (with descriptive column
 headings) the following commands could be included in an input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">reax</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span>
-<span class="n">variable</span> <span class="n">eb</span>           <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-<span class="n">variable</span> <span class="n">ea</span>           <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-<span class="o">...</span>
-<span class="n">variable</span> <span class="n">eqeq</span>         <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">14</span><span class="p">]</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_eb</span> <span class="n">v_ea</span> <span class="o">...</span> <span class="n">v_eqeq</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute reax all pair reax/c
+variable eb           equal c_reax[1]
+variable ea           equal c_reax[2]
+...
+variable eqeq         equal c_reax[14]
+thermo_style custom step temp epair v_eb v_ea ... v_eqeq
+</pre>
 <p>Only a single pair_coeff command is used with the <em>reax/c</em> style which
 specifies a ReaxFF potential file with parameters for all needed
 elements.  These are mapped to LAMMPS atom types by specifying N
@@ -310,14 +310,14 @@ types that will be used with other potentials.</p>
 elements are ordered as C, H, O, N in the <em>ffield</em> file.  If you want
 the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
 H, you would use the following pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="n">C</span> <span class="n">C</span> <span class="n">N</span> <span class="n">H</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * ffield.reax C C N H
+</pre>
 <hr class="docutils" />
 <p>The format of a line in the control file is as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable_name</span> <span class="n">value</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable_name value
+</pre>
 <p>and it may be followed by an &#8221;!&#8221; character and a trailing comment.</p>
 <p>If the value of a control variable is not specified, then default
 values are used.  What follows is the list of variables along with a
diff --git a/doc/html/pair_resquared.html b/doc/html/pair_resquared.html
index edf33d6bdb..70c4fd0ba0 100644
--- a/doc/html/pair_resquared.html
+++ b/doc/html/pair_resquared.html
@@ -134,19 +134,19 @@
 <h1>pair_style resquared/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">resquared</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style resquared cutoff
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">resquared</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.7</span> <span class="mf">3.4</span> <span class="mf">3.4</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style resquared 10.0
+pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_sdk.html b/doc/html/pair_sdk.html
index a8cfc33d42..21a9ded1a5 100644
--- a/doc/html/pair_sdk.html
+++ b/doc/html/pair_sdk.html
@@ -146,9 +146,9 @@
 <h1>pair_style lj/sdk/coul/long/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>lj/sdk</em> or <em>lj/sdk/coul/long</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -163,15 +163,15 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sdk</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">lj12_6</span> <span class="mi">1</span> <span class="mf">1.1</span> <span class="mf">2.8</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sdk</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
-<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sdk</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="mf">12.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">lj9_6</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">12.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/sdk 2.5
+pair_coeff 1 1 lj12_6 1 1.1 2.8
+</pre>
+<pre class="literal-block">
+pair_style lj/sdk/coul/long 10.0
+pair_style lj/sdk/coul/long 10.0 12.0
+pair_coeff 1 1 lj9_6 100.0 3.5 12.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_smd_hertz.html b/doc/html/pair_smd_hertz.html
index 52dd7939f6..25cbc618da 100644
--- a/doc/html/pair_smd_hertz.html
+++ b/doc/html/pair_smd_hertz.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_style smd/hertz command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">smd</span><span class="o">/</span><span class="n">hertz</span> <span class="n">scale_factor</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style smd/hertz scale_factor
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
@@ -146,7 +146,7 @@ The effect is that a particles cannot penetrate into each other.
 The parameter &lt;contact_stiffness&gt; has units of pressure and should equal roughly one half
 of the Young&#8217;s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.</p>
 <p>The parameter <em>scale_factor</em> can be used to scale the particles&#8217; contact radii. This can be useful to control how close
-particles can approach each other. Usually, <em>scale_factor</em>=1.0.</p>
+particles can approach each other. Usually, <a href="#id1"><span class="problematic" id="id2">*</span></a>scale_factor*=1.0.</p>
 <hr class="docutils" />
 <p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
 <p>No mixing is performed automatically.
diff --git a/doc/html/pair_smd_triangulated_surface.html b/doc/html/pair_smd_triangulated_surface.html
index 9f4ba0991d..428893dfc3 100644
--- a/doc/html/pair_smd_triangulated_surface.html
+++ b/doc/html/pair_smd_triangulated_surface.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_style smd/tri_surface command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">smd</span><span class="o">/</span><span class="n">tri_surface</span> <span class="n">scale_factor</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style smd/tri_surface scale_factor
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
@@ -147,7 +147,7 @@ The effect is that a particle cannot penetrate into the triangular surface.
 The parameter &lt;contact_stiffness&gt; has units of pressure and should equal roughly one half
 of the Young&#8217;s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle</p>
 <p>The parameter <em>scale_factor</em> can be used to scale the particles&#8217; contact radii. This can be useful to control how close
-particles can approach the triangulated surface. Usually, <em>scale_factor</em>=1.0.</p>
+particles can approach the triangulated surface. Usually, <a href="#id1"><span class="problematic" id="id2">*</span></a>scale_factor*=1.0.</p>
 <hr class="docutils" />
 <p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
 <p>No mixing is performed automatically.
diff --git a/doc/html/pair_smtbq.html b/doc/html/pair_smtbq.html
index 568539fd0c..f9b3de8f22 100644
--- a/doc/html/pair_smtbq.html
+++ b/doc/html/pair_smtbq.html
@@ -128,16 +128,16 @@
 <span id="index-0"></span><h1>pair_style smtbq command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">smtbq</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style smtbq
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">smtbq</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">smtbq</span><span class="o">.</span><span class="n">Al2O3</span> <span class="n">O</span> <span class="n">Al</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style smtbq
+pair_coeff * * ffield.smtbq.Al2O3 O Al
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -164,9 +164,9 @@ filename in the pair_coeff command. Note that atom type 1 must always
 correspond to oxygen atoms. As an example, to simulate a TiO2 system,
 atom type 1 has to be oxygen and atom type 2 Ti. The following
 pair_coeff command should then be used:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">PathToLammps</span><span class="o">/</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">smtbq</span><span class="o">.</span><span class="n">TiO2</span> <span class="n">O</span> <span class="n">Ti</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
+</pre>
 <p>The electrostatic part of the energy consists of two components</p>
 <p>self-energy of atom <em>i</em> in the form of a second order charge dependent
 polynomial and a long-range Coulombic electrostatic interaction. The
@@ -271,7 +271,7 @@ quotation marks (&#8216;&#8217;).</p>
 </ol>
 <ul class="simple">
 <li>Keyword for element1, element2 and interaction potential (&#8216;second_moment&#8217; or &#8216;buck&#8217; or &#8216;buckPlusAttr&#8217;) between element 1 and 2.  If the potential is &#8216;second_moment&#8217;, specify &#8216;oxide&#8217; or &#8216;metal&#8217; for metal-oxygen or metal-metal interactions respectively.</li>
-<li>Potential parameter: &lt;pre&gt;&lt;br/&gt;       If type of potential is &#8216;second_moment&#8217; : <em>A (eV)</em>, <em>p</em>, <em>&amp;#958&lt;sup&gt;0&lt;/sup&gt;</em> (eV) and <em>q</em> &lt;br/&gt;                                               <em>r&lt;sub&gt;c1&lt;/sub&gt;</em> (&amp;#197), <em>r&lt;sub&gt;c2&lt;/sub&gt;</em> (&amp;#197) and <em>r&lt;sub&gt;0&lt;/sub&gt;</em> (&amp;#197) &lt;br/&gt;  If type of potential is &#8216;buck&#8217; : <em>C</em> (eV) and <em>&amp;#961</em> (&amp;#197) &lt;br/&gt;     If type of potential is &#8216;buckPlusAttr&#8217; : <em>C</em> (eV) and <em>&amp;#961</em> (&amp;#197) &lt;br/&gt;                                              <em>D</em> (eV), <em>B</em> (&amp;#197&lt;sup&gt;-1&lt;/sup&gt;), <em>r&lt;sub&gt;1&lt;/sub&gt;&lt;sup&gt;OO&lt;/sup&gt;</em> (&amp;#197) and <em>r&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;OO&lt;/sup&gt;</em> (&amp;#197) &lt;/pre&gt;</li>
+<li>Potential parameter: &lt;pre&gt;&lt;br/&gt;       If type of potential is &#8216;second_moment&#8217; : <em>A (eV)</em>, <em>p</em>, <em>&amp;#958&lt;sup&gt;0&lt;/sup&gt;</em> (eV) and <em>q</em> &lt;br/&gt;                                              <em>r&lt;sub&gt;c1&lt;/sub&gt;</em> (&amp;#197), <em>r&lt;sub&gt;c2&lt;/sub&gt;</em> (&amp;#197) and <em>r&lt;sub&gt;0&lt;/sub&gt;</em> (&amp;#197) &lt;br/&gt;  If type of potential is &#8216;buck&#8217; : <em>C</em> (eV) and <em>&amp;#961</em> (&amp;#197) &lt;br/&gt;     If type of potential is &#8216;buckPlusAttr&#8217; : <em>C</em> (eV) and <em>&amp;#961</em> (&amp;#197) &lt;br/&gt;                                              <em>D</em> (eV), <em>B</em> (&amp;#197&lt;sup&gt;-1&lt;/sup&gt;), <em>r&lt;sub&gt;1&lt;/sub&gt;&lt;sup&gt;OO&lt;/sup&gt;</em> (&amp;#197) and <em>r&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;OO&lt;/sup&gt;</em> (&amp;#197) &lt;/pre&gt;</li>
 <li>Divided line</li>
 </ul>
 <ol class="arabic simple" start="4">
diff --git a/doc/html/pair_snap.html b/doc/html/pair_snap.html
index bc82ce506e..0589cb40a5 100644
--- a/doc/html/pair_snap.html
+++ b/doc/html/pair_snap.html
@@ -128,16 +128,16 @@
 <span id="index-0"></span><h1>pair_style snap command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">snap</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style snap
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">snap</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">snap</span> <span class="n">InP</span><span class="o">.</span><span class="n">snapcoeff</span> <span class="n">In</span> <span class="n">P</span> <span class="n">InP</span><span class="o">.</span><span class="n">snapparam</span> <span class="n">In</span> <span class="n">In</span> <span class="n">P</span> <span class="n">P</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style snap
+pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -180,9 +180,9 @@ command, where N is the number of LAMMPS atom types:</p>
 <p>As an example, if a LAMMPS indium phosphide simulation has 4 atoms
 types, with the first two being indium and the 3rd and 4th being
 phophorous, the pair_coeff command would look like this:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">snap</span> <span class="n">InP</span><span class="o">.</span><span class="n">snapcoeff</span> <span class="n">In</span> <span class="n">P</span> <span class="n">InP</span><span class="o">.</span><span class="n">snapparam</span> <span class="n">In</span> <span class="n">In</span> <span class="n">P</span> <span class="n">P</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The two filenames are for the element and parameter files, respectively.
 The &#8216;In&#8217; and &#8216;P&#8217; arguments (between the file names) are the two elements
@@ -210,7 +210,8 @@ using the <em>hybrid/overlay</em> pair style. As an example, the SNAP
 tantalum potential provided in the LAMMPS potentials directory
 combines the <em>snap</em> and <em>zbl</em> pair styles. It is invoked
 by the following commands:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable zblcutinner equal 4
+<pre class="literal-block">
+variable zblcutinner equal 4
 variable zblcutouter equal 4.8
 variable zblz equal 73
 pair_style hybrid/overlay &amp;
@@ -219,8 +220,7 @@ pair_coeff * * zbl 0.0
 pair_coeff 1 1 zbl ${zblz}
 pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &amp;
 ../potentials/Ta06A.snapparam Ta
-</pre></div>
-</div>
+</pre>
 <p>It is convenient to keep these commands in a separate file that can
 be inserted in any LAMMPS input script using the <a class="reference internal" href="include.html"><span class="doc">include</span></a>
 command.</p>
diff --git a/doc/html/pair_soft.html b/doc/html/pair_soft.html
index 0929a1f6af..3443927106 100644
--- a/doc/html/pair_soft.html
+++ b/doc/html/pair_soft.html
@@ -134,26 +134,26 @@
 <h1>pair_style soft/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">soft</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style soft cutoff
+</pre>
 <ul class="simple">
 <li>cutoff = global cutoff for soft interactions (distance units)</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">soft</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">10.0</span> <span class="mf">3.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">soft</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.0</span>
-<span class="n">variable</span> <span class="n">prefactor</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">30</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_prefactor</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style soft 1.0
+pair_coeff * * 10.0
+pair_coeff 1 1 10.0 3.0
+</pre>
+<pre class="literal-block">
+pair_style soft 1.0
+pair_coeff * * 0.0
+variable prefactor equal ramp(0,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -193,10 +193,10 @@ pair_coeff settings for A must still be specified, but will be
 overridden.  For example these commands will vary the prefactor A for
 all pairwise interactions from 0.0 at the beginning to 30.0 at the end
 of a run:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">prefactor</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">30</span><span class="p">)</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_prefactor</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable prefactor equal ramp(0,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+</pre>
 <p>Note that a formula defined by an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>
 can use the current timestep, elapsed time in the current run, elapsed
 time since the beginning of a series of runs, as well as access other
diff --git a/doc/html/pair_sph_idealgas.html b/doc/html/pair_sph_idealgas.html
index 130c193d90..602e66a277 100644
--- a/doc/html/pair_sph_idealgas.html
+++ b/doc/html/pair_sph_idealgas.html
@@ -128,16 +128,16 @@
 <span id="index-0"></span><h1>pair_style sph/idealgas command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">sph</span><span class="o">/</span><span class="n">idealgas</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style sph/idealgas
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">sph</span><span class="o">/</span><span class="n">idealgas</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">2.4</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style sph/idealgas
+pair_coeff * * 1.0 2.4
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_sph_taitwater.html b/doc/html/pair_sph_taitwater.html
index 0d56ce2bdd..0ce7b08918 100644
--- a/doc/html/pair_sph_taitwater.html
+++ b/doc/html/pair_sph_taitwater.html
@@ -128,16 +128,16 @@
 <span id="index-0"></span><h1>pair_style sph/taitwater command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">sph</span><span class="o">/</span><span class="n">taitwater</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style sph/taitwater
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">sph</span><span class="o">/</span><span class="n">taitwater</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1000.0</span> <span class="mf">1430.0</span> <span class="mf">1.0</span> <span class="mf">2.4</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style sph/taitwater
+pair_coeff * * 1000.0 1430.0 1.0 2.4
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_sph_taitwater_morris.html b/doc/html/pair_sph_taitwater_morris.html
index 8c6f8c913a..fda93bd07c 100644
--- a/doc/html/pair_sph_taitwater_morris.html
+++ b/doc/html/pair_sph_taitwater_morris.html
@@ -128,16 +128,16 @@
 <span id="index-0"></span><h1>pair_style sph/taitwater/morris command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">sph</span><span class="o">/</span><span class="n">taitwater</span><span class="o">/</span><span class="n">morris</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style sph/taitwater/morris
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">sph</span><span class="o">/</span><span class="n">taitwater</span><span class="o">/</span><span class="n">morris</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1000.0</span> <span class="mf">1430.0</span> <span class="mf">1.0</span> <span class="mf">2.4</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style sph/taitwater/morris
+pair_coeff * * 1000.0 1430.0 1.0 2.4
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_srp.html b/doc/html/pair_srp.html
index caddb4012a..a9e1607ab8 100644
--- a/doc/html/pair_srp.html
+++ b/doc/html/pair_srp.html
@@ -143,24 +143,24 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">dpd</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">12345</span> <span class="n">srp</span> <span class="mf">0.8</span> <span class="mi">1</span> <span class="n">mid</span> <span class="n">exclude</span> <span class="n">yes</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">dpd</span> <span class="mf">60.0</span> <span class="mf">4.5</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">none</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">srp</span> <span class="mf">100.0</span> <span class="mf">0.8</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">dpd</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">12345</span> <span class="n">srp</span> <span class="mf">0.8</span> <span class="o">*</span> <span class="nb">min</span> <span class="n">exclude</span> <span class="n">yes</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">dpd</span> <span class="mf">60.0</span> <span class="mi">50</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">none</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">srp</span> <span class="mf">40.0</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">srp</span> <span class="mf">0.8</span> <span class="mi">2</span> <span class="n">mid</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">none</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">none</span>
-<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">srp</span> <span class="mf">100.0</span> <span class="mf">0.8</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
+pair_coeff 1 1 dpd 60.0 4.5 1.0
+pair_coeff 1 2 none
+pair_coeff 2 2 srp 100.0 0.8
+</pre>
+<pre class="literal-block">
+pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
+pair_coeff 1 1 dpd 60.0 50 1.0
+pair_coeff 1 2 none
+pair_coeff 2 2 srp 40.0
+</pre>
+<pre class="literal-block">
+pair_style hybrid srp 0.8 2 mid
+pair_coeff 1 1 none
+pair_coeff 1 2 none
+pair_coeff 2 2 srp 100.0 0.8
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_style.html b/doc/html/pair_style.html
index 4dc6adc479..86a80963cc 100644
--- a/doc/html/pair_style.html
+++ b/doc/html/pair_style.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>pair_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = one of the styles from the list below</li>
 <li>args = arguments used by a particular style</li>
@@ -138,13 +138,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span>
-<span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span>
-<span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="n">eam</span>
-<span class="n">pair_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
-<span class="n">pair_style</span> <span class="n">none</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut 2.5
+pair_style eam/alloy
+pair_style hybrid lj/charmm/coul/long 10.0 eam
+pair_style table linear 1000
+pair_style none
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -338,9 +338,9 @@ package.</p>
 </div>
 <div class="section" id="default">
 <h2>Default</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">none</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style none
+</pre>
 </div>
 </div>
 
diff --git a/doc/html/pair_sw.html b/doc/html/pair_sw.html
index 099d2de727..687c162b34 100644
--- a/doc/html/pair_sw.html
+++ b/doc/html/pair_sw.html
@@ -140,17 +140,17 @@
 <h1>pair_style sw/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">sw</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style sw
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">sw</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">si</span><span class="o">.</span><span class="n">sw</span> <span class="n">Si</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">GaN</span><span class="o">.</span><span class="n">sw</span> <span class="n">Ga</span> <span class="n">N</span> <span class="n">Ga</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style sw
+pair_coeff * * si.sw Si
+pair_coeff * * GaN.sw Ga N Ga
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -175,9 +175,9 @@ to specify the path for the potential file.</p>
 Si and C.  If your LAMMPS simulation has 4 atoms types and you want
 the 1st 3 to be Si, and the 4th to be C, you would use the following
 pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">sw</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * SiC.sw Si Si Si C
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
 element in the SW file.  The final C argument maps LAMMPS atom type 4
diff --git a/doc/html/pair_table.html b/doc/html/pair_table.html
index 7dd8b8ecf1..703a6081cc 100644
--- a/doc/html/pair_table.html
+++ b/doc/html/pair_table.html
@@ -137,9 +137,9 @@
 <h1>pair_style table/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">N</span> <span class="n">keyword</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style table style N keyword ...
+</pre>
 <ul class="simple">
 <li>style = <em>lookup</em> or <em>linear</em> or <em>spline</em> or <em>bitmap</em> = method of interpolation</li>
 <li>N = use N values in <em>lookup</em>, <em>linear</em>, <em>spline</em> tables</li>
@@ -150,13 +150,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
-<span class="n">pair_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span> <span class="n">pppm</span>
-<span class="n">pair_style</span> <span class="n">table</span> <span class="n">bitmap</span> <span class="mi">12</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">3</span> <span class="n">morse</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">3</span> <span class="n">morse</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="mf">7.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style table linear 1000
+pair_style table linear 1000 pppm
+pair_style table bitmap 12
+pair_coeff * 3 morse.table ENTRY1
+pair_coeff * 3 morse.table ENTRY1 7.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -240,15 +240,15 @@ defined as follows (without the parenthesized comments):</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Morse potential for Fe   (one or more comment or blank lines)</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">MORSE_FE</span>                   <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
-<span class="n">N</span> <span class="mi">500</span> <span class="n">R</span> <span class="mf">1.0</span> <span class="mf">10.0</span>           <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">R</span><span class="p">,</span> <span class="n">RSQ</span><span class="p">,</span> <span class="n">BITMAP</span><span class="p">,</span> <span class="n">FPRIME</span> <span class="n">parameters</span><span class="p">)</span>
-                           <span class="p">(</span><span class="n">blank</span><span class="p">)</span>
-<span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">25.5</span> <span class="mf">102.34</span>          <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">energy</span><span class="p">,</span> <span class="n">force</span><span class="p">)</span>
-<span class="mi">2</span> <span class="mf">1.02</span> <span class="mf">23.4</span> <span class="mf">98.5</span>
-<span class="o">...</span>
-<span class="mi">500</span> <span class="mf">10.0</span> <span class="mf">0.001</span> <span class="mf">0.003</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+MORSE_FE                   (keyword is first text on line)
+N 500 R 1.0 10.0           (N, R, RSQ, BITMAP, FPRIME parameters)
+                           (blank)
+1 1.0 25.5 102.34          (index, r, energy, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+</pre>
 <p>A section begins with a non-blank line whose 1st character is not a
 &#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
 between sections.  The first line begins with a keyword which
diff --git a/doc/html/pair_table_rx.html b/doc/html/pair_table_rx.html
index 18ecd7f404..eab8b7d00c 100644
--- a/doc/html/pair_table_rx.html
+++ b/doc/html/pair_table_rx.html
@@ -128,22 +128,22 @@
 <span id="index-0"></span><h1>pair_style table/rx command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">N</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style table style N
+</pre>
 <p>style = <em>lookup</em> or <em>linear</em> or <em>spline</em> or <em>bitmap</em> = method of interpolation
 N = use N values in <em>lookup</em>, <em>linear</em>, <em>spline</em> tables
 N = use 2^N values in <em>bitmap</em> tables</p>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">table</span><span class="o">/</span><span class="n">rx</span> <span class="n">linear</span> <span class="mi">1000</span>
-<span class="n">pair_style</span> <span class="n">table</span><span class="o">/</span><span class="n">rx</span> <span class="n">bitmap</span> <span class="mi">12</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">rxn</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="n">h2o</span> <span class="n">h2o</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">rxn</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">3</span> <span class="n">rxn</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span> <span class="n">h2o</span> <span class="n">no2</span> <span class="mf">10.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style table/rx linear 1000
+pair_style table/rx bitmap 12
+pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0
+pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0
+pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -226,15 +226,15 @@ defined as follows (without the parenthesized comments):</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Morse potential for Fe   (one or more comment or blank lines)</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">MORSE_FE</span>                   <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
-<span class="n">N</span> <span class="mi">500</span> <span class="n">R</span> <span class="mf">1.0</span> <span class="mf">10.0</span>           <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">R</span><span class="p">,</span> <span class="n">RSQ</span><span class="p">,</span> <span class="n">BITMAP</span><span class="p">,</span> <span class="n">FPRIME</span> <span class="n">parameters</span><span class="p">)</span>
-                           <span class="p">(</span><span class="n">blank</span><span class="p">)</span>
-<span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">25.5</span> <span class="mf">102.34</span>          <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">energy</span><span class="p">,</span> <span class="n">force</span><span class="p">)</span>
-<span class="mi">2</span> <span class="mf">1.02</span> <span class="mf">23.4</span> <span class="mf">98.5</span>
-<span class="o">...</span>
-<span class="mi">500</span> <span class="mf">10.0</span> <span class="mf">0.001</span> <span class="mf">0.003</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+MORSE_FE                   (keyword is first text on line)
+N 500 R 1.0 10.0           (N, R, RSQ, BITMAP, FPRIME parameters)
+                           (blank)
+1 1.0 25.5 102.34          (index, r, energy, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+</pre>
 <p>A section begins with a non-blank line whose 1st character is not a
 &#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
 between sections.  The first line begins with a keyword which
diff --git a/doc/html/pair_tersoff.html b/doc/html/pair_tersoff.html
index 6ea2a43607..8345a1c90b 100644
--- a/doc/html/pair_tersoff.html
+++ b/doc/html/pair_tersoff.html
@@ -146,22 +146,22 @@
 <h1>pair_style tersoff/table/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style
+</pre>
 <p>style = <em>tersoff</em> or <em>tersoff/table</em> or <em>tersoff/gpu</em> or <em>tersoff/omp</em> or <em>tersoff/table/omp</em></p>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Si</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span> <span class="n">C</span> <span class="n">Si</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span><span class="o">/</span><span class="n">table</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiCGe</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span><span class="p">(</span><span class="n">D</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style tersoff
+pair_coeff * * Si.tersoff Si
+pair_coeff * * SiC.tersoff Si C Si
+</pre>
+<pre class="literal-block">
+pair_style tersoff/table
+pair_coeff * * SiCGe.tersoff Si(D)
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -191,9 +191,9 @@ to specify the path for the potential file.</p>
 and C.  If your LAMMPS simulation has 4 atoms types and you want the
 1st 3 to be Si, and the 4th to be C, you would use the following
 pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * SiC.tersoff Si Si Si C
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
 element in the Tersoff file.  The final C argument maps LAMMPS atom
diff --git a/doc/html/pair_tersoff_mod.html b/doc/html/pair_tersoff_mod.html
index b88d02ee18..34a2120f67 100644
--- a/doc/html/pair_tersoff_mod.html
+++ b/doc/html/pair_tersoff_mod.html
@@ -137,16 +137,16 @@
 <h1>pair_style tersoff/mod/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span><span class="o">/</span><span class="n">mod</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style tersoff/mod
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span><span class="o">/</span><span class="n">mod</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Si</span><span class="o">.</span><span class="n">tersoff</span><span class="o">.</span><span class="n">mod</span> <span class="n">Si</span> <span class="n">Si</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style tersoff/mod
+pair_coeff * * Si.tersoff.mod Si Si
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -180,9 +180,9 @@ where N is the number of LAMMPS atom types:</p>
 <p>As an example, imagine the Si.tersoff_mod file has Tersoff values for Si.
 If your LAMMPS simulation has 3 Si atoms types, you would use the following
 pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Si</span><span class="o">.</span><span class="n">tersoff_mod</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * Si.tersoff_mod Si Si Si
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The three Si arguments map LAMMPS atom types 1,2,3 to the Si element
 in the Tersoff/MOD file. If a mapping value is specified as NULL, the
diff --git a/doc/html/pair_tersoff_zbl.html b/doc/html/pair_tersoff_zbl.html
index 90e840acc3..694938f86e 100644
--- a/doc/html/pair_tersoff_zbl.html
+++ b/doc/html/pair_tersoff_zbl.html
@@ -137,16 +137,16 @@
 <h1>pair_style tersoff/zbl/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span><span class="o">/</span><span class="n">zbl</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style tersoff/zbl
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span><span class="o">/</span><span class="n">zbl</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span><span class="o">.</span><span class="n">zbl</span> <span class="n">Si</span> <span class="n">C</span> <span class="n">Si</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style tersoff/zbl
+pair_coeff * * SiC.tersoff.zbl Si C Si
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -188,9 +188,9 @@ to specify the path for the potential file.</p>
 for Si and C.  If your LAMMPS simulation has 4 atoms types and you
 want the 1st 3 to be Si, and the 4th to be C, you would use the
 following pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * SiC.tersoff Si Si Si C
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
 element in the Tersoff/ZBL file.  The final C argument maps LAMMPS
diff --git a/doc/html/pair_thole.html b/doc/html/pair_thole.html
index e3a5f8b9cb..8e8f15daf2 100644
--- a/doc/html/pair_thole.html
+++ b/doc/html/pair_thole.html
@@ -134,9 +134,9 @@
 <h1>pair_style lj/cut/thole/long/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>thole</em> or <em>lj/cut/thole/long</em> or <em>lj/cut/thole/long/omp</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -153,15 +153,15 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="o">...</span> <span class="n">thole</span> <span class="mf">2.6</span> <span class="mf">12.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">thole</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">thole</span> <span class="mf">1.0</span> <span class="mf">2.6</span> <span class="mf">10.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">2</span> <span class="n">thole</span> <span class="mf">1.0</span> <span class="mf">2.6</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">thole</span><span class="o">/</span><span class="n">long</span> <span class="mf">2.6</span> <span class="mf">12.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid/overlay ... thole 2.6 12.0
+pair_coeff 1 1 thole 1.0
+pair_coeff 1 2 thole 1.0 2.6 10.0
+pair_coeff * 2 thole 1.0 2.6
+</pre>
+<pre class="literal-block">
+pair_style lj/cut/thole/long 2.6 12.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -189,8 +189,8 @@ short distances by a function</p>
 \frac{s_{ij} r_{ij} }{2} \right)
 \exp \left( - s_{ij} r_{ij} \right) \end{equation}\]</div>
 <p>This function results from an adaptation to point charges
-<a class="reference internal" href="#noskov"><span class="std std-ref">(Noskov)</span></a> of the dipole screening scheme originally proposed
-by <a class="reference internal" href="#thole"><span class="std std-ref">Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
+<a class="reference internal" href="tutorial_drude.html#noskov"><span class="std std-ref">(Noskov)</span></a> of the dipole screening scheme originally proposed
+by <a class="reference internal" href="tutorial_drude.html#thole"><span class="std std-ref">Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
 by the polarizability of the atoms, <span class="math">\(\alpha_i\)</span>, and by a Thole
 damping parameter <span class="math">\(a\)</span>.  This Thole damping parameter usually takes
 a value of 2.6, but in certain force fields the value can depend upon
diff --git a/doc/html/pair_tri_lj.html b/doc/html/pair_tri_lj.html
index e6c6b24ddd..bdda14e2e2 100644
--- a/doc/html/pair_tri_lj.html
+++ b/doc/html/pair_tri_lj.html
@@ -128,18 +128,18 @@
 <span id="index-0"></span><h1>pair_style tri/lj command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tri</span><span class="o">/</span><span class="n">lj</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style tri/lj cutoff
+</pre>
 <p>cutoff = global cutoff for interactions (distance units)</p>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tri</span><span class="o">/</span><span class="n">lj</span> <span class="mf">3.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.5</span> <span class="mf">2.5</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style tri/lj 3.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_vashishta.html b/doc/html/pair_vashishta.html
index 0bfaceb06c..6dd3e02f8f 100644
--- a/doc/html/pair_vashishta.html
+++ b/doc/html/pair_vashishta.html
@@ -131,16 +131,16 @@
 <h1>pair_style vashishta/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">vashishta</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style vashishta
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">vashishta</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">vashishta</span> <span class="n">Si</span> <span class="n">C</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style vashishta
+pair_coeff * * SiC.vashishta Si C
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -178,9 +178,9 @@ to specify the path for the potential file.</p>
 Si and C.  If your LAMMPS simulation has 4 atoms types and you want
 the 1st 3 to be Si, and the 4th to be C, you would use the following
 pair_coeff command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">vashishta</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * * SiC.vashishta Si Si Si C
+</pre>
 <p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
 element in the file.  The final C argument maps LAMMPS atom type 4
diff --git a/doc/html/pair_yukawa.html b/doc/html/pair_yukawa.html
index 826c7de7ff..3f0d3b3e2c 100644
--- a/doc/html/pair_yukawa.html
+++ b/doc/html/pair_yukawa.html
@@ -134,9 +134,9 @@
 <h1>pair_style yukawa/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">yukawa</span> <span class="n">kappa</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style yukawa kappa cutoff
+</pre>
 <ul class="simple">
 <li>kappa = screening length (inverse distance units)</li>
 <li>cutoff = global cutoff for Yukawa interactions (distance units)</li>
@@ -144,11 +144,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">yukawa</span> <span class="mf">2.0</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.3</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style yukawa 2.0 2.5
+pair_coeff 1 1 100.0 2.3
+pair_coeff * * 100.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/pair_yukawa_colloid.html b/doc/html/pair_yukawa_colloid.html
index 560d253325..0c16f65c1d 100644
--- a/doc/html/pair_yukawa_colloid.html
+++ b/doc/html/pair_yukawa_colloid.html
@@ -134,9 +134,9 @@
 <h1>pair_style yukawa/colloid/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">yukawa</span><span class="o">/</span><span class="n">colloid</span> <span class="n">kappa</span> <span class="n">cutoff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style yukawa/colloid kappa cutoff
+</pre>
 <ul class="simple">
 <li>kappa = screening length (inverse distance units)</li>
 <li>cutoff = global cutoff for colloidal Yukawa interactions (distance units)</li>
@@ -144,11 +144,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">yukawa</span><span class="o">/</span><span class="n">colloid</span> <span class="mf">2.0</span> <span class="mf">2.5</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.3</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style yukawa/colloid 2.0 2.5
+pair_coeff 1 1 100.0 2.3
+pair_coeff * * 100.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -182,9 +182,9 @@ charge and surface potential due to the presence of electrolyte.  Note
 that the A for this potential style has different units than the A
 used in <a class="reference internal" href="pair_yukawa.html"><span class="doc">pair_style yukawa</span></a>.  For low surface
 potentials, i.e. less than about 25 mV, A can be written as:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">A</span> <span class="o">=</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">PI</span> <span class="o">*</span> <span class="n">R</span><span class="o">*</span><span class="n">eps</span><span class="o">*</span><span class="n">eps0</span> <span class="o">*</span> <span class="n">kappa</span> <span class="o">*</span> <span class="n">psi</span><span class="o">^</span><span class="mi">2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+A = 2 * PI * R*eps*eps0 * kappa * psi^2
+</pre>
 <p>where</p>
 <ul class="simple">
 <li>R = colloid radius (distance units)</li>
diff --git a/doc/html/pair_zbl.html b/doc/html/pair_zbl.html
index 71b3bea35c..54ad6b5344 100644
--- a/doc/html/pair_zbl.html
+++ b/doc/html/pair_zbl.html
@@ -134,9 +134,9 @@
 <h1>pair_style zbl/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">zbl</span> <span class="n">inner</span> <span class="n">outer</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style zbl inner outer
+</pre>
 <ul class="simple">
 <li>inner = distance where switching function begins</li>
 <li>outer = global cutoff for ZBL interaction</li>
@@ -144,11 +144,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">zbl</span> <span class="mf">3.0</span> <span class="mf">4.0</span>
-<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">73.0</span> <span class="mf">73.0</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">14.0</span> <span class="mf">14.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style zbl 3.0 4.0
+pair_coeff * * 73.0 73.0
+pair_coeff 1 1 14.0 14.0
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/prd.html b/doc/html/prd.html
index ee0c7948c0..a32fecfdce 100644
--- a/doc/html/prd.html
+++ b/doc/html/prd.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>prd command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">prd</span> <span class="n">N</span> <span class="n">t_event</span> <span class="n">n_dephase</span> <span class="n">t_dephase</span> <span class="n">t_correlate</span> <span class="n">compute</span><span class="o">-</span><span class="n">ID</span> <span class="n">seed</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
+</pre>
 <ul class="simple">
 <li>N = # of timesteps to run (not including dephasing/quenching)</li>
 <li>t_event = timestep interval between event checks</li>
@@ -200,19 +200,19 @@ potentials, etc should be the same for every replica.</p>
 <p>A PRD run has several stages, which are repeated each time an &#8220;event&#8221;
 occurs in one of the replicas, as defined below.  The logic for a PRD
 run is as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">while</span> <span class="p">(</span><span class="n">time</span> <span class="n">remains</span><span class="p">):</span>
-  <span class="n">dephase</span> <span class="k">for</span> <span class="n">n_dephase</span><span class="o">*</span><span class="n">t_dephase</span> <span class="n">steps</span>
-  <span class="n">until</span> <span class="p">(</span><span class="n">event</span> <span class="n">occurs</span> <span class="n">on</span> <span class="n">some</span> <span class="n">replica</span><span class="p">):</span>
-    <span class="n">run</span> <span class="n">dynamics</span> <span class="k">for</span> <span class="n">t_event</span> <span class="n">steps</span>
-    <span class="n">quench</span>
-    <span class="n">check</span> <span class="k">for</span> <span class="n">uncorrelated</span> <span class="n">event</span> <span class="n">on</span> <span class="nb">any</span> <span class="n">replica</span>
-  <span class="n">until</span> <span class="p">(</span><span class="n">no</span> <span class="n">correlated</span> <span class="n">event</span> <span class="n">occurs</span><span class="p">):</span>
-    <span class="n">run</span> <span class="n">dynamics</span> <span class="k">for</span> <span class="n">t_correlate</span> <span class="n">steps</span>
-    <span class="n">quench</span>
-    <span class="n">check</span> <span class="k">for</span> <span class="n">correlated</span> <span class="n">event</span> <span class="n">on</span> <span class="n">this</span> <span class="n">replica</span>
-  <span class="n">event</span> <span class="n">replica</span> <span class="n">shares</span> <span class="n">state</span> <span class="k">with</span> <span class="nb">all</span> <span class="n">replicas</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+while (time remains):
+  dephase for n_dephase*t_dephase steps
+  until (event occurs on some replica):
+    run dynamics for t_event steps
+    quench
+    check for uncorrelated event on any replica
+  until (no correlated event occurs):
+    run dynamics for t_correlate steps
+    quench
+    check for correlated event on this replica
+  event replica shares state with all replicas
+</pre>
 <p>Before this loop begins, the state of the system on replica 0 is
 shared with all replicas, so that all replicas begin from the same
 initial state. The first potential energy basin is identified by
diff --git a/doc/html/processors.html b/doc/html/processors.html
index f0feeb91ba..15f24d6340 100644
--- a/doc/html/processors.html
+++ b/doc/html/processors.html
@@ -162,15 +162,15 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">processors</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">5</span>
-<span class="n">processors</span> <span class="mi">2</span> <span class="mi">4</span> <span class="mi">4</span>
-<span class="n">processors</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">8</span> <span class="nb">map</span> <span class="n">xyz</span>
-<span class="n">processors</span> <span class="o">*</span> <span class="o">*</span> <span class="o">*</span> <span class="n">grid</span> <span class="n">numa</span>
-<span class="n">processors</span> <span class="o">*</span> <span class="o">*</span> <span class="o">*</span> <span class="n">grid</span> <span class="n">twolevel</span> <span class="mi">4</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">1</span>
-<span class="n">processors</span> <span class="mi">4</span> <span class="mi">8</span> <span class="mi">16</span> <span class="n">grid</span> <span class="n">custom</span> <span class="n">myfile</span>
-<span class="n">processors</span> <span class="o">*</span> <span class="o">*</span> <span class="o">*</span> <span class="n">part</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">multiple</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+processors * * 5
+processors 2 4 4
+processors * * 8 map xyz
+processors * * * grid numa
+processors * * * grid twolevel 4 * * 1
+processors 4 8 16 grid custom myfile
+processors * * * part 1 2 multiple
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -428,7 +428,7 @@ option.</p>
 </div>
 <div class="section" id="default">
 <h2>Default</h2>
-<p>The option defaults are Px Py Pz = * * <a href="#id1"><span class="problematic" id="id2">*</span></a>, grid = onelevel, and map =
+<p>The option defaults are Px Py Pz = * * *, grid = onelevel, and map =
 cart.</p>
 </div>
 </div>
diff --git a/doc/html/python.html b/doc/html/python.html
index f78a9df834..6700435a9f 100644
--- a/doc/html/python.html
+++ b/doc/html/python.html
@@ -161,35 +161,35 @@ keyword = <em>invoke</em> or <em>input</em> or <em>return</em> or <em>format</em
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">pForce</span> <span class="nb">input</span> <span class="mi">2</span> <span class="n">v_x</span> <span class="mf">20.0</span> <span class="k">return</span> <span class="n">v_f</span> <span class="nb">format</span> <span class="n">fff</span> <span class="n">file</span> <span class="n">force</span><span class="o">.</span><span class="n">py</span>
-<span class="n">python</span> <span class="n">pForce</span> <span class="n">invoke</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">factorial</span> <span class="nb">input</span> <span class="mi">1</span> <span class="n">myN</span> <span class="k">return</span> <span class="n">v_fac</span> <span class="nb">format</span> <span class="n">ii</span> <span class="n">here</span> <span class="s2">&quot;&quot;&quot;</span>
-<span class="s2">def factorial(n):</span>
-<span class="s2">  if n == 1: return n</span>
-<span class="s2">  return n * factorial(n-1)</span>
-<span class="s2"> &quot;&quot;&quot;</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">loop</span> <span class="nb">input</span> <span class="mi">1</span> <span class="n">SELF</span> <span class="k">return</span> <span class="n">v_value</span> <span class="nb">format</span> <span class="o">-</span><span class="n">f</span> <span class="n">here</span> <span class="s2">&quot;&quot;&quot;</span>
-<span class="s2">def loop(lmpptr,N,cut0):</span>
-<span class="s2">  from lammps import lammps</span>
-<span class="s2">  lmp = lammps(ptr=lmpptr)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+python pForce input 2 v_x 20.0 return v_f format fff file force.py
+python pForce invoke
+</pre>
+<pre class="literal-block">
+python factorial input 1 myN return v_fac format ii here &quot;&quot;&quot;
+def factorial(n):
+  if n == 1: return n
+  return n * factorial(n-1)
+ &quot;&quot;&quot;
+</pre>
+<pre class="literal-block">
+python loop input 1 SELF return v_value format -f here &quot;&quot;&quot;
+def loop(lmpptr,N,cut0):
+  from lammps import lammps
+  lmp = lammps(ptr=lmpptr)
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># loop N times, increasing cutoff each time</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">N</span><span class="p">):</span>
-   <span class="n">cut</span> <span class="o">=</span> <span class="n">cut0</span> <span class="o">+</span> <span class="n">i</span><span class="o">*</span><span class="mf">0.1</span>
-   <span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="s2">&quot;cut&quot;</span><span class="p">,</span><span class="n">cut</span><span class="p">)</span>               <span class="c1"># set a variable in LAMMPS</span>
-   <span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">&quot;pair_style lj/cut $</span><span class="si">{cut}</span><span class="s2">&quot;</span><span class="p">)</span>   <span class="c1"># LAMMPS commands</span>
-   <span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">&quot;pair_coeff * * 1.0 1.0&quot;</span><span class="p">)</span>
-   <span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">&quot;run 100&quot;</span><span class="p">)</span>
-<span class="s2">&quot;&quot;&quot;</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+ for i in range(N):
+   cut = cut0 + i*0.1
+   lmp.set_variable(&quot;cut&quot;,cut)               # set a variable in LAMMPS
+   lmp.command(&quot;pair_style lj/cut ${cut}&quot;)   # LAMMPS commands
+   lmp.command(&quot;pair_coeff * * 1.0 1.0&quot;)
+   lmp.command(&quot;run 100&quot;)
+&quot;&quot;&quot;
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -263,10 +263,10 @@ numeric or string value, as specified by the <em>format</em> keyword.</p>
 of a python-style variable associates a Python function name with the
 variable.  This must match the <em>func</em> setting for this command.  For
 exampe these two commands would be self-consistent:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">foo</span> <span class="n">python</span> <span class="n">myMultiply</span>
-<span class="n">python</span> <span class="n">myMultiply</span> <span class="k">return</span> <span class="n">v_foo</span> <span class="nb">format</span> <span class="n">f</span> <span class="n">file</span> <span class="n">funcs</span><span class="o">.</span><span class="n">py</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable foo python myMultiply
+python myMultiply return v_foo format f file funcs.py
+</pre>
 <p>The two commands can appear in either order in the input script so
 long as both are specified before the Python function is invoked for
 the first time.</p>
@@ -417,29 +417,29 @@ Python wraps the various functions included in the LAMMPS library
 interface.</p>
 <p>A more interesting example is in the examples/python/in.python script
 which loads and runs the following function from examples/python/funcs.py:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">loop</span><span class="p">(</span><span class="n">N</span><span class="p">,</span><span class="n">cut0</span><span class="p">,</span><span class="n">thresh</span><span class="p">,</span><span class="n">lmpptr</span><span class="p">):</span>
-  <span class="nb">print</span> <span class="s2">&quot;LOOP ARGS&quot;</span><span class="p">,</span><span class="n">N</span><span class="p">,</span><span class="n">cut0</span><span class="p">,</span><span class="n">thresh</span><span class="p">,</span><span class="n">lmpptr</span>
-  <span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
-  <span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">ptr</span><span class="o">=</span><span class="n">lmpptr</span><span class="p">)</span>
-  <span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">N</span><span class="p">):</span>
-  <span class="n">cut</span> <span class="o">=</span> <span class="n">cut0</span> <span class="o">+</span> <span class="n">i</span><span class="o">*</span><span class="mf">0.1</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="s2">&quot;cut&quot;</span><span class="p">,</span><span class="n">cut</span><span class="p">)</span>                 <span class="c1"># set a variable in LAMMPS</span>
-<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">&quot;pair_style lj/cut $</span><span class="si">{cut}</span><span class="s2">&quot;</span><span class="p">)</span>     <span class="c1"># LAMMPS command</span>
-<span class="c1">#lmp.command(&quot;pair_style lj/cut %d&quot; % cut)  # LAMMPS command option</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">&quot;pair_coeff * * 1.0 1.0&quot;</span><span class="p">)</span>       <span class="c1"># ditto</span>
-<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">&quot;run 10&quot;</span><span class="p">)</span>                       <span class="c1"># ditto</span>
-<span class="n">pe</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_compute</span><span class="p">(</span><span class="s2">&quot;thermo_pe&quot;</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">)</span>   <span class="c1"># extract total PE from LAMMPS</span>
-<span class="nb">print</span> <span class="s2">&quot;PE&quot;</span><span class="p">,</span><span class="n">pe</span><span class="o">/</span><span class="n">natoms</span><span class="p">,</span><span class="n">thresh</span>
-<span class="k">if</span> <span class="n">pe</span><span class="o">/</span><span class="n">natoms</span> <span class="o">&lt;</span> <span class="n">thresh</span><span class="p">:</span> <span class="k">return</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+def loop(N,cut0,thresh,lmpptr):
+  print &quot;LOOP ARGS&quot;,N,cut0,thresh,lmpptr
+  from lammps import lammps
+  lmp = lammps(ptr=lmpptr)
+  natoms = lmp.get_natoms()
+</pre>
+<pre class="literal-block">
+for i in range(N):
+  cut = cut0 + i*0.1
+</pre>
+<pre class="literal-block">
+lmp.set_variable(&quot;cut&quot;,cut)                 # set a variable in LAMMPS
+lmp.command(&quot;pair_style lj/cut ${cut}&quot;)     # LAMMPS command
+#lmp.command(&quot;pair_style lj/cut %d&quot; % cut)  # LAMMPS command option
+</pre>
+<pre class="literal-block">
+lmp.command(&quot;pair_coeff * * 1.0 1.0&quot;)       # ditto
+lmp.command(&quot;run 10&quot;)                       # ditto
+pe = lmp.extract_compute(&quot;thermo_pe&quot;,0,0)   # extract total PE from LAMMPS
+print &quot;PE&quot;,pe/natoms,thresh
+if pe/natoms &lt; thresh: return
+</pre>
 <p>with these input script commands:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span>          <span class="n">loop</span> <span class="nb">input</span> <span class="mi">4</span> <span class="mi">10</span> <span class="mf">1.0</span> <span class="o">-</span><span class="mf">4.0</span> <span class="n">SELF</span> <span class="nb">format</span> <span class="n">iffp</span> <span class="n">file</span> <span class="n">funcs</span><span class="o">.</span><span class="n">py</span>
 <span class="n">python</span>          <span class="n">loop</span> <span class="n">invoke</span>
diff --git a/doc/html/read_data.html b/doc/html/read_data.html
index 41ce8a8dc9..0087555e4b 100644
--- a/doc/html/read_data.html
+++ b/doc/html/read_data.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>read_data command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_data</span> <span class="n">file</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+read_data file keyword args ...
+</pre>
 <ul class="simple">
 <li>file = name of data file to read in</li>
 <li>zero or more keyword/arg pairs may be appended</li>
@@ -165,13 +165,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">lj</span>
-<span class="n">read_data</span> <span class="o">../</span><span class="n">run7</span><span class="o">/</span><span class="n">data</span><span class="o">.</span><span class="n">polymer</span><span class="o">.</span><span class="n">gz</span>
-<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">protein</span> <span class="n">fix</span> <span class="n">mycmap</span> <span class="n">crossterm</span> <span class="n">CMAP</span>
-<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">water</span> <span class="n">add</span> <span class="n">append</span> <span class="n">offset</span> <span class="mi">3</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">shift</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">50.0</span>
-<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">water</span> <span class="n">add</span> <span class="n">merge</span> <span class="mi">1</span> <span class="n">group</span> <span class="n">solvent</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+read_data data.lj
+read_data ../run7/data.polymer.gz
+read_data data.protein fix mycmap crossterm CMAP
+read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
+read_data data.water add merge 1 group solvent
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -764,9 +764,9 @@ are those that are not the 5 standard ones (ID,type,x,y,z).  For
 example, for the &#8220;charge&#8221; sub-style, a &#8220;q&#8221; value would appear.  For
 the &#8220;full&#8221; sub-style, a &#8220;molecule-ID&#8221; and &#8220;q&#8221; would appear.  These are
 listed in the same order they appear as listed above.  Thus if</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">sphere</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+atom_style hybrid charge sphere
+</pre>
 <p>were used in the input script, each atom line would have these fields:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom</span><span class="o">-</span><span class="n">ID</span> <span class="n">atom</span><span class="o">-</span><span class="nb">type</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">q</span> <span class="n">diameter</span> <span class="n">density</span>
 </pre></div>
@@ -1260,9 +1260,9 @@ are those that are not the 5 standard ones (ID,vx,vy,vz).  For
 example, for the &#8220;sphere&#8221; sub-style, &#8220;wx&#8221;, &#8220;wy&#8221;, &#8220;wz&#8221; values would
 appear.  These are listed in the same order they appear as listed
 above.  Thus if</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">electron</span> <span class="n">sphere</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+atom_style hybrid electron sphere
+</pre>
 <p>were used in the input script, each velocity line would have these
 fields:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom</span><span class="o">-</span><span class="n">ID</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span> <span class="n">ervel</span> <span class="n">wx</span> <span class="n">wy</span> <span class="n">wz</span>
diff --git a/doc/html/read_dump.html b/doc/html/read_dump.html
index 603ab46785..5e2e9f96eb 100644
--- a/doc/html/read_dump.html
+++ b/doc/html/read_dump.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>read_dump command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_dump</span> <span class="n">file</span> <span class="n">Nstep</span> <span class="n">field1</span> <span class="n">field2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+read_dump file Nstep field1 field2 ... keyword values ...
+</pre>
 <ul class="simple">
 <li>file = name of dump file to read</li>
 <li>Nstep = snapshot timestep to read from file</li>
@@ -168,18 +168,18 @@ field = <em>x</em> or <em>y</em> or <em>z</em> or <em>vx</em> or <em>vy</em> or
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">file</span> <span class="mi">5000</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span>
-<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">xyz</span> <span class="mi">5</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">no</span> <span class="nb">format</span> <span class="n">xyz</span>
-<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">xyz</span> <span class="mi">10</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">no</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">xyz</span> <span class="s2">&quot;../plugins&quot;</span>
-<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">dcd</span> <span class="mi">0</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">yes</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">dcd</span>
-<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">file</span> <span class="mi">1000</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span> <span class="n">box</span> <span class="n">yes</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">lammpstrj</span> <span class="o">/</span><span class="n">usr</span><span class="o">/</span><span class="n">local</span><span class="o">/</span><span class="n">lib</span><span class="o">/</span><span class="n">vmd</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">LINUXAMD64</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">molfile</span>
-<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">file</span> <span class="mi">5000</span> <span class="n">x</span> <span class="n">y</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">trim</span> <span class="n">yes</span>
-<span class="n">read_dump</span> <span class="o">../</span><span class="n">run7</span><span class="o">/</span><span class="n">dump</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">gz</span> <span class="mi">10000</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">yes</span>
-<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">xyz</span> <span class="mi">10</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">no</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">xyz</span> <span class="o">../</span><span class="n">plugins</span>
-<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">dcd</span> <span class="mi">0</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">dcd</span>
-<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">file</span> <span class="mi">1000</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">lammpstrj</span> <span class="o">/</span><span class="n">usr</span><span class="o">/</span><span class="n">local</span><span class="o">/</span><span class="n">lib</span><span class="o">/</span><span class="n">vmd</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">LINUXAMD64</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">molfile</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+read_dump dump.file 5000 x y z
+read_dump dump.xyz 5 x y z box no format xyz
+read_dump dump.xyz 10 x y z box no format molfile xyz &quot;../plugins&quot;
+read_dump dump.dcd 0 x y z box yes format molfile dcd
+read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
+read_dump dump.file 5000 x y vx vy trim yes
+read_dump ../run7/dump.file.gz 10000 x y z box yes
+read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
+read_dump dump.dcd 0 x y z format molfile dcd
+read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/region.html b/doc/html/region.html
index de04067047..8e3f0aa71b 100644
--- a/doc/html/region.html
+++ b/doc/html/region.html
@@ -193,14 +193,14 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">region</span> <span class="mi">1</span> <span class="n">block</span> <span class="o">-</span><span class="mf">3.0</span> <span class="mf">5.0</span> <span class="n">INF</span> <span class="mf">10.0</span> <span class="n">INF</span> <span class="n">INF</span>
-<span class="n">region</span> <span class="mi">2</span> <span class="n">sphere</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mi">5</span> <span class="n">side</span> <span class="n">out</span>
-<span class="n">region</span> <span class="n">void</span> <span class="n">cylinder</span> <span class="n">y</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">5</span> <span class="o">-</span><span class="mf">5.0</span> <span class="n">EDGE</span> <span class="n">units</span> <span class="n">box</span>
-<span class="n">region</span> <span class="mi">1</span> <span class="n">prism</span> <span class="mi">0</span> <span class="mi">10</span> <span class="mi">0</span> <span class="mi">10</span> <span class="mi">0</span> <span class="mi">10</span> <span class="mi">2</span> <span class="mi">0</span> <span class="mi">0</span>
-<span class="n">region</span> <span class="n">outside</span> <span class="n">union</span> <span class="mi">4</span> <span class="n">side1</span> <span class="n">side2</span> <span class="n">side3</span> <span class="n">side4</span>
-<span class="n">region</span> <span class="mi">2</span> <span class="n">sphere</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mi">5</span> <span class="n">side</span> <span class="n">out</span> <span class="n">move</span> <span class="n">v_left</span> <span class="n">v_up</span> <span class="n">NULL</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+region 1 block -3.0 5.0 INF 10.0 INF INF
+region 2 sphere 0.0 0.0 0.0 5 side out
+region void cylinder y 2 3 5 -5.0 EDGE units box
+region 1 prism 0 10 0 10 0 10 2 0 0
+region outside union 4 side1 side2 side3 side4
+region 2 sphere 0.0 0.0 0.0 5 side out move v_left v_up NULL
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -380,18 +380,18 @@ fashion.  For the latter, see the <em>start</em> and <em>stop</em> keywords of t
 <p>For example, these commands would displace a region from its initial
 position, in the positive x direction, effectively at a constant
 velocity:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">dx</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
-<span class="n">region</span> <span class="mi">2</span> <span class="n">sphere</span> <span class="mf">10.0</span> <span class="mf">10.0</span> <span class="mf">0.0</span> <span class="mi">5</span> <span class="n">move</span> <span class="n">v_dx</span> <span class="n">NULL</span> <span class="n">NULL</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable dx equal ramp(0,10)
+region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL
+</pre>
 <p>Note that the initial displacemet is 0.0, though that is not required.</p>
 <p>Either of these varaibles would &#8220;wiggle&#8221; the region back and forth in
 the y direction:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">dy</span> <span class="n">equal</span> <span class="n">swiggle</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">5</span><span class="p">,</span><span class="mi">100</span><span class="p">)</span>
-<span class="n">variable</span> <span class="n">dysame</span> <span class="n">equal</span> <span class="mi">5</span><span class="o">*</span><span class="n">sin</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">PI</span><span class="o">*</span><span class="n">elaplong</span><span class="o">*</span><span class="n">dt</span><span class="o">/</span><span class="mi">100</span><span class="p">)</span>
-<span class="n">region</span> <span class="mi">2</span> <span class="n">sphere</span> <span class="mf">10.0</span> <span class="mf">10.0</span> <span class="mf">0.0</span> <span class="mi">5</span> <span class="n">move</span> <span class="n">NULL</span> <span class="n">v_dy</span> <span class="n">NULL</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable dy equal swiggle(0,5,100)
+variable dysame equal 5*sin(2*PI*elaplong*dt/100)
+region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL
+</pre>
 <p>The <em>rotate</em> keyword rotates the region around a rotation axis <em>R</em> =
 (Rx,Ry,Rz) that goes thru a point <em>P</em> = (Px,Py,Pz).  The rotation
 angle is calculated, presumably as a function of time, by a variable
diff --git a/doc/html/restart.html b/doc/html/restart.html
index d6fc25f246..3f169da485 100644
--- a/doc/html/restart.html
+++ b/doc/html/restart.html
@@ -150,14 +150,14 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">restart</span> <span class="mi">0</span>
-<span class="n">restart</span> <span class="mi">1000</span> <span class="n">poly</span><span class="o">.</span><span class="n">restart</span>
-<span class="n">restart</span> <span class="mi">1000</span> <span class="n">poly</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="n">mpiio</span>
-<span class="n">restart</span> <span class="mi">1000</span> <span class="n">restart</span><span class="o">.*.</span><span class="n">equil</span>
-<span class="n">restart</span> <span class="mi">10000</span> <span class="n">poly</span><span class="o">.%.</span><span class="mi">1</span> <span class="n">poly</span><span class="o">.%.</span><span class="mi">2</span> <span class="n">nfile</span> <span class="mi">10</span>
-<span class="n">restart</span> <span class="n">v_mystep</span> <span class="n">poly</span><span class="o">.</span><span class="n">restart</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+restart 0
+restart 1000 poly.restart
+restart 1000 poly.restart.mpiio
+restart 1000 restart.*.equil
+restart 10000 poly.%.1 poly.%.2 nfile 10
+restart v_mystep poly.restart
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -226,10 +226,10 @@ options for <a class="reference internal" href="variable.html"><span class="doc"
 <p>For example, the following commands will write restart files
 every step from 1100 to 1200, and could be useful for debugging
 a simulation where something goes wrong at step 1163:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span>     <span class="n">s</span> <span class="n">equal</span> <span class="n">stride</span><span class="p">(</span><span class="mi">1100</span><span class="p">,</span><span class="mi">1200</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
-<span class="n">restart</span>              <span class="n">v_s</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable     s equal stride(1100,1200,1)
+restart              v_s tmp.restart
+</pre>
 <hr class="docutils" />
 <p>See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for information about
 what is stored in a restart file.</p>
diff --git a/doc/html/run_style.html b/doc/html/run_style.html
index 9ef0e69f67..b00835c7e1 100644
--- a/doc/html/run_style.html
+++ b/doc/html/run_style.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>run_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+run_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>verlet</em> or <em>verlet/split</em> or <em>respa</em> or <em>respa/omp</em></li>
 </ul>
@@ -175,14 +175,14 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run_style</span> <span class="n">verlet</span>
-<span class="n">run_style</span> <span class="n">respa</span> <span class="mi">4</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">bond</span> <span class="mi">1</span> <span class="n">dihedral</span> <span class="mi">2</span> <span class="n">pair</span> <span class="mi">3</span> <span class="n">kspace</span> <span class="mi">4</span>
-<span class="n">run_style</span> <span class="n">respa</span> <span class="mi">4</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">bond</span> <span class="mi">1</span> <span class="n">dihedral</span> <span class="mi">2</span> <span class="n">inner</span> <span class="mi">3</span> <span class="mf">5.0</span> <span class="mf">6.0</span> <span class="n">outer</span> <span class="mi">4</span> <span class="n">kspace</span> <span class="mi">4</span>
-</pre></div>
-</div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run_style</span> <span class="n">respa</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mi">2</span> <span class="n">bond</span> <span class="mi">1</span> <span class="n">hybrid</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">1</span> <span class="n">kspace</span> <span class="mi">3</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+run_style verlet
+run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
+run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
+</pre>
+<pre class="literal-block">
+run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -219,9 +219,9 @@ its onn optimal layout, then require the 2nd partition&#8217;s layout to
 match the integer multiple constraint.  See the
 <a class="reference internal" href="processors.html"><span class="doc">processors</span></a> command with its <em>part</em> keyword for a way
 to control this, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">procssors</span> <span class="o">*</span> <span class="o">*</span> <span class="o">*</span> <span class="n">part</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">multiple</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+procssors * * * part 1 2 multiple
+</pre>
 <p>You can also use the <a class="reference internal" href="partition.html"><span class="doc">partition</span></a> command to explicitly
 specity the processor layout on each partition.  E.g. for 2 partitions
 of 60 and 15 processors each:</p>
@@ -314,10 +314,10 @@ angstrom &#8220;healing distance&#8221; (the distance between the outer and inne
 cutoffs) works reasonably well.  We thus recommend the following
 settings for use of the <em>respa</em> style without SHAKE in biomolecular
 simulations:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">timestep</span>  <span class="mf">4.0</span>
-<span class="n">run_style</span> <span class="n">respa</span> <span class="mi">4</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">inner</span> <span class="mi">2</span> <span class="mf">4.5</span> <span class="mf">6.0</span> <span class="n">middle</span> <span class="mi">3</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="n">outer</span> <span class="mi">4</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+timestep  4.0
+run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
+</pre>
 <p>With these settings, users can expect good energy conservation and
 roughly a 2.5 fold speedup over the <em>verlet</em> style with a 0.5 fmsec
 timestep.</p>
@@ -332,11 +332,11 @@ respa in order to freeze out these high frequency motions and increase
 the size of the time steps in the respa hierarchy.  The following
 settings can be used for biomolecular simulations with SHAKE and
 rRESPA:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span>             <span class="mi">2</span> <span class="nb">all</span> <span class="n">shake</span> <span class="mf">0.000001</span> <span class="mi">500</span> <span class="mi">0</span> <span class="n">m</span> <span class="mf">1.0</span> <span class="n">a</span> <span class="mi">1</span>
-<span class="n">timestep</span>        <span class="mf">4.0</span>
-<span class="n">run_style</span>    <span class="n">respa</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">inner</span> <span class="mi">1</span> <span class="mf">4.0</span> <span class="mf">5.0</span> <span class="n">outer</span> <span class="mi">2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+fix             2 all shake 0.000001 500 0 m 1.0 a 1
+timestep        4.0
+run_style   respa 2 2 inner 1 4.0 5.0 outer 2
+</pre>
 <p>With these settings, users can expect good energy conservation and
 roughly a 1.5 fold speedup over the <em>verlet</em> style with SHAKE and a
 2.0 fmsec timestep.</p>
@@ -348,10 +348,10 @@ keywords.  A 2-fold or more speedup can be obtained while maintaining
 good energy conservation.  In real units, for a pure LJ fluid at
 liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1
 Kcal/mol, the following settings seem to work well:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">timestep</span>  <span class="mf">36.0</span>
-<span class="n">run_style</span> <span class="n">respa</span> <span class="mi">3</span> <span class="mi">3</span> <span class="mi">4</span> <span class="n">inner</span> <span class="mi">1</span> <span class="mf">3.0</span> <span class="mf">4.0</span> <span class="n">middle</span> <span class="mi">2</span> <span class="mf">6.0</span> <span class="mf">7.0</span> <span class="n">outer</span> <span class="mi">3</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+timestep  36.0
+run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
+</pre>
 <hr class="docutils" />
 <p>The <em>respa/omp</em> styles is a variant of <em>respa</em> adapted for use with
 pair, bond, angle, dihedral, improper, or kspace styles with an <em>omp</em>
@@ -384,9 +384,9 @@ conserving energy to adequate precision.</p>
 </div>
 <div class="section" id="default">
 <h2>Default</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run_style</span> <span class="n">verlet</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+run_style verlet
+</pre>
 <hr class="docutils" />
 <p id="tuckerman"><strong>(Tuckerman)</strong> Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990
 (1992).</p>
diff --git a/doc/html/set.html b/doc/html/set.html
index 89ea2eb1ff..075dbb3510 100644
--- a/doc/html/set.html
+++ b/doc/html/set.html
@@ -214,17 +214,17 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">set</span> <span class="n">group</span> <span class="n">solvent</span> <span class="nb">type</span> <span class="mi">2</span>
-<span class="nb">set</span> <span class="n">group</span> <span class="n">solvent</span> <span class="nb">type</span><span class="o">/</span><span class="n">fraction</span> <span class="mi">2</span> <span class="mf">0.5</span> <span class="mi">12393</span>
-<span class="nb">set</span> <span class="n">group</span> <span class="n">edge</span> <span class="n">bond</span> <span class="mi">4</span>
-<span class="nb">set</span> <span class="n">region</span> <span class="n">half</span> <span class="n">charge</span> <span class="mf">0.5</span>
-<span class="nb">set</span> <span class="nb">type</span> <span class="mi">3</span> <span class="n">charge</span> <span class="mf">0.5</span>
-<span class="nb">set</span> <span class="nb">type</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">charge</span> <span class="mf">0.5</span>
-<span class="nb">set</span> <span class="n">atom</span> <span class="o">*</span> <span class="n">charge</span> <span class="n">v_atomfile</span>
-<span class="nb">set</span> <span class="n">atom</span> <span class="mi">100</span><span class="o">*</span><span class="mi">200</span> <span class="n">x</span> <span class="mf">0.5</span> <span class="n">y</span> <span class="mf">1.0</span>
-<span class="nb">set</span> <span class="n">atom</span> <span class="mi">1492</span> <span class="nb">type</span> <span class="mi">3</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+set group solvent type 2
+set group solvent type/fraction 2 0.5 12393
+set group edge bond 4
+set region half charge 0.5
+set type 3 charge 0.5
+set type 1*3 charge 0.5
+set atom * charge v_atomfile
+set atom 100*200 x 0.5 y 1.0
+set atom 1492 type 3
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -252,7 +252,7 @@ style <em>type</em> selects all the atoms in a range of types.  The style
 <em>mol</em> selects all the atoms in a range of molecule IDs.</p>
 <p>In each of the range cases, the range can be specified as a single
 numeric value, or a wildcard asterisk can be used to specify a range
-of values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  For
+of values.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  For
 example, for the style <em>type</em>, if N = the number of atom types, then
 an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
diff --git a/doc/html/special_bonds.html b/doc/html/special_bonds.html
index 08a1e3f74c..d431cc49b3 100644
--- a/doc/html/special_bonds.html
+++ b/doc/html/special_bonds.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>special_bonds command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+special_bonds keyword values ...
+</pre>
 <ul class="simple">
 <li>one or more keyword/value pairs may be appended</li>
 <li>keyword = <em>amber</em> or <em>charmm</em> or <em>dreiding</em> or <em>fene</em> or <em>lj/coul</em> or <em>lj</em> or <em>coul</em> or <em>angle</em> or <em>dihedral</em> or <em>extra</em></li>
@@ -152,14 +152,14 @@
   N = number of extra 1-2,1-3,1-4 interactions to save space for
 </pre>
 <p>Examples:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">amber</span>
-<span class="n">special_bonds</span> <span class="n">charmm</span>
-<span class="n">special_bonds</span> <span class="n">fene</span> <span class="n">dihedral</span> <span class="n">no</span>
-<span class="n">special_bonds</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.5</span> <span class="n">angle</span> <span class="n">yes</span> <span class="n">dihedral</span> <span class="n">yes</span>
-<span class="n">special_bonds</span> <span class="n">lj</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.5</span> <span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">dihedral</span> <span class="n">yes</span>
-<span class="n">special_bonds</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">extra</span> <span class="mi">2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+special_bonds amber
+special_bonds charmm
+special_bonds fene dihedral no
+special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
+special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
+special_bonds lj/coul 0 1 1 extra 2
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -301,7 +301,7 @@ current system has.</p>
 the system).  If new bonds are created (or molecules added containing
 atoms with more special neighbors), the size of this list needs to
 grow.  Note that adding a single bond always adds a new 1st neighbor
-but may also induce <em>many</em> new 2nd and 3rd neighbors, depending on the
+but may also induce *many* new 2nd and 3rd neighbors, depending on the
 molecular topology of your system.  Using the <em>extra</em> keyword leaves
 empty space in the list for this N additional 1st, 2nd, or 3rd
 neighbors to be added.  If you do not do this, you may get an error
@@ -325,14 +325,14 @@ Coul: coul 0.0 0.0 1.0</p>
 <p>because the LJ settings are reset to their default values
 each time the command is issued.</p>
 <p>Likewise</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">amber</span>
-<span class="n">special_bonds</span> <span class="n">extra</span> <span class="mi">2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+special_bonds amber
+special_bonds extra 2
+</pre>
 <p>is not the same as this single command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">amber</span> <span class="n">extra</span> <span class="mi">2</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+special_bonds amber extra 2
+</pre>
 <p>since in the former case, the 2nd command will reset all the LJ and
 Coulombic weights to 0.0 (the default).</p>
 <p>One exception to this rule is the <em>extra</em> option itself.  It is not
diff --git a/doc/html/tad.html b/doc/html/tad.html
index d4f05d75ae..e4bab3f210 100644
--- a/doc/html/tad.html
+++ b/doc/html/tad.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>tad command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">tad</span> <span class="n">N</span> <span class="n">t_event</span> <span class="n">T_lo</span> <span class="n">T_hi</span> <span class="n">delta</span> <span class="n">tmax</span> <span class="n">compute</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...
+</pre>
 <ul class="simple">
 <li>N = # of timesteps to run (not including dephasing/quenching)</li>
 <li>t_event = timestep interval between event checks</li>
@@ -162,15 +162,15 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">tad</span> <span class="mi">2000</span> <span class="mi">50</span> <span class="mi">1800</span> <span class="mi">2300</span> <span class="mf">0.01</span> <span class="mf">0.01</span> <span class="n">event</span>
-<span class="n">tad</span> <span class="mi">2000</span> <span class="mi">50</span> <span class="mi">1800</span> <span class="mi">2300</span> <span class="mf">0.01</span> <span class="mf">0.01</span> <span class="n">event</span> <span class="o">&amp;</span>
-    <span class="nb">min</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">05</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">05</span> <span class="mi">100</span> <span class="mi">100</span> <span class="o">&amp;</span>
-    <span class="n">neb</span> <span class="mf">0.0</span> <span class="mf">0.01</span> <span class="mi">200</span> <span class="mi">200</span> <span class="mi">20</span> <span class="o">&amp;</span>
-    <span class="n">min_style</span> <span class="n">cg</span> <span class="o">&amp;</span>
-    <span class="n">neb_style</span> <span class="n">fire</span> <span class="o">&amp;</span>
-    <span class="n">neb_log</span> <span class="n">log</span><span class="o">.</span><span class="n">neb</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+tad 2000 50 1800 2300 0.01 0.01 event
+tad 2000 50 1800 2300 0.01 0.01 event &amp;
+    min 1e-05 1e-05 100 100 &amp;
+    neb 0.0 0.01 200 200 20 &amp;
+    min_style cg &amp;
+    neb_style fire &amp;
+    neb_log log.neb
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -215,19 +215,19 @@ partitions remain idle. See <a class="reference internal" href="Section_howto.ht
 multi-replica simulations.</p>
 <p>A TAD run has several stages, which are repeated each time an event is
 performed.  The logic for a TAD run is as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">while</span> <span class="p">(</span><span class="n">time</span> <span class="n">remains</span><span class="p">):</span>
-  <span class="k">while</span> <span class="p">(</span><span class="n">time</span> <span class="o">&lt;</span> <span class="n">tstop</span><span class="p">):</span>
-    <span class="n">until</span> <span class="p">(</span><span class="n">event</span> <span class="n">occurs</span><span class="p">):</span>
-      <span class="n">run</span> <span class="n">dynamics</span> <span class="k">for</span> <span class="n">t_event</span> <span class="n">steps</span>
-      <span class="n">quench</span>
-    <span class="n">run</span> <span class="n">neb</span> <span class="n">calculation</span> <span class="n">using</span> <span class="nb">all</span> <span class="n">replicas</span>
-    <span class="n">compute</span> <span class="n">tlo</span> <span class="kn">from</span> <span class="nn">energy</span> <span class="n">barrier</span>
-    <span class="n">update</span> <span class="n">earliest</span> <span class="n">event</span>
-    <span class="n">update</span> <span class="n">tstop</span>
-    <span class="n">reflect</span> <span class="n">back</span> <span class="n">into</span> <span class="n">current</span> <span class="n">basin</span>
-  <span class="n">execute</span> <span class="n">earliest</span> <span class="n">event</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+while (time remains):
+  while (time &lt; tstop):
+    until (event occurs):
+      run dynamics for t_event steps
+      quench
+    run neb calculation using all replicas
+    compute tlo from energy barrier
+    update earliest event
+    update tstop
+    reflect back into current basin
+  execute earliest event
+</pre>
 <p>Before this outer loop begins, the initial potential energy basin is
 identified by quenching (an energy minimization, see below) the
 initial state and storing the resulting coordinates for reference.</p>
@@ -298,7 +298,7 @@ at the low temperature.</p>
 current basin to the stopping time. This last number can be used to
 judge whether the stopping time is too short or too long (see above).</p>
 <p><em>t_lo</em> is the low-temperature event time when the current basin was
-entered, in units of timestep.  del<em>t_lo</em> is the time of each detected
+entered, in units of timestep.  del*t_lo* is the time of each detected
 event, measured relative to <em>t_lo</em>.  <em>delt_lo</em> is equal to the
 high-temperature time since entering the current basin, scaled by an
 exponential factor that depends on the hi/lo temperature ratio and the
diff --git a/doc/html/thermo.html b/doc/html/thermo.html
index 8567a3fd63..7a5cb15c32 100644
--- a/doc/html/thermo.html
+++ b/doc/html/thermo.html
@@ -162,10 +162,10 @@ this context.  Other similar math functions could easily be added as
 options for <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a>.</p>
 <p>For example, the following commands will output thermodynamic info at
 timesteps 0,10,20,30,100,200,300,1000,2000,etc:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span>     <span class="n">s</span> <span class="n">equal</span> <span class="n">logfreq</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
-<span class="n">thermo</span>               <span class="n">v_s</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable     s equal logfreq(10,3,10)
+thermo               v_s
+</pre>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
diff --git a/doc/html/thermo_style.html b/doc/html/thermo_style.html
index 5a6e41bfc9..4f0f68acae 100644
--- a/doc/html/thermo_style.html
+++ b/doc/html/thermo_style.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>thermo_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_style</span> <span class="n">style</span> <span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+thermo_style style args
+</pre>
 <ul class="simple">
 <li>style = <em>one</em> or <em>multi</em> or <em>custom</em></li>
 <li>args = list of arguments for a particular style</li>
@@ -207,12 +207,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_style</span> <span class="n">multi</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">pe</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">vol</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">c_myTemp</span> <span class="n">v_abc</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">v_abc</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+thermo_style multi
+thermo_style custom step temp pe etotal press vol
+thermo_style custom step temp etotal c_myTemp v_abc
+thermo_style custom step temp etotal c_myTemp[*] v_abc
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -260,9 +260,9 @@ the thermo_modify command after it.</p>
 computed: &#8220;temp&#8221;, &#8220;press&#8221;, &#8220;ke&#8221;, &#8220;etotal&#8221;, &#8220;enthalpy&#8221;, &#8220;pxx&#8221;, etc.  By
 default this is done by using a <em>temperature</em> compute which is created
 when LAMMPS starts up, as if this command had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_temp</span> <span class="nb">all</span> <span class="n">temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute thermo_temp all temp
+</pre>
 <p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details.  Note
 that the ID of this compute is <em>thermo_temp</em> and the group is <em>all</em>.
 You can change the attributes of this temperature (e.g. its
@@ -275,9 +275,9 @@ This is done via the <a class="reference internal" href="thermo_modify.html"><sp
 computed: &#8220;press&#8221;, &#8220;enthalpy&#8221;, &#8220;pxx&#8221;, etc.  By default this is done by
 using a <em>pressure</em> compute which is created when LAMMPS starts up, as
 if this command had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute thermo_press all pressure thermo_temp
+</pre>
 <p>See the <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> command for details.
 Note that the ID of this compute is <em>thermo_press</em> and the group is
 <em>all</em>.  You can change the attributes of this pressure via the
@@ -290,9 +290,9 @@ that requires a pressure.  This is done via the
 be computed: &#8220;pe&#8221;, &#8220;etotal&#8221;, &#8220;ebond&#8221;, etc.  This is done by using a
 <em>pe</em> compute which is created when LAMMPS starts up, as if this
 command had been issued:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_pe</span> <span class="nb">all</span> <span class="n">pe</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute thermo_pe all pe
+</pre>
 <p>See the <a class="reference internal" href="compute_pe.html"><span class="doc">compute pe</span></a> command for details.  Note that
 the ID of this compute is <em>thermo_pe</em> and the group is <em>all</em>.  You can
 change the attributes of this potential energy via the
@@ -394,7 +394,7 @@ of these quantities in terms of the internal LAMMPS cell dimensions
 <p>For output values from a compute or fix, the bracketed index I used to
 index a vector, as in <em>c_ID[I]</em> or <em>f_ID[I]</em>, can be specified
 using a wildcard asterisk with the index to effectively specify
-multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.
+multiple values.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.
 If N = the size of the vector (for <em>mode</em> = scalar) or the number of
 columns in the array (for <em>mode</em> = vector), then an asterisk with no
 numeric values means all indices from 1 to N.  A leading asterisk
@@ -405,13 +405,13 @@ indices from m to n (inclusive).</p>
 vector had been listed one by one.  E.g. these 2 thermo_style commands
 are equivalent, since the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command
 creates a global vector with 6 values.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myTemp</span> <span class="nb">all</span> <span class="n">temp</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="o">&amp;</span>
-             <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
-             <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute myTemp all temp
+thermo_style custom step temp etotal c_myTemp[*]
+thermo_style custom step temp etotal &amp;
+             c_myTemp[1] c_myTemp[2] c_myTemp[3] &amp;
+             c_myTemp[4] c_myTemp[5] c_myTemp[6]
+</pre>
 <hr class="docutils" />
 <p>The <em>c_ID</em> and <em>c_ID[I]</em> and <em>c_ID[I][J]</em> keywords allow global
 values calculated by a compute to be output.  As discussed on the
@@ -490,9 +490,9 @@ division by &#8220;natoms&#8221; in the variable formula if this is not the case
 </div>
 <div class="section" id="default">
 <h2>Default</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_style</span> <span class="n">one</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+thermo_style one
+</pre>
 </div>
 </div>
 
diff --git a/doc/html/tutorial_drude.html b/doc/html/tutorial_drude.html
index e414d5d007..1f4763d477 100644
--- a/doc/html/tutorial_drude.html
+++ b/doc/html/tutorial_drude.html
@@ -204,14 +204,14 @@ The masses and charges of DCs and DPs are computed
 from <em>phenol.dff</em>, as well as the DC-DP bond constants.  The file
 <em>phenol.dff</em> contains the polarizabilities of the atom types
 and the mass of the Drude particles, for instance:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># units: kJ/mol, A, deg</span>
-<span class="c1"># kforce is in the form k/2 r_D^2</span>
-<span class="c1"># type  m_D/u   q_D/e    k_D   alpha/A3  thole</span>
-<span class="n">OH</span>      <span class="mf">0.4</span>    <span class="o">-</span><span class="mf">1.0</span>    <span class="mf">4184.0</span>   <span class="mf">0.63</span>     <span class="mf">0.67</span>
-<span class="n">CA</span>      <span class="mf">0.4</span>    <span class="o">-</span><span class="mf">1.0</span>    <span class="mf">4184.0</span>   <span class="mf">1.36</span>     <span class="mf">2.51</span>
-<span class="n">CAI</span>     <span class="mf">0.4</span>    <span class="o">-</span><span class="mf">1.0</span>    <span class="mf">4184.0</span>   <span class="mf">1.09</span>     <span class="mf">2.51</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+# units: kJ/mol, A, deg
+# kforce is in the form k/2 r_D^2
+# type  m_D/u   q_D/e    k_D   alpha/A3  thole
+OH      0.4    -1.0    4184.0   0.63     0.67
+CA      0.4    -1.0    4184.0   1.36     2.51
+CAI     0.4    -1.0    4184.0   1.09     2.51
+</pre>
 <p>The hydrogen atoms are absent from this file, so they will be treated
 as non-polarizable atoms.  In the non-polarizable data file
 <em>data.102494.lmp</em>, atom names corresponding to the atom type numbers
@@ -252,9 +252,9 @@ be reserved by using the <em>extra</em> keyword of the <em>special_bonds</em>
 command.  With our phenol, there is 1 more special neighbor for which
 space is required.  Otherwise LAMMPS crashes and gives the required
 value.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.5</span> <span class="n">extra</span> <span class="mi">1</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+special_bonds lj/coul 0.0 0.0 0.5 extra 1
+</pre>
 <p>Let us assume we want to run a simple NVT simulation at 300 K.  Note
 that Drude oscillators need to be thermalized at a low temperature in
 order to approximate a self-consistent field (SCF), therefore it is not
@@ -263,17 +263,17 @@ are approximated by a charged DC-DP pair, the <em>pair_style</em> must
 include Coulomb interactions, for instance <em>lj/cut/coul/long</em> with
 <em>kspace_style pppm</em>. For example, with a cutoff of 10. and a precision
 1.e-4:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
-<span class="n">kspace_style</span> <span class="n">pppm</span> <span class="mf">1.0e-4</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style lj/cut/coul/long 10.0
+kspace_style pppm 1.0e-4
+</pre>
 <p>As compared to the non-polarizable input file, <em>pair_coeff</em> lines need
 to be added for the DPs.  Since the DPs have no Lennard-Jones
 interactions, their <em>epsilon</em> is 0. so the only <em>pair_coeff</em> line
 that needs to be added is</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">6</span><span class="o">*</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="c1"># All-DPs</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff * 6* 0.0 0.0 # All-DPs
+</pre>
 <p>Now for the thermalization, the simplest choice is to use the <a class="reference internal" href="fix_langevin_drude.html"><span class="doc">fix langevin/drude</span></a>.</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">LANG</span> <span class="nb">all</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="mf">300.</span> <span class="mi">100</span> <span class="mi">12435</span> <span class="mf">1.</span> <span class="mi">20</span> <span class="mi">13977</span>
 </pre></div>
@@ -286,9 +286,9 @@ time 20 and random seed 13977.  Only the DCs and non-polarizable
 atoms need to be in this fix&#8217;s group.  LAMMPS will thermostate the DPs
 together with their DC.  For this, ghost atoms need to know their
 velocities. Thus you need to add the following command:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+comm_modify vel yes
+</pre>
 <p>In order to avoid that the center of mass of the whole system
 drifts due to the random forces of the Langevin thermostat on DCs, you
 can add the <em>zero yes</em> option at the end of the fix line.</p>
@@ -311,10 +311,10 @@ modification of forces but no position/velocity updates), the fix
 <p>Finally, do not forget to update the atom type elements if you use
 them in a <em>dump_modify ... element ...</em> command, by adding the element
 type of the DPs. Here for instance</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">DUMP</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">10</span> <span class="n">dump</span><span class="o">.</span><span class="n">lammpstrj</span> <span class="nb">id</span> <span class="n">mol</span> <span class="nb">type</span> <span class="n">element</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">ix</span> <span class="n">iy</span> <span class="n">iz</span>
-<span class="n">dump_modify</span> <span class="n">DUMP</span> <span class="n">element</span> <span class="n">C</span> <span class="n">C</span> <span class="n">O</span> <span class="n">H</span> <span class="n">H</span> <span class="n">D</span> <span class="n">D</span> <span class="n">D</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+dump DUMP all custom 10 dump.lammpstrj id mol type element x y z ix iy iz
+dump_modify DUMP element C C O H H D D D
+</pre>
 <p>The input file should now be ready for use!</p>
 <p>You will notice that the global temperature <em>thermo_temp</em> computed by
 LAMMPS is not 300. K as wanted.  This is because LAMMPS treats DPs as
@@ -327,9 +327,9 @@ to their DCs, you should use the <a class="reference internal" href="compute_tem
 <p>And then output the correct temperatures of the Drude oscillators
 using <em>thermo_style custom</em> with respectively <em>c_TDRUDE[1]</em> and
 <em>c_TDRUDE[2]</em>. These should be close to 300.0 and 1.0 on average.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+thermo_style custom step temp c_TDRUDE[1] c_TDRUDE[2]
+</pre>
 <hr class="docutils" />
 <p><strong>Thole screening</strong></p>
 <p>Dipolar interactions represented by point charges on springs may not
@@ -346,9 +346,9 @@ correction to the Coulomb pair_styles, which dampens at short distance
 the interactions between the charges representing the induced dipoles.
 It is to be used as <em>hybrid/overlay</em> with any standard <em>coul</em> pair
 style.  In our example, we would use</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="n">thole</span> <span class="mf">2.6</span> <span class="mf">10.0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0
+</pre>
 <p>This tells LAMMPS that we are using two pair_styles.  The first one is
 as above (<em>lj/cut/coul/long 10.0</em>).  The second one is a <em>thole</em>
 pair_style with default screening factor 2.6 (<a class="reference internal" href="#noskov"><span class="std std-ref">Noskov</span></a>) and
@@ -358,50 +358,48 @@ coefficients of all the pairs of atom types with i &lt; j should be
 explicitly defined.  The output of the <em>polarizer</em> script can be used
 to complete the <em>pair_coeff</em> section of the input file.  In our
 example, this will look like:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span>    <span class="mi">1</span>    <span class="mi">1</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.0700</span>   <span class="mf">3.550</span>
-<span class="n">pair_coeff</span>    <span class="mi">1</span>    <span class="mi">2</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.0700</span>   <span class="mf">3.550</span>
-<span class="n">pair_coeff</span>    <span class="mi">1</span>    <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.1091</span>   <span class="mf">3.310</span>
-<span class="n">pair_coeff</span>    <span class="mi">1</span>    <span class="mi">4</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.0458</span>   <span class="mf">2.985</span>
-<span class="n">pair_coeff</span>    <span class="mi">2</span>    <span class="mi">2</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.0700</span>   <span class="mf">3.550</span>
-<span class="n">pair_coeff</span>    <span class="mi">2</span>    <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.1091</span>   <span class="mf">3.310</span>
-<span class="n">pair_coeff</span>    <span class="mi">2</span>    <span class="mi">4</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.0458</span>   <span class="mf">2.985</span>
-<span class="n">pair_coeff</span>    <span class="mi">3</span>    <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.1700</span>   <span class="mf">3.070</span>
-<span class="n">pair_coeff</span>    <span class="mi">3</span>    <span class="mi">4</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.0714</span>   <span class="mf">2.745</span>
-<span class="n">pair_coeff</span>    <span class="mi">4</span>    <span class="mi">4</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.0300</span>   <span class="mf">2.420</span>
-<span class="n">pair_coeff</span>    <span class="o">*</span>    <span class="mi">5</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.0000</span>   <span class="mf">0.000</span>
-<span class="n">pair_coeff</span>    <span class="o">*</span>   <span class="mi">6</span><span class="o">*</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span>    <span class="mf">0.0000</span>   <span class="mf">0.000</span>
-<span class="n">pair_coeff</span>    <span class="mi">1</span>    <span class="mi">1</span> <span class="n">thole</span>   <span class="mf">1.090</span>   <span class="mf">2.510</span>
-<span class="n">pair_coeff</span>    <span class="mi">1</span>    <span class="mi">2</span> <span class="n">thole</span>   <span class="mf">1.218</span>   <span class="mf">2.510</span>
-<span class="n">pair_coeff</span>    <span class="mi">1</span>    <span class="mi">3</span> <span class="n">thole</span>   <span class="mf">0.829</span>   <span class="mf">1.590</span>
-<span class="n">pair_coeff</span>    <span class="mi">1</span>    <span class="mi">6</span> <span class="n">thole</span>   <span class="mf">1.090</span>   <span class="mf">2.510</span>
-<span class="n">pair_coeff</span>    <span class="mi">1</span>    <span class="mi">7</span> <span class="n">thole</span>   <span class="mf">1.218</span>   <span class="mf">2.510</span>
-<span class="n">pair_coeff</span>    <span class="mi">1</span>    <span class="mi">8</span> <span class="n">thole</span>   <span class="mf">0.829</span>   <span class="mf">1.590</span>
-<span class="n">pair_coeff</span>    <span class="mi">2</span>    <span class="mi">2</span> <span class="n">thole</span>   <span class="mf">1.360</span>   <span class="mf">2.510</span>
-<span class="n">pair_coeff</span>    <span class="mi">2</span>    <span class="mi">3</span> <span class="n">thole</span>   <span class="mf">0.926</span>   <span class="mf">1.590</span>
-<span class="n">pair_coeff</span>    <span class="mi">2</span>    <span class="mi">6</span> <span class="n">thole</span>   <span class="mf">1.218</span>   <span class="mf">2.510</span>
-<span class="n">pair_coeff</span>    <span class="mi">2</span>    <span class="mi">7</span> <span class="n">thole</span>   <span class="mf">1.360</span>   <span class="mf">2.510</span>
-<span class="n">pair_coeff</span>    <span class="mi">2</span>    <span class="mi">8</span> <span class="n">thole</span>   <span class="mf">0.926</span>   <span class="mf">1.590</span>
-<span class="n">pair_coeff</span>    <span class="mi">3</span>    <span class="mi">3</span> <span class="n">thole</span>   <span class="mf">0.630</span>   <span class="mf">0.670</span>
-<span class="n">pair_coeff</span>    <span class="mi">3</span>    <span class="mi">6</span> <span class="n">thole</span>   <span class="mf">0.829</span>   <span class="mf">1.590</span>
-<span class="n">pair_coeff</span>    <span class="mi">3</span>    <span class="mi">7</span> <span class="n">thole</span>   <span class="mf">0.926</span>   <span class="mf">1.590</span>
-<span class="n">pair_coeff</span>    <span class="mi">3</span>    <span class="mi">8</span> <span class="n">thole</span>   <span class="mf">0.630</span>   <span class="mf">0.670</span>
-<span class="n">pair_coeff</span>    <span class="mi">6</span>    <span class="mi">6</span> <span class="n">thole</span>   <span class="mf">1.090</span>   <span class="mf">2.510</span>
-<span class="n">pair_coeff</span>    <span class="mi">6</span>    <span class="mi">7</span> <span class="n">thole</span>   <span class="mf">1.218</span>   <span class="mf">2.510</span>
-<span class="n">pair_coeff</span>    <span class="mi">6</span>    <span class="mi">8</span> <span class="n">thole</span>   <span class="mf">0.829</span>   <span class="mf">1.590</span>
-<span class="n">pair_coeff</span>    <span class="mi">7</span>    <span class="mi">7</span> <span class="n">thole</span>   <span class="mf">1.360</span>   <span class="mf">2.510</span>
-<span class="n">pair_coeff</span>    <span class="mi">7</span>    <span class="mi">8</span> <span class="n">thole</span>   <span class="mf">0.926</span>   <span class="mf">1.590</span>
-<span class="n">pair_coeff</span>    <span class="mi">8</span>    <span class="mi">8</span> <span class="n">thole</span>   <span class="mf">0.630</span>   <span class="mf">0.670</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff    1    1 lj/cut/coul/long    0.0700   3.550
+pair_coeff    1    2 lj/cut/coul/long    0.0700   3.550
+pair_coeff    1    3 lj/cut/coul/long    0.1091   3.310
+pair_coeff    1    4 lj/cut/coul/long    0.0458   2.985
+pair_coeff    2    2 lj/cut/coul/long    0.0700   3.550
+pair_coeff    2    3 lj/cut/coul/long    0.1091   3.310
+pair_coeff    2    4 lj/cut/coul/long    0.0458   2.985
+pair_coeff    3    3 lj/cut/coul/long    0.1700   3.070
+pair_coeff    3    4 lj/cut/coul/long    0.0714   2.745
+pair_coeff    4    4 lj/cut/coul/long    0.0300   2.420
+pair_coeff    *    5 lj/cut/coul/long    0.0000   0.000
+pair_coeff    *   6* lj/cut/coul/long    0.0000   0.000
+pair_coeff    1    1 thole   1.090   2.510
+pair_coeff    1    2 thole   1.218   2.510
+pair_coeff    1    3 thole   0.829   1.590
+pair_coeff    1    6 thole   1.090   2.510
+pair_coeff    1    7 thole   1.218   2.510
+pair_coeff    1    8 thole   0.829   1.590
+pair_coeff    2    2 thole   1.360   2.510
+pair_coeff    2    3 thole   0.926   1.590
+pair_coeff    2    6 thole   1.218   2.510
+pair_coeff    2    7 thole   1.360   2.510
+pair_coeff    2    8 thole   0.926   1.590
+pair_coeff    3    3 thole   0.630   0.670
+pair_coeff    3    6 thole   0.829   1.590
+pair_coeff    3    7 thole   0.926   1.590
+pair_coeff    3    8 thole   0.630   0.670
+pair_coeff    6    6 thole   1.090   2.510
+pair_coeff    6    7 thole   1.218   2.510
+pair_coeff    6    8 thole   0.829   1.590
+pair_coeff    7    7 thole   1.360   2.510
+pair_coeff    7    8 thole   0.926   1.590
+pair_coeff    8    8 thole   0.630   0.670
+</pre>
 <p>For the <em>thole</em> pair style the coefficients are</p>
 <ol class="arabic simple">
 <li>the atom polarizability in units of cubic length</li>
 <li>the screening factor of the Thole function (optional, default value
 specified by the pair_style command)</li>
-</ol>
-<ul class="simple">
 <li>the cutoff (optional, default value defined by the pair_style command)</li>
-</ul>
+</ol>
 <p>The special neighbors have charge-charge and charge-dipole
 interactions screened by the <em>coul</em> factors of the <em>special_bonds</em>
 command (0.0, 0.0, and 0.5 in the example above).  Without using the
@@ -458,14 +456,14 @@ We do want the pressure to correspond to the whole system, but we want
 the temperature to correspond to the fix group only.  We must then use
 the <em>fix_modify</em> command for this.  In the end, the block of
 instructions for thermostating and barostating will look like</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">TATOMS</span> <span class="n">ATOMS</span> <span class="n">temp</span>
-<span class="n">fix</span> <span class="n">DIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
-<span class="n">fix</span> <span class="n">NPT</span> <span class="n">ATOMS</span> <span class="n">npt</span> <span class="n">temp</span> <span class="mf">300.</span> <span class="mf">300.</span> <span class="mi">100</span> <span class="n">iso</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">500</span>
-<span class="n">fix_modify</span> <span class="n">NPT</span> <span class="n">temp</span> <span class="n">TATOMS</span> <span class="n">press</span> <span class="n">thermo_press</span>
-<span class="n">fix</span> <span class="n">NVT</span> <span class="n">DRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">20</span>
-<span class="n">fix</span> <span class="n">INVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute TATOMS ATOMS temp
+fix DIRECT all drude/transform/direct
+fix NPT ATOMS npt temp 300. 300. 100 iso 1. 1. 500
+fix_modify NPT temp TATOMS press thermo_press
+fix NVT DRUDES nvt temp 1. 1. 20
+fix INVERSE all drude/transform/inverse
+</pre>
 <hr class="docutils" />
 <p><strong>Rigid bodies</strong></p>
 <p>You may want to simulate molecules as rigid bodies (but polarizable).
@@ -474,12 +472,12 @@ kind of polarizable TIP4P water.  The rigid bodies and the DPs should
 be integrated separately, even with the Langevin thermostat.  Let us
 review the different thermostats and ensemble combinations.</p>
 <p>NVT ensemble using Langevin thermostat:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
-<span class="n">fix</span> <span class="n">LANG</span> <span class="nb">all</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="mf">300.</span> <span class="mi">100</span> <span class="mi">12435</span> <span class="mf">1.</span> <span class="mi">20</span> <span class="mi">13977</span>
-<span class="n">fix</span> <span class="n">RIGID</span> <span class="n">ATOMS</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nve</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span>
-<span class="n">fix</span> <span class="n">NVE</span> <span class="n">DRUDES</span> <span class="n">nve</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+comm_modify vel yes
+fix LANG all langevin/drude 300. 100 12435 1. 20 13977
+fix RIGID ATOMS rigid/nve/small molecule
+fix NVE DRUDES nve
+</pre>
 <p>NVT ensemble using Nose-Hoover thermostat:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">DIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
 <span class="n">fix</span> <span class="n">RIGID</span> <span class="n">ATOMS</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nvt</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">300.</span> <span class="mf">300.</span> <span class="mi">100</span>
@@ -488,21 +486,21 @@ review the different thermostats and ensemble combinations.</p>
 </pre></div>
 </div>
 <p>NPT ensemble with Langevin thermostat:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
-<span class="n">fix</span> <span class="n">LANG</span> <span class="nb">all</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="mf">300.</span> <span class="mi">100</span> <span class="mi">12435</span> <span class="mf">1.</span> <span class="mi">20</span> <span class="mi">13977</span>
-<span class="n">fix</span> <span class="n">RIGID</span> <span class="n">ATOMS</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nph</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">iso</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">500</span>
-<span class="n">fix</span> <span class="n">NVE</span> <span class="n">DRUDES</span> <span class="n">nve</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+comm_modify vel yes
+fix LANG all langevin/drude 300. 100 12435 1. 20 13977
+fix RIGID ATOMS rigid/nph/small molecule iso 1. 1. 500
+fix NVE DRUDES nve
+</pre>
 <p>NPT ensemble using Nose-Hoover thermostat:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">TATOM</span> <span class="n">ATOMS</span> <span class="n">temp</span>
-<span class="n">fix</span> <span class="n">DIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
-<span class="n">fix</span> <span class="n">RIGID</span> <span class="n">ATOMS</span> <span class="n">rigid</span><span class="o">/</span><span class="n">npt</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">300.</span> <span class="mf">300.</span> <span class="mi">100</span> <span class="n">iso</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">500</span>
-<span class="n">fix_modify</span> <span class="n">RIGID</span> <span class="n">temp</span> <span class="n">TATOM</span> <span class="n">press</span> <span class="n">thermo_press</span>
-<span class="n">fix</span> <span class="n">NVT</span> <span class="n">DRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mi">20</span>
-<span class="n">fix</span> <span class="n">INVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute TATOM ATOMS temp
+fix DIRECT all drude/transform/direct
+fix RIGID ATOMS rigid/npt/small molecule temp 300. 300. 100 iso 1. 1. 500
+fix_modify RIGID temp TATOM press thermo_press
+fix NVT DRUDES nvt temp 1. 1. 20
+fix INVERSE all drude/transform/inverse
+</pre>
 <hr class="docutils" />
 <p id="lamoureux"><strong>(Lamoureux)</strong> Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)</p>
 <p id="schroeder"><strong>(Schroeder)</strong>  Schroeder and Steinhauser, J Chem Phys, 133,
diff --git a/doc/html/tutorial_github.html b/doc/html/tutorial_github.html
index e6170b8961..ad4a731ba8 100644
--- a/doc/html/tutorial_github.html
+++ b/doc/html/tutorial_github.html
@@ -135,14 +135,14 @@ git. You may want to have a look at the <a class="reference external" href="http
 <p><strong>Making an account</strong></p>
 <p>First of all, you need a GitHub account. This is fairly simple, just
 go to <a class="reference external" href="https://github.com">GitHub</a> and create an account by clicking
-the <a href="#id1"><span class="problematic" id="id2">``</span></a>Sign up for GitHub&#8217;&#8217; button. Once your account is created, you
+the &#8220;Sign up for GitHub&#8221; button. Once your account is created, you
 can sign in by clicking the button in the top left and filling in your
 username or e-mail address and password.</p>
 <hr class="docutils" />
 <p><strong>Forking the repository</strong></p>
 <p>To get changes into LAMMPS, you need to first fork the repository. At
 the time of writing, LAMMPS-ICMS is the preferred fork. Go to <a class="reference external" href="https://github.com/lammps/lammps">LAMMPS on GitHub</a> and make sure branch is
-set to <a href="#id3"><span class="problematic" id="id4">``</span></a>lammps-icms&#8217;&#8216;, see the figure below.</p>
+set to &#8220;lammps-icms&#8221;, see the figure below.</p>
 <img alt="_images/tutorial_branch.png" class="align-center" src="_images/tutorial_branch.png" />
 <p>Now, click on fork in the top right corner:</p>
 <img alt="_images/tutorial_fork.png" class="align-center" src="_images/tutorial_fork.png" />
@@ -158,7 +158,7 @@ will contain these changes, a so-called feature branch.</p>
 <p><strong>Feature branches</strong></p>
 <p>Since LAMMPS is such a big project and most user contributions come in
 small portions, the most ideal workflow for LAMMPS is the so-called
-<a href="#id5"><span class="problematic" id="id6">``</span></a>Feature branch&#8217;&#8217; workflow. It is explained in great detail here:
+&#8220;Feature branch&#8221; workflow. It is explained in great detail here:
 <a class="reference external" href="https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow">feature branch workflow</a>.</p>
 <p>The idea is that every new feature for LAMMPS gets its own
 branch. This way, it is fairly painless to incorporate new features
@@ -172,7 +172,7 @@ to use a command line.</p>
 </div>
 <p>You can find the proper url to the right of the &#8220;HTTPS&#8221; block, see figure.</p>
 <img alt="_images/tutorial_https_block.png" class="align-center" src="_images/tutorial_https_block.png" />
-<p>The above command copies (<a href="#id7"><span class="problematic" id="id8">``</span></a>clones&#8217;&#8216;) the git repository to your local
+<p>The above command copies (&#8220;clones&#8221;) the git repository to your local
 machine. You can use this local clone to make changes and test them
 without interfering with the repository on github. First, however, it
 is recommended to make a new branch for a particular feature you would
@@ -192,7 +192,7 @@ you should switch branches!</p>
 <p>After everything is done, add the files to the branch and commit them:</p>
 <pre class="literal-block">
 $ git add src/USER-MANIFOLD examples/USER/manifold/
-$ git add doc/fix_nv<em>t,e</em>_manifold_rattle.txt
+$ git add doc/fix_nv{t,e}_manifold_rattle.txt
 $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt
 </pre>
 <p>After the files are added, the change should be comitted:</p>
@@ -203,14 +203,14 @@ $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt
 indicate what type of change was commited.</p>
 <p><strong>Wisdom by Axel</strong></p>
 <p><em>&#8220;Do not use &#8220;git commit -a&#8221;.  the -a flag will automatically include
-*all</em> modified or new files.  mercurial does that and it find it
+*all* modified or new files.  mercurial does that and it find it
 hugely annoying and often leading to accidental commits of files you
 don&#8217;t want.  use git add, git rm, git mv for adding, removing,
 renaming and then git commit to finalize the commit.  personally, i
 find it very convenient to use the bundled gui for commits, i.e. git
 gui.  typically, i will do git add and other operations, but then
 verify and review them with git gui.  git gui also allows to do
-line-by-line unstaging and other convenient operations.&#8221;*</p>
+line-by-line unstaging and other convenient operations.&#8221;</em></p>
 <p>After the commit, the changes can be pushed to the same branch on GitHub:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span>$ git push
 </pre></div>
@@ -234,7 +234,7 @@ branch. GitHub will now look like this:</p>
 this case, is &#8220;add-user-manifold&#8221;. Now click &#8220;New pull request&#8221;. If
 done correctly, the only changes you will see are those that were made
 on this branch, so in my case, I will see nothing related to
-$mathrm*pair_dzugatov*.$</p>
+$mathrm*pair\_dzugatov*.$</p>
 <p>This will open up a new window that lists changes made to the
 repository. If you are just adding new files, there is not much to do,
 but I suppose merge conflicts are to be resolved here if there are
diff --git a/doc/html/units.html b/doc/html/units.html
index 9dc8285c6d..e80e207a23 100644
--- a/doc/html/units.html
+++ b/doc/html/units.html
@@ -187,7 +187,7 @@ results from a unitless LJ simulation into physical quantities.</p>
 <li>pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon</li>
 <li>dynamic viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau</li>
 <li>charge = reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)^1/2</li>
-<li>dipole = reduced LJ dipole, moment where <a href="#id1"><span class="problematic" id="id2">*</span></a>mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2</li>
+<li>dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2</li>
 <li>electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon</li>
 <li>density = mass/volume, where rho* = rho sigma^dim</li>
 </ul>
diff --git a/doc/html/variable.html b/doc/html/variable.html
index f5eb258506..f7fd72fac0 100644
--- a/doc/html/variable.html
+++ b/doc/html/variable.html
@@ -197,7 +197,8 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable x index run1 run2 run3 run4 run5 run6 run7 run8
+<pre class="literal-block">
+variable x index run1 run2 run3 run4 run5 run6 run7 run8
 variable LoopVar loop $n
 variable beta equal temp/3.0
 variable b1 equal x[234]+0.5*vol
@@ -214,8 +215,7 @@ variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
 variable x uloop 15 pad
 variable str format x %.6g
 variable x delete
-</pre></div>
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -470,10 +470,10 @@ appear in the set, will remain 0.0.</p>
 to match a function name specified in a <a class="reference internal" href="python.html"><span class="doc">python</span></a> command
 which returns a value to this variable as defined by its <em>return</em>
 keyword.  For example these two commands would be self-consistent:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">foo</span> <span class="n">python</span> <span class="n">myMultiply</span>
-<span class="n">python</span> <span class="n">myMultiply</span> <span class="k">return</span> <span class="n">v_foo</span> <span class="nb">format</span> <span class="n">f</span> <span class="n">file</span> <span class="n">funcs</span><span class="o">.</span><span class="n">py</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable foo python myMultiply
+python myMultiply return v_foo format f file funcs.py
+</pre>
 <p>The two commands can appear in either order so long as both are
 specified before the Python function is invoked for the first time.</p>
 <p>Each time the variable is evaluated, the associated Python function is
@@ -527,9 +527,9 @@ variety of quantities.  The syntax for each kind of quantity is
 simple, but multiple quantities can be nested and combined in various
 ways to build up formulas of arbitrary complexity.  For example, this
 is a valid (though strange) variable formula:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">x</span> <span class="n">equal</span> <span class="s2">&quot;pe + c_MyTemp / vol^(1/3)&quot;</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable x equal &quot;pe + c_MyTemp / vol^(1/3)&quot;
+</pre>
 <p>Specifically, a formula can contain numbers, constants, thermo
 keywords, math operators, math functions, group functions, region
 functions, atom values, atom vectors, compute references, fix
@@ -618,9 +618,9 @@ of LAMMPS will be smaller. This can be used to have input scripts
 adapt automatically to LAMMPS versions, when non-backwards compatible
 syntax changes are introduced. Here is an illustrative example (which
 will not work, since the <em>version</em> has been introduced more recently):</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>if $(version&lt;20140513) then &quot;communicate vel yes&quot; else &quot;comm_modify vel yes&quot;
-</pre></div>
-</div>
+<pre class="literal-block">
+if $(version&lt;20140513) then &quot;communicate vel yes&quot; else &quot;comm_modify vel yes&quot;
+</pre>
 <p>The thermo keywords allowed in a formula are those defined by the
 <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command.  Thermo keywords that
 require a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> to calculate their values such as
@@ -719,9 +719,9 @@ is the nearest integer to its argument.</p>
 <p>The ramp(x,y) function uses the current timestep to generate a value
 linearly intepolated between the specified x,y values over the course
 of a run, according to this formula:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">value</span> <span class="o">=</span> <span class="n">x</span> <span class="o">+</span> <span class="p">(</span><span class="n">y</span><span class="o">-</span><span class="n">x</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">timestep</span><span class="o">-</span><span class="n">startstep</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">stopstep</span><span class="o">-</span><span class="n">startstep</span><span class="p">)</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)
+</pre>
 <p>The run begins on startstep and ends on stopstep.  Startstep and
 stopstep can span multiple runs, using the <em>start</em> and <em>stop</em> keywords
 of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.  See the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command for
@@ -790,9 +790,9 @@ sequence of output timesteps:</p>
 velocity, and uses the elapsed time to change the value by a linear
 displacement due to the applied velocity over the course of a run,
 according to this formula:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">value</span> <span class="o">=</span> <span class="n">value0</span> <span class="o">+</span> <span class="n">velocity</span><span class="o">*</span><span class="p">(</span><span class="n">timestep</span><span class="o">-</span><span class="n">startstep</span><span class="p">)</span><span class="o">*</span><span class="n">dt</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+value = value0 + velocity*(timestep-startstep)*dt
+</pre>
 <p>where dt = the timestep size.</p>
 <p>The run begins on startstep.  Startstep can span multiple runs, using
 the <em>start</em> keyword of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.  See the
@@ -803,10 +803,10 @@ timestep-startstep.</p>
 x = value0, y = amplitude, z = period.  They use the elapsed time to
 oscillate the value by a sin() or cos() function over the course of a
 run, according to one of these formulas, where omega = 2 PI / period:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">value</span> <span class="o">=</span> <span class="n">value0</span> <span class="o">+</span> <span class="n">Amplitude</span> <span class="o">*</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="p">(</span><span class="n">timestep</span><span class="o">-</span><span class="n">startstep</span><span class="p">)</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
-<span class="n">value</span> <span class="o">=</span> <span class="n">value0</span> <span class="o">+</span> <span class="n">Amplitude</span> <span class="o">*</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="p">(</span><span class="n">timestep</span><span class="o">-</span><span class="n">startstep</span><span class="p">)</span><span class="o">*</span><span class="n">dt</span><span class="p">))</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt)
+value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt))
+</pre>
 <p>where dt = the timestep size.</p>
 <p>The run begins on startstep.  Startstep can span multiple runs, using
 the <em>start</em> keyword of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.  See the
@@ -952,16 +952,16 @@ features or LAMMPS, <em>respa</em> allows to check whether the inner/middle/oute
 mode of r-RESPA is supported. In the various style categories,
 the checking is also done using suffix flags, if available and enabled.</p>
 <p>Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP).</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>pair_style lj/cut/coul/long 14.0
+<pre class="literal-block">
+pair_style lj/cut/coul/long 14.0
 if $(is_active(package,gpu)) then &quot;suffix off&quot;
 kspace_style pppm
-</pre></div>
-</div>
+</pre>
 <p>Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>timestep $(2.0*(1.0+*is_active(pair,respa))
+<pre class="literal-block">
+timestep $(2.0*(1.0+*is_active(pair,respa))
 if $(is_active(pair,respa)) then &quot;run_style respa 4 3 2 2  improper 1 inner 2 5.5 7.0 outer 3 kspace 4&quot; else &quot;run_style respa 3 3 2  improper 1 pair 2 kspace 3&quot;
-</pre></div>
-</div>
+</pre>
 <p>The <em>is_defined()</em> function allows to query categories like <em>compute</em>,
 <em>dump</em>, <em>fix</em>, <em>group</em>, <em>region</em>, and <em>variable</em> whether an entry
 with the provided name or id is defined.</p>
@@ -1022,8 +1022,8 @@ reference means, since computes only produce either global or per-atom
 quantities, never both.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="10%" />
-<col width="90%" />
+<col width="11%" />
+<col width="89%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>c_ID</td>
@@ -1046,9 +1046,9 @@ variable refers to a compute that produces both a global scalar and a
 global vector.  Consider a compute with ID &#8220;foo&#8221; that does this,
 referenced as follows by variable &#8220;a&#8221;, where &#8220;myVec&#8221; is another
 vector-style variable:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">a</span> <span class="n">vector</span> <span class="n">c_foo</span><span class="o">*</span><span class="n">v_myVec</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+variable a vector c_foo*v_myVec
+</pre>
 <p>The reference &#8220;c_foo&#8221; could refer to either the global scalar or
 global vector produced by compute &#8220;foo&#8221;.  In this case, &#8220;c_foo&#8221; will
 always refer to the global scalar, and &#8220;C_foo&#8221; can be used to
@@ -1077,14 +1077,14 @@ vector values.  A vector value can be a per-atom vector itself, or a
 column of an per-atom array.  See the doc pages for individual fixes
 to see what kind of values they produce.</p>
 <p>The different kinds of fix references are exactly the same as the
-compute references listed in the above table, where &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221; is replaced
-by &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;.  Again, there is typically no ambiguity (see exception below)
+compute references listed in the above table, where &#8220;c_&#8221; is replaced
+by &#8220;f_&#8221;.  Again, there is typically no ambiguity (see exception below)
 as to what a reference means, since fixes only produce either global
 or per-atom quantities, never both.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="10%" />
-<col width="90%" />
+<col width="11%" />
+<col width="89%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>f_ID</td>
@@ -1152,8 +1152,8 @@ There is no ambiguity as to what a reference means, since variables
 produce only a global scalar or global vector or per-atom vector.</p>
 <table border="1" class="docutils">
 <colgroup>
-<col width="14%" />
-<col width="86%" />
+<col width="15%" />
+<col width="85%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>v_name</td>
@@ -1188,7 +1188,7 @@ same syntax as equal-style variables described on this page.  This
 effectively evaluates a formula immediately without using the variable
 command to define a named variable.</p>
 <p>More generally, there is a difference between referencing a variable
-with a leading $ sign (e.g. $x or ${abc}) versus with a leading &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;
+with a leading $ sign (e.g. $x or ${abc}) versus with a leading &#8220;v_&#8221;
 (e.g. v_x or v_abc).  The former can be used in any input script
 command, including a variable command.  The input script parser
 evaluates the reference variable immediately and substitutes its value
@@ -1197,7 +1197,7 @@ un-named &#8220;immediate&#8221; variables for this purpose.  For example, a
 string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
 command evaluates the string between the parenthesis as an equal-style
 variable formula.</p>
-<p>Referencing a variable with a leading &#8220;<a href="#id7"><span class="problematic" id="id8">v_</span></a>&#8221; is an optional or required
+<p>Referencing a variable with a leading &#8220;v_&#8221; is an optional or required
 kind of argument for some commands (e.g. the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> or <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> or
 <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> commands) if you wish it to evaluate
 a variable periodically during a run.  It can also be used in a
@@ -1224,9 +1224,9 @@ variable v0 equal $v
 <p>The second command will force &#8220;v&#8221; to be evaluated (yielding the
 initial volume) and assign that value to the variable &#8220;v0&#8221;.  Thus the
 command</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">v_v</span> <span class="n">v_v0</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+thermo_style custom step v_v v_v0
+</pre>
 <p>would print out both the current and initial volume periodically
 during the run.</p>
 <p>Note that it is a mistake to enclose a variable formula in double
@@ -1317,13 +1317,13 @@ a 0-timestep run before printing the variable has the desired effect.</p>
 <p>(3) The variable may be evaluated incorrectly and LAMMPS may have no
 way to detect this has occurred.  Consider the following sequence of
 commands:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">run</span> <span class="mi">1000</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.5</span> <span class="mf">1.0</span>
-<span class="n">variable</span> <span class="n">e</span> <span class="n">equal</span> <span class="n">pe</span>
-<span class="nb">print</span> <span class="s2">&quot;Final potential energy = $e&quot;</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff 1 1 1.0 1.0
+run 1000
+pair_coeff 1 1 1.5 1.0
+variable e equal pe
+print &quot;Final potential energy = $e&quot;
+</pre>
 <p>The first run is performed using one setting for the pairwise
 potential defined by the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> and
 <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> commands.  The potential energy is
@@ -1340,14 +1340,14 @@ perform a 0-timestep run before the variable is evaluated to insure
 the system is up-to-date.  For example, this sequence of commands
 would print a potential energy that reflected the changed pairwise
 coefficient:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
-<span class="n">run</span> <span class="mi">1000</span>
-<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.5</span> <span class="mf">1.0</span>
-<span class="n">run</span> <span class="mi">0</span>
-<span class="n">variable</span> <span class="n">e</span> <span class="n">equal</span> <span class="n">pe</span>
-<span class="nb">print</span> <span class="s2">&quot;Final potential energy = $e&quot;</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+pair_coeff 1 1 1.0 1.0
+run 1000
+pair_coeff 1 1 1.5 1.0
+run 0
+variable e equal pe
+print &quot;Final potential energy = $e&quot;
+</pre>
 </div>
 </div>
 <hr class="docutils" />
diff --git a/doc/html/velocity.html b/doc/html/velocity.html
index 06accf9593..af9be7196c 100644
--- a/doc/html/velocity.html
+++ b/doc/html/velocity.html
@@ -172,13 +172,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">velocity</span> <span class="nb">all</span> <span class="n">create</span> <span class="mf">300.0</span> <span class="mi">4928459</span> <span class="n">rot</span> <span class="n">yes</span> <span class="n">dist</span> <span class="n">gaussian</span>
-<span class="n">velocity</span> <span class="n">border</span> <span class="nb">set</span> <span class="n">NULL</span> <span class="mf">4.0</span> <span class="n">v_vz</span> <span class="nb">sum</span> <span class="n">yes</span> <span class="n">units</span> <span class="n">box</span>
-<span class="n">velocity</span> <span class="n">flow</span> <span class="n">scale</span> <span class="mf">300.0</span>
-<span class="n">velocity</span> <span class="n">flow</span> <span class="n">ramp</span> <span class="n">vx</span> <span class="mf">0.0</span> <span class="mf">5.0</span> <span class="n">y</span> <span class="mi">5</span> <span class="mi">25</span> <span class="n">temp</span> <span class="n">mytemp</span>
-<span class="n">velocity</span> <span class="nb">all</span> <span class="n">zero</span> <span class="n">linear</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+velocity all create 300.0 4928459 rot yes dist gaussian
+velocity border set NULL 4.0 v_vz sum yes units box
+velocity flow scale 300.0
+velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
+velocity all zero linear
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -244,7 +244,7 @@ replace them if sum = no.</p>
 <p>The <em>mom</em> and <em>rot</em> keywords are used by <em>create</em>.  If mom = yes, the
 linear momentum of the newly created ensemble of velocities is zeroed;
 if rot = yes, the angular momentum is zeroed.</p>
-<p><a href="#id1"><span class="problematic" id="id2">*</span></a>line</p>
+<p>*line</p>
 <p>If specified, the <em>temp</em> keyword is used by <em>create</em> and <em>scale</em> to
 specify a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> that calculates temperature in a
 desired way, e.g. by first subtracting out a velocity bias, as
@@ -252,9 +252,9 @@ discussed in <a class="reference internal" href="Section_howto.html#howto-15"><s
 pages.  If this keyword is not specified, <em>create</em> and <em>scale</em>
 calculate temperature using a compute that is defined internally as
 follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">velocity_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+compute velocity_temp group-ID temp
+</pre>
 <p>where group-ID is the same ID used in the velocity command. i.e. the
 group of atoms whose velocity is being altered.  This compute is
 deleted when the velocity command is finished.  See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details.  If the calculated
diff --git a/doc/html/write_coeff.html b/doc/html/write_coeff.html
index 1698ec2615..d4d15e1ddf 100644
--- a/doc/html/write_coeff.html
+++ b/doc/html/write_coeff.html
@@ -128,18 +128,18 @@
 <span id="index-0"></span><h1>write_coeff command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">write_coeff</span> <span class="n">file</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+write_coeff file
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">file</span> <span class="o">=</span> <span class="n">name</span> <span class="n">of</span> <span class="n">data</span> <span class="n">file</span> <span class="n">to</span> <span class="n">write</span> <span class="n">out</span>
 </pre></div>
 </div>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">write_coeff</span> <span class="n">polymer</span><span class="o">.</span><span class="n">coeff</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+write_coeff polymer.coeff
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
diff --git a/doc/html/write_dump.html b/doc/html/write_dump.html
index 413887f469..0fcd373eb7 100644
--- a/doc/html/write_dump.html
+++ b/doc/html/write_dump.html
@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>write_dump command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">write_dump</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">file</span> <span class="n">dump</span><span class="o">-</span><span class="n">args</span> <span class="n">modify</span> <span class="n">dump_modify</span><span class="o">-</span><span class="n">args</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+write_dump group-ID style file dump-args modify dump_modify-args
+</pre>
 <ul class="simple">
 <li>group-ID = ID of the group of atoms to be dumped</li>
 <li>style = any of the supported <a class="reference internal" href="dump.html"><span class="doc">dump styles</span></a></li>
@@ -142,17 +142,17 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">write_dump</span> <span class="nb">all</span> <span class="n">atom</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span>
-<span class="n">write_dump</span> <span class="n">subgroup</span> <span class="n">atom</span> <span class="n">dump</span><span class="o">.</span><span class="n">run</span><span class="o">.</span><span class="n">bin</span>
-<span class="n">write_dump</span> <span class="nb">all</span> <span class="n">custom</span> <span class="n">dump</span><span class="o">.</span><span class="n">myforce</span><span class="o">.*</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">x</span> <span class="n">y</span> <span class="n">vx</span> <span class="n">fx</span>
-<span class="n">write_dump</span> <span class="n">flow</span> <span class="n">custom</span> <span class="n">dump</span><span class="o">.%.</span><span class="n">myforce</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myF</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">v_ke</span> <span class="n">modify</span> <span class="n">sort</span> <span class="nb">id</span>
-<span class="n">write_dump</span> <span class="nb">all</span> <span class="n">xyz</span> <span class="n">system</span><span class="o">.</span><span class="n">xyz</span> <span class="n">modify</span> <span class="n">sort</span> <span class="nb">id</span> <span class="n">elements</span> <span class="n">O</span> <span class="n">H</span>
-<span class="n">write_dump</span> <span class="nb">all</span> <span class="n">image</span> <span class="n">snap</span><span class="o">*.</span><span class="n">jpg</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">size</span> <span class="mi">960</span> <span class="mi">960</span> <span class="n">modify</span> <span class="n">backcolor</span> <span class="n">white</span>
-<span class="n">write_dump</span> <span class="nb">all</span> <span class="n">image</span> <span class="n">snap</span><span class="o">*.</span><span class="n">jpg</span> <span class="n">element</span> <span class="n">element</span> <span class="o">&amp;</span>
-   <span class="n">bond</span> <span class="n">atom</span> <span class="mf">0.3</span> <span class="n">shiny</span> <span class="mf">0.1</span> <span class="n">ssao</span> <span class="n">yes</span> <span class="mi">6345</span> <span class="mf">0.2</span> <span class="n">size</span> <span class="mi">1600</span> <span class="mi">1600</span>  <span class="o">&amp;</span>
-   <span class="n">modify</span> <span class="n">backcolor</span> <span class="n">white</span> <span class="n">element</span> <span class="n">C</span> <span class="n">C</span> <span class="n">O</span> <span class="n">H</span> <span class="n">N</span> <span class="n">C</span> <span class="n">C</span> <span class="n">C</span> <span class="n">O</span> <span class="n">H</span> <span class="n">H</span> <span class="n">S</span> <span class="n">O</span> <span class="n">H</span>
-</pre></div>
-</div>
+<pre class="literal-block">
+write_dump all atom dump.atom
+write_dump subgroup atom dump.run.bin
+write_dump all custom dump.myforce.* id type x y vx fx
+write_dump flow custom dump.%.myforce id type c_myF[3] v_ke modify sort id
+write_dump all xyz system.xyz modify sort id elements O H
+write_dump all image snap*.jpg type type size 960 960 modify backcolor white
+write_dump all image snap*.jpg element element &amp;
+   bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600  &amp;
+   modify backcolor white element C C O H N C C C O H H S O H
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
-- 
GitLab


From 346ff4249833619793efda918f5bc18b7fc5d0ba Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Sep 2016 10:10:12 -0400
Subject: [PATCH 28/52] correct reference in modify section

---
 doc/src/Section_modify.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt
index a3ac505946..d5657c7db6 100644
--- a/doc/src/Section_modify.txt
+++ b/doc/src/Section_modify.txt
@@ -21,7 +21,7 @@ and extending its source code.
 10.6 "Fix styles"_#mod_6 which include integrators, \
      temperature and pressure control, force constraints, \
      boundary conditions, diagnostic output, etc
-10.7 "Input script commands"_mod_7
+10.7 "Input script commands"_#mod_7
 10.8 "Kspace computations"_#mod_8
 10.9 "Minimization styles"_#mod_9
 10.10 "Pairwise potentials"_#mod_10
-- 
GitLab


From 0fe7d1d3612cac3cee27ef0c9d2939f20fa65395 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 7 Sep 2016 10:13:34 -0400
Subject: [PATCH 29/52] correct internal links for Modify LAMMPS section

---
 doc/html/Section_modify.html | 4 ++--
 doc/src/Section_modify.txt   | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/html/Section_modify.html b/doc/html/Section_modify.html
index 41c466042e..b760c3c002 100644
--- a/doc/html/Section_modify.html
+++ b/doc/html/Section_modify.html
@@ -1040,7 +1040,7 @@ compute values = c_mytemp[0], c_thermo_press[3], ...
 </pre>
 <p>Adding keywords for the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command
 (which can then be accessed by variables) was discussed
-<a class="reference internal" href="Section_howto.html#thermo"><span class="std std-ref">here</span></a> on this page.</p>
+<a class="reference internal" href="#mod-13"><span class="std std-ref">here</span></a> on this page.</p>
 <p>Adding a new math function of one or two arguments can be done by
 editing one section of the Variable::evaulate() method.  Search for
 the word &#8220;customize&#8221; to find the appropriate location.</p>
@@ -1053,7 +1053,7 @@ of the Variable::evaulate() method.  Search for the word &#8220;customize&#8221;
 to find the appropriate location.</p>
 <p>Adding new <a class="reference internal" href="compute.html"><span class="doc">compute styles</span></a> (whose calculated values can
 then be accessed by variables) was discussed
-<a class="reference internal" href="Section_howto.html#compute"><span class="std std-ref">here</span></a> on this page.</p>
+<a class="reference internal" href="#mod-3"><span class="std std-ref">here</span></a> on this page.</p>
 </div>
 <div class="section" id="submitting-new-features-for-inclusion-in-lammps">
 <span id="mod-15"></span><h2>10.15. Submitting new features for inclusion in LAMMPS</h2>
diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt
index d5657c7db6..67b38d6936 100644
--- a/doc/src/Section_modify.txt
+++ b/doc/src/Section_modify.txt
@@ -598,7 +598,7 @@ compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre
 
 Adding keywords for the "thermo_style custom"_thermo_style.html command
 (which can then be accessed by variables) was discussed
-"here"_Section_modify.html#thermo on this page.
+"here"_Section_modify.html#mod_13 on this page.
 
 Adding a new math function of one or two arguments can be done by
 editing one section of the Variable::evaulate() method.  Search for
@@ -615,7 +615,7 @@ to find the appropriate location.
 
 Adding new "compute styles"_compute.html (whose calculated values can
 then be accessed by variables) was discussed
-"here"_Section_modify.html#compute on this page.
+"here"_Section_modify.html#mod_3 on this page.
 
 :line
 :line
-- 
GitLab


From 06e3a11c2dd52dc7935027b28086fda9f8f63a25 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 14:28:32 -0400
Subject: [PATCH 30/52] Add styles output to info command

Adds the ability to list all available styles in LAMMPS with:

```
info styles
```

Each style can also be printed separately using one of the following:

```
info atom_styles
info integrate_styles
info minimize_styles
info pair_styles
info bond_styles
info angle_styles
info dihedral_styles
info improper_styles
info kspace_styles
info fix_styles
info compute_styles
info region_styles
info dump_styles
```
---
 src/info.cpp | 332 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 src/info.h   |  18 +++
 2 files changed, 345 insertions(+), 5 deletions(-)

diff --git a/src/info.cpp b/src/info.cpp
index a791becf0e..0e8136278d 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -1,4 +1,5 @@
 /* ----------------------------------------------------------------------
+  fputs
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -12,7 +13,8 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing author:  Axel Kohlmeyer (Temple U)
+   Contributing authors:  Axel Kohlmeyer (Temple U),
+                          Richard Berger (Temple U)
 ------------------------------------------------------------------------- */
 
 #include <string.h>
@@ -39,6 +41,9 @@
 #include "error.h"
 
 #include <time.h>
+#include <vector>
+#include <string>
+#include <algorithm>
 
 #ifdef _WIN32
 #define PSAPI_VERSION=1
@@ -70,9 +75,29 @@ enum {COMPUTES=1<<0,
       VARIABLES=1<<7,
       SYSTEM=1<<8,
       COMM=1<<9,
+      ATOM_STYLES=1<<10,
+      INTEGRATE_STYLES=1<<11,
+      MINIMIZE_STYLES=1<<12,
+      PAIR_STYLES=1<<13,
+      BOND_STYLES=1<<14,
+      ANGLE_STYLES=1<<15,
+      DIHEDRAL_STYLES=1<<16,
+      IMPROPER_STYLES=1<<17,
+      KSPACE_STYLES=1<<18,
+      FIX_STYLES=1<<19,
+      COMPUTE_STYLES=1<<20,
+      REGION_STYLES=1<<21,
+      DUMP_STYLES=1<<22,
+      COMMAND_STYLES=1<<23,
       ALL=~0};
+
+static const int STYLES = ATOM_STYLES | INTEGRATE_STYLES | MINIMIZE_STYLES | PAIR_STYLES | BOND_STYLES | \
+                         ANGLE_STYLES | DIHEDRAL_STYLES | IMPROPER_STYLES | KSPACE_STYLES | FIX_STYLES | \
+                         COMPUTE_STYLES | REGION_STYLES | DUMP_STYLES | COMMAND_STYLES;
+
 }
 
+
 static const char *varstyles[] = {
   "index", "loop", "world", "universe", "uloop", "string", "getenv",
   "file", "atomfile", "format", "equal", "atom", "python", "(unknown)"};
@@ -85,6 +110,9 @@ static const char *commlayout[] = { "uniform", "nonuniform", "irregular" };
 static const char bstyles[] = "pfsm";
 
 using namespace LAMMPS_NS;
+using namespace std;
+
+static void print_columns(FILE* fp, vector<string> & styles);
 
 /* ---------------------------------------------------------------------- */
 
@@ -122,16 +150,58 @@ void Info::command(int narg, char **arg)
       if ((out != screen) && (out != logfile)) fclose(out);
       out = fopen(arg[idx+2],"w");
       idx += 3;
-    } else if (strncmp(arg[idx],"communication",4) == 0) {
+    } else if (strncmp(arg[idx],"atom_styles",3) == 0) {
+      flags |= ATOM_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"integrate_styles",3) == 0) {
+      flags |= INTEGRATE_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"minimize_styles",3) == 0) {
+      flags |= MINIMIZE_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"pair_styles",3) == 0) {
+      flags |= PAIR_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"bond_styles",3) == 0) {
+      flags |= BOND_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"angle_styles",3) == 0) {
+      flags |= ANGLE_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"dihedral_styles",3) == 0) {
+      flags |= DIHEDRAL_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"improper_styles",3) == 0) {
+      flags |= IMPROPER_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"kspace_styles",3) == 0) {
+      flags |= KSPACE_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"fix_styles",3) == 0) {
+      flags |= FIX_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"compute_styles",5) == 0) {
+      flags |= COMPUTE_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"region_styles",3) == 0) {
+      flags |= REGION_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"dump_styles",3) == 0) {
+      flags |= DUMP_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"command_styles",5) == 0) {
+      flags |= COMMAND_STYLES;
+      ++idx;
+    } else if (strncmp(arg[idx],"communication",5) == 0) {
       flags |= COMM;
       ++idx;
-    } else if (strncmp(arg[idx],"computes",4) == 0) {
+    } else if (strncmp(arg[idx],"computes",5) == 0) {
       flags |= COMPUTES;
       ++idx;
-    } else if (strncmp(arg[idx],"dumps",3) == 0) {
+    } else if (strncmp(arg[idx],"dumps",5) == 0) {
       flags |= DUMPS;
       ++idx;
-    } else if (strncmp(arg[idx],"fixes",3) == 0) {
+    } else if (strncmp(arg[idx],"fixes",5) == 0) {
       flags |= FIXES;
       ++idx;
     } else if (strncmp(arg[idx],"groups",3) == 0) {
@@ -152,6 +222,9 @@ void Info::command(int narg, char **arg)
     } else if (strncmp(arg[idx],"system",3) == 0) {
       flags |= SYSTEM;
       ++idx;
+    } else if (strncmp(arg[idx],"styles",3) == 0) {
+      flags |= STYLES;
+      ++idx;
     } else {
       error->warning(FLERR,"Ignoring unknown or incorrect info command flag");
       ++idx;
@@ -457,6 +530,10 @@ void Info::command(int narg, char **arg)
             cpuh,cpum,cpus,wallh,wallm,walls);
   }
 
+  if (flags & STYLES) {
+    available_styles(out, flags);
+  }
+
   fputs("\nInfo-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info\n\n",out);
 
   // close output file pointer if opened locally thus forcing a hard sync.
@@ -464,6 +541,211 @@ void Info::command(int narg, char **arg)
     fclose(out);
 }
 
+
+void Info::available_styles(FILE * out, int flags)
+{
+
+  fprintf(out,"\nStyles information:\n");
+
+  if(flags & ATOM_STYLES)      atom_styles(out);
+  if(flags & INTEGRATE_STYLES) integrate_styles(out);
+  if(flags & MINIMIZE_STYLES)  minimize_styles(out);
+  if(flags & PAIR_STYLES)      pair_styles(out);
+  if(flags & BOND_STYLES)      bond_styles(out);
+  if(flags & ANGLE_STYLES)     angle_styles(out);
+  if(flags & DIHEDRAL_STYLES)  dihedral_styles(out);
+  if(flags & IMPROPER_STYLES)  improper_styles(out);
+  if(flags & KSPACE_STYLES)    kspace_styles(out);
+  if(flags & FIX_STYLES)       fix_styles(out);
+  if(flags & COMPUTE_STYLES)   compute_styles(out);
+  if(flags & REGION_STYLES)    region_styles(out);
+  if(flags & DUMP_STYLES)      dump_styles(out);
+  if(flags & COMMAND_STYLES)   command_styles(out);
+}
+
+void Info::atom_styles(FILE * out)
+{
+  fprintf(out, "\nAtom styles:\n");
+
+  vector<string> styles;
+#define ATOM_CLASS
+#define AtomStyle(key,Class) styles.push_back(#key);
+#include "style_atom.h"
+#undef ATOM_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::integrate_styles(FILE * out)
+{
+  fprintf(out, "\nIntegrate styles:\n");
+
+  vector<string> styles;
+#define INTEGRATE_CLASS
+#define IntegrateStyle(key,Class) styles.push_back(#key);
+#include "style_integrate.h"
+#undef INTEGRATE_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::minimize_styles(FILE * out)
+{
+  fprintf(out, "\nMinimize styles:\n");
+
+  vector<string> styles;
+#define MINIMIZE_CLASS
+#define MinimizeStyle(key,Class) styles.push_back(#key);
+#include "style_minimize.h"
+#undef MINIMIZE_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::pair_styles(FILE * out)
+{
+  fprintf(out, "\nPair styles:\n");
+
+  vector<string> styles;
+#define PAIR_CLASS
+#define PairStyle(key,Class) styles.push_back(#key);
+#include "style_pair.h"
+#undef PAIR_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::bond_styles(FILE * out)
+{
+  fprintf(out, "\nBond styles:\n");
+
+  vector<string> styles;
+#define BOND_CLASS
+#define BondStyle(key,Class) styles.push_back(#key);
+#include "style_bond.h"
+#undef BOND_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::angle_styles(FILE * out)
+{
+  fprintf(out, "\nAngle styles:\n");
+
+  vector<string> styles;
+#define ANGLE_CLASS
+#define AngleStyle(key,Class) styles.push_back(#key);
+#include "style_angle.h"
+#undef ANGLE_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::dihedral_styles(FILE * out)
+{
+  fprintf(out, "\nDihedral styles:\n");
+
+  vector<string> styles;
+#define DIHEDRAL_CLASS
+#define DihedralStyle(key,Class) styles.push_back(#key);
+#include "style_dihedral.h"
+#undef DIHEDRAL_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::improper_styles(FILE * out)
+{
+  fprintf(out, "\nImproper styles:\n");
+
+  vector<string> styles;
+#define IMPROPER_CLASS
+#define ImproperStyle(key,Class) styles.push_back(#key);
+#include "style_improper.h"
+#undef IMPROPER_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::kspace_styles(FILE * out)
+{
+  fprintf(out, "\nKSpace styles:\n");
+
+  vector<string> styles;
+#define KSPACE_CLASS
+#define KSpaceStyle(key,Class) styles.push_back(#key);
+#include "style_kspace.h"
+#undef KSPACE_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::fix_styles(FILE * out)
+{
+  fprintf(out, "\nFix styles:\n");
+
+  vector<string> styles;
+#define FIX_CLASS
+#define FixStyle(key,Class) styles.push_back(#key);
+#include "style_fix.h"
+#undef FIX_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::compute_styles(FILE * out)
+{
+  fprintf(out, "\nCompute styles:\n");
+
+  vector<string> styles;
+#define COMPUTE_CLASS
+#define ComputeStyle(key,Class) styles.push_back(#key);
+#include "style_compute.h"
+#undef COMPUTE_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::region_styles(FILE * out)
+{
+  fprintf(out, "\nRegion styles:\n");
+
+  vector<string> styles;
+#define REGION_CLASS
+#define RegionStyle(key,Class) styles.push_back(#key);
+#include "style_region.h"
+#undef REGION_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::dump_styles(FILE * out)
+{
+  fprintf(out, "\nDump styles:\n");
+
+  vector<string> styles;
+#define DUMP_CLASS
+#define DumpStyle(key,Class) styles.push_back(#key);
+#include "style_dump.h"
+#undef DUMP_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+void Info::command_styles(FILE * out)
+{
+  fprintf(out, "\nCommand styles (add-on input script commands):\n");
+
+  vector<string> styles;
+#define COMMAND_CLASS
+#define CommandStyle(key,Class) styles.push_back(#key);
+#include "style_command.h"
+#undef COMMAND_CLASS
+  print_columns(out, styles);
+  fprintf(out, "\n\n\n");
+}
+
+
 /* ---------------------------------------------------------------------- */
 
 // the is_active() function returns true if the selected style or name
@@ -681,3 +963,43 @@ bool Info::is_defined(const char *category, const char *name)
 
   return false;
 }
+
+static void print_columns(FILE* fp, vector<string> & styles)
+{
+  if (styles.size() == 0) {
+    fprintf(fp, "\nNone");
+    return;
+  }
+
+  std::sort(styles.begin(), styles.end());
+
+  int pos = 80;
+  for (int i = 0; i < styles.size(); ++i) {
+
+    // skip "secret" styles
+    if (isupper(styles[i][0])) continue;
+
+    int len = styles[i].length();
+    if (pos + len > 80) {
+      fprintf(fp,"\n");
+      pos = 0;
+    }
+
+    if (len < 16) {
+      fprintf(fp,"%-16s",styles[i].c_str());
+      pos += 16;
+    } else if (len < 32) {
+      fprintf(fp,"%-32s",styles[i].c_str());
+      pos += 32;
+    } else if (len < 48) {
+      fprintf(fp,"%-48s",styles[i].c_str());
+      pos += 48;
+    } else if (len < 64) {
+      fprintf(fp,"%-64s",styles[i].c_str());
+      pos += 64;
+    } else {
+      fprintf(fp,"%-80s",styles[i].c_str());
+      pos += 80;
+    }
+  }
+}
diff --git a/src/info.h b/src/info.h
index 4a7388d186..f4549badf7 100644
--- a/src/info.h
+++ b/src/info.h
@@ -32,6 +32,24 @@ class Info : protected Pointers {
   bool is_active(const char *, const char *);
   bool is_defined(const char *, const char *);
   bool is_available(const char *, const char *);
+
+private:
+  void available_styles(FILE * out, int flags);
+
+  void atom_styles(FILE * out);
+  void integrate_styles(FILE * out);
+  void minimize_styles(FILE * out);
+  void pair_styles(FILE * out);
+  void bond_styles(FILE * out);
+  void angle_styles(FILE * out);
+  void dihedral_styles(FILE * out);
+  void improper_styles(FILE * out);
+  void kspace_styles(FILE * out);
+  void fix_styles(FILE * out);
+  void compute_styles(FILE * out);
+  void region_styles(FILE * out);
+  void dump_styles(FILE * out);
+  void command_styles(FILE * out);
 };
 
 }
-- 
GitLab


From e483cb9ef97714d196a044a22ac55c7e455991da Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 16:30:14 -0400
Subject: [PATCH 31/52] Use command_map to list command styles

---
 src/info.cpp  | 7 +++----
 src/input.cpp | 2 +-
 src/input.h   | 6 ++++--
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/info.cpp b/src/info.cpp
index 0e8136278d..bb8380aa19 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -737,10 +737,9 @@ void Info::command_styles(FILE * out)
   fprintf(out, "\nCommand styles (add-on input script commands):\n");
 
   vector<string> styles;
-#define COMMAND_CLASS
-#define CommandStyle(key,Class) styles.push_back(#key);
-#include "style_command.h"
-#undef COMMAND_CLASS
+  for(Input::CommandCreatorMap::iterator it = input->command_map->begin(); it != input->command_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
diff --git a/src/input.cpp b/src/input.cpp
index 4ab4a6b968..905e7f0590 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -93,7 +93,7 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp)
 
   // fill map with commands listed in style_command.h
 
-  command_map = new std::map<std::string,CommandCreator>();
+  command_map = new CommandCreatorMap();
 
 #define COMMAND_CLASS
 #define CommandStyle(key,Class) \
diff --git a/src/input.h b/src/input.h
index c1947fee03..33a271ccdf 100644
--- a/src/input.h
+++ b/src/input.h
@@ -53,10 +53,12 @@ class Input : protected Pointers {
 
   FILE **infiles;              // list of open input files
 
- protected:
+ public:
   typedef void (*CommandCreator)(LAMMPS *, int, char **);
-  std::map<std::string,CommandCreator> *command_map;
+  typedef std::map<std::string,CommandCreator> CommandCreatorMap;
+  CommandCreatorMap *command_map;
 
+ protected:
   template <typename T> static void command_creator(LAMMPS *, int, char **);
 
  private:
-- 
GitLab


From 00b08bb5e1fe80d6ab5d953f29f01d2cc73c9867 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 16:37:10 -0400
Subject: [PATCH 32/52] Use compute_map and fix_map to list compute and fix
 styles

---
 src/info.cpp   | 20 ++++++++++++--------
 src/modify.cpp |  6 ++----
 src/modify.h   |  9 ++++++---
 3 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/src/info.cpp b/src/info.cpp
index bb8380aa19..4166238e66 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -685,10 +685,11 @@ void Info::fix_styles(FILE * out)
   fprintf(out, "\nFix styles:\n");
 
   vector<string> styles;
-#define FIX_CLASS
-#define FixStyle(key,Class) styles.push_back(#key);
-#include "style_fix.h"
-#undef FIX_CLASS
+
+  for(Modify::FixCreatorMap::iterator it = modify->fix_map->begin(); it != modify->fix_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
@@ -698,10 +699,11 @@ void Info::compute_styles(FILE * out)
   fprintf(out, "\nCompute styles:\n");
 
   vector<string> styles;
-#define COMPUTE_CLASS
-#define ComputeStyle(key,Class) styles.push_back(#key);
-#include "style_compute.h"
-#undef COMPUTE_CLASS
+
+  for(Modify::ComputeCreatorMap::iterator it = modify->compute_map->begin(); it != modify->compute_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
@@ -737,9 +739,11 @@ void Info::command_styles(FILE * out)
   fprintf(out, "\nCommand styles (add-on input script commands):\n");
 
   vector<string> styles;
+
   for(Input::CommandCreatorMap::iterator it = input->command_map->begin(); it != input->command_map->end(); ++it) {
     styles.push_back(it->first);
   }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
diff --git a/src/modify.cpp b/src/modify.cpp
index 219c233f2b..dea0d9dc08 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -28,8 +28,6 @@
 #include "memory.h"
 #include "error.h"
 
-#include <map>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
@@ -80,7 +78,7 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
 
   // fill map with fixes listed in style_fix.h
 
-  fix_map = new std::map<std::string,FixCreator>();
+  fix_map = new FixCreatorMap();
 
 #define FIX_CLASS
 #define FixStyle(key,Class) \
@@ -91,7 +89,7 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
 
   // fill map with computes listed in style_compute.h
 
-  compute_map = new std::map<std::string,ComputeCreator>();
+  compute_map = new ComputeCreatorMap();
 
 #define COMPUTE_CLASS
 #define ComputeStyle(key,Class) \
diff --git a/src/modify.h b/src/modify.h
index 934ceb13dc..6472c9bf6a 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -149,13 +149,16 @@ class Modify : protected Pointers {
   void list_init_dofflag(int &, int *&);
   void list_init_compute();
 
- protected:
+ public:
   typedef Compute *(*ComputeCreator)(LAMMPS *, int, char **);
-  std::map<std::string,ComputeCreator> *compute_map;
+  typedef std::map<std::string,ComputeCreator> ComputeCreatorMap;
+  ComputeCreatorMap *compute_map;
 
   typedef Fix *(*FixCreator)(LAMMPS *, int, char **);
-  std::map<std::string,FixCreator> *fix_map;
+  typedef std::map<std::string,FixCreator> FixCreatorMap;
+  FixCreatorMap *fix_map;
 
+ protected:
   template <typename T> static Compute *compute_creator(LAMMPS *, int, char **);
   template <typename T> static Fix *fix_creator(LAMMPS *, int, char **);
 };
-- 
GitLab


From 95ee6440add06a51bcd7cf62852607642f5d2d42 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 16:42:50 -0400
Subject: [PATCH 33/52] Use pair_map to list pair styles

---
 src/force.cpp | 2 +-
 src/force.h   | 3 ++-
 src/info.cpp  | 9 +++++----
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/force.cpp b/src/force.cpp
index 37ac4f4ee6..9d751d0b31 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -78,7 +78,7 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
 
   // fill pair map with pair styles listed in style_pair.h
 
-  pair_map = new std::map<std::string,PairCreator>();
+  pair_map = new PairCreatorMap();
 
 #define PAIR_CLASS
 #define PairStyle(key,Class) \
diff --git a/src/force.h b/src/force.h
index 1873173a74..4c1f81c21f 100644
--- a/src/force.h
+++ b/src/force.h
@@ -49,7 +49,8 @@ class Force : protected Pointers {
   char *pair_style;
 
   typedef Pair *(*PairCreator)(LAMMPS *);
-  std::map<std::string,PairCreator> *pair_map;
+  typedef std::map<std::string,PairCreator> PairCreatorMap;
+  PairCreatorMap *pair_map;
 
   class Bond *bond;
   char *bond_style;
diff --git a/src/info.cpp b/src/info.cpp
index 4166238e66..52f1f56cf7 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -607,10 +607,11 @@ void Info::pair_styles(FILE * out)
   fprintf(out, "\nPair styles:\n");
 
   vector<string> styles;
-#define PAIR_CLASS
-#define PairStyle(key,Class) styles.push_back(#key);
-#include "style_pair.h"
-#undef PAIR_CLASS
+
+  for(Force::PairCreatorMap::iterator it = force->pair_map->begin(); it != force->pair_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
-- 
GitLab


From 69c58ef0d5dff9610607fa72f7f1ce6debd6668a Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 18:05:17 -0400
Subject: [PATCH 34/52] Use factory for bond style creation

---
 src/force.cpp | 58 +++++++++++++++++++++++++++++----------------------
 src/force.h   |  5 +++++
 src/info.cpp  |  9 ++++----
 3 files changed, 43 insertions(+), 29 deletions(-)

diff --git a/src/force.cpp b/src/force.cpp
index 9d751d0b31..7a7bd281c3 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -86,6 +86,15 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
 #include "style_pair.h"
 #undef PairStyle
 #undef PAIR_CLASS
+
+  bond_map = new BondCreatorMap();
+
+#define BOND_CLASS
+#define BondStyle(key,Class) \
+  (*bond_map)[#key] = &bond_creator<Class>;
+#include "style_bond.h"
+#undef BondStyle
+#undef BOND_CLASS
 }
 
 /* ---------------------------------------------------------------------- */
@@ -114,6 +123,7 @@ Force::~Force()
   kspace = NULL;
 
   delete pair_map;
+  delete bond_map;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -288,46 +298,44 @@ Bond *Force::new_bond(const char *style, int trysuffix, int &sflag)
       sflag = 1;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix);
-
-      if (0) return NULL;
-
-#define BOND_CLASS
-#define BondStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp);
-#include "style_bond.h"
-#undef BondStyle
-#undef BOND_CLASS
+      if (bond_map->find(estyle) != bond_map->end()) {
+        BondCreator bond_creator = (*bond_map)[estyle];
+        return bond_creator(lmp);
+      }
     }
 
     if (lmp->suffix2) {
       sflag = 2;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix2);
-
-      if (0) return NULL;
-
-#define BOND_CLASS
-#define BondStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp);
-#include "style_bond.h"
-#undef BondStyle
-#undef BOND_CLASS
+      if (bond_map->find(estyle) != bond_map->end()) {
+        BondCreator bond_creator = (*bond_map)[estyle];
+        return bond_creator(lmp);
+      }
     }
   }
 
   sflag = 0;
   if (strcmp(style,"none") == 0) return NULL;
+  if (bond_map->find(style) != bond_map->end()) {
+    BondCreator bond_creator = (*bond_map)[style];
+    return bond_creator(lmp);
+  }
 
-#define BOND_CLASS
-#define BondStyle(key,Class) \
-  else if (strcmp(style,#key) == 0) return new Class(lmp);
-#include "style_bond.h"
-#undef BOND_CLASS
-
-  else error->all(FLERR,"Unknown bond style");
+  error->all(FLERR,"Unknown bond style");
   return NULL;
 }
 
+/* ----------------------------------------------------------------------
+   one instance per bond style in style_bond.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+Bond *Force::bond_creator(LAMMPS *lmp)
+{
+  return new T(lmp);
+}
+
 /* ----------------------------------------------------------------------
    return ptr to current bond class or hybrid sub-class if matches style
 ------------------------------------------------------------------------- */
diff --git a/src/force.h b/src/force.h
index 4c1f81c21f..0a692b6dc7 100644
--- a/src/force.h
+++ b/src/force.h
@@ -55,6 +55,10 @@ class Force : protected Pointers {
   class Bond *bond;
   char *bond_style;
 
+  typedef Bond *(*BondCreator)(LAMMPS *);
+  typedef std::map<std::string,BondCreator> BondCreatorMap;
+  BondCreatorMap *bond_map;
+
   class Angle *angle;
   char *angle_style;
 
@@ -122,6 +126,7 @@ class Force : protected Pointers {
 
  private:
   template <typename T> static Pair *pair_creator(LAMMPS *);
+  template <typename T> static Bond *bond_creator(LAMMPS *);
 };
 
 }
diff --git a/src/info.cpp b/src/info.cpp
index 52f1f56cf7..c607b73881 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -621,10 +621,11 @@ void Info::bond_styles(FILE * out)
   fprintf(out, "\nBond styles:\n");
 
   vector<string> styles;
-#define BOND_CLASS
-#define BondStyle(key,Class) styles.push_back(#key);
-#include "style_bond.h"
-#undef BOND_CLASS
+
+  for(Force::BondCreatorMap::iterator it = force->bond_map->begin(); it != force->bond_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
-- 
GitLab


From 35bdeb63e266aacacbdfbdded721f5c40869ff40 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 18:19:33 -0400
Subject: [PATCH 35/52] Use factory for angle style creation

---
 src/force.cpp | 59 +++++++++++++++++++++++++++++----------------------
 src/force.h   |  5 +++++
 src/info.cpp  |  9 ++++----
 3 files changed, 44 insertions(+), 29 deletions(-)

diff --git a/src/force.cpp b/src/force.cpp
index 7a7bd281c3..91d43a876e 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -95,6 +95,15 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
 #include "style_bond.h"
 #undef BondStyle
 #undef BOND_CLASS
+
+  angle_map = new AngleCreatorMap();
+
+#define ANGLE_CLASS
+#define AngleStyle(key,Class) \
+  (*angle_map)[#key] = &angle_creator<Class>;
+#include "style_angle.h"
+#undef AngleStyle
+#undef ANGLE_CLASS
 }
 
 /* ---------------------------------------------------------------------- */
@@ -124,6 +133,7 @@ Force::~Force()
 
   delete pair_map;
   delete bond_map;
+  delete angle_map;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -376,46 +386,45 @@ Angle *Force::new_angle(const char *style, int trysuffix, int &sflag)
       sflag = 1;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix);
-
-      if (0) return NULL;
-
-#define ANGLE_CLASS
-#define AngleStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp);
-#include "style_angle.h"
-#undef AngleStyle
-#undef ANGLE_CLASS
+      if (angle_map->find(estyle) != angle_map->end()) {
+        AngleCreator angle_creator = (*angle_map)[estyle];
+        return angle_creator(lmp);
+      }
     }
 
     if (lmp->suffix2) {
       sflag = 2;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix);
-
-      if (0) return NULL;
-
-#define ANGLE_CLASS
-#define AngleStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp);
-#include "style_angle.h"
-#undef AngleStyle
-#undef ANGLE_CLASS
+      if (angle_map->find(estyle) != angle_map->end()) {
+        AngleCreator angle_creator = (*angle_map)[estyle];
+        return angle_creator(lmp);
+      }
     }
   }
 
   sflag = 0;
   if (strcmp(style,"none") == 0) return NULL;
+  if (angle_map->find(style) != angle_map->end()) {
+    AngleCreator angle_creator = (*angle_map)[style];
+    return angle_creator(lmp);
+  }
 
-#define ANGLE_CLASS
-#define AngleStyle(key,Class) \
-  else if (strcmp(style,#key) == 0) return new Class(lmp);
-#include "style_angle.h"
-#undef ANGLE_CLASS
-
-  else error->all(FLERR,"Unknown angle style");
+  error->all(FLERR,"Unknown angle style");
   return NULL;
 }
 
+/* ----------------------------------------------------------------------
+   one instance per angle style in style_angle.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+Angle *Force::angle_creator(LAMMPS *lmp)
+{
+  return new T(lmp);
+}
+
+
 /* ----------------------------------------------------------------------
    return ptr to current angle class or hybrid sub-class if matches style
 ------------------------------------------------------------------------- */
diff --git a/src/force.h b/src/force.h
index 0a692b6dc7..0f79fe041d 100644
--- a/src/force.h
+++ b/src/force.h
@@ -62,6 +62,10 @@ class Force : protected Pointers {
   class Angle *angle;
   char *angle_style;
 
+  typedef Angle *(*AngleCreator)(LAMMPS *);
+  typedef std::map<std::string,AngleCreator> AngleCreatorMap;
+  AngleCreatorMap *angle_map;
+
   class Dihedral *dihedral;
   char *dihedral_style;
 
@@ -127,6 +131,7 @@ class Force : protected Pointers {
  private:
   template <typename T> static Pair *pair_creator(LAMMPS *);
   template <typename T> static Bond *bond_creator(LAMMPS *);
+  template <typename T> static Angle *angle_creator(LAMMPS *);
 };
 
 }
diff --git a/src/info.cpp b/src/info.cpp
index c607b73881..86a4626037 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -635,10 +635,11 @@ void Info::angle_styles(FILE * out)
   fprintf(out, "\nAngle styles:\n");
 
   vector<string> styles;
-#define ANGLE_CLASS
-#define AngleStyle(key,Class) styles.push_back(#key);
-#include "style_angle.h"
-#undef ANGLE_CLASS
+
+  for(Force::AngleCreatorMap::iterator it = force->angle_map->begin(); it != force->angle_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
-- 
GitLab


From 906c50223af60182ce2a0e81432cfe607e725f72 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 22:07:21 -0400
Subject: [PATCH 36/52] Use factory for dihedral style creation

---
 src/force.cpp | 59 ++++++++++++++++++++++++++++-----------------------
 src/force.h   |  5 +++++
 src/info.cpp  |  9 ++++----
 3 files changed, 43 insertions(+), 30 deletions(-)

diff --git a/src/force.cpp b/src/force.cpp
index 91d43a876e..aed8c8c766 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -104,6 +104,15 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
 #include "style_angle.h"
 #undef AngleStyle
 #undef ANGLE_CLASS
+
+  dihedral_map = new DihedralCreatorMap();
+
+#define DIHEDRAL_CLASS
+#define DihedralStyle(key,Class) \
+  (*dihedral_map)[#key] = &dihedral_creator<Class>;
+#include "style_dihedral.h"
+#undef DihedralStyle
+#undef DIHEDRAL_CLASS
 }
 
 /* ---------------------------------------------------------------------- */
@@ -134,6 +143,7 @@ Force::~Force()
   delete pair_map;
   delete bond_map;
   delete angle_map;
+  delete dihedral_map;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -465,47 +475,44 @@ Dihedral *Force::new_dihedral(const char *style, int trysuffix, int &sflag)
       sflag = 1;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix);
-
-      if (0) return NULL;
-
-#define DIHEDRAL_CLASS
-#define DihedralStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp);
-#include "style_dihedral.h"
-#undef DihedralStyle
-#undef DIHEDRAL_CLASS
+      if (dihedral_map->find(estyle) != dihedral_map->end()) {
+        DihedralCreator dihedral_creator = (*dihedral_map)[estyle];
+        return dihedral_creator(lmp);
+      }
     }
 
     if (lmp->suffix2) {
       sflag = 2;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix2);
-
-      if (0) return NULL;
-
-#define DIHEDRAL_CLASS
-#define DihedralStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp);
-#include "style_dihedral.h"
-#undef DihedralStyle
-#undef DIHEDRAL_CLASS
+      if (dihedral_map->find(estyle) != dihedral_map->end()) {
+        DihedralCreator dihedral_creator = (*dihedral_map)[estyle];
+        return dihedral_creator(lmp);
+      }
     }
   }
 
   sflag = 0;
   if (strcmp(style,"none") == 0) return NULL;
+  if (dihedral_map->find(style) != dihedral_map->end()) {
+    DihedralCreator dihedral_creator = (*dihedral_map)[style];
+    return dihedral_creator(lmp);
+  }
 
-#define DIHEDRAL_CLASS
-#define DihedralStyle(key,Class) \
-  else if (strcmp(style,#key) == 0) return new Class(lmp);
-#include "style_dihedral.h"
-#undef DihedralStyle
-#undef DIHEDRAL_CLASS
-
-  else error->all(FLERR,"Unknown dihedral style");
+  error->all(FLERR,"Unknown dihedral style");
   return NULL;
 }
 
+/* ----------------------------------------------------------------------
+   one instance per dihedral style in style_dihedral.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+Dihedral *Force::dihedral_creator(LAMMPS *lmp)
+{
+  return new T(lmp);
+}
+
 /* ----------------------------------------------------------------------
    return ptr to current angle class or hybrid sub-class if matches style
 ------------------------------------------------------------------------- */
diff --git a/src/force.h b/src/force.h
index 0f79fe041d..555094170a 100644
--- a/src/force.h
+++ b/src/force.h
@@ -69,6 +69,10 @@ class Force : protected Pointers {
   class Dihedral *dihedral;
   char *dihedral_style;
 
+  typedef Dihedral *(*DihedralCreator)(LAMMPS *);
+  typedef std::map<std::string,DihedralCreator> DihedralCreatorMap;
+  DihedralCreatorMap *dihedral_map;
+
   class Improper *improper;
   char *improper_style;
 
@@ -132,6 +136,7 @@ class Force : protected Pointers {
   template <typename T> static Pair *pair_creator(LAMMPS *);
   template <typename T> static Bond *bond_creator(LAMMPS *);
   template <typename T> static Angle *angle_creator(LAMMPS *);
+  template <typename T> static Dihedral *dihedral_creator(LAMMPS *);
 };
 
 }
diff --git a/src/info.cpp b/src/info.cpp
index 86a4626037..276461b507 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -649,10 +649,11 @@ void Info::dihedral_styles(FILE * out)
   fprintf(out, "\nDihedral styles:\n");
 
   vector<string> styles;
-#define DIHEDRAL_CLASS
-#define DihedralStyle(key,Class) styles.push_back(#key);
-#include "style_dihedral.h"
-#undef DIHEDRAL_CLASS
+
+  for(Force::DihedralCreatorMap::iterator it = force->dihedral_map->begin(); it != force->dihedral_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
-- 
GitLab


From 0745a9f33f412607a7b9c95efafc4545641761bb Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 22:31:26 -0400
Subject: [PATCH 37/52] Use factory for improper style creation

---
 src/force.cpp | 58 +++++++++++++++++++++++++++++----------------------
 src/force.h   |  5 +++++
 src/info.cpp  |  9 ++++----
 3 files changed, 43 insertions(+), 29 deletions(-)

diff --git a/src/force.cpp b/src/force.cpp
index aed8c8c766..f02ba1c5ee 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -113,6 +113,15 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
 #include "style_dihedral.h"
 #undef DihedralStyle
 #undef DIHEDRAL_CLASS
+
+  improper_map = new ImproperCreatorMap();
+
+#define IMPROPER_CLASS
+#define ImproperStyle(key,Class) \
+  (*improper_map)[#key] = &improper_creator<Class>;
+#include "style_improper.h"
+#undef ImproperStyle
+#undef IMPROPER_CLASS
 }
 
 /* ---------------------------------------------------------------------- */
@@ -144,6 +153,7 @@ Force::~Force()
   delete bond_map;
   delete angle_map;
   delete dihedral_map;
+  delete improper_map;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -553,46 +563,44 @@ Improper *Force::new_improper(const char *style, int trysuffix, int &sflag)
       sflag = 1;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix);
-
-      if (0) return NULL;
-
-#define IMPROPER_CLASS
-#define ImproperStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp);
-#include "style_improper.h"
-#undef ImproperStyle
-#undef IMPROPER_CLASS
+      if (improper_map->find(estyle) != improper_map->end()) {
+        ImproperCreator improper_creator = (*improper_map)[estyle];
+        return improper_creator(lmp);
+      }
     }
 
     if (lmp->suffix2) {
       sflag = 2;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix2);
-
-      if (0) return NULL;
-
-#define IMPROPER_CLASS
-#define ImproperStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp);
-#include "style_improper.h"
-#undef ImproperStyle
-#undef IMPROPER_CLASS
+      if (improper_map->find(estyle) != improper_map->end()) {
+        ImproperCreator improper_creator = (*improper_map)[estyle];
+        return improper_creator(lmp);
+      }
     }
   }
 
   sflag = 0;
   if (strcmp(style,"none") == 0) return NULL;
+  if (improper_map->find(style) != improper_map->end()) {
+    ImproperCreator improper_creator = (*improper_map)[style];
+    return improper_creator(lmp);
+  }
 
-#define IMPROPER_CLASS
-#define ImproperStyle(key,Class) \
-  else if (strcmp(style,#key) == 0) return new Class(lmp);
-#include "style_improper.h"
-#undef IMPROPER_CLASS
-
-  else error->all(FLERR,"Unknown improper style");
+  error->all(FLERR,"Unknown improper style");
   return NULL;
 }
 
+/* ----------------------------------------------------------------------
+   one instance per improper style in style_improper.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+Improper *Force::improper_creator(LAMMPS *lmp)
+{
+  return new T(lmp);
+}
+
 /* ----------------------------------------------------------------------
    return ptr to current improper class or hybrid sub-class if matches style
 ------------------------------------------------------------------------- */
diff --git a/src/force.h b/src/force.h
index 555094170a..02f7e30811 100644
--- a/src/force.h
+++ b/src/force.h
@@ -76,6 +76,10 @@ class Force : protected Pointers {
   class Improper *improper;
   char *improper_style;
 
+  typedef Improper *(*ImproperCreator)(LAMMPS *);
+  typedef std::map<std::string,ImproperCreator> ImproperCreatorMap;
+  ImproperCreatorMap *improper_map;
+
   class KSpace *kspace;
   char *kspace_style;
                              // index [0] is not used in these arrays
@@ -137,6 +141,7 @@ class Force : protected Pointers {
   template <typename T> static Bond *bond_creator(LAMMPS *);
   template <typename T> static Angle *angle_creator(LAMMPS *);
   template <typename T> static Dihedral *dihedral_creator(LAMMPS *);
+  template <typename T> static Improper *improper_creator(LAMMPS *);
 };
 
 }
diff --git a/src/info.cpp b/src/info.cpp
index 276461b507..06a80b8995 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -663,10 +663,11 @@ void Info::improper_styles(FILE * out)
   fprintf(out, "\nImproper styles:\n");
 
   vector<string> styles;
-#define IMPROPER_CLASS
-#define ImproperStyle(key,Class) styles.push_back(#key);
-#include "style_improper.h"
-#undef IMPROPER_CLASS
+
+  for(Force::ImproperCreatorMap::iterator it = force->improper_map->begin(); it != force->improper_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
-- 
GitLab


From 1d03913aa307503cb0ad629a93bc1b92b8f6df71 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 22:51:50 -0400
Subject: [PATCH 38/52] Use factory for kspace style creation

---
 src/force.cpp | 57 +++++++++++++++++++++++++++++----------------------
 src/force.h   |  6 ++++++
 src/info.cpp  |  9 ++++----
 3 files changed, 43 insertions(+), 29 deletions(-)

diff --git a/src/force.cpp b/src/force.cpp
index f02ba1c5ee..c4de7f841d 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -122,6 +122,15 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
 #include "style_improper.h"
 #undef ImproperStyle
 #undef IMPROPER_CLASS
+
+  kspace_map = new KSpaceCreatorMap();
+
+#define KSPACE_CLASS
+#define KSpaceStyle(key,Class) \
+  (*kspace_map)[#key] = &kspace_creator<Class>;
+#include "style_kspace.h"
+#undef KSpaceStyle
+#undef KSPACE_CLASS
 }
 
 /* ---------------------------------------------------------------------- */
@@ -645,46 +654,44 @@ KSpace *Force::new_kspace(int narg, char **arg, int trysuffix, int &sflag)
       sflag = 1;
       char estyle[256];
       sprintf(estyle,"%s/%s",arg[0],lmp->suffix);
-
-      if (0) return NULL;
-
-#define KSPACE_CLASS
-#define KSpaceStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp,narg-1,&arg[1]);
-#include "style_kspace.h"
-#undef KSpaceStyle
-#undef KSPACE_CLASS
+      if (kspace_map->find(estyle) != kspace_map->end()) {
+        KSpaceCreator kspace_creator = (*kspace_map)[estyle];
+        return kspace_creator(lmp, narg-1, &arg[1]);
+      }
     }
 
     if (lmp->suffix2) {
       sflag = 1;
       char estyle[256];
       sprintf(estyle,"%s/%s",arg[0],lmp->suffix2);
-
-      if (0) return NULL;
-
-#define KSPACE_CLASS
-#define KSpaceStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp,narg-1,&arg[1]);
-#include "style_kspace.h"
-#undef KSpaceStyle
-#undef KSPACE_CLASS
+      if (kspace_map->find(estyle) != kspace_map->end()) {
+        KSpaceCreator kspace_creator = (*kspace_map)[estyle];
+        return kspace_creator(lmp, narg-1, &arg[1]);
+      }
     }
   }
 
   sflag = 0;
   if (strcmp(arg[0],"none") == 0) return NULL;
+  if (kspace_map->find(arg[0]) != kspace_map->end()) {
+    KSpaceCreator kspace_creator = (*kspace_map)[arg[0]];
+    return kspace_creator(lmp, narg-1, &arg[1]);
+  }
 
-#define KSPACE_CLASS
-#define KSpaceStyle(key,Class) \
-  else if (strcmp(arg[0],#key) == 0) return  new Class(lmp,narg-1,&arg[1]);
-#include "style_kspace.h"
-#undef KSPACE_CLASS
-
-  else error->all(FLERR,"Unknown kspace style");
+  error->all(FLERR,"Unknown kspace style");
   return NULL;
 }
 
+/* ----------------------------------------------------------------------
+   one instance per kspace style in style_kspace.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+KSpace *Force::kspace_creator(LAMMPS *lmp, int narg, char ** arg)
+{
+  return new T(lmp, narg, arg);
+}
+
 /* ----------------------------------------------------------------------
    return ptr to Kspace class if matches word
    if exact, then style name must be exact match to word
diff --git a/src/force.h b/src/force.h
index 02f7e30811..f49a3f8ad6 100644
--- a/src/force.h
+++ b/src/force.h
@@ -82,6 +82,11 @@ class Force : protected Pointers {
 
   class KSpace *kspace;
   char *kspace_style;
+
+  typedef KSpace *(*KSpaceCreator)(LAMMPS *,int,char**);
+  typedef std::map<std::string,KSpaceCreator> KSpaceCreatorMap;
+  KSpaceCreatorMap *kspace_map;
+
                              // index [0] is not used in these arrays
   double special_lj[4];      // 1-2, 1-3, 1-4 prefactors for LJ
   double special_coul[4];    // 1-2, 1-3, 1-4 prefactors for Coulombics
@@ -142,6 +147,7 @@ class Force : protected Pointers {
   template <typename T> static Angle *angle_creator(LAMMPS *);
   template <typename T> static Dihedral *dihedral_creator(LAMMPS *);
   template <typename T> static Improper *improper_creator(LAMMPS *);
+  template <typename T> static KSpace *kspace_creator(LAMMPS *, int, char **);
 };
 
 }
diff --git a/src/info.cpp b/src/info.cpp
index 06a80b8995..111bddf0ad 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -677,10 +677,11 @@ void Info::kspace_styles(FILE * out)
   fprintf(out, "\nKSpace styles:\n");
 
   vector<string> styles;
-#define KSPACE_CLASS
-#define KSpaceStyle(key,Class) styles.push_back(#key);
-#include "style_kspace.h"
-#undef KSPACE_CLASS
+
+  for(Force::KSpaceCreatorMap::iterator it = force->kspace_map->begin(); it != force->kspace_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
-- 
GitLab


From 88e10b401d5ed5f85ce9507e76115b2ec7b61151 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 23:05:53 -0400
Subject: [PATCH 39/52] Cleanup force.h after refactoring

---
 src/force.h | 37 +++++++++++++++++--------------------
 1 file changed, 17 insertions(+), 20 deletions(-)

diff --git a/src/force.h b/src/force.h
index f49a3f8ad6..78788826a4 100644
--- a/src/force.h
+++ b/src/force.h
@@ -48,43 +48,40 @@ class Force : protected Pointers {
   class Pair *pair;
   char *pair_style;
 
-  typedef Pair *(*PairCreator)(LAMMPS *);
-  typedef std::map<std::string,PairCreator> PairCreatorMap;
-  PairCreatorMap *pair_map;
-
   class Bond *bond;
   char *bond_style;
 
-  typedef Bond *(*BondCreator)(LAMMPS *);
-  typedef std::map<std::string,BondCreator> BondCreatorMap;
-  BondCreatorMap *bond_map;
-
   class Angle *angle;
   char *angle_style;
 
-  typedef Angle *(*AngleCreator)(LAMMPS *);
-  typedef std::map<std::string,AngleCreator> AngleCreatorMap;
-  AngleCreatorMap *angle_map;
-
   class Dihedral *dihedral;
   char *dihedral_style;
 
-  typedef Dihedral *(*DihedralCreator)(LAMMPS *);
-  typedef std::map<std::string,DihedralCreator> DihedralCreatorMap;
-  DihedralCreatorMap *dihedral_map;
-
   class Improper *improper;
   char *improper_style;
 
-  typedef Improper *(*ImproperCreator)(LAMMPS *);
-  typedef std::map<std::string,ImproperCreator> ImproperCreatorMap;
-  ImproperCreatorMap *improper_map;
-
   class KSpace *kspace;
   char *kspace_style;
 
+  typedef Pair *(*PairCreator)(LAMMPS *);
+  typedef Bond *(*BondCreator)(LAMMPS *);
+  typedef Angle *(*AngleCreator)(LAMMPS *);
+  typedef Dihedral *(*DihedralCreator)(LAMMPS *);
+  typedef Improper *(*ImproperCreator)(LAMMPS *);
   typedef KSpace *(*KSpaceCreator)(LAMMPS *,int,char**);
+
+  typedef std::map<std::string,PairCreator> PairCreatorMap;
+  typedef std::map<std::string,BondCreator> BondCreatorMap;
+  typedef std::map<std::string,AngleCreator> AngleCreatorMap;
+  typedef std::map<std::string,DihedralCreator> DihedralCreatorMap;
+  typedef std::map<std::string,ImproperCreator> ImproperCreatorMap;
   typedef std::map<std::string,KSpaceCreator> KSpaceCreatorMap;
+
+  PairCreatorMap *pair_map;
+  BondCreatorMap *bond_map;
+  AngleCreatorMap *angle_map;
+  DihedralCreatorMap *dihedral_map;
+  ImproperCreatorMap *improper_map;
   KSpaceCreatorMap *kspace_map;
 
                              // index [0] is not used in these arrays
-- 
GitLab


From a1e5fc0fca8facf03fa4f0edfa9fb6416b877891 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 23:37:19 -0400
Subject: [PATCH 40/52] Use factory for AtomVec style creation

---
 src/atom.cpp | 59 +++++++++++++++++++++++++++++-----------------------
 src/atom.h   | 11 ++++++++++
 src/info.cpp |  9 ++++----
 3 files changed, 49 insertions(+), 30 deletions(-)

diff --git a/src/atom.cpp b/src/atom.cpp
index 86b1dea3d6..2db73d4325 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -210,6 +210,15 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
 
   datamask = ALL_MASK;
   datamask_ext = ALL_MASK;
+
+  avec_map = new AtomVecCreatorMap();
+
+#define ATOM_CLASS
+#define AtomStyle(key,Class) \
+  (*avec_map)[#key] = &avec_creator<Class>;
+#include "style_atom.h"
+#undef AtomStyle
+#undef ATOM_CLASS
 }
 
 /* ---------------------------------------------------------------------- */
@@ -218,6 +227,7 @@ Atom::~Atom()
 {
   delete [] atom_style;
   delete avec;
+  delete avec_map;
 
   delete [] firstgroupname;
   memory->destroy(binhead);
@@ -445,46 +455,43 @@ AtomVec *Atom::new_avec(const char *style, int trysuffix, int &sflag)
       sflag = 1;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix);
-
-      if (0) return NULL;
-
-#define ATOM_CLASS
-#define AtomStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp);
-#include "style_atom.h"
-#undef AtomStyle
-#undef ATOM_CLASS
+      if (avec_map->find(estyle) != avec_map->end()) {
+        AtomVecCreator avec_creator = (*avec_map)[estyle];
+        return avec_creator(lmp);
+      }
     }
 
     if (lmp->suffix2) {
       sflag = 2;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix2);
-
-      if (0) return NULL;
-
-#define ATOM_CLASS
-#define AtomStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) return new Class(lmp);
-#include "style_atom.h"
-#undef AtomStyle
-#undef ATOM_CLASS
+      if (avec_map->find(estyle) != avec_map->end()) {
+        AtomVecCreator avec_creator = (*avec_map)[estyle];
+        return avec_creator(lmp);
+      }
     }
   }
 
   sflag = 0;
-  if (0) return NULL;
-
-#define ATOM_CLASS
-#define AtomStyle(key,Class) \
-  else if (strcmp(style,#key) == 0) return new Class(lmp);
-#include "style_atom.h"
-#undef ATOM_CLASS
+  if (avec_map->find(style) != avec_map->end()) {
+    AtomVecCreator avec_creator = (*avec_map)[style];
+    return avec_creator(lmp);
+  }
 
-  else error->all(FLERR,"Unknown atom style");
+  error->all(FLERR,"Unknown atom style");
   return NULL;
 }
 
+/* ----------------------------------------------------------------------
+   one instance per AtomVec style in style_atom.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+AtomVec *Atom::avec_creator(LAMMPS *lmp)
+{
+  return new T(lmp);
+}
+
 /* ---------------------------------------------------------------------- */
 
 void Atom::init()
diff --git a/src/atom.h b/src/atom.h
index 6d0b881b75..31fd355f9a 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -15,6 +15,8 @@
 #define LMP_ATOM_H
 
 #include "pointers.h"
+#include <map>
+#include <string>
 
 namespace LAMMPS_NS {
 
@@ -197,6 +199,12 @@ class Atom : protected Pointers {
 
   int *sametag;      // sametag[I] = next atom with same ID, -1 if no more
 
+  // AtomVec factory types and map
+
+  typedef AtomVec *(*AtomVecCreator)(LAMMPS *);
+  typedef std::map<std::string,AtomVecCreator> AtomVecCreatorMap;
+  AtomVecCreatorMap *avec_map;
+
   // functions
 
   Atom(class LAMMPS *);
@@ -322,6 +330,9 @@ class Atom : protected Pointers {
 
   void setup_sort_bins();
   int next_prime(int);
+
+ private:
+  template <typename T> static AtomVec *avec_creator(LAMMPS *);
 };
 
 }
diff --git a/src/info.cpp b/src/info.cpp
index 111bddf0ad..8978f06b73 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -568,10 +568,11 @@ void Info::atom_styles(FILE * out)
   fprintf(out, "\nAtom styles:\n");
 
   vector<string> styles;
-#define ATOM_CLASS
-#define AtomStyle(key,Class) styles.push_back(#key);
-#include "style_atom.h"
-#undef ATOM_CLASS
+
+  for(Atom::AtomVecCreatorMap::iterator it = atom->avec_map->begin(); it != atom->avec_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
-- 
GitLab


From 55260ad53e5b10297cac7189c75c605702235f0e Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 7 Sep 2016 23:57:29 -0400
Subject: [PATCH 41/52] Add missing delete in destructor

---
 src/force.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/force.cpp b/src/force.cpp
index c4de7f841d..dbc71b49a9 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -163,6 +163,7 @@ Force::~Force()
   delete angle_map;
   delete dihedral_map;
   delete improper_map;
+  delete kspace_map;
 }
 
 /* ---------------------------------------------------------------------- */
-- 
GitLab


From 85c132943ed5574d07d346e23409a558bbb73dbd Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 8 Sep 2016 00:12:09 -0400
Subject: [PATCH 42/52] Use factory for integrate style creation

---
 src/info.cpp   |  9 ++++---
 src/update.cpp | 70 ++++++++++++++++++++++++++------------------------
 src/update.h   |  7 +++++
 3 files changed, 48 insertions(+), 38 deletions(-)

diff --git a/src/info.cpp b/src/info.cpp
index 8978f06b73..97b0ac1cf7 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -582,10 +582,11 @@ void Info::integrate_styles(FILE * out)
   fprintf(out, "\nIntegrate styles:\n");
 
   vector<string> styles;
-#define INTEGRATE_CLASS
-#define IntegrateStyle(key,Class) styles.push_back(#key);
-#include "style_integrate.h"
-#undef INTEGRATE_CLASS
+
+  for(Update::IntegrateCreatorMap::iterator it = update->integrate_map->begin(); it != update->integrate_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
diff --git a/src/update.cpp b/src/update.cpp
index faf3a8c148..2e85798941 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -61,6 +61,15 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
   minimize_style = NULL;
   minimize = NULL;
 
+  integrate_map = new IntegrateCreatorMap();
+
+#define INTEGRATE_CLASS
+#define IntegrateStyle(key,Class) \
+  (*integrate_map)[#key] = &integrate_creator<Class>;
+#include "style_integrate.h"
+#undef IntegrateStyle
+#undef INTEGRATE_CLASS
+
   str = (char *) "verlet";
   create_integrate(1,&str,1);
 
@@ -79,6 +88,8 @@ Update::~Update()
 
   delete [] minimize_style;
   delete minimize;
+
+  delete integrate_map;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -319,52 +330,43 @@ void Update::new_integrate(char *style, int narg, char **arg,
       sflag = 1;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix);
-      int success = 1;
-
-      if (0) return;
-
-#define INTEGRATE_CLASS
-#define IntegrateStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) integrate = new Class(lmp,narg,arg);
-#include "style_integrate.h"
-#undef IntegrateStyle
-#undef INTEGRATE_CLASS
-
-      else success = 0;
-      if (success) return;
+      if (integrate_map->find(estyle) != integrate_map->end()) {
+        IntegrateCreator integrate_creator = (*integrate_map)[estyle];
+        integrate = integrate_creator(lmp, narg, arg);
+        return;
+      }
     }
 
     if (lmp->suffix2) {
       sflag = 2;
       char estyle[256];
       sprintf(estyle,"%s/%s",style,lmp->suffix2);
-      int success = 1;
-
-      if (0) return;
-
-#define INTEGRATE_CLASS
-#define IntegrateStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) integrate = new Class(lmp,narg,arg);
-#include "style_integrate.h"
-#undef IntegrateStyle
-#undef INTEGRATE_CLASS
-
-      else success = 0;
-      if (success) return;
+      if (integrate_map->find(estyle) != integrate_map->end()) {
+        IntegrateCreator integrate_creator = (*integrate_map)[estyle];
+        integrate = integrate_creator(lmp, narg, arg);
+        return;
+      }
     }
   }
 
   sflag = 0;
-  if (0) return;
+  if (integrate_map->find(style) != integrate_map->end()) {
+    IntegrateCreator integrate_creator = (*integrate_map)[style];
+    integrate = integrate_creator(lmp, narg, arg);
+    return;
+  }
 
-#define INTEGRATE_CLASS
-#define IntegrateStyle(key,Class) \
-  else if (strcmp(style,#key) == 0) integrate = new Class(lmp,narg,arg);
-#include "style_integrate.h"
-#undef IntegrateStyle
-#undef INTEGRATE_CLASS
+  error->all(FLERR,"Illegal integrate style");
+}
 
-  else error->all(FLERR,"Illegal integrate style");
+/* ----------------------------------------------------------------------
+   one instance per integrate style in style_integrate.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+Integrate *Update::integrate_creator(LAMMPS *lmp, int narg, char ** arg)
+{
+  return new T(lmp, narg, arg);
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/update.h b/src/update.h
index bbb29bc7ee..3241d64d1f 100644
--- a/src/update.h
+++ b/src/update.h
@@ -15,6 +15,8 @@
 #define LMP_UPDATE_H
 
 #include "pointers.h"
+#include <map>
+#include <string>
 
 namespace LAMMPS_NS {
 
@@ -46,6 +48,10 @@ class Update : protected Pointers {
   class Min *minimize;
   char *minimize_style;
 
+  typedef Integrate *(*IntegrateCreator)(LAMMPS *,int,char**);
+  typedef std::map<std::string,IntegrateCreator> IntegrateCreatorMap;
+  IntegrateCreatorMap *integrate_map;
+
   Update(class LAMMPS *);
   ~Update();
   void init();
@@ -60,6 +66,7 @@ class Update : protected Pointers {
  private:
   void new_integrate(char *, int, char **, int, int &);
 
+  template <typename T> static Integrate *integrate_creator(LAMMPS *, int, char **);
 };
 
 }
-- 
GitLab


From 9952d8a210fc3e56932dc0af496cbfae86aeacf4 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 8 Sep 2016 00:30:21 -0400
Subject: [PATCH 43/52] Use factory for minimize style creation

---
 src/info.cpp   |  9 +++++----
 src/update.cpp | 32 ++++++++++++++++++++++++--------
 src/update.h   |  6 ++++++
 3 files changed, 35 insertions(+), 12 deletions(-)

diff --git a/src/info.cpp b/src/info.cpp
index 97b0ac1cf7..dfd901fc35 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -596,10 +596,11 @@ void Info::minimize_styles(FILE * out)
   fprintf(out, "\nMinimize styles:\n");
 
   vector<string> styles;
-#define MINIMIZE_CLASS
-#define MinimizeStyle(key,Class) styles.push_back(#key);
-#include "style_minimize.h"
-#undef MINIMIZE_CLASS
+
+  for(Update::MinimizeCreatorMap::iterator it = update->minimize_map->begin(); it != update->minimize_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
diff --git a/src/update.cpp b/src/update.cpp
index 2e85798941..35492006cc 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -70,6 +70,15 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
 #undef IntegrateStyle
 #undef INTEGRATE_CLASS
 
+  minimize_map = new MinimizeCreatorMap();
+
+#define MINIMIZE_CLASS
+#define MinimizeStyle(key,Class) \
+  (*minimize_map)[#key] = &minimize_creator<Class>;
+#include "style_minimize.h"
+#undef MinimizeStyle
+#undef MINIMIZE_CLASS
+
   str = (char *) "verlet";
   create_integrate(1,&str,1);
 
@@ -90,6 +99,7 @@ Update::~Update()
   delete minimize;
 
   delete integrate_map;
+  delete minimize_map;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -378,14 +388,10 @@ void Update::create_minimize(int narg, char **arg)
   delete [] minimize_style;
   delete minimize;
 
-  if (0) return;      // dummy line to enable else-if macro expansion
-
-#define MINIMIZE_CLASS
-#define MinimizeStyle(key,Class) \
-  else if (strcmp(arg[0],#key) == 0) minimize = new Class(lmp);
-#include "style_minimize.h"
-#undef MINIMIZE_CLASS
-
+  if (minimize_map->find(arg[0]) != minimize_map->end()) {
+    MinimizeCreator minimize_creator = (*minimize_map)[arg[0]];
+    minimize = minimize_creator(lmp);
+  }
   else error->all(FLERR,"Illegal min_style command");
 
   int n = strlen(arg[0]) + 1;
@@ -393,6 +399,16 @@ void Update::create_minimize(int narg, char **arg)
   strcpy(minimize_style,arg[0]);
 }
 
+/* ----------------------------------------------------------------------
+   one instance per minimize style in style_minimize.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+Min *Update::minimize_creator(LAMMPS *lmp)
+{
+  return new T(lmp);
+}
+
 /* ----------------------------------------------------------------------
    reset timestep as called from input script
 ------------------------------------------------------------------------- */
diff --git a/src/update.h b/src/update.h
index 3241d64d1f..fe17dc6bb4 100644
--- a/src/update.h
+++ b/src/update.h
@@ -49,8 +49,13 @@ class Update : protected Pointers {
   char *minimize_style;
 
   typedef Integrate *(*IntegrateCreator)(LAMMPS *,int,char**);
+  typedef Min *(*MinimizeCreator)(LAMMPS *);
+
   typedef std::map<std::string,IntegrateCreator> IntegrateCreatorMap;
+  typedef std::map<std::string,MinimizeCreator> MinimizeCreatorMap;
+
   IntegrateCreatorMap *integrate_map;
+  MinimizeCreatorMap *minimize_map;
 
   Update(class LAMMPS *);
   ~Update();
@@ -67,6 +72,7 @@ class Update : protected Pointers {
   void new_integrate(char *, int, char **, int, int &);
 
   template <typename T> static Integrate *integrate_creator(LAMMPS *, int, char **);
+  template <typename T> static Min *minimize_creator(LAMMPS *);
 };
 
 }
-- 
GitLab


From fd2b8864227830d3241950bff0715f6be1eec331 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 8 Sep 2016 00:45:03 -0400
Subject: [PATCH 44/52] Use factory for dump style creation

---
 src/info.cpp   |  9 +++++----
 src/output.cpp | 33 +++++++++++++++++++++++++--------
 src/output.h   | 10 ++++++++++
 3 files changed, 40 insertions(+), 12 deletions(-)

diff --git a/src/info.cpp b/src/info.cpp
index dfd901fc35..22cb432acc 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -735,10 +735,11 @@ void Info::dump_styles(FILE * out)
   fprintf(out, "\nDump styles:\n");
 
   vector<string> styles;
-#define DUMP_CLASS
-#define DumpStyle(key,Class) styles.push_back(#key);
-#include "style_dump.h"
-#undef DUMP_CLASS
+
+  for(Output::DumpCreatorMap::iterator it = output->dump_map->begin(); it != output->dump_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
diff --git a/src/output.cpp b/src/output.cpp
index 073171735f..df7c33e101 100644
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -89,6 +89,15 @@ Output::Output(LAMMPS *lmp) : Pointers(lmp)
   restart1 = restart2a = restart2b = NULL;
   var_restart_single = var_restart_double = NULL;
   restart = NULL;
+
+  dump_map = new DumpCreatorMap();
+
+#define DUMP_CLASS
+#define DumpStyle(key,Class) \
+  (*dump_map)[#key] = &dump_creator<Class>;
+#include "style_dump.h"
+#undef DumpStyle
+#undef DUMP_CLASS
 }
 
 /* ----------------------------------------------------------------------
@@ -115,6 +124,8 @@ Output::~Output()
   delete [] var_restart_single;
   delete [] var_restart_double;
   delete restart;
+
+  delete dump_map;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -571,14 +582,10 @@ void Output::add_dump(int narg, char **arg)
 
   // create the Dump
 
-  if (0) return;         // dummy line to enable else-if macro expansion
-
-#define DUMP_CLASS
-#define DumpStyle(key,Class) \
-  else if (strcmp(arg[2],#key) == 0) dump[ndump] = new Class(lmp,narg,arg);
-#include "style_dump.h"
-#undef DUMP_CLASS
-
+  if (dump_map->find(arg[2]) != dump_map->end()) {
+    DumpCreator dump_creator = (*dump_map)[arg[2]];
+    dump[ndump] = dump_creator(lmp, narg, arg);
+  }
   else error->all(FLERR,"Unknown dump style");
 
   every_dump[ndump] = force->inumeric(FLERR,arg[3]);
@@ -588,6 +595,16 @@ void Output::add_dump(int narg, char **arg)
   ndump++;
 }
 
+/* ----------------------------------------------------------------------
+   one instance per dump style in style_dump.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+Dump *Output::dump_creator(LAMMPS *lmp, int narg, char ** arg)
+{
+  return new T(lmp, narg, arg);
+}
+
 /* ----------------------------------------------------------------------
    modify parameters of a Dump
 ------------------------------------------------------------------------- */
diff --git a/src/output.h b/src/output.h
index 6bbd92a259..cc282cbedd 100644
--- a/src/output.h
+++ b/src/output.h
@@ -15,6 +15,8 @@
 #define LMP_OUTPUT_H
 
 #include "pointers.h"
+#include <map>
+#include <string>
 
 namespace LAMMPS_NS {
 
@@ -57,6 +59,11 @@ class Output : protected Pointers {
   char *restart2a,*restart2b;  // names of double restart files
   class WriteRestart *restart; // class for writing restart files
 
+
+  typedef Dump *(*DumpCreator)(LAMMPS *,int,char**);
+  typedef std::map<std::string,DumpCreator> DumpCreatorMap;
+  DumpCreatorMap *dump_map;
+
   Output(class LAMMPS *);
   ~Output();
   void init();
@@ -75,6 +82,9 @@ class Output : protected Pointers {
   void create_restart(int, char **); // create Restart and restart files
 
   void memory_usage();               // print out memory usage
+
+ private:
+  template <typename T> static Dump *dump_creator(LAMMPS *, int, char **);
 };
 
 }
-- 
GitLab


From ba2b523bf4b7c4dc91aac2d0ea61c3e4966594ea Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 8 Sep 2016 01:00:53 -0400
Subject: [PATCH 45/52] Use factory for region style creation

---
 src/domain.cpp | 71 ++++++++++++++++++++++++++------------------------
 src/domain.h   |  9 +++++++
 src/info.cpp   |  9 ++++---
 3 files changed, 51 insertions(+), 38 deletions(-)

diff --git a/src/domain.cpp b/src/domain.cpp
index 0590b956dd..2c3f61401d 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -105,6 +105,15 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp)
   regions = NULL;
 
   copymode = 0;
+
+  region_map = new RegionCreatorMap();
+
+#define REGION_CLASS
+#define RegionStyle(key,Class) \
+  (*region_map)[#key] = &region_creator<Class>;
+#include "style_region.h"
+#undef RegionStyle
+#undef REGION_CLASS
 }
 
 /* ---------------------------------------------------------------------- */
@@ -116,6 +125,8 @@ Domain::~Domain()
   delete lattice;
   for (int i = 0; i < nregion; i++) delete regions[i];
   memory->sfree(regions);
+
+  delete region_map;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1524,51 +1535,33 @@ void Domain::add_region(int narg, char **arg)
     if (lmp->suffix) {
       char estyle[256];
       sprintf(estyle,"%s/%s",arg[1],lmp->suffix);
-
-      if (0) return;
-
-#define REGION_CLASS
-#define RegionStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) { \
-            regions[nregion] = new Class(lmp,narg,arg); \
-            regions[nregion]->init(); \
-            nregion++; \
-            return; \
+      if (region_map->find(estyle) != region_map->end()) {
+        RegionCreator region_creator = (*region_map)[estyle];
+        regions[nregion] = region_creator(lmp, narg, arg);
+        regions[nregion]->init();
+        nregion++;
+        return;
       }
-#include "style_region.h"
-#undef RegionStyle
-#undef REGION_CLASS
     }
 
     if (lmp->suffix2) {
       char estyle[256];
       sprintf(estyle,"%s/%s",arg[1],lmp->suffix2);
-
-      if (0) return;
-
-#define REGION_CLASS
-#define RegionStyle(key,Class) \
-      else if (strcmp(estyle,#key) == 0) { \
-            regions[nregion] = new Class(lmp,narg,arg); \
-            regions[nregion]->init(); \
-            nregion++; \
-            return; \
+      if (region_map->find(estyle) != region_map->end()) {
+        RegionCreator region_creator = (*region_map)[estyle];
+        regions[nregion] = region_creator(lmp, narg, arg);
+        regions[nregion]->init();
+        nregion++;
+        return;
       }
-#include "style_region.h"
-#undef RegionStyle
-#undef REGION_CLASS
     }
   }
 
   if (strcmp(arg[1],"none") == 0) error->all(FLERR,"Unknown region style");
-
-#define REGION_CLASS
-#define RegionStyle(key,Class) \
-  else if (strcmp(arg[1],#key) == 0) \
-    regions[nregion] = new Class(lmp,narg,arg);
-#include "style_region.h"
-#undef REGION_CLASS
-
+  if (region_map->find(arg[1]) != region_map->end()) {
+    RegionCreator region_creator = (*region_map)[arg[1]];
+    regions[nregion] = region_creator(lmp, narg, arg);
+  }
   else error->all(FLERR,"Unknown region style");
 
   // initialize any region variables via init()
@@ -1578,6 +1571,16 @@ void Domain::add_region(int narg, char **arg)
   nregion++;
 }
 
+/* ----------------------------------------------------------------------
+   one instance per region style in style_region.h
+------------------------------------------------------------------------- */
+
+template <typename T>
+Region *Domain::region_creator(LAMMPS *lmp, int narg, char ** arg)
+{
+  return new T(lmp, narg, arg);
+}
+
 /* ----------------------------------------------------------------------
    delete a region
 ------------------------------------------------------------------------- */
diff --git a/src/domain.h b/src/domain.h
index 8654b59168..ef3de42071 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -16,6 +16,8 @@
 
 #include <math.h>
 #include "pointers.h"
+#include <map>
+#include <string>
 
 namespace LAMMPS_NS {
 
@@ -92,6 +94,10 @@ class Domain : protected Pointers {
 
   int copymode;
 
+  typedef Region *(*RegionCreator)(LAMMPS *,int,char**);
+  typedef std::map<std::string,RegionCreator> RegionCreatorMap;
+  RegionCreatorMap *region_map;
+
   Domain(class LAMMPS *);
   virtual ~Domain();
   virtual void init();
@@ -151,6 +157,9 @@ class Domain : protected Pointers {
 
  protected:
   double small[3];                  // fractions of box lengths
+
+ private:
+  template <typename T> static Region *region_creator(LAMMPS *,int,char**);
 };
 
 }
diff --git a/src/info.cpp b/src/info.cpp
index 22cb432acc..c150e0a886 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -722,10 +722,11 @@ void Info::region_styles(FILE * out)
   fprintf(out, "\nRegion styles:\n");
 
   vector<string> styles;
-#define REGION_CLASS
-#define RegionStyle(key,Class) styles.push_back(#key);
-#include "style_region.h"
-#undef REGION_CLASS
+
+  for(Domain::RegionCreatorMap::iterator it = domain->region_map->begin(); it != domain->region_map->end(); ++it) {
+    styles.push_back(it->first);
+  }
+
   print_columns(out, styles);
   fprintf(out, "\n\n\n");
 }
-- 
GitLab


From 2dcfb51d180758a2c8c5932aaf6a013a187e1a79 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 8 Sep 2016 01:20:19 -0400
Subject: [PATCH 46/52] Change info command styles syntax

Change to `info styles [all|atom|pair|compute|...]`.
By default, `info styles` will print all styles.
---
 src/info.cpp | 98 +++++++++++++++++++++++++++++-----------------------
 1 file changed, 54 insertions(+), 44 deletions(-)

diff --git a/src/info.cpp b/src/info.cpp
index c150e0a886..175ea7c94f 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -150,48 +150,6 @@ void Info::command(int narg, char **arg)
       if ((out != screen) && (out != logfile)) fclose(out);
       out = fopen(arg[idx+2],"w");
       idx += 3;
-    } else if (strncmp(arg[idx],"atom_styles",3) == 0) {
-      flags |= ATOM_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"integrate_styles",3) == 0) {
-      flags |= INTEGRATE_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"minimize_styles",3) == 0) {
-      flags |= MINIMIZE_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"pair_styles",3) == 0) {
-      flags |= PAIR_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"bond_styles",3) == 0) {
-      flags |= BOND_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"angle_styles",3) == 0) {
-      flags |= ANGLE_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"dihedral_styles",3) == 0) {
-      flags |= DIHEDRAL_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"improper_styles",3) == 0) {
-      flags |= IMPROPER_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"kspace_styles",3) == 0) {
-      flags |= KSPACE_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"fix_styles",3) == 0) {
-      flags |= FIX_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"compute_styles",5) == 0) {
-      flags |= COMPUTE_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"region_styles",3) == 0) {
-      flags |= REGION_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"dump_styles",3) == 0) {
-      flags |= DUMP_STYLES;
-      ++idx;
-    } else if (strncmp(arg[idx],"command_styles",5) == 0) {
-      flags |= COMMAND_STYLES;
-      ++idx;
     } else if (strncmp(arg[idx],"communication",5) == 0) {
       flags |= COMM;
       ++idx;
@@ -223,8 +181,60 @@ void Info::command(int narg, char **arg)
       flags |= SYSTEM;
       ++idx;
     } else if (strncmp(arg[idx],"styles",3) == 0) {
-      flags |= STYLES;
-      ++idx;
+      if (idx+1 < narg) {
+        ++idx;
+        if (strncmp(arg[idx],"all",3) == 0) {
+          flags |= STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"atom",3) == 0) {
+          flags |= ATOM_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"integrate",3) == 0) {
+          flags |= INTEGRATE_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"minimize",3) == 0) {
+          flags |= MINIMIZE_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"pair",3) == 0) {
+          flags |= PAIR_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"bond",3) == 0) {
+          flags |= BOND_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"angle",3) == 0) {
+          flags |= ANGLE_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"dihedral",3) == 0) {
+          flags |= DIHEDRAL_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"improper",3) == 0) {
+          flags |= IMPROPER_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"kspace",3) == 0) {
+          flags |= KSPACE_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"fix",3) == 0) {
+          flags |= FIX_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"compute",4) == 0) {
+          flags |= COMPUTE_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"region",3) == 0) {
+          flags |= REGION_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"dump",3) == 0) {
+          flags |= DUMP_STYLES;
+          ++idx;
+        } else if (strncmp(arg[idx],"command",4) == 0) {
+          flags |= COMMAND_STYLES;
+          ++idx;
+        } else {
+          flags |= STYLES;
+        }
+      } else {
+        flags |= STYLES;
+        ++idx;
+      }
     } else {
       error->warning(FLERR,"Ignoring unknown or incorrect info command flag");
       ++idx;
-- 
GitLab


From 79b8f6320d622d78c48c7a1114686a7055670e4d Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 8 Sep 2016 09:53:14 -0400
Subject: [PATCH 47/52] Update docs of info command

---
 doc/src/info.txt | 29 ++++++++++++++++++++++++++---
 1 file changed, 26 insertions(+), 3 deletions(-)

diff --git a/doc/src/info.txt b/doc/src/info.txt
index b973b3f199..73bc07eb13 100644
--- a/doc/src/info.txt
+++ b/doc/src/info.txt
@@ -12,15 +12,18 @@ info command :h3
 
 info args :pre
 
-args = one or more of the following keywords: {out}, {all}, {system}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {time}, or {configuration}
-     {out} values = {screen}, {log}, {append} filename, {overwrite} filename:ul
+args = one or more of the following keywords: {out}, {all}, {system}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {styles}, {time}, or {configuration}
+     {out} values = {screen}, {log}, {append} filename, {overwrite} filename
+     {styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {region} :ul
 
 [Examples:]
 
 info system
 info groups computes variables
 info all out log
-info all out append info.txt :pre
+info all out append info.txt
+info styles all
+info styles atom :pre
 
 [Description:]
 
@@ -67,6 +70,24 @@ The {variables} category prints a list of all currently defined
 variables, their names, styles, definition and last computed value, if
 available.
 
+The {styles} category prints the list of styles available in LAMMPS. It
+supports one of the following options to control what is printed out:
+
+all
+angle
+atom
+bond
+compute
+command
+dump
+dihedral
+fix
+improper
+integrate
+kspace
+minimize
+region :ul
+
 The {time} category prints the accumulated CPU and wall time for the
 process that writes output (usually MPI rank 0).
 
@@ -84,3 +105,5 @@ reported.
 [Default:]
 
 The {out} option has the default {screen}.
+
+The {styles} option has the default {all}.
-- 
GitLab


From 1f901c9b2daac713972efa30d7925e904bb1d2c0 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 8 Sep 2016 09:53:57 -0400
Subject: [PATCH 48/52] Update generated HTML docs of info command

---
 doc/html/info.html | 30 ++++++++++++++++++++++++++----
 1 file changed, 26 insertions(+), 4 deletions(-)

diff --git a/doc/html/info.html b/doc/html/info.html
index 8b263884ae..b60c5a6b9d 100644
--- a/doc/html/info.html
+++ b/doc/html/info.html
@@ -131,10 +131,11 @@
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">info</span> <span class="n">args</span>
 </pre></div>
 </div>
-<dl class="docutils">
-<dt>args = one or more of the following keywords: <em>out</em>, <em>all</em>, <em>system</em>, <em>communication</em>, <em>computes</em>, <em>dumps</em>, <em>fixes</em>, <em>groups</em>, <em>regions</em>, <em>variables</em>, <em>time</em>, or <em>configuration</em></dt>
-<dd><em>out</em> values = <em>screen</em>, <em>log</em>, <em>append</em> filename, <em>overwrite</em> filename:ul</dd>
-</dl>
+<ul class="simple">
+<li>args = one or more of the following keywords: <em>out</em>, <em>all</em>, <em>system</em>, <em>communication</em>, <em>computes</em>, <em>dumps</em>, <em>fixes</em>, <em>groups</em>, <em>regions</em>, <em>variables</em>, <em>styles</em>, <em>time</em>, or <em>configuration</em></li>
+<li><em>out</em> values = <em>screen</em>, <em>log</em>, <em>append</em> filename, <em>overwrite</em> filename</li>
+<li><em>styles</em> values = <em>all</em>, <em>angle</em>, <em>atom</em>, <em>bond</em>, <em>compute</em>, <em>command</em>, <em>dump</em>, <em>dihedral</em>, <em>fix</em>, <em>improper</em>, <em>integrate</em>, <em>kspace</em>, <em>minimize</em>, <em>region</em></li>
+</ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
@@ -142,6 +143,8 @@
 <span class="n">info</span> <span class="n">groups</span> <span class="n">computes</span> <span class="n">variables</span>
 <span class="n">info</span> <span class="nb">all</span> <span class="n">out</span> <span class="n">log</span>
 <span class="n">info</span> <span class="nb">all</span> <span class="n">out</span> <span class="n">append</span> <span class="n">info</span><span class="o">.</span><span class="n">txt</span>
+<span class="n">info</span> <span class="n">styles</span> <span class="nb">all</span>
+<span class="n">info</span> <span class="n">styles</span> <span class="n">atom</span>
 </pre></div>
 </div>
 </div>
@@ -179,6 +182,24 @@ selected.</p>
 <p>The <em>variables</em> category prints a list of all currently defined
 variables, their names, styles, definition and last computed value, if
 available.</p>
+<p>The <em>styles</em> category prints the list of styles available in LAMMPS. It
+supports one of the following options to control what is printed out:</p>
+<ul class="simple">
+<li>all</li>
+<li>angle</li>
+<li>atom</li>
+<li>bond</li>
+<li>compute</li>
+<li>command</li>
+<li>dump</li>
+<li>dihedral</li>
+<li>fix</li>
+<li>improper</li>
+<li>integrate</li>
+<li>kspace</li>
+<li>minimize</li>
+<li>region</li>
+</ul>
 <p>The <em>time</em> category prints the accumulated CPU and wall time for the
 process that writes output (usually MPI rank 0).</p>
 <p>The <em>configuration</em> command prints some information about the LAMMPS
@@ -198,6 +219,7 @@ reported.</p>
 <div class="section" id="default">
 <h2>Default</h2>
 <p>The <em>out</em> option has the default <em>screen</em>.</p>
+<p>The <em>styles</em> option has the default <em>all</em>.</p>
 </div>
 </div>
 
-- 
GitLab


From c33e1049d8dd312cd2f6bd67577d696bf610f9c2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Sep 2016 11:51:22 -0400
Subject: [PATCH 49/52] delete duplicate fclose() in fix ttm/mod constructor

---
 src/USER-MISC/fix_ttm_mod.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp
index f7b81c7206..4bf90fdca3 100644
--- a/src/USER-MISC/fix_ttm_mod.cpp
+++ b/src/USER-MISC/fix_ttm_mod.cpp
@@ -282,7 +282,6 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
   if (me == 0) read_initial_electron_temperatures(fpr);
   MPI_Bcast(&T_electron[0][0][0],total_nnodes,MPI_DOUBLE,0,world);
   fclose(fpr);
-  fclose(fpr_2);
 }
 
 /* ---------------------------------------------------------------------- */
-- 
GitLab


From 9b2d5ff3e72df39f52623032c36d8263ff6d8e8d Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Sep 2016 14:45:07 -0400
Subject: [PATCH 50/52] remove executable permissions on non-executables and
 non-scripts

---
 src/ASPHERE/compute_temp_asphere.cpp         | 0
 src/ASPHERE/compute_temp_asphere.h           | 0
 src/ASPHERE/fix_npt_asphere.cpp              | 0
 src/ASPHERE/fix_npt_asphere.h                | 0
 src/ASPHERE/fix_nve_asphere.cpp              | 0
 src/ASPHERE/fix_nve_asphere.h                | 0
 src/ASPHERE/fix_nve_asphere_noforce.h        | 0
 src/ASPHERE/fix_nvt_asphere.cpp              | 0
 src/ASPHERE/fix_nvt_asphere.h                | 0
 src/ASPHERE/pair_gayberne.cpp                | 0
 src/ASPHERE/pair_gayberne.h                  | 0
 src/ASPHERE/pair_resquared.cpp               | 0
 src/ASPHERE/pair_resquared.h                 | 0
 src/BODY/compute_temp_body.cpp               | 0
 src/BODY/compute_temp_body.h                 | 0
 src/BODY/fix_npt_body.cpp                    | 0
 src/BODY/fix_npt_body.h                      | 0
 src/BODY/fix_nvt_body.cpp                    | 0
 src/BODY/fix_nvt_body.h                      | 0
 src/COLLOID/pair_brownian.cpp                | 0
 src/COLLOID/pair_lubricate.cpp               | 0
 src/DIPOLE/pair_lj_cut_dipole_cut.cpp        | 0
 src/DIPOLE/pair_lj_cut_dipole_cut.h          | 0
 src/DIPOLE/pair_lj_cut_dipole_long.cpp       | 0
 src/DIPOLE/pair_lj_cut_dipole_long.h         | 0
 src/DIPOLE/pair_lj_long_dipole_long.cpp      | 0
 src/DIPOLE/pair_lj_long_dipole_long.h        | 0
 src/GPU/pair_lj_cut_dipole_cut_gpu.cpp       | 0
 src/GPU/pair_lj_cut_dipole_cut_gpu.h         | 0
 src/GPU/pair_lj_sf_dipole_sf_gpu.cpp         | 0
 src/GPU/pair_lj_sf_dipole_sf_gpu.h           | 0
 src/KOKKOS/angle_charmm_kokkos.cpp           | 0
 src/KOKKOS/angle_charmm_kokkos.h             | 0
 src/KOKKOS/angle_harmonic_kokkos.cpp         | 0
 src/KOKKOS/angle_harmonic_kokkos.h           | 0
 src/KOKKOS/bond_fene_kokkos.cpp              | 0
 src/KOKKOS/bond_fene_kokkos.h                | 0
 src/KOKKOS/bond_harmonic_kokkos.cpp          | 0
 src/KOKKOS/bond_harmonic_kokkos.h            | 0
 src/KOKKOS/compute_temp_kokkos.cpp           | 0
 src/KOKKOS/compute_temp_kokkos.h             | 0
 src/KOKKOS/dihedral_charmm_kokkos.cpp        | 0
 src/KOKKOS/dihedral_charmm_kokkos.h          | 0
 src/KOKKOS/dihedral_opls_kokkos.cpp          | 0
 src/KOKKOS/dihedral_opls_kokkos.h            | 0
 src/KOKKOS/fix_deform_kokkos.cpp             | 0
 src/KOKKOS/fix_deform_kokkos.h               | 0
 src/KOKKOS/fix_nh_kokkos.cpp                 | 0
 src/KOKKOS/fix_nh_kokkos.h                   | 0
 src/KOKKOS/fix_nph_kokkos.cpp                | 0
 src/KOKKOS/fix_nph_kokkos.h                  | 0
 src/KOKKOS/fix_npt_kokkos.cpp                | 0
 src/KOKKOS/fix_npt_kokkos.h                  | 0
 src/KOKKOS/fix_nvt_kokkos.cpp                | 0
 src/KOKKOS/fix_nvt_kokkos.h                  | 0
 src/KOKKOS/fix_setforce_kokkos.cpp           | 0
 src/KOKKOS/fix_setforce_kokkos.h             | 0
 src/KOKKOS/fix_wall_reflect_kokkos.cpp       | 0
 src/KOKKOS/fix_wall_reflect_kokkos.h         | 0
 src/KOKKOS/improper_harmonic_kokkos.cpp      | 0
 src/KOKKOS/improper_harmonic_kokkos.h        | 0
 src/KOKKOS/neigh_bond_kokkos.cpp             | 0
 src/KOKKOS/neigh_bond_kokkos.h               | 0
 src/KOKKOS/pair_buck_kokkos.cpp              | 0
 src/KOKKOS/pair_buck_kokkos.h                | 0
 src/KOKKOS/pair_coul_dsf_kokkos.cpp          | 0
 src/KOKKOS/pair_coul_dsf_kokkos.h            | 0
 src/KOKKOS/pair_coul_wolf_kokkos.cpp         | 0
 src/KOKKOS/pair_coul_wolf_kokkos.h           | 0
 src/KOKKOS/pair_eam_alloy_kokkos.cpp         | 0
 src/KOKKOS/pair_eam_alloy_kokkos.h           | 0
 src/KOKKOS/pair_eam_fs_kokkos.cpp            | 0
 src/KOKKOS/pair_eam_fs_kokkos.h              | 0
 src/KOKKOS/pair_eam_kokkos.cpp               | 0
 src/KOKKOS/pair_eam_kokkos.h                 | 0
 src/KOKKOS/pair_sw_kokkos.cpp                | 0
 src/KOKKOS/pair_sw_kokkos.h                  | 0
 src/KOKKOS/pair_tersoff_kokkos.cpp           | 0
 src/KOKKOS/pair_tersoff_kokkos.h             | 0
 src/KOKKOS/pair_tersoff_mod_kokkos.cpp       | 0
 src/KOKKOS/pair_tersoff_mod_kokkos.h         | 0
 src/KOKKOS/pair_tersoff_zbl_kokkos.cpp       | 0
 src/KOKKOS/pair_tersoff_zbl_kokkos.h         | 0
 src/KOKKOS/region_block_kokkos.cpp           | 0
 src/KOKKOS/region_block_kokkos.h             | 0
 src/KSPACE/pair_lj_long_tip4p_long.cpp       | 0
 src/KSPACE/pair_lj_long_tip4p_long.h         | 0
 src/KSPACE/pppm_disp.cpp                     | 0
 src/KSPACE/pppm_disp.h                       | 0
 src/KSPACE/pppm_disp_tip4p.cpp               | 0
 src/KSPACE/pppm_disp_tip4p.h                 | 0
 src/KSPACE/pppm_stagger.cpp                  | 0
 src/KSPACE/pppm_stagger.h                    | 0
 src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi | 0
 src/MAKE/OPTIONS/Makefile.intel_cpu_mpich    | 0
 src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi  | 0
 src/MAKE/OPTIONS/Makefile.knl                | 0
 src/MANYBODY/pair_polymorphic.cpp            | 0
 src/MANYBODY/pair_polymorphic.h              | 0
 src/MANYBODY/pair_sw.cpp                     | 0
 src/MANYBODY/pair_sw.h                       | 0
 src/MANYBODY/pair_tersoff.cpp                | 0
 src/MANYBODY/pair_tersoff.h                  | 0
 src/MANYBODY/pair_tersoff_zbl.h              | 0
 src/MANYBODY/pair_vashishta.cpp              | 0
 src/MANYBODY/pair_vashishta.h                | 0
 src/MC/fix_bond_break.cpp                    | 0
 src/MC/fix_bond_break.h                      | 0
 src/MC/fix_bond_create.cpp                   | 0
 src/MC/fix_bond_create.h                     | 0
 src/MC/fix_tfmc.cpp                          | 0
 src/MC/fix_tfmc.h                            | 0
 src/MOLECULE/bond_quartic.cpp                | 0
 src/Makefile                                 | 0
 src/PERI/atom_vec_peri.h                     | 0
 src/USER-INTEL/bond_fene_intel.cpp           | 0
 src/USER-INTEL/bond_fene_intel.h             | 0
 src/USER-INTEL/fix_nve_asphere_intel.cpp     | 0
 src/USER-INTEL/fix_nve_asphere_intel.h       | 0
 src/USER-INTEL/pair_sw_intel.cpp             | 0
 src/USER-INTEL/pair_sw_intel.h               | 0
 src/USER-LB/README                           | 0
 src/USER-LB/fix_lb_fluid.cpp                 | 0
 src/USER-LB/fix_lb_fluid.h                   | 0
 src/USER-LB/fix_lb_momentum.cpp              | 0
 src/USER-LB/fix_lb_momentum.h                | 0
 src/USER-LB/fix_lb_pc.cpp                    | 0
 src/USER-LB/fix_lb_pc.h                      | 0
 src/USER-LB/fix_lb_rigid_pc_sphere.cpp       | 0
 src/USER-LB/fix_lb_rigid_pc_sphere.h         | 0
 src/USER-LB/fix_lb_viscous.cpp               | 0
 src/USER-LB/fix_lb_viscous.h                 | 0
 src/USER-MISC/fix_ti_rs.cpp                  | 0
 src/USER-MISC/fix_ti_rs.h                    | 0
 src/USER-MISC/fix_ti_spring.cpp              | 0
 src/USER-MISC/fix_ti_spring.h                | 0
 src/USER-MISC/pair_edip.cpp                  | 0
 src/USER-MISC/pair_edip.h                    | 0
 src/USER-MISC/pair_lj_sf_dipole_sf.cpp       | 0
 src/USER-MISC/pair_lj_sf_dipole_sf.h         | 0
 src/USER-OMP/msm_omp.cpp                     | 0
 src/USER-OMP/msm_omp.h                       | 0
 src/USER-OMP/pair_born_coul_msm_omp.cpp      | 0
 src/USER-OMP/pair_born_coul_msm_omp.h        | 0
 src/USER-OMP/pair_buck_coul_msm_omp.cpp      | 0
 src/USER-OMP/pair_buck_coul_msm_omp.h        | 0
 src/USER-OMP/pair_coul_msm_omp.cpp           | 0
 src/USER-OMP/pair_coul_msm_omp.h             | 0
 src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp | 0
 src/USER-OMP/pair_lj_charmm_coul_msm_omp.h   | 0
 src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp    | 0
 src/USER-OMP/pair_lj_cut_coul_msm_omp.h      | 0
 src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp  | 0
 src/USER-OMP/pair_lj_cut_dipole_cut_omp.h    | 0
 src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp    | 0
 src/USER-OMP/pair_lj_sf_dipole_sf_omp.h      | 0
 src/atom_vec_ellipsoid.cpp                   | 0
 src/atom_vec_ellipsoid.h                     | 0
 src/compute_pe_atom.cpp                      | 0
 src/compute_pe_atom.h                        | 0
 src/compute_vacf.cpp                         | 0
 src/compute_vacf.h                           | 0
 src/dump_cfg.cpp                             | 0
 src/dump_cfg.h                               | 0
 src/fix_controller.h                         | 0
 src/math_extra.h                             | 0
 166 files changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 src/ASPHERE/compute_temp_asphere.cpp
 mode change 100755 => 100644 src/ASPHERE/compute_temp_asphere.h
 mode change 100755 => 100644 src/ASPHERE/fix_npt_asphere.cpp
 mode change 100755 => 100644 src/ASPHERE/fix_npt_asphere.h
 mode change 100755 => 100644 src/ASPHERE/fix_nve_asphere.cpp
 mode change 100755 => 100644 src/ASPHERE/fix_nve_asphere.h
 mode change 100755 => 100644 src/ASPHERE/fix_nve_asphere_noforce.h
 mode change 100755 => 100644 src/ASPHERE/fix_nvt_asphere.cpp
 mode change 100755 => 100644 src/ASPHERE/fix_nvt_asphere.h
 mode change 100755 => 100644 src/ASPHERE/pair_gayberne.cpp
 mode change 100755 => 100644 src/ASPHERE/pair_gayberne.h
 mode change 100755 => 100644 src/ASPHERE/pair_resquared.cpp
 mode change 100755 => 100644 src/ASPHERE/pair_resquared.h
 mode change 100755 => 100644 src/BODY/compute_temp_body.cpp
 mode change 100755 => 100644 src/BODY/compute_temp_body.h
 mode change 100755 => 100644 src/BODY/fix_npt_body.cpp
 mode change 100755 => 100644 src/BODY/fix_npt_body.h
 mode change 100755 => 100644 src/BODY/fix_nvt_body.cpp
 mode change 100755 => 100644 src/BODY/fix_nvt_body.h
 mode change 100755 => 100644 src/COLLOID/pair_brownian.cpp
 mode change 100755 => 100644 src/COLLOID/pair_lubricate.cpp
 mode change 100755 => 100644 src/DIPOLE/pair_lj_cut_dipole_cut.cpp
 mode change 100755 => 100644 src/DIPOLE/pair_lj_cut_dipole_cut.h
 mode change 100755 => 100644 src/DIPOLE/pair_lj_cut_dipole_long.cpp
 mode change 100755 => 100644 src/DIPOLE/pair_lj_cut_dipole_long.h
 mode change 100755 => 100644 src/DIPOLE/pair_lj_long_dipole_long.cpp
 mode change 100755 => 100644 src/DIPOLE/pair_lj_long_dipole_long.h
 mode change 100755 => 100644 src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
 mode change 100755 => 100644 src/GPU/pair_lj_cut_dipole_cut_gpu.h
 mode change 100755 => 100644 src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
 mode change 100755 => 100644 src/GPU/pair_lj_sf_dipole_sf_gpu.h
 mode change 100755 => 100644 src/KOKKOS/angle_charmm_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/angle_charmm_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/angle_harmonic_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/angle_harmonic_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/bond_fene_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/bond_fene_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/bond_harmonic_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/bond_harmonic_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/compute_temp_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/compute_temp_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/dihedral_charmm_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/dihedral_charmm_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/dihedral_opls_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/dihedral_opls_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/fix_deform_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/fix_deform_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/fix_nh_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/fix_nh_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/fix_nph_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/fix_nph_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/fix_npt_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/fix_npt_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/fix_nvt_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/fix_nvt_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/fix_setforce_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/fix_setforce_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/fix_wall_reflect_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/fix_wall_reflect_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/improper_harmonic_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/improper_harmonic_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/neigh_bond_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/neigh_bond_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/pair_buck_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/pair_buck_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/pair_coul_dsf_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/pair_coul_dsf_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/pair_coul_wolf_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/pair_coul_wolf_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/pair_eam_alloy_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/pair_eam_alloy_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/pair_eam_fs_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/pair_eam_fs_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/pair_eam_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/pair_eam_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/pair_sw_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/pair_sw_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/pair_tersoff_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/pair_tersoff_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/pair_tersoff_mod_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/pair_tersoff_mod_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/pair_tersoff_zbl_kokkos.h
 mode change 100755 => 100644 src/KOKKOS/region_block_kokkos.cpp
 mode change 100755 => 100644 src/KOKKOS/region_block_kokkos.h
 mode change 100755 => 100644 src/KSPACE/pair_lj_long_tip4p_long.cpp
 mode change 100755 => 100644 src/KSPACE/pair_lj_long_tip4p_long.h
 mode change 100755 => 100644 src/KSPACE/pppm_disp.cpp
 mode change 100755 => 100644 src/KSPACE/pppm_disp.h
 mode change 100755 => 100644 src/KSPACE/pppm_disp_tip4p.cpp
 mode change 100755 => 100644 src/KSPACE/pppm_disp_tip4p.h
 mode change 100755 => 100644 src/KSPACE/pppm_stagger.cpp
 mode change 100755 => 100644 src/KSPACE/pppm_stagger.h
 mode change 100755 => 100644 src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
 mode change 100755 => 100644 src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
 mode change 100755 => 100644 src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi
 mode change 100755 => 100644 src/MAKE/OPTIONS/Makefile.knl
 mode change 100755 => 100644 src/MANYBODY/pair_polymorphic.cpp
 mode change 100755 => 100644 src/MANYBODY/pair_polymorphic.h
 mode change 100755 => 100644 src/MANYBODY/pair_sw.cpp
 mode change 100755 => 100644 src/MANYBODY/pair_sw.h
 mode change 100755 => 100644 src/MANYBODY/pair_tersoff.cpp
 mode change 100755 => 100644 src/MANYBODY/pair_tersoff.h
 mode change 100755 => 100644 src/MANYBODY/pair_tersoff_zbl.h
 mode change 100755 => 100644 src/MANYBODY/pair_vashishta.cpp
 mode change 100755 => 100644 src/MANYBODY/pair_vashishta.h
 mode change 100755 => 100644 src/MC/fix_bond_break.cpp
 mode change 100755 => 100644 src/MC/fix_bond_break.h
 mode change 100755 => 100644 src/MC/fix_bond_create.cpp
 mode change 100755 => 100644 src/MC/fix_bond_create.h
 mode change 100755 => 100644 src/MC/fix_tfmc.cpp
 mode change 100755 => 100644 src/MC/fix_tfmc.h
 mode change 100755 => 100644 src/MOLECULE/bond_quartic.cpp
 mode change 100755 => 100644 src/Makefile
 mode change 100755 => 100644 src/PERI/atom_vec_peri.h
 mode change 100755 => 100644 src/USER-INTEL/bond_fene_intel.cpp
 mode change 100755 => 100644 src/USER-INTEL/bond_fene_intel.h
 mode change 100755 => 100644 src/USER-INTEL/fix_nve_asphere_intel.cpp
 mode change 100755 => 100644 src/USER-INTEL/fix_nve_asphere_intel.h
 mode change 100755 => 100644 src/USER-INTEL/pair_sw_intel.cpp
 mode change 100755 => 100644 src/USER-INTEL/pair_sw_intel.h
 mode change 100755 => 100644 src/USER-LB/README
 mode change 100755 => 100644 src/USER-LB/fix_lb_fluid.cpp
 mode change 100755 => 100644 src/USER-LB/fix_lb_fluid.h
 mode change 100755 => 100644 src/USER-LB/fix_lb_momentum.cpp
 mode change 100755 => 100644 src/USER-LB/fix_lb_momentum.h
 mode change 100755 => 100644 src/USER-LB/fix_lb_pc.cpp
 mode change 100755 => 100644 src/USER-LB/fix_lb_pc.h
 mode change 100755 => 100644 src/USER-LB/fix_lb_rigid_pc_sphere.cpp
 mode change 100755 => 100644 src/USER-LB/fix_lb_rigid_pc_sphere.h
 mode change 100755 => 100644 src/USER-LB/fix_lb_viscous.cpp
 mode change 100755 => 100644 src/USER-LB/fix_lb_viscous.h
 mode change 100755 => 100644 src/USER-MISC/fix_ti_rs.cpp
 mode change 100755 => 100644 src/USER-MISC/fix_ti_rs.h
 mode change 100755 => 100644 src/USER-MISC/fix_ti_spring.cpp
 mode change 100755 => 100644 src/USER-MISC/fix_ti_spring.h
 mode change 100755 => 100644 src/USER-MISC/pair_edip.cpp
 mode change 100755 => 100644 src/USER-MISC/pair_edip.h
 mode change 100755 => 100644 src/USER-MISC/pair_lj_sf_dipole_sf.cpp
 mode change 100755 => 100644 src/USER-MISC/pair_lj_sf_dipole_sf.h
 mode change 100755 => 100644 src/USER-OMP/msm_omp.cpp
 mode change 100755 => 100644 src/USER-OMP/msm_omp.h
 mode change 100755 => 100644 src/USER-OMP/pair_born_coul_msm_omp.cpp
 mode change 100755 => 100644 src/USER-OMP/pair_born_coul_msm_omp.h
 mode change 100755 => 100644 src/USER-OMP/pair_buck_coul_msm_omp.cpp
 mode change 100755 => 100644 src/USER-OMP/pair_buck_coul_msm_omp.h
 mode change 100755 => 100644 src/USER-OMP/pair_coul_msm_omp.cpp
 mode change 100755 => 100644 src/USER-OMP/pair_coul_msm_omp.h
 mode change 100755 => 100644 src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
 mode change 100755 => 100644 src/USER-OMP/pair_lj_charmm_coul_msm_omp.h
 mode change 100755 => 100644 src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
 mode change 100755 => 100644 src/USER-OMP/pair_lj_cut_coul_msm_omp.h
 mode change 100755 => 100644 src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
 mode change 100755 => 100644 src/USER-OMP/pair_lj_cut_dipole_cut_omp.h
 mode change 100755 => 100644 src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
 mode change 100755 => 100644 src/USER-OMP/pair_lj_sf_dipole_sf_omp.h
 mode change 100755 => 100644 src/atom_vec_ellipsoid.cpp
 mode change 100755 => 100644 src/atom_vec_ellipsoid.h
 mode change 100755 => 100644 src/compute_pe_atom.cpp
 mode change 100755 => 100644 src/compute_pe_atom.h
 mode change 100755 => 100644 src/compute_vacf.cpp
 mode change 100755 => 100644 src/compute_vacf.h
 mode change 100755 => 100644 src/dump_cfg.cpp
 mode change 100755 => 100644 src/dump_cfg.h
 mode change 100755 => 100644 src/fix_controller.h
 mode change 100755 => 100644 src/math_extra.h

diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp
old mode 100755
new mode 100644
diff --git a/src/ASPHERE/compute_temp_asphere.h b/src/ASPHERE/compute_temp_asphere.h
old mode 100755
new mode 100644
diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp
old mode 100755
new mode 100644
diff --git a/src/ASPHERE/fix_npt_asphere.h b/src/ASPHERE/fix_npt_asphere.h
old mode 100755
new mode 100644
diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp
old mode 100755
new mode 100644
diff --git a/src/ASPHERE/fix_nve_asphere.h b/src/ASPHERE/fix_nve_asphere.h
old mode 100755
new mode 100644
diff --git a/src/ASPHERE/fix_nve_asphere_noforce.h b/src/ASPHERE/fix_nve_asphere_noforce.h
old mode 100755
new mode 100644
diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp
old mode 100755
new mode 100644
diff --git a/src/ASPHERE/fix_nvt_asphere.h b/src/ASPHERE/fix_nvt_asphere.h
old mode 100755
new mode 100644
diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp
old mode 100755
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-- 
GitLab


From a6df1e53b43f9104fad5e5b54b595d013bde2e64 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Sep 2016 14:46:09 -0400
Subject: [PATCH 51/52] ignore all variants of the vashishta pair styles in
 src/

---
 src/.gitignore | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/.gitignore b/src/.gitignore
index 6e8f637d95..b18bfe8a6e 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -1010,6 +1010,6 @@
 /pair_morse_smooth_linear.h
 /pair_smtbq.cpp
 /pair_smtbq.h
-/pair_vashishta.cpp
-/pair_vashishta.h
+/pair_vashishta*.cpp
+/pair_vashishta*.h
 
-- 
GitLab


From 236ebf7fabbb3dc07b231b9a74c378c40540b1b4 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Thu, 8 Sep 2016 13:56:18 -0600
Subject: [PATCH 52/52] Kokkos lib update

---
 lib/kokkos/CMakeLists.txt                     |   54 +-
 lib/kokkos/Makefile.kokkos                    |   23 +-
 lib/kokkos/Makefile.targets                   |   14 +-
 lib/kokkos/README                             |   31 +-
 lib/kokkos/algorithms/src/Kokkos_Random.hpp   |  349 +-
 .../algorithms/unit_tests/TestRandom.hpp      |   35 +-
 lib/kokkos/cmake/deps/CUDA.cmake              |   79 +
 lib/kokkos/cmake/deps/CUSPARSE.cmake          |   64 +
 lib/kokkos/cmake/deps/HWLOC.cmake             |   70 +
 lib/kokkos/cmake/deps/Pthread.cmake           |   83 +
 lib/kokkos/cmake/deps/QTHREAD.cmake           |   70 +
 lib/kokkos/cmake/tribits.cmake                |  485 +++
 .../kokkos-trilinos-integration-procedure.txt |  153 +
 lib/kokkos/config/master_history.txt          |    3 +
 lib/kokkos/config/nvcc_wrapper                |   46 +-
 lib/kokkos/config/test_all_sandia             |  201 +-
 .../performance_tests/CMakeLists.txt          |   17 +-
 .../containers/performance_tests/TestCuda.cpp |    9 +
 .../performance_tests/TestDynRankView.hpp     |  265 ++
 .../performance_tests/TestGlobal2LocalIds.hpp |    2 +-
 .../performance_tests/TestOpenMP.cpp          |    9 +
 .../performance_tests/TestThreads.cpp         |    9 +
 .../TestUnorderedMapPerformance.hpp           |    4 +-
 .../containers/src/Kokkos_DynRankView.hpp     | 1367 +++++--
 .../containers/src/Kokkos_DynamicView.hpp     |    9 +-
 .../src/impl/Kokkos_Bitset_impl.hpp           |  110 +-
 .../containers/unit_tests/TestDynViewAPI.hpp  |  374 +-
 .../containers/unit_tests/TestDynamicView.hpp |    7 +-
 lib/kokkos/core/cmake/KokkosCore_config.h.in  |    1 +
 lib/kokkos/core/perf_test/CMakeLists.txt      |   15 +-
 lib/kokkos/core/perf_test/PerfTestCuda.cpp    |    2 +-
 .../core/perf_test/PerfTestGramSchmidt.hpp    |    2 +-
 lib/kokkos/core/perf_test/PerfTestHexGrad.hpp |    2 +-
 lib/kokkos/core/perf_test/test_atomic.cpp     |   19 +-
 lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp  |   38 +-
 lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp |  163 +-
 .../core/src/Cuda/Kokkos_Cuda_Alloc.hpp       |    1 -
 .../src/Cuda/Kokkos_Cuda_BasicAllocators.cpp  |  198 -
 .../src/Cuda/Kokkos_Cuda_BasicAllocators.hpp  |  190 -
 lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp |  111 +-
 .../core/src/Cuda/Kokkos_Cuda_Internal.hpp    |   40 +-
 .../core/src/Cuda/Kokkos_Cuda_Parallel.hpp    |  774 ++--
 .../core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp  |   18 +-
 lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.cpp |  179 +
 lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp |  519 +++
 .../core/src/Cuda/Kokkos_Cuda_TaskPolicy.cpp  |   12 +-
 .../core/src/Cuda/Kokkos_Cuda_TaskPolicy.hpp  |   24 +-
 lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp |  339 --
 .../core/src/KokkosExp_MDRangePolicy.hpp      |  611 +++
 lib/kokkos/core/src/KokkosExp_View.hpp        | 2306 ------------
 lib/kokkos/core/src/Kokkos_Complex.hpp        |   15 +-
 ...asicAllocators.hpp => Kokkos_Concepts.hpp} |   99 +-
 lib/kokkos/core/src/Kokkos_Core.hpp           |   72 -
 lib/kokkos/core/src/Kokkos_Core_fwd.hpp       |    7 +-
 lib/kokkos/core/src/Kokkos_Cuda.hpp           |   15 +-
 lib/kokkos/core/src/Kokkos_CudaSpace.hpp      |   93 +-
 lib/kokkos/core/src/Kokkos_ExecPolicy.hpp     |  231 +-
 lib/kokkos/core/src/Kokkos_HBWSpace.hpp       |   15 -
 lib/kokkos/core/src/Kokkos_HostSpace.hpp      |   22 -
 lib/kokkos/core/src/Kokkos_Macros.hpp         |   31 +-
 lib/kokkos/core/src/Kokkos_MemoryPool.hpp     | 1701 +++++++--
 lib/kokkos/core/src/Kokkos_OpenMP.hpp         |   11 +-
 lib/kokkos/core/src/Kokkos_Pair.hpp           |   25 +-
 lib/kokkos/core/src/Kokkos_Parallel.hpp       |  431 +--
 .../core/src/Kokkos_Parallel_Reduce.hpp       | 1240 ++++++
 lib/kokkos/core/src/Kokkos_ScratchSpace.hpp   |   68 +-
 lib/kokkos/core/src/Kokkos_Serial.hpp         |  185 +-
 lib/kokkos/core/src/Kokkos_TaskPolicy.hpp     |  652 +++-
 lib/kokkos/core/src/Kokkos_Threads.hpp        |   10 +-
 lib/kokkos/core/src/Kokkos_View.hpp           | 3322 +++++++++--------
 .../src/OpenMP/Kokkos_OpenMP_Parallel.hpp     |  120 +-
 .../core/src/OpenMP/Kokkos_OpenMP_Task.cpp    |  329 ++
 .../core/src/OpenMP/Kokkos_OpenMP_Task.hpp    |  356 ++
 .../core/src/OpenMP/Kokkos_OpenMPexec.cpp     |   32 +-
 .../core/src/OpenMP/Kokkos_OpenMPexec.hpp     |  138 +-
 .../core/src/Qthread/Kokkos_QthreadExec.cpp   |    2 +-
 .../core/src/Qthread/Kokkos_QthreadExec.hpp   |   32 +-
 .../src/Qthread/Kokkos_Qthread_Parallel.hpp   |  110 +-
 .../src/Qthread/Kokkos_Qthread_TaskPolicy.cpp |   37 +-
 .../src/Qthread/Kokkos_Qthread_TaskPolicy.hpp |  107 +-
 lib/kokkos/core/src/Qthread/README            |   21 +-
 .../core/src/Threads/Kokkos_ThreadsExec.cpp   |   43 +-
 .../core/src/Threads/Kokkos_ThreadsExec.hpp   |   14 -
 .../core/src/Threads/Kokkos_ThreadsTeam.hpp   |   58 +-
 .../src/Threads/Kokkos_Threads_Parallel.hpp   |  100 +-
 .../src/Threads/Kokkos_Threads_TaskPolicy.cpp |   14 +-
 .../src/Threads/Kokkos_Threads_TaskPolicy.hpp |    5 +-
 .../core/src/impl/KokkosExp_SharedAlloc.hpp   |    2 +-
 .../core/src/impl/KokkosExp_ViewCtor.hpp      |    4 -
 .../core/src/impl/KokkosExp_ViewMapping.hpp   |   24 +-
 .../src/impl/Kokkos_AllocationTracker.cpp     |  848 -----
 .../src/impl/Kokkos_AllocationTracker.hpp     |  574 ---
 .../core/src/impl/Kokkos_AnalyzePolicy.hpp    |  197 +
 .../Kokkos_Atomic_Compare_Exchange_Strong.hpp |   22 +-
 .../core/src/impl/Kokkos_Atomic_Exchange.hpp  |   24 +-
 .../core/src/impl/Kokkos_Atomic_Fetch_Add.hpp |   41 +-
 .../core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp |    2 +-
 .../core/src/impl/Kokkos_Atomic_Generic.hpp   |   40 +
 .../core/src/impl/Kokkos_Atomic_View.hpp      |   36 -
 .../core/src/impl/Kokkos_BasicAllocators.cpp  |  287 --
 lib/kokkos/core/src/impl/Kokkos_BitOps.hpp    |  122 +
 lib/kokkos/core/src/impl/Kokkos_Core.cpp      |    4 +-
 .../core/src/impl/Kokkos_FunctorAdapter.hpp   |  120 +-
 lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp  |   18 -
 lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp |   16 -
 .../src/impl/Kokkos_MemoryPool_Inline.hpp     |  446 ---
 .../core/src/impl/Kokkos_PhysicalLayout.hpp   |   13 +-
 .../src/impl/Kokkos_Profiling_DeviceInfo.hpp  |    2 +-
 .../src/impl/Kokkos_Profiling_Interface.cpp   |   13 +-
 .../src/impl/Kokkos_Profiling_Interface.hpp   |    2 +-
 .../core/src/impl/Kokkos_Serial_Task.cpp      |  147 +
 .../core/src/impl/Kokkos_Serial_Task.hpp      |  271 ++
 .../src/impl/Kokkos_Serial_TaskPolicy.cpp     |   18 +-
 .../src/impl/Kokkos_Serial_TaskPolicy.hpp     |   10 +-
 lib/kokkos/core/src/impl/Kokkos_Tags.hpp      |  137 +-
 lib/kokkos/core/src/impl/Kokkos_TaskQueue.hpp |  499 +++
 .../core/src/impl/Kokkos_TaskQueue_impl.hpp   |  569 +++
 lib/kokkos/core/src/impl/Kokkos_Timer.hpp     |    3 +
 lib/kokkos/core/src/impl/Kokkos_Traits.hpp    |   25 +-
 .../core/src/impl/Kokkos_ViewSupport.hpp      |  129 -
 .../core/src/impl/Kokkos_ViewTileLeft.hpp     |  153 -
 lib/kokkos/core/unit_test/CMakeLists.txt      |   19 +-
 lib/kokkos/core/unit_test/Makefile            |   23 +-
 lib/kokkos/core/unit_test/TestAggregate.hpp   |  661 ----
 .../core/unit_test/TestAggregateReduction.hpp |   14 +-
 .../core/unit_test/TestAllocationTracker.cpp  |  159 -
 lib/kokkos/core/unit_test/TestAtomic.hpp      |   11 +-
 .../core/unit_test/TestAtomicOperations.hpp   |  841 +++++
 lib/kokkos/core/unit_test/TestCuda.cpp        |  361 +-
 lib/kokkos/core/unit_test/TestCuda_a.cpp      |  443 +--
 lib/kokkos/core/unit_test/TestCuda_b.cpp      |  486 +--
 lib/kokkos/core/unit_test/TestCuda_c.cpp      |  480 +--
 ...Init.cpp => TestDefaultDeviceTypeInit.hpp} |   35 +-
 .../unit_test/TestDefaultDeviceTypeInit_1.cpp |    2 +
 .../TestDefaultDeviceTypeInit_10.cpp          |    2 +
 .../TestDefaultDeviceTypeInit_11.cpp          |    2 +
 .../TestDefaultDeviceTypeInit_12.cpp          |    2 +
 .../TestDefaultDeviceTypeInit_13.cpp          |    2 +
 .../TestDefaultDeviceTypeInit_14.cpp          |    2 +
 .../TestDefaultDeviceTypeInit_15.cpp          |    2 +
 .../TestDefaultDeviceTypeInit_16.cpp          |    2 +
 .../unit_test/TestDefaultDeviceTypeInit_2.cpp |    2 +
 .../unit_test/TestDefaultDeviceTypeInit_3.cpp |    2 +
 .../unit_test/TestDefaultDeviceTypeInit_4.cpp |    2 +
 .../unit_test/TestDefaultDeviceTypeInit_5.cpp |    2 +
 .../unit_test/TestDefaultDeviceTypeInit_6.cpp |    2 +
 .../unit_test/TestDefaultDeviceTypeInit_7.cpp |    2 +
 .../unit_test/TestDefaultDeviceTypeInit_8.cpp |    2 +
 .../unit_test/TestDefaultDeviceTypeInit_9.cpp |    2 +
 .../TestDefaultDeviceType_a.cpp}              |   42 +-
 lib/kokkos/core/unit_test/TestMDRange.hpp     |  555 +++
 lib/kokkos/core/unit_test/TestMemoryPool.hpp  |  558 ++-
 lib/kokkos/core/unit_test/TestOpenMP.cpp      |   78 +
 lib/kokkos/core/unit_test/TestOpenMP_a.cpp    |   23 +-
 lib/kokkos/core/unit_test/TestOpenMP_b.cpp    |   54 +-
 lib/kokkos/core/unit_test/TestOpenMP_c.cpp    |   62 +-
 .../core/unit_test/TestPolicyConstruction.hpp |   26 +-
 lib/kokkos/core/unit_test/TestQthread.cpp     |   12 +-
 lib/kokkos/core/unit_test/TestRange.hpp       |    5 +-
 lib/kokkos/core/unit_test/TestReduce.hpp      | 1408 +++++++
 lib/kokkos/core/unit_test/TestSerial.cpp      |  131 +-
 lib/kokkos/core/unit_test/TestTaskPolicy.hpp  |  516 ++-
 lib/kokkos/core/unit_test/TestTeam.hpp        |  291 +-
 lib/kokkos/core/unit_test/TestThreads.cpp     |  120 +-
 lib/kokkos/core/unit_test/TestViewAPI.hpp     |    4 +-
 lib/kokkos/example/fenl/CGSolve.hpp           |    4 +-
 lib/kokkos/example/fenl/fenl_functors.hpp     |    2 +-
 lib/kokkos/example/fenl/fenl_impl.hpp         |    2 +-
 lib/kokkos/example/global_2_local_ids/G2L.hpp |    2 +-
 .../example_chol_performance_device.hpp       |    2 +-
 lib/kokkos/example/md_skeleton/main.cpp       |    4 +-
 lib/kokkos/example/multi_fem/Explicit.hpp     |    2 +-
 lib/kokkos/example/multi_fem/Implicit.hpp     |    2 +-
 lib/kokkos/example/multi_fem/Nonlinear.hpp    |    2 +-
 .../example/multi_fem/SparseLinearSystem.hpp  |    2 +-
 lib/kokkos/example/sort_array/CMakeLists.txt  |    1 -
 lib/kokkos/example/sort_array/sort_array.hpp  |    2 +-
 .../example/tutorial/01_hello_world/Makefile  |    2 +-
 .../tutorial/01_hello_world_lambda/Makefile   |    2 +-
 .../tutorial/02_simple_reduce/Makefile        |    2 +-
 .../tutorial/02_simple_reduce_lambda/Makefile |    2 +-
 .../example/tutorial/03_simple_view/Makefile  |    2 +-
 .../tutorial/03_simple_view_lambda/Makefile   |    2 +-
 .../tutorial/04_simple_memoryspaces/Makefile  |    2 +-
 .../tutorial/05_simple_atomics/Makefile       |    2 +-
 .../Advanced_Views/01_data_layouts/Makefile   |    2 +-
 .../01_data_layouts/data_layouts.cpp          |    4 +-
 .../Advanced_Views/02_memory_traits/Makefile  |    2 +-
 .../02_memory_traits/memory_traits.cpp        |    4 +-
 .../Advanced_Views/03_subviews/Makefile       |    2 +-
 .../Advanced_Views/04_dualviews/Makefile      |    2 +-
 .../Advanced_Views/04_dualviews/dual_view.cpp |   10 +-
 .../Advanced_Views/05_NVIDIA_UVM/Makefile     |    2 +-
 .../05_NVIDIA_UVM/uvm_example.cpp             |    2 +-
 .../Advanced_Views/06_AtomicViews/Makefile    |    2 +-
 .../07_Overlapping_DeepCopy/Makefile          |    2 +-
 .../overlapping_deepcopy.cpp                  |    2 +-
 .../Algorithms/01_random_numbers/Makefile     |    2 +-
 .../01_random_numbers/random_numbers.cpp      |    2 +-
 .../01_thread_teams/Makefile                  |    2 +-
 .../01_thread_teams_lambda/Makefile           |    3 +-
 .../thread_teams_lambda.cpp                   |    3 +-
 .../02_nested_parallel_for/Makefile           |    2 +-
 .../03_vectorization/Makefile                 |    2 +-
 .../03_vectorization/vectorization.cpp        |    6 +-
 .../04_team_scan/Makefile                     |    2 +-
 .../04_team_scan/team_scan.cpp                |    2 +-
 lib/kokkos/generate_makefile.bash             |    2 +-
 src/MANYBODY/pair_vashishta.cpp               |    2 +-
 src/MANYBODY/pair_vashishta.h                 |   14 +-
 src/fix_nve_sphere.cpp                        |   31 +-
 src/group.cpp                                 |  113 +-
 212 files changed, 18620 insertions(+), 13184 deletions(-)
 create mode 100644 lib/kokkos/cmake/deps/CUDA.cmake
 create mode 100644 lib/kokkos/cmake/deps/CUSPARSE.cmake
 create mode 100644 lib/kokkos/cmake/deps/HWLOC.cmake
 create mode 100644 lib/kokkos/cmake/deps/Pthread.cmake
 create mode 100644 lib/kokkos/cmake/deps/QTHREAD.cmake
 create mode 100644 lib/kokkos/cmake/tribits.cmake
 create mode 100644 lib/kokkos/config/kokkos-trilinos-integration-procedure.txt
 create mode 100644 lib/kokkos/config/master_history.txt
 create mode 100644 lib/kokkos/containers/performance_tests/TestDynRankView.hpp
 delete mode 100644 lib/kokkos/core/src/Cuda/Kokkos_Cuda_BasicAllocators.cpp
 delete mode 100644 lib/kokkos/core/src/Cuda/Kokkos_Cuda_BasicAllocators.hpp
 create mode 100644 lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.cpp
 create mode 100644 lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp
 create mode 100644 lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp
 delete mode 100644 lib/kokkos/core/src/KokkosExp_View.hpp
 rename lib/kokkos/core/src/{impl/Kokkos_BasicAllocators.hpp => Kokkos_Concepts.hpp} (56%)
 create mode 100644 lib/kokkos/core/src/Kokkos_Parallel_Reduce.hpp
 create mode 100644 lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.cpp
 create mode 100644 lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.hpp
 delete mode 100644 lib/kokkos/core/src/impl/Kokkos_AllocationTracker.cpp
 delete mode 100644 lib/kokkos/core/src/impl/Kokkos_AllocationTracker.hpp
 create mode 100644 lib/kokkos/core/src/impl/Kokkos_AnalyzePolicy.hpp
 delete mode 100644 lib/kokkos/core/src/impl/Kokkos_BasicAllocators.cpp
 create mode 100644 lib/kokkos/core/src/impl/Kokkos_BitOps.hpp
 delete mode 100644 lib/kokkos/core/src/impl/Kokkos_MemoryPool_Inline.hpp
 create mode 100644 lib/kokkos/core/src/impl/Kokkos_Serial_Task.cpp
 create mode 100644 lib/kokkos/core/src/impl/Kokkos_Serial_Task.hpp
 create mode 100644 lib/kokkos/core/src/impl/Kokkos_TaskQueue.hpp
 create mode 100644 lib/kokkos/core/src/impl/Kokkos_TaskQueue_impl.hpp
 delete mode 100644 lib/kokkos/core/unit_test/TestAllocationTracker.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestAtomicOperations.hpp
 rename lib/kokkos/core/unit_test/{TestDefaultDeviceTypeInit.cpp => TestDefaultDeviceTypeInit.hpp} (93%)
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_1.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_10.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_11.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_12.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_13.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_14.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_15.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_16.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_2.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_3.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_4.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_5.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_6.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_7.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_8.cpp
 create mode 100644 lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_9.cpp
 rename lib/kokkos/core/{src/impl/Kokkos_MemoryPool.cpp => unit_test/TestDefaultDeviceType_a.cpp} (77%)
 create mode 100644 lib/kokkos/core/unit_test/TestMDRange.hpp

diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt
index f45fc8d9fc..1219352f73 100644
--- a/lib/kokkos/CMakeLists.txt
+++ b/lib/kokkos/CMakeLists.txt
@@ -1,4 +1,15 @@
 
+IF(COMMAND TRIBITS_PACKAGE_DECL)
+  SET(KOKKOS_HAS_TRILINOS ON CACHE BOOL "")
+ELSE()
+  SET(KOKKOS_HAS_TRILINOS OFF CACHE BOOL "")
+ENDIF()
+
+IF(NOT KOKKOS_HAS_TRILINOS)
+  CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11 FATAL_ERROR)
+  INCLUDE(cmake/tribits.cmake)
+ENDIF()
+
 #
 # A) Forward delcare the package so that certain options are also defined for
 # subpackages
@@ -12,7 +23,22 @@ TRIBITS_PACKAGE_DECL(Kokkos) # ENABLE_SHADOWING_WARNINGS)
 # subpackages as well.
 #
 
-TRIBITS_ADD_DEBUG_OPTION()
+
+
+# mfh 01 Aug 2016: See Issue #61:
+#
+# https://github.com/kokkos/kokkos/issues/61
+#
+# Don't use TRIBITS_ADD_DEBUG_OPTION() here, because that defines
+# HAVE_KOKKOS_DEBUG.  We define KOKKOS_HAVE_DEBUG here instead,
+# for compatibility with Kokkos' Makefile build system.
+
+TRIBITS_ADD_OPTION_AND_DEFINE(
+  ${PACKAGE_NAME}_ENABLE_DEBUG
+  ${PACKAGE_NAME_UC}_HAVE_DEBUG
+  "Enable run-time debug checks.  These checks may be expensive, so they are disabled by default in a release build."
+  ${${PROJECT_NAME}_ENABLE_DEBUG}
+)
 
 TRIBITS_ADD_OPTION_AND_DEFINE(
   Kokkos_ENABLE_SIERRA_BUILD
@@ -82,11 +108,33 @@ TRIBITS_ADD_OPTION_AND_DEFINE(
   "${TPL_ENABLE_MPI}"
   )
 
+# Set default value of Kokkos_ENABLE_Debug_Bounds_Check option
+#
+# CMake is case sensitive.  The Kokkos_ENABLE_Debug_Bounds_Check
+# option (defined below) is annoyingly not all caps, but we need to
+# keep it that way for backwards compatibility.  If users forget and
+# try using an all-caps variable, then make it count by using the
+# all-caps version as the default value of the original, not-all-caps
+# option.  Otherwise, the default value of this option comes from
+# Kokkos_ENABLE_DEBUG (see Issue #367).
+
+ASSERT_DEFINED(${PACKAGE_NAME}_ENABLE_DEBUG)
+IF(DEFINED Kokkos_ENABLE_DEBUG_BOUNDS_CHECK)
+  IF(Kokkos_ENABLE_DEBUG_BOUNDS_CHECK)
+    SET(Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT ON)
+  ELSE()
+    SET(Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT "${${PACKAGE_NAME}_ENABLE_DEBUG}")
+  ENDIF()
+ELSE()
+  SET(Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT "${${PACKAGE_NAME}_ENABLE_DEBUG}")
+ENDIF()
+ASSERT_DEFINED(Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT)
+
 TRIBITS_ADD_OPTION_AND_DEFINE(
   Kokkos_ENABLE_Debug_Bounds_Check
   KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK
-  "Enable bounds checking support in Kokkos."
-  OFF
+  "Enable Kokkos::View run-time bounds checking."
+  "${Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT}"
   )
 
 TRIBITS_ADD_OPTION_AND_DEFINE(
diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos
index c01ceaf64d..c9b6cc464d 100644
--- a/lib/kokkos/Makefile.kokkos
+++ b/lib/kokkos/Makefile.kokkos
@@ -7,7 +7,7 @@ CXXFLAGS=$(CCFLAGS)
 #Options: OpenMP,Serial,Pthreads,Cuda
 KOKKOS_DEVICES ?= "OpenMP"
 #KOKKOS_DEVICES ?= "Pthreads"
-#Options: KNC,SNB,HSW,Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,ARMv8,BGQ,Power7,Power8,KNL
+#Options: KNC,SNB,HSW,Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal61,ARMv8,BGQ,Power7,Power8,KNL,BDW
 KOKKOS_ARCH ?= ""
 #Options: yes,no
 KOKKOS_DEBUG ?= "no"
@@ -97,6 +97,7 @@ KOKKOS_INTERNAL_USE_CUDA := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Cuda |
 KOKKOS_INTERNAL_USE_ARCH_KNC := $(strip $(shell echo $(KOKKOS_ARCH) | grep KNC | wc -l))
 KOKKOS_INTERNAL_USE_ARCH_SNB := $(strip $(shell echo $(KOKKOS_ARCH) | grep SNB | wc -l))
 KOKKOS_INTERNAL_USE_ARCH_HSW := $(strip $(shell echo $(KOKKOS_ARCH) | grep HSW | wc -l))
+KOKKOS_INTERNAL_USE_ARCH_BDW := $(strip $(shell echo $(KOKKOS_ARCH) | grep BDW | wc -l))
 KOKKOS_INTERNAL_USE_ARCH_KNL := $(strip $(shell echo $(KOKKOS_ARCH) | grep KNL | wc -l))
 
 #NVIDIA based
@@ -108,10 +109,12 @@ KOKKOS_INTERNAL_USE_ARCH_KEPLER37 := $(strip $(shell echo $(KOKKOS_ARCH) | grep
 KOKKOS_INTERNAL_USE_ARCH_MAXWELL50 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Maxwell50 | wc -l))
 KOKKOS_INTERNAL_USE_ARCH_MAXWELL52 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Maxwell52 | wc -l))
 KOKKOS_INTERNAL_USE_ARCH_MAXWELL53 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Maxwell53 | wc -l))
+KOKKOS_INTERNAL_USE_ARCH_PASCAL61 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Pascal61 | wc -l))
 KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30)  \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32)  \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35)  \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37)  \
+                                                      + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61)  \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53) | bc))
@@ -123,6 +126,7 @@ KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_AR
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32)  \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35)  \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37)  \
+                                                      + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61)  \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
                                                       + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53) | bc))
@@ -142,11 +146,11 @@ KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(strip $(shell echo $(KOKKOS_ARCH) | grep AM
 
 #Any AVX?
 KOKKOS_INTERNAL_USE_ARCH_AVX       := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_SNB)+$(KOKKOS_INTERNAL_USE_ARCH_AMDAVX) | bc ))
-KOKKOS_INTERNAL_USE_ARCH_AVX2      := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_HSW) | bc ))
+KOKKOS_INTERNAL_USE_ARCH_AVX2      := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_HSW)+$(KOKKOS_INTERNAL_USE_ARCH_BDW) | bc ))
 KOKKOS_INTERNAL_USE_ARCH_AVX512MIC := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_KNL) | bc ))
 
 # Decide what ISA level we are able to support
-KOKKOS_INTERNAL_USE_ISA_X86_64     := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_SNB)+$(KOKKOS_INTERNAL_USE_ARCH_HSW)+$(KOKKOS_INTERNAL_USE_ARCH_KNL) | bc ))
+KOKKOS_INTERNAL_USE_ISA_X86_64     := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_SNB)+$(KOKKOS_INTERNAL_USE_ARCH_HSW)+$(KOKKOS_INTERNAL_USE_ARCH_BDW)+$(KOKKOS_INTERNAL_USE_ARCH_KNL) | bc ))
 KOKKOS_INTERNAL_USE_ISA_KNC        := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_KNC) | bc ))
 KOKKOS_INTERNAL_USE_ISA_POWERPCLE  := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_POWER8) | bc ))
 
@@ -304,8 +308,8 @@ endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER8), 1)
     tmp := $(shell echo "\#define KOKKOS_ARCH_POWER8 1" >> KokkosCore_config.tmp )
-	KOKKOS_CXXFLAGS += -mcpu=power8
-	KOKKOS_LDFLAGS  += -mcpu=power8
+	KOKKOS_CXXFLAGS += -mcpu=power8 -mtune=power8
+	KOKKOS_LDFLAGS  += -mcpu=power8 -mtune=power8
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX2), 1)
@@ -321,8 +325,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX2), 1)
 
 			else
 				# Assume that this is a really a GNU compiler
-				KOKKOS_CXXFLAGS += -march=core-avx2
-				KOKKOS_LDFLAGS  += -march=core-avx2
+				KOKKOS_CXXFLAGS += -march=core-avx2 -mtune=core-avx2
+				KOKKOS_LDFLAGS  += -march=core-avx2 -mtune=core-avx2
 			endif
 		endif
 	endif
@@ -390,6 +394,11 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53), 1)
     tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL53 1" >> KokkosCore_config.tmp )
 	KOKKOS_CXXFLAGS += -arch=sm_53
 endif
+ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL61), 1)
+    tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp )
+    tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL61 1" >> KokkosCore_config.tmp )
+        KOKKOS_CXXFLAGS += -arch=sm_61
+endif
 endif
  
 KOKKOS_INTERNAL_LS_CONFIG := $(shell ls KokkosCore_config.h)
diff --git a/lib/kokkos/Makefile.targets b/lib/kokkos/Makefile.targets
index 876ae033b7..86929ea0fe 100644
--- a/lib/kokkos/Makefile.targets
+++ b/lib/kokkos/Makefile.targets
@@ -1,9 +1,5 @@
 Kokkos_UnorderedMap_impl.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/containers/src/impl/Kokkos_UnorderedMap_impl.cpp
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/containers/src/impl/Kokkos_UnorderedMap_impl.cpp
-Kokkos_AllocationTracker.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_AllocationTracker.cpp
-	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_AllocationTracker.cpp
-Kokkos_BasicAllocators.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_BasicAllocators.cpp
-	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_BasicAllocators.cpp
 Kokkos_Core.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Core.cpp
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Core.cpp
 Kokkos_CPUDiscovery.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_CPUDiscovery.cpp
@@ -20,6 +16,10 @@ Kokkos_Serial.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Seria
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial.cpp
 Kokkos_Serial_TaskPolicy.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial_TaskPolicy.cpp
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial_TaskPolicy.cpp
+Kokkos_TaskQueue.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_TaskQueue.cpp
+	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_TaskQueue.cpp
+Kokkos_Serial_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial_Task.cpp
+	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial_Task.cpp
 Kokkos_Shape.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Shape.cpp
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Shape.cpp
 Kokkos_spinwait.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_spinwait.cpp
@@ -32,12 +32,12 @@ Kokkos_MemoryPool.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_M
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_MemoryPool.cpp
 
 ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
-Kokkos_Cuda_BasicAllocators.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_BasicAllocators.cpp
-	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_BasicAllocators.cpp
 Kokkos_Cuda_Impl.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Impl.cpp
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Impl.cpp
 Kokkos_CudaSpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_CudaSpace.cpp
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_CudaSpace.cpp
+Kokkos_Cuda_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Task.cpp
+	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Task.cpp
 Kokkos_Cuda_TaskPolicy.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_TaskPolicy.cpp
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_TaskPolicy.cpp
 endif
@@ -61,6 +61,8 @@ endif
 ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
 Kokkos_OpenMPexec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMPexec.cpp
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMPexec.cpp
+Kokkos_OpenMP_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp
+	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp
 endif
 
 Kokkos_HBWSpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp
diff --git a/lib/kokkos/README b/lib/kokkos/README
index 25b3778d95..b094578af6 100644
--- a/lib/kokkos/README
+++ b/lib/kokkos/README
@@ -37,7 +37,7 @@ hcedwar(at)sandia.gov and crtrott(at)sandia.gov
 ====Requirements============================================================
 ============================================================================
 
-Primary tested compilers are:
+Primary tested compilers on X86 are:
   GCC 4.7.2
   GCC 4.8.4
   GCC 4.9.2
@@ -48,26 +48,43 @@ Primary tested compilers are:
   Clang 3.5.2
   Clang 3.6.1
 
+Primary tested compilers on Power 8 are:
+  IBM XL 13.1.3 (OpenMP,Serial)
+  GCC 4.9.2 (OpenMP,Serial)
+  GCC 5.3.0 (OpenMP,Serial)
+
 Secondary tested compilers are:
   CUDA 6.5 (with gcc 4.7.2)
   CUDA 7.0 (with gcc 4.7.2)
   CUDA 7.5 (with gcc 4.8.4)
 
 Other compilers working:
-  PGI 15.4
-  IBM XL 13.1.2
-  Cygwin 2.1.0 64bit with gcc 4.9.3
+  X86:
+   Intel 17.0.042 (the FENL example causes internal compiler error)
+   PGI 15.4
+   Cygwin 2.1.0 64bit with gcc 4.9.3
+  KNL:
+   Intel 16.2.181 (the FENL example causes internal compiler error)
+   Intel 17.0.042 (the FENL example causes internal compiler error)
+
+Known non-working combinations:
+  Power8:
+   GCC 6.1.0
+   Pthreads backend
+
 
 Primary tested compiler are passing in release mode
-with warnings as errors. We are using the following set
-of flags:
+with warnings as errors. They also are tested with a comprehensive set of 
+backend combinations (i.e. OpenMP, Pthreads, Serial, OpenMP+Serial, ...).
+We are using the following set of flags:
 GCC:   -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits
        -Wignored-qualifiers -Wempty-body -Wclobbered -Wuninitialized
 Intel: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wuninitialized
 Clang: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wuninitialized
 
 Secondary compilers are passing without -Werror.
-Other compilers are tested occasionally.
+Other compilers are tested occasionally, in particular when pushing from develop to 
+master branch, without -Werror and only for a select set of backends.
 
 ============================================================================
 ====Getting started=========================================================
diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp
index 192b1d64f8..d7c06dc14b 100644
--- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp
+++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp
@@ -771,6 +771,7 @@ namespace Kokkos {
     friend class Random_XorShift1024_Pool<DeviceType>;
   public:
 
+    typedef Random_XorShift1024_Pool<DeviceType> pool_type;
     typedef DeviceType device_type;
 
     enum {MAX_URAND = 0xffffffffU};
@@ -779,10 +780,10 @@ namespace Kokkos {
     enum {MAX_RAND64 = static_cast<int64_t>(0xffffffffffffffffULL/2-1)};
 
     KOKKOS_INLINE_FUNCTION
-    Random_XorShift1024 (uint64_t* state, int p, int state_idx = 0):
+    Random_XorShift1024 (const typename pool_type::state_data_type& state, int p, int state_idx = 0):
       p_(p),state_idx_(state_idx){
       for(int i=0 ; i<16; i++)
-        state_[i] = state[i];
+        state_[i] = state(state_idx,i);
     }
 
     KOKKOS_INLINE_FUNCTION
@@ -933,6 +934,7 @@ namespace Kokkos {
     state_data_type state_;
     int_view_type p_;
     int num_states_;
+    friend class Random_XorShift1024<DeviceType>;
 
   public:
     typedef Random_XorShift1024<DeviceType> generator_type;
@@ -1001,7 +1003,7 @@ namespace Kokkos {
     KOKKOS_INLINE_FUNCTION
     Random_XorShift1024<DeviceType> get_state() const {
       const int i = DeviceType::hardware_thread_id();
-      return Random_XorShift1024<DeviceType>(&state_(i,0),p_(i),i);
+      return Random_XorShift1024<DeviceType>(state_,p_(i),i);
     };
 
     KOKKOS_INLINE_FUNCTION
@@ -1020,10 +1022,12 @@ namespace Kokkos {
     int p_;
     const int state_idx_;
     uint64_t* state_;
+    const int stride_;
     friend class Random_XorShift1024_Pool<Kokkos::Cuda>;
   public:
 
     typedef Kokkos::Cuda device_type;
+    typedef Random_XorShift1024_Pool<device_type> pool_type;
 
     enum {MAX_URAND = 0xffffffffU};
     enum {MAX_URAND64 = 0xffffffffffffffffULL-1};
@@ -1031,30 +1035,30 @@ namespace Kokkos {
     enum {MAX_RAND64 = static_cast<int64_t>(0xffffffffffffffffULL/2-1)};
 
     KOKKOS_INLINE_FUNCTION
-    Random_XorShift1024 (uint64_t* state, int p, int state_idx = 0):
-      p_(p),state_idx_(state_idx),state_(state){
+    Random_XorShift1024 (const typename pool_type::state_data_type& state, int p, int state_idx = 0):
+      p_(p),state_idx_(state_idx),state_(&state(state_idx,0)),stride_(state.stride_1()){
     }
 
     KOKKOS_INLINE_FUNCTION
     uint32_t urand() {
-      uint64_t state_0 = state_[ p_ ];
-      uint64_t state_1 = state_[ p_ = ( p_ + 1 ) & 15 ];
+      uint64_t state_0 = state_[ p_ * stride_ ];
+      uint64_t state_1 = state_[ (p_ = ( p_ + 1 ) & 15) * stride_ ];
       state_1 ^= state_1 << 31;
       state_1 ^= state_1 >> 11;
       state_0 ^= state_0 >> 30;
-      uint64_t tmp = ( state_[ p_ ] = state_0 ^ state_1 ) * 1181783497276652981ULL;
+      uint64_t tmp = ( state_[ p_ * stride_ ] = state_0 ^ state_1 ) * 1181783497276652981ULL;
       tmp = tmp>>16;
       return static_cast<uint32_t>(tmp&MAX_URAND);
     }
 
     KOKKOS_INLINE_FUNCTION
     uint64_t urand64() {
-      uint64_t state_0 = state_[ p_ ];
-      uint64_t state_1 = state_[ p_ = ( p_ + 1 ) & 15 ];
+      uint64_t state_0 = state_[ p_ * stride_ ];
+      uint64_t state_1 = state_[ (p_ = ( p_ + 1 ) & 15) * stride_ ];
       state_1 ^= state_1 << 31;
       state_1 ^= state_1 >> 11;
       state_0 ^= state_0 >> 30;
-      return (( state_[ p_ ] = state_0 ^ state_1 ) * 1181783497276652981LL) - 1;
+      return (( state_[ p_ * stride_ ] = state_0 ^ state_1 ) * 1181783497276652981LL) - 1;
     }
 
     KOKKOS_INLINE_FUNCTION
@@ -1227,9 +1231,9 @@ Random_XorShift1024<Kokkos::Cuda> Random_XorShift1024_Pool<Kokkos::Cuda>::get_st
       if(i>=num_states_) {i = i_offset;}
   }
 
-  return Random_XorShift1024<Kokkos::Cuda>(&state_(i,0), p_(i), i);
+  return Random_XorShift1024<Kokkos::Cuda>(state_, p_(i), i);
 #else
-  return Random_XorShift1024<Kokkos::Cuda>(&state_(0,0), p_(0), 0);
+  return Random_XorShift1024<Kokkos::Cuda>(state_, p_(0), 0);
 #endif
 }
 
@@ -1248,14 +1252,15 @@ void Random_XorShift1024_Pool<Kokkos::Cuda>::free_state(const Random_XorShift102
 #endif
 
 
+namespace Impl {
 
-template<class ViewType, class RandomPool, int loops, int rank>
+template<class ViewType, class RandomPool, int loops, int rank, class IndexType>
 struct fill_random_functor_range;
-template<class ViewType, class RandomPool, int loops, int rank>
+template<class ViewType, class RandomPool, int loops, int rank, class IndexType>
 struct fill_random_functor_begin_end;
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_range<ViewType,RandomPool,loops,1>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_range<ViewType,RandomPool,loops,1,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1268,19 +1273,19 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,1>{
     a(a_),rand_pool(rand_pool_),range(range_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (const IndexType& i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0())
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0()))
         a(idx) = Rand::draw(gen,range);
     }
     rand_pool.free_state(gen);
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_range<ViewType,RandomPool,loops,2>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_range<ViewType,RandomPool,loops,2,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1293,12 +1298,12 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,2>{
     a(a_),rand_pool(rand_pool_),range(range_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
           a(idx,k) = Rand::draw(gen,range);
       }
     }
@@ -1307,8 +1312,8 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,2>{
 };
 
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_range<ViewType,RandomPool,loops,3>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_range<ViewType,RandomPool,loops,3,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1321,13 +1326,13 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,3>{
     a(a_),rand_pool(rand_pool_),range(range_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
             a(idx,k,l) = Rand::draw(gen,range);
       }
     }
@@ -1335,8 +1340,8 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,3>{
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_range<ViewType,RandomPool,loops,4>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_range<ViewType,RandomPool,loops,4, IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1349,14 +1354,14 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,4>{
     a(a_),rand_pool(rand_pool_),range(range_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
-            for(unsigned int m=0;m<a.dimension_3();m++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
+            for(IndexType m=0;m<static_cast<IndexType>(a.dimension_3());m++)
               a(idx,k,l,m) = Rand::draw(gen,range);
       }
     }
@@ -1364,8 +1369,8 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,4>{
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_range<ViewType,RandomPool,loops,5>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_range<ViewType,RandomPool,loops,5,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1378,15 +1383,15 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,5>{
     a(a_),rand_pool(rand_pool_),range(range_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
-            for(unsigned int m=0;m<a.dimension_3();m++)
-              for(unsigned int n=0;n<a.dimension_4();n++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
+            for(IndexType m=0;m<static_cast<IndexType>(a.dimension_3());m++)
+              for(IndexType n=0;n<static_cast<IndexType>(a.dimension_4());n++)
               a(idx,k,l,m,n) = Rand::draw(gen,range);
       }
     }
@@ -1394,8 +1399,8 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,5>{
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_range<ViewType,RandomPool,loops,6>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_range<ViewType,RandomPool,loops,6,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1408,16 +1413,16 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,6>{
     a(a_),rand_pool(rand_pool_),range(range_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
-            for(unsigned int m=0;m<a.dimension_3();m++)
-              for(unsigned int n=0;n<a.dimension_4();n++)
-                for(unsigned int o=0;o<a.dimension_5();o++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
+            for(IndexType m=0;m<static_cast<IndexType>(a.dimension_3());m++)
+              for(IndexType n=0;n<static_cast<IndexType>(a.dimension_4());n++)
+                for(IndexType o=0;o<static_cast<IndexType>(a.dimension_5());o++)
               a(idx,k,l,m,n,o) = Rand::draw(gen,range);
       }
     }
@@ -1425,8 +1430,8 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,6>{
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_range<ViewType,RandomPool,loops,7>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_range<ViewType,RandomPool,loops,7,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1439,17 +1444,17 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,7>{
     a(a_),rand_pool(rand_pool_),range(range_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
-            for(unsigned int m=0;m<a.dimension_3();m++)
-              for(unsigned int n=0;n<a.dimension_4();n++)
-                for(unsigned int o=0;o<a.dimension_5();o++)
-                  for(unsigned int p=0;p<a.dimension_6();p++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
+            for(IndexType m=0;m<static_cast<IndexType>(a.dimension_3());m++)
+              for(IndexType n=0;n<static_cast<IndexType>(a.dimension_4());n++)
+                for(IndexType o=0;o<static_cast<IndexType>(a.dimension_5());o++)
+                  for(IndexType p=0;p<static_cast<IndexType>(a.dimension_6());p++)
               a(idx,k,l,m,n,o,p) = Rand::draw(gen,range);
       }
     }
@@ -1457,8 +1462,8 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,7>{
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_range<ViewType,RandomPool,loops,8>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_range<ViewType,RandomPool,loops,8,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1471,26 +1476,26 @@ struct fill_random_functor_range<ViewType,RandomPool,loops,8>{
     a(a_),rand_pool(rand_pool_),range(range_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
-            for(unsigned int m=0;m<a.dimension_3();m++)
-              for(unsigned int n=0;n<a.dimension_4();n++)
-                for(unsigned int o=0;o<a.dimension_5();o++)
-                  for(unsigned int p=0;p<a.dimension_6();p++)
-                    for(unsigned int q=0;q<a.dimension_7();q++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
+            for(IndexType m=0;m<static_cast<IndexType>(a.dimension_3());m++)
+              for(IndexType n=0;n<static_cast<IndexType>(a.dimension_4());n++)
+                for(IndexType o=0;o<static_cast<IndexType>(a.dimension_5());o++)
+                  for(IndexType p=0;p<static_cast<IndexType>(a.dimension_6());p++)
+                    for(IndexType q=0;q<static_cast<IndexType>(a.dimension_7());q++)
               a(idx,k,l,m,n,o,p,q) = Rand::draw(gen,range);
       }
     }
     rand_pool.free_state(gen);
   }
 };
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_begin_end<ViewType,RandomPool,loops,1>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_begin_end<ViewType,RandomPool,loops,1,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1503,19 +1508,19 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,1>{
     a(a_),rand_pool(rand_pool_),begin(begin_),end(end_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0())
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0()))
         a(idx) = Rand::draw(gen,begin,end);
     }
     rand_pool.free_state(gen);
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_begin_end<ViewType,RandomPool,loops,2>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_begin_end<ViewType,RandomPool,loops,2,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1528,12 +1533,12 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,2>{
     a(a_),rand_pool(rand_pool_),begin(begin_),end(end_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
           a(idx,k) = Rand::draw(gen,begin,end);
       }
     }
@@ -1542,8 +1547,8 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,2>{
 };
 
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_begin_end<ViewType,RandomPool,loops,3>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_begin_end<ViewType,RandomPool,loops,3,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1556,13 +1561,13 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,3>{
     a(a_),rand_pool(rand_pool_),begin(begin_),end(end_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
             a(idx,k,l) = Rand::draw(gen,begin,end);
       }
     }
@@ -1570,8 +1575,8 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,3>{
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_begin_end<ViewType,RandomPool,loops,4>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_begin_end<ViewType,RandomPool,loops,4,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1584,14 +1589,14 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,4>{
     a(a_),rand_pool(rand_pool_),begin(begin_),end(end_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
-            for(unsigned int m=0;m<a.dimension_3();m++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
+            for(IndexType m=0;m<static_cast<IndexType>(a.dimension_3());m++)
               a(idx,k,l,m) = Rand::draw(gen,begin,end);
       }
     }
@@ -1599,8 +1604,8 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,4>{
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_begin_end<ViewType,RandomPool,loops,5>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_begin_end<ViewType,RandomPool,loops,5,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1613,15 +1618,15 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,5>{
     a(a_),rand_pool(rand_pool_),begin(begin_),end(end_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()){
-        for(unsigned int l=0;l<a.dimension_1();l++)
-          for(unsigned int m=0;m<a.dimension_2();m++)
-            for(unsigned int n=0;n<a.dimension_3();n++)
-              for(unsigned int o=0;o<a.dimension_4();o++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())){
+        for(IndexType l=0;l<static_cast<IndexType>(a.dimension_1());l++)
+          for(IndexType m=0;m<static_cast<IndexType>(a.dimension_2());m++)
+            for(IndexType n=0;n<static_cast<IndexType>(a.dimension_3());n++)
+              for(IndexType o=0;o<static_cast<IndexType>(a.dimension_4());o++)
           a(idx,l,m,n,o) = Rand::draw(gen,begin,end);
       }
     }
@@ -1629,8 +1634,8 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,5>{
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_begin_end<ViewType,RandomPool,loops,6>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_begin_end<ViewType,RandomPool,loops,6,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1643,16 +1648,16 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,6>{
     a(a_),rand_pool(rand_pool_),begin(begin_),end(end_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
-            for(unsigned int m=0;m<a.dimension_3();m++)
-              for(unsigned int n=0;n<a.dimension_4();n++)
-                for(unsigned int o=0;o<a.dimension_5();o++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
+            for(IndexType m=0;m<static_cast<IndexType>(a.dimension_3());m++)
+              for(IndexType n=0;n<static_cast<IndexType>(a.dimension_4());n++)
+                for(IndexType o=0;o<static_cast<IndexType>(a.dimension_5());o++)
           a(idx,k,l,m,n,o) = Rand::draw(gen,begin,end);
       }
     }
@@ -1661,8 +1666,8 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,6>{
 };
 
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_begin_end<ViewType,RandomPool,loops,7>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_begin_end<ViewType,RandomPool,loops,7,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1675,17 +1680,17 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,7>{
     a(a_),rand_pool(rand_pool_),begin(begin_),end(end_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
-            for(unsigned int m=0;m<a.dimension_3();m++)
-              for(unsigned int n=0;n<a.dimension_4();n++)
-                for(unsigned int o=0;o<a.dimension_5();o++)
-                  for(unsigned int p=0;p<a.dimension_6();p++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
+            for(IndexType m=0;m<static_cast<IndexType>(a.dimension_3());m++)
+              for(IndexType n=0;n<static_cast<IndexType>(a.dimension_4());n++)
+                for(IndexType o=0;o<static_cast<IndexType>(a.dimension_5());o++)
+                  for(IndexType p=0;p<static_cast<IndexType>(a.dimension_6());p++)
             a(idx,k,l,m,n,o,p) = Rand::draw(gen,begin,end);
       }
     }
@@ -1693,8 +1698,8 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,7>{
   }
 };
 
-template<class ViewType, class RandomPool, int loops>
-struct fill_random_functor_begin_end<ViewType,RandomPool,loops,8>{
+template<class ViewType, class RandomPool, int loops, class IndexType>
+struct fill_random_functor_begin_end<ViewType,RandomPool,loops,8,IndexType>{
   typedef typename ViewType::execution_space execution_space;
   ViewType a;
   RandomPool rand_pool;
@@ -1707,18 +1712,18 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,8>{
     a(a_),rand_pool(rand_pool_),begin(begin_),end(end_) {}
 
   KOKKOS_INLINE_FUNCTION
-  void operator() (unsigned int i) const {
+  void operator() (IndexType i) const {
     typename RandomPool::generator_type gen = rand_pool.get_state();
-    for(unsigned int j=0;j<loops;j++) {
-      const uint64_t idx = i*loops+j;
-      if(idx<a.dimension_0()) {
-        for(unsigned int k=0;k<a.dimension_1();k++)
-          for(unsigned int l=0;l<a.dimension_2();l++)
-            for(unsigned int m=0;m<a.dimension_3();m++)
-              for(unsigned int n=0;n<a.dimension_4();n++)
-                for(unsigned int o=0;o<a.dimension_5();o++)
-                  for(unsigned int p=0;p<a.dimension_6();p++)
-                    for(unsigned int q=0;q<a.dimension_7();q++)
+    for(IndexType j=0;j<loops;j++) {
+      const IndexType idx = i*loops+j;
+      if(idx<static_cast<IndexType>(a.dimension_0())) {
+        for(IndexType k=0;k<static_cast<IndexType>(a.dimension_1());k++)
+          for(IndexType l=0;l<static_cast<IndexType>(a.dimension_2());l++)
+            for(IndexType m=0;m<static_cast<IndexType>(a.dimension_3());m++)
+              for(IndexType n=0;n<static_cast<IndexType>(a.dimension_4());n++)
+                for(IndexType o=0;o<static_cast<IndexType>(a.dimension_5());o++)
+                  for(IndexType p=0;p<static_cast<IndexType>(a.dimension_6());p++)
+                    for(IndexType q=0;q<static_cast<IndexType>(a.dimension_7());q++)
               a(idx,k,l,m,n,o,p,q) = Rand::draw(gen,begin,end);
       }
     }
@@ -1726,18 +1731,20 @@ struct fill_random_functor_begin_end<ViewType,RandomPool,loops,8>{
   }
 };
 
-template<class ViewType, class RandomPool>
+}
+
+template<class ViewType, class RandomPool, class IndexType = int64_t>
 void fill_random(ViewType a, RandomPool g, typename ViewType::const_value_type range) {
   int64_t LDA = a.dimension_0();
   if(LDA>0)
-    parallel_for((LDA+127)/128,fill_random_functor_range<ViewType,RandomPool,128,ViewType::Rank>(a,g,range));
+    parallel_for((LDA+127)/128,Impl::fill_random_functor_range<ViewType,RandomPool,128,ViewType::Rank,IndexType>(a,g,range));
 }
 
-template<class ViewType, class RandomPool>
+template<class ViewType, class RandomPool, class IndexType = int64_t>
 void fill_random(ViewType a, RandomPool g, typename ViewType::const_value_type begin,typename ViewType::const_value_type end ) {
   int64_t LDA = a.dimension_0();
   if(LDA>0)
-    parallel_for((LDA+127)/128,fill_random_functor_begin_end<ViewType,RandomPool,128,ViewType::Rank>(a,g,begin,end));
+    parallel_for((LDA+127)/128,Impl::fill_random_functor_begin_end<ViewType,RandomPool,128,ViewType::Rank,IndexType>(a,g,begin,end));
 }
 }
 
diff --git a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp
index eade74ed93..c906b9f2cd 100644
--- a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp
+++ b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp
@@ -50,6 +50,7 @@
 #include <Kokkos_Core.hpp>
 #include <Kokkos_Random.hpp>
 #include <cmath>
+#include <chrono>
 
 namespace Test {
 
@@ -207,7 +208,6 @@ struct test_histogram1d_functor {
     density_1d (d1d),
     mean (1.0*num_draws/HIST_DIM1D*3)
   {
-    printf ("Mean: %e\n", mean);
   }
 
   KOKKOS_INLINE_FUNCTION void
@@ -295,7 +295,7 @@ struct test_random_scalar {
       parallel_reduce (num_draws/1024, functor_type (pool, density_1d, density_3d), result);
 
       //printf("Result: %lf %lf %lf\n",result.mean/num_draws/3,result.variance/num_draws/3,result.covariance/num_draws/2);
-      double tolerance = 2.0*sqrt(1.0/num_draws);
+      double tolerance = 1.6*sqrt(1.0/num_draws);
       double mean_expect = 0.5*Kokkos::rand<rnd_type,Scalar>::max();
       double variance_expect = 1.0/3.0*mean_expect*mean_expect;
       double mean_eps = mean_expect/(result.mean/num_draws/3)-1.0;
@@ -303,10 +303,10 @@ struct test_random_scalar {
       double covariance_eps = result.covariance/num_draws/2/variance_expect;
       pass_mean  = ((-tolerance < mean_eps) &&
                     ( tolerance > mean_eps)) ? 1:0;
-      pass_var   = ((-tolerance < variance_eps) &&
-                    ( tolerance > variance_eps)) ? 1:0;
-      pass_covar = ((-1.4*tolerance < covariance_eps) &&
-                    ( 1.4*tolerance > covariance_eps)) ? 1:0;
+      pass_var   = ((-1.5*tolerance < variance_eps) &&
+                    ( 1.5*tolerance > variance_eps)) ? 1:0;
+      pass_covar = ((-2.0*tolerance < covariance_eps) &&
+                    ( 2.0*tolerance > covariance_eps)) ? 1:0;
       cerr << "Pass: " << pass_mean
            << " " << pass_var
            << " " << mean_eps
@@ -328,12 +328,12 @@ struct test_random_scalar {
       double mean_eps = mean_expect/(result.mean/HIST_DIM1D)-1.0;
       double variance_eps = variance_expect/(result.variance/HIST_DIM1D)-1.0;
       double covariance_eps = (result.covariance/HIST_DIM1D - covariance_expect)/mean_expect;
-      pass_hist1d_mean  = ((-tolerance < mean_eps) &&
-                           ( tolerance > mean_eps)) ? 1:0;
-      pass_hist1d_var   = ((-tolerance < variance_eps) &&
-                           ( tolerance > variance_eps)) ? 1:0;
-      pass_hist1d_covar = ((-tolerance < covariance_eps) &&
-                           ( tolerance > covariance_eps)) ? 1:0;
+      pass_hist1d_mean  = ((-0.0001 < mean_eps) &&
+                           ( 0.0001 > mean_eps)) ? 1:0;
+      pass_hist1d_var   = ((-0.07 < variance_eps) &&
+                           ( 0.07 > variance_eps)) ? 1:0;
+      pass_hist1d_covar = ((-0.06 < covariance_eps) &&
+                           ( 0.06 > covariance_eps)) ? 1:0;
 
       cerr << "Density 1D: " << mean_eps
            << " " << variance_eps
@@ -363,8 +363,8 @@ struct test_random_scalar {
       double covariance_eps = (result.covariance/HIST_DIM1D - covariance_expect)/mean_expect;
       pass_hist3d_mean  = ((-tolerance < mean_eps) &&
                            ( tolerance > mean_eps)) ? 1:0;
-      pass_hist3d_var   = ((-tolerance < variance_eps) &&
-                           ( tolerance > variance_eps)) ? 1:0;
+      pass_hist3d_var   = ((-1.2*tolerance < variance_eps) &&
+                           ( 1.2*tolerance > variance_eps)) ? 1:0;
       pass_hist3d_covar = ((-tolerance < covariance_eps) &&
                            ( tolerance > covariance_eps)) ? 1:0;
 
@@ -386,8 +386,13 @@ void test_random(unsigned int num_draws)
   typename test_random_functor<RandomGenerator,int>::type_1d density_1d("D1d");
   typename test_random_functor<RandomGenerator,int>::type_3d density_3d("D3d");
 
+
+  uint64_t ticks = std::chrono::high_resolution_clock::now().time_since_epoch().count();
+  cerr << "Test Seed:" << ticks << endl;
+
+  RandomGenerator pool(ticks);
+
   cerr << "Test Scalar=int" << endl;
-  RandomGenerator pool(31891);
   test_random_scalar<RandomGenerator,int> test_int(density_1d,density_3d,pool,num_draws);
   ASSERT_EQ( test_int.pass_mean,1);
   ASSERT_EQ( test_int.pass_var,1);
diff --git a/lib/kokkos/cmake/deps/CUDA.cmake b/lib/kokkos/cmake/deps/CUDA.cmake
new file mode 100644
index 0000000000..801c20067b
--- /dev/null
+++ b/lib/kokkos/cmake/deps/CUDA.cmake
@@ -0,0 +1,79 @@
+# @HEADER
+# ************************************************************************
+#
+#            Trilinos: An Object-Oriented Solver Framework
+#                 Copyright (2001) Sandia Corporation
+#
+#
+# Copyright (2001) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000, there is a non-exclusive license for use of this
+# work by or on behalf of the U.S. Government.  Export of this program
+# may require a license from the United States Government.
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# NOTICE:  The United States Government is granted for itself and others
+# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
+# license in this data to reproduce, prepare derivative works, and
+# perform publicly and display publicly.  Beginning five (5) years from
+# July 25, 2001, the United States Government is granted for itself and
+# others acting on its behalf a paid-up, nonexclusive, irrevocable
+# worldwide license in this data to reproduce, prepare derivative works,
+# distribute copies to the public, perform publicly and display
+# publicly, and to permit others to do so.
+#
+# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
+# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
+# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
+# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
+# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
+# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
+#
+# ************************************************************************
+# @HEADER
+
+# Check for CUDA support
+
+SET(_CUDA_FAILURE OFF)
+
+# Have CMake find CUDA
+IF(NOT _CUDA_FAILURE)
+  FIND_PACKAGE(CUDA 3.2)
+  IF (NOT CUDA_FOUND)
+    SET(_CUDA_FAILURE ON)
+  ENDIF()
+ENDIF()
+
+IF(NOT _CUDA_FAILURE)
+  # if we haven't met failure
+  macro(PACKAGE_ADD_CUDA_LIBRARY cuda_target)
+    TRIBITS_ADD_LIBRARY(${cuda_target} ${ARGN} CUDALIBRARY)
+  endmacro()
+  GLOBAL_SET(TPL_CUDA_LIBRARY_DIRS)
+  GLOBAL_SET(TPL_CUDA_INCLUDE_DIRS ${CUDA_TOOLKIT_INCLUDE})
+  GLOBAL_SET(TPL_CUDA_LIBRARIES ${CUDA_CUDART_LIBRARY} ${CUDA_cublas_LIBRARY} ${CUDA_cufft_LIBRARY})
+  TIBITS_CREATE_IMPORTED_TPL_LIBRARY(CUSPARSE)
+ELSE()
+  SET(TPL_ENABLE_CUDA OFF)
+ENDIF()
diff --git a/lib/kokkos/cmake/deps/CUSPARSE.cmake b/lib/kokkos/cmake/deps/CUSPARSE.cmake
new file mode 100644
index 0000000000..205f5e2a98
--- /dev/null
+++ b/lib/kokkos/cmake/deps/CUSPARSE.cmake
@@ -0,0 +1,64 @@
+# @HEADER
+# ************************************************************************
+#
+#            Trilinos: An Object-Oriented Solver Framework
+#                 Copyright (2001) Sandia Corporation
+#
+#
+# Copyright (2001) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000, there is a non-exclusive license for use of this
+# work by or on behalf of the U.S. Government.  Export of this program
+# may require a license from the United States Government.
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# NOTICE:  The United States Government is granted for itself and others
+# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
+# license in this data to reproduce, prepare derivative works, and
+# perform publicly and display publicly.  Beginning five (5) years from
+# July 25, 2001, the United States Government is granted for itself and
+# others acting on its behalf a paid-up, nonexclusive, irrevocable
+# worldwide license in this data to reproduce, prepare derivative works,
+# distribute copies to the public, perform publicly and display
+# publicly, and to permit others to do so.
+#
+# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
+# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
+# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
+# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
+# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
+# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
+#
+# ************************************************************************
+# @HEADER
+
+include(${TRIBITS_DEPS_DIR}/CUDA.cmake)
+
+IF (TPL_ENABLE_CUDA)
+  GLOBAL_SET(TPL_CUSPARSE_LIBRARY_DIRS)
+  GLOBAL_SET(TPL_CUSPARSE_INCLUDE_DIRS ${TPL_CUDA_INCLUDE_DIRS})
+  GLOBAL_SET(TPL_CUSPARSE_LIBRARIES    ${CUDA_cusparse_LIBRARY})
+  TIBITS_CREATE_IMPORTED_TPL_LIBRARY(CUSPARSE)
+ENDIF()
+
diff --git a/lib/kokkos/cmake/deps/HWLOC.cmake b/lib/kokkos/cmake/deps/HWLOC.cmake
new file mode 100644
index 0000000000..275abd3a5d
--- /dev/null
+++ b/lib/kokkos/cmake/deps/HWLOC.cmake
@@ -0,0 +1,70 @@
+# @HEADER
+# ************************************************************************
+#
+#            Trilinos: An Object-Oriented Solver Framework
+#                 Copyright (2001) Sandia Corporation
+#
+#
+# Copyright (2001) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000, there is a non-exclusive license for use of this
+# work by or on behalf of the U.S. Government.  Export of this program
+# may require a license from the United States Government.
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# NOTICE:  The United States Government is granted for itself and others
+# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
+# license in this data to reproduce, prepare derivative works, and
+# perform publicly and display publicly.  Beginning five (5) years from
+# July 25, 2001, the United States Government is granted for itself and
+# others acting on its behalf a paid-up, nonexclusive, irrevocable
+# worldwide license in this data to reproduce, prepare derivative works,
+# distribute copies to the public, perform publicly and display
+# publicly, and to permit others to do so.
+#
+# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
+# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
+# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
+# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
+# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
+# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
+#
+# ************************************************************************
+# @HEADER
+
+
+#-----------------------------------------------------------------------------
+#  Hardware locality detection and control library.
+#
+#  Acquisition information:
+#    Date checked:  November 2011
+#    Checked by:    H. Carter Edwards <hcedwar AT sandia.gov>
+#    Source:        http://www.open-mpi.org/projects/hwloc/
+#    Version:       1.3
+#
+
+TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( HWLOC
+  REQUIRED_HEADERS hwloc.h
+  REQUIRED_LIBS_NAMES "hwloc"
+  )
diff --git a/lib/kokkos/cmake/deps/Pthread.cmake b/lib/kokkos/cmake/deps/Pthread.cmake
new file mode 100644
index 0000000000..46d0a939ca
--- /dev/null
+++ b/lib/kokkos/cmake/deps/Pthread.cmake
@@ -0,0 +1,83 @@
+# @HEADER
+# ************************************************************************
+#
+#            Trilinos: An Object-Oriented Solver Framework
+#                 Copyright (2001) Sandia Corporation
+#
+#
+# Copyright (2001) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000, there is a non-exclusive license for use of this
+# work by or on behalf of the U.S. Government.  Export of this program
+# may require a license from the United States Government.
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# NOTICE:  The United States Government is granted for itself and others
+# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
+# license in this data to reproduce, prepare derivative works, and
+# perform publicly and display publicly.  Beginning five (5) years from
+# July 25, 2001, the United States Government is granted for itself and
+# others acting on its behalf a paid-up, nonexclusive, irrevocable
+# worldwide license in this data to reproduce, prepare derivative works,
+# distribute copies to the public, perform publicly and display
+# publicly, and to permit others to do so.
+#
+# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
+# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
+# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
+# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
+# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
+# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
+#
+# ************************************************************************
+# @HEADER
+
+
+SET(USE_THREADS FALSE)
+
+IF(NOT TPL_Pthread_INCLUDE_DIRS AND NOT TPL_Pthread_LIBRARY_DIRS AND NOT TPL_Pthread_LIBRARIES)
+  # Use CMake's Thread finder since it is a bit smarter in determining
+  # whether pthreads is already built into the compiler and doesn't need
+  # a library to link.
+  FIND_PACKAGE(Threads)
+  #If Threads found a copy of pthreads make sure it is one of the cases the tribits
+  #tpl system cannot handle.
+  IF(Threads_FOUND AND CMAKE_USE_PTHREADS_INIT)
+    IF(CMAKE_THREAD_LIBS_INIT STREQUAL "" OR CMAKE_THREAD_LIBS_INIT STREQUAL "-pthread")
+      SET(USE_THREADS TRUE)
+    ENDIF()
+  ENDIF()
+ENDIF()
+
+IF(USE_THREADS)
+  SET(TPL_Pthread_INCLUDE_DIRS "")
+  SET(TPL_Pthread_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
+  SET(TPL_Pthread_LIBRARY_DIRS "")
+  TIBITS_CREATE_IMPORTED_TPL_LIBRARY(Pthread)
+ELSE()
+  TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( Pthread
+    REQUIRED_HEADERS pthread.h
+    REQUIRED_LIBS_NAMES pthread
+      )
+ENDIF()
diff --git a/lib/kokkos/cmake/deps/QTHREAD.cmake b/lib/kokkos/cmake/deps/QTHREAD.cmake
new file mode 100644
index 0000000000..994b72b200
--- /dev/null
+++ b/lib/kokkos/cmake/deps/QTHREAD.cmake
@@ -0,0 +1,70 @@
+# @HEADER
+# ************************************************************************
+#
+#            Trilinos: An Object-Oriented Solver Framework
+#                 Copyright (2001) Sandia Corporation
+#
+#
+# Copyright (2001) Sandia Corporation. Under the terms of Contract
+# DE-AC04-94AL85000, there is a non-exclusive license for use of this
+# work by or on behalf of the U.S. Government.  Export of this program
+# may require a license from the United States Government.
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the Corporation nor the names of the
+# contributors may be used to endorse or promote products derived from
+# this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# NOTICE:  The United States Government is granted for itself and others
+# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
+# license in this data to reproduce, prepare derivative works, and
+# perform publicly and display publicly.  Beginning five (5) years from
+# July 25, 2001, the United States Government is granted for itself and
+# others acting on its behalf a paid-up, nonexclusive, irrevocable
+# worldwide license in this data to reproduce, prepare derivative works,
+# distribute copies to the public, perform publicly and display
+# publicly, and to permit others to do so.
+#
+# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
+# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
+# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
+# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
+# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
+# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
+#
+# ************************************************************************
+# @HEADER
+
+
+#-----------------------------------------------------------------------------
+#  Hardware locality detection and control library.
+#
+#  Acquisition information:
+#    Date checked:  July 2014
+#    Checked by:    H. Carter Edwards <hcedwar AT sandia.gov>
+#    Source:        https://code.google.com/p/qthreads
+#
+
+TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( QTHREAD
+  REQUIRED_HEADERS qthread.h
+  REQUIRED_LIBS_NAMES "qthread"
+  )
+
diff --git a/lib/kokkos/cmake/tribits.cmake b/lib/kokkos/cmake/tribits.cmake
new file mode 100644
index 0000000000..34cd216f81
--- /dev/null
+++ b/lib/kokkos/cmake/tribits.cmake
@@ -0,0 +1,485 @@
+INCLUDE(CMakeParseArguments)
+INCLUDE(CTest)
+
+FUNCTION(ASSERT_DEFINED VARS)
+  FOREACH(VAR ${VARS})
+    IF(NOT DEFINED ${VAR})
+      MESSAGE(SEND_ERROR "Error, the variable ${VAR} is not defined!")
+    ENDIF()
+  ENDFOREACH()
+ENDFUNCTION()
+
+MACRO(GLOBAL_SET VARNAME)
+  SET(${VARNAME} ${ARGN} CACHE INTERNAL "")
+ENDMACRO()
+
+MACRO(PREPEND_GLOBAL_SET VARNAME)
+  ASSERT_DEFINED(${VARNAME})
+  GLOBAL_SET(${VARNAME} ${ARGN} ${${VARNAME}})
+ENDMACRO()
+
+FUNCTION(REMOVE_GLOBAL_DUPLICATES VARNAME)
+  ASSERT_DEFINED(${VARNAME})
+  IF (${VARNAME})
+    SET(TMP ${${VARNAME}})
+    LIST(REMOVE_DUPLICATES TMP)
+    GLOBAL_SET(${VARNAME} ${TMP})
+  ENDIF()
+ENDFUNCTION()
+
+MACRO(TRIBITS_ADD_OPTION_AND_DEFINE  USER_OPTION_NAME  MACRO_DEFINE_NAME DOCSTRING  DEFAULT_VALUE)
+  MESSAGE(STATUS "TRIBITS_ADD_OPTION_AND_DEFINE: '${USER_OPTION_NAME}' '${MACRO_DEFINE_NAME}' '${DEFAULT_VALUE}'")
+  SET( ${USER_OPTION_NAME} "${DEFAULT_VALUE}" CACHE BOOL "${DOCSTRING}" )
+  IF(NOT ${MACRO_DEFINE_NAME} STREQUAL "")
+    IF(${USER_OPTION_NAME})
+      GLOBAL_SET(${MACRO_DEFINE_NAME} ON)
+    ELSE()
+      GLOBAL_SET(${MACRO_DEFINE_NAME} OFF)
+    ENDIF()
+  ENDIF()
+ENDMACRO()
+
+FUNCTION(TRIBITS_CONFIGURE_FILE  PACKAGE_NAME_CONFIG_FILE)
+
+  # Configure the file
+  CONFIGURE_FILE(
+    ${PACKAGE_SOURCE_DIR}/cmake/${PACKAGE_NAME_CONFIG_FILE}.in
+    ${CMAKE_CURRENT_BINARY_DIR}/${PACKAGE_NAME_CONFIG_FILE}
+    )
+
+ENDFUNCTION()
+
+MACRO(TRIBITS_ADD_DEBUG_OPTION)
+  TRIBITS_ADD_OPTION_AND_DEFINE(
+    ${PROJECT_NAME}_ENABLE_DEBUG
+    HAVE_${PROJECT_NAME_UC}_DEBUG
+    "Enable a host of runtime debug checking."
+    OFF
+    )
+ENDMACRO()
+
+
+MACRO(TRIBITS_ADD_TEST_DIRECTORIES)
+  FOREACH(TEST_DIR ${ARGN})
+    ADD_SUBDIRECTORY(${TEST_DIR})
+  ENDFOREACH()
+ENDMACRO()
+
+MACRO(TRIBITS_ADD_EXAMPLE_DIRECTORIES)
+
+  IF(${PACKAGE_NAME}_ENABLE_EXAMPLES OR ${PARENT_PACKAGE_NAME}_ENABLE_EXAMPLES)
+    FOREACH(EXAMPLE_DIR ${ARGN})
+      ADD_SUBDIRECTORY(${EXAMPLE_DIR})
+    ENDFOREACH()
+  ENDIF()
+
+ENDMACRO()
+
+MACRO(TARGET_TRANSFER_PROPERTY TARGET_NAME PROP_IN PROP_OUT)
+  SET(PROP_VALUES)
+  FOREACH(TARGET_X ${ARGN})
+    LIST(APPEND PROP_VALUES "$<TARGET_PROPERTY:${TARGET_X},${PROP_IN}>")
+  ENDFOREACH()
+  SET_TARGET_PROPERTIES(${TARGET_NAME} PROPERTIES ${PROP_OUT} "${PROP_VALUES}")
+ENDMACRO()
+
+MACRO(ADD_INTERFACE_LIBRARY LIB_NAME)
+  FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/dummy.cpp "")
+  ADD_LIBRARY(${LIB_NAME} STATIC ${CMAKE_CURRENT_BINARY_DIR}/dummy.cpp)
+  SET_TARGET_PROPERTIES(${LIB_NAME} PROPERTIES INTERFACE TRUE)
+ENDMACRO()
+
+# Older versions of cmake does not make include directories transitive
+MACRO(TARGET_LINK_AND_INCLUDE_LIBRARIES TARGET_NAME)
+  TARGET_LINK_LIBRARIES(${TARGET_NAME} LINK_PUBLIC ${ARGN})
+  FOREACH(DEP_LIB ${ARGN})
+    TARGET_INCLUDE_DIRECTORIES(${TARGET_NAME} PUBLIC $<TARGET_PROPERTY:${DEP_LIB},INTERFACE_INCLUDE_DIRECTORIES>)
+    TARGET_INCLUDE_DIRECTORIES(${TARGET_NAME} PUBLIC $<TARGET_PROPERTY:${DEP_LIB},INCLUDE_DIRECTORIES>)
+  ENDFOREACH()
+ENDMACRO()
+
+FUNCTION(TRIBITS_ADD_LIBRARY LIBRARY_NAME)
+
+  SET(options STATIC SHARED TESTONLY NO_INSTALL_LIB_OR_HEADERS CUDALIBRARY)
+  SET(oneValueArgs)
+  SET(multiValueArgs HEADERS HEADERS_INSTALL_SUBDIR NOINSTALLHEADERS SOURCES DEPLIBS IMPORTEDLIBS DEFINES ADDED_LIB_TARGET_NAME_OUT)
+
+  CMAKE_PARSE_ARGUMENTS(PARSE "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+  IF(PARSE_HEADERS)
+    LIST(REMOVE_DUPLICATES PARSE_HEADERS)
+  ENDIF()
+  IF(PARSE_SOURCES)
+    LIST(REMOVE_DUPLICATES PARSE_SOURCES)
+  ENDIF()
+
+  # Local variable to hold all of the libraries that will be directly linked
+  # to this library.
+  SET(LINK_LIBS ${${PACKAGE_NAME}_DEPS})
+
+  # Add dependent libraries passed directly in
+
+  IF (PARSE_IMPORTEDLIBS)
+    LIST(APPEND LINK_LIBS ${PARSE_IMPORTEDLIBS})
+  ENDIF()
+
+  IF (PARSE_DEPLIBS)
+    LIST(APPEND LINK_LIBS ${PARSE_DEPLIBS})
+  ENDIF()
+
+  # Add the library and all the dependencies
+
+  IF (PARSE_DEFINES)
+    ADD_DEFINITIONS(${PARSE_DEFINES})
+  ENDIF()
+
+  IF (PARSE_STATIC)
+    SET(STATIC_KEYWORD "STATIC")
+  ELSE()
+    SET(STATIC_KEYWORD)
+  ENDIF()
+
+  IF (PARSE_SHARED)
+    SET(SHARED_KEYWORD "SHARED")
+  ELSE()
+    SET(SHARED_KEYWORD)
+  ENDIF()
+
+  IF (PARSE_TESTONLY)
+    SET(EXCLUDE_FROM_ALL_KEYWORD "EXCLUDE_FROM_ALL")
+  ELSE()
+    SET(EXCLUDE_FROM_ALL_KEYWORD)
+  ENDIF()
+  IF (NOT PARSE_CUDALIBRARY)
+    ADD_LIBRARY(
+      ${LIBRARY_NAME}
+      ${STATIC_KEYWORD}
+      ${SHARED_KEYWORD}
+      ${EXCLUDE_FROM_ALL_KEYWORD}
+      ${PARSE_HEADERS}
+      ${PARSE_NOINSTALLHEADERS}
+      ${PARSE_SOURCES}
+      )
+  ELSE()
+    CUDA_ADD_LIBRARY(
+      ${LIBRARY_NAME}
+      ${PARSE_HEADERS}
+      ${PARSE_NOINSTALLHEADERS}
+      ${PARSE_SOURCES}
+      )
+  ENDIF()
+
+  TARGET_LINK_AND_INCLUDE_LIBRARIES(${LIBRARY_NAME} ${LINK_LIBS})
+
+  IF (NOT PARSE_TESTONLY OR PARSE_NO_INSTALL_LIB_OR_HEADERS)
+
+    INSTALL(
+      TARGETS ${LIBRARY_NAME}
+      EXPORT ${PROJECT_NAME}
+      RUNTIME DESTINATION bin
+      LIBRARY DESTINATION lib
+      ARCHIVE DESTINATION lib
+      COMPONENT ${PACKAGE_NAME}
+      )
+
+    INSTALL(
+      FILES  ${PARSE_HEADERS}
+      EXPORT ${PROJECT_NAME}
+      DESTINATION include
+      COMPONENT ${PACKAGE_NAME}
+      )
+
+      INSTALL(
+      DIRECTORY  ${PARSE_HEADERS_INSTALL_SUBDIR}
+      EXPORT ${PROJECT_NAME}
+      DESTINATION include
+      COMPONENT ${PACKAGE_NAME}
+      )
+
+  ENDIF()
+
+  IF (NOT PARSE_TESTONLY)
+    PREPEND_GLOBAL_SET(${PACKAGE_NAME}_LIBS ${LIBRARY_NAME})
+    REMOVE_GLOBAL_DUPLICATES(${PACKAGE_NAME}_LIBS)
+  ENDIF()
+
+ENDFUNCTION()
+
+FUNCTION(TRIBITS_ADD_EXECUTABLE EXE_NAME)
+
+  SET(options NOEXEPREFIX NOEXESUFFIX ADD_DIR_TO_NAME INSTALLABLE TESTONLY)
+  SET(oneValueArgs ADDED_EXE_TARGET_NAME_OUT)
+  SET(multiValueArgs SOURCES CATEGORIES HOST XHOST HOSTTYPE XHOSTTYPE DIRECTORY TESTONLYLIBS IMPORTEDLIBS DEPLIBS COMM LINKER_LANGUAGE TARGET_DEFINES DEFINES)
+
+  CMAKE_PARSE_ARGUMENTS(PARSE "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+  IF (PARSE_TARGET_DEFINES)
+    TARGET_COMPILE_DEFINITIONS(${EXE_NAME} PUBLIC ${PARSE_TARGET_DEFINES})
+  ENDIF()
+
+  SET(LINK_LIBS PACKAGE_${PACKAGE_NAME})
+
+  IF (PARSE_TESTONLYLIBS)
+    LIST(APPEND LINK_LIBS ${PARSE_TESTONLYLIBS})
+  ENDIF()
+
+  IF (PARSE_IMPORTEDLIBS)
+    LIST(APPEND LINK_LIBS ${PARSE_IMPORTEDLIBS})
+  ENDIF()
+
+  SET (EXE_SOURCES)
+  IF(PARSE_DIRECTORY)
+    FOREACH( SOURCE_FILE ${PARSE_SOURCES} )
+      IF(IS_ABSOLUTE ${SOURCE_FILE})
+        SET (EXE_SOURCES ${EXE_SOURCES} ${SOURCE_FILE})
+      ELSE()
+        SET (EXE_SOURCES ${EXE_SOURCES} ${PARSE_DIRECTORY}/${SOURCE_FILE})
+      ENDIF()
+    ENDFOREACH( )
+  ELSE()
+    FOREACH( SOURCE_FILE ${PARSE_SOURCES} )
+      SET (EXE_SOURCES ${EXE_SOURCES} ${SOURCE_FILE})
+    ENDFOREACH( )
+  ENDIF()
+
+  SET(EXE_BINARY_NAME ${EXE_NAME})
+  IF(DEFINED PACKAGE_NAME AND NOT PARSE_NOEXEPREFIX)
+    SET(EXE_BINARY_NAME ${PACKAGE_NAME}_${EXE_BINARY_NAME})
+  ENDIF()
+
+  IF (PARSE_TESTONLY)
+    SET(EXCLUDE_FROM_ALL_KEYWORD "EXCLUDE_FROM_ALL")
+  ELSE()
+    SET(EXCLUDE_FROM_ALL_KEYWORD)
+  ENDIF()
+  ADD_EXECUTABLE(${EXE_BINARY_NAME} ${EXCLUDE_FROM_ALL_KEYWORD} ${EXE_SOURCES})
+
+  TARGET_LINK_AND_INCLUDE_LIBRARIES(${EXE_BINARY_NAME} ${LINK_LIBS})
+
+  IF(PARSE_ADDED_EXE_TARGET_NAME_OUT)
+    SET(${PARSE_ADDED_EXE_TARGET_NAME_OUT} ${EXE_BINARY_NAME} PARENT_SCOPE)
+  ENDIF()
+
+  IF(PARSE_INSTALLABLE)
+    INSTALL(
+      TARGETS ${EXE_BINARY_NAME}
+      EXPORT ${PROJECT_NAME}
+        DESTINATION bin
+    )
+  ENDIF()
+ENDFUNCTION()
+
+ADD_CUSTOM_TARGET(check COMMAND ${CMAKE_CTEST_COMMAND} -VV -C ${CMAKE_CFG_INTDIR})
+
+FUNCTION(TRIBITS_ADD_EXECUTABLE_AND_TEST EXE_NAME)
+
+  SET(options STANDARD_PASS_OUTPUT WILL_FAIL)
+  SET(oneValueArgs PASS_REGULAR_EXPRESSION FAIL_REGULAR_EXPRESSION ENVIRONMENT TIMEOUT CATEGORIES ADDED_TESTS_NAMES_OUT ADDED_EXE_TARGET_NAME_OUT)
+  SET(multiValueArgs)
+
+  CMAKE_PARSE_ARGUMENTS(PARSE "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+  TRIBITS_ADD_EXECUTABLE(${EXE_NAME} TESTONLY ADDED_EXE_TARGET_NAME_OUT TEST_NAME ${PARSE_UNPARSED_ARGUMENTS})
+
+  IF(WIN32)
+    ADD_TEST(NAME ${TEST_NAME} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH} COMMAND ${TEST_NAME}${CMAKE_EXECUTABLE_SUFFIX})
+  ELSE()
+    ADD_TEST(NAME ${TEST_NAME} COMMAND ${TEST_NAME})
+  ENDIF()
+  ADD_DEPENDENCIES(check ${TEST_NAME})
+
+  IF(PARSE_FAIL_REGULAR_EXPRESSION)
+    SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES FAIL_REGULAR_EXPRESSION ${PARSE_FAIL_REGULAR_EXPRESSION})
+  ENDIF()
+
+  IF(PARSE_PASS_REGULAR_EXPRESSION)
+    SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES PASS_REGULAR_EXPRESSION ${PARSE_PASS_REGULAR_EXPRESSION})
+  ENDIF()
+
+  IF(PARSE_WILL_FAIL)
+    SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES WILL_FAIL ${PARSE_WILL_FAIL})
+  ENDIF()
+
+  IF(PARSE_ADDED_TESTS_NAMES_OUT)
+    SET(${PARSE_ADDED_TESTS_NAMES_OUT} ${TEST_NAME} PARENT_SCOPE)
+  ENDIF()
+
+  IF(PARSE_ADDED_EXE_TARGET_NAME_OUT)
+    SET(${PARSE_ADDED_EXE_TARGET_NAME_OUT} ${TEST_NAME} PARENT_SCOPE)
+  ENDIF()
+
+ENDFUNCTION()
+
+MACRO(TIBITS_CREATE_IMPORTED_TPL_LIBRARY TPL_NAME)
+  ADD_INTERFACE_LIBRARY(TPL_LIB_${TPL_NAME})
+  TARGET_LINK_LIBRARIES(TPL_LIB_${TPL_NAME} LINK_PUBLIC ${TPL_${TPL_NAME}_LIBRARIES})
+  TARGET_INCLUDE_DIRECTORIES(TPL_LIB_${TPL_NAME} INTERFACE ${TPL_${TPL_NAME}_INCLUDE_DIRS})
+ENDMACRO()
+
+FUNCTION(TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES TPL_NAME)
+
+  SET(options MUST_FIND_ALL_LIBS MUST_FIND_ALL_HEADERS NO_PRINT_ENABLE_SUCCESS_FAIL)
+  SET(oneValueArgs)
+  SET(multiValueArgs REQUIRED_HEADERS REQUIRED_LIBS_NAMES)
+
+  CMAKE_PARSE_ARGUMENTS(PARSE "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+  SET(_${TPL_NAME}_ENABLE_SUCCESS TRUE)
+  IF (PARSE_REQUIRED_LIBS_NAMES)
+    FIND_LIBRARY(TPL_${TPL_NAME}_LIBRARIES NAMES ${PARSE_REQUIRED_LIBS_NAMES})
+    IF(NOT TPL_${TPL_NAME}_LIBRARIES)
+      SET(_${TPL_NAME}_ENABLE_SUCCESS FALSE)
+    ENDIF()
+  ENDIF()
+  IF (PARSE_REQUIRED_HEADERS)
+    FIND_PATH(TPL_${TPL_NAME}_INCLUDE_DIRS NAMES ${PARSE_REQUIRED_HEADERS})
+    IF(NOT TPL_${TPL_NAME}_INCLUDE_DIRS)
+      SET(_${TPL_NAME}_ENABLE_SUCCESS FALSE)
+    ENDIF()
+  ENDIF()
+
+
+  IF (_${TPL_NAME}_ENABLE_SUCCESS)
+    TIBITS_CREATE_IMPORTED_TPL_LIBRARY(${TPL_NAME})
+  ENDIF()
+
+ENDFUNCTION()
+
+MACRO(TRIBITS_PROCESS_TPL_DEP_FILE TPL_FILE)
+  GET_FILENAME_COMPONENT(TPL_NAME ${TPL_FILE} NAME_WE)
+  INCLUDE("${TPL_FILE}")
+  IF(TARGET TPL_LIB_${TPL_NAME})
+    MESSAGE(STATUS "Found tpl library: ${TPL_NAME}")
+    SET(TPL_ENABLE_${TPL_NAME} TRUE)
+  ELSE()
+    MESSAGE(STATUS "Tpl library not found: ${TPL_NAME}")
+    SET(TPL_ENABLE_${TPL_NAME} FALSE)
+  ENDIF()
+ENDMACRO()
+
+MACRO(PREPEND_TARGET_SET VARNAME TARGET_NAME TYPE)
+  IF(TYPE STREQUAL "REQUIRED")
+    SET(REQUIRED TRUE)
+  ELSE()
+    SET(REQUIRED FALSE)
+  ENDIF()
+  IF(TARGET ${TARGET_NAME})
+    PREPEND_GLOBAL_SET(${VARNAME} ${TARGET_NAME})
+  ELSE()
+    IF(REQUIRED)
+      MESSAGE(FATAL_ERROR "Missing dependency ${TARGET_NAME}")
+    ENDIF()
+  ENDIF()
+ENDMACRO()
+
+MACRO(TRIBITS_APPEND_PACKAGE_DEPS DEP_LIST TYPE)
+  FOREACH(DEP ${ARGN})
+    PREPEND_GLOBAL_SET(${DEP_LIST} PACKAGE_${DEP})
+  ENDFOREACH()
+ENDMACRO()
+
+MACRO(TRIBITS_APPEND_TPLS_DEPS DEP_LIST TYPE)
+  FOREACH(DEP ${ARGN})
+    PREPEND_TARGET_SET(${DEP_LIST} TPL_LIB_${DEP} ${TYPE})
+  ENDFOREACH()
+ENDMACRO()
+
+MACRO(TRIBITS_ENABLE_TPLS)
+  FOREACH(TPL ${ARGN})
+    IF(TARGET ${TPL})
+      GLOBAL_SET(${PACKAGE_NAME}_ENABLE_${TPL} TRUE)
+    ELSE()
+      GLOBAL_SET(${PACKAGE_NAME}_ENABLE_${TPL} FALSE)
+    ENDIF()
+  ENDFOREACH()
+ENDMACRO()
+
+MACRO(TRIBITS_PACKAGE_DEFINE_DEPENDENCIES)
+
+  SET(options)
+  SET(oneValueArgs)
+  SET(multiValueArgs 
+    LIB_REQUIRED_PACKAGES
+    LIB_OPTIONAL_PACKAGES
+    TEST_REQUIRED_PACKAGES
+    TEST_OPTIONAL_PACKAGES
+    LIB_REQUIRED_TPLS
+    LIB_OPTIONAL_TPLS
+    TEST_REQUIRED_TPLS
+    TEST_OPTIONAL_TPLS
+    REGRESSION_EMAIL_LIST
+    SUBPACKAGES_DIRS_CLASSIFICATIONS_OPTREQS
+  )
+  CMAKE_PARSE_ARGUMENTS(PARSE "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+  GLOBAL_SET(${PACKAGE_NAME}_DEPS "")
+  TRIBITS_APPEND_PACKAGE_DEPS(${PACKAGE_NAME}_DEPS REQUIRED ${PARSE_LIB_REQUIRED_PACKAGES})
+  TRIBITS_APPEND_PACKAGE_DEPS(${PACKAGE_NAME}_DEPS OPTIONAL ${PARSE_LIB_OPTIONAL_PACKAGES})
+  TRIBITS_APPEND_TPLS_DEPS(${PACKAGE_NAME}_DEPS REQUIRED ${PARSE_LIB_REQUIRED_TPLS})
+  TRIBITS_APPEND_TPLS_DEPS(${PACKAGE_NAME}_DEPS OPTIONAL ${PARSE_LIB_OPTIONAL_TPLS})
+
+  GLOBAL_SET(${PACKAGE_NAME}_TEST_DEPS "")
+  TRIBITS_APPEND_PACKAGE_DEPS(${PACKAGE_NAME}_TEST_DEPS REQUIRED ${PARSE_TEST_REQUIRED_PACKAGES})
+  TRIBITS_APPEND_PACKAGE_DEPS(${PACKAGE_NAME}_TEST_DEPS OPTIONAL ${PARSE_TEST_OPTIONAL_PACKAGES})
+  TRIBITS_APPEND_TPLS_DEPS(${PACKAGE_NAME}_TEST_DEPS REQUIRED ${PARSE_TEST_REQUIRED_TPLS})
+  TRIBITS_APPEND_TPLS_DEPS(${PACKAGE_NAME}_TEST_DEPS OPTIONAL ${PARSE_TEST_OPTIONAL_TPLS})
+
+  TRIBITS_ENABLE_TPLS(${PARSE_LIB_REQUIRED_TPLS} ${PARSE_LIB_OPTIONAL_TPLS} ${PARSE_TEST_REQUIRED_TPLS} ${PARSE_TEST_OPTIONAL_TPLS})
+
+ENDMACRO()
+
+MACRO(TRIBITS_SUBPACKAGE NAME)
+  SET(PACKAGE_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+  SET(PARENT_PACKAGE_NAME ${PACKAGE_NAME})
+  SET(PACKAGE_NAME ${PACKAGE_NAME}${NAME})
+  STRING(TOUPPER ${PACKAGE_NAME} PACKAGE_NAME_UC)
+
+  ADD_INTERFACE_LIBRARY(PACKAGE_${PACKAGE_NAME})
+
+  GLOBAL_SET(${PACKAGE_NAME}_LIBS "")
+
+  INCLUDE(${PACKAGE_SOURCE_DIR}/cmake/Dependencies.cmake)
+
+ENDMACRO(TRIBITS_SUBPACKAGE)
+
+MACRO(TRIBITS_SUBPACKAGE_POSTPROCESS)
+  TARGET_LINK_AND_INCLUDE_LIBRARIES(PACKAGE_${PACKAGE_NAME} ${${PACKAGE_NAME}_LIBS})
+ENDMACRO(TRIBITS_SUBPACKAGE_POSTPROCESS)
+
+MACRO(TRIBITS_PACKAGE_DECL NAME)
+
+  PROJECT(${NAME})
+  STRING(TOUPPER ${PROJECT_NAME} PROJECT_NAME_UC)
+  SET(PACKAGE_NAME ${PROJECT_NAME})
+  STRING(TOUPPER ${PACKAGE_NAME} PACKAGE_NAME_UC)
+
+  SET(TRIBITS_DEPS_DIR "${CMAKE_SOURCE_DIR}/cmake/deps")
+  FILE(GLOB TPLS_FILES "${TRIBITS_DEPS_DIR}/*.cmake")
+  FOREACH(TPL_FILE ${TPLS_FILES})
+    TRIBITS_PROCESS_TPL_DEP_FILE(${TPL_FILE})
+  ENDFOREACH()
+
+ENDMACRO()
+
+
+MACRO(TRIBITS_PROCESS_SUBPACKAGES)
+  FILE(GLOB SUBPACKAGES RELATIVE ${CMAKE_SOURCE_DIR} */cmake/Dependencies.cmake)
+  FOREACH(SUBPACKAGE ${SUBPACKAGES})
+    GET_FILENAME_COMPONENT(SUBPACKAGE_CMAKE ${SUBPACKAGE} DIRECTORY)
+    GET_FILENAME_COMPONENT(SUBPACKAGE_DIR ${SUBPACKAGE_CMAKE} DIRECTORY)
+    ADD_SUBDIRECTORY(${SUBPACKAGE_DIR})
+  ENDFOREACH()
+ENDMACRO(TRIBITS_PROCESS_SUBPACKAGES)
+
+MACRO(TRIBITS_PACKAGE_DEF)
+ENDMACRO(TRIBITS_PACKAGE_DEF)
+
+MACRO(TRIBITS_EXCLUDE_AUTOTOOLS_FILES)
+ENDMACRO(TRIBITS_EXCLUDE_AUTOTOOLS_FILES)
+
+MACRO(TRIBITS_EXCLUDE_FILES)
+ENDMACRO(TRIBITS_EXCLUDE_FILES)
+
+MACRO(TRIBITS_PACKAGE_POSTPROCESS)
+ENDMACRO(TRIBITS_PACKAGE_POSTPROCESS)
+
diff --git a/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt b/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt
new file mode 100644
index 0000000000..9f56f2fd48
--- /dev/null
+++ b/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt
@@ -0,0 +1,153 @@
+// -------------------------------------------------------------------------------- //
+
+The following steps are for workstations/servers with the SEMS environment installed.
+
+// -------------------------------------------------------------------------------- //
+Summary:
+
+- Step 1: Rigorous testing of Kokkos' develop branch for each backend (Serial, OpenMP, Threads, Cuda) with all supported compilers.
+
+- Step 2: Snapshot Kokkos' develop branch into current Trilinos develop branch.
+
+- Step 3: Build and test Trilinos with combinations of compilers, types, backends.
+
+- Step 4: Promote Kokkos develop branch to master if the snapshot does not cause any new tests to fail; else track/fix causes of new failures.
+
+- Step 5: Snapshot Kokkos tagged master branch into Trilinos and push Trilinos.
+// -------------------------------------------------------------------------------- //
+
+
+// -------------------------------------------------------------------------------- //
+
+Step 1:
+  1.1. Update kokkos develop branch (NOT a fork)
+
+         (From kokkos directory):
+         git fetch --all
+         git checkout develop
+         git reset --hard origin/develop
+
+  1.2. Create a testing directory - here the directory is created within the kokkos directory
+
+         mkdir testing
+         cd testing
+
+  1.3. Run the test_all_sandia script; various compiler and build-list options can be specified
+
+         ../config/test_all_sandia
+
+  1.4 Clean repository of untracked files
+
+        cd ../
+        git clean -df
+
+// -------------------------------------------------------------------------------- //
+
+Step 2:
+  2.1 Update Trilinos develop branch
+
+        (From Trilinos directory):
+        git checkout develop
+        git fetch --all
+        git reset --hard origin/develop
+        git clean -df
+
+  2.2 Snapshot Kokkos into Trilinos - this requires python/2.7.9 and that both Trilinos and Kokkos be clean - no untracked or modified files
+
+        module load python/2.7.9
+        python KOKKOS_PATH/config/snapshot.py KOKKOS_PATH TRILINOS_PATH/packages
+
+// -------------------------------------------------------------------------------- //
+
+Step 3:
+  3.1. Build and test Trilinos with 3 different configurations; a configure-all script is provided in Trilinos and should be modified to test each of the following 3 configurations with appropriate environment variable(s):
+
+      - GCC/4.7.2-OpenMP/Complex
+          Run tests with the following environment variable:
+
+            export OMP_NUM_THREADS=2
+
+
+      - Intel/15.0.2-Serial/NoComplex
+
+
+      - GCC/4.8.4/CUDA/7.5.18-Cuda/Serial/NoComplex
+          Run tests with the following environment variables:
+
+            export CUDA_LAUNCH_BLOCKING=1
+            export CUDA_MANAGED_FORCE_DEVICE_ALLOC=1
+
+
+        mkdir Build
+        cd Build
+        cp TRILINOS_PATH/sampleScripts/Sandia-SEMS/configure-all ./
+            ** Set the path to Trilinos appropriately within the configure-all script **
+        source $SEMS_MODULE_ROOT/utils/sems-modules-init.sh kokkos
+        source configure-all
+        make -k  (-k means "keep going" to get past build errors; -j12 can also be specified to build with 12 threads, for example)
+        ctest
+
+  3.2. Compare the failed test output to the test output on the dashboard ( testing.sandia.gov/cdash select Trilinos ); investigate and fix problems if new tests fail after the Kokkos snapshot
+
+// -------------------------------------------------------------------------------- //
+
+Step 4:
+  4.1. Once all Trilinos tests pass promote Kokkos develop branch to master on Github
+
+       - DO NOT fast-forward the merge!!!!
+
+       (From kokkos directory):
+       git checkout master
+       git fetch --all
+       # Ensure we are on the current origin/master
+       git reset --hard origin/master
+       git merge --no-ff origin/develop
+
+  4.2. Update the tag in kokkos/config/master_history.txt
+       Tag description: MajorNumber.MinorNumber.WeeksSinceMinorNumberUpdate
+       Tag format: #.#.##
+
+       # Prepend master_history.txt with 
+       
+       # tag: #.#.##
+       # date: mm/dd/yyyy
+       # master: sha1
+       # develop: sha1
+       # -----------------------
+
+       git commit --amend -a
+
+       git tag -a #.#.##
+         tag: #.#.##
+         date: mm/dd/yyyy
+         master: sha1
+         develop: sha1
+
+       git push --follow-tags origin master
+
+// -------------------------------------------------------------------------------- //
+
+Step 5:
+  5.1. Make sure Trilinos is up-to-date - chances are other changes have been committed since the integration testing process began. If a substantial change has occurred that may be affected by the snapshot the testing procedure may need to be repeated
+
+       (From Trilinos directory):
+       git checkout develop
+       git fetch --all
+       git reset --hard origin/develop
+       git clean -df
+
+  5.2. Snapshot Kokkos master branch into Trilinos
+
+       (From kokkos directory):
+       git fetch --all
+       git checkout tags/#.#.##
+       git clean -df
+
+       python KOKKOS_PATH/config/snapshot.py KOKKOS_PATH TRILINOS_PATH/packages
+       
+  5.3. Push the updated develop branch of Trilinos to Github - congratulations!!!
+
+       (From Trilinos directory):
+       git push
+
+// -------------------------------------------------------------------------------- //
diff --git a/lib/kokkos/config/master_history.txt b/lib/kokkos/config/master_history.txt
new file mode 100644
index 0000000000..f2eb674578
--- /dev/null
+++ b/lib/kokkos/config/master_history.txt
@@ -0,0 +1,3 @@
+tag:  2.01.00    date: 07:21:2016    master: xxxxxxxx    develop: fa6dfcc4
+tag:  2.01.06    date: 09:02:2016    master: 9afaa87f    develop: 555f1a3a
+
diff --git a/lib/kokkos/config/nvcc_wrapper b/lib/kokkos/config/nvcc_wrapper
index d583866191..6093cb61bd 100755
--- a/lib/kokkos/config/nvcc_wrapper
+++ b/lib/kokkos/config/nvcc_wrapper
@@ -1,17 +1,12 @@
 #!/bin/bash
 #
 # This shell script (nvcc_wrapper) wraps both the host compiler and
-# NVCC, if you are building Trilinos with CUDA enabled.  The script
-# remedies some differences between the interface of NVCC and that of
-# the host compiler, in particular for linking.  It also means that
-# Trilinos doesn't need separate .cu files; it can just use .cpp
-# files.
+# NVCC, if you are building legacy C or C++ code with CUDA enabled.
+# The script remedies some differences between the interface of NVCC
+# and that of the host compiler, in particular for linking.
+# It also means that a legacy code doesn't need separate .cu files;
+# it can just use .cpp files.
 #
-# Hopefully, at some point, NVIDIA may fix NVCC so as to make this
-# script obsolete.  For now, this script exists and if you want to
-# build Trilinos with CUDA enabled, you must use this script as your
-# compiler.
-
 # Default settings: change those according to your machine.  For
 # example, you may have have two different wrappers with either icpc
 # or g++ as their back-end compiler.  The defaults can be overwritten
@@ -53,6 +48,10 @@ object_files=""
 # Link objects for the host linker only
 object_files_xlinker=""
 
+# Shared libraries with version numbers are not handled correctly by NVCC
+shared_versioned_libraries_host=""
+shared_versioned_libraries=""
+
 # Does the User set the architecture 
 arch_set=0
 
@@ -76,6 +75,9 @@ first_xcompiler_arg=1
 
 temp_dir=${TMPDIR:-/tmp}
 
+# Check if we have an optimization argument already
+optimization_applied=0
+
 #echo "Arguments: $# $@"
 
 while [ $# -gt 0 ]
@@ -97,8 +99,17 @@ do
   *.cpp|*.cxx|*.cc|*.C|*.c++|*.cu)
     cpp_files="$cpp_files $1"
     ;;
+   # Ensure we only have one optimization flag because NVCC doesn't allow muliple
+  -O*)
+    if [ $optimization_applied -eq 1 ]; then
+       echo "nvcc_wrapper - *warning* you have set multiple optimization flags (-O*), only the first is used because nvcc can only accept a single optimization setting."
+    else
+       shared_args="$shared_args $1"
+       optimization_applied=1
+    fi
+    ;;
   #Handle shared args (valid for both nvcc and the host compiler)
-  -O*|-D*|-c|-I*|-L*|-l*|-g|--help|--version|-E|-M|-shared)
+  -D*|-c|-I*|-L*|-l*|-g|--help|--version|-E|-M|-shared)
     shared_args="$shared_args $1"
     ;;
   #Handle shared args that have an argument
@@ -107,7 +118,7 @@ do
     shift
     ;;
   #Handle known nvcc args
-  -gencode*|--dryrun|--verbose|--keep|--keep-dir*|-G|--relocatable-device-code*|-lineinfo|-expt-extended-lambda|--resource-usage)
+  -gencode*|--dryrun|--verbose|--keep|--keep-dir*|-G|--relocatable-device-code*|-lineinfo|-expt-extended-lambda|--resource-usage|-Xptxas*)
     cuda_args="$cuda_args $1"
     ;;
   #Handle known nvcc args that have an argument
@@ -175,10 +186,15 @@ do
     object_files_xlinker="$object_files_xlinker -Xlinker $1"
     ;;
   #Handle object files which always need to use "-Xlinker": -x cu applies to all input files, so give them to linker, except if only linking
-  *.so.*|*.dylib)
+  *.dylib)
     object_files="$object_files -Xlinker $1"
     object_files_xlinker="$object_files_xlinker -Xlinker $1"
     ;;
+  #Handle shared libraries with *.so.* names which nvcc can't do.
+  *.so.*)
+    shared_versioned_libraries_host="$shared_versioned_libraries_host $1"
+    shared_versioned_libraries="$shared_versioned_libraries -Xlinker $1"
+  ;;
   #All other args are sent to the host compiler
   *)
     if [ $first_xcompiler_arg -eq 1 ]; then
@@ -204,13 +220,13 @@ if [ $arch_set -ne 1 ]; then
 fi
 
 #Compose compilation command
-nvcc_command="nvcc $cuda_args $shared_args $xlinker_args"
+nvcc_command="nvcc $cuda_args $shared_args $xlinker_args $shared_versioned_libraries"
 if [ $first_xcompiler_arg -eq 0 ]; then
   nvcc_command="$nvcc_command -Xcompiler $xcompiler_args"
 fi
 
 #Compose host only command
-host_command="$host_compiler $shared_args $xcompiler_args $host_linker_args"
+host_command="$host_compiler $shared_args $xcompiler_args $host_linker_args $shared_versioned_libraries_host"
 
 #nvcc does not accept '#pragma ident SOME_MACRO_STRING' but it does accept '#ident SOME_MACRO_STRING'
 if [ $replace_pragma_ident -eq 1 ]; then
diff --git a/lib/kokkos/config/test_all_sandia b/lib/kokkos/config/test_all_sandia
index add45b77b4..aac036a8f3 100755
--- a/lib/kokkos/config/test_all_sandia
+++ b/lib/kokkos/config/test_all_sandia
@@ -6,18 +6,132 @@
 
 set -o pipefail
 
+# Determine current machine
+
+MACHINE=""
+HOSTNAME=$(hostname)
+if [[ "$HOSTNAME" =~ (white|ride).* ]]; then
+    MACHINE=white
+elif [[ "$HOSTNAME" =~ .*bowman.* ]]; then
+    MACHINE=bowman
+elif [[ "$HOSTNAME" =~ node.* ]]; then # Warning: very generic name
+    MACHINE=shepard
+elif [ ! -z "$SEMS_MODULEFILES_ROOT" ]; then
+    MACHINE=sems
+else
+    echo "Unrecognized machine" >&2
+    exit 1
+fi
+
 GCC_BUILD_LIST="OpenMP,Pthread,Serial,OpenMP_Serial,Pthread_Serial"
+IBM_BUILD_LIST="OpenMP,Serial,OpenMP_Serial"
 INTEL_BUILD_LIST="OpenMP,Pthread,Serial,OpenMP_Serial,Pthread_Serial"
 CLANG_BUILD_LIST="Pthread,Serial,Pthread_Serial"
 CUDA_BUILD_LIST="Cuda_OpenMP,Cuda_Pthread,Cuda_Serial"
 
 GCC_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wignored-qualifiers,-Wempty-body,-Wclobbered,-Wuninitialized"
+IBM_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized"
 CLANG_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized"
 INTEL_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized"
 CUDA_WARNING_FLAGS=""
 
-BASE_MODULE_LIST="<COMPILER_NAME>/<COMPILER_VERSION>/base,hwloc/1.10.1/<COMPILER_NAME>/<COMPILER_VERSION>/base"
-CUDA_MODULE_LIST="<COMPILER_NAME>/<COMPILER_VERSION>,gcc/4.7.2/base"
+# Default. Machine specific can override
+DEBUG=False
+ARGS=""
+CUSTOM_BUILD_LIST=""
+DRYRUN=False
+BUILD_ONLY=False
+declare -i NUM_JOBS_TO_RUN_IN_PARALLEL=3
+TEST_SCRIPT=False
+SKIP_HWLOC=False
+
+ARCH_FLAG=""
+
+#
+# Machine specific config
+#
+
+if [ "$MACHINE" = "sems" ]; then
+    source /projects/modulefiles/utils/sems-modules-init.sh
+    source /projects/modulefiles/utils/kokkos-modules-init.sh
+
+    BASE_MODULE_LIST="<COMPILER_NAME>/<COMPILER_VERSION>/base,hwloc/1.10.1/<COMPILER_NAME>/<COMPILER_VERSION>/base"
+    CUDA_MODULE_LIST="<COMPILER_NAME>/<COMPILER_VERSION>,gcc/4.7.2/base"
+
+    # Format: (compiler module-list build-list exe-name warning-flag)
+    COMPILERS=("gcc/4.7.2 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS"
+               "gcc/4.8.4 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS"
+               "gcc/4.9.2 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS"
+               "gcc/5.1.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS"
+               "intel/14.0.4 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS"
+               "intel/15.0.2 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS"
+               "intel/16.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS"
+               "clang/3.5.2 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS"
+               "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS"
+               "cuda/6.5.14 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS"
+               "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS"
+               "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS"
+    )
+
+elif [ "$MACHINE" = "white" ]; then
+    source /etc/profile.d/modules.sh
+    SKIP_HWLOC=True
+    export SLURM_TASKS_PER_NODE=32
+
+    BASE_MODULE_LIST="<COMPILER_NAME>/<COMPILER_VERSION>"
+    IBM_MODULE_LIST="<COMPILER_NAME>/xl/<COMPILER_VERSION>"
+    CUDA_MODULE_LIST="<COMPILER_NAME>/<COMPILER_VERSION>,gcc/4.9.2"
+
+    # Don't do pthread on white
+    GCC_BUILD_LIST="OpenMP,Serial,OpenMP_Serial"
+
+    # Format: (compiler module-list build-list exe-name warning-flag)
+    COMPILERS=("gcc/4.9.2 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS"
+               "gcc/5.3.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS"
+               "ibm/13.1.3 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS"
+    )
+
+    ARCH_FLAG="--arch=Power8"
+    NUM_JOBS_TO_RUN_IN_PARALLEL=8
+
+elif [ "$MACHINE" = "bowman" ]; then
+    source /etc/profile.d/modules.sh
+    SKIP_HWLOC=True
+    export SLURM_TASKS_PER_NODE=32
+
+    BASE_MODULE_LIST="<COMPILER_NAME>/compilers/<COMPILER_VERSION>"
+
+    OLD_INTEL_BUILD_LIST="Pthread,Serial,Pthread_Serial"
+
+    # Format: (compiler module-list build-list exe-name warning-flag)
+    COMPILERS=("intel/16.2.181 $BASE_MODULE_LIST $OLD_INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS"
+               "intel/17.0.064 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS"
+    )
+
+    ARCH_FLAG="--arch=KNL"
+    NUM_JOBS_TO_RUN_IN_PARALLEL=8
+
+elif [ "$MACHINE" = "shepard" ]; then
+    source /etc/profile.d/modules.sh
+    SKIP_HWLOC=True
+    export SLURM_TASKS_PER_NODE=32
+
+    BASE_MODULE_LIST="<COMPILER_NAME>/compilers/<COMPILER_VERSION>"
+
+    OLD_INTEL_BUILD_LIST="Pthread,Serial,Pthread_Serial"
+
+    # Format: (compiler module-list build-list exe-name warning-flag)
+    COMPILERS=("intel/16.2.181 $BASE_MODULE_LIST $OLD_INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS"
+               "intel/17.0.064 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS"
+    )
+
+    ARCH_FLAG="--arch=HSW"
+    NUM_JOBS_TO_RUN_IN_PARALLEL=8
+
+else
+    echo "Unhandled machine $MACHINE" >&2
+    exit 1
+fi
 
 export OMP_NUM_THREADS=4
 
@@ -25,23 +139,12 @@ declare -i NUM_RESULTS_TO_KEEP=7
 
 RESULT_ROOT_PREFIX=TestAll
 
-source /projects/modulefiles/utils/sems-modules-init.sh
-source /projects/modulefiles/utils/kokkos-modules-init.sh
-
 SCRIPT_KOKKOS_ROOT=$( cd "$( dirname "$0" )" && cd .. && pwd )
 
 #
 # Handle arguments
 #
 
-DEBUG=False
-ARGS=""
-CUSTOM_BUILD_LIST=""
-DRYRUN=False
-BUILD_ONLY=False
-declare -i NUM_JOBS_TO_RUN_IN_PARALLEL=3
-TEST_SCRIPT=False
-
 while [[ $# > 0 ]]
 do
 key="$1"
@@ -61,6 +164,9 @@ BUILD_ONLY=True
 --test-script*)
 TEST_SCRIPT=True
 ;;
+--skip-hwloc*)
+SKIP_HWLOC=True
+;;
 --num*)
 NUM_JOBS_TO_RUN_IN_PARALLEL="${key#*=}"
 ;;
@@ -73,6 +179,7 @@ echo "--kokkos-path=/Path/To/Kokkos: Path to the Kokkos root directory"
 echo "    Defaults to root repo containing this script"
 echo "--debug: Run tests in debug. Defaults to False"
 echo "--test-script: Test this script, not Kokkos"
+echo "--skip-hwloc: Do not do hwloc tests"
 echo "--num=N: Number of jobs to run in parallel "
 echo "--dry-run: Just print what would be executed"
 echo "--build-only: Just do builds, don't run anything"
@@ -82,21 +189,16 @@ echo "    Valid items:"
 echo "      OpenMP, Pthread, Serial, OpenMP_Serial, Pthread_Serial"
 echo "      Cuda_OpenMP, Cuda_Pthread, Cuda_Serial"
 echo ""
+
 echo "ARGS: list of expressions matching compilers to test"
-echo "  supported compilers"
-echo "    gcc/4.7.2"
-echo "    gcc/4.8.4"
-echo "    gcc/4.9.2"
-echo "    gcc/5.1.0"
-echo "    intel/14.0.4"
-echo "    intel/15.0.2"
-echo "    intel/16.0.1"
-echo "    clang/3.5.2"
-echo "    clang/3.6.1"
-echo "    cuda/6.5.14"
-echo "    cuda/7.0.28"
-echo "    cuda/7.5.18"
+echo "  supported compilers sems"
+for COMPILER_DATA in "${COMPILERS[@]}"; do
+    ARR=($COMPILER_DATA)
+    COMPILER=${ARR[0]}
+    echo "    $COMPILER"
+done
 echo ""
+
 echo "Examples:"
 echo "  Run all tests"
 echo "  % test_all_sandia"
@@ -147,21 +249,6 @@ if [ -z "$ARGS" ]; then
     ARGS='?'
 fi
 
-# Format: (compiler module-list build-list exe-name warning-flag)
-COMPILERS=("gcc/4.7.2 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS"
-           "gcc/4.8.4 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS"
-           "gcc/4.9.2 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS"
-           "gcc/5.1.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS"
-           "intel/14.0.4 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS"
-           "intel/15.0.2 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS"
-           "intel/16.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS"
-           "clang/3.5.2 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS"
-           "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS"
-           "cuda/6.5.14 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS"
-           "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS"
-           "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS"
-           )
-
 # Process args to figure out which compilers to test
 COMPILERS_TO_TEST=""
 for ARG in $ARGS; do
@@ -240,18 +327,19 @@ run_cmd() {
     fi
 }
 
-# report_and_log_test_results <SUCCESS> <DESC> <PHASE>
+# report_and_log_test_results <SUCCESS> <DESC> <COMMENT>
 report_and_log_test_result() {
     # Use sane var names
-    local success=$1; local desc=$2; local phase=$3;
+    local success=$1; local desc=$2; local comment=$3;
 
     if [ "$success" = "0" ]; then
 	echo "  PASSED $desc"
-        touch $PASSED_DIR/$desc
+        echo $comment > $PASSED_DIR/$desc
     else
+        # For failures, comment should be the name of the phase that failed
 	echo "  FAILED $desc" >&2
-        echo $phase > $FAILED_DIR/$desc
-        cat ${desc}.${phase}.log
+        echo $comment > $FAILED_DIR/$desc
+        cat ${desc}.${comment}.log
     fi
 }
 
@@ -309,6 +397,8 @@ single_build_and_test() {
 
     echo "  Starting job $desc"
 
+    local comment="no_comment"
+
     if [ "$TEST_SCRIPT" = "True" ]; then
         local rand=$[ 1 + $[ RANDOM % 10 ]]
         sleep $rand
@@ -316,14 +406,19 @@ single_build_and_test() {
             run_cmd ls fake_problem >& ${desc}.configure.log || { report_and_log_test_result 1 $desc configure && return 0; }
         fi
     else
-        run_cmd ${KOKKOS_PATH}/generate_makefile.bash --with-devices=$build --compiler=$(which $compiler_exe) --cxxflags=\"$cxxflags\" $extra_args &>> ${desc}.configure.log || { report_and_log_test_result 1 ${desc} configure && return 0; }
+        run_cmd ${KOKKOS_PATH}/generate_makefile.bash --with-devices=$build $ARCH_FLAG --compiler=$(which $compiler_exe) --cxxflags=\"$cxxflags\" $extra_args &>> ${desc}.configure.log || { report_and_log_test_result 1 ${desc} configure && return 0; }
+        local -i build_start_time=$(date +%s)
         run_cmd make build-test >& ${desc}.build.log || { report_and_log_test_result 1 ${desc} build && return 0; }
+        local -i build_end_time=$(date +%s)
+        comment="build_time=$(($build_end_time-$build_start_time))"
         if [[ "$BUILD_ONLY" == False ]]; then
             run_cmd make test >& ${desc}.test.log || { report_and_log_test_result 1 ${desc} test && return 0; }
+            local -i run_end_time=$(date +%s)
+            comment="$comment run_time=$(($run_end_time-$build_end_time))"
         fi
     fi
 
-    report_and_log_test_result 0 $desc
+    report_and_log_test_result 0 $desc "$comment"
 
     return 0
 }
@@ -374,7 +469,7 @@ build_and_test_all() {
 	run_in_background $compiler $build $BUILD_TYPE
 
         # If not cuda, do a hwloc test too
-        if [[ "$compiler" != cuda* ]]; then
+        if [[ "$compiler" != cuda* && "$SKIP_HWLOC" == False ]]; then
             run_in_background $compiler $build "hwloc-$BUILD_TYPE"
         fi
     done
@@ -401,7 +496,11 @@ wait_summarize_and_exit() {
     echo "PASSED TESTS"
     echo "#######################################################"
 
-    \ls -1 $PASSED_DIR | sort
+    local passed_test
+    for passed_test in $(\ls -1 $PASSED_DIR | sort)
+    do
+        echo $passed_test $(cat $PASSED_DIR/$passed_test)
+    done
 
     echo "#######################################################"
     echo "FAILED TESTS"
@@ -409,7 +508,7 @@ wait_summarize_and_exit() {
 
     local failed_test
     local -i rv=0
-    for failed_test in $(\ls -1 $FAILED_DIR)
+    for failed_test in $(\ls -1 $FAILED_DIR | sort)
     do
         echo $failed_test "("$(cat $FAILED_DIR/$failed_test)" failed)"
         rv=$rv+1
diff --git a/lib/kokkos/containers/performance_tests/CMakeLists.txt b/lib/kokkos/containers/performance_tests/CMakeLists.txt
index 6b57802935..726d403452 100644
--- a/lib/kokkos/containers/performance_tests/CMakeLists.txt
+++ b/lib/kokkos/containers/performance_tests/CMakeLists.txt
@@ -16,11 +16,22 @@ IF(Kokkos_ENABLE_OpenMP)
   LIST( APPEND SOURCES TestOpenMP.cpp)
 ENDIF()
 
-TRIBITS_ADD_EXECUTABLE_AND_TEST(
-  PerformanceTest
+# Per #374, we always want to build this test, but we only want to run
+# it as a PERFORMANCE test.  That's why we separate building the test
+# from running the test.
+
+TRIBITS_ADD_EXECUTABLE(
+  PerfTestExec
   SOURCES ${SOURCES}
   COMM serial mpi
+  TESTONLYLIBS kokkos_gtest
+  )
+
+TRIBITS_ADD_TEST(
+  PerformanceTest
+  NAME PerfTestExec
+  COMM serial mpi
   NUM_MPI_PROCS 1
+  CATEGORIES PERFORMANCE
   FAIL_REGULAR_EXPRESSION "  FAILED  "
-  TESTONLYLIBS kokkos_gtest
   )
diff --git a/lib/kokkos/containers/performance_tests/TestCuda.cpp b/lib/kokkos/containers/performance_tests/TestCuda.cpp
index aee262de93..8183adaa60 100644
--- a/lib/kokkos/containers/performance_tests/TestCuda.cpp
+++ b/lib/kokkos/containers/performance_tests/TestCuda.cpp
@@ -54,6 +54,8 @@
 
 #if defined( KOKKOS_HAVE_CUDA )
 
+#include <TestDynRankView.hpp>
+
 #include <Kokkos_UnorderedMap.hpp>
 
 #include <TestGlobal2LocalIds.hpp>
@@ -77,6 +79,13 @@ protected:
   }
 };
 
+TEST_F( cuda, dynrankview_perf ) 
+{
+  std::cout << "Cuda" << std::endl;
+  std::cout << " DynRankView vs View: Initialization Only " << std::endl;
+  test_dynrankview_op_perf<Kokkos::Cuda>( 4096 );
+}
+
 TEST_F( cuda, global_2_local)
 {
   std::cout << "Cuda" << std::endl;
diff --git a/lib/kokkos/containers/performance_tests/TestDynRankView.hpp b/lib/kokkos/containers/performance_tests/TestDynRankView.hpp
new file mode 100644
index 0000000000..aab6e6988f
--- /dev/null
+++ b/lib/kokkos/containers/performance_tests/TestDynRankView.hpp
@@ -0,0 +1,265 @@
+
+//@HEADER
+// ************************************************************************
+// 
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+// 
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+// 
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+// 
+// ************************************************************************
+//@HEADER
+
+#ifndef KOKKOS_TEST_DYNRANKVIEW_HPP
+#define KOKKOS_TEST_DYNRANKVIEW_HPP
+
+#include <Kokkos_Core.hpp>
+#include <Kokkos_DynRankView.hpp>
+#include <vector>
+
+#include <impl/Kokkos_Timer.hpp>
+
+// Compare performance of DynRankView to View, specific focus on the parenthesis operators
+
+namespace Performance {
+
+//View functor
+template <typename DeviceType>
+struct InitViewFunctor {
+  typedef Kokkos::View<double***, DeviceType> inviewtype;
+  inviewtype _inview;
+
+  InitViewFunctor( inviewtype &inview_ ) : _inview(inview_)
+  {}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(const int i) const {
+    for (unsigned j = 0; j < _inview.dimension(1); ++j) {
+      for (unsigned k = 0; k < _inview.dimension(2); ++k) {
+        _inview(i,j,k) = i/2 -j*j + k/3;
+      }
+    }
+  }
+
+  struct SumComputationTest
+  {
+    typedef Kokkos::View<double***, DeviceType> inviewtype;
+    inviewtype _inview;
+
+    typedef Kokkos::View<double*, DeviceType> outviewtype;
+    outviewtype _outview;
+
+    KOKKOS_INLINE_FUNCTION
+    SumComputationTest(inviewtype &inview_ , outviewtype &outview_) : _inview(inview_), _outview(outview_) {}
+
+    KOKKOS_INLINE_FUNCTION
+    void operator()(const int i) const {
+      for (unsigned j = 0; j < _inview.dimension(1); ++j) {
+        for (unsigned k = 0; k < _inview.dimension(2); ++k) {
+          _outview(i) += _inview(i,j,k) ;
+        }
+      }
+    }
+  };
+
+};
+
+template <typename DeviceType>
+struct InitStrideViewFunctor {
+  typedef Kokkos::View<double***, Kokkos::LayoutStride, DeviceType> inviewtype;
+  inviewtype _inview;
+
+  InitStrideViewFunctor( inviewtype &inview_ ) : _inview(inview_)
+  {}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(const int i) const {
+    for (unsigned j = 0; j < _inview.dimension(1); ++j) {
+      for (unsigned k = 0; k < _inview.dimension(2); ++k) {
+        _inview(i,j,k) = i/2 -j*j + k/3;
+      }
+    }
+  }
+
+};
+
+template <typename DeviceType>
+struct InitViewRank7Functor {
+  typedef Kokkos::View<double*******, DeviceType> inviewtype;
+  inviewtype _inview;
+
+  InitViewRank7Functor( inviewtype &inview_ ) : _inview(inview_)
+  {}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(const int i) const {
+    for (unsigned j = 0; j < _inview.dimension(1); ++j) {
+      for (unsigned k = 0; k < _inview.dimension(2); ++k) {
+        _inview(i,j,k,0,0,0,0) = i/2 -j*j + k/3;
+      }
+    }
+  }
+
+};
+
+//DynRankView functor
+template <typename DeviceType>
+struct InitDynRankViewFunctor {
+  typedef Kokkos::DynRankView<double, DeviceType> inviewtype;
+  inviewtype _inview;
+
+  InitDynRankViewFunctor( inviewtype &inview_ ) : _inview(inview_)
+  {}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(const int i) const {
+    for (unsigned j = 0; j < _inview.dimension(1); ++j) {
+      for (unsigned k = 0; k < _inview.dimension(2); ++k) {
+        _inview(i,j,k) = i/2 -j*j + k/3;
+      }
+    }
+  }
+
+  struct SumComputationTest
+  {
+    typedef Kokkos::DynRankView<double, DeviceType> inviewtype;
+    inviewtype _inview;
+
+    typedef Kokkos::DynRankView<double, DeviceType> outviewtype;
+    outviewtype _outview;
+
+    KOKKOS_INLINE_FUNCTION
+    SumComputationTest(inviewtype &inview_ , outviewtype &outview_) : _inview(inview_), _outview(outview_) {}
+
+    KOKKOS_INLINE_FUNCTION
+    void operator()(const int i) const {
+      for (unsigned j = 0; j < _inview.dimension(1); ++j) {
+        for (unsigned k = 0; k < _inview.dimension(2); ++k) {
+          _outview(i) += _inview(i,j,k) ;
+        }
+      }
+    }
+  };
+
+};
+
+
+template <typename DeviceType>
+void test_dynrankview_op_perf( const int par_size )
+{
+
+  typedef DeviceType execution_space;
+  typedef typename execution_space::size_type size_type;
+  const size_type dim2 = 900;
+  const size_type dim3 = 300;
+
+  double elapsed_time_view = 0;
+  double elapsed_time_compview = 0;
+  double elapsed_time_strideview = 0;
+  double elapsed_time_view_rank7 = 0;
+  double elapsed_time_drview = 0;
+  double elapsed_time_compdrview = 0;
+  Kokkos::Timer timer;
+  {
+    Kokkos::View<double***,DeviceType> testview("testview",par_size,dim2,dim3);
+    typedef InitViewFunctor<DeviceType> FunctorType;
+
+    timer.reset();
+    Kokkos::RangePolicy<DeviceType> policy(0,par_size);
+    Kokkos::parallel_for( policy , FunctorType(testview) );
+    DeviceType::fence();
+    elapsed_time_view = timer.seconds();
+    std::cout << " View time (init only): " << elapsed_time_view << std::endl;
+
+
+    timer.reset();
+    Kokkos::View<double*,DeviceType> sumview("sumview",par_size);
+    Kokkos::parallel_for( policy , typename FunctorType::SumComputationTest(testview, sumview) );
+    DeviceType::fence();
+    elapsed_time_compview = timer.seconds();
+    std::cout << " View sum computation time: " << elapsed_time_view << std::endl;
+
+
+    Kokkos::View<double***,Kokkos::LayoutStride, DeviceType> teststrideview = Kokkos::subview(testview, Kokkos::ALL, Kokkos::ALL,Kokkos::ALL);
+    typedef InitStrideViewFunctor<DeviceType> FunctorStrideType;
+
+    timer.reset();
+    Kokkos::parallel_for( policy , FunctorStrideType(teststrideview) );
+    DeviceType::fence();
+    elapsed_time_strideview = timer.seconds();
+    std::cout << " Strided View time (init only): " << elapsed_time_strideview << std::endl;
+  }
+  {
+    Kokkos::View<double*******,DeviceType> testview("testview",par_size,dim2,dim3,1,1,1,1);
+    typedef InitViewRank7Functor<DeviceType> FunctorType;
+
+    timer.reset();
+    Kokkos::RangePolicy<DeviceType> policy(0,par_size);
+    Kokkos::parallel_for( policy , FunctorType(testview) );
+    DeviceType::fence();
+    elapsed_time_view_rank7 = timer.seconds();
+    std::cout << " View Rank7 time (init only): " << elapsed_time_view_rank7 << std::endl;
+  }
+  {
+    Kokkos::DynRankView<double,DeviceType> testdrview("testdrview",par_size,dim2,dim3);
+    typedef InitDynRankViewFunctor<DeviceType> FunctorType;
+
+    timer.reset();
+    Kokkos::RangePolicy<DeviceType> policy(0,par_size);
+    Kokkos::parallel_for( policy , FunctorType(testdrview) );
+    DeviceType::fence();
+    elapsed_time_drview = timer.seconds();
+    std::cout << " DynRankView time (init only): " << elapsed_time_drview << std::endl;
+
+    timer.reset();
+    Kokkos::DynRankView<double,DeviceType> sumview("sumview",par_size);
+    Kokkos::parallel_for( policy , typename FunctorType::SumComputationTest(testdrview, sumview) );
+    DeviceType::fence();
+    elapsed_time_compdrview = timer.seconds();
+    std::cout << " DynRankView sum computation time: " << elapsed_time_compdrview << std::endl;
+
+  }
+
+  std::cout << " Ratio of View to DynRankView time: " << elapsed_time_view / elapsed_time_drview << std::endl; //expect < 1
+  std::cout << " Ratio of View to DynRankView sum computation time: " << elapsed_time_compview / elapsed_time_compdrview << std::endl; //expect < 1
+  std::cout << " Ratio of View to View Rank7  time: " << elapsed_time_view / elapsed_time_view_rank7 << std::endl; //expect < 1
+  std::cout << " Ratio of StrideView to DynRankView time: " << elapsed_time_strideview / elapsed_time_drview << std::endl; //expect < 1
+  std::cout << " Ratio of DynRankView to View Rank7  time: " << elapsed_time_drview / elapsed_time_view_rank7 << std::endl; //expect ?
+
+  timer.reset();
+
+} //end test_dynrankview
+
+
+} //end Performance
+#endif
diff --git a/lib/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp b/lib/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp
index fb70b8fe2e..66f1fbf092 100644
--- a/lib/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp
+++ b/lib/kokkos/containers/performance_tests/TestGlobal2LocalIds.hpp
@@ -178,7 +178,7 @@ void test_global_to_local_ids(unsigned num_ids)
   std::cout << num_ids << ", ";
 
   double elasped_time = 0;
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
 
   local_id_view local_2_global("local_ids", num_ids);
   global_id_view global_2_local((3u*num_ids)/2u);
diff --git a/lib/kokkos/containers/performance_tests/TestOpenMP.cpp b/lib/kokkos/containers/performance_tests/TestOpenMP.cpp
index 82a9311df7..da74d32ac1 100644
--- a/lib/kokkos/containers/performance_tests/TestOpenMP.cpp
+++ b/lib/kokkos/containers/performance_tests/TestOpenMP.cpp
@@ -50,6 +50,8 @@
 #include <TestGlobal2LocalIds.hpp>
 #include <TestUnorderedMapPerformance.hpp>
 
+#include <TestDynRankView.hpp>
+
 #include <iomanip>
 #include <sstream>
 #include <string>
@@ -91,6 +93,13 @@ protected:
   }
 };
 
+TEST_F( openmp, dynrankview_perf ) 
+{
+  std::cout << "OpenMP" << std::endl;
+  std::cout << " DynRankView vs View: Initialization Only " << std::endl;
+  test_dynrankview_op_perf<Kokkos::OpenMP>( 8192 );
+}
+
 TEST_F( openmp, global_2_local)
 {
   std::cout << "OpenMP" << std::endl;
diff --git a/lib/kokkos/containers/performance_tests/TestThreads.cpp b/lib/kokkos/containers/performance_tests/TestThreads.cpp
index 04d9dc0c18..4179b7de4c 100644
--- a/lib/kokkos/containers/performance_tests/TestThreads.cpp
+++ b/lib/kokkos/containers/performance_tests/TestThreads.cpp
@@ -52,6 +52,8 @@
 #include <TestGlobal2LocalIds.hpp>
 #include <TestUnorderedMapPerformance.hpp>
 
+#include <TestDynRankView.hpp>
+
 #include <iomanip>
 #include <sstream>
 #include <string>
@@ -85,6 +87,13 @@ protected:
   }
 };
 
+TEST_F( threads, dynrankview_perf ) 
+{
+  std::cout << "Threads" << std::endl;
+  std::cout << " DynRankView vs View: Initialization Only " << std::endl;
+  test_dynrankview_op_perf<Kokkos::Threads>( 8192 );
+}
+
 TEST_F( threads, global_2_local)
 {
   std::cout << "Threads" << std::endl;
diff --git a/lib/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp b/lib/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp
index 975800229c..71d1182cbe 100644
--- a/lib/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp
+++ b/lib/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp
@@ -80,7 +80,7 @@ struct UnorderedMapTest
     , map(capacity)
     , histogram(map.get_histogram())
   {
-    Kokkos::Impl::Timer wall_clock ;
+    Kokkos::Timer wall_clock ;
     wall_clock.reset();
 
     value_type v = {};
@@ -228,7 +228,7 @@ void run_performance_tests(std::string const & base_file_name)
   distance_out << "\b\b\b   " << std::endl;
   block_distance_out << "\b\b\b   " << std::endl;
 
-  Kokkos::Impl::Timer wall_clock ;
+  Kokkos::Timer wall_clock ;
   for (int i=0;  i < num_collisions ; ++i) {
     wall_clock.reset();
     std::cout << "Collisions: " << collisions[i] << std::endl;
diff --git a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp
index 0fc722c140..f72277700a 100644
--- a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp
+++ b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp
@@ -52,6 +52,12 @@
  *   2. Max rank of a DynRankView is 7
  *   3. subview name is subdynrankview
  *   4. Every subdynrankview is returned with LayoutStride
+ *
+ *   NEW: Redesigned DynRankView
+ *   5. subview function name now available
+ *   6. Copy and Copy-Assign View to DynRankView
+ *   7. deep_copy between Views and DynRankViews
+ *   8. rank( view ); returns the rank of View or DynRankView
  */
 
 #ifndef KOKKOS_DYNRANKVIEW_HPP
@@ -64,11 +70,16 @@
 namespace Kokkos {
 namespace Experimental {
 
+template< typename DataType , class ... Properties >
+class DynRankView;  //forward declare
+
 namespace Impl {
 
 template <typename Specialize>
 struct DynRankDimTraits {
 
+  enum : size_t{unspecified = ~size_t(0)};
+
   // Compute the rank of the view from the nonzero dimension arguments.
   KOKKOS_INLINE_FUNCTION
   static size_t computeRank( const size_t N0
@@ -81,13 +92,13 @@ struct DynRankDimTraits {
                            , const size_t N7 )
   {
     return
-      (   (N6 == 0 && N5 == 0 && N4 == 0 && N3 == 0 && N2 == 0 && N1 == 0 && N0 == 0) ? 0
-      : ( (N6 == 0 && N5 == 0 && N4 == 0 && N3 == 0 && N2 == 0 && N1 == 0) ? 1
-      : ( (N6 == 0 && N5 == 0 && N4 == 0 && N3 == 0 && N2 == 0) ? 2
-      : ( (N6 == 0 && N5 == 0 && N4 == 0 && N3 == 0) ? 3
-      : ( (N6 == 0 && N5 == 0 && N4 == 0) ? 4
-      : ( (N6 == 0 && N5 == 0) ? 5
-      : ( (N6 == 0) ? 6
+      (   (N6 == unspecified && N5 == unspecified && N4 == unspecified && N3 == unspecified && N2 == unspecified && N1 == unspecified && N0 == unspecified) ? 0
+      : ( (N6 == unspecified && N5 == unspecified && N4 == unspecified && N3 == unspecified && N2 == unspecified && N1 == unspecified) ? 1
+      : ( (N6 == unspecified && N5 == unspecified && N4 == unspecified && N3 == unspecified && N2 == unspecified) ? 2
+      : ( (N6 == unspecified && N5 == unspecified && N4 == unspecified && N3 == unspecified) ? 3
+      : ( (N6 == unspecified && N5 == unspecified && N4 == unspecified) ? 4
+      : ( (N6 == unspecified && N5 == unspecified) ? 5
+      : ( (N6 == unspecified) ? 6
       : 7 ) ) ) ) ) ) );
   }
 
@@ -112,14 +123,14 @@ struct DynRankDimTraits {
   KOKKOS_INLINE_FUNCTION
   static typename std::enable_if< (std::is_same<Layout , Kokkos::LayoutRight>::value || std::is_same<Layout , Kokkos::LayoutLeft>::value) , Layout >::type createLayout( const Layout& layout )
   {
-    return Layout( layout.dimension[0] != 0 ? layout.dimension[0] : 1
-                 , layout.dimension[1] != 0 ? layout.dimension[1] : 1
-                 , layout.dimension[2] != 0 ? layout.dimension[2] : 1
-                 , layout.dimension[3] != 0 ? layout.dimension[3] : 1
-                 , layout.dimension[4] != 0 ? layout.dimension[4] : 1
-                 , layout.dimension[5] != 0 ? layout.dimension[5] : 1
-                 , layout.dimension[6] != 0 ? layout.dimension[6] : 1
-                 , layout.dimension[7] != 0 ? layout.dimension[7] : 1
+    return Layout( layout.dimension[0] != unspecified ? layout.dimension[0] : 1
+                 , layout.dimension[1] != unspecified ? layout.dimension[1] : 1
+                 , layout.dimension[2] != unspecified ? layout.dimension[2] : 1
+                 , layout.dimension[3] != unspecified ? layout.dimension[3] : 1
+                 , layout.dimension[4] != unspecified ? layout.dimension[4] : 1
+                 , layout.dimension[5] != unspecified ? layout.dimension[5] : 1
+                 , layout.dimension[6] != unspecified ? layout.dimension[6] : 1
+                 , layout.dimension[7] != unspecified ? layout.dimension[7] : 1
                  );
   }
 
@@ -128,21 +139,21 @@ struct DynRankDimTraits {
   KOKKOS_INLINE_FUNCTION
   static typename std::enable_if< (std::is_same<Layout , Kokkos::LayoutStride>::value) , Layout>::type createLayout( const Layout& layout )
   {
-    return Layout( layout.dimension[0] != 0 ? layout.dimension[0] : 1
+    return Layout( layout.dimension[0] != unspecified ? layout.dimension[0] : 1
                  , layout.stride[0] 
-                 , layout.dimension[1] != 0 ? layout.dimension[1] : 1
+                 , layout.dimension[1] != unspecified ? layout.dimension[1] : 1
                  , layout.stride[1] 
-                 , layout.dimension[2] != 0 ? layout.dimension[2] : 1
+                 , layout.dimension[2] != unspecified ? layout.dimension[2] : 1
                  , layout.stride[2] 
-                 , layout.dimension[3] != 0 ? layout.dimension[3] : 1
+                 , layout.dimension[3] != unspecified ? layout.dimension[3] : 1
                  , layout.stride[3] 
-                 , layout.dimension[4] != 0 ? layout.dimension[4] : 1
+                 , layout.dimension[4] != unspecified ? layout.dimension[4] : 1
                  , layout.stride[4] 
-                 , layout.dimension[5] != 0 ? layout.dimension[5] : 1
+                 , layout.dimension[5] != unspecified ? layout.dimension[5] : 1
                  , layout.stride[5] 
-                 , layout.dimension[6] != 0 ? layout.dimension[6] : 1
+                 , layout.dimension[6] != unspecified ? layout.dimension[6] : 1
                  , layout.stride[6] 
-                 , layout.dimension[7] != 0 ? layout.dimension[7] : 1
+                 , layout.dimension[7] != unspecified ? layout.dimension[7] : 1
                  , layout.stride[7] 
                  );
   }
@@ -161,17 +172,141 @@ struct DynRankDimTraits {
                             , const size_t N7 )
   {
     return ViewType( arg
-                   , N0 != 0 ? N0 : 1
-                   , N1 != 0 ? N1 : 1
-                   , N2 != 0 ? N2 : 1
-                   , N3 != 0 ? N3 : 1
-                   , N4 != 0 ? N4 : 1
-                   , N5 != 0 ? N5 : 1
-                   , N6 != 0 ? N6 : 1
-                   , N7 != 0 ? N7 : 1 );
+                   , N0 != unspecified ? N0 : 1
+                   , N1 != unspecified ? N1 : 1
+                   , N2 != unspecified ? N2 : 1
+                   , N3 != unspecified ? N3 : 1
+                   , N4 != unspecified ? N4 : 1
+                   , N5 != unspecified ? N5 : 1
+                   , N6 != unspecified ? N6 : 1
+                   , N7 != unspecified ? N7 : 1 );
   }
 };
 
+  // Non-strided Layout
+  template <typename Layout , typename iType>
+  KOKKOS_INLINE_FUNCTION
+  static typename std::enable_if< (std::is_same<Layout , Kokkos::LayoutRight>::value || std::is_same<Layout , Kokkos::LayoutLeft>::value) && std::is_integral<iType>::value , Layout >::type reconstructLayout( const Layout& layout , iType dynrank )
+  {
+    return Layout( dynrank > 0 ? layout.dimension[0] : ~size_t(0) 
+                 , dynrank > 1 ? layout.dimension[1] : ~size_t(0)
+                 , dynrank > 2 ? layout.dimension[2] : ~size_t(0)
+                 , dynrank > 3 ? layout.dimension[3] : ~size_t(0)
+                 , dynrank > 4 ? layout.dimension[4] : ~size_t(0)
+                 , dynrank > 5 ? layout.dimension[5] : ~size_t(0)
+                 , dynrank > 6 ? layout.dimension[6] : ~size_t(0)
+                 , dynrank > 7 ? layout.dimension[7] : ~size_t(0)
+                 );
+  }
+
+  // LayoutStride
+  template <typename Layout , typename iType>
+  KOKKOS_INLINE_FUNCTION
+  static typename std::enable_if< (std::is_same<Layout , Kokkos::LayoutStride>::value) && std::is_integral<iType>::value , Layout >::type reconstructLayout( const Layout& layout , iType dynrank )
+  {
+    return Layout( dynrank > 0 ? layout.dimension[0] : ~size_t(0)
+                 , dynrank > 0 ? layout.stride[0] : (0) 
+                 , dynrank > 1 ? layout.dimension[1] : ~size_t(0)
+                 , dynrank > 1 ? layout.stride[1] : (0) 
+                 , dynrank > 2 ? layout.dimension[2] : ~size_t(0)
+                 , dynrank > 2 ? layout.stride[2] : (0) 
+                 , dynrank > 3 ? layout.dimension[3] : ~size_t(0)
+                 , dynrank > 3 ? layout.stride[3] : (0) 
+                 , dynrank > 4 ? layout.dimension[4] : ~size_t(0)
+                 , dynrank > 4 ? layout.stride[4] : (0) 
+                 , dynrank > 5 ? layout.dimension[5] : ~size_t(0)
+                 , dynrank > 5 ? layout.stride[5] : (0) 
+                 , dynrank > 6 ? layout.dimension[6] : ~size_t(0)
+                 , dynrank > 6 ? layout.stride[6] : (0) 
+                 , dynrank > 7 ? layout.dimension[7] : ~size_t(0)
+                 , dynrank > 7 ? layout.stride[7] : (0) 
+                 );
+  }
+
+  template < typename DynRankViewType , typename iType >
+  void verify_dynrankview_rank ( iType N , const DynRankViewType &drv )
+  {
+    if ( static_cast<iType>(drv.rank()) > N )
+       {
+         Kokkos::abort( "Need at least rank arguments to the operator()" ); 
+       }
+  }
+
+
+/** \brief  Assign compatible default mappings */
+struct ViewToDynRankViewTag {};
+
+template< class DstTraits , class SrcTraits >
+class ViewMapping< DstTraits , SrcTraits ,
+  typename std::enable_if<(
+    std::is_same< typename DstTraits::memory_space , typename SrcTraits::memory_space >::value
+    &&
+    std::is_same< typename DstTraits::specialize , void >::value
+    &&
+    std::is_same< typename SrcTraits::specialize , void >::value
+    &&
+    (
+      std::is_same< typename DstTraits::array_layout , typename SrcTraits::array_layout >::value
+      ||
+      (
+        (
+          std::is_same< typename DstTraits::array_layout , Kokkos::LayoutLeft >::value ||
+          std::is_same< typename DstTraits::array_layout , Kokkos::LayoutRight >::value ||
+          std::is_same< typename DstTraits::array_layout , Kokkos::LayoutStride >::value
+        )
+        &&
+        (
+          std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutLeft >::value ||
+          std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutRight >::value ||
+          std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutStride >::value
+        )
+      )
+    )
+  ) , ViewToDynRankViewTag >::type >
+{
+private:
+
+  enum { is_assignable_value_type =
+    std::is_same< typename DstTraits::value_type
+                , typename SrcTraits::value_type >::value ||
+    std::is_same< typename DstTraits::value_type
+                , typename SrcTraits::const_value_type >::value };
+
+  enum { is_assignable_layout =
+    std::is_same< typename DstTraits::array_layout
+                , typename SrcTraits::array_layout >::value ||
+    std::is_same< typename DstTraits::array_layout
+                , Kokkos::LayoutStride >::value 
+    };
+
+public:
+
+  enum { is_assignable = is_assignable_value_type &&
+                         is_assignable_layout };
+
+  typedef ViewMapping< DstTraits , void >  DstType ;
+  typedef ViewMapping< SrcTraits , void >  SrcType ;
+
+  template < typename DT , typename ... DP , typename ST , typename ... SP >
+  KOKKOS_INLINE_FUNCTION
+  static void assign( Kokkos::Experimental::DynRankView< DT , DP...> & dst ,  const Kokkos::View< ST , SP... > & src )
+    {
+      static_assert( is_assignable_value_type
+                   , "View assignment must have same value type or const = non-const" );
+
+      static_assert( is_assignable_layout
+                   , "View assignment must have compatible layout or have rank <= 1" );
+
+    // Removed dimension checks...
+
+      typedef typename DstType::offset_type  dst_offset_type ;
+      dst.m_map.m_offset = dst_offset_type(std::integral_constant<unsigned,0>() , src.layout() ); //Check this for integer input1 for padding, etc
+      dst.m_map.m_handle = Kokkos::Experimental::Impl::ViewDataHandle< DstTraits >::assign( src.m_map.m_handle , src.m_track );
+      dst.m_track.assign( src.m_track , DstTraits::is_managed );
+      dst.m_rank = src.Rank ;
+    }
+};
+
 } //end Impl
 
 /* \class DynRankView
@@ -185,145 +320,228 @@ struct DynRankDimTraits {
  *   3. subview name is subdynrankview
  *   4. Every subdynrankview is returned with LayoutStride
  *
+ *   NEW: Redesigned DynRankView
+ *   5. subview function name now available
+ *   6. Copy and Copy-Assign View to DynRankView
+ *   7. deep_copy between Views and DynRankViews
+ *   8. rank( view ); returns the rank of View or DynRankView
+ *
  */
 
+template< class > struct is_dyn_rank_view : public std::false_type {};
+
+template< class D, class ... P >
+struct is_dyn_rank_view< Kokkos::Experimental::DynRankView<D,P...> > : public std::true_type {};
+
+
 template< typename DataType , class ... Properties >
-class DynRankView : private View< DataType*******, Properties... >
+class DynRankView : public ViewTraits< DataType , Properties ... >
 {
   static_assert( !std::is_array<DataType>::value && !std::is_pointer<DataType>::value , "Cannot template DynRankView with array or pointer datatype - must be pod" );
 
-public: 
-  using view_type = View< DataType******* , Properties...>;
-  using reference_type = typename view_type::reference_type; 
-
 private: 
   template < class , class ... > friend class DynRankView ;
-  template< class , class ... > friend class Impl::ViewMapping ;
-  unsigned m_rank;
-
-public:
-  KOKKOS_INLINE_FUNCTION
-  view_type & DownCast() const { return static_cast< view_type & > (*this); }
-  KOKKOS_INLINE_FUNCTION
-  const view_type & ConstDownCast() const { return static_cast< const view_type & > (*this); }
+//  template < class , class ... > friend class Kokkos::Experimental::View ; //unnecessary now...
+  template < class , class ... > friend class Impl::ViewMapping ;
 
-  typedef ViewTraits< DataType , Properties ... > traits ;
+public: 
+  typedef ViewTraits< DataType , Properties ... > drvtraits ;
 
-  // Data type traits:
-  typedef typename traits::data_type            data_type;
-  typedef typename traits::const_data_type      const_data_type;
-  typedef typename traits::non_const_data_type  non_const_data_type;
+  typedef View< DataType******* , Properties...> view_type ; 
 
-  // Compatible array of trivial type traits:
-  typedef typename traits::scalar_array_type            scalar_array_type ;
-  typedef typename traits::const_scalar_array_type      const_scalar_array_type ;
-  typedef typename traits::non_const_scalar_array_type  non_const_scalar_array_type ;
+  typedef ViewTraits< DataType******* , Properties ... > traits ;
 
-  // Value type traits:
-  typedef typename traits::value_type            value_type ;
-  typedef typename traits::const_value_type      const_value_type ;
-  typedef typename traits::non_const_value_type  non_const_value_type ;
 
-  // Mapping traits:
-  typedef typename traits::array_layout   array_layout ;
-  typedef typename traits::specialize     specialize ;
+private:
+  typedef Kokkos::Experimental::Impl::ViewMapping< traits , void > map_type ;
+  typedef Kokkos::Experimental::Impl::SharedAllocationTracker      track_type ;
 
-  // Execution space, memory space, memory access traits, and host mirror space:
-  typedef typename traits::execution_space    execution_space ;
-  typedef typename traits::memory_space       memory_space ;
-  typedef typename traits::device_type        device_type ;
-  typedef typename traits::memory_traits      memory_traits ;
-  typedef typename traits::host_mirror_space  host_mirror_space ;
+  track_type  m_track ;
+  map_type    m_map ;
+  unsigned m_rank;
 
-  typedef typename traits::size_type size_type ;
+public: 
+  KOKKOS_INLINE_FUNCTION
+  view_type & DownCast() const { return ( view_type & ) (*this); }
+  KOKKOS_INLINE_FUNCTION
+  const view_type & ConstDownCast() const { return (const view_type & ) (*this); }
 
-  using view_type::is_hostspace ;
-  using view_type::is_managed ;
-  using view_type::is_random_access ;
+  //Types below - at least the HostMirror requires the value_type, NOT the rank 7 data_type of the traits
 
   /** \brief  Compatible view of array of scalar types */
-  typedef DynRankView< typename traits::scalar_array_type ,
-                       typename traits::array_layout ,
-                       typename traits::device_type ,
-                       typename traits::memory_traits >
+  typedef DynRankView< typename drvtraits::scalar_array_type ,
+                typename drvtraits::array_layout ,
+                typename drvtraits::device_type ,
+                typename drvtraits::memory_traits >
     array_type ;
 
   /** \brief  Compatible view of const data type */
-  typedef DynRankView< typename traits::const_data_type ,
-                       typename traits::array_layout ,
-                       typename traits::device_type ,
-                       typename traits::memory_traits >
+  typedef DynRankView< typename drvtraits::const_data_type ,
+                typename drvtraits::array_layout ,
+                typename drvtraits::device_type ,
+                typename drvtraits::memory_traits >
     const_type ;
 
   /** \brief  Compatible view of non-const data type */
-  typedef DynRankView< typename traits::non_const_data_type ,
-                       typename traits::array_layout ,
-                       typename traits::device_type ,
-                       typename traits::memory_traits >
+  typedef DynRankView< typename drvtraits::non_const_data_type ,
+                typename drvtraits::array_layout ,
+                typename drvtraits::device_type ,
+                typename drvtraits::memory_traits >
     non_const_type ;
 
   /** \brief  Compatible HostMirror view */
-  typedef DynRankView< typename traits::non_const_data_type ,
-                       typename traits::array_layout ,
-                       typename traits::host_mirror_space >
+  typedef DynRankView< typename drvtraits::non_const_data_type ,
+                typename drvtraits::array_layout ,
+                typename drvtraits::host_mirror_space >
     HostMirror ;
 
+
   //----------------------------------------
   // Domain rank and extents
 
+//  enum { Rank = map_type::Rank }; //Will be dyn rank of 7 always, keep the enum?
+
+  template< typename iType >
+  KOKKOS_INLINE_FUNCTION constexpr
+  typename std::enable_if< std::is_integral<iType>::value , size_t >::type
+  extent( const iType & r ) const
+    { return m_map.extent(r); }
+
+  template< typename iType >
+  KOKKOS_INLINE_FUNCTION constexpr
+  typename std::enable_if< std::is_integral<iType>::value , int >::type
+  extent_int( const iType & r ) const
+    { return static_cast<int>(m_map.extent(r)); }
+
+  KOKKOS_INLINE_FUNCTION constexpr
+  typename traits::array_layout layout() const
+    { return m_map.layout(); }
+
+  //----------------------------------------
+  /*  Deprecate all 'dimension' functions in favor of
+   *  ISO/C++ vocabulary 'extent'.
+   */
+
+  template< typename iType >
+  KOKKOS_INLINE_FUNCTION constexpr
+  typename std::enable_if< std::is_integral<iType>::value , size_t >::type
+  dimension( const iType & r ) const { return extent( r ); }
+
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_0() const { return m_map.dimension_0(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_1() const { return m_map.dimension_1(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_2() const { return m_map.dimension_2(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_3() const { return m_map.dimension_3(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_4() const { return m_map.dimension_4(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_5() const { return m_map.dimension_5(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_6() const { return m_map.dimension_6(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_7() const { return m_map.dimension_7(); }
+
+  //----------------------------------------
+
+  KOKKOS_INLINE_FUNCTION constexpr size_t size() const { return m_map.dimension_0() *
+                                                                m_map.dimension_1() *
+                                                                m_map.dimension_2() *
+                                                                m_map.dimension_3() *
+                                                                m_map.dimension_4() *
+                                                                m_map.dimension_5() *
+                                                                m_map.dimension_6() *
+                                                                m_map.dimension_7(); }
+
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_0() const { return m_map.stride_0(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_1() const { return m_map.stride_1(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_2() const { return m_map.stride_2(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_3() const { return m_map.stride_3(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_4() const { return m_map.stride_4(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_5() const { return m_map.stride_5(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_6() const { return m_map.stride_6(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_7() const { return m_map.stride_7(); }
+
+  template< typename iType >
+  KOKKOS_INLINE_FUNCTION void stride( iType * const s ) const { m_map.stride(s); }
+
+  //----------------------------------------
+  // Range span is the span which contains all members.
+
+  typedef typename map_type::reference_type  reference_type ;
+  typedef typename map_type::pointer_type    pointer_type ;
+
+  enum { reference_type_is_lvalue_reference = std::is_lvalue_reference< reference_type >::value };
+
+  KOKKOS_INLINE_FUNCTION constexpr size_t span() const { return m_map.span(); }
+  // Deprecated, use 'span()' instead
+  KOKKOS_INLINE_FUNCTION constexpr size_t capacity() const { return m_map.span(); }
+  KOKKOS_INLINE_FUNCTION constexpr bool   span_is_contiguous() const { return m_map.span_is_contiguous(); }
+  KOKKOS_INLINE_FUNCTION constexpr pointer_type data() const { return m_map.data(); }
+
+  // Deprecated, use 'span_is_contigous()' instead
+  KOKKOS_INLINE_FUNCTION constexpr bool   is_contiguous() const { return m_map.span_is_contiguous(); }
+  // Deprecated, use 'data()' instead
+  KOKKOS_INLINE_FUNCTION constexpr pointer_type ptr_on_device() const { return m_map.data(); }
+
+  //----------------------------------------
+  // Allow specializations to query their specialized map
+
   KOKKOS_INLINE_FUNCTION
-  DynRankView() : view_type() , m_rank(0) {}
+  const Kokkos::Experimental::Impl::ViewMapping< traits , void > &
+  implementation_map() const { return m_map ; }
+
+  //----------------------------------------
+
+private:
+
+  enum {
+    is_layout_left = std::is_same< typename traits::array_layout
+                                  , Kokkos::LayoutLeft >::value ,
+
+    is_layout_right = std::is_same< typename traits::array_layout
+                                  , Kokkos::LayoutRight >::value ,
+
+    is_layout_stride = std::is_same< typename traits::array_layout
+                                   , Kokkos::LayoutStride >::value ,
+
+    is_default_map =
+      std::is_same< typename traits::specialize , void >::value &&
+      ( is_layout_left || is_layout_right || is_layout_stride )
+  };
+
+// Bounds checking macros
+#if defined( KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK )
+
+#define KOKKOS_VIEW_OPERATOR_VERIFY( N , ARG ) \
+  Kokkos::Impl::VerifyExecutionCanAccessMemorySpace \
+    < Kokkos::Impl::ActiveExecutionMemorySpace , typename traits::memory_space >::verify(); \
+  Kokkos::Experimental::Impl::verify_dynrankview_rank ( N , *this ) ; \
+  Kokkos::Experimental::Impl::view_verify_operator_bounds ARG ; 
+
+#else
+
+#define KOKKOS_VIEW_OPERATOR_VERIFY( N , ARG ) \
+  Kokkos::Impl::VerifyExecutionCanAccessMemorySpace \
+    < Kokkos::Impl::ActiveExecutionMemorySpace , typename traits::memory_space >::verify();
+
+#endif
+
+public:
 
   KOKKOS_INLINE_FUNCTION
   constexpr unsigned rank() const { return m_rank; }
 
-  using view_type::extent; 
-  using view_type::extent_int; 
-  using view_type::layout;
-  using view_type::dimension;
-  using view_type::size;
-  using view_type::stride;
-
-  using pointer_type = typename view_type::pointer_type;
-  using view_type::reference_type_is_lvalue_reference;
-  using view_type::span;
-  using view_type::capacity;
-  using view_type::span_is_contiguous;
-  using view_type::data;
-  using view_type::implementation_map;
-
-  using view_type::is_contiguous;
-  using view_type::ptr_on_device;
-
-  //Deprecated, remove soon (add for test)
-  using view_type::dimension_0;
-  using view_type::dimension_1;
-  using view_type::dimension_2;
-  using view_type::dimension_3;
-  using view_type::dimension_4;
-  using view_type::dimension_5;
-  using view_type::dimension_6;
-  using view_type::dimension_7;
-  using view_type::stride_0;
-  using view_type::stride_1;
-  using view_type::stride_2;
-  using view_type::stride_3;
-  using view_type::stride_4;
-  using view_type::stride_5;
-  using view_type::stride_6;
-  using view_type::stride_7;
 
   //operators ()
   // Rank 0
   KOKKOS_INLINE_FUNCTION
   reference_type operator()() const
-    { return view_type::operator()(0,0,0,0,0,0,0); }
-  
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 0 , ( implementation_map() ) )
+      return implementation_map().reference();
+      //return m_map.reference(0,0,0,0,0,0,0); 
+    }
+
   // Rank 1
   // This assumes a contiguous underlying memory (i.e. no padding, no striding...)
   template< typename iType >
   KOKKOS_INLINE_FUNCTION
-  typename std::enable_if< std::is_same<value_type, scalar_array_type>::value && std::is_integral<iType>::value, reference_type>::type
+  typename std::enable_if< std::is_same<typename drvtraits::value_type, typename drvtraits::scalar_array_type>::value && std::is_integral<iType>::value, reference_type>::type
   operator[](const iType & i0) const
     {
       return data()[i0];
@@ -333,59 +551,141 @@ public:
   // AND a Trilinos/Sacado scalar type )
   template< typename iType >
   KOKKOS_INLINE_FUNCTION
-  typename std::enable_if< !std::is_same<value_type, scalar_array_type>::value && std::is_integral<iType>::value, reference_type>::type
+  typename std::enable_if< !std::is_same<typename drvtraits::value_type, typename drvtraits::scalar_array_type>::value && std::is_integral<iType>::value, reference_type>::type
   operator[](const iType & i0) const
     {
-      auto map = implementation_map();
-
-      const size_t dim_scalar = map.dimension_scalar();
+//      auto map = implementation_map();
+      const size_t dim_scalar = m_map.dimension_scalar();
       const size_t bytes = this->span() / dim_scalar;
 
-      typedef Kokkos::View<DataType*, array_layout, device_type, Kokkos::MemoryTraits<Kokkos::Unmanaged | memory_traits::RandomAccess | memory_traits::Atomic> > tmp_view_type;
+      typedef Kokkos::View<DataType*, typename traits::array_layout, typename traits::device_type, Kokkos::MemoryTraits<Kokkos::Unmanaged | traits::memory_traits::RandomAccess | traits::memory_traits::Atomic> > tmp_view_type;
       tmp_view_type rankone_view(this->data(), bytes, dim_scalar);
       return rankone_view(i0);
     }
 
   template< typename iType >
   KOKKOS_INLINE_FUNCTION
-  reference_type operator()(const iType & i0 ) const 
-    { return view_type::operator()(i0,0,0,0,0,0,0); }
+  typename std::enable_if< (std::is_same<typename traits::specialize , void>::value && std::is_integral<iType>::value), reference_type>::type
+  operator()(const iType & i0 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 1 , ( m_map , i0 ) )
+      return m_map.reference(i0); 
+    }
+
+  template< typename iType >
+  KOKKOS_INLINE_FUNCTION
+  typename std::enable_if< !(std::is_same<typename traits::specialize , void>::value && std::is_integral<iType>::value), reference_type>::type
+  operator()(const iType & i0 ) const
+    {
+      return m_map.reference(i0,0,0,0,0,0,0);
+    }
 
   // Rank 2
   template< typename iType0 , typename iType1 >
   KOKKOS_INLINE_FUNCTION
-  reference_type operator()(const iType0 & i0 , const iType1 & i1 ) const 
-    { return view_type::operator()(i0,i1,0,0,0,0,0); }
+  typename std::enable_if< (std::is_same<typename traits::specialize , void>::value && std::is_integral<iType0>::value  && std::is_integral<iType1>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 2 , ( m_map , i0 , i1 ) )
+      return m_map.reference(i0,i1); 
+    }
+
+  template< typename iType0 , typename iType1 >
+  KOKKOS_INLINE_FUNCTION
+  typename std::enable_if< !(std::is_same<typename drvtraits::specialize , void>::value && std::is_integral<iType0>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 2 , ( m_map , i0 , i1 ) )
+      return m_map.reference(i0,i1,0,0,0,0,0); 
+    }
 
   // Rank 3
   template< typename iType0 , typename iType1 , typename iType2 >
   KOKKOS_INLINE_FUNCTION
-  reference_type operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const 
-    { return view_type::operator()(i0,i1,i2,0,0,0,0); }
+  typename std::enable_if< (std::is_same<typename traits::specialize , void>::value && std::is_integral<iType0>::value  && std::is_integral<iType1>::value && std::is_integral<iType2>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 3 , ( m_map , i0 , i1 , i2 ) )
+      return m_map.reference(i0,i1,i2); 
+    }
+
+  template< typename iType0 , typename iType1 , typename iType2 >
+  KOKKOS_INLINE_FUNCTION
+  typename std::enable_if< !(std::is_same<typename drvtraits::specialize , void>::value && std::is_integral<iType0>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 3 , ( m_map , i0 , i1 , i2 ) )
+      return m_map.reference(i0,i1,i2,0,0,0,0); 
+    }
 
   // Rank 4
   template< typename iType0 , typename iType1 , typename iType2 , typename iType3 >
   KOKKOS_INLINE_FUNCTION
-  reference_type operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const 
-    { return view_type::operator()(i0,i1,i2,i3,0,0,0); }
+  typename std::enable_if< (std::is_same<typename traits::specialize , void>::value && std::is_integral<iType0>::value  && std::is_integral<iType1>::value && std::is_integral<iType2>::value && std::is_integral<iType3>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 4 , ( m_map , i0 , i1 , i2 , i3 ) )
+      return m_map.reference(i0,i1,i2,i3); 
+    }
+
+  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 >
+  KOKKOS_INLINE_FUNCTION
+  typename std::enable_if< !(std::is_same<typename drvtraits::specialize , void>::value && std::is_integral<iType0>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 4 , ( m_map , i0 , i1 , i2 , i3 ) )
+      return m_map.reference(i0,i1,i2,i3,0,0,0); 
+    }
 
   // Rank 5
   template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 >
   KOKKOS_INLINE_FUNCTION
-  reference_type operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const 
-    { return view_type::operator()(i0,i1,i2,i3,i4,0,0); }
+  typename std::enable_if< (std::is_same<typename traits::specialize , void>::value && std::is_integral<iType0>::value  && std::is_integral<iType1>::value && std::is_integral<iType2>::value && std::is_integral<iType3>::value && std::is_integral<iType4>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 5 , ( m_map , i0 , i1 , i2 , i3 , i4 ) )
+      return m_map.reference(i0,i1,i2,i3,i4); 
+    }
+
+  template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 >
+  KOKKOS_INLINE_FUNCTION
+  typename std::enable_if< !(std::is_same<typename drvtraits::specialize , void>::value && std::is_integral<iType0>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 5 , ( m_map , i0 , i1 , i2 , i3 , i4 ) )
+      return m_map.reference(i0,i1,i2,i3,i4,0,0); 
+    }
 
   // Rank 6
   template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 >
   KOKKOS_INLINE_FUNCTION
-  reference_type operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const 
-    { return view_type::operator()(i0,i1,i2,i3,i4,i5,0); }
+  typename std::enable_if< (std::is_same<typename traits::specialize , void>::value && std::is_integral<iType0>::value  && std::is_integral<iType1>::value && std::is_integral<iType2>::value && std::is_integral<iType3>::value && std::is_integral<iType4>::value && std::is_integral<iType5>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 6 , ( m_map , i0 , i1 , i2 , i3 , i4 , i5 ) )
+      return m_map.reference(i0,i1,i2,i3,i4,i5); 
+    }
+
+  template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 >
+  KOKKOS_INLINE_FUNCTION
+  typename std::enable_if< !(std::is_same<typename drvtraits::specialize , void>::value && std::is_integral<iType0>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 6 , ( m_map , i0 , i1 , i2 , i3 , i4 , i5 ) )
+      return m_map.reference(i0,i1,i2,i3,i4,i5,0); 
+    }
 
   // Rank 7
   template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 , typename iType6 >
   KOKKOS_INLINE_FUNCTION
-  reference_type operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 , const iType6 & i6 ) const 
-    { return view_type::operator()(i0,i1,i2,i3,i4,i5,i6); }
+  typename std::enable_if< (std::is_integral<iType0>::value  && std::is_integral<iType1>::value && std::is_integral<iType2>::value && std::is_integral<iType3>::value && std::is_integral<iType4>::value && std::is_integral<iType5>::value && std::is_integral<iType6>::value), reference_type>::type
+  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 , const iType6 & i6 ) const 
+    { 
+      KOKKOS_VIEW_OPERATOR_VERIFY( 7 , ( m_map , i0 , i1 , i2 , i3 , i4 , i5 , i6 ) )
+      return m_map.reference(i0,i1,i2,i3,i4,i5,i6); 
+    }
+
+#undef KOKKOS_VIEW_OPERATOR_VERIFY
 
   //----------------------------------------
   // Standard constructor, destructor, and assignment operators... 
@@ -394,46 +694,89 @@ public:
   ~DynRankView() {}
 
   KOKKOS_INLINE_FUNCTION
-  DynRankView( const DynRankView & ) = default ;
+  DynRankView() : m_track(), m_map(), m_rank() {} //Default ctor
 
   KOKKOS_INLINE_FUNCTION
-  DynRankView( DynRankView && ) = default ;
+  DynRankView( const DynRankView & rhs ) : m_track( rhs.m_track ), m_map( rhs.m_map ), m_rank(rhs.m_rank) {}
 
   KOKKOS_INLINE_FUNCTION
-  DynRankView & operator = ( const DynRankView & ) = default ;
+  DynRankView( DynRankView && rhs ) : m_track( rhs.m_track ), m_map( rhs.m_map ), m_rank(rhs.m_rank) {}
 
   KOKKOS_INLINE_FUNCTION
-  DynRankView & operator = ( DynRankView && ) = default ;
+  DynRankView & operator = ( const DynRankView & rhs ) { m_track = rhs.m_track; m_map = rhs.m_map; m_rank = rhs.m_rank; return *this; }
+
+  KOKKOS_INLINE_FUNCTION
+  DynRankView & operator = ( DynRankView && rhs ) { m_track = rhs.m_track; m_map = rhs.m_map; m_rank = rhs.m_rank; return *this; } 
 
   //----------------------------------------
   // Compatible view copy constructor and assignment
   // may assign unmanaged from managed.
-
   template< class RT , class ... RP >
   KOKKOS_INLINE_FUNCTION
   DynRankView( const DynRankView<RT,RP...> & rhs )
-    : view_type( rhs.ConstDownCast() )  
+    : m_track( rhs.m_track , traits::is_managed )
+    , m_map()
     , m_rank(rhs.m_rank)
-    {}
+    {
+      typedef typename DynRankView<RT,RP...> ::traits SrcTraits ;
+      typedef Kokkos::Experimental::Impl::ViewMapping< traits , SrcTraits , void > Mapping ;
+      static_assert( Mapping::is_assignable , "Incompatible DynRankView copy construction" );
+      Mapping::assign( m_map , rhs.m_map , rhs.m_track );
+    }
 
   template< class RT , class ... RP >
   KOKKOS_INLINE_FUNCTION
   DynRankView & operator = (const DynRankView<RT,RP...> & rhs )
-  {
-    view_type::operator = ( rhs.ConstDownCast() );
-    m_rank = rhs.rank();
-    return *this;
-  }
+    {
+      typedef typename DynRankView<RT,RP...> ::traits SrcTraits ;
+      typedef Kokkos::Experimental::Impl::ViewMapping< traits , SrcTraits , void > Mapping ;
+      static_assert( Mapping::is_assignable , "Incompatible DynRankView copy construction" );
+      Mapping::assign( m_map , rhs.m_map , rhs.m_track );
+      m_track.assign( rhs.m_track , traits::is_managed );
+      m_rank = rhs.rank();
+      return *this;
+    }
+
+// Experimental
+// Copy/Assign View to DynRankView
+  template< class RT , class ... RP >
+  KOKKOS_INLINE_FUNCTION
+  DynRankView( const View<RT,RP...> & rhs )
+    : m_track()
+    , m_map()
+    , m_rank( rhs.Rank )
+    {
+      typedef typename View<RT,RP...>::traits  SrcTraits ;
+      typedef Kokkos::Experimental::Impl::ViewMapping< traits , SrcTraits , Kokkos::Experimental::Impl::ViewToDynRankViewTag >  Mapping ;
+      static_assert( Mapping::is_assignable , "Incompatible DynRankView copy construction" );
+      Mapping::assign( *this , rhs );
+    }
+
+  template< class RT , class ... RP >
+  KOKKOS_INLINE_FUNCTION
+  DynRankView & operator = ( const View<RT,RP...> & rhs )
+    {
+      typedef typename View<RT,RP...>::traits  SrcTraits ;
+      typedef Kokkos::Experimental::Impl::ViewMapping< traits , SrcTraits , Kokkos::Experimental::Impl::ViewToDynRankViewTag >  Mapping ;
+      static_assert( Mapping::is_assignable , "Incompatible View to DynRankView copy assignment" );
+      Mapping::assign( *this , rhs );
+      return *this ;
+    }
 
   //----------------------------------------
   // Allocation tracking properties
 
-  using view_type::use_count;
-  using view_type::label;
+  KOKKOS_INLINE_FUNCTION
+  int use_count() const
+    { return m_track.use_count(); }
+
+  inline
+  const std::string label() const
+    { return m_track.template get_label< typename traits::memory_space >(); }
 
   //----------------------------------------
   // Allocation according to allocation properties and array layout
-
+  // unused arg_layout dimensions must be set to ~size_t(0) so that rank deduction can properly take place
   template< class ... P >
   explicit inline
   DynRankView( const Impl::ViewCtorProp< P ... > & arg_prop
@@ -441,12 +784,77 @@ public:
                                , typename traits::array_layout
                                >::type const & arg_layout
       )
-      : view_type( arg_prop
-                 , Impl::DynRankDimTraits<typename traits::specialize>::createLayout(arg_layout) )
+      : m_track()
+      , m_map()
       , m_rank( Impl::DynRankDimTraits<typename traits::specialize>::computeRank(arg_layout) )
-    {}
+    {
+      // Append layout and spaces if not input
+      typedef Impl::ViewCtorProp< P ... > alloc_prop_input ;
+
+      // use 'std::integral_constant<unsigned,I>' for non-types
+      // to avoid duplicate class error.
+      typedef Impl::ViewCtorProp
+        < P ...
+        , typename std::conditional
+            < alloc_prop_input::has_label
+            , std::integral_constant<unsigned,0>
+            , typename std::string
+            >::type
+        , typename std::conditional
+            < alloc_prop_input::has_memory_space
+            , std::integral_constant<unsigned,1>
+            , typename traits::device_type::memory_space
+            >::type
+        , typename std::conditional
+            < alloc_prop_input::has_execution_space
+            , std::integral_constant<unsigned,2>
+            , typename traits::device_type::execution_space
+            >::type
+        > alloc_prop ;
+
+      static_assert( traits::is_managed
+                   , "View allocation constructor requires managed memory" );
+
+      if ( alloc_prop::initialize &&
+           ! alloc_prop::execution_space::is_initialized() ) {
+        // If initializing view data then
+        // the execution space must be initialized.
+        Kokkos::Impl::throw_runtime_exception("Constructing DynRankView and initializing data with uninitialized execution space");
+      }
+
+      // Copy the input allocation properties with possibly defaulted properties
+      alloc_prop prop( arg_prop );
+
+//------------------------------------------------------------
+#if defined( KOKKOS_HAVE_CUDA )
+      // If allocating in CudaUVMSpace must fence before and after
+      // the allocation to protect against possible concurrent access
+      // on the CPU and the GPU.
+      // Fence using the trait's executon space (which will be Kokkos::Cuda)
+      // to avoid incomplete type errors from usng Kokkos::Cuda directly.
+      if ( std::is_same< Kokkos::CudaUVMSpace , typename traits::device_type::memory_space >::value ) {
+        traits::device_type::memory_space::execution_space::fence();
+      }
+#endif
+//------------------------------------------------------------
 
-//Wrappers
+      Kokkos::Experimental::Impl::SharedAllocationRecord<> *
+        record = m_map.allocate_shared( prop , Impl::DynRankDimTraits<typename traits::specialize>::createLayout(arg_layout) );
+
+//------------------------------------------------------------
+#if defined( KOKKOS_HAVE_CUDA )
+      if ( std::is_same< Kokkos::CudaUVMSpace , typename traits::device_type::memory_space >::value ) {
+        traits::device_type::memory_space::execution_space::fence();
+      }
+#endif
+//------------------------------------------------------------
+
+      // Setup and initialization complete, start tracking
+      m_track.assign_allocated_record_to_uninitialized( record );
+    }
+
+
+  // Wrappers
   template< class ... P >
   explicit KOKKOS_INLINE_FUNCTION
   DynRankView( const Impl::ViewCtorProp< P ... > & arg_prop
@@ -454,10 +862,16 @@ public:
                                , typename traits::array_layout
                                >::type const & arg_layout
       )
-      : view_type( arg_prop
-                 , Impl::DynRankDimTraits<typename traits::specialize>::createLayout(arg_layout) )
+      : m_track() // No memory tracking
+      , m_map( arg_prop , Impl::DynRankDimTraits<typename traits::specialize>::createLayout(arg_layout) )
       , m_rank( Impl::DynRankDimTraits<typename traits::specialize>::computeRank(arg_layout) )
-    {}
+    {
+      static_assert(
+        std::is_same< pointer_type
+                    , typename Impl::ViewCtorProp< P... >::pointer_type
+                    >::value ,
+        "Constructing DynRankView to wrap user memory must supply matching pointer type" );
+    }
 
   //----------------------------------------
   //Constructor(s)
@@ -468,14 +882,14 @@ public:
   DynRankView( const Impl::ViewCtorProp< P ... > & arg_prop
       , typename std::enable_if< ! Impl::ViewCtorProp< P... >::has_pointer
                                , size_t
-                               >::type const arg_N0 = 0
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0
+                               >::type const arg_N0 = ~size_t(0)
+      , const size_t arg_N1 = ~size_t(0)
+      , const size_t arg_N2 = ~size_t(0)
+      , const size_t arg_N3 = ~size_t(0)
+      , const size_t arg_N4 = ~size_t(0)
+      , const size_t arg_N5 = ~size_t(0)
+      , const size_t arg_N6 = ~size_t(0)
+      , const size_t arg_N7 = ~size_t(0)
       )
     : DynRankView( arg_prop
     , typename traits::array_layout
@@ -488,14 +902,14 @@ public:
   DynRankView( const Impl::ViewCtorProp< P ... > & arg_prop
       , typename std::enable_if< Impl::ViewCtorProp< P... >::has_pointer
                                , size_t
-                               >::type const arg_N0 = 0
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0
+                               >::type const arg_N0 = ~size_t(0)
+      , const size_t arg_N1 = ~size_t(0)
+      , const size_t arg_N2 = ~size_t(0)
+      , const size_t arg_N3 = ~size_t(0)
+      , const size_t arg_N4 = ~size_t(0)
+      , const size_t arg_N5 = ~size_t(0)
+      , const size_t arg_N6 = ~size_t(0)
+      , const size_t arg_N7 = ~size_t(0)
       )
     : DynRankView( arg_prop
     , typename traits::array_layout
@@ -514,20 +928,20 @@ public:
     : DynRankView( Impl::ViewCtorProp< std::string >( arg_label ) , arg_layout )
     {}
 
-  // Allocate label and layout
+  // Allocate label and layout, must disambiguate from subview constructor
   template< typename Label >
   explicit inline
   DynRankView( const Label & arg_label
       , typename std::enable_if<
           Kokkos::Experimental::Impl::is_view_label<Label>::value ,
-        const size_t >::type arg_N0 = 0
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0
+        const size_t >::type arg_N0 = ~size_t(0) 
+      , const size_t arg_N1 = ~size_t(0)
+      , const size_t arg_N2 = ~size_t(0)
+      , const size_t arg_N3 = ~size_t(0)
+      , const size_t arg_N4 = ~size_t(0)
+      , const size_t arg_N5 = ~size_t(0)
+      , const size_t arg_N6 = ~size_t(0)
+      , const size_t arg_N7 = ~size_t(0)
       )
     : DynRankView( Impl::ViewCtorProp< std::string >( arg_label )
     , typename traits::array_layout
@@ -536,44 +950,58 @@ public:
     {}
 
   // For backward compatibility
-/*
   explicit inline
   DynRankView( const ViewAllocateWithoutInitializing & arg_prop
       , const typename traits::array_layout & arg_layout
       )
-    : view_type( Impl::ViewCtorProp< std::string , Kokkos::Experimental::Impl::WithoutInitializing_t >( arg_prop.label , Kokkos::Experimental::WithoutInitializing )
-          , arg_layout
-          )
-    //, m_rank(arg_N0 == 0 ? 0 : ( arg_N1 == 0 ? 1 : ( arg_N2 == 0 ? 2 : ( arg_N3 == 0 ? 3 : ( arg_N4 == 0 ? 4 : ( arg_N5 == 0 ? 5 : ( arg_N6 == 0 ? 6 : ( arg_N7 == 0 ? 7 : 8 ) ) ) ) ) ) ) ) //how to extract rank?
+    : DynRankView( Impl::ViewCtorProp< std::string , Kokkos::Experimental::Impl::WithoutInitializing_t >( arg_prop.label , Kokkos::Experimental::WithoutInitializing )
+          , Impl::DynRankDimTraits<typename traits::specialize>::createLayout(arg_layout)
+      )
     {}
-*/
 
   explicit inline
   DynRankView( const ViewAllocateWithoutInitializing & arg_prop
-      , const size_t arg_N0 = 0
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0
+      , const size_t arg_N0 = ~size_t(0)
+      , const size_t arg_N1 = ~size_t(0)
+      , const size_t arg_N2 = ~size_t(0)
+      , const size_t arg_N3 = ~size_t(0)
+      , const size_t arg_N4 = ~size_t(0)
+      , const size_t arg_N5 = ~size_t(0)
+      , const size_t arg_N6 = ~size_t(0)
+      , const size_t arg_N7 = ~size_t(0)
       )
     : DynRankView(Impl::ViewCtorProp< std::string , Kokkos::Experimental::Impl::WithoutInitializing_t >( arg_prop.label , Kokkos::Experimental::WithoutInitializing ), arg_N0, arg_N1, arg_N2, arg_N3, arg_N4, arg_N5, arg_N6, arg_N7 ) 
     {}
 
-  using view_type::memory_span;
+  //----------------------------------------
+  // Memory span required to wrap these dimensions.
+  static constexpr size_t required_allocation_size(
+                                       const size_t arg_N0 = 0
+                                     , const size_t arg_N1 = 0
+                                     , const size_t arg_N2 = 0
+                                     , const size_t arg_N3 = 0
+                                     , const size_t arg_N4 = 0
+                                     , const size_t arg_N5 = 0
+                                     , const size_t arg_N6 = 0
+                                     , const size_t arg_N7 = 0
+                                     )
+    {
+      return map_type::memory_span(
+        typename traits::array_layout
+          ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+          , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) );
+    }
 
   explicit KOKKOS_INLINE_FUNCTION
   DynRankView( pointer_type arg_ptr
-      , const size_t arg_N0 = 0
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0
+      , const size_t arg_N0 = ~size_t(0)
+      , const size_t arg_N1 = ~size_t(0)
+      , const size_t arg_N2 = ~size_t(0)
+      , const size_t arg_N3 = ~size_t(0)
+      , const size_t arg_N4 = ~size_t(0)
+      , const size_t arg_N5 = ~size_t(0)
+      , const size_t arg_N6 = ~size_t(0)
+      , const size_t arg_N7 = ~size_t(0)
       )
     : DynRankView( Impl::ViewCtorProp<pointer_type>(arg_ptr) , arg_N0, arg_N1, arg_N2, arg_N3, arg_N4, arg_N5, arg_N6, arg_N7 )
     {}
@@ -589,39 +1017,76 @@ public:
   //----------------------------------------
   // Shared scratch memory constructor
 
-  using view_type::shmem_size; 
+  static inline
+  size_t shmem_size( const size_t arg_N0 = ~size_t(0) ,
+                     const size_t arg_N1 = ~size_t(0) ,
+                     const size_t arg_N2 = ~size_t(0) ,
+                     const size_t arg_N3 = ~size_t(0) ,
+                     const size_t arg_N4 = ~size_t(0) ,
+                     const size_t arg_N5 = ~size_t(0) ,
+                     const size_t arg_N6 = ~size_t(0) ,
+                     const size_t arg_N7 = ~size_t(0) )
+  {
+    const size_t num_passed_args =
+      ( arg_N0 != ~size_t(0) ) + ( arg_N1 != ~size_t(0) ) + ( arg_N2 != ~size_t(0) ) +
+      ( arg_N3 != ~size_t(0) ) + ( arg_N4 != ~size_t(0) ) + ( arg_N5 != ~size_t(0) ) +
+      ( arg_N6 != ~size_t(0) ) + ( arg_N7 != ~size_t(0) );
+
+    if ( std::is_same<typename traits::specialize , void>::value && num_passed_args != traits::rank_dynamic ) {
+      Kokkos::abort( "Kokkos::View::shmem_size() rank_dynamic != number of arguments.\n" );
+    }
+    {}
+
+    return map_type::memory_span(
+           typename traits::array_layout
+            ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+            , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) );
+  }
+
+  explicit KOKKOS_INLINE_FUNCTION
+  DynRankView( const typename traits::execution_space::scratch_memory_space & arg_space
+      , const typename traits::array_layout & arg_layout )
+    : DynRankView( Impl::ViewCtorProp<pointer_type>(
+              reinterpret_cast<pointer_type>(
+                arg_space.get_shmem( map_type::memory_span( 
+                  Impl::DynRankDimTraits<typename traits::specialize>::createLayout( arg_layout ) //is this correct?
+                ) ) ) )
+         , arg_layout )
+     {}
 
   explicit KOKKOS_INLINE_FUNCTION
   DynRankView( const typename traits::execution_space::scratch_memory_space & arg_space
-      , const size_t arg_N0 = 0
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0 )
-    : view_type( Impl::DynRankDimTraits<typename traits::specialize>::template createView<view_type>( arg_space
-                                                                                                    , arg_N0
-                                                                                                    , arg_N1
-                                                                                                    , arg_N2
-                                                                                                    , arg_N3
-                                                                                                    , arg_N4
-                                                                                                    , arg_N5
-                                                                                                    , arg_N6
-                                                                                                    , arg_N7 ) )
-    , m_rank( Impl::DynRankDimTraits<typename traits::specialize>::computeRank( arg_N0
-                                                                              , arg_N1
-                                                                              , arg_N2
-                                                                              , arg_N3
-                                                                              , arg_N4
-                                                                              , arg_N5
-                                                                              , arg_N6
-                                                                              , arg_N7 ) )
+      , const size_t arg_N0 = ~size_t(0)
+      , const size_t arg_N1 = ~size_t(0)
+      , const size_t arg_N2 = ~size_t(0)
+      , const size_t arg_N3 = ~size_t(0)
+      , const size_t arg_N4 = ~size_t(0)
+      , const size_t arg_N5 = ~size_t(0)
+      , const size_t arg_N6 = ~size_t(0)
+      , const size_t arg_N7 = ~size_t(0) )
+
+    : DynRankView( Impl::ViewCtorProp<pointer_type>(
+                   reinterpret_cast<pointer_type>(
+                     arg_space.get_shmem(
+                       map_type::memory_span(
+                       Impl::DynRankDimTraits<typename traits::specialize>::createLayout(
+                       typename traits::array_layout
+                       ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+                       , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) ) ) ) ) 
+                    )
+                  , typename traits::array_layout
+                    ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+                    , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
+        )
     {}
 
 };
 
+
+  template < typename D , class ... P >
+  KOKKOS_INLINE_FUNCTION
+  constexpr unsigned rank( const DynRankView<D , P...> & DRV ) { return DRV.rank(); } //needed for transition to common constexpr method in view and dynrankview to return rank
+
 //----------------------------------------------------------------------------
 // Subview mapping.
 // Deduce destination view type from source view traits and subview arguments
@@ -719,11 +1184,11 @@ public:
 
   template < typename T , class ... P >
   KOKKOS_INLINE_FUNCTION
-  static ret_type subview( const unsigned src_rank , Kokkos::Experimental::View< T******* , P...> const & src 
+  static ret_type subview( const unsigned src_rank , Kokkos::Experimental::DynRankView< T , P...> const & src 
                     , Args ... args )
     {
 
-      typedef ViewMapping< traits_type, void >  DstType ;
+       typedef ViewMapping< traits_type, void >  DstType ;
 
        typedef typename std::conditional< (rank==0) , ViewDimension<>
                                                     , typename std::conditional< (rank==1) , ViewDimension<0>
@@ -801,13 +1266,21 @@ subdynrankview( const Kokkos::Experimental::DynRankView< D , P... > &src , Args.
   
     typedef Kokkos::Experimental::Impl::ViewMapping< Kokkos::Experimental::Impl::DynRankSubviewTag , Kokkos::Experimental::ViewTraits< D*******, P... > , Args... > metafcn ;
 
-    return metafcn::subview( src.rank() , src.ConstDownCast() , args... );
+    return metafcn::subview( src.rank() , src , args... );
+  }
+
+//Wrapper to allow subview function name
+template< class D , class ... P , class ...Args >
+KOKKOS_INLINE_FUNCTION
+Subdynrankview< ViewTraits<D******* , P...> , Args... > 
+subview( const Kokkos::Experimental::DynRankView< D , P... > &src , Args...args)
+  {
+    return subdynrankview( src , args... );
   }
 
 } // namespace Experimental
 } // namespace Kokkos
 
-
 namespace Kokkos {
 namespace Experimental {
 
@@ -854,6 +1327,109 @@ bool operator != ( const DynRankView<LT,LP...> & lhs ,
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
+namespace Kokkos {
+namespace Experimental {
+namespace Impl {
+
+template< class OutputView , typename Enable = void >
+struct DynRankViewFill {
+
+  typedef typename OutputView::traits::const_value_type  const_value_type ;
+
+  const OutputView output ;
+  const_value_type input ;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()( const size_t i0 ) const
+  {
+    const size_t n1 = output.dimension_1();
+    const size_t n2 = output.dimension_2();
+    const size_t n3 = output.dimension_3();
+    const size_t n4 = output.dimension_4();
+    const size_t n5 = output.dimension_5();
+    const size_t n6 = output.dimension_6();
+
+    for ( size_t i1 = 0 ; i1 < n1 ; ++i1 ) {
+    for ( size_t i2 = 0 ; i2 < n2 ; ++i2 ) {
+    for ( size_t i3 = 0 ; i3 < n3 ; ++i3 ) {
+    for ( size_t i4 = 0 ; i4 < n4 ; ++i4 ) {
+    for ( size_t i5 = 0 ; i5 < n5 ; ++i5 ) {
+    for ( size_t i6 = 0 ; i6 < n6 ; ++i6 ) {
+      output(i0,i1,i2,i3,i4,i5,i6) = input ;
+    }}}}}}
+  }
+
+  DynRankViewFill( const OutputView & arg_out , const_value_type & arg_in )
+    : output( arg_out ), input( arg_in )
+    {
+      typedef typename OutputView::execution_space  execution_space ;
+      typedef Kokkos::RangePolicy< execution_space > Policy ;
+
+      const Kokkos::Impl::ParallelFor< DynRankViewFill , Policy > closure( *this , Policy( 0 , output.dimension_0() ) );
+
+      closure.execute();
+
+      execution_space::fence();
+    }
+};
+
+template< class OutputView >
+struct DynRankViewFill< OutputView , typename std::enable_if< OutputView::Rank == 0 >::type > { 
+  DynRankViewFill( const OutputView & dst , const typename OutputView::const_value_type & src )
+    {
+      Kokkos::Impl::DeepCopy< typename OutputView::memory_space , Kokkos::HostSpace >
+        ( dst.data() , & src , sizeof(typename OutputView::const_value_type) );
+    }
+};
+
+template< class OutputView , class InputView , class ExecSpace = typename OutputView::execution_space >
+struct DynRankViewRemap {
+
+  const OutputView output ;
+  const InputView  input ;
+  const size_t n0 ;
+  const size_t n1 ;
+  const size_t n2 ;
+  const size_t n3 ;
+  const size_t n4 ;
+  const size_t n5 ;
+  const size_t n6 ;
+  const size_t n7 ;
+
+  DynRankViewRemap( const OutputView & arg_out , const InputView & arg_in )
+    : output( arg_out ), input( arg_in )
+    , n0( std::min( (size_t)arg_out.dimension_0() , (size_t)arg_in.dimension_0() ) )
+    , n1( std::min( (size_t)arg_out.dimension_1() , (size_t)arg_in.dimension_1() ) )
+    , n2( std::min( (size_t)arg_out.dimension_2() , (size_t)arg_in.dimension_2() ) )
+    , n3( std::min( (size_t)arg_out.dimension_3() , (size_t)arg_in.dimension_3() ) )
+    , n4( std::min( (size_t)arg_out.dimension_4() , (size_t)arg_in.dimension_4() ) )
+    , n5( std::min( (size_t)arg_out.dimension_5() , (size_t)arg_in.dimension_5() ) )
+    , n6( std::min( (size_t)arg_out.dimension_6() , (size_t)arg_in.dimension_6() ) )
+    , n7( std::min( (size_t)arg_out.dimension_7() , (size_t)arg_in.dimension_7() ) )
+    {
+      typedef Kokkos::RangePolicy< ExecSpace > Policy ;
+      const Kokkos::Impl::ParallelFor< DynRankViewRemap , Policy > closure( *this , Policy( 0 , n0 ) );
+      closure.execute();
+    }
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()( const size_t i0 ) const
+  {
+    for ( size_t i1 = 0 ; i1 < n1 ; ++i1 ) {
+    for ( size_t i2 = 0 ; i2 < n2 ; ++i2 ) {
+    for ( size_t i3 = 0 ; i3 < n3 ; ++i3 ) {
+    for ( size_t i4 = 0 ; i4 < n4 ; ++i4 ) {
+    for ( size_t i5 = 0 ; i5 < n5 ; ++i5 ) {
+    for ( size_t i6 = 0 ; i6 < n6 ; ++i6 ) {
+      output(i0,i1,i2,i3,i4,i5,i6) = input(i0,i1,i2,i3,i4,i5,i6);
+    }}}}}}
+  }
+};
+
+} /* namespace Impl */
+} /* namespace Experimental */
+} /* namespace Kokkos */
+
 
 namespace Kokkos {
 namespace Experimental {
@@ -863,9 +1439,17 @@ template< class DT , class ... DP >
 inline
 void deep_copy
   ( const DynRankView<DT,DP...> & dst
-  , typename ViewTraits<DT,DP...>::const_value_type & value )
+  , typename ViewTraits<DT,DP...>::const_value_type & value
+  , typename std::enable_if<
+    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value
+    >::type * = 0 )
 {
-  deep_copy( dst.ConstDownCast() , value );
+  static_assert(
+    std::is_same< typename ViewTraits<DT,DP...>::non_const_value_type ,
+                  typename ViewTraits<DT,DP...>::value_type >::value
+    , "deep_copy requires non-const type" );
+
+  Kokkos::Experimental::Impl::DynRankViewFill< DynRankView<DT,DP...> >( dst , value );
 }
 
 /** \brief  Deep copy into a value in Host memory from a view.  */
@@ -873,21 +1457,156 @@ template< class ST , class ... SP >
 inline
 void deep_copy
   ( typename ViewTraits<ST,SP...>::non_const_value_type & dst
-  , const DynRankView<ST,SP...> & src )
+  , const DynRankView<ST,SP...> & src
+  , typename std::enable_if<
+    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value
+    >::type * = 0 )
 {
-  deep_copy( dst , src.ConstDownCast() );
-}
+  if ( src.rank() != 0 )
+  {
+    Kokkos::abort("");
+  }
 
+  typedef ViewTraits<ST,SP...>               src_traits ;
+  typedef typename src_traits::memory_space  src_memory_space ;
+  Kokkos::Impl::DeepCopy< HostSpace , src_memory_space >( & dst , src.data() , sizeof(ST) );
+}
 
 //----------------------------------------------------------------------------
-/** \brief  A deep copy between views of compatible type */
-template< class DT , class ... DP , class ST , class ... SP >
+/** \brief  A deep copy between views of the default specialization, compatible type,
+ *          same rank, same contiguous layout.
+ */
+template< class DstType , class SrcType >
 inline
 void deep_copy
-  ( const DynRankView<DT,DP...> & dst
-  , const DynRankView<ST,SP...> & src )
+  ( const DstType & dst
+  , const SrcType & src
+  , typename std::enable_if<(
+    std::is_same< typename DstType::traits::specialize , void >::value &&
+    std::is_same< typename SrcType::traits::specialize , void >::value
+    &&
+    ( Kokkos::Experimental::is_dyn_rank_view<DstType>::value || Kokkos::Experimental::is_dyn_rank_view<SrcType>::value)
+  )>::type * = 0 )
 {
-  deep_copy( dst.ConstDownCast() , src.ConstDownCast() );
+  static_assert(
+    std::is_same< typename DstType::traits::value_type ,
+                  typename DstType::traits::non_const_value_type >::value
+    , "deep_copy requires non-const destination type" );
+
+  typedef DstType  dst_type ;
+  typedef SrcType  src_type ;
+
+  typedef typename dst_type::execution_space  dst_execution_space ;
+  typedef typename src_type::execution_space  src_execution_space ;
+  typedef typename dst_type::memory_space     dst_memory_space ;
+  typedef typename src_type::memory_space     src_memory_space ;
+
+  enum { DstExecCanAccessSrc =
+   Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< typename dst_execution_space::memory_space , src_memory_space >::value };
+
+  enum { SrcExecCanAccessDst =
+   Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< typename src_execution_space::memory_space , dst_memory_space >::value };
+
+  if ( (void *) dst.data() != (void*) src.data() ) {
+
+    // Concern: If overlapping views then a parallel copy will be erroneous.
+    // ...
+
+    // If same type, equal layout, equal dimensions, equal span, and contiguous memory then can byte-wise copy
+    if ( rank(src) == 0 && rank(dst) == 0 )
+    { 
+      typedef typename dst_type::value_type    value_type ;
+      Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.data() , src.data() , sizeof(value_type) ); 
+    }
+    else if ( std::is_same< typename DstType::traits::value_type ,
+                       typename SrcType::traits::non_const_value_type >::value &&
+         (
+           ( std::is_same< typename DstType::traits::array_layout ,
+                           typename SrcType::traits::array_layout >::value
+             &&
+             ( std::is_same< typename DstType::traits::array_layout ,
+                             typename Kokkos::LayoutLeft>::value
+             ||
+               std::is_same< typename DstType::traits::array_layout ,
+                             typename Kokkos::LayoutRight>::value
+             )
+           )
+           ||
+           (
+             rank(dst) == 1
+             &&
+             rank(src) == 1
+           )
+         ) &&
+         dst.span_is_contiguous() &&
+         src.span_is_contiguous() &&
+         dst.span() == src.span() &&
+         dst.dimension_0() == src.dimension_0() &&
+         dst.dimension_1() == src.dimension_1() &&
+         dst.dimension_2() == src.dimension_2() &&
+         dst.dimension_3() == src.dimension_3() &&
+         dst.dimension_4() == src.dimension_4() &&
+         dst.dimension_5() == src.dimension_5() &&
+         dst.dimension_6() == src.dimension_6() &&
+         dst.dimension_7() == src.dimension_7() ) {
+
+      const size_t nbytes = sizeof(typename dst_type::value_type) * dst.span();
+
+      Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.data() , src.data() , nbytes );
+    }
+    else if ( std::is_same< typename DstType::traits::value_type ,
+                            typename SrcType::traits::non_const_value_type >::value &&
+         (
+           ( std::is_same< typename DstType::traits::array_layout ,
+                           typename SrcType::traits::array_layout >::value
+             &&
+             std::is_same< typename DstType::traits::array_layout ,
+                          typename Kokkos::LayoutStride>::value
+           )
+           ||
+           (
+             rank(dst) == 1
+             &&
+             rank(src) == 1
+           )
+         ) &&
+         dst.span_is_contiguous() &&
+         src.span_is_contiguous() &&
+         dst.span() == src.span() &&
+         dst.dimension_0() == src.dimension_0() &&
+         dst.dimension_1() == src.dimension_1() &&
+         dst.dimension_2() == src.dimension_2() &&
+         dst.dimension_3() == src.dimension_3() &&
+         dst.dimension_4() == src.dimension_4() &&
+         dst.dimension_5() == src.dimension_5() &&
+         dst.dimension_6() == src.dimension_6() &&
+         dst.dimension_7() == src.dimension_7() &&
+         dst.stride_0() == src.stride_0() &&
+         dst.stride_1() == src.stride_1() &&
+         dst.stride_2() == src.stride_2() &&
+         dst.stride_3() == src.stride_3() &&
+         dst.stride_4() == src.stride_4() &&
+         dst.stride_5() == src.stride_5() &&
+         dst.stride_6() == src.stride_6() &&
+         dst.stride_7() == src.stride_7()
+         ) {
+
+      const size_t nbytes = sizeof(typename dst_type::value_type) * dst.span();
+
+      Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.data() , src.data() , nbytes );
+    }
+    else if ( DstExecCanAccessSrc ) {
+      // Copying data between views in accessible memory spaces and either non-contiguous or incompatible shape.
+      Kokkos::Experimental::Impl::DynRankViewRemap< dst_type , src_type >( dst , src );
+    }
+    else if ( SrcExecCanAccessDst ) {
+      // Copying data between views in accessible memory spaces and either non-contiguous or incompatible shape.
+      Kokkos::Experimental::Impl::DynRankViewRemap< dst_type , src_type , src_execution_space >( dst , src );
+    }
+    else {
+      Kokkos::Impl::throw_runtime_exception("deep_copy given views that would require a temporary allocation");
+    }
+  }
 }
 
 } //end Experimental
@@ -900,6 +1619,48 @@ void deep_copy
 namespace Kokkos {
 namespace Experimental {
 
+namespace Impl {
+
+
+// Deduce Mirror Types
+template<class Space, class T, class ... P>
+struct MirrorDRViewType {
+  // The incoming view_type
+  typedef typename Kokkos::Experimental::DynRankView<T,P...> src_view_type;
+  // The memory space for the mirror view
+  typedef typename Space::memory_space memory_space;
+  // Check whether it is the same memory space
+  enum { is_same_memspace = std::is_same<memory_space,typename src_view_type::memory_space>::value };
+  // The array_layout
+  typedef typename src_view_type::array_layout array_layout;
+  // The data type (we probably want it non-const since otherwise we can't even deep_copy to it.
+  typedef typename src_view_type::non_const_data_type data_type;
+  // The destination view type if it is not the same memory space
+  typedef Kokkos::Experimental::DynRankView<data_type,array_layout,Space> dest_view_type;
+  // If it is the same memory_space return the existsing view_type
+  // This will also keep the unmanaged trait if necessary
+  typedef typename std::conditional<is_same_memspace,src_view_type,dest_view_type>::type view_type;
+};
+
+template<class Space, class T, class ... P>
+struct MirrorDRVType {
+  // The incoming view_type
+  typedef typename Kokkos::Experimental::DynRankView<T,P...> src_view_type;
+  // The memory space for the mirror view
+  typedef typename Space::memory_space memory_space;
+  // Check whether it is the same memory space
+  enum { is_same_memspace = std::is_same<memory_space,typename src_view_type::memory_space>::value };
+  // The array_layout
+  typedef typename src_view_type::array_layout array_layout;
+  // The data type (we probably want it non-const since otherwise we can't even deep_copy to it.
+  typedef typename src_view_type::non_const_data_type data_type;
+  // The destination view type if it is not the same memory space
+  typedef Kokkos::Experimental::DynRankView<data_type,array_layout,Space> view_type;
+};
+
+}
+
+
 template< class T , class ... P >
 inline
 typename DynRankView<T,P...>::HostMirror
@@ -914,14 +1675,7 @@ create_mirror( const DynRankView<T,P...> & src
   typedef typename src_type::HostMirror  dst_type ;
 
   return dst_type( std::string( src.label() ).append("_mirror")
-                 , src.dimension(0)
-                 , src.dimension(1)
-                 , src.dimension(2)
-                 , src.dimension(3)
-                 , src.dimension(4)
-                 , src.dimension(5)
-                 , src.dimension(6)
-                 , src.dimension(7) );
+                 , Impl::reconstructLayout(src.layout(), src.rank()) );
 }
 
 
@@ -938,27 +1692,15 @@ create_mirror( const DynRankView<T,P...> & src
   typedef DynRankView<T,P...>                   src_type ;
   typedef typename src_type::HostMirror  dst_type ;
 
-  Kokkos::LayoutStride layout ;
-
-  layout.dimension[0] = src.dimension(0);
-  layout.dimension[1] = src.dimension(1);
-  layout.dimension[2] = src.dimension(2);
-  layout.dimension[3] = src.dimension(3);
-  layout.dimension[4] = src.dimension(4);
-  layout.dimension[5] = src.dimension(5);
-  layout.dimension[6] = src.dimension(6);
-  layout.dimension[7] = src.dimension(7);
-
-  layout.stride[0] = src.stride(0);
-  layout.stride[1] = src.stride(1);
-  layout.stride[2] = src.stride(2);
-  layout.stride[3] = src.stride(3);
-  layout.stride[4] = src.stride(4);
-  layout.stride[5] = src.stride(5);
-  layout.stride[6] = src.stride(6);
-  layout.stride[7] = src.stride(7);
-
-  return dst_type( std::string( src.label() ).append("_mirror") , layout );
+  return dst_type( std::string( src.label() ).append("_mirror") 
+                 , Impl::reconstructLayout(src.layout(), src.rank()) );
+}
+
+
+// Create a mirror in a new space (specialization for different space)
+template<class Space, class T, class ... P>
+typename Impl::MirrorDRVType<Space,T,P ...>::view_type create_mirror(const Space& , const Kokkos::Experimental::DynRankView<T,P...> & src) {
+  return typename Impl::MirrorDRVType<Space,T,P ...>::view_type(src.label(), Impl::reconstructLayout(src.layout(), src.rank()) );
 }
 
 template< class T , class ... P >
@@ -997,6 +1739,22 @@ create_mirror_view( const DynRankView<T,P...> & src
   return Kokkos::Experimental::create_mirror( src ); 
 }
 
+// Create a mirror view in a new space (specialization for same space)
+template<class Space, class T, class ... P>
+typename Impl::MirrorDRViewType<Space,T,P ...>::view_type
+create_mirror_view(const Space& , const Kokkos::Experimental::DynRankView<T,P...> & src
+  , typename std::enable_if<Impl::MirrorDRViewType<Space,T,P ...>::is_same_memspace>::type* = 0 ) {
+  return src;
+}
+
+// Create a mirror view in a new space (specialization for different space)
+template<class Space, class T, class ... P>
+typename Impl::MirrorDRViewType<Space,T,P ...>::view_type
+create_mirror_view(const Space& , const Kokkos::Experimental::DynRankView<T,P...> & src
+  , typename std::enable_if<!Impl::MirrorDRViewType<Space,T,P ...>::is_same_memspace>::type* = 0 ) {
+  return typename Impl::MirrorDRViewType<Space,T,P ...>::view_type(src.label(), Impl::reconstructLayout(src.layout(), src.rank()) );
+}
+
 } //end Experimental
 } //end Kokkos
 
@@ -1006,27 +1764,26 @@ create_mirror_view( const DynRankView<T,P...> & src
 
 namespace Kokkos {
 namespace Experimental {
-
 /** \brief  Resize a view with copying old data to new data at the corresponding indices. */
 template< class T , class ... P >
 inline
 void resize( DynRankView<T,P...> & v ,
-             const size_t n0 = 0 ,
-             const size_t n1 = 0 ,
-             const size_t n2 = 0 ,
-             const size_t n3 = 0 ,
-             const size_t n4 = 0 ,
-             const size_t n5 = 0 ,
-             const size_t n6 = 0 ,
-             const size_t n7 = 0 )
+             const size_t n0 = ~size_t(0) ,
+             const size_t n1 = ~size_t(0) ,
+             const size_t n2 = ~size_t(0) ,
+             const size_t n3 = ~size_t(0) ,
+             const size_t n4 = ~size_t(0) ,
+             const size_t n5 = ~size_t(0) ,
+             const size_t n6 = ~size_t(0) ,
+             const size_t n7 = ~size_t(0) )
 {
   typedef DynRankView<T,P...>  drview_type ;
 
   static_assert( Kokkos::Experimental::ViewTraits<T,P...>::is_managed , "Can only resize managed views" );
 
-  drview_type v_resized( v.label(), n0, n1, n2, n3, n4, n5, n6, n7 );
+  drview_type v_resized( v.label(), n0, n1, n2, n3, n4, n5, n6 );
 
-  Kokkos::Experimental::Impl::ViewRemap< drview_type , drview_type >( v_resized , v );
+  Kokkos::Experimental::Impl::DynRankViewRemap< drview_type , drview_type >( v_resized, v );
 
   v = v_resized ;
 }
@@ -1035,29 +1792,30 @@ void resize( DynRankView<T,P...> & v ,
 template< class T , class ... P >
 inline
 void realloc( DynRankView<T,P...> & v ,
-              const size_t n0 = 0 ,
-              const size_t n1 = 0 ,
-              const size_t n2 = 0 ,
-              const size_t n3 = 0 ,
-              const size_t n4 = 0 ,
-              const size_t n5 = 0 ,
-              const size_t n6 = 0 ,
-              const size_t n7 = 0 )
+              const size_t n0 = ~size_t(0) ,
+              const size_t n1 = ~size_t(0) ,
+              const size_t n2 = ~size_t(0) ,
+              const size_t n3 = ~size_t(0) ,
+              const size_t n4 = ~size_t(0) ,
+              const size_t n5 = ~size_t(0) ,
+              const size_t n6 = ~size_t(0) ,
+              const size_t n7 = ~size_t(0) )
 {
-  typedef DynRankView<T,P...>  view_type ;
+  typedef DynRankView<T,P...>  drview_type ;
 
   static_assert( Kokkos::Experimental::ViewTraits<T,P...>::is_managed , "Can only realloc managed views" );
 
   const std::string label = v.label();
 
-  v = view_type(); // Deallocate first, if the only view to allocation
-  v = view_type( label, n0, n1, n2, n3, n4, n5, n6, n7 );
+  v = drview_type(); // Deallocate first, if the only view to allocation
+  v = drview_type( label, n0, n1, n2, n3, n4, n5, n6 );
 }
 
 } //end Experimental
 
 } //end Kokkos
 
+using Kokkos::Experimental::is_dyn_rank_view ;
 
 namespace Kokkos {
 
@@ -1068,6 +1826,7 @@ using Kokkos::Experimental::deep_copy ;
 using Kokkos::Experimental::create_mirror ;
 using Kokkos::Experimental::create_mirror_view ;
 using Kokkos::Experimental::subdynrankview ;
+using Kokkos::Experimental::subview ;
 using Kokkos::Experimental::resize ;
 using Kokkos::Experimental::realloc ;
 
diff --git a/lib/kokkos/containers/src/Kokkos_DynamicView.hpp b/lib/kokkos/containers/src/Kokkos_DynamicView.hpp
index b1f9e95ed0..fb364f0bf2 100644
--- a/lib/kokkos/containers/src/Kokkos_DynamicView.hpp
+++ b/lib/kokkos/containers/src/Kokkos_DynamicView.hpp
@@ -77,10 +77,7 @@ private:
 
 public:
 
-  typedef Kokkos::Experimental::MemoryPool
-    < typename traits::memory_space
-    , typename traits::execution_space
-    > memory_pool ;
+  typedef Kokkos::Experimental::MemoryPool< typename traits::device_type > memory_pool ;
 
 private:
 
@@ -338,7 +335,7 @@ public:
     void operator()( unsigned i ) const
       {
         if ( m_destroy && i < m_chunk_max && 0 != m_chunks[i] ) {
-          m_pool.deallocate( m_chunks[i] , m_pool.get_min_chunk_size() );
+          m_pool.deallocate( m_chunks[i] , m_pool.get_min_block_size() );
         }
         m_chunks[i] = 0 ;
       }
@@ -397,7 +394,7 @@ public:
     // The memory pool chunk is guaranteed to be a power of two
     , m_chunk_shift(
         Kokkos::Impl::integral_power_of_two(
-          m_pool.get_min_chunk_size()/sizeof(typename traits::value_type)) )
+          m_pool.get_min_block_size()/sizeof(typename traits::value_type)) )
     , m_chunk_mask( ( 1 << m_chunk_shift ) - 1 )
     , m_chunk_max( ( arg_size_max + m_chunk_mask ) >> m_chunk_shift )
     {
diff --git a/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp b/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp
index 7de290e711..df2fbed5a6 100644
--- a/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp
+++ b/lib/kokkos/containers/src/impl/Kokkos_Bitset_impl.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -45,6 +45,7 @@
 #define KOKKOS_BITSET_IMPL_HPP
 
 #include <Kokkos_Macros.hpp>
+#include <impl/Kokkos_BitOps.hpp>
 #include <stdint.h>
 
 #include <cstdio>
@@ -52,122 +53,57 @@
 #include <iostream>
 #include <iomanip>
 
-namespace Kokkos { namespace Impl {
+namespace Kokkos {
+namespace Impl {
 
 KOKKOS_FORCEINLINE_FUNCTION
-unsigned rotate_right(unsigned i, int r)
+unsigned rotate_right( unsigned i, int r )
 {
-  enum { size = static_cast<int>(sizeof(unsigned)*CHAR_BIT) };
-  return r ? ((i >> r) | (i << (size-r))) : i ;
+  enum { size = static_cast<int>( sizeof(unsigned) * CHAR_BIT ) };
+  return r ? ( ( i >> r ) | ( i << ( size - r ) ) ) : i ;
 }
 
-KOKKOS_FORCEINLINE_FUNCTION
-int bit_scan_forward(unsigned i)
-{
-#if defined( __CUDA_ARCH__ )
-  return __ffs(i) - 1;
-#elif defined( __GNUC__ ) || defined( __GNUG__ )
-  return __builtin_ffs(i) - 1;
-#elif defined( __INTEL_COMPILER )
-  return _bit_scan_forward(i);
-#else
-
-  unsigned t = 1u;
-  int r = 0;
-  while (i && (i & t == 0))
-  {
-    t = t << 1;
-    ++r;
-  }
-  return r;
-#endif
-}
-
-
-KOKKOS_FORCEINLINE_FUNCTION
-int bit_scan_reverse(unsigned i)
-{
-  enum { shift = static_cast<int>(sizeof(unsigned)*CHAR_BIT - 1) };
-#if defined( __CUDA_ARCH__ )
-  return shift - __clz(i);
-#elif defined( __GNUC__ ) || defined( __GNUG__ )
-  return shift - __builtin_clz(i);
-#elif defined( __INTEL_COMPILER )
-  return _bit_scan_reverse(i);
-#else
-  unsigned t = 1u << shift;
-  int r = 0;
-  while (i && (i & t == 0))
-  {
-    t = t >> 1;
-    ++r;
-  }
-  return r;
-#endif
-}
-
-
-// count the bits set
-KOKKOS_FORCEINLINE_FUNCTION
-int popcount(unsigned i)
-{
-#if defined( __CUDA_ARCH__ )
-  return __popc(i);
-#elif defined( __GNUC__ ) || defined( __GNUG__ )
-  return __builtin_popcount(i);
-#elif defined ( __INTEL_COMPILER )
-  return _popcnt32(i);
-#else
-  // http://graphics.stanford.edu/~seander/bithacks.html#CountBitsSetNaive
-  i = i - ((i >> 1) & ~0u/3u);                                         // temp
-  i = (i & ~0u/15u*3u) + ((i >> 2) & ~0u/15u*3u);                      // temp
-  i = (i + (i >> 4)) & ~0u/255u*15u;                                   // temp
-  return (int)((i * (~0u/255u)) >> (sizeof(unsigned) - 1) * CHAR_BIT); // count
-#endif
-}
-
-
-template <typename Bitset>
+template < typename Bitset >
 struct BitsetCount
 {
-  typedef Bitset bitset_type;
-  typedef typename bitset_type::execution_space::execution_space execution_space;
-  typedef typename bitset_type::size_type size_type;
-  typedef size_type value_type;
+  typedef Bitset                                                  bitset_type;
+  typedef typename bitset_type::execution_space::execution_space  execution_space;
+  typedef typename bitset_type::size_type                         size_type;
+  typedef size_type                                               value_type;
 
   bitset_type m_bitset;
 
-  BitsetCount( bitset_type const& bitset)
+  BitsetCount( bitset_type const& bitset )
     : m_bitset(bitset)
   {}
 
   size_type apply() const
   {
     size_type count = 0u;
-    parallel_reduce(m_bitset.m_blocks.dimension_0(), *this, count);
+    parallel_reduce( m_bitset.m_blocks.dimension_0(), *this, count );
     return count;
   }
 
   KOKKOS_INLINE_FUNCTION
-  static void init( value_type & count)
+  void init( value_type & count ) const
   {
     count = 0u;
   }
 
   KOKKOS_INLINE_FUNCTION
-  static void join( volatile value_type & count, const volatile size_type & incr )
+  void join( volatile value_type & count, const volatile size_type & incr ) const
   {
     count += incr;
   }
 
   KOKKOS_INLINE_FUNCTION
-  void operator()( size_type i, value_type & count) const
+  void operator()( size_type i, value_type & count ) const
   {
-    count += popcount(m_bitset.m_blocks[i]);
+    count += bit_count( m_bitset.m_blocks[i] );
   }
 };
 
-}} //Kokkos::Impl
+} // namespace Impl
+} // namespace Kokkos
 
 #endif // KOKKOS_BITSET_IMPL_HPP
-
diff --git a/lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp b/lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp
index 3c4aed7bec..e71ccc0091 100644
--- a/lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp
+++ b/lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp
@@ -713,13 +713,20 @@ public:
   typedef Kokkos::Experimental::DynRankView< const T , device > const_dView0 ;
 
   typedef Kokkos::Experimental::DynRankView< T, device, Kokkos::MemoryUnmanaged > dView0_unmanaged ;
-  typedef typename dView0::host_mirror_space host ;
+  typedef typename dView0::host_mirror_space host_drv_space ;
+
+  typedef Kokkos::Experimental::View< T , device >        View0 ;
+  typedef Kokkos::Experimental::View< T* , device >       View1 ;
+  typedef Kokkos::Experimental::View< T******* , device > View7 ;
+
+  typedef typename View0::host_mirror_space  host_view_space ;
 
   TestDynViewAPI()
   {
+    run_test_resize_realloc();
     run_test_mirror();
-    run_test();
     run_test_scalar();
+    run_test();
     run_test_const();
     run_test_subview();
     run_test_subview_strided();
@@ -735,19 +742,147 @@ public:
     TestViewOperator_LeftAndRight< int , device , 1 >::testit(2);
   }
 
+  static void run_test_resize_realloc()
+  {
+    dView0 drv0("drv0", 10, 20, 30);
+    ASSERT_EQ( drv0.rank(), 3);
+
+    Kokkos::Experimental::resize(drv0, 5, 10);
+    ASSERT_EQ( drv0.rank(), 2);
+    ASSERT_EQ( drv0.dimension_0(), 5);
+    ASSERT_EQ( drv0.dimension_1(), 10);
+    ASSERT_EQ( drv0.dimension_2(), 1);
+
+    Kokkos::Experimental::realloc(drv0, 10, 20);
+    ASSERT_EQ( drv0.rank(), 2);
+    ASSERT_EQ( drv0.dimension_0(), 10);
+    ASSERT_EQ( drv0.dimension_1(), 20);
+    ASSERT_EQ( drv0.dimension_2(), 1);
+
+  }
+
   static void run_test_mirror()
   {
-    typedef Kokkos::Experimental::DynRankView< int , host > view_type ;
+    typedef Kokkos::Experimental::DynRankView< int , host_drv_space > view_type ;
     typedef typename view_type::HostMirror mirror_type ;
     view_type a("a");
     mirror_type am = Kokkos::Experimental::create_mirror_view(a);
     mirror_type ax = Kokkos::Experimental::create_mirror(a);
     ASSERT_EQ( & a() , & am() );
+    ASSERT_EQ( a.rank() , am.rank() );
+    ASSERT_EQ( ax.rank() , am.rank() );
+
+    if (Kokkos::HostSpace::execution_space::is_initialized() )
+    {
+      Kokkos::DynRankView<double, Kokkos::LayoutLeft, Kokkos::HostSpace> a_h("A",1000);
+      auto a_h2 = Kokkos::create_mirror(Kokkos::HostSpace(),a_h);
+      auto a_d = Kokkos::create_mirror(typename device::memory_space(),a_h);
+  
+      int equal_ptr_h_h2  = (a_h.data() ==a_h2.data())?1:0;
+      int equal_ptr_h_d   = (a_h.data() ==a_d. data())?1:0;
+      int equal_ptr_h2_d  = (a_h2.data()==a_d. data())?1:0;
+  
+      ASSERT_EQ(equal_ptr_h_h2,0);
+      ASSERT_EQ(equal_ptr_h_d ,0);
+      ASSERT_EQ(equal_ptr_h2_d,0);
+  
+      ASSERT_EQ(a_h.dimension_0(),a_h2.dimension_0());
+      ASSERT_EQ(a_h.dimension_0(),a_d .dimension_0());
+
+      ASSERT_EQ(a_h.rank(),a_h2.rank());
+      ASSERT_EQ(a_h.rank(),a_d.rank());
+    }
+    if (Kokkos::HostSpace::execution_space::is_initialized() )
+    {
+      Kokkos::DynRankView<double, Kokkos::LayoutRight, Kokkos::HostSpace> a_h("A",1000);
+      auto a_h2 = Kokkos::create_mirror(Kokkos::HostSpace(),a_h);
+      auto a_d = Kokkos::create_mirror(typename device::memory_space(),a_h);
+  
+      int equal_ptr_h_h2  = (a_h.data() ==a_h2.data())?1:0;
+      int equal_ptr_h_d   = (a_h.data() ==a_d. data())?1:0;
+      int equal_ptr_h2_d  = (a_h2.data()==a_d. data())?1:0;
+  
+      ASSERT_EQ(equal_ptr_h_h2,0);
+      ASSERT_EQ(equal_ptr_h_d ,0);
+      ASSERT_EQ(equal_ptr_h2_d,0);
+  
+      ASSERT_EQ(a_h.dimension_0(),a_h2.dimension_0());
+      ASSERT_EQ(a_h.dimension_0(),a_d .dimension_0());
+
+      ASSERT_EQ(a_h.rank(),a_h2.rank());
+      ASSERT_EQ(a_h.rank(),a_d.rank());
+    }
+
+    if (Kokkos::HostSpace::execution_space::is_initialized() )
+    {
+      Kokkos::DynRankView<double, Kokkos::LayoutLeft, Kokkos::HostSpace> a_h("A",1000);
+      auto a_h2 = Kokkos::create_mirror_view(Kokkos::HostSpace(),a_h);
+      auto a_d = Kokkos::create_mirror_view(typename device::memory_space(),a_h);
+  
+      int equal_ptr_h_h2  = a_h.data() ==a_h2.data()?1:0;
+      int equal_ptr_h_d   = a_h.data() ==a_d. data()?1:0;
+      int equal_ptr_h2_d  = a_h2.data()==a_d. data()?1:0;
+  
+      int is_same_memspace = std::is_same<Kokkos::HostSpace,typename device::memory_space>::value?1:0; 
+      ASSERT_EQ(equal_ptr_h_h2,1);
+      ASSERT_EQ(equal_ptr_h_d ,is_same_memspace);
+      ASSERT_EQ(equal_ptr_h2_d ,is_same_memspace);
+  
+      ASSERT_EQ(a_h.dimension_0(),a_h2.dimension_0());
+      ASSERT_EQ(a_h.dimension_0(),a_d .dimension_0());
+
+      ASSERT_EQ(a_h.rank(),a_h2.rank());
+      ASSERT_EQ(a_h.rank(),a_d.rank());
+    } 
+    if (Kokkos::HostSpace::execution_space::is_initialized() )
+    {
+      Kokkos::DynRankView<double, Kokkos::LayoutRight, Kokkos::HostSpace> a_h("A",1000);
+      auto a_h2 = Kokkos::create_mirror_view(Kokkos::HostSpace(),a_h);
+      auto a_d = Kokkos::create_mirror_view(typename device::memory_space(),a_h);
+  
+      int equal_ptr_h_h2  = a_h.data() ==a_h2.data()?1:0;
+      int equal_ptr_h_d   = a_h.data() ==a_d. data()?1:0;
+      int equal_ptr_h2_d  = a_h2.data()==a_d. data()?1:0;
+  
+      int is_same_memspace = std::is_same<Kokkos::HostSpace,typename device::memory_space>::value?1:0; 
+      ASSERT_EQ(equal_ptr_h_h2,1);
+      ASSERT_EQ(equal_ptr_h_d ,is_same_memspace);
+      ASSERT_EQ(equal_ptr_h2_d ,is_same_memspace);
+  
+      ASSERT_EQ(a_h.dimension_0(),a_h2.dimension_0());
+      ASSERT_EQ(a_h.dimension_0(),a_d .dimension_0());
+
+      ASSERT_EQ(a_h.rank(),a_h2.rank());
+      ASSERT_EQ(a_h.rank(),a_d.rank());
+    } 
+    if (Kokkos::HostSpace::execution_space::is_initialized() )
+    {
+      typedef Kokkos::DynRankView< int , Kokkos::LayoutStride , Kokkos::HostSpace > view_stride_type ;
+      unsigned order[] = { 6,5,4,3,2,1,0 }, dimen[] = { N0, N1, N2, 2, 2, 2, 2 }; //LayoutRight equivalent
+      view_stride_type a_h( "a" , Kokkos::LayoutStride::order_dimensions(7, order, dimen) );
+      auto a_h2 = Kokkos::create_mirror_view(Kokkos::HostSpace(),a_h);
+      auto a_d = Kokkos::create_mirror_view(typename device::memory_space(),a_h);
+  
+      int equal_ptr_h_h2  = a_h.data() ==a_h2.data()?1:0;
+      int equal_ptr_h_d   = a_h.data() ==a_d. data()?1:0;
+      int equal_ptr_h2_d  = a_h2.data()==a_d. data()?1:0;
+  
+      int is_same_memspace = std::is_same<Kokkos::HostSpace,typename device::memory_space>::value?1:0; 
+      ASSERT_EQ(equal_ptr_h_h2,1);
+      ASSERT_EQ(equal_ptr_h_d ,is_same_memspace);
+      ASSERT_EQ(equal_ptr_h2_d ,is_same_memspace);
+  
+      ASSERT_EQ(a_h.dimension_0(),a_h2.dimension_0());
+      ASSERT_EQ(a_h.dimension_0(),a_d .dimension_0());
+
+      ASSERT_EQ(a_h.rank(),a_h2.rank());
+      ASSERT_EQ(a_h.rank(),a_d.rank());
+    }
   }
 
   static void run_test_scalar()
   {
-    typedef typename dView0::HostMirror  hView0 ;
+    typedef typename dView0::HostMirror  hView0 ; //HostMirror of DynRankView is a DynRankView
 
     dView0 dx , dy ;
     hView0 hx , hy ;
@@ -765,6 +900,79 @@ public:
     Kokkos::Experimental::deep_copy( hy , dy );
 
     ASSERT_EQ( hx(), hy() );
+    ASSERT_EQ( dx.rank() , hx.rank() );
+    ASSERT_EQ( dy.rank() , hy.rank() );
+
+  //View - DynRankView Interoperability tests
+  // deep_copy DynRankView to View
+    View0 vx("vx");
+    Kokkos::deep_copy( vx , dx );
+    ASSERT_EQ( rank(dx) , rank(vx) );
+
+    View0 vy("vy");
+    Kokkos::deep_copy( vy , dy );
+    ASSERT_EQ( rank(dy) , rank(vy) );
+
+  // deep_copy View to DynRankView 
+    dView0 dxx("dxx");
+    Kokkos::deep_copy( dxx , vx );
+    ASSERT_EQ( rank(dxx) , rank(vx) );
+
+
+    View7 vcast = dx.ConstDownCast();
+    ASSERT_EQ( dx.dimension_0() , vcast.dimension_0() );
+    ASSERT_EQ( dx.dimension_1() , vcast.dimension_1() );
+    ASSERT_EQ( dx.dimension_2() , vcast.dimension_2() );
+    ASSERT_EQ( dx.dimension_3() , vcast.dimension_3() );
+    ASSERT_EQ( dx.dimension_4() , vcast.dimension_4() );
+
+    View7 vcast1( dy.ConstDownCast() );
+    ASSERT_EQ( dy.dimension_0() , vcast1.dimension_0() );
+    ASSERT_EQ( dy.dimension_1() , vcast1.dimension_1() );
+    ASSERT_EQ( dy.dimension_2() , vcast1.dimension_2() );
+    ASSERT_EQ( dy.dimension_3() , vcast1.dimension_3() );
+    ASSERT_EQ( dy.dimension_4() , vcast1.dimension_4() );
+
+  //View - DynRankView Interoperability tests
+  // copy View to DynRankView
+    dView0 dfromvx( vx );
+    auto hmx = Kokkos::create_mirror_view(dfromvx) ;
+    Kokkos::deep_copy(hmx , dfromvx);
+    auto hvx = Kokkos::create_mirror_view(vx) ;
+    Kokkos::deep_copy(hvx , vx);
+    ASSERT_EQ( rank(hvx) , rank(hmx) );
+    ASSERT_EQ( hvx.dimension_0() , hmx.dimension_0() );
+    ASSERT_EQ( hvx.dimension_1() , hmx.dimension_1() );
+
+  // copy-assign View to DynRankView
+    dView0 dfromvy = vy ;
+    auto hmy = Kokkos::create_mirror_view(dfromvy) ;
+    Kokkos::deep_copy(hmy , dfromvy);
+    auto hvy = Kokkos::create_mirror_view(vy) ;
+    Kokkos::deep_copy(hvy , vy);
+    ASSERT_EQ( rank(hvy) , rank(hmy) );
+    ASSERT_EQ( hvy.dimension_0() , hmy.dimension_0() );
+    ASSERT_EQ( hvy.dimension_1() , hmy.dimension_1() );
+
+
+    View7 vtest1("vtest1",2,2,2,2,2,2,2);
+    dView0 dfromv1( vtest1 );
+    ASSERT_EQ( dfromv1.rank() , vtest1.Rank );
+    ASSERT_EQ( dfromv1.dimension_0() , vtest1.dimension_0() );
+    ASSERT_EQ( dfromv1.dimension_1() , vtest1.dimension_1() );
+    ASSERT_EQ( dfromv1.use_count() , vtest1.use_count() );
+
+    dView0 dfromv2( vcast );
+    ASSERT_EQ( dfromv2.rank() , vcast.Rank );
+    ASSERT_EQ( dfromv2.dimension_0() , vcast.dimension_0() );
+    ASSERT_EQ( dfromv2.dimension_1() , vcast.dimension_1() );
+    ASSERT_EQ( dfromv2.use_count() , vcast.use_count() );
+
+    dView0 dfromv3 = vcast1;
+    ASSERT_EQ( dfromv3.rank() , vcast1.Rank );
+    ASSERT_EQ( dfromv3.dimension_0() , vcast1.dimension_0() );
+    ASSERT_EQ( dfromv3.dimension_1() , vcast1.dimension_1() );
+    ASSERT_EQ( dfromv3.use_count() , vcast1.use_count() );
   }
 
   static void run_test()
@@ -782,22 +990,32 @@ public:
       (void) thing;
     }
 
+    dView0 d_uninitialized(Kokkos::ViewAllocateWithoutInitializing("uninit"),10,20);
+    ASSERT_TRUE( d_uninitialized.data() != nullptr );
+    ASSERT_EQ( d_uninitialized.rank() , 2 );
+    ASSERT_EQ( d_uninitialized.dimension_0() , 10 );
+    ASSERT_EQ( d_uninitialized.dimension_1() , 20 );
+    ASSERT_EQ( d_uninitialized.dimension_2() , 1  );
+
     dView0 dx , dy , dz ;
     hView0 hx , hy , hz ;
 
-    ASSERT_TRUE( dx.ptr_on_device() == 0 );
-    ASSERT_TRUE( dy.ptr_on_device() == 0 );
-    ASSERT_TRUE( dz.ptr_on_device() == 0 );
+    ASSERT_TRUE( Kokkos::Experimental::is_dyn_rank_view<dView0>::value );
+    ASSERT_FALSE( Kokkos::Experimental::is_dyn_rank_view< Kokkos::View<double> >::value );
+
+    ASSERT_TRUE( dx.ptr_on_device() == 0 ); //Okay with UVM
+    ASSERT_TRUE( dy.ptr_on_device() == 0 );  //Okay with UVM
+    ASSERT_TRUE( dz.ptr_on_device() == 0 ); //Okay with UVM
     ASSERT_TRUE( hx.ptr_on_device() == 0 );
     ASSERT_TRUE( hy.ptr_on_device() == 0 );
     ASSERT_TRUE( hz.ptr_on_device() == 0 );
-    ASSERT_EQ( dx.dimension_0() , 0u );
-    ASSERT_EQ( dy.dimension_0() , 0u );
-    ASSERT_EQ( dz.dimension_0() , 0u );
+    ASSERT_EQ( dx.dimension_0() , 0u ); //Okay with UVM
+    ASSERT_EQ( dy.dimension_0() , 0u ); //Okay with UVM
+    ASSERT_EQ( dz.dimension_0() , 0u ); //Okay with UVM
     ASSERT_EQ( hx.dimension_0() , 0u );
     ASSERT_EQ( hy.dimension_0() , 0u );
     ASSERT_EQ( hz.dimension_0() , 0u );
-    ASSERT_EQ( dx.rank() , 0u );
+    ASSERT_EQ( dx.rank() , 0u ); //Okay with UVM
     ASSERT_EQ( hx.rank() , 0u );
 
     dx = dView0( "dx" , N1 , N2 , N3 );
@@ -806,11 +1024,11 @@ public:
     hx = hView0( "hx" , N1 , N2 , N3 );
     hy = hView0( "hy" , N1 , N2 , N3 );
 
-    ASSERT_EQ( dx.dimension_0() , unsigned(N1) );
-    ASSERT_EQ( dy.dimension_0() , unsigned(N1) );
+    ASSERT_EQ( dx.dimension_0() , unsigned(N1) ); //Okay with UVM
+    ASSERT_EQ( dy.dimension_0() , unsigned(N1) ); //Okay with UVM
     ASSERT_EQ( hx.dimension_0() , unsigned(N1) );
     ASSERT_EQ( hy.dimension_0() , unsigned(N1) );
-    ASSERT_EQ( dx.rank() , 3 );
+    ASSERT_EQ( dx.rank() , 3 ); //Okay with UVM
     ASSERT_EQ( hx.rank() , 3 );
 
     dx = dView0( "dx" , N0 , N1 , N2 , N3 );
@@ -823,19 +1041,23 @@ public:
     ASSERT_EQ( hx.dimension_0() , unsigned(N0) );
     ASSERT_EQ( hy.dimension_0() , unsigned(N0) );
     ASSERT_EQ( dx.rank() , 4 );
+    ASSERT_EQ( dy.rank() , 4 );
     ASSERT_EQ( hx.rank() , 4 );
+    ASSERT_EQ( hy.rank() , 4 );
 
     ASSERT_EQ( dx.use_count() , size_t(1) );
 
     dView0_unmanaged unmanaged_dx = dx;
     ASSERT_EQ( dx.use_count() , size_t(1) );
 
+
     dView0_unmanaged unmanaged_from_ptr_dx = dView0_unmanaged(dx.ptr_on_device(),
                                                               dx.dimension_0(),
                                                               dx.dimension_1(),
                                                               dx.dimension_2(),
                                                               dx.dimension_3());
 
+
     {
       // Destruction of this view should be harmless
       const_dView0 unmanaged_from_ptr_const_dx( dx.ptr_on_device() ,
@@ -888,6 +1110,19 @@ public:
     hx = Kokkos::Experimental::create_mirror( dx );
     hy = Kokkos::Experimental::create_mirror( dy );
 
+    ASSERT_EQ( hx.rank() , dx.rank() );
+    ASSERT_EQ( hy.rank() , dy.rank() );
+
+    ASSERT_EQ( hx.dimension_0() , unsigned(N0) );
+    ASSERT_EQ( hx.dimension_1() , unsigned(N1) );
+    ASSERT_EQ( hx.dimension_2() , unsigned(N2) );
+    ASSERT_EQ( hx.dimension_3() , unsigned(N3) );
+
+    ASSERT_EQ( hy.dimension_0() , unsigned(N0) );
+    ASSERT_EQ( hy.dimension_1() , unsigned(N1) );
+    ASSERT_EQ( hy.dimension_2() , unsigned(N2) );
+    ASSERT_EQ( hy.dimension_3() , unsigned(N3) );
+
     // T v1 = hx() ;    // Generates compile error as intended
     // T v2 = hx(0,0) ; // Generates compile error as intended
     // hx(0,0) = v2 ;   // Generates compile error as intended
@@ -990,7 +1225,9 @@ public:
       for ( size_t i3 = 0 ; i3 < N3 ; ++i3 ) {
         { ASSERT_EQ( hx(ip,i1,i2,i3) , T(0) ); }
       }}}}
+//    ASSERT_EQ( hx(0,0,0,0,0,0,0,0) , T(0) ); //Test rank8 op behaves properly - if implemented
     }
+
     dz = dx ; ASSERT_EQ( dx, dz); ASSERT_NE( dy, dz);
     dz = dy ; ASSERT_EQ( dy, dz); ASSERT_NE( dx, dz);
 
@@ -1006,6 +1243,35 @@ public:
     ASSERT_TRUE( dx.ptr_on_device() == 0 );
     ASSERT_TRUE( dy.ptr_on_device() == 0 );
     ASSERT_TRUE( dz.ptr_on_device() == 0 );
+
+  //View - DynRankView Interoperability tests
+    // deep_copy from view to dynrankview
+    const int testdim = 4;
+    dView0 dxx("dxx",testdim);
+    View1  vxx("vxx",testdim);
+    auto hvxx = Kokkos::create_mirror_view(vxx); 
+    for (int i = 0; i < testdim; ++i)
+      { hvxx(i) = i; }
+    Kokkos::deep_copy(vxx,hvxx);
+    Kokkos::deep_copy(dxx,vxx);
+    auto hdxx = Kokkos::create_mirror_view(dxx);
+    Kokkos::deep_copy(hdxx,dxx);
+    for (int i = 0; i < testdim; ++i)
+      { ASSERT_EQ( hvxx(i) , hdxx(i) ); }
+
+    ASSERT_EQ( rank(hdxx) , rank(hvxx) );
+    ASSERT_EQ( hdxx.dimension_0() , testdim );
+    ASSERT_EQ( hdxx.dimension_0() , hvxx.dimension_0() );
+
+    // deep_copy from dynrankview to view
+    View1 vdxx("vdxx",testdim);
+    auto hvdxx = Kokkos::create_mirror_view(vdxx);
+    Kokkos::deep_copy(hvdxx , hdxx);
+    ASSERT_EQ( rank(hdxx) , rank(hvdxx) );
+    ASSERT_EQ( hvdxx.dimension_0() , testdim );
+    ASSERT_EQ( hdxx.dimension_0() , hvdxx.dimension_0() );
+    for (int i = 0; i < testdim; ++i)
+      { ASSERT_EQ( hvxx(i) , hvdxx(i) ); }
   }
 
   typedef T DataType ;
@@ -1059,35 +1325,66 @@ public:
   //  N0 = 1000,N1 = 3,N2 = 5,N3 = 7 
     unsigned order[] = { 6,5,4,3,2,1,0 }, dimen[] = { N0, N1, N2, 2, 2, 2, 2 }; //LayoutRight equivalent
     sdView d7( "d7" , Kokkos::LayoutStride::order_dimensions(7, order, dimen) );
+    ASSERT_EQ( d7.rank() , 7 );
 
-    sdView ds0 = Kokkos::subdynrankview( d7 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ); //Should be rank0 subview
+    sdView ds0 = Kokkos::subdynrankview( d7 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ); 
+    ASSERT_EQ( ds0.rank() , 0 );
 
 //Basic test - ALL
-    sdView dsALL = Kokkos::Experimental::subdynrankview( d7 , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() ); //compiles and runs
+    sdView dsALL = Kokkos::Experimental::subdynrankview( d7 , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() ); 
+    ASSERT_EQ( dsALL.rank() , 7 );
 
-//  Send a single value for one rank
+//  Send a value to final rank returning rank 6 subview
     sdView dsm1 = Kokkos::Experimental::subdynrankview( d7 , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , 1 );
+    ASSERT_EQ( dsm1.rank() , 6 );
 
-//  Send a std::pair as a rank
+//  Send a std::pair as argument to a rank
     sdView dssp = Kokkos::Experimental::subdynrankview( d7 , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , std::pair<unsigned,unsigned>(1,2) );
+    ASSERT_EQ( dssp.rank() , 7 );
 
-//  Send a kokkos::pair as a rank; take default layout as input
+//  Send a kokkos::pair as argument to a rank; take default layout as input
     dView0 dd0("dd0" , N0 , N1 , N2 , 2 , 2 , 2 , 2 ); //default layout
+    ASSERT_EQ( dd0.rank() , 7 );
     sdView dtkp = Kokkos::Experimental::subdynrankview( dd0 , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::pair<unsigned,unsigned>(0,1) );
+    ASSERT_EQ( dtkp.rank() , 7 );
 
 // Return rank 7 subview, taking a pair as one argument, layout stride input
     sdView ds7 = Kokkos::Experimental::subdynrankview( d7 , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::pair<unsigned,unsigned>(0,1) );
+    ASSERT_EQ( ds7.rank() , 7 );
 
 // Default Layout DynRankView
     dView dv6("dv6" , N0 , N1 , N2 , N3 , 2 , 2 );
+    ASSERT_EQ( dv6.rank() , 6 );
 
 // DynRankView with LayoutRight
     typedef Kokkos::Experimental::DynRankView< T , Kokkos::LayoutRight , device > drView ;
     drView dr5( "dr5" , N0 , N1 , N2 , 2 , 2 );
+    ASSERT_EQ( dr5.rank() , 5 );
 
 // LayoutStride but arranged as LayoutRight
-    unsigned order3[] = { 4,3,2,1,0 }, dimen3[] = { N0, N1, N2, 2, 2 };
-    sdView d5( "d5" , Kokkos::LayoutStride::order_dimensions(5, order3, dimen3) );
+  // NOTE: unused arg_layout dimensions must be set to ~size_t(0) so that 
+  //  rank deduction can properly take place
+    unsigned order5[] = { 4,3,2,1,0 }, dimen5[] = { N0, N1, N2, 2, 2 };
+    Kokkos::LayoutStride ls = Kokkos::LayoutStride::order_dimensions(5, order5, dimen5);
+    ls.dimension[5] = ~size_t(0);
+    ls.dimension[6] = ~size_t(0);
+    ls.dimension[7] = ~size_t(0);
+    sdView d5("d5", ls);
+    ASSERT_EQ( d5.rank() , 5 );
+
+//  LayoutStride arranged as LayoutRight - commented out as example that fails unit test
+//    unsigned order5[] = { 4,3,2,1,0 }, dimen5[] = { N0, N1, N2, 2, 2 };
+//    sdView d5( "d5" , Kokkos::LayoutStride::order_dimensions(5, order5, dimen5) );
+//
+//  Fails the following unit test:
+//    ASSERT_EQ( d5.rank() , dr5.rank() );
+//
+//  Explanation: In construction of the Kokkos::LayoutStride below, since the 
+//   remaining dimensions are not specified, they will default to values of 0 
+//   rather than ~size_t(0). 
+//  When passed to the DynRankView constructor the default dimensions (of 0) 
+//   will be counted toward the dynamic rank and returning an incorrect value 
+//   (i.e. rank 7 rather than 5).
 
 // Check LayoutRight dr5 and LayoutStride d5 dimensions agree (as they should) 
     ASSERT_EQ( d5.dimension_0() , dr5.dimension_0() );
@@ -1100,21 +1397,21 @@ public:
 
 // Rank 5 subview of rank 5 dynamic rank view, layout stride input
     sdView ds5 = Kokkos::Experimental::subdynrankview( d5 , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::pair<unsigned,unsigned>(0,1) );
+    ASSERT_EQ( ds5.rank() , 5 );
 
 // Pass in extra ALL arguments beyond the rank of the DynRank View.
 // This behavior is allowed - ignore the extra ALL arguments when
 //  the src.rank() < number of arguments, but be careful!
     sdView ds5plus = Kokkos::Experimental::subdynrankview( d5 , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::ALL() , Kokkos::pair<unsigned,unsigned>(0,1) , Kokkos::ALL() );
 
+    ASSERT_EQ( ds5.rank() , ds5plus.rank() );
     ASSERT_EQ( ds5.dimension_0() , ds5plus.dimension_0() );
     ASSERT_EQ( ds5.dimension_4() , ds5plus.dimension_4() );
     ASSERT_EQ( ds5.dimension_5() , ds5plus.dimension_5() );
-    ASSERT_EQ( ds5.rank() , ds5plus.rank() );
-    ASSERT_EQ( ds5.rank() , 5 );
 
 #if ! defined( KOKKOS_HAVE_CUDA ) || defined ( KOKKOS_USE_CUDA_UVM )
-    ASSERT_EQ( & ds5(1,1,1,1) - & ds5plus(1,1,1,1) , 0 );
     ASSERT_EQ( & ds5(1,1,1,1,0) - & ds5plus(1,1,1,1,0) , 0 );
+    ASSERT_EQ( & ds5(1,1,1,1,0,0) - & ds5plus(1,1,1,1,0,0) , 0 );  // passing argument to rank beyond the view's rank is allowed iff it is a 0. 
 #endif
 
 // Similar test to rank 5 above, but create rank 4 subview
@@ -1131,9 +1428,9 @@ public:
 
   static void run_test_subview_strided()
   {
-    typedef Kokkos::Experimental::DynRankView < int , Kokkos::LayoutLeft , host > drview_left ;
-    typedef Kokkos::Experimental::DynRankView < int , Kokkos::LayoutRight , host > drview_right ;
-    typedef Kokkos::Experimental::DynRankView < int , Kokkos::LayoutStride , host > drview_stride ;
+    typedef Kokkos::Experimental::DynRankView < int , Kokkos::LayoutLeft , host_drv_space > drview_left ;
+    typedef Kokkos::Experimental::DynRankView < int , Kokkos::LayoutRight , host_drv_space > drview_right ;
+    typedef Kokkos::Experimental::DynRankView < int , Kokkos::LayoutStride , host_drv_space > drview_stride ;
 
     drview_left  xl2( "xl2", 100 , 200 );
     drview_right xr2( "xr2", 100 , 200 );
@@ -1159,35 +1456,37 @@ public:
     drview_left  xl4( "xl4", 10 , 20 , 30 , 40 );
     drview_right xr4( "xr4", 10 , 20 , 30 , 40 );
 
-    drview_stride yl4 = Kokkos::Experimental::subdynrankview( xl4 , 1 , Kokkos::ALL() , 2 , Kokkos::ALL() );
-    drview_stride yr4 = Kokkos::Experimental::subdynrankview( xr4 , 1 , Kokkos::ALL() , 2 , Kokkos::ALL() );
+    //Replace subdynrankview with subview - test
+    drview_stride yl4 = Kokkos::Experimental::subview( xl4 , 1 , Kokkos::ALL() , 2 , Kokkos::ALL() );
+    drview_stride yr4 = Kokkos::Experimental::subview( xr4 , 1 , Kokkos::ALL() , 2 , Kokkos::ALL() );
 
     ASSERT_EQ( yl4.dimension_0() , xl4.dimension_1() );
     ASSERT_EQ( yl4.dimension_1() , xl4.dimension_3() );
     ASSERT_EQ( yr4.dimension_0() , xr4.dimension_1() );
     ASSERT_EQ( yr4.dimension_1() , xr4.dimension_3() );
+    ASSERT_EQ( yl4.rank() , 2);
+    ASSERT_EQ( yr4.rank() , 2);
 
     ASSERT_EQ( & yl4(4,4) - & xl4(1,4,2,4) , 0 );
     ASSERT_EQ( & yr4(4,4) - & xr4(1,4,2,4) , 0 );
-
   }
 
   static void run_test_vector()
   {
     static const unsigned Length = 1000 , Count = 8 ;
 
-    typedef typename Kokkos::Experimental::DynRankView< T , Kokkos::LayoutLeft , host > multivector_type ; 
+    typedef typename Kokkos::Experimental::DynRankView< T , Kokkos::LayoutLeft , host_drv_space > multivector_type ; 
 
-    typedef typename Kokkos::Experimental::DynRankView< T , Kokkos::LayoutRight , host > multivector_right_type ;
+    typedef typename Kokkos::Experimental::DynRankView< T , Kokkos::LayoutRight , host_drv_space > multivector_right_type ;
 
     multivector_type mv = multivector_type( "mv" , Length , Count );
     multivector_right_type mv_right = multivector_right_type( "mv" , Length , Count );
 
-    typedef typename Kokkos::Experimental::DynRankView< T , Kokkos::LayoutStride , host > svector_type ;
-    typedef typename Kokkos::Experimental::DynRankView< T , Kokkos::LayoutStride , host > smultivector_type ;
-    typedef typename Kokkos::Experimental::DynRankView< const T , Kokkos::LayoutStride , host > const_svector_right_type ; //LayoutStride, not right; setup to match original ViewAPI calls... update
-    typedef typename Kokkos::Experimental::DynRankView< const T , Kokkos::LayoutStride , host > const_svector_type ;
-    typedef typename Kokkos::Experimental::DynRankView< const T , Kokkos::LayoutStride , host > const_smultivector_type ;
+    typedef typename Kokkos::Experimental::DynRankView< T , Kokkos::LayoutStride , host_drv_space > svector_type ;
+    typedef typename Kokkos::Experimental::DynRankView< T , Kokkos::LayoutStride , host_drv_space > smultivector_type ;
+    typedef typename Kokkos::Experimental::DynRankView< const T , Kokkos::LayoutStride , host_drv_space > const_svector_right_type ; 
+    typedef typename Kokkos::Experimental::DynRankView< const T , Kokkos::LayoutStride , host_drv_space > const_svector_type ;
+    typedef typename Kokkos::Experimental::DynRankView< const T , Kokkos::LayoutStride , host_drv_space > const_smultivector_type ;
 
     svector_type v1 = Kokkos::Experimental::subdynrankview( mv , Kokkos::ALL() , 0 );
     svector_type v2 = Kokkos::Experimental::subdynrankview( mv , Kokkos::ALL() , 1 );
@@ -1251,7 +1550,6 @@ public:
     const_smultivector_type cmv( mv );
     typename smultivector_type::const_type cmvX( cmv );
     typename const_smultivector_type::const_type ccmvX( cmv );
-
   }
 };
 
diff --git a/lib/kokkos/containers/unit_tests/TestDynamicView.hpp b/lib/kokkos/containers/unit_tests/TestDynamicView.hpp
index fd37f16f0a..7e3ca005f4 100644
--- a/lib/kokkos/containers/unit_tests/TestDynamicView.hpp
+++ b/lib/kokkos/containers/unit_tests/TestDynamicView.hpp
@@ -61,8 +61,7 @@ struct TestDynamicView
   typedef typename Space::execution_space  execution_space ;
   typedef typename Space::memory_space     memory_space ;
 
-  typedef Kokkos::Experimental::MemoryPool< memory_space , execution_space >
-    memory_pool_type ;
+  typedef Kokkos::Experimental::MemoryPool<typename Space::device_type> memory_pool_type;
 
   typedef Kokkos::Experimental::DynamicView<Scalar*,Space> view_type;
 
@@ -129,11 +128,9 @@ struct TestDynamicView
     typedef Kokkos::TeamPolicy<execution_space,TEST> TestPolicy ;
     typedef Kokkos::TeamPolicy<execution_space,VERIFY> VerifyPolicy ;
 
-    const unsigned int chunk_size = 1024 ;
-
 // printf("TestDynamicView::run(%d) construct memory pool\n",arg_total_size);
 
-    memory_pool_type pool( memory_space() , chunk_size , arg_total_size * sizeof(Scalar) );
+    memory_pool_type pool( memory_space() , arg_total_size * sizeof(Scalar) * 1.2 );
 
 // printf("TestDynamicView::run(%d) construct dynamic view\n",arg_total_size);
 
diff --git a/lib/kokkos/core/cmake/KokkosCore_config.h.in b/lib/kokkos/core/cmake/KokkosCore_config.h.in
index 961ad58ec5..27e3ba1c31 100644
--- a/lib/kokkos/core/cmake/KokkosCore_config.h.in
+++ b/lib/kokkos/core/cmake/KokkosCore_config.h.in
@@ -34,6 +34,7 @@
 #cmakedefine KOKKOS_HAVE_Winthread
 #cmakedefine KOKKOS_HAVE_OPENMP
 #cmakedefine KOKKOS_HAVE_HWLOC
+#cmakedefine KOKKOS_HAVE_DEBUG
 #cmakedefine KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK
 #cmakedefine KOKKOS_HAVE_CXX11
 #cmakedefine KOKKOS_HAVE_CUSPARSE
diff --git a/lib/kokkos/core/perf_test/CMakeLists.txt b/lib/kokkos/core/perf_test/CMakeLists.txt
index 34aa81e92c..d93ca14d96 100644
--- a/lib/kokkos/core/perf_test/CMakeLists.txt
+++ b/lib/kokkos/core/perf_test/CMakeLists.txt
@@ -8,11 +8,22 @@ SET(SOURCES
   PerfTestCuda.cpp
   )
 
+# Per #374, we always want to build this test, but we only want to run
+# it as a PERFORMANCE test.  That's why we separate building the test
+# from running the test.
+
+TRIBITS_ADD_EXECUTABLE(
+  PerfTestExec
+  SOURCES ${SOURCES}
+  COMM serial mpi
+  TESTONLYLIBS kokkos_gtest
+  )
+
 TRIBITS_ADD_EXECUTABLE_AND_TEST(
   PerfTest
-  SOURCES ${SOURCES}
+  NAME PerfTestExec
   COMM serial mpi
   NUM_MPI_PROCS 1
+  CATEGORIES PERFORMANCE
   FAIL_REGULAR_EXPRESSION "  FAILED  "
-  TESTONLYLIBS kokkos_gtest
   )
diff --git a/lib/kokkos/core/perf_test/PerfTestCuda.cpp b/lib/kokkos/core/perf_test/PerfTestCuda.cpp
index 4a4bc13cd4..524beb8b90 100644
--- a/lib/kokkos/core/perf_test/PerfTestCuda.cpp
+++ b/lib/kokkos/core/perf_test/PerfTestCuda.cpp
@@ -159,7 +159,7 @@ struct TextureFetch
 
     Kokkos::Cuda::fence();
 
-    Kokkos::Impl::Timer timer;
+    Kokkos::Timer timer;
     for (int j=0; j<10; ++j) {
       RandomReduce f(array,indexes);
       f.apply(reduce);
diff --git a/lib/kokkos/core/perf_test/PerfTestGramSchmidt.hpp b/lib/kokkos/core/perf_test/PerfTestGramSchmidt.hpp
index 03805dcdf5..516696b141 100644
--- a/lib/kokkos/core/perf_test/PerfTestGramSchmidt.hpp
+++ b/lib/kokkos/core/perf_test/PerfTestGramSchmidt.hpp
@@ -153,7 +153,7 @@ struct ModifiedGramSchmidt
 
     Kokkos::deep_copy( one , (Scalar) 1 );
 
-    Kokkos::Impl::Timer timer ;
+    Kokkos::Timer timer ;
 
     for ( size_type j = 0 ; j < count ; ++j ) {
       // Reduction   : tmp = dot( Q(:,j) , Q(:,j) );
diff --git a/lib/kokkos/core/perf_test/PerfTestHexGrad.hpp b/lib/kokkos/core/perf_test/PerfTestHexGrad.hpp
index d13d9a49e8..ed5371f29c 100644
--- a/lib/kokkos/core/perf_test/PerfTestHexGrad.hpp
+++ b/lib/kokkos/core/perf_test/PerfTestHexGrad.hpp
@@ -252,7 +252,7 @@ struct HexGrad
     execution_space::fence();
 
     for ( int i = 0 ; i < iter ; ++i ) {
-      Kokkos::Impl::Timer timer ;
+      Kokkos::Timer timer ;
       Kokkos::parallel_for( count , HexGrad<execution_space>( coord , grad ) );
       execution_space::fence();
       const double dt = timer.seconds();
diff --git a/lib/kokkos/core/perf_test/test_atomic.cpp b/lib/kokkos/core/perf_test/test_atomic.cpp
index 882a5c615e..ab73f2505e 100644
--- a/lib/kokkos/core/perf_test/test_atomic.cpp
+++ b/lib/kokkos/core/perf_test/test_atomic.cpp
@@ -414,24 +414,27 @@ void Loop(int loop, int test, const char* type_name) {
 
   Kokkos::Impl::Timer timer;
   T res = LoopVariant<T>(loop,test);
-  double time1 = timer.seconds();
+  double time = timer.seconds();
 
   timer.reset();
   T resNonAtomic = LoopVariantNonAtomic<T>(loop,test);
-  double time2 = timer.seconds();
+  double timeNonAtomic = timer.seconds();
 
   timer.reset();
   T resSerial = LoopVariantSerial<T>(loop,test);
-  double time3 = timer.seconds();
+  double timeSerial = timer.seconds();
 
-  time1*=1e6/loop;
-  time2*=1e6/loop;
-  time3*=1e6/loop;
+  time         *=1e6/loop;
+  timeNonAtomic*=1e6/loop;
+  timeSerial   *=1e6/loop;
   //textcolor_standard();
   bool passed = true;
   if(resSerial!=res) passed = false;
   //if(!passed) textcolor(RESET,BLACK,YELLOW);
-  printf("%s Test %i %s  --- Loop: %i Value (S,A,NA): %e %e %e Time: %7.4e %7.4e %7.4e Size of Type %i)",type_name,test,passed?"PASSED":"FAILED",loop,1.0*resSerial,1.0*res,1.0*resNonAtomic,time1,time2,time3,(int)sizeof(T));
+  printf("%s Test %i %s  --- Loop: %i Value (S,A,NA): %e %e %e Time: %7.4e %7.4e %7.4e Size of Type %i)",
+         type_name,test,passed?"PASSED":"FAILED",loop,
+         1.0*resSerial,1.0*res,1.0*resNonAtomic,
+         timeSerial,time,timeNonAtomic,(int)sizeof(T));
   //if(!passed) textcolor_standard();
   printf("\n");
 }
@@ -452,7 +455,7 @@ void Test(int loop, int test, const char* type_name) {
 int main(int argc, char* argv[])
 {
   int type = -1;
-  int loop = 1000000;
+  int loop = 100000;
   int test = -1;
 
   for(int i=0;i<argc;i++)
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp b/lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp
index 9930cdf1ba..d1a560ee04 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp
@@ -124,15 +124,31 @@ unsigned long kokkos_impl_cuda_constant_memory_buffer[ Kokkos::Impl::CudaTraits:
 
 #endif
 
+
+namespace Kokkos {
+namespace Impl {
+  struct CudaLockArraysStruct {
+    int* atomic;
+    int* scratch;
+    int* threadid;
+  };
+}
+}
 __device__ __constant__
 #ifdef KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
 extern
 #endif
-int* kokkos_impl_cuda_atomic_lock_array ;
+Kokkos::Impl::CudaLockArraysStruct kokkos_impl_cuda_lock_arrays ;
 
 #define CUDA_SPACE_ATOMIC_MASK 0x1FFFF
 #define CUDA_SPACE_ATOMIC_XOR_MASK 0x15A39
 
+namespace Kokkos {
+namespace Impl {
+  void* cuda_resize_scratch_space(size_t bytes, bool force_shrink = false);
+}
+}
+
 namespace Kokkos {
 namespace Impl {
 __device__ inline
@@ -140,8 +156,7 @@ bool lock_address_cuda_space(void* ptr) {
   size_t offset = size_t(ptr);
   offset = offset >> 2;
   offset = offset & CUDA_SPACE_ATOMIC_MASK;
-  //offset = offset xor CUDA_SPACE_ATOMIC_XOR_MASK;
-  return (0 == atomicCAS(&kokkos_impl_cuda_atomic_lock_array[offset],0,1));
+  return (0 == atomicCAS(&kokkos_impl_cuda_lock_arrays.atomic[offset],0,1));
 }
 
 __device__ inline
@@ -149,8 +164,7 @@ void unlock_address_cuda_space(void* ptr) {
   size_t offset = size_t(ptr);
   offset = offset >> 2;
   offset = offset & CUDA_SPACE_ATOMIC_MASK;
-  //offset = offset xor CUDA_SPACE_ATOMIC_XOR_MASK;
-  atomicExch( &kokkos_impl_cuda_atomic_lock_array[ offset ], 0);
+  atomicExch( &kokkos_impl_cuda_lock_arrays.atomic[ offset ], 0);
 }
 
 }
@@ -232,8 +246,11 @@ struct CudaParallelLaunch< DriverType , true > {
       cudaMemcpyToSymbol( kokkos_impl_cuda_constant_memory_buffer , & driver , sizeof(DriverType) );
 
       #ifndef KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
-      int* lock_array_ptr = lock_array_cuda_space_ptr();
-      cudaMemcpyToSymbol( kokkos_impl_cuda_atomic_lock_array , & lock_array_ptr , sizeof(int*) );
+      Kokkos::Impl::CudaLockArraysStruct locks;
+      locks.atomic = atomic_lock_array_cuda_space_ptr(false);
+      locks.scratch = scratch_lock_array_cuda_space_ptr(false);
+      locks.threadid = threadid_lock_array_cuda_space_ptr(false);
+      cudaMemcpyToSymbol( kokkos_impl_cuda_lock_arrays , & locks , sizeof(CudaLockArraysStruct) );
       #endif
 
       // Invoke the driver function on the device
@@ -271,8 +288,11 @@ struct CudaParallelLaunch< DriverType , false > {
       #endif
 
       #ifndef KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
-      int* lock_array_ptr = lock_array_cuda_space_ptr();
-      cudaMemcpyToSymbol( kokkos_impl_cuda_atomic_lock_array , & lock_array_ptr , sizeof(int*) );
+      Kokkos::Impl::CudaLockArraysStruct locks;
+      locks.atomic = atomic_lock_array_cuda_space_ptr(false);
+      locks.scratch = scratch_lock_array_cuda_space_ptr(false);
+      locks.threadid = threadid_lock_array_cuda_space_ptr(false);
+      cudaMemcpyToSymbol( kokkos_impl_cuda_lock_arrays , & locks , sizeof(CudaLockArraysStruct) );
       #endif
 
       cuda_parallel_launch_local_memory< DriverType ><<< grid , block , shmem , stream >>>( driver );
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp
index 863488c3b0..a4f372d65d 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp
@@ -51,10 +51,10 @@
 /* only compile this file if CUDA is enabled for Kokkos */
 #ifdef KOKKOS_HAVE_CUDA
 
+#include <Kokkos_Core.hpp>
 #include <Kokkos_Cuda.hpp>
 #include <Kokkos_CudaSpace.hpp>
 
-#include <Cuda/Kokkos_Cuda_BasicAllocators.hpp>
 #include <Cuda/Kokkos_Cuda_Internal.hpp>
 #include <impl/Kokkos_Error.hpp>
 
@@ -107,68 +107,6 @@ void DeepCopyAsyncCuda( void * dst , const void * src , size_t n) {
 
 namespace Kokkos {
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-namespace {
-
-void texture_object_attach_impl(  Impl::AllocationTracker const & tracker
-                                , unsigned type_size
-                                , ::cudaChannelFormatDesc const & desc
-                               )
-{
-  enum { TEXTURE_BOUND_1D = 2u << 27 };
-
-  if ( tracker.attribute() == NULL ) {
-    // check for correct allocator
-    const bool ok_alloc =  tracker.allocator()->support_texture_binding();
-
-    const bool ok_count = (tracker.alloc_size() / type_size) < TEXTURE_BOUND_1D;
-
-    if (ok_alloc && ok_count) {
-      Impl::TextureAttribute * attr = new Impl::TextureAttribute( tracker.alloc_ptr(), tracker.alloc_size(), desc );
-      tracker.set_attribute( attr );
-    }
-    else {
-      std::ostringstream oss;
-      oss << "Error: Cannot attach texture object";
-      if (!ok_alloc) {
-        oss << ", incompatabile allocator " << tracker.allocator()->name();
-      }
-      if (!ok_count) {
-        oss << ", array " << tracker.label() << " too large";
-      }
-      oss << ".";
-      Kokkos::Impl::throw_runtime_exception( oss.str() );
-    }
-  }
-
-  if ( NULL == dynamic_cast<Impl::TextureAttribute *>(tracker.attribute()) ) {
-    std::ostringstream oss;
-    oss << "Error: Allocation " << tracker.label() << " already has an attribute attached.";
-    Kokkos::Impl::throw_runtime_exception( oss.str() );
-  }
-
-}
-
-} // unnamed namespace
-
-/*--------------------------------------------------------------------------*/
-
-Impl::AllocationTracker CudaSpace::allocate_and_track( const std::string & label, const size_t size )
-{
-  return Impl::AllocationTracker( allocator(), size, label);
-}
-
-void CudaSpace::texture_object_attach(  Impl::AllocationTracker const & tracker
-                                      , unsigned type_size
-                                      , ::cudaChannelFormatDesc const & desc
-                                     )
-{
-  texture_object_attach_impl( tracker, type_size, desc );
-}
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
 void CudaSpace::access_error()
 {
   const std::string msg("Kokkos::CudaSpace::access_error attempt to execute Cuda function from non-Cuda space" );
@@ -183,23 +121,6 @@ void CudaSpace::access_error( const void * const )
 
 /*--------------------------------------------------------------------------*/
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-Impl::AllocationTracker CudaUVMSpace::allocate_and_track( const std::string & label, const size_t size )
-{
-  return Impl::AllocationTracker( allocator(), size, label);
-}
-
-void CudaUVMSpace::texture_object_attach(  Impl::AllocationTracker const & tracker
-                                         , unsigned type_size
-                                         , ::cudaChannelFormatDesc const & desc
-                                        )
-{
-  texture_object_attach_impl( tracker, type_size, desc );
-}
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
 bool CudaUVMSpace::available()
 {
 #if defined( CUDA_VERSION ) && ( 6000 <= CUDA_VERSION ) && !defined(__APPLE__)
@@ -212,15 +133,6 @@ bool CudaUVMSpace::available()
 
 /*--------------------------------------------------------------------------*/
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-Impl::AllocationTracker CudaHostPinnedSpace::allocate_and_track( const std::string & label, const size_t size )
-{
-  return Impl::AllocationTracker( allocator(), size, label);
-}
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
 } // namespace Kokkos
 
 /*--------------------------------------------------------------------------*/
@@ -824,16 +736,26 @@ print_records( std::ostream & s , const Kokkos::CudaHostPinnedSpace & space , bo
 
 namespace Kokkos {
 namespace {
-  __global__ void init_lock_array_kernel() {
+  __global__ void init_lock_array_kernel_atomic() {
     unsigned i = blockIdx.x*blockDim.x + threadIdx.x;
 
     if(i<CUDA_SPACE_ATOMIC_MASK+1)
-      kokkos_impl_cuda_atomic_lock_array[i] = 0;
+      kokkos_impl_cuda_lock_arrays.atomic[i] = 0;
+  }
+
+  __global__ void init_lock_array_kernel_scratch_threadid(int N) {
+    unsigned i = blockIdx.x*blockDim.x + threadIdx.x;
+
+    if(i<N) {
+      kokkos_impl_cuda_lock_arrays.scratch[i] = 0;
+      kokkos_impl_cuda_lock_arrays.threadid[i] = 0;
+    }
   }
 }
 
+
 namespace Impl {
-int* lock_array_cuda_space_ptr(bool deallocate) {
+int* atomic_lock_array_cuda_space_ptr(bool deallocate) {
   static int* ptr = NULL;
   if(deallocate) {
     cudaFree(ptr);
@@ -845,15 +767,62 @@ int* lock_array_cuda_space_ptr(bool deallocate) {
   return ptr;
 }
 
-void init_lock_array_cuda_space() {
-  int is_initialized = 0;
+int* scratch_lock_array_cuda_space_ptr(bool deallocate) {
+  static int* ptr = NULL;
+  if(deallocate) {
+    cudaFree(ptr);
+    ptr = NULL;
+  }
+
+  if(ptr==NULL && !deallocate)
+    cudaMalloc(&ptr,sizeof(int)*(Cuda::concurrency()));
+  return ptr;
+}
+
+int* threadid_lock_array_cuda_space_ptr(bool deallocate) {
+  static int* ptr = NULL;
+  if(deallocate) {
+    cudaFree(ptr);
+    ptr = NULL;
+  }
+
+  if(ptr==NULL && !deallocate)
+    cudaMalloc(&ptr,sizeof(int)*(Cuda::concurrency()));
+  return ptr;
+}
+
+void init_lock_arrays_cuda_space() {
+  static int is_initialized = 0;
   if(! is_initialized) {
-    int* lock_array_ptr = lock_array_cuda_space_ptr();
-    cudaMemcpyToSymbol( kokkos_impl_cuda_atomic_lock_array , & lock_array_ptr , sizeof(int*) );
-    init_lock_array_kernel<<<(CUDA_SPACE_ATOMIC_MASK+255)/256,256>>>();
+    Kokkos::Impl::CudaLockArraysStruct locks;
+    locks.atomic = atomic_lock_array_cuda_space_ptr(false);
+    locks.scratch = scratch_lock_array_cuda_space_ptr(false);
+    locks.threadid = threadid_lock_array_cuda_space_ptr(false);
+    cudaMemcpyToSymbol( kokkos_impl_cuda_lock_arrays , & locks , sizeof(CudaLockArraysStruct) );
+    init_lock_array_kernel_atomic<<<(CUDA_SPACE_ATOMIC_MASK+255)/256,256>>>();
+    init_lock_array_kernel_scratch_threadid<<<(Kokkos::Cuda::concurrency()+255)/256,256>>>(Kokkos::Cuda::concurrency());
   }
 }
 
+void* cuda_resize_scratch_space(size_t bytes, bool force_shrink) {
+  static void* ptr = NULL;
+  static size_t current_size = 0;
+  if(current_size == 0) {
+    current_size = bytes;
+    ptr = Kokkos::kokkos_malloc<Kokkos::CudaSpace>("CudaSpace::ScratchMemory",current_size);
+  }
+  if(bytes > current_size) {
+    current_size = bytes;
+    ptr = Kokkos::kokkos_realloc<Kokkos::CudaSpace>(ptr,current_size);
+  }
+  if((bytes < current_size) && (force_shrink)) {
+    current_size = bytes;
+    Kokkos::kokkos_free<Kokkos::CudaSpace>(ptr);
+    ptr = Kokkos::kokkos_malloc<Kokkos::CudaSpace>("CudaSpace::ScratchMemory",current_size);
+  }
+  return ptr;
+}
+
 }
 }
 #endif // KOKKOS_HAVE_CUDA
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Alloc.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Alloc.hpp
index 5746176274..10999ee57b 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Alloc.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Alloc.hpp
@@ -50,7 +50,6 @@
 #ifdef KOKKOS_HAVE_CUDA
 
 #include <impl/Kokkos_Traits.hpp>
-#include <impl/Kokkos_AllocationTracker.hpp> // AllocatorAttributeBase
 
 namespace Kokkos {
 namespace Impl {
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BasicAllocators.cpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BasicAllocators.cpp
deleted file mode 100644
index 05c73121bc..0000000000
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BasicAllocators.cpp
+++ /dev/null
@@ -1,198 +0,0 @@
-/*
-//@HEADER
-// ************************************************************************
-// 
-//                        Kokkos v. 2.0
-//              Copyright (2014) Sandia Corporation
-// 
-// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
-// the U.S. Government retains certain rights in this software.
-// 
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are
-// met:
-//
-// 1. Redistributions of source code must retain the above copyright
-// notice, this list of conditions and the following disclaimer.
-//
-// 2. Redistributions in binary form must reproduce the above copyright
-// notice, this list of conditions and the following disclaimer in the
-// documentation and/or other materials provided with the distribution.
-//
-// 3. Neither the name of the Corporation nor the names of the
-// contributors may be used to endorse or promote products derived from
-// this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
-// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
-// ************************************************************************
-//@HEADER
-*/
-
-#include <Kokkos_Macros.hpp>
-
-#if ! KOKKOS_USING_EXP_VIEW
-
-/* only compile this file if CUDA is enabled for Kokkos */
-#ifdef KOKKOS_HAVE_CUDA
-
-#include <impl/Kokkos_Error.hpp>
-#include <Cuda/Kokkos_Cuda_BasicAllocators.hpp>
-#include <Cuda/Kokkos_Cuda_Error.hpp>
-
-#include <sstream>
-
-namespace Kokkos { namespace Impl {
-
-
-/*--------------------------------------------------------------------------*/
-
-TextureAttribute::TextureAttribute(  void * const alloc_ptr
-                                   , size_t alloc_size
-                                   , cudaChannelFormatDesc const & desc
-                                  )
-  : m_tex_obj(0)
-{
-  cuda_device_synchronize();
-
-  struct cudaResourceDesc resDesc ;
-  struct cudaTextureDesc  texDesc ;
-
-  memset( & resDesc , 0 , sizeof(resDesc) );
-  memset( & texDesc , 0 , sizeof(texDesc) );
-
-  resDesc.resType                = cudaResourceTypeLinear ;
-  resDesc.res.linear.desc        = desc ;
-  resDesc.res.linear.sizeInBytes = alloc_size ;
-  resDesc.res.linear.devPtr      = alloc_ptr ;
-
-  CUDA_SAFE_CALL( cudaCreateTextureObject( & m_tex_obj , & resDesc, & texDesc, NULL) );
-
-  cuda_device_synchronize();
-}
-
-
-TextureAttribute::~TextureAttribute()
-{
-  if (m_tex_obj) {
-    cudaDestroyTextureObject( m_tex_obj );
-  }
-}
-
-/*--------------------------------------------------------------------------*/
-
-void * CudaMallocAllocator::allocate( size_t size )
-{
-  void * ptr = NULL;
-
-  CUDA_SAFE_CALL( cudaMalloc( &ptr, size ) );
-
-  return ptr;
-}
-
-void CudaMallocAllocator::deallocate( void * ptr, size_t /*size*/ )
-{
-  try {
-    CUDA_SAFE_CALL( cudaFree( ptr ) );
-  } catch(...) {}
-}
-
-void * CudaMallocAllocator::reallocate(void * old_ptr, size_t old_size, size_t new_size)
-{
-  void * ptr = old_ptr;
-  if (old_size != new_size) {
-    ptr = allocate( new_size );
-    size_t copy_size = old_size < new_size ? old_size : new_size;
-
-    CUDA_SAFE_CALL( cudaMemcpy( ptr , old_ptr , copy_size , cudaMemcpyDefault ) );
-
-    deallocate( old_ptr, old_size );
-  }
-  return ptr;
-}
-
-/*--------------------------------------------------------------------------*/
-
-void * CudaUVMAllocator::allocate( size_t size )
-{
-#if defined( CUDA_VERSION ) && ( 6000 <= CUDA_VERSION )
-  void * ptr = NULL;
-  CUDA_SAFE_CALL( cudaMallocManaged( &ptr, size, cudaMemAttachGlobal ) );
-  return ptr;
-#else
-  throw_runtime_exception( "CUDA VERSION does not support UVM" );
-  return NULL;
-#endif
-}
-
-void CudaUVMAllocator::deallocate( void * ptr, size_t /*size*/ )
-{
-  try {
-    CUDA_SAFE_CALL( cudaFree( ptr ) );
-  } catch(...) {}
-}
-
-void * CudaUVMAllocator::reallocate(void * old_ptr, size_t old_size, size_t new_size)
-{
-  void * ptr = old_ptr;
-  if (old_size != new_size) {
-    ptr = allocate( new_size );
-    size_t copy_size = old_size < new_size ? old_size : new_size;
-
-    CUDA_SAFE_CALL( cudaMemcpy( ptr , old_ptr , copy_size , cudaMemcpyDefault ) );
-
-    deallocate( old_ptr, old_size );
-  }
-  return ptr;
-}
-
-/*--------------------------------------------------------------------------*/
-
-void * CudaHostAllocator::allocate( size_t size )
-{
-  void * ptr = NULL;
-  CUDA_SAFE_CALL( cudaHostAlloc( &ptr , size , cudaHostAllocDefault ) );
-  return ptr;
-}
-
-void CudaHostAllocator::deallocate( void * ptr, size_t /*size*/ )
-{
-  try {
-    CUDA_SAFE_CALL( cudaFreeHost( ptr ) );
-  } catch(...) {}
-}
-
-void * CudaHostAllocator::reallocate(void * old_ptr, size_t old_size, size_t new_size)
-{
-  void * ptr = old_ptr;
-  if (old_size != new_size) {
-    ptr = allocate( new_size );
-    size_t copy_size = old_size < new_size ? old_size : new_size;
-
-    CUDA_SAFE_CALL( cudaMemcpy( ptr , old_ptr , copy_size , cudaMemcpyHostToHost ) );
-
-    deallocate( old_ptr, old_size );
-  }
-  return ptr;
-}
-
-/*--------------------------------------------------------------------------*/
-
-}} // namespace Kokkos::Impl
-
-#endif //KOKKOS_HAVE_CUDA
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BasicAllocators.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BasicAllocators.hpp
deleted file mode 100644
index 80bc986ad7..0000000000
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_BasicAllocators.hpp
+++ /dev/null
@@ -1,190 +0,0 @@
-/*
-//@HEADER
-// ************************************************************************
-// 
-//                        Kokkos v. 2.0
-//              Copyright (2014) Sandia Corporation
-// 
-// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
-// the U.S. Government retains certain rights in this software.
-// 
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are
-// met:
-//
-// 1. Redistributions of source code must retain the above copyright
-// notice, this list of conditions and the following disclaimer.
-//
-// 2. Redistributions in binary form must reproduce the above copyright
-// notice, this list of conditions and the following disclaimer in the
-// documentation and/or other materials provided with the distribution.
-//
-// 3. Neither the name of the Corporation nor the names of the
-// contributors may be used to endorse or promote products derived from
-// this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
-// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
-// ************************************************************************
-//@HEADER
-*/
-
-#ifndef KOKKOS_CUDA_BASIC_ALLOCATORS_HPP
-#define KOKKOS_CUDA_BASIC_ALLOCATORS_HPP
-
-#include <Kokkos_Macros.hpp>
-
-#if ! KOKKOS_USING_EXP_VIEW
-
-/* only compile this file if CUDA is enabled for Kokkos */
-#ifdef KOKKOS_HAVE_CUDA
-
-#include <impl/Kokkos_Traits.hpp>
-#include <impl/Kokkos_AllocationTracker.hpp> // AllocatorAttributeBase
-
-namespace Kokkos { namespace Impl {
-
-
-// Cuda 5.0 <texture_types.h> defines 'cudaTextureObject_t'
-// to be an 'unsigned long long'.  This chould change with
-// future version of Cuda and this typedef would have to
-// change accordingly.
-
-#if defined( CUDA_VERSION ) && ( 5000 <= CUDA_VERSION )
-
-typedef enable_if<
-  sizeof(::cudaTextureObject_t) == sizeof(const void *) ,
-  ::cudaTextureObject_t >::type cuda_texture_object_type ;
-
-#else
-
-typedef const void * cuda_texture_object_type ;
-
-#endif
-
-
-struct TextureAttribute : public AllocatorAttributeBase
-{
-  cuda_texture_object_type m_tex_obj ;
-
-  TextureAttribute(  void * const alloc_ptr
-                   , size_t alloc_size
-                   , cudaChannelFormatDesc const & desc
-                  );
-
-  ~TextureAttribute();
-};
-
-/// class CudaUnmanagedAllocator
-/// does nothing when deallocate(ptr,size) is called
-struct CudaUnmanagedAllocator
-{
-  static const char * name()
-  {
-    return "Cuda Unmanaged Allocator";
-  }
-
-  static void deallocate(void * /*ptr*/, size_t /*size*/) {}
-
-  static bool support_texture_binding() { return true; }
-};
-
-/// class CudaUnmanagedAllocator
-/// does nothing when deallocate(ptr,size) is called
-struct CudaUnmanagedUVMAllocator
-{
-  static const char * name()
-  {
-    return "Cuda Unmanaged UVM Allocator";
-  }
-
-  static void deallocate(void * /*ptr*/, size_t /*size*/) {}
-
-  static bool support_texture_binding() { return true; }
-};
-
-/// class CudaUnmanagedHostAllocator
-/// does nothing when deallocate(ptr,size) is called
-class CudaUnmanagedHostAllocator
-{
-public:
-  static const char * name()
-  {
-    return "Cuda Unmanaged Host Allocator";
-  }
-  // Unmanaged deallocate does nothing
-  static void deallocate(void * /*ptr*/, size_t /*size*/) {}
-};
-
-/// class CudaMallocAllocator
-class CudaMallocAllocator
-{
-public:
-  static const char * name()
-  {
-    return "Cuda Malloc Allocator";
-  }
-
-  static void* allocate(size_t size);
-
-  static void deallocate(void * ptr, size_t);
-
-  static void * reallocate(void * old_ptr, size_t old_size, size_t new_size);
-
-  static bool support_texture_binding() { return true; }
-};
-
-/// class CudaUVMAllocator
-class CudaUVMAllocator
-{
-public:
-  static const char * name()
-  {
-    return "Cuda UVM Allocator";
-  }
-
-  static void* allocate(size_t size);
-
-  static void deallocate(void * ptr, size_t);
-
-  static void * reallocate(void * old_ptr, size_t old_size, size_t new_size);
-
-  static bool support_texture_binding() { return true; }
-};
-
-/// class CudaHostAllocator
-class CudaHostAllocator
-{
-public:
-  static const char * name()
-  {
-    return "Cuda Host Allocator";
-  }
-
-  static void* allocate(size_t size);
-
-  static void deallocate(void * ptr, size_t);
-
-  static void * reallocate(void * old_ptr, size_t old_size, size_t new_size);
-};
-
-
-}} // namespace Kokkos::Impl
-
-#endif //KOKKOS_HAVE_CUDA
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-#endif //KOKKOS_CUDA_BASIC_ALLOCATORS_HPP
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp
index 02c85d268c..2d8d07d077 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp
@@ -51,8 +51,8 @@
 
 #include <Cuda/Kokkos_Cuda_Error.hpp>
 #include <Cuda/Kokkos_Cuda_Internal.hpp>
-#include <impl/Kokkos_AllocationTracker.hpp>
 #include <impl/Kokkos_Error.hpp>
+#include <impl/Kokkos_Profiling_Interface.hpp>
 
 /*--------------------------------------------------------------------------*/
 /* Standard 'C' libraries */
@@ -70,7 +70,7 @@ __device__ __constant__
 unsigned long kokkos_impl_cuda_constant_memory_buffer[ Kokkos::Impl::CudaTraits::ConstantMemoryUsage / sizeof(unsigned long) ] ;
 
 __device__ __constant__
-int* kokkos_impl_cuda_atomic_lock_array ;
+Kokkos::Impl::CudaLockArraysStruct kokkos_impl_cuda_lock_arrays ;
 
 #endif
 
@@ -190,7 +190,7 @@ namespace {
 
 class CudaInternalDevices {
 public:
-  enum { MAXIMUM_DEVICE_COUNT = 8 };
+  enum { MAXIMUM_DEVICE_COUNT = 64 };
   struct cudaDeviceProp  m_cudaProp[ MAXIMUM_DEVICE_COUNT ] ;
   int                    m_cudaDevCount ;
 
@@ -206,6 +206,9 @@ CudaInternalDevices::CudaInternalDevices()
 
   CUDA_SAFE_CALL (cudaGetDeviceCount( & m_cudaDevCount ) );
 
+  if(m_cudaDevCount > MAXIMUM_DEVICE_COUNT) {
+    Kokkos::abort("Sorry, you have more GPUs per node than we thought anybody would ever have. Please report this to github.com/kokkos/kokkos.");
+  }
   for ( int i = 0 ; i < m_cudaDevCount ; ++i ) {
     CUDA_SAFE_CALL( cudaGetDeviceProperties( m_cudaProp + i , i ) );
   }
@@ -226,14 +229,6 @@ private:
   CudaInternal( const CudaInternal & );
   CudaInternal & operator = ( const CudaInternal & );
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-  AllocationTracker m_scratchFlagsTracker;
-  AllocationTracker m_scratchSpaceTracker;
-  AllocationTracker m_scratchUnifiedTracker;
-
-#endif
-
 
 public:
 
@@ -255,6 +250,8 @@ public:
   size_type * m_scratchUnified ;
   cudaStream_t * m_stream ;
 
+  static int was_initialized;
+  static int was_finalized;
 
   static CudaInternal & singleton();
 
@@ -293,6 +290,8 @@ public:
   size_type * scratch_unified( const size_type size );
 };
 
+int CudaInternal::was_initialized = 0;
+int CudaInternal::was_finalized = 0;
 //----------------------------------------------------------------------------
 
 
@@ -367,6 +366,10 @@ CudaInternal & CudaInternal::singleton()
 
 void CudaInternal::initialize( int cuda_device_id , int stream_count )
 {
+  if ( was_finalized ) Kokkos::abort("Calling Cuda::initialize after Cuda::finalize is illegal\n");
+  was_initialized = 1;
+  if ( is_initialized() ) return;
+
   enum { WordSize = sizeof(size_type) };
 
   if ( ! HostSpace::execution_space::is_initialized() ) {
@@ -526,11 +529,14 @@ void CudaInternal::initialize( int cuda_device_id , int stream_count )
   cudaThreadSetCacheConfig(cudaFuncCachePreferShared);
 
   // Init the array for used for arbitrarily sized atomics
-  Impl::init_lock_array_cuda_space();
+  Impl::init_lock_arrays_cuda_space();
 
   #ifdef KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
-  int* lock_array_ptr = lock_array_cuda_space_ptr();
-  cudaMemcpyToSymbol( kokkos_impl_cuda_atomic_lock_array , & lock_array_ptr , sizeof(int*) );
+  Kokkos::Impl::CudaLockArraysStruct locks;
+  locks.atomic = atomic_lock_array_cuda_space_ptr(false);
+  locks.scratch = scratch_lock_array_cuda_space_ptr(false);
+  locks.threadid = threadid_lock_array_cuda_space_ptr(false);
+  cudaMemcpyToSymbol( kokkos_impl_cuda_lock_arrays , & locks , sizeof(CudaLockArraysStruct) );
   #endif
 }
 
@@ -548,14 +554,6 @@ CudaInternal::scratch_flags( const Cuda::size_type size )
 
     m_scratchFlagsCount = ( size + sizeScratchGrain - 1 ) / sizeScratchGrain ;
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-    m_scratchFlagsTracker = CudaSpace::allocate_and_track( std::string("InternalScratchFlags") , sizeof( ScratchGrain ) * m_scratchFlagsCount );
-
-    m_scratchFlags = reinterpret_cast<size_type *>(m_scratchFlagsTracker.alloc_ptr());
-
-#else
-
     typedef Kokkos::Experimental::Impl::SharedAllocationRecord< Kokkos::CudaSpace , void > Record ;
 
     Record * const r = Record::allocate( Kokkos::CudaSpace()
@@ -566,9 +564,6 @@ CudaInternal::scratch_flags( const Cuda::size_type size )
 
     m_scratchFlags = reinterpret_cast<size_type *>( r->data() );
 
-#endif
-
-
     CUDA_SAFE_CALL( cudaMemset( m_scratchFlags , 0 , m_scratchFlagsCount * sizeScratchGrain ) );
   }
 
@@ -582,26 +577,15 @@ CudaInternal::scratch_space( const Cuda::size_type size )
 
     m_scratchSpaceCount = ( size + sizeScratchGrain - 1 ) / sizeScratchGrain ;
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-    m_scratchSpaceTracker = CudaSpace::allocate_and_track( std::string("InternalScratchSpace") , sizeof( ScratchGrain ) * m_scratchSpaceCount );
-
-    m_scratchSpace = reinterpret_cast<size_type *>(m_scratchSpaceTracker.alloc_ptr());
-
-#else
-
-    typedef Kokkos::Experimental::Impl::SharedAllocationRecord< Kokkos::CudaSpace , void > Record ;
-
-    Record * const r = Record::allocate( Kokkos::CudaSpace()
-                                       , "InternalScratchSpace"
-                                       , ( sizeof( ScratchGrain ) * m_scratchSpaceCount ) );
-
-    Record::increment( r );
+     typedef Kokkos::Experimental::Impl::SharedAllocationRecord< Kokkos::CudaSpace , void > Record ;
 
-    m_scratchSpace = reinterpret_cast<size_type *>( r->data() );
+     Record * const r = Record::allocate( Kokkos::CudaSpace()
+                                        , "InternalScratchSpace"
+                                        , ( sizeof( ScratchGrain ) * m_scratchSpaceCount ) );
 
-#endif
+     Record::increment( r );
 
+     m_scratchSpace = reinterpret_cast<size_type *>( r->data() );
   }
 
   return m_scratchSpace ;
@@ -615,14 +599,6 @@ CudaInternal::scratch_unified( const Cuda::size_type size )
 
     m_scratchUnifiedCount = ( size + sizeScratchGrain - 1 ) / sizeScratchGrain ;
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-    m_scratchUnifiedTracker = CudaHostPinnedSpace::allocate_and_track( std::string("InternalScratchUnified") , sizeof( ScratchGrain ) * m_scratchUnifiedCount );
-
-    m_scratchUnified = reinterpret_cast<size_type *>( m_scratchUnifiedTracker.alloc_ptr() );
-
-#else
-
     typedef Kokkos::Experimental::Impl::SharedAllocationRecord< Kokkos::CudaHostPinnedSpace , void > Record ;
 
     Record * const r = Record::allocate( Kokkos::CudaHostPinnedSpace()
@@ -632,9 +608,6 @@ CudaInternal::scratch_unified( const Cuda::size_type size )
     Record::increment( r );
 
     m_scratchUnified = reinterpret_cast<size_type *>( r->data() );
-
-#endif
-
   }
 
   return m_scratchUnified ;
@@ -644,9 +617,13 @@ CudaInternal::scratch_unified( const Cuda::size_type size )
 
 void CudaInternal::finalize()
 {
+  was_finalized = 1;
   if ( 0 != m_scratchSpace || 0 != m_scratchFlags ) {
 
-    lock_array_cuda_space_ptr(true);
+    atomic_lock_array_cuda_space_ptr(false);
+    scratch_lock_array_cuda_space_ptr(false);
+    threadid_lock_array_cuda_space_ptr(false);
+
     if ( m_stream ) {
       for ( size_type i = 1 ; i < m_streamCount ; ++i ) {
         cudaStreamDestroy( m_stream[i] );
@@ -655,14 +632,6 @@ void CudaInternal::finalize()
       ::free( m_stream );
     }
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-    m_scratchSpaceTracker.clear();
-    m_scratchFlagsTracker.clear();
-    m_scratchUnifiedTracker.clear();
-
-#else
-
     typedef Kokkos::Experimental::Impl::SharedAllocationRecord< CudaSpace > RecordCuda ;
     typedef Kokkos::Experimental::Impl::SharedAllocationRecord< CudaHostPinnedSpace > RecordHost ;
 
@@ -670,8 +639,6 @@ void CudaInternal::finalize()
     RecordCuda::decrement( RecordCuda::get_record( m_scratchSpace ) );
     RecordHost::decrement( RecordHost::get_record( m_scratchUnified ) );
 
-#endif
-
     m_cudaDev             = -1 ;
     m_multiProcCount      = 0 ;
     m_maxWarpCount        = 0 ;
@@ -730,7 +697,13 @@ int Cuda::is_initialized()
 { return Impl::CudaInternal::singleton().is_initialized(); }
 
 void Cuda::initialize( const Cuda::SelectDevice config , size_t num_instances )
-{ Impl::CudaInternal::singleton().initialize( config.cuda_device_id , num_instances ); }
+{
+  Impl::CudaInternal::singleton().initialize( config.cuda_device_id , num_instances );
+
+  #if (KOKKOS_ENABLE_PROFILING)
+    Kokkos::Profiling::initialize();
+  #endif
+}
 
 std::vector<unsigned>
 Cuda::detect_device_arch()
@@ -763,7 +736,13 @@ Cuda::size_type Cuda::device_arch()
 }
 
 void Cuda::finalize()
-{ Impl::CudaInternal::singleton().finalize(); }
+{
+  Impl::CudaInternal::singleton().finalize();
+
+  #if (KOKKOS_ENABLE_PROFILING)
+    Kokkos::Profiling::finalize();
+  #endif
+}
 
 Cuda::Cuda()
   : m_device( Impl::CudaInternal::singleton().m_cudaDev )
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp
index 328857d997..8b10d47f88 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp
@@ -57,17 +57,20 @@ template<class DriverType, bool Large>
 struct CudaGetMaxBlockSize;
 
 template<class DriverType, bool Large = (CudaTraits::ConstantMemoryUseThreshold < sizeof(DriverType))>
-int cuda_get_max_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra) {
-  return CudaGetMaxBlockSize<DriverType,Large>::get_block_size(f,vector_length, shmem_extra);
+int cuda_get_max_block_size(const typename DriverType::functor_type & f, const size_t vector_length,
+                            const size_t shmem_extra_block, const size_t shmem_extra_thread) {
+  return CudaGetMaxBlockSize<DriverType,Large>::get_block_size(f,vector_length, shmem_extra_block,shmem_extra_thread);
 }
 
 
 template<class DriverType>
 struct CudaGetMaxBlockSize<DriverType,true> {
-  static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra) {
+  static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length,
+                            const size_t shmem_extra_block, const size_t shmem_extra_thread) {
     int numBlocks;
     int blockSize=32;
-    int sharedmem = shmem_extra + FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
+    int sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) +
+                    FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
     cudaOccupancyMaxActiveBlocksPerMultiprocessor(
         &numBlocks,
         cuda_parallel_launch_constant_memory<DriverType>,
@@ -76,7 +79,8 @@ struct CudaGetMaxBlockSize<DriverType,true> {
 
     while (blockSize<1024 && numBlocks>0) {
       blockSize*=2;
-      sharedmem = shmem_extra + FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length);
+      sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) +
+                  FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
 
       cudaOccupancyMaxActiveBlocksPerMultiprocessor(
           &numBlocks,
@@ -91,11 +95,13 @@ struct CudaGetMaxBlockSize<DriverType,true> {
 
 template<class DriverType>
 struct CudaGetMaxBlockSize<DriverType,false> {
-  static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra) {
+  static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length,
+                            const size_t shmem_extra_block, const size_t shmem_extra_thread) {
     int numBlocks;
 
     int blockSize=32;
-    int sharedmem = shmem_extra + FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
+    int sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) +
+                    FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
     cudaOccupancyMaxActiveBlocksPerMultiprocessor(
         &numBlocks,
         cuda_parallel_launch_local_memory<DriverType>,
@@ -104,7 +110,8 @@ struct CudaGetMaxBlockSize<DriverType,false> {
 
     while (blockSize<1024 && numBlocks>0) {
       blockSize*=2;
-      sharedmem = shmem_extra + FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
+      sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) +
+                  FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
 
       cudaOccupancyMaxActiveBlocksPerMultiprocessor(
           &numBlocks,
@@ -123,13 +130,15 @@ template<class DriverType, bool Large>
 struct CudaGetOptBlockSize;
 
 template<class DriverType, bool Large = (CudaTraits::ConstantMemoryUseThreshold < sizeof(DriverType))>
-int cuda_get_opt_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra) {
-  return CudaGetOptBlockSize<DriverType,Large>::get_block_size(f,vector_length,shmem_extra);
+int cuda_get_opt_block_size(const typename DriverType::functor_type & f, const size_t vector_length,
+                            const size_t shmem_extra_block, const size_t shmem_extra_thread) {
+  return CudaGetOptBlockSize<DriverType,Large>::get_block_size(f,vector_length,shmem_extra_block,shmem_extra_thread);
 }
 
 template<class DriverType>
 struct CudaGetOptBlockSize<DriverType,true> {
-  static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra) {
+  static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length,
+                            const size_t shmem_extra_block, const size_t shmem_extra_thread) {
     int blockSize=16;
     int numBlocks;
     int sharedmem;
@@ -140,7 +149,8 @@ struct CudaGetOptBlockSize<DriverType,true> {
       blockSize*=2;
 
       //calculate the occupancy with that optBlockSize and check whether its larger than the largest one found so far
-      sharedmem = shmem_extra + FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
+      sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) +
+                  FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
       cudaOccupancyMaxActiveBlocksPerMultiprocessor(
               &numBlocks,
               cuda_parallel_launch_constant_memory<DriverType>,
@@ -157,7 +167,8 @@ struct CudaGetOptBlockSize<DriverType,true> {
 
 template<class DriverType>
 struct CudaGetOptBlockSize<DriverType,false> {
-  static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra) {
+  static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length,
+                            const size_t shmem_extra_block, const size_t shmem_extra_thread) {
     int blockSize=16;
     int numBlocks;
     int sharedmem;
@@ -166,7 +177,8 @@ struct CudaGetOptBlockSize<DriverType,false> {
 
     while(blockSize<1024) {
       blockSize*=2;
-      sharedmem = shmem_extra + FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
+      sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) +
+                  FunctorTeamShmemSize< typename DriverType::functor_type  >::value( f , blockSize/vector_length );
 
       cudaOccupancyMaxActiveBlocksPerMultiprocessor(
               &numBlocks,
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp
index 99296dd273..7afa06fdf5 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp
@@ -99,13 +99,13 @@ public:
 
   __device__ inline
   const execution_space::scratch_memory_space & team_shmem() const
-    { return m_team_shared.set_team_thread_mode(1,0) ; }
+    { return m_team_shared.set_team_thread_mode(0,1,0) ; }
   __device__ inline
-  const execution_space::scratch_memory_space & team_scratch(int) const
-    { return m_team_shared.set_team_thread_mode(1,0) ; }
+  const execution_space::scratch_memory_space & team_scratch(const int& level) const
+    { return m_team_shared.set_team_thread_mode(level,1,0) ; }
   __device__ inline
-  const execution_space::scratch_memory_space & thread_scratch(int) const
-    { return m_team_shared.set_team_thread_mode(team_size(),team_rank()) ; }
+  const execution_space::scratch_memory_space & thread_scratch(const int& level) const
+    { return m_team_shared.set_team_thread_mode(level,team_size(),team_rank()) ; }
 
   __device__ inline int league_rank() const { return m_league_rank ; }
   __device__ inline int league_size() const { return m_league_size ; }
@@ -122,6 +122,7 @@ public:
     }
     team_barrier();
     value = sh_val;
+    team_barrier();
   }
 
 #ifdef KOKKOS_HAVE_CXX11
@@ -203,10 +204,12 @@ public:
   CudaTeamMember( void * shared
                 , const int shared_begin
                 , const int shared_size
+                , void*     scratch_level_1_ptr
+                , const int scratch_level_1_size
                 , const int arg_league_rank
                 , const int arg_league_size )
     : m_team_reduce( shared )
-    , m_team_shared( ((char *)shared) + shared_begin , shared_size )
+    , m_team_shared( ((char *)shared) + shared_begin , shared_size,  scratch_level_1_ptr, scratch_level_1_size)
     , m_league_rank( arg_league_rank ) 
     , m_league_size( arg_league_size ) 
     {}
@@ -214,11 +217,11 @@ public:
 #else
 
   const execution_space::scratch_memory_space & team_shmem() const
-    { return m_team_shared.set_team_thread_mode(1,0) ; }
-  const execution_space::scratch_memory_space & team_scratch(int) const
-    { return m_team_shared.set_team_thread_mode(1,0) ; }
-  const execution_space::scratch_memory_space & thread_scratch(int) const
-    { return m_team_shared.set_team_thread_mode(team_size(),team_rank()) ; }
+    { return m_team_shared.set_team_thread_mode(0, 1,0) ; }
+  const execution_space::scratch_memory_space & team_scratch(const int& level) const
+    { return m_team_shared.set_team_thread_mode(level,1,0) ; }
+  const execution_space::scratch_memory_space & thread_scratch(const int& level) const
+    { return m_team_shared.set_team_thread_mode(level,team_size(),team_rank()) ; }
 
   int league_rank() const {return 0;}
   int league_size() const {return 1;}
@@ -245,6 +248,8 @@ public:
   CudaTeamMember( void * shared
                 , const int shared_begin
                 , const int shared_end
+                , void*     scratch_level_1_ptr
+                , const int scratch_level_1_size
                 , const int arg_league_rank
                 , const int arg_league_size );
 
@@ -272,8 +277,8 @@ private:
   int m_league_size ;
   int m_team_size ;
   int m_vector_length ;
-  int m_team_scratch_size ;
-  int m_thread_scratch_size ;
+  int m_team_scratch_size[2] ;
+  int m_thread_scratch_size[2] ;
   int m_chunk_size;
 
 public:
@@ -285,8 +290,10 @@ public:
     m_league_size = p.m_league_size;
     m_team_size = p.m_team_size;
     m_vector_length = p.m_vector_length;
-    m_team_scratch_size = p.m_team_scratch_size;
-    m_thread_scratch_size = p.m_thread_scratch_size;
+    m_team_scratch_size[0] = p.m_team_scratch_size[0];
+    m_team_scratch_size[1] = p.m_team_scratch_size[1];
+    m_thread_scratch_size[0] = p.m_thread_scratch_size[0];
+    m_thread_scratch_size[1] = p.m_thread_scratch_size[1];
     m_chunk_size = p.m_chunk_size;
     return *this;
   }
@@ -332,14 +339,23 @@ public:
   inline int vector_length()   const { return m_vector_length ; }
   inline int team_size()   const { return m_team_size ; }
   inline int league_size() const { return m_league_size ; }
-  inline size_t scratch_size() const { return m_team_scratch_size + m_team_size*m_thread_scratch_size; }
+  inline int scratch_size(int level, int team_size_ = -1) const {
+    if(team_size_<0) team_size_ = m_team_size;
+    return m_team_scratch_size[level] + team_size_*m_thread_scratch_size[level];
+  }
+  inline size_t team_scratch_size(int level) const {
+    return m_team_scratch_size[level];
+  }
+  inline size_t thread_scratch_size(int level) const {
+    return m_thread_scratch_size[level];
+  }
 
   TeamPolicyInternal()
     : m_league_size( 0 )
     , m_team_size( 0 )
     , m_vector_length( 0 )
-    , m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    , m_team_scratch_size {0,0}
+    , m_thread_scratch_size {0,0}
     , m_chunk_size ( 32 ) 
    {}
 
@@ -351,8 +367,8 @@ public:
     : m_league_size( league_size_ )
     , m_team_size( team_size_request )
     , m_vector_length( vector_length_request )
-    , m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    , m_team_scratch_size {0,0}
+    , m_thread_scratch_size {0,0}
     , m_chunk_size ( 32 )
     {
       // Allow only power-of-two vector_length
@@ -378,8 +394,8 @@ public:
     : m_league_size( league_size_ )
     , m_team_size( -1 )
     , m_vector_length( vector_length_request )
-    , m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    , m_team_scratch_size {0,0}
+    , m_thread_scratch_size {0,0}
     , m_chunk_size ( 32 )
     {
       // Allow only power-of-two vector_length
@@ -398,8 +414,8 @@ public:
     : m_league_size( league_size_ )
     , m_team_size( team_size_request )
     , m_vector_length ( vector_length_request )
-    , m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    , m_team_scratch_size {0,0}
+    , m_thread_scratch_size {0,0}
     , m_chunk_size ( 32 )
     {
       // Allow only power-of-two vector_length
@@ -423,8 +439,8 @@ public:
     : m_league_size( league_size_ )
     , m_team_size( -1 )
     , m_vector_length ( vector_length_request )
-    , m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    , m_team_scratch_size {0,0}
+    , m_thread_scratch_size {0,0}
     , m_chunk_size ( 32 )
     {
       // Allow only power-of-two vector_length
@@ -448,26 +464,23 @@ public:
 
   /** \brief set per team scratch size for a specific level of the scratch hierarchy */
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerTeamValue& per_team) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_team_scratch_size = per_team.value;
+    p.m_team_scratch_size[level] = per_team.value;
     return p;
   };
 
   /** \brief set per thread scratch size for a specific level of the scratch hierarchy */
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerThreadValue& per_thread) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_thread_scratch_size = per_thread.value;
+    p.m_thread_scratch_size[level] = per_thread.value;
     return p;
   };
 
   /** \brief set per thread and per team scratch size for a specific level of the scratch hierarchy */
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerTeamValue& per_team, const PerThreadValue& per_thread) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_team_scratch_size = per_team.value;
-    p.m_thread_scratch_size = per_thread.value;
+    p.m_team_scratch_size[level] = per_team.value;
+    p.m_thread_scratch_size[level] = per_thread.value;
     return p;
   };
 
@@ -580,6 +593,8 @@ private:
   const size_type   m_vector_size ;
   const size_type   m_shmem_begin ;
   const size_type   m_shmem_size ;
+  void*             m_scratch_ptr[2] ;
+  const int         m_scratch_size[2] ;
 
   template< class TagType >
   __device__ inline
@@ -605,6 +620,8 @@ public:
         typename Policy::member_type( kokkos_impl_cuda_shared_memory<void>()
                                     , m_shmem_begin
                                     , m_shmem_size
+                                    , m_scratch_ptr[1]
+                                    , m_scratch_size[1]
                                     , league_rank
                                     , m_league_size ) );
     }
@@ -627,22 +644,24 @@ public:
     : m_functor( arg_functor )
     , m_league_size( arg_policy.league_size() )
     , m_team_size( 0 <= arg_policy.team_size() ? arg_policy.team_size() :
-        Kokkos::Impl::cuda_get_opt_block_size< ParallelFor >( arg_functor , arg_policy.vector_length(), arg_policy.scratch_size() ) / arg_policy.vector_length() )
+        Kokkos::Impl::cuda_get_opt_block_size< ParallelFor >( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length() )
     , m_vector_size( arg_policy.vector_length() )
     , m_shmem_begin( sizeof(double) * ( m_team_size + 2 ) )
-    , m_shmem_size( arg_policy.scratch_size() + FunctorTeamShmemSize< FunctorType >::value( m_functor , m_team_size ) )
+    , m_shmem_size( arg_policy.scratch_size(0,m_team_size) + FunctorTeamShmemSize< FunctorType >::value( m_functor , m_team_size ) )
+    , m_scratch_ptr{NULL,NULL}
+    , m_scratch_size{arg_policy.scratch_size(0,m_team_size),arg_policy.scratch_size(1,m_team_size)}
     {
       // Functor's reduce memory, team scan memory, and team shared memory depend upon team size.
+      m_scratch_ptr[1] = cuda_resize_scratch_space(m_scratch_size[1]*(Cuda::concurrency()/(m_team_size*m_vector_size)));
 
       const int shmem_size_total = m_shmem_begin + m_shmem_size ;
-
       if ( CudaTraits::SharedMemoryCapacity < shmem_size_total ) {
         Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelFor< Cuda > insufficient shared memory"));
       }
 
-      if ( m_team_size >
-           Kokkos::Impl::cuda_get_max_block_size< ParallelFor >
-                 ( arg_functor , arg_policy.vector_length(), arg_policy.scratch_size() ) / arg_policy.vector_length()) {
+      if ( int(m_team_size) >
+           int(Kokkos::Impl::cuda_get_max_block_size< ParallelFor >
+                 ( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length())) {
         Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelFor< Cuda > requested too large team size."));
       }
     }
@@ -657,9 +676,10 @@ public:
 namespace Kokkos {
 namespace Impl {
 
-template< class FunctorType , class ... Traits >
+template< class FunctorType , class ReducerType, class ... Traits >
 class ParallelReduce< FunctorType
                     , Kokkos::RangePolicy< Traits ... >
+                    , ReducerType
                     , Kokkos::Cuda 
                     >
 {
@@ -671,8 +691,12 @@ private:
   typedef typename Policy::work_tag     WorkTag ;
   typedef typename Policy::member_type  Member ;
 
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType, WorkTag > ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueInit<   FunctorType, WorkTag > ValueInit ;
+  typedef Kokkos::Impl::if_c< std::is_same<InvalidType,ReducerType>::value, FunctorType, ReducerType> ReducerConditional;
+  typedef typename ReducerConditional::type ReducerTypeFwd;
+
+  typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd, WorkTag > ValueTraits ;
+  typedef Kokkos::Impl::FunctorValueInit<   ReducerTypeFwd, WorkTag > ValueInit ;
+  typedef Kokkos::Impl::FunctorValueJoin<   ReducerTypeFwd, WorkTag > ValueJoin ;
 
 public:
 
@@ -686,11 +710,20 @@ public:
 
   const FunctorType   m_functor ;
   const Policy        m_policy ;
+  const ReducerType   m_reducer ;
   const pointer_type  m_result_ptr ;
   size_type *         m_scratch_space ;
   size_type *         m_scratch_flags ;
   size_type *         m_unified_space ;
 
+  // Shall we use the shfl based reduction or not (only use it for static sized types of more than 128bit
+  enum { UseShflReduction = ((sizeof(value_type)>2*sizeof(double)) && ValueTraits::StaticValueSize) };
+  // Some crutch to do function overloading
+private:
+  typedef double DummyShflReductionType;
+  typedef int DummySHMEMReductionType;
+
+public:
   template< class TagType >
   __device__ inline
   typename std::enable_if< std::is_same< TagType , void >::value >::type
@@ -703,17 +736,20 @@ public:
   exec_range( const Member & i , reference_type update ) const
     { m_functor( TagType() , i , update ); }
 
-#if ! defined( KOKKOS_EXPERIMENTAL_CUDA_SHFL_REDUCTION )
+  __device__ inline
+  void operator() () const {
+    run(Kokkos::Impl::if_c<UseShflReduction, DummyShflReductionType, DummySHMEMReductionType>::select(1,1.0) );
+  }
 
   __device__ inline
-  void operator()(void) const
+  void run(const DummySHMEMReductionType& ) const
   {
     const integral_nonzero_constant< size_type , ValueTraits::StaticValueSize / sizeof(size_type) >
-      word_count( ValueTraits::value_size( m_functor ) / sizeof(size_type) );
+      word_count( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) / sizeof(size_type) );
 
     {
       reference_type value =
-        ValueInit::init( m_functor , kokkos_impl_cuda_shared_memory<size_type>() + threadIdx.y * word_count.value );
+        ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , kokkos_impl_cuda_shared_memory<size_type>() + threadIdx.y * word_count.value );
 
       // Number of blocks is bounded so that the reduction can be limited to two passes.
       // Each thread block is given an approximately equal amount of work to perform.
@@ -729,8 +765,8 @@ public:
     }
 
     // Reduce with final value at blockDim.y - 1 location.
-    if ( cuda_single_inter_block_reduce_scan<false,FunctorType,WorkTag>(
-           m_functor , blockIdx.x , gridDim.x ,
+    if ( cuda_single_inter_block_reduce_scan<false,ReducerTypeFwd,WorkTag>(
+           ReducerConditional::select(m_functor , m_reducer) , blockIdx.x , gridDim.x ,
            kokkos_impl_cuda_shared_memory<size_type>() , m_scratch_space , m_scratch_flags ) ) {
 
       // This is the final block with the final result at the final threads' location
@@ -739,7 +775,7 @@ public:
       size_type * const global = m_unified_space ? m_unified_space : m_scratch_space ;
 
       if ( threadIdx.y == 0 ) {
-        Kokkos::Impl::FunctorFinal< FunctorType , WorkTag >::final( m_functor , shared );
+        Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTag >::final( ReducerConditional::select(m_functor , m_reducer) , shared );
       }
 
       if ( CudaTraits::WarpSize < word_count.value ) { __syncthreads(); }
@@ -748,20 +784,18 @@ public:
     }
   }
 
-#else /* defined( KOKKOS_EXPERIMENTAL_CUDA_SHFL_REDUCTION ) */
-
   __device__ inline
-   void operator()(void) const
+   void run(const DummyShflReductionType&) const
    {
 
-     value_type value = 0;
-
+     value_type value;
+     ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , &value);
      // Number of blocks is bounded so that the reduction can be limited to two passes.
      // Each thread block is given an approximately equal amount of work to perform.
      // Accumulate the values for this block.
      // The accumulation ordering does not match the final pass, but is arithmatically equivalent.
 
-     const Policy range( m_policy , blockIdx.x , gridDim.x );
+     const WorkRange range( m_policy , blockIdx.x , gridDim.x );
 
      for ( Member iwork = range.begin() + threadIdx.y , iwork_end = range.end() ;
            iwork < iwork_end ; iwork += blockDim.y ) {
@@ -769,20 +803,23 @@ public:
      }
 
      pointer_type const result = (pointer_type) (m_unified_space ? m_unified_space : m_scratch_space) ;
+
      int max_active_thread = range.end()-range.begin() < blockDim.y ? range.end() - range.begin():blockDim.y;
-     max_active_thread = max_active_thread == 0?blockDim.y:max_active_thread;
-     if(Impl::cuda_inter_block_reduction<FunctorType,Impl::JoinAdd<value_type> >
-            (value,Impl::JoinAdd<value_type>(),m_scratch_space,result,m_scratch_flags,max_active_thread)) {
+
+     max_active_thread = (max_active_thread == 0)?blockDim.y:max_active_thread;
+
+    value_type init;
+    ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , &init);
+     if(Impl::cuda_inter_block_reduction<ReducerTypeFwd,ValueJoin,WorkTag>
+            (value,init,ValueJoin(ReducerConditional::select(m_functor , m_reducer)),m_scratch_space,result,m_scratch_flags,max_active_thread)) {
        const unsigned id = threadIdx.y*blockDim.x + threadIdx.x;
        if(id==0) {
-         Kokkos::Impl::FunctorFinal< FunctorType , WorkTag >::final( m_functor , (void*) &value );
+         Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTag >::final( ReducerConditional::select(m_functor , m_reducer) , (void*) &value );
          *result = value;
        }
      }
    }
 
-#endif
-
   // Determine block size constrained by shared memory:
   static inline
   unsigned local_block_size( const FunctorType & f )
@@ -799,20 +836,17 @@ public:
       if ( nwork ) {
         const int block_size = local_block_size( m_functor );
   
-        m_scratch_space = cuda_internal_scratch_space( ValueTraits::value_size( m_functor ) * block_size /* block_size == max block_count */ );
+        m_scratch_space = cuda_internal_scratch_space( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) * block_size /* block_size == max block_count */ );
         m_scratch_flags = cuda_internal_scratch_flags( sizeof(size_type) );
-        m_unified_space = cuda_internal_scratch_unified( ValueTraits::value_size( m_functor ) );
+        m_unified_space = cuda_internal_scratch_unified( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) );
   
         // REQUIRED ( 1 , N , 1 )
         const dim3 block( 1 , block_size , 1 );
         // Required grid.x <= block.y
         const dim3 grid( std::min( int(block.y) , int( ( nwork + block.y - 1 ) / block.y ) ) , 1 , 1 );
   
-#ifdef KOKKOS_EXPERIMENTAL_CUDA_SHFL_REDUCTION
-      const int shmem = 0;
-#else
-      const int shmem = cuda_single_inter_block_reduce_scan_shmem<false,FunctorType,WorkTag>( m_functor , block.y );
-#endif
+      const int shmem = UseShflReduction?0:cuda_single_inter_block_reduce_scan_shmem<false,FunctorType,WorkTag>( m_functor , block.y );
+
   
       CudaParallelLaunch< ParallelReduce >( *this, grid, block, shmem ); // copy to device and execute
   
@@ -820,18 +854,18 @@ public:
   
       if ( m_result_ptr ) {
         if ( m_unified_space ) {
-          const int count = ValueTraits::value_count( m_functor );
+          const int count = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer)  );
           for ( int i = 0 ; i < count ; ++i ) { m_result_ptr[i] = pointer_type(m_unified_space)[i] ; }
         }
         else {
-          const int size = ValueTraits::value_size( m_functor );
+          const int size = ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer)  );
           DeepCopy<HostSpace,CudaSpace>( m_result_ptr , m_scratch_space , size );
         }
       }
     }
     else {
       if (m_result_ptr) {
-        ValueInit::init( m_functor , m_result_ptr ); 
+        ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , m_result_ptr );
       }
     }
   }
@@ -840,21 +874,37 @@ public:
   ParallelReduce( const FunctorType  & arg_functor 
                 , const Policy       & arg_policy 
                 , const HostViewType & arg_result
-                )
+                , typename std::enable_if<
+                   Kokkos::is_view< HostViewType >::value
+                ,void*>::type = NULL)
   : m_functor( arg_functor )
   , m_policy(  arg_policy )
+  , m_reducer( InvalidType() )
   , m_result_ptr( arg_result.ptr_on_device() )
   , m_scratch_space( 0 )
   , m_scratch_flags( 0 )
   , m_unified_space( 0 )
   { }
+
+  ParallelReduce( const FunctorType  & arg_functor
+                , const Policy       & arg_policy
+                , const ReducerType & reducer)
+  : m_functor( arg_functor )
+  , m_policy(  arg_policy )
+  , m_reducer( reducer )
+  , m_result_ptr( reducer.result_view().ptr_on_device() )
+  , m_scratch_space( 0 )
+  , m_scratch_flags( 0 )
+  , m_unified_space( 0 )
+  { }
 };
 
 //----------------------------------------------------------------------------
 
-template< class FunctorType , class ... Properties >
+template< class FunctorType , class ReducerType, class ... Properties >
 class ParallelReduce< FunctorType
                     , Kokkos::TeamPolicy< Properties ... >
+                    , ReducerType
                     , Kokkos::Cuda
                     >
 {
@@ -864,18 +914,29 @@ private:
   typedef typename Policy::member_type  Member ;
   typedef typename Policy::work_tag     WorkTag ;
 
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType, WorkTag > ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueInit<   FunctorType, WorkTag > ValueInit ;
+  typedef Kokkos::Impl::if_c< std::is_same<InvalidType,ReducerType>::value, FunctorType, ReducerType> ReducerConditional;
+  typedef typename ReducerConditional::type ReducerTypeFwd;
+
+  typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd, WorkTag > ValueTraits ;
+  typedef Kokkos::Impl::FunctorValueInit<   ReducerTypeFwd, WorkTag > ValueInit ;
+  typedef Kokkos::Impl::FunctorValueJoin<   ReducerTypeFwd, WorkTag > ValueJoin ;
 
   typedef typename ValueTraits::pointer_type    pointer_type ;
   typedef typename ValueTraits::reference_type  reference_type ;
+  typedef typename ValueTraits::value_type      value_type ;
+
 
 public:
 
   typedef FunctorType      functor_type ;
   typedef Cuda::size_type  size_type ;
 
+  enum { UseShflReduction = (true && ValueTraits::StaticValueSize) };
+
 private:
+  typedef double DummyShflReductionType;
+  typedef int DummySHMEMReductionType;
+
 
   // Algorithmic constraints: blockDim.y is a power of two AND blockDim.y == blockDim.z == 1
   // shared memory utilization:
@@ -886,6 +947,7 @@ private:
   //
 
   const FunctorType   m_functor ;
+  const ReducerType   m_reducer ;
   const pointer_type  m_result_ptr ;
   size_type *         m_scratch_space ;
   size_type *         m_scratch_flags ;
@@ -893,8 +955,11 @@ private:
   size_type           m_team_begin ;
   size_type           m_shmem_begin ;
   size_type           m_shmem_size ;
+  void*               m_scratch_ptr[2] ;
+  int                 m_scratch_size[2] ;
   const size_type     m_league_size ;
   const size_type     m_team_size ;
+  const size_type     m_vector_size ;
 
   template< class TagType >
   __device__ inline
@@ -911,13 +976,18 @@ private:
 public:
 
   __device__ inline
-  void operator()(void) const
+  void operator() () const {
+    run(Kokkos::Impl::if_c<UseShflReduction, DummyShflReductionType, DummySHMEMReductionType>::select(1,1.0) );
+  }
+
+  __device__ inline
+  void run(const DummySHMEMReductionType&) const
   {
     const integral_nonzero_constant< size_type , ValueTraits::StaticValueSize / sizeof(size_type) >
-      word_count( ValueTraits::value_size( m_functor ) / sizeof(size_type) );
+      word_count( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) / sizeof(size_type) );
 
     reference_type value =
-      ValueInit::init( m_functor , kokkos_impl_cuda_shared_memory<size_type>() + threadIdx.y * word_count.value );
+      ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , kokkos_impl_cuda_shared_memory<size_type>() + threadIdx.y * word_count.value );
 
     // Iterate this block through the league
     for ( int league_rank = blockIdx.x ; league_rank < m_league_size ; league_rank += gridDim.x ) {
@@ -925,6 +995,8 @@ public:
         ( Member( kokkos_impl_cuda_shared_memory<char>() + m_team_begin
                                         , m_shmem_begin
                                         , m_shmem_size
+                                        , m_scratch_ptr[1]
+                                        , m_scratch_size[1]
                                         , league_rank
                                         , m_league_size )
         , value );
@@ -932,7 +1004,7 @@ public:
 
     // Reduce with final value at blockDim.y - 1 location.
     if ( cuda_single_inter_block_reduce_scan<false,FunctorType,WorkTag>(
-           m_functor , blockIdx.x , gridDim.x ,
+           ReducerConditional::select(m_functor , m_reducer) , blockIdx.x , gridDim.x ,
            kokkos_impl_cuda_shared_memory<size_type>() , m_scratch_space , m_scratch_flags ) ) {
 
       // This is the final block with the final result at the final threads' location
@@ -941,7 +1013,7 @@ public:
       size_type * const global = m_unified_space ? m_unified_space : m_scratch_space ;
 
       if ( threadIdx.y == 0 ) {
-        Kokkos::Impl::FunctorFinal< FunctorType , WorkTag >::final( m_functor , shared );
+        Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTag >::final( ReducerConditional::select(m_functor , m_reducer) , shared );
       }
 
       if ( CudaTraits::WarpSize < word_count.value ) { __syncthreads(); }
@@ -950,18 +1022,51 @@ public:
     }
   }
 
+  __device__ inline
+  void run(const DummyShflReductionType&) const
+  {
+    value_type value;
+    ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , &value);
+
+    // Iterate this block through the league
+    for ( int league_rank = blockIdx.x ; league_rank < m_league_size ; league_rank += gridDim.x ) {
+      this-> template exec_team< WorkTag >
+        ( Member( kokkos_impl_cuda_shared_memory<char>() + m_team_begin
+                                        , m_shmem_begin
+                                        , m_shmem_size
+                                        , m_scratch_ptr[1]
+                                        , m_scratch_size[1]
+                                        , league_rank
+                                        , m_league_size )
+        , value );
+    }
+
+    pointer_type const result = (pointer_type) (m_unified_space ? m_unified_space : m_scratch_space) ;
+
+    value_type init;
+    ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , &init);
+    if(Impl::cuda_inter_block_reduction<FunctorType,ValueJoin,WorkTag>
+           (value,init,ValueJoin(ReducerConditional::select(m_functor , m_reducer)),m_scratch_space,result,m_scratch_flags,blockDim.y)) {
+      const unsigned id = threadIdx.y*blockDim.x + threadIdx.x;
+      if(id==0) {
+        Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTag >::final( ReducerConditional::select(m_functor , m_reducer) , (void*) &value );
+        *result = value;
+      }
+    }
+  }
+
   inline
   void execute()
     {
-      const int block_count = std::min( m_league_size , m_team_size );
+      const int block_count = UseShflReduction? std::min( m_league_size , size_type(1024) )
+                                               :std::min( m_league_size , m_team_size );
 
-      m_scratch_space = cuda_internal_scratch_space( ValueTraits::value_size( m_functor ) * block_count );
+      m_scratch_space = cuda_internal_scratch_space( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) * block_count );
       m_scratch_flags = cuda_internal_scratch_flags( sizeof(size_type) );
-      m_unified_space = cuda_internal_scratch_unified( ValueTraits::value_size( m_functor ) );
+      m_unified_space = cuda_internal_scratch_unified( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) );
 
-      // REQUIRED DIMENSIONS ( 1 , N , 1 )
-      const dim3 block( 1 , m_team_size , 1 );
-      const dim3 grid( std::min( int(m_league_size) , int(m_team_size) ) , 1 , 1 );
+      const dim3 block( m_vector_size , m_team_size , 1 );
+      const dim3 grid( block_count , 1 , 1 );
       const int shmem_size_total = m_team_begin + m_shmem_begin + m_shmem_size ;
 
       CudaParallelLaunch< ParallelReduce >( *this, grid, block, shmem_size_total ); // copy to device and execute
@@ -970,11 +1075,11 @@ public:
 
       if ( m_result_ptr ) {
         if ( m_unified_space ) {
-          const int count = ValueTraits::value_count( m_functor );
+          const int count = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) );
           for ( int i = 0 ; i < count ; ++i ) { m_result_ptr[i] = pointer_type(m_unified_space)[i] ; }
         }
         else {
-          const int size = ValueTraits::value_size( m_functor );
+          const int size = ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) );
           DeepCopy<HostSpace,CudaSpace>( m_result_ptr, m_scratch_space, size );
         }
       }
@@ -984,8 +1089,11 @@ public:
   ParallelReduce( const FunctorType  & arg_functor 
                 , const Policy       & arg_policy 
                 , const HostViewType & arg_result
-                )
+                , typename std::enable_if<
+                                   Kokkos::is_view< HostViewType >::value
+                                ,void*>::type = NULL)
   : m_functor( arg_functor )
+  , m_reducer( InvalidType() )
   , m_result_ptr( arg_result.ptr_on_device() )
   , m_scratch_space( 0 )
   , m_scratch_flags( 0 )
@@ -993,39 +1101,107 @@ public:
   , m_team_begin( 0 )
   , m_shmem_begin( 0 )
   , m_shmem_size( 0 )
+  , m_scratch_ptr{NULL,NULL}
   , m_league_size( arg_policy.league_size() )
   , m_team_size( 0 <= arg_policy.team_size() ? arg_policy.team_size() :
-      Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce >( arg_functor , arg_policy.vector_length(), arg_policy.scratch_size() ) / arg_policy.vector_length() )
+      Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce >( arg_functor , arg_policy.vector_length(),
+                                                               arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) /
+      arg_policy.vector_length() )
+  , m_vector_size( arg_policy.vector_length() )
+  , m_scratch_size{arg_policy.scratch_size(0,m_team_size),arg_policy.scratch_size(1,m_team_size)}
   {
     // Return Init value if the number of worksets is zero
     if( arg_policy.league_size() == 0) {
-      ValueInit::init( m_functor , arg_result.ptr_on_device() );
+      ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , arg_result.ptr_on_device() );
       return ;
     }
 
-    m_team_begin = cuda_single_inter_block_reduce_scan_shmem<false,FunctorType,WorkTag>( arg_functor , m_team_size );
+    m_team_begin = UseShflReduction?0:cuda_single_inter_block_reduce_scan_shmem<false,FunctorType,WorkTag>( arg_functor , m_team_size );
     m_shmem_begin = sizeof(double) * ( m_team_size + 2 );
-    m_shmem_size = arg_policy.scratch_size() + FunctorTeamShmemSize< FunctorType >::value( arg_functor , m_team_size );
+    m_shmem_size = arg_policy.scratch_size(0,m_team_size) + FunctorTeamShmemSize< FunctorType >::value( arg_functor , m_team_size );
+    m_scratch_ptr[1] = cuda_resize_scratch_space(m_scratch_size[1]*(Cuda::concurrency()/(m_team_size*m_vector_size)));
+    m_scratch_size[0] = m_shmem_size;
+    m_scratch_size[1] = arg_policy.scratch_size(1,m_team_size);
 
     // The global parallel_reduce does not support vector_length other than 1 at the moment
-    if( arg_policy.vector_length() > 1)
-      Impl::throw_runtime_exception( "Kokkos::parallel_reduce with a TeamPolicy using a vector length of greater than 1 is not currently supported for CUDA.");
+    if( (arg_policy.vector_length() > 1) && !UseShflReduction )
+      Impl::throw_runtime_exception( "Kokkos::parallel_reduce with a TeamPolicy using a vector length of greater than 1 is not currently supported for CUDA for dynamic sized reduction types.");
 
-    if( m_team_size < 32)
-      Impl::throw_runtime_exception( "Kokkos::parallel_reduce with a TeamPolicy using a team_size smaller than 32 is not currently supported with CUDA.");
+    if( (m_team_size < 32) && !UseShflReduction )
+      Impl::throw_runtime_exception( "Kokkos::parallel_reduce with a TeamPolicy using a team_size smaller than 32 is not currently supported with CUDA for dynamic sized reduction types.");
 
     // Functor's reduce memory, team scan memory, and team shared memory depend upon team size.
 
     const int shmem_size_total = m_team_begin + m_shmem_begin + m_shmem_size ;
 
-    if ( ! Kokkos::Impl::is_integral_power_of_two( m_team_size ) ||
-         CudaTraits::SharedMemoryCapacity < shmem_size_total ) {
+    if (! Kokkos::Impl::is_integral_power_of_two( m_team_size )  && !UseShflReduction ) {
       Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelReduce< Cuda > bad team size"));
     }
 
+    if ( CudaTraits::SharedMemoryCapacity < shmem_size_total ) {
+      Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelReduce< Cuda > requested too much L0 scratch memory"));
+    }
+
     if ( m_team_size >
          Kokkos::Impl::cuda_get_max_block_size< ParallelReduce >
-               ( arg_functor , arg_policy.vector_length(), arg_policy.scratch_size() ) / arg_policy.vector_length()) {
+               ( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length()) {
+      Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelReduce< Cuda > requested too large team size."));
+    }
+
+  }
+
+  ParallelReduce( const FunctorType  & arg_functor
+                , const Policy       & arg_policy
+                , const ReducerType & reducer)
+  : m_functor( arg_functor )
+  , m_reducer( reducer )
+  , m_result_ptr( reducer.result_view().ptr_on_device() )
+  , m_scratch_space( 0 )
+  , m_scratch_flags( 0 )
+  , m_unified_space( 0 )
+  , m_team_begin( 0 )
+  , m_shmem_begin( 0 )
+  , m_shmem_size( 0 )
+  , m_scratch_ptr{NULL,NULL}
+  , m_league_size( arg_policy.league_size() )
+  , m_team_size( 0 <= arg_policy.team_size() ? arg_policy.team_size() :
+      Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce >( arg_functor , arg_policy.vector_length(),
+                                                               arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) /
+      arg_policy.vector_length() )
+  , m_vector_size( arg_policy.vector_length() )
+  {
+    // Return Init value if the number of worksets is zero
+    if( arg_policy.league_size() == 0) {
+      ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , m_result_ptr );
+      return ;
+    }
+
+    m_team_begin = UseShflReduction?0:cuda_single_inter_block_reduce_scan_shmem<false,FunctorType,WorkTag>( arg_functor , m_team_size );
+    m_shmem_begin = sizeof(double) * ( m_team_size + 2 );
+    m_shmem_size = arg_policy.scratch_size(0,m_team_size) + FunctorTeamShmemSize< FunctorType >::value( arg_functor , m_team_size );
+    m_scratch_ptr[1] = cuda_resize_scratch_space(m_scratch_size[1]*(Cuda::concurrency()/(m_team_size*m_vector_size)));
+    m_scratch_size[0] = m_shmem_size;
+    m_scratch_size[1] = arg_policy.scratch_size(1,m_team_size);
+
+    // The global parallel_reduce does not support vector_length other than 1 at the moment
+    if( (arg_policy.vector_length() > 1) && !UseShflReduction )
+      Impl::throw_runtime_exception( "Kokkos::parallel_reduce with a TeamPolicy using a vector length of greater than 1 is not currently supported for CUDA for dynamic sized reduction types.");
+
+    if( (m_team_size < 32) && !UseShflReduction )
+      Impl::throw_runtime_exception( "Kokkos::parallel_reduce with a TeamPolicy using a team_size smaller than 32 is not currently supported with CUDA for dynamic sized reduction types.");
+
+    // Functor's reduce memory, team scan memory, and team shared memory depend upon team size.
+
+    const int shmem_size_total = m_team_begin + m_shmem_begin + m_shmem_size ;
+
+    if ( (! Kokkos::Impl::is_integral_power_of_two( m_team_size )  && !UseShflReduction ) ||
+         CudaTraits::SharedMemoryCapacity < shmem_size_total ) {
+      Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelReduce< Cuda > bad team size"));
+    }
+
+    if ( int(m_team_size) >
+         int(Kokkos::Impl::cuda_get_max_block_size< ParallelReduce >
+               ( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length())) {
       Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelReduce< Cuda > requested too large team size."));
     }
 
@@ -1453,14 +1629,12 @@ KOKKOS_INLINE_FUNCTION
 void parallel_reduce(const Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::CudaTeamMember >&
       loop_boundaries, const Lambda & lambda, ValueType& result) {
 #ifdef __CUDA_ARCH__
-  ValueType val = ValueType();
+  result = ValueType();
 
   for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
-    lambda(i,val);
+    lambda(i,result);
   }
 
-  result = val;
-
   if (loop_boundaries.increment > 1)
     result += shfl_down(result, 1,loop_boundaries.increment);
   if (loop_boundaries.increment > 2)
@@ -1659,6 +1833,11 @@ namespace Impl {
       //Insert Static Assert with decltype on ValueType equals second argument type of FunctorType::operator()
       f(i,val);
     }
+    __device__ inline
+    void operator() (typename ExecPolicy::member_type& i, ValueType& val) const {
+      //Insert Static Assert with decltype on ValueType equals second argument type of FunctorType::operator()
+      f(i,val);
+    }
 
   };
 
@@ -1692,11 +1871,22 @@ namespace Impl {
     enum {value = true};
   };
 
+  template< class FunctorType, class Enable = void>
+    struct ReduceFunctorHasShmemSize {
+      enum {value = false};
+    };
+
+    template< class FunctorType>
+    struct ReduceFunctorHasShmemSize<FunctorType, typename Impl::enable_if< 0 < sizeof( & FunctorType::team_shmem_size ) >::type > {
+      enum {value = true};
+    };
+
   template< class FunctorType, bool Enable =
       ( FunctorDeclaresValueType<FunctorType,void>::value) ||
       ( ReduceFunctorHasInit<FunctorType>::value  ) ||
       ( ReduceFunctorHasJoin<FunctorType>::value  ) ||
-      ( ReduceFunctorHasFinal<FunctorType>::value )
+      ( ReduceFunctorHasFinal<FunctorType>::value ) ||
+      ( ReduceFunctorHasShmemSize<FunctorType>::value )
       >
   struct IsNonTrivialReduceFunctor {
     enum {value = false};
@@ -1717,376 +1907,18 @@ namespace Impl {
     typedef typename Kokkos::Impl::FunctorValueTraits< FunctorType ,Tag >::reference_type reference_type;
   };
 
-}
-
-// general policy and view ouput
-template< class ExecPolicy , class FunctorTypeIn , class ViewType >
-inline
-void parallel_reduce( const ExecPolicy  & policy
-                    , const FunctorTypeIn & functor_in
-                    , const ViewType    & result_view
-                    , const std::string& str = "" 
-                    , typename Impl::enable_if<
-                      ( Kokkos::is_view<ViewType>::value && ! Impl::is_integral< ExecPolicy >::value &&
-                        Impl::is_same<typename ExecPolicy::execution_space,Kokkos::Cuda>::value
-                      )>::type * = 0 )
-{
-  enum {FunctorHasValueType = Impl::IsNonTrivialReduceFunctor<FunctorTypeIn>::value };
-  typedef typename Kokkos::Impl::if_c<FunctorHasValueType, FunctorTypeIn, Impl::CudaFunctorAdapter<FunctorTypeIn,ExecPolicy,typename ViewType::value_type> >::type FunctorType;
-  FunctorType functor = Impl::if_c<FunctorHasValueType,FunctorTypeIn,FunctorType>::select(functor_in,FunctorType(functor_in));
-
-#if (KOKKOS_ENABLE_PROFILING)
-    uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelScan("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType, ExecPolicy > closure( functor , policy , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-    
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelScan(kpID);
-     }
-#endif
-}
-
-// general policy and pod or array of pod output
-template< class ExecPolicy , class FunctorTypeIn , class ResultType>
-inline
-void parallel_reduce( const ExecPolicy  & policy
-                    , const FunctorTypeIn & functor_in
-                    , ResultType& result_ref
-                    , const std::string& str = "" 
-                    , typename Impl::enable_if<
-                      ( ! Kokkos::is_view<ResultType>::value &&
-                        ! Impl::IsNonTrivialReduceFunctor<FunctorTypeIn>::value &&
-                        ! Impl::is_integral< ExecPolicy >::value  &&
-                          Impl::is_same<typename ExecPolicy::execution_space,Kokkos::Cuda>::value )>::type * = 0 )
-{
-  typedef typename Impl::CudaFunctorAdapter<FunctorTypeIn,ExecPolicy,ResultType> FunctorType;
-
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , typename ExecPolicy::work_tag >  ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueOps<    FunctorType , typename ExecPolicy::work_tag >  ValueOps ;
-
-  // Wrap the result output request in a view to inform the implementation
-  // of the type and memory space.
-
-  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
-                                     , typename ValueTraits::value_type
-                                     , typename ValueTraits::pointer_type
-                                     >::type value_type ;
-  Kokkos::View< value_type
-              , HostSpace
-              , Kokkos::MemoryUnmanaged
-              >
-    result_view( ValueOps::pointer( result_ref )
-               , 1
-               );
-
-#if (KOKKOS_ENABLE_PROFILING)
-    uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelScan("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-    
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType, ExecPolicy > closure( FunctorType(functor_in) , policy , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-    
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelScan(kpID);
-     }
-#endif
-}
-
-// general policy and pod or array of pod output
-template< class ExecPolicy , class FunctorType>
-inline
-void parallel_reduce( const ExecPolicy  & policy
-                    , const FunctorType & functor
-                    , typename Kokkos::Impl::FunctorValueTraits< FunctorType , typename ExecPolicy::work_tag >::reference_type result_ref
-                    , const std::string& str = "" 
-                    , typename Impl::enable_if<
-                      (   Impl::IsNonTrivialReduceFunctor<FunctorType>::value &&
-                        ! Impl::is_integral< ExecPolicy >::value  &&
-                          Impl::is_same<typename ExecPolicy::execution_space,Kokkos::Cuda>::value )>::type * = 0 )
-{
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , typename ExecPolicy::work_tag >  ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueOps<    FunctorType , typename ExecPolicy::work_tag >  ValueOps ;
-
-  // Wrap the result output request in a view to inform the implementation
-  // of the type and memory space.
-
-  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
-                                     , typename ValueTraits::value_type
-                                     , typename ValueTraits::pointer_type
-                                     >::type value_type ;
-
-  Kokkos::View< value_type
-              , HostSpace
-              , Kokkos::MemoryUnmanaged
-              >
-    result_view( ValueOps::pointer( result_ref )
-               , ValueTraits::value_count( functor )
-               );
-
-#if (KOKKOS_ENABLE_PROFILING)
-    uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelScan("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-    
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType, ExecPolicy > closure( functor , policy , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-    
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelScan(kpID);
-     }
-#endif
-}
-
-// integral range policy and view ouput
-template< class FunctorTypeIn , class ViewType >
-inline
-void parallel_reduce( const size_t        work_count
-                    , const FunctorTypeIn & functor_in
-                    , const ViewType    & result_view
-                    , const std::string& str = "" 
-                    , typename Impl::enable_if<( Kokkos::is_view<ViewType>::value &&
-                                                 Impl::is_same<
-                          typename Impl::FunctorPolicyExecutionSpace< FunctorTypeIn , void >::execution_space,
-                          Kokkos::Cuda>::value
-                        )>::type * = 0 )
-{
-  enum {FunctorHasValueType = Impl::IsNonTrivialReduceFunctor<FunctorTypeIn>::value };
-  typedef typename
-    Impl::FunctorPolicyExecutionSpace< FunctorTypeIn , void >::execution_space
-      execution_space ;
-
-  typedef RangePolicy< execution_space > ExecPolicy ;
-
-  typedef typename Kokkos::Impl::if_c<FunctorHasValueType, FunctorTypeIn, Impl::CudaFunctorAdapter<FunctorTypeIn,ExecPolicy,typename ViewType::value_type> >::type FunctorType;
-
-  FunctorType functor = Impl::if_c<FunctorHasValueType,FunctorTypeIn,FunctorType>::select(functor_in,FunctorType(functor_in));
-
-#if (KOKKOS_ENABLE_PROFILING)
-    uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelScan("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-    
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType, ExecPolicy > closure( functor , ExecPolicy(0,work_count) , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelScan(kpID);
-     }
-#endif
-
-}
-
-// integral range policy and pod or array of pod output
-template< class FunctorTypeIn , class ResultType>
-inline
-void parallel_reduce( const size_t        work_count
-                    , const FunctorTypeIn & functor_in
-                    , ResultType& result
-                    , const std::string& str = "" 
-                    , typename Impl::enable_if< ! Kokkos::is_view<ResultType>::value &&
-                                                ! Impl::IsNonTrivialReduceFunctor<FunctorTypeIn>::value &&
-                                                Impl::is_same<
-                             typename Impl::FunctorPolicyExecutionSpace< FunctorTypeIn , void >::execution_space,
-                             Kokkos::Cuda>::value >::type * = 0 )
-{
-  typedef typename
-    Kokkos::Impl::FunctorPolicyExecutionSpace< FunctorTypeIn , void >::execution_space
-      execution_space ;
-  typedef Kokkos::RangePolicy< execution_space > ExecPolicy ;
-
-  typedef Impl::CudaFunctorAdapter<FunctorTypeIn,ExecPolicy,ResultType> FunctorType;
-
-
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , void >  ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueOps<    FunctorType , void >  ValueOps ;
-
-
-  // Wrap the result output request in a view to inform the implementation
-  // of the type and memory space.
-
-  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
-                                     , typename ValueTraits::value_type
-                                     , typename ValueTraits::pointer_type
-                                     >::type value_type ;
-
-  Kokkos::View< value_type
-              , HostSpace
-              , Kokkos::MemoryUnmanaged
-              >
-    result_view( ValueOps::pointer( result )
-               , 1
-               );
-
-#if (KOKKOS_ENABLE_PROFILING)
-    uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelScan("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-    
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType , ExecPolicy > closure( FunctorType(functor_in) , ExecPolicy(0,work_count) , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-    
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelScan(kpID);
-     }
-#endif
-}
-
-template< class FunctorType>
-inline
-void parallel_reduce( const size_t        work_count
-                    , const FunctorType & functor
-                    , typename Kokkos::Impl::FunctorValueTraits< FunctorType , void >::reference_type result
-                    , const std::string& str = "" 
-                    , typename Impl::enable_if< Impl::IsNonTrivialReduceFunctor<FunctorType>::value &&
-                                                Impl::is_same<
-                             typename Impl::FunctorPolicyExecutionSpace< FunctorType , void >::execution_space,
-                             Kokkos::Cuda>::value >::type * = 0 )
-{
-
-  typedef typename
-    Kokkos::Impl::FunctorPolicyExecutionSpace< FunctorType , void >::execution_space
-      execution_space ;
-  typedef Kokkos::RangePolicy< execution_space > ExecPolicy ;
-
-
-
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , void >  ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueOps<    FunctorType , void >  ValueOps ;
-
-
-  // Wrap the result output request in a view to inform the implementation
-  // of the type and memory space.
-
-  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
-                                     , typename ValueTraits::value_type
-                                     , typename ValueTraits::pointer_type
-                                     >::type value_type ;
-
-  Kokkos::View< value_type
-              , HostSpace
-              , Kokkos::MemoryUnmanaged
-              >
-    result_view( ValueOps::pointer( result )
-               , ValueTraits::value_count( functor )
-               );
-
-#if (KOKKOS_ENABLE_PROFILING)
-    uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelScan("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-    
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType , ExecPolicy > closure( functor , ExecPolicy(0,work_count) , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-    
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelScan(kpID);
-     }
-#endif
-}
-
-#ifdef KOKKOS_HAVE_CUDA
-template< class ExecPolicy , class FunctorType , class ResultType >
-inline
-void parallel_reduce( const std::string & str
-                    , const ExecPolicy  & policy
-                    , const FunctorType & functor
-                    , ResultType * result)
-{
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG Start parallel_reduce kernel: " << str << std::endl;
-  #endif
-
-  parallel_reduce(policy,functor,result,str);
-
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG End   parallel_reduce kernel: " << str << std::endl;
-  #endif
-  (void) str;
-}
-
-template< class ExecPolicy , class FunctorType , class ResultType >
-inline
-void parallel_reduce( const std::string & str
-                    , const ExecPolicy  & policy
-                    , const FunctorType & functor
-                    , ResultType & result)
-{
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG Start parallel_reduce kernel: " << str << std::endl;
-  #endif
+  template< class FunctorTypeIn, class ExecPolicy, class ValueType>
+  struct ParallelReduceFunctorType<FunctorTypeIn,ExecPolicy,ValueType,Cuda> {
 
-  parallel_reduce(policy,functor,result,str);
+    enum {FunctorHasValueType = IsNonTrivialReduceFunctor<FunctorTypeIn>::value };
+    typedef typename Kokkos::Impl::if_c<FunctorHasValueType, FunctorTypeIn, Impl::CudaFunctorAdapter<FunctorTypeIn,ExecPolicy,ValueType> >::type functor_type;
+    static functor_type functor(const FunctorTypeIn& functor_in) {
+      return Impl::if_c<FunctorHasValueType,FunctorTypeIn,functor_type>::select(functor_in,functor_type(functor_in));
+    }
+  };
 
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG End   parallel_reduce kernel: " << str << std::endl;
-  #endif
-  (void) str;
 }
 
-template< class ExecPolicy , class FunctorType >
-inline
-void parallel_reduce( const std::string & str
-                    , const ExecPolicy  & policy
-                    , const FunctorType & functor)
-{
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG Start parallel_reduce kernel: " << str << std::endl;
-  #endif
-
-  parallel_reduce(policy,functor,str);
-
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG End   parallel_reduce kernel: " << str << std::endl;
-  #endif
-  (void) str;
-}
-#endif
 } // namespace Kokkos
 #endif /* defined( __CUDACC__ ) */
 
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp
index 11871a6abc..1778f631c0 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp
@@ -130,16 +130,17 @@ inline void cuda_intra_block_reduction( ValueType& value,
   cuda_inter_warp_reduction(value,join,max_active_thread);
 }
 
-template< class FunctorType , class JoinOp>
+template< class FunctorType , class JoinOp , class ArgTag = void >
 __device__
-bool cuda_inter_block_reduction( typename FunctorValueTraits< FunctorType , void >::reference_type  value,
+bool cuda_inter_block_reduction( typename FunctorValueTraits< FunctorType , ArgTag >::reference_type  value,
+                                 typename FunctorValueTraits< FunctorType , ArgTag >::reference_type  neutral,
                                  const JoinOp& join,
                                  Cuda::size_type * const m_scratch_space,
-                                 typename FunctorValueTraits< FunctorType , void >::pointer_type const result,
+                                 typename FunctorValueTraits< FunctorType , ArgTag >::pointer_type const result,
                                  Cuda::size_type * const m_scratch_flags,
                                  const int max_active_thread = blockDim.y) {
-  typedef typename FunctorValueTraits< FunctorType , void >::pointer_type pointer_type;
-  typedef typename FunctorValueTraits< FunctorType , void >::value_type value_type;
+  typedef typename FunctorValueTraits< FunctorType , ArgTag >::pointer_type pointer_type;
+  typedef typename FunctorValueTraits< FunctorType , ArgTag >::value_type value_type;
 
   //Do the intra-block reduction with shfl operations and static shared memory
   cuda_intra_block_reduction(value,join,max_active_thread);
@@ -170,7 +171,7 @@ bool cuda_inter_block_reduction( typename FunctorValueTraits< FunctorType , void
       if(id == 0)
         *m_scratch_flags = 0;
       last_block = true;
-      value = 0;
+      value = neutral;
 
       pointer_type const volatile global = (pointer_type) m_scratch_space ;
 
@@ -366,7 +367,12 @@ bool cuda_single_inter_block_reduce_scan( const FunctorType     & functor ,
     size_type * const shared = shared_data + word_count.value * BlockSizeMask ;
     size_type * const global = global_data + word_count.value * block_id ;
 
+#if (__CUDA_ARCH__ < 500)
     for ( size_type i = threadIdx.y ; i < word_count.value ; i += blockDim.y ) { global[i] = shared[i] ; }
+#else
+    for ( size_type i = 0 ; i < word_count.value ; i += 1 ) { global[i] = shared[i] ; }
+#endif
+
   }
 
   // Contributing blocks note that their contribution has been completed via an atomic-increment flag
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.cpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.cpp
new file mode 100644
index 0000000000..701d267e1b
--- /dev/null
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.cpp
@@ -0,0 +1,179 @@
+/*
+//@HEADER
+// ************************************************************************
+// 
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+// 
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+// 
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+// 
+// ************************************************************************
+//@HEADER
+*/
+
+#include <Kokkos_Core.hpp>
+
+#if defined( KOKKOS_HAVE_CUDA ) && defined( KOKKOS_ENABLE_TASKPOLICY )
+
+#include <impl/Kokkos_TaskQueue_impl.hpp>
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+namespace Impl {
+
+template class TaskQueue< Kokkos::Cuda > ;
+
+//----------------------------------------------------------------------------
+
+__device__
+void TaskQueueSpecialization< Kokkos::Cuda >::driver
+  ( TaskQueueSpecialization< Kokkos::Cuda >::queue_type * const queue )
+{
+  using Member = TaskExec< Kokkos::Cuda > ;
+  using Queue  = TaskQueue< Kokkos::Cuda > ;
+  using task_root_type = TaskBase< Kokkos::Cuda , void , void > ;
+
+  task_root_type * const end = (task_root_type *) task_root_type::EndTag ;
+
+  Member single_exec( 1 );
+  Member team_exec( blockDim.y );
+
+  const int warp_lane = threadIdx.x + threadIdx.y * blockDim.x ;
+
+  union {
+    task_root_type * ptr ;
+    int              raw[2] ;
+  } task ;
+
+  // Loop until all queues are empty and no tasks in flight
+
+  do {
+
+    // Each team lead attempts to acquire either a thread team task
+    // or collection of single thread tasks for the team.
+
+    if ( 0 == warp_lane ) {
+
+      task.ptr = 0 < *((volatile int *) & queue->m_ready_count) ? end : 0 ;
+
+      // Loop by priority and then type
+      for ( int i = 0 ; i < Queue::NumQueue && end == task.ptr ; ++i ) {
+        for ( int j = 0 ; j < 2 && end == task.ptr ; ++j ) {
+          task.ptr = Queue::pop_task( & queue->m_ready[i][j] );
+        }
+      }
+
+#if 0
+printf("TaskQueue<Cuda>::driver(%d,%d) task(%lx)\n",threadIdx.z,blockIdx.x
+      , uintptr_t(task.ptr));
+#endif
+
+    }
+
+    // shuffle broadcast
+
+    task.raw[0] = __shfl( task.raw[0] , 0 );
+    task.raw[1] = __shfl( task.raw[1] , 0 );
+
+    if ( 0 == task.ptr ) break ; // 0 == queue->m_ready_count
+
+    if ( end != task.ptr ) {
+      if ( task_root_type::TaskTeam == task.ptr->m_task_type ) {
+        // Thread Team Task
+        (*task.ptr->m_apply)( task.ptr , & team_exec );
+      }
+      else if ( 0 == threadIdx.y ) {
+        // Single Thread Task
+        (*task.ptr->m_apply)( task.ptr , & single_exec );
+      }
+
+      if ( 0 == warp_lane ) {
+        queue->complete( task.ptr ); 
+      }
+    }
+  } while(1);
+}
+
+namespace {
+
+__global__
+void cuda_task_queue_execute( TaskQueue< Kokkos::Cuda > * queue )
+{ TaskQueueSpecialization< Kokkos::Cuda >::driver( queue ); }
+
+}
+
+void TaskQueueSpecialization< Kokkos::Cuda >::execute
+  ( TaskQueue< Kokkos::Cuda > * const queue )
+{
+  const int warps_per_block = 4 ;
+  const dim3 grid( Kokkos::Impl::cuda_internal_multiprocessor_count() , 1 , 1 );
+  const dim3 block( 1 , Kokkos::Impl::CudaTraits::WarpSize , warps_per_block );
+  const int shared = 0 ;
+  const cudaStream_t stream = 0 ;
+
+  CUDA_SAFE_CALL( cudaDeviceSynchronize() );
+
+#if 0
+printf("cuda_task_queue_execute before\n");
+#endif
+
+  // Query the stack size, in bytes:
+  //
+  // size_t stack_size = 0 ;
+  // CUDA_SAFE_CALL( cudaDeviceGetLimit( & stack_size , cudaLimitStackSize ) );
+  //
+  // If not large enough then set the stack size, in bytes:
+  //
+  // CUDA_SAFE_CALL( cudaDeviceSetLimit( cudaLimitStackSize , stack_size ) );
+ 
+  cuda_task_queue_execute<<< grid , block , shared , stream >>>( queue );
+
+  CUDA_SAFE_CALL( cudaGetLastError() );
+
+  CUDA_SAFE_CALL( cudaDeviceSynchronize() );
+
+#if 0
+printf("cuda_task_queue_execute after\n");
+#endif
+
+}
+
+}} /* namespace Kokkos::Impl */
+
+//----------------------------------------------------------------------------
+
+#endif /* #if defined( KOKKOS_HAVE_CUDA ) && defined( KOKKOS_ENABLE_TASKPOLICY ) */
+
+
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp
new file mode 100644
index 0000000000..9d9347cc8d
--- /dev/null
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp
@@ -0,0 +1,519 @@
+/*
+//@HEADER
+// ************************************************************************
+// 
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+// 
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+// 
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+// 
+// ************************************************************************
+//@HEADER
+*/
+
+#ifndef KOKKOS_IMPL_CUDA_TASK_HPP
+#define KOKKOS_IMPL_CUDA_TASK_HPP
+
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+namespace Impl {
+namespace {
+
+template< typename TaskType >
+__global__
+void set_cuda_task_base_apply_function_pointer
+  ( TaskBase<Kokkos::Cuda,void,void>::function_type * ptr )
+{ *ptr = TaskType::apply ; }
+
+}
+
+template<>
+class TaskQueueSpecialization< Kokkos::Cuda >
+{
+public:
+
+  using execution_space = Kokkos::Cuda ;
+  using memory_space    = Kokkos::CudaUVMSpace ;
+  using queue_type      = TaskQueue< execution_space > ;
+
+  static
+  void iff_single_thread_recursive_execute( queue_type * const ) {}
+
+  __device__
+  static void driver( queue_type * const );
+
+  static
+  void execute( queue_type * const );
+
+  template< typename FunctorType >
+  static
+  void proc_set_apply( TaskBase<execution_space,void,void>::function_type * ptr )
+    {
+      using TaskType = TaskBase< execution_space
+                               , typename FunctorType::value_type
+                               , FunctorType > ;
+
+      CUDA_SAFE_CALL( cudaDeviceSynchronize() );
+
+      set_cuda_task_base_apply_function_pointer<TaskType><<<1,1>>>(ptr);
+
+      CUDA_SAFE_CALL( cudaGetLastError() );
+      CUDA_SAFE_CALL( cudaDeviceSynchronize() );
+    }
+};
+
+extern template class TaskQueue< Kokkos::Cuda > ;
+
+//----------------------------------------------------------------------------
+/**\brief  Impl::TaskExec<Cuda> is the TaskPolicy<Cuda>::member_type
+ *         passed to tasks running in a Cuda space.
+ *
+ *  Cuda thread blocks for tasking are dimensioned:
+ *    blockDim.x == vector length
+ *    blockDim.y == team size
+ *    blockDim.z == number of teams
+ *  where
+ *    blockDim.x * blockDim.y == WarpSize
+ *
+ *  Both single thread and thread team tasks are run by a full Cuda warp.
+ *  A single thread task is called by warp lane #0 and the remaining
+ *  lanes of the warp are idle.
+ */
+template<>
+class TaskExec< Kokkos::Cuda >
+{
+private:
+
+  TaskExec( TaskExec && ) = delete ;
+  TaskExec( TaskExec const & ) = delete ;
+  TaskExec & operator = ( TaskExec && ) = delete ;
+  TaskExec & operator = ( TaskExec const & ) = delete ;
+
+  friend class Kokkos::Impl::TaskQueue< Kokkos::Cuda > ;
+  friend class Kokkos::Impl::TaskQueueSpecialization< Kokkos::Cuda > ;
+
+  const int m_team_size ;
+
+  __device__
+  TaskExec( int arg_team_size = blockDim.y )
+    : m_team_size( arg_team_size ) {}
+
+public:
+
+#if defined( __CUDA_ARCH__ )
+  __device__ void team_barrier() { /* __threadfence_block(); */ }
+  __device__ int  team_rank() const { return threadIdx.y ; }
+  __device__ int  team_size() const { return m_team_size ; }
+#else
+  __host__ void team_barrier() {}
+  __host__ int  team_rank() const { return 0 ; }
+  __host__ int  team_size() const { return 0 ; }
+#endif
+
+};
+
+//----------------------------------------------------------------------------
+
+template<typename iType>
+struct TeamThreadRangeBoundariesStruct<iType, TaskExec< Kokkos::Cuda > >
+{
+  typedef iType index_type;
+  const iType start ;
+  const iType end ;
+  const iType increment ;
+  const TaskExec< Kokkos::Cuda > & thread;
+
+#if defined( __CUDA_ARCH__ )
+
+  __device__ inline
+  TeamThreadRangeBoundariesStruct
+    ( const TaskExec< Kokkos::Cuda > & arg_thread, const iType& arg_count)
+    : start( threadIdx.y )
+    , end(arg_count)
+    , increment( blockDim.y )
+    , thread(arg_thread)
+    {}
+
+  __device__ inline
+  TeamThreadRangeBoundariesStruct
+    ( const TaskExec< Kokkos::Cuda > & arg_thread
+    , const iType & arg_start
+    , const iType & arg_end
+    )
+    : start( arg_start + threadIdx.y )
+    , end(   arg_end)
+    , increment( blockDim.y )
+    , thread( arg_thread )
+    {}
+
+#else
+
+  TeamThreadRangeBoundariesStruct
+    ( const TaskExec< Kokkos::Cuda > & arg_thread, const iType& arg_count);
+
+  TeamThreadRangeBoundariesStruct
+    ( const TaskExec< Kokkos::Cuda > & arg_thread
+    , const iType & arg_start
+    , const iType & arg_end
+    );
+
+#endif
+
+};
+
+//----------------------------------------------------------------------------
+
+template<typename iType>
+struct ThreadVectorRangeBoundariesStruct<iType, TaskExec< Kokkos::Cuda > >
+{
+  typedef iType index_type;
+  const iType start ;
+  const iType end ;
+  const iType increment ;
+  const TaskExec< Kokkos::Cuda > & thread;
+
+#if defined( __CUDA_ARCH__ )
+
+  __device__ inline
+  ThreadVectorRangeBoundariesStruct
+    ( const TaskExec< Kokkos::Cuda > & arg_thread, const iType& arg_count)
+    : start( threadIdx.x )
+    , end(arg_count)
+    , increment( blockDim.x )
+    , thread(arg_thread)
+    {}
+
+#else
+
+  ThreadVectorRangeBoundariesStruct
+    ( const TaskExec< Kokkos::Cuda > & arg_thread, const iType& arg_count);
+
+#endif
+
+};
+
+}} /* namespace Kokkos::Impl */
+
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+
+template<typename iType>
+KOKKOS_INLINE_FUNCTION
+Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >
+TeamThreadRange( const Impl::TaskExec< Kokkos::Cuda > & thread
+               , const iType & count )
+{
+  return Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >(thread,count);
+}
+
+template<typename iType>
+KOKKOS_INLINE_FUNCTION
+Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >
+TeamThreadRange( const Impl::TaskExec< Kokkos::Cuda > & thread, const iType & start , const iType & end )
+{
+  return Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::Cuda > >(thread,start,end);
+}
+
+template<typename iType>
+KOKKOS_INLINE_FUNCTION
+Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >
+ThreadVectorRange( const Impl::TaskExec< Kokkos::Cuda > & thread
+               , const iType & count )
+{
+  return Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >(thread,count);
+}
+
+/** \brief  Inter-thread parallel_for. Executes lambda(iType i) for each i=0..N-1.
+ *
+ * The range i=0..N-1 is mapped to all threads of the the calling thread team.
+ * This functionality requires C++11 support.
+*/
+template<typename iType, class Lambda>
+KOKKOS_INLINE_FUNCTION
+void parallel_for
+  ( const Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::Cuda > >& loop_boundaries
+  , const Lambda& lambda
+  )
+{
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    lambda(i);
+  }
+}
+
+// reduce across corresponding lanes between team members within warp
+// assume stride*team_size == warp_size
+template< typename ValueType, class JoinType >
+KOKKOS_INLINE_FUNCTION
+void strided_shfl_warp_reduction
+  (const JoinType& join,
+   ValueType& val,
+   int team_size,
+   int stride)
+{
+  for (int lane_delta=(team_size*stride)>>1; lane_delta>=stride; lane_delta>>=1) {
+    join(val, Kokkos::shfl_down(val, lane_delta, team_size*stride));
+  }
+}
+
+// multiple within-warp non-strided reductions
+template< typename ValueType, class JoinType >
+KOKKOS_INLINE_FUNCTION
+void multi_shfl_warp_reduction
+  (const JoinType& join,
+   ValueType& val,
+   int vec_length)
+{
+  for (int lane_delta=vec_length>>1; lane_delta; lane_delta>>=1) {
+    join(val, Kokkos::shfl_down(val, lane_delta, vec_length));
+  }
+}
+
+// broadcast within warp
+template< class ValueType >
+KOKKOS_INLINE_FUNCTION
+ValueType shfl_warp_broadcast
+  (ValueType& val,
+   int src_lane,
+   int width)
+{
+  return Kokkos::shfl(val, src_lane, width);
+}
+
+// all-reduce across corresponding vector lanes between team members within warp
+// assume vec_length*team_size == warp_size 
+// blockDim.x == vec_length == stride
+// blockDim.y == team_size
+// threadIdx.x == position in vec
+// threadIdx.y == member number
+template< typename iType, class Lambda, typename ValueType, class JoinType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >& loop_boundaries,
+   const Lambda & lambda,
+   const JoinType& join,
+   ValueType& initialized_result) {
+
+  ValueType result = initialized_result;
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    lambda(i,result);
+  }
+  initialized_result = result;
+
+  strided_shfl_warp_reduction<ValueType, JoinType>(
+                          join,
+                          initialized_result,
+                          loop_boundaries.thread.team_size(),
+                          blockDim.x);
+  initialized_result = shfl_warp_broadcast<ValueType>( initialized_result, threadIdx.x, Impl::CudaTraits::WarpSize );
+}
+
+// all-reduce across corresponding vector lanes between team members within warp
+// if no join() provided, use sum
+// assume vec_length*team_size == warp_size 
+// blockDim.x == vec_length == stride
+// blockDim.y == team_size
+// threadIdx.x == position in vec
+// threadIdx.y == member number
+template< typename iType, class Lambda, typename ValueType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >& loop_boundaries,
+   const Lambda & lambda,
+   ValueType& initialized_result) {
+
+  //TODO what is the point of creating this temporary?
+  ValueType result = initialized_result;
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    lambda(i,result);
+  }
+  initialized_result = result;
+
+  strided_shfl_warp_reduction(
+                          [&] (ValueType& val1, const ValueType& val2) { val1 += val2; },
+                          initialized_result,
+                          loop_boundaries.thread.team_size(),
+                          blockDim.x);
+  initialized_result = shfl_warp_broadcast<ValueType>( initialized_result, threadIdx.x, Impl::CudaTraits::WarpSize );
+}
+
+// all-reduce within team members within warp
+// assume vec_length*team_size == warp_size 
+// blockDim.x == vec_length == stride
+// blockDim.y == team_size
+// threadIdx.x == position in vec
+// threadIdx.y == member number
+template< typename iType, class Lambda, typename ValueType, class JoinType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >& loop_boundaries,
+   const Lambda & lambda,
+   const JoinType& join,
+   ValueType& initialized_result) {
+
+  ValueType result = initialized_result;
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    lambda(i,result);
+  }
+  initialized_result = result;
+
+  multi_shfl_warp_reduction<ValueType, JoinType>(join, initialized_result, blockDim.x);
+  initialized_result = shfl_warp_broadcast<ValueType>( initialized_result, 0, blockDim.x );
+}
+
+// all-reduce within team members within warp
+// if no join() provided, use sum
+// assume vec_length*team_size == warp_size 
+// blockDim.x == vec_length == stride
+// blockDim.y == team_size
+// threadIdx.x == position in vec
+// threadIdx.y == member number
+template< typename iType, class Lambda, typename ValueType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >& loop_boundaries,
+   const Lambda & lambda,
+   ValueType& initialized_result) {
+
+  ValueType result = initialized_result;
+
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    lambda(i,result);
+  }
+
+  initialized_result = result;
+
+  //initialized_result = multi_shfl_warp_reduction(
+  multi_shfl_warp_reduction(
+                          [&] (ValueType& val1, const ValueType& val2) { val1 += val2; },
+                          initialized_result,
+                          blockDim.x);
+  initialized_result = shfl_warp_broadcast<ValueType>( initialized_result, 0, blockDim.x );
+}
+
+// scan across corresponding vector lanes between team members within warp
+// assume vec_length*team_size == warp_size 
+// blockDim.x == vec_length == stride
+// blockDim.y == team_size
+// threadIdx.x == position in vec
+// threadIdx.y == member number
+template< typename ValueType, typename iType, class Lambda >
+KOKKOS_INLINE_FUNCTION
+void parallel_scan
+  (const Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >& loop_boundaries,
+   const Lambda & lambda) {
+
+  ValueType accum = 0 ;
+  ValueType val, y, local_total;
+
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    val = 0;
+    lambda(i,val,false);
+
+    // intra-blockDim.y exclusive scan on 'val'
+    // accum = accumulated, sum in total for this iteration
+
+    // INCLUSIVE scan
+    for( int offset = blockDim.x ; offset < Impl::CudaTraits::WarpSize ; offset <<= 1 ) {
+      y = Kokkos::shfl_up(val, offset, Impl::CudaTraits::WarpSize);
+      if(threadIdx.y*blockDim.x >= offset) { val += y; }
+    }
+
+    // pass accum to all threads
+    local_total = shfl_warp_broadcast<ValueType>(val,
+                                            threadIdx.x+Impl::CudaTraits::WarpSize-blockDim.x,
+                                            Impl::CudaTraits::WarpSize);
+
+    // make EXCLUSIVE scan by shifting values over one
+    val = Kokkos::shfl_up(val, blockDim.x, Impl::CudaTraits::WarpSize);
+    if ( threadIdx.y == 0 ) { val = 0 ; }
+
+    val += accum;
+    lambda(i,val,true);
+    accum += local_total;
+  }
+}
+
+// scan within team member (vector) within warp
+// assume vec_length*team_size == warp_size 
+// blockDim.x == vec_length == stride
+// blockDim.y == team_size
+// threadIdx.x == position in vec
+// threadIdx.y == member number
+template< typename iType, class Lambda, typename ValueType >
+KOKKOS_INLINE_FUNCTION
+void parallel_scan
+  (const Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Cuda > >& loop_boundaries,
+   const Lambda & lambda)
+{
+  ValueType accum = 0 ;
+  ValueType val, y, local_total;
+
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    val = 0;
+    lambda(i,val,false);
+
+    // intra-blockDim.x exclusive scan on 'val'
+    // accum = accumulated, sum in total for this iteration
+
+    // INCLUSIVE scan
+    for( int offset = 1 ; offset < blockDim.x ; offset <<= 1 ) {
+      y = Kokkos::shfl_up(val, offset, blockDim.x);
+      if(threadIdx.x >= offset) { val += y; }
+    }
+
+    // pass accum to all threads
+    local_total = shfl_warp_broadcast<ValueType>(val, blockDim.x-1, blockDim.x);
+
+    // make EXCLUSIVE scan by shifting values over one
+    val = Kokkos::shfl_up(val, 1, blockDim.x);
+    if ( threadIdx.x == 0 ) { val = 0 ; }
+
+    val += accum;
+    lambda(i,val,true);
+    accum += local_total;
+  }
+}
+
+} /* namespace Kokkos */
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
+#endif /* #ifndef KOKKOS_IMPL_CUDA_TASK_HPP */
+
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_TaskPolicy.cpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_TaskPolicy.cpp
index f470a0a6ef..bb3cd2640d 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_TaskPolicy.cpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_TaskPolicy.cpp
@@ -46,9 +46,10 @@
 #include <stdio.h>
 #include <iostream>
 #include <sstream>
+#include <Kokkos_Core.hpp>
 #include <Cuda/Kokkos_Cuda_TaskPolicy.hpp>
 
-#if defined( KOKKOS_ENABLE_CUDA_TASK_POLICY )
+#if defined( KOKKOS_HAVE_CUDA ) && defined( KOKKOS_ENABLE_TASKPOLICY )
 
 // #define DETAILED_PRINT
 
@@ -93,9 +94,8 @@ CudaTaskPolicyQueue
   , const unsigned arg_team_size
   )
   : m_space( Kokkos::CudaUVMSpace()
-           , arg_task_max_size
-           , arg_task_max_size * arg_task_max_count
-           , 1 /* only one level of memory pool */
+           , arg_task_max_size * arg_task_max_count * 1.2
+           , 16 /* log2(superblock size) */
            )
   , m_team { 0 , 0 , 0 }
   , m_serial { 0 , 0 , 0 }
@@ -172,6 +172,8 @@ if ( IS_TEAM_LEAD && 0 != team_task ) {
           member( kokkos_impl_cuda_shared_memory<void>()
                 , 16                      /* shared_begin */
                 , team_task->m_shmem_size /* shared size */
+                , 0                       /* scratch level 1 pointer */
+                , 0                       /* scratch level 1 size */
                 , 0                       /* league rank */
                 , 1                       /* league size */
                 );
@@ -926,5 +928,5 @@ void Task::clear_dependence()
 } /* namespace Kokkos */
 
 
-#endif  /* #if defined( KOKKOS_ENABLE_CUDA_TASK_POLICY ) */
+#endif  /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
 
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_TaskPolicy.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_TaskPolicy.hpp
index 1b645c8819..e71512f039 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_TaskPolicy.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_TaskPolicy.hpp
@@ -47,19 +47,11 @@
 #define KOKKOS_CUDA_TASKPOLICY_HPP
 
 #include <Kokkos_Core_fwd.hpp>
-
-#if defined( KOKKOS_HAVE_CUDA ) && \
-    defined( KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE )
-
-#define KOKKOS_ENABLE_CUDA_TASK_POLICY
-
-/* The TaskPolicy< Cuda > capability requires nvcc using the option:
- *    --relocatable-device-code=true
- */
-
 #include <Kokkos_Cuda.hpp>
 #include <Kokkos_TaskPolicy.hpp>
 
+#if defined( KOKKOS_HAVE_CUDA ) && defined( KOKKOS_ENABLE_TASKPOLICY )
+
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
@@ -81,8 +73,6 @@ public:
 
 private:
 
-  friend struct CudaTaskPolicyQueue ;
-
   CudaTaskPolicyQueue   * m_policy ;
   TaskMember * volatile * m_queue ;
   function_team_type      m_team ;    ///< Apply function on CUDA
@@ -819,9 +809,11 @@ public:
   static member_type member_single()
     {
       return
-        member_type( 0 /* shared memory */
-                   , 0 /* shared memory begin */
-                   , 0 /* shared memory size */
+        member_type( 0 /* shared memory pointer */
+                   , 0 /* shared memory begin offset */
+                   , 0 /* shared memory end offset */
+                   , 0 /* scratch level_1 pointer */
+                   , 0 /* scratch level_1 size */
                    , 0 /* league rank */
                    , 1 /* league size */ );
     }
@@ -832,10 +824,10 @@ public:
 } /* namespace Experimental */
 } /* namespace Kokkos */
 
-#endif /* #if defined( KOKKOS_HAVE_CUDA ) && defined( KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE ) */
 
 //----------------------------------------------------------------------------
 
+#endif /* #if defined( KOKKOS_HAVE_CUDA ) && defined( KOKKOS_ENABLE_TASKPOLICY ) */
 #endif /* #ifndef KOKKOS_CUDA_TASKPOLICY_HPP */
 
 
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp
index 84c2e75dc2..92f6fc1f5f 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp
@@ -56,8 +56,6 @@
 #include <impl/Kokkos_Shape.hpp>
 #include <Kokkos_View.hpp>
 
-#include <Cuda/Kokkos_Cuda_BasicAllocators.hpp>
-
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
@@ -90,343 +88,6 @@ struct AssertShapeBoundsAbort< CudaSpace >
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-namespace Kokkos {
-namespace Impl {
-
-//----------------------------------------------------------------------------
-// Cuda Texture fetches can be performed for 4, 8 and 16 byte objects (int,int2,int4)
-// Via reinterpret_case this can be used to support all scalar types of those sizes.
-// Any other scalar type falls back to either normal reads out of global memory,
-// or using the __ldg intrinsic on Kepler GPUs or newer (Compute Capability >= 3.0)
-
-template< typename ValueType
-        , class MemorySpace
-        , class AliasType =
-            typename Kokkos::Impl::if_c< ( sizeof(ValueType) ==  4 ) , int ,
-            typename Kokkos::Impl::if_c< ( sizeof(ValueType) ==  8 ) , ::int2 ,
-            typename Kokkos::Impl::if_c< ( sizeof(ValueType) == 16 ) , ::int4 ,
-            typename Kokkos::Impl::if_c< ( sizeof(ValueType) == 32 ) , ::float4 ,void
-            >::type
-            >::type
-            >::type
-            >::type
-        >
-class CudaTextureFetch {
-private:
-
-  cuda_texture_object_type  m_obj ;
-  const ValueType         * m_alloc_ptr ;
-  int                       m_offset ;
-
-  void attach( const ValueType * const arg_ptr, AllocationTracker const & tracker )
-  {
-    typedef char const * const byte;
-
-    m_alloc_ptr = reinterpret_cast<ValueType *>(tracker.alloc_ptr());
-
-    size_t byte_offset = reinterpret_cast<byte>(arg_ptr) - reinterpret_cast<byte>(m_alloc_ptr);
-    const bool ok_aligned = 0 == byte_offset % sizeof(ValueType);
-
-    const size_t count = tracker.alloc_size() / sizeof(ValueType);
-    const bool ok_contains = (m_alloc_ptr <= arg_ptr) && (arg_ptr < (m_alloc_ptr + count));
-
-    if (ok_aligned && ok_contains) {
-      if (tracker.attribute() == NULL ) {
-        MemorySpace::texture_object_attach(
-            tracker
-            , sizeof(ValueType)
-            , cudaCreateChannelDesc< AliasType >()
-            );
-      }
-      m_obj = dynamic_cast<TextureAttribute*>(tracker.attribute())->m_tex_obj;
-      m_offset = arg_ptr - m_alloc_ptr;
-    }
-    else if( !ok_contains ) {
-      throw_runtime_exception("Error: cannot attach a texture object to a tracker which does not bound the pointer.");
-    }
-    else {
-      throw_runtime_exception("Error: cannot attach a texture object to an incorrectly aligned pointer.");
-    }
-  }
-
-public:
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch() : m_obj() , m_alloc_ptr() , m_offset() {}
-
-  KOKKOS_INLINE_FUNCTION
-  ~CudaTextureFetch() {}
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch( const CudaTextureFetch & rhs )
-    : m_obj(       rhs.m_obj )
-    , m_alloc_ptr( rhs.m_alloc_ptr )
-    , m_offset(    rhs.m_offset )
-    {}
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch & operator = ( const CudaTextureFetch & rhs )
-    {
-      m_obj       = rhs.m_obj ;
-      m_alloc_ptr = rhs.m_alloc_ptr ;
-      m_offset    = rhs.m_offset ;
-      return *this ;
-    }
-
-  KOKKOS_INLINE_FUNCTION explicit
-  CudaTextureFetch( const ValueType * const arg_ptr, AllocationTracker const & tracker )
-    : m_obj( 0 ) , m_alloc_ptr(0) , m_offset(0)
-    {
-      #if defined( KOKKOS_USE_LDG_INTRINSIC )
-        m_alloc_ptr(arg_ptr);
-      #elif defined( __CUDACC__ ) && ! defined( __CUDA_ARCH__ )
-        if ( arg_ptr != NULL ) {
-          if ( tracker.is_valid() ) {
-            attach( arg_ptr, tracker );
-          }
-          else {
-            AllocationTracker found_tracker = AllocationTracker::find<typename MemorySpace::allocator>(arg_ptr);
-            if ( found_tracker.is_valid() ) {
-              attach( arg_ptr, found_tracker );
-            } else {
-              throw_runtime_exception("Error: cannot attach a texture object to an untracked pointer!");
-            }
-          }
-        }
-      #endif
-    }
-
-  KOKKOS_INLINE_FUNCTION
-  operator const ValueType * () const { return m_alloc_ptr + m_offset ; }
-
-
-  template< typename iType >
-  KOKKOS_INLINE_FUNCTION
-  ValueType operator[]( const iType & i ) const
-    {
-      #if defined( KOKKOS_USE_LDG_INTRINSIC ) && defined( __CUDA_ARCH__ ) && ( 300 <= __CUDA_ARCH__ )
-        AliasType v = __ldg(reinterpret_cast<AliasType*>(&m_alloc_ptr[i]));
-        return  *(reinterpret_cast<ValueType*> (&v));
-      #elif defined( __CUDA_ARCH__ ) && ( 300 <= __CUDA_ARCH__ )
-        AliasType v = tex1Dfetch<AliasType>( m_obj , i + m_offset );
-        return  *(reinterpret_cast<ValueType*> (&v));
-      #else
-        return m_alloc_ptr[ i + m_offset ];
-      #endif
-  }
-};
-
-
-template< typename ValueType, class MemorySpace >
-class CudaTextureFetch< const ValueType, MemorySpace, float4 > {
-private:
-  typedef float4 AliasType;
-  cuda_texture_object_type  m_obj ;
-  const ValueType         * m_alloc_ptr ;
-  int                       m_offset ;
-
-  void attach( const ValueType * const arg_ptr, AllocationTracker const & tracker )
-  {
-    typedef char const * const byte;
-
-    m_alloc_ptr = reinterpret_cast<ValueType *>(tracker.alloc_ptr());
-
-    size_t byte_offset = reinterpret_cast<byte>(arg_ptr) - reinterpret_cast<byte>(m_alloc_ptr);
-    const bool ok_aligned = 0 == byte_offset % sizeof(ValueType);
-
-    const size_t count = tracker.alloc_size() / sizeof(ValueType);
-    const bool ok_contains = (m_alloc_ptr <= arg_ptr) && (arg_ptr < (m_alloc_ptr + count));
-
-    if (ok_aligned && ok_contains) {
-      if (tracker.attribute() == NULL ) {
-        MemorySpace::texture_object_attach(
-            tracker
-            , sizeof(ValueType)
-            , cudaCreateChannelDesc< AliasType >()
-            );
-      }
-      m_obj = dynamic_cast<TextureAttribute*>(tracker.attribute())->m_tex_obj;
-      m_offset = arg_ptr - m_alloc_ptr;
-    }
-    else if( !ok_contains ) {
-      throw_runtime_exception("Error: cannot attach a texture object to a tracker which does not bound the pointer.");
-    }
-    else {
-      throw_runtime_exception("Error: cannot attach a texture object to an incorrectly aligned pointer.");
-    }
-  }
-
-public:
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch() : m_obj() , m_alloc_ptr() , m_offset() {}
-
-  KOKKOS_INLINE_FUNCTION
-  ~CudaTextureFetch() {}
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch( const CudaTextureFetch & rhs )
-    : m_obj(       rhs.m_obj )
-    , m_alloc_ptr( rhs.m_alloc_ptr )
-    , m_offset(    rhs.m_offset )
-    {}
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch & operator = ( const CudaTextureFetch & rhs )
-    {
-      m_obj       = rhs.m_obj ;
-      m_alloc_ptr = rhs.m_alloc_ptr ;
-      m_offset    = rhs.m_offset ;
-      return *this ;
-    }
-
-  KOKKOS_INLINE_FUNCTION explicit
-  CudaTextureFetch( const ValueType * const arg_ptr, AllocationTracker const & tracker )
-    : m_obj( 0 ) , m_alloc_ptr(0) , m_offset(0)
-    {
-      #if defined( KOKKOS_USE_LDG_INTRINSIC )
-        m_alloc_ptr(arg_ptr);
-      #elif defined( __CUDACC__ ) && ! defined( __CUDA_ARCH__ )
-        if ( arg_ptr != NULL ) {
-          if ( tracker.is_valid() ) {
-            attach( arg_ptr, tracker );
-          }
-          else {
-            AllocationTracker found_tracker = AllocationTracker::find<typename MemorySpace::allocator>(arg_ptr);
-            if ( found_tracker.is_valid() ) {
-              attach( arg_ptr, found_tracker );
-            } else {
-              throw_runtime_exception("Error: cannot attach a texture object to an untracked pointer!");
-            }
-          }
-        }
-      #endif
-    }
-
-  KOKKOS_INLINE_FUNCTION
-  operator const ValueType * () const { return m_alloc_ptr + m_offset ; }
-
-
-  template< typename iType >
-  KOKKOS_INLINE_FUNCTION
-  ValueType operator[]( const iType & i ) const
-    {
-      #if defined( KOKKOS_USE_LDG_INTRINSIC ) && defined( __CUDA_ARCH__ ) && ( 300 <= __CUDA_ARCH__ )
-        AliasType v = __ldg(reinterpret_cast<AliasType*>(&m_alloc_ptr[i]));
-        return  *(reinterpret_cast<ValueType*> (&v));
-      #elif defined( __CUDA_ARCH__ ) && ( 300 <= __CUDA_ARCH__ )
-        union Float4ValueType {
-          float4 f4[2];
-          ValueType val;
-        };
-        Float4ValueType convert;
-        convert.f4[0] = tex1Dfetch<AliasType>( m_obj , 2*(i + m_offset) );
-        convert.f4[1] = tex1Dfetch<AliasType>( m_obj , 2*(i + m_offset)+1 );
-        return  convert.val;
-      #else
-        return m_alloc_ptr[ i + m_offset ];
-      #endif
-  }
-};
-
-template< typename ValueType, class MemorySpace >
-class CudaTextureFetch< const ValueType, MemorySpace, void >
-{
-private:
-  const ValueType * m_ptr ;
-public:
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch() : m_ptr(0) {};
-
-  KOKKOS_INLINE_FUNCTION
-  ~CudaTextureFetch() {
-  }
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch( const ValueType * ptr, const AllocationTracker & ) : m_ptr(ptr) {}
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch( const CudaTextureFetch & rhs ) : m_ptr(rhs.m_ptr) {}
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch & operator = ( const CudaTextureFetch & rhs ) {
-    m_ptr = rhs.m_ptr;
-    return *this ;
-  }
-
-  explicit KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch( ValueType * const base_view_ptr, AllocationTracker const & /*tracker*/ ) {
-    m_ptr = base_view_ptr;
-  }
-
-  KOKKOS_INLINE_FUNCTION
-  CudaTextureFetch & operator = (const ValueType* base_view_ptr) {
-    m_ptr = base_view_ptr;
-    return *this;
-  }
-
-
-  KOKKOS_INLINE_FUNCTION
-  operator const ValueType * () const { return m_ptr ; }
-
-
-  template< typename iType >
-  KOKKOS_INLINE_FUNCTION
-  ValueType operator[]( const iType & i ) const
-  {
-    return m_ptr[ i ];
-  }
-};
-
-} // namespace Impl
-} // namespace Kokkos
-
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Impl {
-
-/** \brief  Replace Default ViewDataHandle with Cuda texture fetch specialization
- *          if 'const' value type, CudaSpace and random access.
- */
-template< class ViewTraits >
-class ViewDataHandle< ViewTraits ,
-  typename enable_if< ( is_same< typename ViewTraits::memory_space,CudaSpace>::value ||
-                        is_same< typename ViewTraits::memory_space,CudaUVMSpace>::value )
-                      &&
-                      is_same<typename ViewTraits::const_value_type,typename ViewTraits::value_type>::value
-                      &&
-                      ViewTraits::memory_traits::RandomAccess
-                    >::type >
-{
-public:
-  enum { ReturnTypeIsReference = false };
-
-  typedef Impl::CudaTextureFetch< typename ViewTraits::value_type
-                                , typename ViewTraits::memory_space> handle_type;
-
-  KOKKOS_INLINE_FUNCTION
-  static handle_type create_handle( typename ViewTraits::value_type * arg_data_ptr, AllocationTracker const & arg_tracker )
-  {
-    return handle_type(arg_data_ptr, arg_tracker);
-  }
-
-  typedef typename ViewTraits::value_type return_type;
-};
-
-}
-}
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
 #endif // KOKKOS_HAVE_CUDA
 #endif /* #ifndef KOKKOS_CUDA_VIEW_HPP */
 
diff --git a/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp b/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp
new file mode 100644
index 0000000000..e813285fc7
--- /dev/null
+++ b/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp
@@ -0,0 +1,611 @@
+/*
+//@HEADER
+// ************************************************************************
+//
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+//
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+//
+// ************************************************************************
+//@HEADER
+*/
+
+#ifndef KOKKOS_CORE_EXP_MD_RANGE_POLICY_HPP
+#define KOKKOS_CORE_EXP_MD_RANGE_POLICY_HPP
+
+#include <Kokkos_ExecPolicy.hpp>
+#include <Kokkos_Parallel.hpp>
+#include <initializer_list>
+
+#if defined(KOKKOS_OPT_RANGE_AGGRESSIVE_VECTORIZATION) && defined(KOKKOS_HAVE_PRAGMA_IVDEP) && !defined(__CUDA_ARCH__)
+#define KOKKOS_MDRANGE_IVDEP
+#endif
+
+namespace Kokkos { namespace Experimental {
+
+enum class Iterate
+{
+  Default, // Default for the device
+  Left,    // Left indices stride fastest
+  Right,   // Right indices stride fastest
+  Flat,    // Do not tile, only valid for inner direction
+};
+
+template <typename ExecSpace>
+struct default_outer_direction
+{
+  using type = Iterate;
+  static constexpr Iterate value = Iterate::Right;
+};
+
+template <typename ExecSpace>
+struct default_inner_direction
+{
+  using type = Iterate;
+  static constexpr Iterate value = Iterate::Right;
+};
+
+
+// Iteration Pattern
+template < unsigned N
+         , Iterate OuterDir = Iterate::Default
+         , Iterate InnerDir = Iterate::Default
+         >
+struct Rank
+{
+  static_assert( N != 0u, "Kokkos Error: rank 0 undefined");
+  static_assert( N != 1u, "Kokkos Error: rank 1 is not a multi-dimensional range");
+  static_assert( N < 4u, "Kokkos Error: Unsupported rank...");
+
+  using iteration_pattern = Rank<N, OuterDir, InnerDir>;
+
+  static constexpr int rank = N;
+  static constexpr Iterate outer_direction = OuterDir;
+  static constexpr Iterate inner_direction = InnerDir;
+};
+
+
+
+// multi-dimensional iteration pattern
+template <typename... Properties>
+struct MDRangePolicy
+{
+  using range_policy = RangePolicy<Properties...>;
+
+  static_assert( !std::is_same<range_policy,void>::value
+               , "Kokkos Error: MD iteration pattern not defined" );
+
+  using iteration_pattern   = typename range_policy::iteration_pattern;
+  using work_tag            = typename range_policy::work_tag;
+
+  static constexpr int rank = iteration_pattern::rank;
+
+  static constexpr int outer_direction = static_cast<int> (
+      (iteration_pattern::outer_direction != Iterate::Default && iteration_pattern::outer_direction != Iterate::Flat)
+    ? iteration_pattern::outer_direction
+    : default_outer_direction< typename range_policy::execution_space>::value );
+
+  static constexpr int inner_direction = static_cast<int> (
+      iteration_pattern::inner_direction != Iterate::Default
+    ? iteration_pattern::inner_direction
+    : default_inner_direction< typename range_policy::execution_space>::value ) ;
+
+
+  // Ugly ugly workaround intel 14 not handling scoped enum correctly
+  static constexpr int Flat = static_cast<int>( Iterate::Flat );
+  static constexpr int Right = static_cast<int>( Iterate::Right );
+
+
+  using size_type   = typename range_policy::index_type;
+  using index_type  = typename std::make_signed<size_type>::type;
+
+
+  template <typename I>
+  MDRangePolicy( std::initializer_list<I> upper_corner )
+  {
+    static_assert( std::is_integral<I>::value, "Kokkos Error: corner defined with non-integral type" );
+
+    // TODO check size of lists equal to rank
+    // static_asserts on initializer_list.size() require c++14
+
+    //static_assert( upper_corner.size() == rank, "Kokkos Error: upper_corner has incorrect rank" );
+
+    const auto u = upper_corner.begin();
+
+    m_num_tiles = 1;
+    for (int i=0; i<rank; ++i) {
+      m_offset[i] = static_cast<index_type>(0);
+      m_dim[i]    = static_cast<index_type>(u[i]);
+      if (inner_direction != Flat) {
+        // default tile size to 4
+        m_tile[i] = 4;
+      } else {
+        m_tile[i] = 1;
+      }
+      m_tile_dim[i] = (m_dim[i] + (m_tile[i] - 1)) / m_tile[i];
+      m_num_tiles *= m_tile_dim[i];
+    }
+  }
+
+  template <typename IA, typename IB>
+  MDRangePolicy( std::initializer_list<IA> corner_a
+               , std::initializer_list<IB> corner_b
+               )
+  {
+    static_assert( std::is_integral<IA>::value, "Kokkos Error: corner A defined with non-integral type" );
+    static_assert( std::is_integral<IB>::value, "Kokkos Error: corner B defined with non-integral type" );
+
+    // TODO check size of lists equal to rank
+    // static_asserts on initializer_list.size() require c++14
+    //static_assert( corner_a.size() == rank, "Kokkos Error: corner_a has incorrect rank" );
+    //static_assert( corner_b.size() == rank, "Kokkos Error: corner_b has incorrect rank" );
+
+
+    using A = typename std::make_signed<IA>::type;
+    using B = typename std::make_signed<IB>::type;
+
+    const auto a = [=](int i) { return static_cast<A>(corner_a.begin()[i]); };
+    const auto b = [=](int i) { return static_cast<B>(corner_b.begin()[i]); };
+
+    m_num_tiles = 1;
+    for (int i=0; i<rank; ++i) {
+      m_offset[i] = static_cast<index_type>(a(i) <= b(i) ? a(i) : b(i));
+      m_dim[i]    = static_cast<index_type>(a(i) <= b(i) ? b(i) - a(i) : a(i) - b(i));
+      if (inner_direction != Flat) {
+        // default tile size to 4
+        m_tile[i] = 4;
+      } else {
+        m_tile[i] = 1;
+      }
+      m_tile_dim[i] = (m_dim[i] + (m_tile[i] - 1)) / m_tile[i];
+      m_num_tiles *= m_tile_dim[i];
+    }
+  }
+
+  template <typename IA, typename IB, typename T>
+  MDRangePolicy( std::initializer_list<IA> corner_a
+               , std::initializer_list<IB> corner_b
+               , std::initializer_list<T> tile
+               )
+  {
+    static_assert( std::is_integral<IA>::value, "Kokkos Error: corner A defined with non-integral type" );
+    static_assert( std::is_integral<IB>::value, "Kokkos Error: corner B defined with non-integral type" );
+    static_assert( std::is_integral<T>::value, "Kokkos Error: tile defined with non-integral type" );
+    static_assert( inner_direction != Flat, "Kokkos Error: tiling not support with flat iteration" );
+
+    // TODO check size of lists equal to rank
+    // static_asserts on initializer_list.size() require c++14
+    //static_assert( corner_a.size() == rank, "Kokkos Error: corner_a has incorrect rank" );
+    //static_assert( corner_b.size() == rank, "Kokkos Error: corner_b has incorrect rank" );
+    //static_assert( tile.size() == rank, "Kokkos Error: tile has incorrect rank" );
+
+    using A = typename std::make_signed<IA>::type;
+    using B = typename std::make_signed<IB>::type;
+
+    const auto a = [=](int i) { return static_cast<A>(corner_a.begin()[i]); };
+    const auto b = [=](int i) { return static_cast<B>(corner_b.begin()[i]); };
+    const auto t = tile.begin();
+
+    m_num_tiles = 1;
+    for (int i=0; i<rank; ++i) {
+      m_offset[i] = static_cast<index_type>(a(i) <= b(i) ? a(i) : b(i));
+      m_dim[i]    = static_cast<index_type>(a(i) <= b(i) ? b(i) - a(i) : a(i) - b(i));
+      m_tile[i]   = static_cast<int>(t[i] > (T)0 ? t[i] : (T)1 );
+      m_tile_dim[i] = (m_dim[i] + (m_tile[i] - 1)) / m_tile[i];
+      m_num_tiles *= m_tile_dim[i];
+    }
+  }
+
+  index_type   m_offset[rank];
+  index_type   m_dim[rank];
+  int          m_tile[rank];
+  index_type   m_tile_dim[rank];
+  size_type    m_num_tiles;       // product of tile dims
+};
+
+namespace Impl {
+
+// Serial, Threads, OpenMP
+// use enable_if to overload for Cuda
+template < typename MDRange, typename Functor, typename Enable = void >
+struct MDForFunctor
+{
+  using work_tag   = typename MDRange::work_tag;
+  using index_type = typename MDRange::index_type;
+  using size_type  = typename MDRange::size_type;
+
+  MDRange m_range;
+  Functor m_func;
+
+  KOKKOS_INLINE_FUNCTION
+  MDForFunctor( MDRange const& range, Functor const& f )
+    : m_range(range)
+    , m_func( f )
+  {}
+
+  KOKKOS_INLINE_FUNCTION
+  MDForFunctor( MDRange const& range, Functor && f )
+    : m_range(range)
+    , m_func( std::forward<Functor>(f) )
+  {}
+
+  KOKKOS_INLINE_FUNCTION
+  MDForFunctor( MDRange && range, Functor const& f )
+    : m_range( std::forward<MDRange>(range) )
+    , m_func( f )
+  {}
+
+  KOKKOS_INLINE_FUNCTION
+  MDForFunctor( MDRange && range, Functor && f )
+    : m_range( std::forward<MDRange>(range) )
+    , m_func( std::forward<Functor>(f) )
+  {}
+
+
+  KOKKOS_INLINE_FUNCTION
+  MDForFunctor( MDForFunctor const& ) = default;
+
+  KOKKOS_INLINE_FUNCTION
+  MDForFunctor& operator=( MDForFunctor const& ) = default;
+
+  KOKKOS_INLINE_FUNCTION
+  MDForFunctor( MDForFunctor && ) = default;
+
+  KOKKOS_INLINE_FUNCTION
+  MDForFunctor& operator=( MDForFunctor && ) = default;
+
+  // Rank-2, Flat, No Tag
+  template <typename Idx>
+  KOKKOS_FORCEINLINE_FUNCTION
+  typename std::enable_if<(  std::is_integral<Idx>::value
+                          && std::is_same<void, work_tag>::value
+                          && MDRange::rank == 2
+                          && MDRange::inner_direction == MDRange::Flat
+                          )>::type
+  operator()(Idx t) const
+  {
+    if (  MDRange::outer_direction == MDRange::Right ) {
+      m_func( m_range.m_offset[0] + ( t / m_range.m_dim[1] )
+            , m_range.m_offset[1] + ( t % m_range.m_dim[1] ) );
+    } else {
+      m_func( m_range.m_offset[0] + ( t % m_range.m_dim[0] )
+            , m_range.m_offset[1] + ( t / m_range.m_dim[0] ) );
+    }
+  }
+
+  // Rank-2, Flat, Tag
+  template <typename Idx>
+  KOKKOS_FORCEINLINE_FUNCTION
+  typename std::enable_if<(  std::is_integral<Idx>::value
+                          && !std::is_same<void, work_tag>::value
+                          && MDRange::rank == 2
+                          && MDRange::inner_direction == MDRange::Flat
+                          )>::type
+  operator()(Idx t) const
+  {
+    if (  MDRange::outer_direction == MDRange::Right ) {
+      m_func( work_tag{}, m_range.m_offset[0] + ( t / m_range.m_dim[1] )
+            , m_range.m_offset[1] + ( t % m_range.m_dim[1] ) );
+    } else {
+      m_func( work_tag{}, m_range.m_offset[0] + ( t % m_range.m_dim[0] )
+            , m_range.m_offset[1] + ( t / m_range.m_dim[0] ) );
+    }
+  }
+
+  // Rank-2, Not Flat, No Tag
+  template <typename Idx>
+  KOKKOS_FORCEINLINE_FUNCTION
+  typename std::enable_if<(  std::is_integral<Idx>::value
+                          && std::is_same<void, work_tag>::value
+                          && MDRange::rank == 2
+                          && MDRange::inner_direction != MDRange::Flat
+                          )>::type
+  operator()(Idx t) const
+  {
+    index_type t0, t1;
+    if (  MDRange::outer_direction == MDRange::Right ) {
+      t0 = t / m_range.m_tile_dim[1];
+      t1 = t % m_range.m_tile_dim[1];
+    } else {
+      t0 = t % m_range.m_tile_dim[0];
+      t1 = t / m_range.m_tile_dim[0];
+    }
+
+    const index_type b0 = t0 * m_range.m_tile[0] + m_range.m_offset[0];
+    const index_type b1 = t1 * m_range.m_tile[1] + m_range.m_offset[1];
+
+    const index_type e0 = b0 + m_range.m_tile[0] <= (m_range.m_dim[0] + m_range.m_offset[0] ) ? b0 + m_range.m_tile[0] : ( m_range.m_dim[0] + m_range.m_offset[0] );
+    const index_type e1 = b1 + m_range.m_tile[1] <= (m_range.m_dim[1] + m_range.m_offset[1] ) ? b1 + m_range.m_tile[1] : ( m_range.m_dim[1] + m_range.m_offset[1] );
+
+    if (  MDRange::inner_direction == MDRange::Right ) {
+      for (int i0=b0; i0<e0; ++i0) {
+      #if defined(KOKKOS_MDRANGE_IVDEP)
+      #pragma ivdep
+      #endif
+      for (int i1=b1; i1<e1; ++i1) {
+        m_func( i0, i1 );
+      }}
+    } else {
+      for (int i1=b1; i1<e1; ++i1) {
+      #if defined(KOKKOS_MDRANGE_IVDEP)
+      #pragma ivdep
+      #endif
+      for (int i0=b0; i0<e0; ++i0) {
+        m_func( i0, i1 );
+      }}
+    }
+  }
+
+  // Rank-2, Not Flat, Tag
+  template <typename Idx>
+  KOKKOS_FORCEINLINE_FUNCTION
+  typename std::enable_if<(  std::is_integral<Idx>::value
+                          && !std::is_same<void, work_tag>::value
+                          && MDRange::rank == 2
+                          && MDRange::inner_direction != MDRange::Flat
+                          )>::type
+  operator()(Idx t) const
+  {
+    work_tag tag;
+
+    index_type t0, t1;
+    if (  MDRange::outer_direction == MDRange::Right ) {
+      t0 = t / m_range.m_tile_dim[1];
+      t1 = t % m_range.m_tile_dim[1];
+    } else {
+      t0 = t % m_range.m_tile_dim[0];
+      t1 = t / m_range.m_tile_dim[0];
+    }
+
+    const index_type b0 = t0 * m_range.m_tile[0] + m_range.m_offset[0];
+    const index_type b1 = t1 * m_range.m_tile[1] + m_range.m_offset[1];
+
+    const index_type e0 = b0 + m_range.m_tile[0] <= (m_range.m_dim[0] + m_range.m_offset[0] ) ? b0 + m_range.m_tile[0] : ( m_range.m_dim[0] + m_range.m_offset[0] );
+    const index_type e1 = b1 + m_range.m_tile[1] <= (m_range.m_dim[1] + m_range.m_offset[1] ) ? b1 + m_range.m_tile[1] : ( m_range.m_dim[1] + m_range.m_offset[1] );
+
+    if (  MDRange::inner_direction == MDRange::Right ) {
+      for (int i0=b0; i0<e0; ++i0) {
+      #if defined(KOKKOS_MDRANGE_IVDEP)
+      #pragma ivdep
+      #endif
+      for (int i1=b1; i1<e1; ++i1) {
+        m_func( tag, i0, i1 );
+      }}
+    } else {
+      for (int i1=b1; i1<e1; ++i1) {
+      #if defined(KOKKOS_MDRANGE_IVDEP)
+      #pragma ivdep
+      #endif
+      for (int i0=b0; i0<e0; ++i0) {
+        m_func( tag, i0, i1 );
+      }}
+    }
+  }
+
+  //---------------------------------------------------------------------------
+
+  // Rank-3, Flat, No Tag
+  template <typename Idx>
+  KOKKOS_FORCEINLINE_FUNCTION
+  typename std::enable_if<(  std::is_integral<Idx>::value
+                          && std::is_same<void, work_tag>::value
+                          && MDRange::rank == 3
+                          && MDRange::inner_direction == MDRange::Flat
+                          )>::type
+  operator()(Idx t) const
+  {
+    if (  MDRange::outer_direction == MDRange::Right ) {
+    const int64_t tmp_prod = m_range.m_dim[1]*m_range.m_dim[2];
+    m_func( m_range.m_offset[0] + (  t / tmp_prod )
+          , m_range.m_offset[1] + ( (t % tmp_prod) / m_range.m_dim[2] )
+          , m_range.m_offset[2] + ( (t % tmp_prod) % m_range.m_dim[2] )
+          );
+    } else {
+    const int64_t tmp_prod = m_range.m_dim[0]*m_range.m_dim[1];
+    m_func( m_range.m_offset[0] + ( (t % tmp_prod) % m_range.m_dim[0] )
+          , m_range.m_offset[1] + ( (t % tmp_prod) / m_range.m_dim[0] )
+          , m_range.m_offset[2] + (  t / tmp_prod )
+          );
+    }
+  }
+
+  // Rank-3, Flat, Tag
+  template <typename Idx>
+  KOKKOS_FORCEINLINE_FUNCTION
+  typename std::enable_if<(  std::is_integral<Idx>::value
+                          && !std::is_same<void, work_tag>::value
+                          && MDRange::rank == 3
+                          && MDRange::inner_direction == MDRange::Flat
+                          )>::type
+  operator()(Idx t) const
+  {
+    if (  MDRange::outer_direction == MDRange::Right ) {
+      const int64_t tmp_prod = m_range.m_dim[1]*m_range.m_dim[2];
+      m_func( work_tag{}
+            , m_range.m_offset[0] + (  t / tmp_prod )
+            , m_range.m_offset[1] + ( (t % tmp_prod) / m_range.m_dim[2] )
+            , m_range.m_offset[2] + ( (t % tmp_prod) % m_range.m_dim[2] )
+            );
+    } else {
+      const int64_t tmp_prod = m_range.m_dim[0]*m_range.m_dim[1];
+      m_func( work_tag{}
+            , m_range.m_offset[0] + ( (t % tmp_prod) % m_range.m_dim[0] )
+            , m_range.m_offset[1] + ( (t % tmp_prod) / m_range.m_dim[0] )
+            , m_range.m_offset[2] + (  t / tmp_prod )
+            );
+    }
+  }
+
+  // Rank-3, Not Flat, No Tag
+  template <typename Idx>
+  KOKKOS_FORCEINLINE_FUNCTION
+  typename std::enable_if<(  std::is_integral<Idx>::value
+                          && std::is_same<void, work_tag>::value
+                          && MDRange::rank == 3
+                          && MDRange::inner_direction != MDRange::Flat
+                          )>::type
+  operator()(Idx t) const
+  {
+    index_type t0, t1, t2;
+    if (  MDRange::outer_direction == MDRange::Right ) {
+      const index_type tmp_prod = ( m_range.m_tile_dim[1]*m_range.m_tile_dim[2]);
+      t0 = t / tmp_prod;
+      t1 = ( t % tmp_prod ) / m_range.m_tile_dim[2];
+      t2 = ( t % tmp_prod ) % m_range.m_tile_dim[2];
+    } else {
+      const index_type tmp_prod = ( m_range.m_tile_dim[0]*m_range.m_tile_dim[1]);
+      t0 = ( t % tmp_prod ) % m_range.m_tile_dim[0];
+      t1 = ( t % tmp_prod ) / m_range.m_tile_dim[0];
+      t2 = t / tmp_prod;
+    }
+
+    const index_type b0 = t0 * m_range.m_tile[0] + m_range.m_offset[0];
+    const index_type b1 = t1 * m_range.m_tile[1] + m_range.m_offset[1];
+    const index_type b2 = t2 * m_range.m_tile[2] + m_range.m_offset[2];
+
+    const index_type e0 = b0 + m_range.m_tile[0] <= (m_range.m_dim[0] + m_range.m_offset[0] ) ? b0 + m_range.m_tile[0] : ( m_range.m_dim[0] + m_range.m_offset[0] );
+    const index_type e1 = b1 + m_range.m_tile[1] <= (m_range.m_dim[1] + m_range.m_offset[1] ) ? b1 + m_range.m_tile[1] : ( m_range.m_dim[1] + m_range.m_offset[1] );
+    const index_type e2 = b2 + m_range.m_tile[2] <= (m_range.m_dim[2] + m_range.m_offset[2] ) ? b2 + m_range.m_tile[2] : ( m_range.m_dim[2] + m_range.m_offset[2] );
+
+    if (  MDRange::inner_direction == MDRange::Right ) {
+      for (int i0=b0; i0<e0; ++i0) {
+      for (int i1=b1; i1<e1; ++i1) {
+      #if defined(KOKKOS_MDRANGE_IVDEP)
+      #pragma ivdep
+      #endif
+      for (int i2=b2; i2<e2; ++i2) {
+        m_func( i0, i1, i2 );
+      }}}
+    } else {
+      for (int i2=b2; i2<e2; ++i2) {
+      for (int i1=b1; i1<e1; ++i1) {
+      #if defined(KOKKOS_MDRANGE_IVDEP)
+      #pragma ivdep
+      #endif
+      for (int i0=b0; i0<e0; ++i0) {
+        m_func( i0, i1, i2 );
+      }}}
+    }
+  }
+
+  // Rank-3, Not Flat, Tag
+  template <typename Idx>
+  KOKKOS_FORCEINLINE_FUNCTION
+  typename std::enable_if<(  std::is_integral<Idx>::value
+                          && !std::is_same<void, work_tag>::value
+                          && MDRange::rank == 3
+                          && MDRange::inner_direction != MDRange::Flat
+                          )>::type
+  operator()(Idx t) const
+  {
+    work_tag tag;
+
+    index_type t0, t1, t2;
+    if (  MDRange::outer_direction == MDRange::Right ) {
+      const index_type tmp_prod = ( m_range.m_tile_dim[1]*m_range.m_tile_dim[2]);
+      t0 = t / tmp_prod;
+      t1 = ( t % tmp_prod ) / m_range.m_tile_dim[2];
+      t2 = ( t % tmp_prod ) % m_range.m_tile_dim[2];
+    } else {
+      const index_type tmp_prod = ( m_range.m_tile_dim[0]*m_range.m_tile_dim[1]);
+      t0 = ( t % tmp_prod ) % m_range.m_tile_dim[0];
+      t1 = ( t % tmp_prod ) / m_range.m_tile_dim[0];
+      t2 = t / tmp_prod;
+    }
+
+    const index_type b0 = t0 * m_range.m_tile[0] + m_range.m_offset[0];
+    const index_type b1 = t1 * m_range.m_tile[1] + m_range.m_offset[1];
+    const index_type b2 = t2 * m_range.m_tile[2] + m_range.m_offset[2];
+
+    const index_type e0 = b0 + m_range.m_tile[0] <= (m_range.m_dim[0] + m_range.m_offset[0] ) ? b0 + m_range.m_tile[0] : ( m_range.m_dim[0] + m_range.m_offset[0] );
+    const index_type e1 = b1 + m_range.m_tile[1] <= (m_range.m_dim[1] + m_range.m_offset[1] ) ? b1 + m_range.m_tile[1] : ( m_range.m_dim[1] + m_range.m_offset[1] );
+    const index_type e2 = b2 + m_range.m_tile[2] <= (m_range.m_dim[2] + m_range.m_offset[2] ) ? b2 + m_range.m_tile[2] : ( m_range.m_dim[2] + m_range.m_offset[2] );
+
+    if (  MDRange::inner_direction == MDRange::Right ) {
+      for (int i0=b0; i0<e0; ++i0) {
+      for (int i1=b1; i1<e1; ++i1) {
+      #if defined(KOKKOS_MDRANGE_IVDEP)
+      #pragma ivdep
+      #endif
+      for (int i2=b2; i2<e2; ++i2) {
+        m_func( tag, i0, i1, i2 );
+      }}}
+    } else {
+      for (int i2=b2; i2<e2; ++i2) {
+      for (int i1=b1; i1<e1; ++i1) {
+      #if defined(KOKKOS_MDRANGE_IVDEP)
+      #pragma ivdep
+      #endif
+      for (int i0=b0; i0<e0; ++i0) {
+        m_func( tag, i0, i1, i2 );
+      }}}
+    }
+  }
+};
+
+
+
+} // namespace Impl
+
+
+template <typename MDRange, typename Functor>
+void md_parallel_for( MDRange const& range
+                    , Functor const& f
+                    , const std::string& str = ""
+                    )
+{
+  Impl::MDForFunctor<MDRange, Functor> g(range, f);
+
+  using range_policy = typename MDRange::range_policy;
+
+  Kokkos::parallel_for( range_policy(0, range.m_num_tiles).set_chunk_size(1), g, str );
+}
+
+template <typename MDRange, typename Functor>
+void md_parallel_for( const std::string& str
+                    , MDRange const& range
+                    , Functor const& f
+                    )
+{
+  Impl::MDForFunctor<MDRange, Functor> g(range, f);
+
+  using range_policy = typename MDRange::range_policy;
+
+  Kokkos::parallel_for( range_policy(0, range.m_num_tiles).set_chunk_size(1), g, str );
+}
+
+}} // namespace Kokkos::Experimental
+
+#endif //KOKKOS_CORE_EXP_MD_RANGE_POLICY_HPP
+
diff --git a/lib/kokkos/core/src/KokkosExp_View.hpp b/lib/kokkos/core/src/KokkosExp_View.hpp
deleted file mode 100644
index f62d318f2e..0000000000
--- a/lib/kokkos/core/src/KokkosExp_View.hpp
+++ /dev/null
@@ -1,2306 +0,0 @@
-/*
-//@HEADER
-// ************************************************************************
-// 
-//                        Kokkos v. 2.0
-//              Copyright (2014) Sandia Corporation
-// 
-// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
-// the U.S. Government retains certain rights in this software.
-// 
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are
-// met:
-//
-// 1. Redistributions of source code must retain the above copyright
-// notice, this list of conditions and the following disclaimer.
-//
-// 2. Redistributions in binary form must reproduce the above copyright
-// notice, this list of conditions and the following disclaimer in the
-// documentation and/or other materials provided with the distribution.
-//
-// 3. Neither the name of the Corporation nor the names of the
-// contributors may be used to endorse or promote products derived from
-// this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
-// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
-// ************************************************************************
-//@HEADER
-*/
-
-#ifndef KOKKOS_EXP_VIEW_HPP
-#define KOKKOS_EXP_VIEW_HPP
-
-#include <string>
-#include <algorithm>
-#include <type_traits>
-#include <initializer_list>
-
-#include <Kokkos_Core_fwd.hpp>
-#include <Kokkos_HostSpace.hpp>
-#include <Kokkos_MemoryTraits.hpp>
-#include <Kokkos_ExecPolicy.hpp>
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-namespace Impl {
-
-template< class DstMemorySpace , class SrcMemorySpace >
-struct DeepCopy ;
-
-template< class DataType >
-struct ViewArrayAnalysis ;
-
-template< class DataType , class ArrayLayout 
-        , typename ValueType =
-          typename ViewArrayAnalysis< DataType >::non_const_value_type
-        >
-struct ViewDataAnalysis ;
-
-template< class , class ... >
-class ViewMapping { public: enum { is_assignable = false }; };
-
-template< class MemorySpace >
-struct ViewOperatorBoundsErrorAbort ;
-
-template<>
-struct ViewOperatorBoundsErrorAbort< Kokkos::HostSpace > {
-  static void apply( const size_t rank
-                   , const size_t n0 , const size_t n1 
-                   , const size_t n2 , const size_t n3 
-                   , const size_t n4 , const size_t n5 
-                   , const size_t n6 , const size_t n7 
-                   , const size_t i0 , const size_t i1 
-                   , const size_t i2 , const size_t i3 
-                   , const size_t i4 , const size_t i5 
-                   , const size_t i6 , const size_t i7 );
-};
-
-} /* namespace Impl */
-} /* namespace Experimental */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-
-/** \class ViewTraits
- *  \brief Traits class for accessing attributes of a View.
- *
- * This is an implementation detail of View.  It is only of interest
- * to developers implementing a new specialization of View.
- *
- * Template argument options:
- *   - View< DataType >
- *   - View< DataType , Space >
- *   - View< DataType , Space , MemoryTraits >
- *   - View< DataType , ArrayLayout >
- *   - View< DataType , ArrayLayout , Space >
- *   - View< DataType , ArrayLayout , MemoryTraits >
- *   - View< DataType , ArrayLayout , Space , MemoryTraits >
- *   - View< DataType , MemoryTraits >
- */
-
-template< class DataType , class ... Properties >
-struct ViewTraits ;
-
-template<>
-struct ViewTraits< void >
-{
-  typedef void  execution_space ;
-  typedef void  memory_space ;
-  typedef void  HostMirrorSpace ;
-  typedef void  array_layout ;
-  typedef void  memory_traits ;
-};
-
-template< class ... Prop >
-struct ViewTraits< void , void , Prop ... >
-{
-  // Ignore an extraneous 'void'
-  typedef typename ViewTraits<void,Prop...>::execution_space  execution_space ;
-  typedef typename ViewTraits<void,Prop...>::memory_space     memory_space ;
-  typedef typename ViewTraits<void,Prop...>::HostMirrorSpace  HostMirrorSpace ;
-  typedef typename ViewTraits<void,Prop...>::array_layout     array_layout ;
-  typedef typename ViewTraits<void,Prop...>::memory_traits    memory_traits ;
-};
-
-template< class ArrayLayout , class ... Prop >
-struct ViewTraits< typename std::enable_if< Kokkos::Impl::is_array_layout<ArrayLayout>::value >::type , ArrayLayout , Prop ... >
-{
-  // Specify layout, keep subsequent space and memory traits arguments
-
-  typedef typename ViewTraits<void,Prop...>::execution_space  execution_space ;
-  typedef typename ViewTraits<void,Prop...>::memory_space     memory_space ;
-  typedef typename ViewTraits<void,Prop...>::HostMirrorSpace  HostMirrorSpace ;
-  typedef          ArrayLayout                                array_layout ;
-  typedef typename ViewTraits<void,Prop...>::memory_traits    memory_traits ;
-};
-
-template< class Space , class ... Prop >
-struct ViewTraits< typename std::enable_if< Kokkos::Impl::is_space<Space>::value >::type , Space , Prop ... >
-{
-  // Specify Space, memory traits should be the only subsequent argument.
-
-  static_assert( std::is_same< typename ViewTraits<void,Prop...>::execution_space , void >::value ||
-                 std::is_same< typename ViewTraits<void,Prop...>::memory_space    , void >::value ||
-                 std::is_same< typename ViewTraits<void,Prop...>::HostMirrorSpace , void >::value ||
-                 std::is_same< typename ViewTraits<void,Prop...>::array_layout    , void >::value
-               , "Only one View Execution or Memory Space template argument" );
-
-  typedef typename Space::execution_space                   execution_space ;
-  typedef typename Space::memory_space                      memory_space ;
-  typedef typename Kokkos::Impl::is_space< Space >::host_mirror_space
-      HostMirrorSpace ;
-  typedef typename execution_space::array_layout            array_layout ;
-  typedef typename ViewTraits<void,Prop...>::memory_traits  memory_traits ;
-};
-
-template< class MemoryTraits , class ... Prop >
-struct ViewTraits< typename std::enable_if< Kokkos::Impl::is_memory_traits<MemoryTraits>::value >::type , MemoryTraits , Prop ... >
-{
-  // Specify memory trait, should not be any subsequent arguments
-
-  static_assert( std::is_same< typename ViewTraits<void,Prop...>::execution_space , void >::value ||
-                 std::is_same< typename ViewTraits<void,Prop...>::memory_space    , void >::value ||
-                 std::is_same< typename ViewTraits<void,Prop...>::array_layout    , void >::value ||
-                 std::is_same< typename ViewTraits<void,Prop...>::memory_traits   , void >::value
-               , "MemoryTrait is the final optional template argument for a View" );
-
-  typedef void          execution_space ;
-  typedef void          memory_space ;
-  typedef void          HostMirrorSpace ;
-  typedef void          array_layout ;
-  typedef MemoryTraits  memory_traits ;
-};
-
-
-template< class DataType , class ... Properties >
-struct ViewTraits {
-private:
-
-  // Unpack the properties arguments
-  typedef ViewTraits< void , Properties ... >  prop ;
-
-  typedef typename
-    std::conditional< ! std::is_same< typename prop::execution_space , void >::value
-                    , typename prop::execution_space
-                    , Kokkos::DefaultExecutionSpace
-                    >::type
-      ExecutionSpace ;
-
-  typedef typename
-    std::conditional< ! std::is_same< typename prop::memory_space , void >::value
-                    , typename prop::memory_space
-                    , typename ExecutionSpace::memory_space
-                    >::type
-      MemorySpace ;
-
-  typedef typename
-    std::conditional< ! std::is_same< typename prop::array_layout , void >::value
-                    , typename prop::array_layout
-                    , typename ExecutionSpace::array_layout
-                    >::type
-      ArrayLayout ;
-
-  typedef typename
-    std::conditional
-      < ! std::is_same< typename prop::HostMirrorSpace , void >::value
-      , typename prop::HostMirrorSpace
-      , typename Kokkos::Impl::is_space< ExecutionSpace >::host_mirror_space
-      >::type
-      HostMirrorSpace ;
-
-  typedef typename
-    std::conditional< ! std::is_same< typename prop::memory_traits , void >::value
-                    , typename prop::memory_traits
-                    , typename Kokkos::MemoryManaged
-                    >::type
-      MemoryTraits ;
-
-  // Analyze data type's properties,
-  // May be specialized based upon the layout and value type
-  typedef Kokkos::Experimental::Impl::ViewDataAnalysis< DataType , ArrayLayout > data_analysis ;
-
-public:
-
-  //------------------------------------
-  // Data type traits:
-
-  typedef typename data_analysis::type            data_type ;
-  typedef typename data_analysis::const_type      const_data_type ;
-  typedef typename data_analysis::non_const_type  non_const_data_type ;
-
-  //------------------------------------
-  // Compatible array of trivial type traits:
-
-  typedef typename data_analysis::scalar_array_type            scalar_array_type ;
-  typedef typename data_analysis::const_scalar_array_type      const_scalar_array_type ;
-  typedef typename data_analysis::non_const_scalar_array_type  non_const_scalar_array_type ;
-
-  //------------------------------------
-  // Value type traits:
-
-  typedef typename data_analysis::value_type            value_type ;
-  typedef typename data_analysis::const_value_type      const_value_type ;
-  typedef typename data_analysis::non_const_value_type  non_const_value_type ;
-
-  //------------------------------------
-  // Mapping traits:
-
-  typedef ArrayLayout                         array_layout ;
-  typedef typename data_analysis::dimension   dimension ;
-  typedef typename data_analysis::specialize  specialize /* mapping specialization tag */ ;
-
-  enum { rank         = dimension::rank };
-  enum { rank_dynamic = dimension::rank_dynamic };
-
-  //------------------------------------
-  // Execution space, memory space, memory access traits, and host mirror space.
-
-  typedef ExecutionSpace                              execution_space ;
-  typedef MemorySpace                                 memory_space ;
-  typedef Kokkos::Device<ExecutionSpace,MemorySpace>  device_type ;
-  typedef MemoryTraits                                memory_traits ;
-  typedef HostMirrorSpace                             host_mirror_space ;
-
-  typedef typename MemorySpace::size_type  size_type ;
-
-  enum { is_hostspace      = std::is_same< MemorySpace , HostSpace >::value };
-  enum { is_managed        = MemoryTraits::Unmanaged    == 0 };
-  enum { is_random_access  = MemoryTraits::RandomAccess == 1 };
-
-  //------------------------------------
-};
-
-/** \class View
- *  \brief View to an array of data.
- *
- * A View represents an array of one or more dimensions.
- * For details, please refer to Kokkos' tutorial materials.
- *
- * \section Kokkos_View_TemplateParameters Template parameters
- *
- * This class has both required and optional template parameters.  The
- * \c DataType parameter must always be provided, and must always be
- * first. The parameters \c Arg1Type, \c Arg2Type, and \c Arg3Type are
- * placeholders for different template parameters.  The default value
- * of the fifth template parameter \c Specialize suffices for most use
- * cases.  When explaining the template parameters, we won't refer to
- * \c Arg1Type, \c Arg2Type, and \c Arg3Type; instead, we will refer
- * to the valid categories of template parameters, in whatever order
- * they may occur.
- *
- * Valid ways in which template arguments may be specified:
- *   - View< DataType >
- *   - View< DataType , Layout >
- *   - View< DataType , Layout , Space >
- *   - View< DataType , Layout , Space , MemoryTraits >
- *   - View< DataType , Space >
- *   - View< DataType , Space , MemoryTraits >
- *   - View< DataType , MemoryTraits >
- *
- * \tparam DataType (required) This indicates both the type of each
- *   entry of the array, and the combination of compile-time and
- *   run-time array dimension(s).  For example, <tt>double*</tt>
- *   indicates a one-dimensional array of \c double with run-time
- *   dimension, and <tt>int*[3]</tt> a two-dimensional array of \c int
- *   with run-time first dimension and compile-time second dimension
- *   (of 3).  In general, the run-time dimensions (if any) must go
- *   first, followed by zero or more compile-time dimensions.  For
- *   more examples, please refer to the tutorial materials.
- *
- * \tparam Space (required) The memory space.
- *
- * \tparam Layout (optional) The array's layout in memory.  For
- *   example, LayoutLeft indicates a column-major (Fortran style)
- *   layout, and LayoutRight a row-major (C style) layout.  If not
- *   specified, this defaults to the preferred layout for the
- *   <tt>Space</tt>.
- *
- * \tparam MemoryTraits (optional) Assertion of the user's intended
- *   access behavior.  For example, RandomAccess indicates read-only
- *   access with limited spatial locality, and Unmanaged lets users
- *   wrap externally allocated memory in a View without automatic
- *   deallocation.
- *
- * \section Kokkos_View_MT MemoryTraits discussion
- *
- * \subsection Kokkos_View_MT_Interp MemoryTraits interpretation depends on Space
- *
- * Some \c MemoryTraits options may have different interpretations for
- * different \c Space types.  For example, with the Cuda device,
- * \c RandomAccess tells Kokkos to fetch the data through the texture
- * cache, whereas the non-GPU devices have no such hardware construct.
- *
- * \subsection Kokkos_View_MT_PrefUse Preferred use of MemoryTraits
- *
- * Users should defer applying the optional \c MemoryTraits parameter
- * until the point at which they actually plan to rely on it in a
- * computational kernel.  This minimizes the number of template
- * parameters exposed in their code, which reduces the cost of
- * compilation.  Users may always assign a View without specified
- * \c MemoryTraits to a compatible View with that specification.
- * For example:
- * \code
- * // Pass in the simplest types of View possible.
- * void
- * doSomething (View<double*, Cuda> out,
- *              View<const double*, Cuda> in)
- * {
- *   // Assign the "generic" View in to a RandomAccess View in_rr.
- *   // Note that RandomAccess View objects must have const data.
- *   View<const double*, Cuda, RandomAccess> in_rr = in;
- *   // ... do something with in_rr and out ...
- * }
- * \endcode
- */
-template< class DataType , class ... Properties >
-class View ;
-
-} /* namespace Experimental */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-#include <impl/KokkosExp_ViewMapping.hpp>
-#include <impl/KokkosExp_ViewArray.hpp>
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-
-namespace {
-
-constexpr Kokkos::Experimental::Impl::ALL_t
-  ALL = Kokkos::Experimental::Impl::ALL_t();
-
-constexpr Kokkos::Experimental::Impl::WithoutInitializing_t
-  WithoutInitializing = Kokkos::Experimental::Impl::WithoutInitializing_t();
-
-constexpr Kokkos::Experimental::Impl::AllowPadding_t       
-  AllowPadding        = Kokkos::Experimental::Impl::AllowPadding_t();
-
-}
-
-/** \brief  Create View allocation parameter bundle from argument list.
- *
- *  Valid argument list members are:
- *    1) label as a "string" or std::string
- *    2) memory space instance of the View::memory_space type
- *    3) execution space instance compatible with the View::memory_space
- *    4) Kokkos::WithoutInitializing to bypass initialization
- *    4) Kokkos::AllowPadding to allow allocation to pad dimensions for memory alignment
- */
-template< class ... Args >
-inline
-Impl::ViewCtorProp< typename Impl::ViewCtorProp< void , Args >::type ... >
-view_alloc( Args const & ... args )
-{
-  typedef 
-    Impl::ViewCtorProp< typename Impl::ViewCtorProp< void , Args >::type ... >
-      return_type ;
-
-  static_assert( ! return_type::has_pointer
-               , "Cannot give pointer-to-memory for view allocation" );
-
-  return return_type( args... );
-}
-
-template< class ... Args >
-inline
-Impl::ViewCtorProp< typename Impl::ViewCtorProp< void , Args >::type ... >
-view_wrap( Args const & ... args )
-{
-  typedef 
-    Impl::ViewCtorProp< typename Impl::ViewCtorProp< void , Args >::type ... >
-      return_type ;
-
-  static_assert( ! return_type::has_memory_space &&
-                 ! return_type::has_execution_space &&
-                 ! return_type::has_label &&
-                 return_type::has_pointer
-               , "Must only give pointer-to-memory for view wrapping" );
-
-  return return_type( args... );
-}
-
-} /* namespace Experimental */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-
-template< class DataType , class ... Properties >
-class View ;
-
-template< class > struct is_view : public std::false_type {};
-
-template< class D, class ... P >
-struct is_view< View<D,P...> > : public std::true_type {};
-
-template< class DataType , class ... Properties >
-class View : public ViewTraits< DataType , Properties ... > {
-private:
-
-  template< class , class ... > friend class View ;
-  template< class , class ... > friend class Impl::ViewMapping ;
-
-public:
-
-  typedef ViewTraits< DataType , Properties ... > traits ;
-
-private:
-
-  typedef Kokkos::Experimental::Impl::ViewMapping< traits , void > map_type ;
-  typedef Kokkos::Experimental::Impl::SharedAllocationTracker      track_type ;
-
-  track_type  m_track ;
-  map_type    m_map ;
-
-public:
-
-  //----------------------------------------
-  /** \brief  Compatible view of array of scalar types */
-  typedef View< typename traits::scalar_array_type ,
-                typename traits::array_layout ,
-                typename traits::device_type ,
-                typename traits::memory_traits > 
-    array_type ;
-
-  /** \brief  Compatible view of const data type */
-  typedef View< typename traits::const_data_type ,
-                typename traits::array_layout ,
-                typename traits::device_type ,
-                typename traits::memory_traits > 
-    const_type ;
-
-  /** \brief  Compatible view of non-const data type */
-  typedef View< typename traits::non_const_data_type ,
-                typename traits::array_layout ,
-                typename traits::device_type ,
-                typename traits::memory_traits > 
-    non_const_type ;
-
-  /** \brief  Compatible HostMirror view */
-  typedef View< typename traits::non_const_data_type ,
-                typename traits::array_layout ,
-                typename traits::host_mirror_space >
-    HostMirror ;
-
-  //----------------------------------------
-  // Domain rank and extents
-
-  enum { Rank = map_type::Rank };
-
-  template< typename iType >
-  KOKKOS_INLINE_FUNCTION constexpr
-  typename std::enable_if< std::is_integral<iType>::value , size_t >::type
-  extent( const iType & r ) const
-    { return m_map.extent(r); }
-
-  template< typename iType >
-  KOKKOS_INLINE_FUNCTION constexpr
-  typename std::enable_if< std::is_integral<iType>::value , int >::type
-  extent_int( const iType & r ) const
-    { return static_cast<int>(m_map.extent(r)); }
-
-  KOKKOS_INLINE_FUNCTION constexpr
-  typename traits::array_layout layout() const
-    { return m_map.layout(); }
-
-  //----------------------------------------
-  /*  Deprecate all 'dimension' functions in favor of
-   *  ISO/C++ vocabulary 'extent'.
-   */
-
-  template< typename iType >
-  KOKKOS_INLINE_FUNCTION constexpr
-  typename std::enable_if< std::is_integral<iType>::value , size_t >::type
-  dimension( const iType & r ) const { return extent( r ); }
-
-  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_0() const { return m_map.dimension_0(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_1() const { return m_map.dimension_1(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_2() const { return m_map.dimension_2(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_3() const { return m_map.dimension_3(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_4() const { return m_map.dimension_4(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_5() const { return m_map.dimension_5(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_6() const { return m_map.dimension_6(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_7() const { return m_map.dimension_7(); }
-
-  //----------------------------------------
-
-  KOKKOS_INLINE_FUNCTION constexpr size_t size() const { return m_map.dimension_0() *
-                                                                m_map.dimension_1() *
-                                                                m_map.dimension_2() *
-                                                                m_map.dimension_3() *
-                                                                m_map.dimension_4() *
-                                                                m_map.dimension_5() *
-                                                                m_map.dimension_6() *
-                                                                m_map.dimension_7(); }
-
-  KOKKOS_INLINE_FUNCTION constexpr size_t stride_0() const { return m_map.stride_0(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t stride_1() const { return m_map.stride_1(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t stride_2() const { return m_map.stride_2(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t stride_3() const { return m_map.stride_3(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t stride_4() const { return m_map.stride_4(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t stride_5() const { return m_map.stride_5(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t stride_6() const { return m_map.stride_6(); }
-  KOKKOS_INLINE_FUNCTION constexpr size_t stride_7() const { return m_map.stride_7(); }
-
-  template< typename iType >
-  KOKKOS_INLINE_FUNCTION void stride( iType * const s ) const { m_map.stride(s); }
-
-  //----------------------------------------
-  // Range span is the span which contains all members.
-
-  typedef typename map_type::reference_type  reference_type ;
-  typedef typename map_type::pointer_type    pointer_type ;
-
-  enum { reference_type_is_lvalue_reference = std::is_lvalue_reference< reference_type >::value };
-
-  KOKKOS_INLINE_FUNCTION constexpr size_t span() const { return m_map.span(); }
-  // Deprecated, use 'span()' instead
-  KOKKOS_INLINE_FUNCTION constexpr size_t capacity() const { return m_map.span(); }
-  KOKKOS_INLINE_FUNCTION constexpr bool   span_is_contiguous() const { return m_map.span_is_contiguous(); }
-  KOKKOS_INLINE_FUNCTION constexpr pointer_type data() const { return m_map.data(); }
-
-  // Deprecated, use 'span_is_contigous()' instead
-  KOKKOS_INLINE_FUNCTION constexpr bool   is_contiguous() const { return m_map.span_is_contiguous(); }
-  // Deprecated, use 'data()' instead
-  KOKKOS_INLINE_FUNCTION constexpr pointer_type ptr_on_device() const { return m_map.data(); }
-
-  //----------------------------------------
-  // Allow specializations to query their specialized map
-
-  KOKKOS_INLINE_FUNCTION
-  const Kokkos::Experimental::Impl::ViewMapping< traits , void > &
-  implementation_map() const { return m_map ; }
-
-  //----------------------------------------
-
-private:
-
-  enum {
-    is_layout_left = std::is_same< typename traits::array_layout
-                                  , Kokkos::LayoutLeft >::value ,
-
-    is_layout_right = std::is_same< typename traits::array_layout
-                                  , Kokkos::LayoutRight >::value ,
-
-    is_layout_stride = std::is_same< typename traits::array_layout
-                                   , Kokkos::LayoutStride >::value ,
-
-    is_default_map =
-      std::is_same< typename traits::specialize , void >::value &&
-      ( is_layout_left || is_layout_right || is_layout_stride )
-  };
-
-#if defined( KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK )
-
-#define KOKKOS_VIEW_OPERATOR_VERIFY( ARG ) \
-  Kokkos::Impl::VerifyExecutionCanAccessMemorySpace \
-    < Kokkos::Impl::ActiveExecutionMemorySpace , typename traits::memory_space >::verify(); \
-  Kokkos::Experimental::Impl::view_verify_operator_bounds ARG ;
-
-#else
-
-#define KOKKOS_VIEW_OPERATOR_VERIFY( ARG ) \
-  Kokkos::Impl::VerifyExecutionCanAccessMemorySpace \
-    < Kokkos::Impl::ActiveExecutionMemorySpace , typename traits::memory_space >::verify();
-
-#endif
-
-public:
-
-  //------------------------------
-  // Rank 0 operator()
-
-  template< class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<( Kokkos::Impl::are_integral<Args...>::value
-                            && ( 0 == Rank )
-                          ), reference_type >::type
-  operator()( Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,args...) )
-
-      return m_map.reference();
-    }
-
-  //------------------------------
-  // Rank 1 operator()
-
-  template< typename I0
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,Args...>::value
-      && ( 1 == Rank )
-      && ! is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,args...) )
-
-      return m_map.reference(i0);
-    }
-
-  template< typename I0
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,Args...>::value
-      && ( 1 == Rank )
-      && is_default_map
-      && ! is_layout_stride
-    ), reference_type >::type
-  operator()( const I0 & i0
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,args...) )
-
-      return m_map.m_handle[ i0 ];
-    }
-
-  template< typename I0
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,Args...>::value
-      && ( 1 == Rank )
-      && is_default_map
-      && is_layout_stride
-    ), reference_type >::type
-  operator()( const I0 & i0
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,args...) )
-
-      return m_map.m_handle[ m_map.m_offset.m_stride.S0 * i0 ];
-    }
-
-  //------------------------------
-  // Rank 1 operator[]
-
-  template< typename I0 >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0>::value
-      && ( 1 == Rank )
-      && ! is_default_map
-    ), reference_type >::type
-  operator[]( const I0 & i0 ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0) )
-
-      return m_map.reference(i0);
-    }
-
-  template< typename I0 >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0>::value
-      && ( 1 == Rank )
-      && is_default_map
-      && ! is_layout_stride
-    ), reference_type >::type
-  operator[]( const I0 & i0 ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0) )
-
-      return m_map.m_handle[ i0 ];
-    }
-
-  template< typename I0 >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0>::value
-      && ( 1 == Rank )
-      && is_default_map
-      && is_layout_stride
-    ), reference_type >::type
-  operator[]( const I0 & i0 ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0) )
-
-      return m_map.m_handle[ m_map.m_offset.m_stride.S0 * i0 ];
-    }
-
-  //------------------------------
-  // Rank 2
-
-  template< typename I0 , typename I1
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
-      && ( 2 == Rank )
-      && ! is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
-
-      return m_map.reference(i0,i1);
-    }
-
-  template< typename I0 , typename I1
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
-      && ( 2 == Rank )
-      && is_default_map
-      && is_layout_left && ( traits::rank_dynamic == 0 )
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
-
-      return m_map.m_handle[ i0 + m_map.m_offset.m_dim.N0 * i1 ];
-    }
-
-  template< typename I0 , typename I1
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
-      && ( 2 == Rank )
-      && is_default_map
-      && is_layout_left && ( traits::rank_dynamic != 0 )
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
-
-      return m_map.m_handle[ i0 + m_map.m_offset.m_stride * i1 ];
-    }
-
-  template< typename I0 , typename I1
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
-      && ( 2 == Rank )
-      && is_default_map
-      && is_layout_right && ( traits::rank_dynamic == 0 )
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
-
-      return m_map.m_handle[ i1 + m_map.m_offset.m_dim.N1 * i0 ];
-    }
-
-  template< typename I0 , typename I1
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
-      && ( 2 == Rank )
-      && is_default_map
-      && is_layout_right && ( traits::rank_dynamic != 0 )
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
-
-      return m_map.m_handle[ i1 + m_map.m_offset.m_stride * i0 ];
-    }
-
-  template< typename I0 , typename I1
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
-      && ( 2 == Rank )
-      && is_default_map
-      && is_layout_stride
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
-
-      return m_map.m_handle[ i0 * m_map.m_offset.m_stride.S0 +
-                             i1 * m_map.m_offset.m_stride.S1 ];
-    }
-
-  //------------------------------
-  // Rank 3
-
-  template< typename I0 , typename I1 , typename I2
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,Args...>::value
-      && ( 3 == Rank )
-      && is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,args...) )
-
-      return m_map.m_handle[ m_map.m_offset(i0,i1,i2) ];
-    }
-
-  template< typename I0 , typename I1 , typename I2
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,Args...>::value
-      && ( 3 == Rank )
-      && ! is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,args...) )
-
-      return m_map.reference(i0,i1,i2);
-    }
-
-  //------------------------------
-  // Rank 4
-
-  template< typename I0 , typename I1 , typename I2 , typename I3
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,Args...>::value
-      && ( 4 == Rank )
-      && is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,args...) )
-
-      return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3) ];
-    }
-
-  template< typename I0 , typename I1 , typename I2 , typename I3
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,Args...>::value
-      && ( 4 == Rank )
-      && ! is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,args...) )
-
-      return m_map.reference(i0,i1,i2,i3);
-    }
-
-  //------------------------------
-  // Rank 5
-
-  template< typename I0 , typename I1 , typename I2 , typename I3
-          , typename I4
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,Args...>::value
-      && ( 5 == Rank )
-      && is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
-            , const I4 & i4
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,args...) )
-
-      return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4) ];
-    }
-
-  template< typename I0 , typename I1 , typename I2 , typename I3
-          , typename I4
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,Args...>::value
-      && ( 5 == Rank )
-      && ! is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
-            , const I4 & i4
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,args...) )
-
-      return m_map.reference(i0,i1,i2,i3,i4);
-    }
-
-  //------------------------------
-  // Rank 6
-
-  template< typename I0 , typename I1 , typename I2 , typename I3
-          , typename I4 , typename I5
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,Args...>::value
-      && ( 6 == Rank )
-      && is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
-            , const I4 & i4 , const I5 & i5
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,args...) )
-
-      return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5) ];
-    }
-
-  template< typename I0 , typename I1 , typename I2 , typename I3
-          , typename I4 , typename I5
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,Args...>::value
-      && ( 6 == Rank )
-      && ! is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
-            , const I4 & i4 , const I5 & i5
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,args...) )
-
-      return m_map.reference(i0,i1,i2,i3,i4,i5);
-    }
-
-  //------------------------------
-  // Rank 7
-
-  template< typename I0 , typename I1 , typename I2 , typename I3
-          , typename I4 , typename I5 , typename I6
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,I6,Args...>::value
-      && ( 7 == Rank )
-      && is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
-            , const I4 & i4 , const I5 & i5 , const I6 & i6
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,i6,args...) )
-
-      return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5,i6) ];
-    }
-
-  template< typename I0 , typename I1 , typename I2 , typename I3
-          , typename I4 , typename I5 , typename I6
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,I6,Args...>::value
-      && ( 7 == Rank )
-      && ! is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
-            , const I4 & i4 , const I5 & i5 , const I6 & i6
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,i6,args...) )
-
-      return m_map.reference(i0,i1,i2,i3,i4,i5,i6);
-    }
-
-  //------------------------------
-  // Rank 8
-
-  template< typename I0 , typename I1 , typename I2 , typename I3
-          , typename I4 , typename I5 , typename I6 , typename I7
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,I6,I7,Args...>::value
-      && ( 8 == Rank )
-      && is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
-            , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,i6,i7,args...) )
-
-      return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5,i6,i7) ];
-    }
-
-  template< typename I0 , typename I1 , typename I2 , typename I3
-          , typename I4 , typename I5 , typename I6 , typename I7
-          , class ... Args >
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename std::enable_if<
-    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,I6,I7,Args...>::value
-      && ( 8 == Rank )
-      && ! is_default_map
-    ), reference_type >::type
-  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
-            , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7
-            , Args ... args ) const
-    {
-      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,i6,i7,args...) )
-
-      return m_map.reference(i0,i1,i2,i3,i4,i5,i6,i7);
-    }
-
-#undef KOKKOS_VIEW_OPERATOR_VERIFY
-
-  //----------------------------------------
-  // Standard destructor, constructors, and assignment operators
-
-  KOKKOS_INLINE_FUNCTION
-  ~View() {}
-
-  KOKKOS_INLINE_FUNCTION
-  View() : m_track(), m_map() {}
-
-  KOKKOS_INLINE_FUNCTION
-  View( const View & rhs ) : m_track( rhs.m_track ), m_map( rhs.m_map ) {}
-
-  KOKKOS_INLINE_FUNCTION
-  View( View && rhs ) : m_track( rhs.m_track ), m_map( rhs.m_map ) {}
-
-  KOKKOS_INLINE_FUNCTION
-  View & operator = ( const View & rhs ) { m_track = rhs.m_track ; m_map = rhs.m_map ; return *this ; }
-
-  KOKKOS_INLINE_FUNCTION
-  View & operator = ( View && rhs ) { m_track = rhs.m_track ; m_map = rhs.m_map ; return *this ; }
-
-  //----------------------------------------
-  // Compatible view copy constructor and assignment
-  // may assign unmanaged from managed.
-
-  template< class RT , class ... RP >
-  KOKKOS_INLINE_FUNCTION
-  View( const View<RT,RP...> & rhs )
-    : m_track( rhs.m_track , traits::is_managed )
-    , m_map()
-    {
-      typedef typename View<RT,RP...>::traits  SrcTraits ;
-      typedef Kokkos::Experimental::Impl::ViewMapping< traits , SrcTraits , void >  Mapping ;
-      static_assert( Mapping::is_assignable , "Incompatible View copy construction" );
-      Mapping::assign( m_map , rhs.m_map , rhs.m_track );
-    }
-
-  template< class RT , class ... RP >
-  KOKKOS_INLINE_FUNCTION
-  View & operator = ( const View<RT,RP...> & rhs )
-    {
-      typedef typename View<RT,RP...>::traits  SrcTraits ;
-      typedef Kokkos::Experimental::Impl::ViewMapping< traits , SrcTraits , void >  Mapping ;
-      static_assert( Mapping::is_assignable , "Incompatible View copy assignment" );
-      Mapping::assign( m_map , rhs.m_map , rhs.m_track );
-      m_track.assign( rhs.m_track , traits::is_managed );
-      return *this ;
-    }
-
-  //----------------------------------------
-  // Compatible subview constructor
-  // may assign unmanaged from managed.
-
-  template< class RT , class ... RP , class Arg0 , class ... Args >
-  KOKKOS_INLINE_FUNCTION
-  View( const View< RT , RP... > & src_view
-      , const Arg0 & arg0 , Args ... args )
-    : m_track( src_view.m_track , traits::is_managed )
-    , m_map()
-    {
-      typedef View< RT , RP... > SrcType ;
-
-      typedef Kokkos::Experimental::Impl::ViewMapping
-        < void /* deduce destination view type from source view traits */
-        , typename SrcType::traits
-        , Arg0 , Args... > Mapping ;
-
-      typedef typename Mapping::type DstType ;
-
-      static_assert( Kokkos::Experimental::Impl::ViewMapping< traits , typename DstType::traits , void >::is_assignable
-        , "Subview construction requires compatible view and subview arguments" );
-
-      Mapping::assign( m_map, src_view.m_map, arg0 , args... );
-    }
-
-  //----------------------------------------
-  // Allocation tracking properties
-
-  KOKKOS_INLINE_FUNCTION
-  int use_count() const
-    { return m_track.use_count(); }
-
-  inline
-  const std::string label() const
-    { return m_track.template get_label< typename traits::memory_space >(); }
-
-  //----------------------------------------
-  // Allocation according to allocation properties and array layout
-
-  template< class ... P >
-  explicit inline
-  View( const Impl::ViewCtorProp< P ... > & arg_prop
-      , typename std::enable_if< ! Impl::ViewCtorProp< P... >::has_pointer
-                               , typename traits::array_layout
-                               >::type const & arg_layout
-      )
-    : m_track()
-    , m_map()
-    {
-      // Append layout and spaces if not input
-      typedef Impl::ViewCtorProp< P ... > alloc_prop_input ;
-
-      // use 'std::integral_constant<unsigned,I>' for non-types
-      // to avoid duplicate class error.
-      typedef Impl::ViewCtorProp
-        < P ...
-        , typename std::conditional
-            < alloc_prop_input::has_label
-            , std::integral_constant<unsigned,0>
-            , typename std::string
-            >::type
-        , typename std::conditional
-            < alloc_prop_input::has_memory_space
-            , std::integral_constant<unsigned,1>
-            , typename traits::device_type::memory_space
-            >::type
-        , typename std::conditional
-            < alloc_prop_input::has_execution_space
-            , std::integral_constant<unsigned,2>
-            , typename traits::device_type::execution_space
-            >::type
-        > alloc_prop ;
-
-      static_assert( traits::is_managed
-                   , "View allocation constructor requires managed memory" );
-
-      if ( alloc_prop::initialize &&
-           ! alloc_prop::execution_space::is_initialized() ) {
-        // If initializing view data then
-        // the execution space must be initialized.
-        Kokkos::Impl::throw_runtime_exception("Constructing View and initializing data with uninitialized execution space");
-      }
-
-      // Copy the input allocation properties with possibly defaulted properties
-      alloc_prop prop( arg_prop );
-
-//------------------------------------------------------------
-#if defined( KOKKOS_HAVE_CUDA )
-      // If allocating in CudaUVMSpace must fence before and after
-      // the allocation to protect against possible concurrent access
-      // on the CPU and the GPU.
-      // Fence using the trait's executon space (which will be Kokkos::Cuda)
-      // to avoid incomplete type errors from usng Kokkos::Cuda directly.
-      if ( std::is_same< Kokkos::CudaUVMSpace , typename traits::device_type::memory_space >::value ) {
-        traits::device_type::memory_space::execution_space::fence();
-      }
-#endif
-//------------------------------------------------------------
-
-      Kokkos::Experimental::Impl::SharedAllocationRecord<> *
-        record = m_map.allocate_shared( prop , arg_layout );
-
-//------------------------------------------------------------
-#if defined( KOKKOS_HAVE_CUDA )
-      if ( std::is_same< Kokkos::CudaUVMSpace , typename traits::device_type::memory_space >::value ) {
-        traits::device_type::memory_space::execution_space::fence();
-      }
-#endif
-//------------------------------------------------------------
-
-      // Setup and initialization complete, start tracking
-      m_track.assign_allocated_record_to_uninitialized( record );
-    }
-
-  // Wrap memory according to properties and array layout
-  template< class ... P >
-  explicit KOKKOS_INLINE_FUNCTION
-  View( const Impl::ViewCtorProp< P ... > & arg_prop
-      , typename std::enable_if< Impl::ViewCtorProp< P... >::has_pointer
-                               , typename traits::array_layout
-                               >::type const & arg_layout
-      )
-    : m_track() // No memory tracking
-    , m_map( arg_prop , arg_layout )
-    {
-      static_assert(
-        std::is_same< pointer_type
-                    , typename Impl::ViewCtorProp< P... >::pointer_type
-                    >::value ,
-        "Constructing View to wrap user memory must supply matching pointer type" );
-    }
-
-  // Simple dimension-only layout
-  template< class ... P >
-  explicit inline
-  View( const Impl::ViewCtorProp< P ... > & arg_prop
-      , typename std::enable_if< ! Impl::ViewCtorProp< P... >::has_pointer
-                               , size_t 
-                               >::type const arg_N0 = 0 
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0
-      )
-    : View( arg_prop
-          , typename traits::array_layout
-              ( arg_N0 , arg_N1 , arg_N2 , arg_N3
-              , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
-          )
-    {}
-
-  template< class ... P >
-  explicit KOKKOS_INLINE_FUNCTION
-  View( const Impl::ViewCtorProp< P ... > & arg_prop
-      , typename std::enable_if< Impl::ViewCtorProp< P... >::has_pointer
-                               , size_t 
-                               >::type const arg_N0 = 0 
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0
-      )
-    : View( arg_prop
-          , typename traits::array_layout
-              ( arg_N0 , arg_N1 , arg_N2 , arg_N3
-              , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
-          )
-    {}
-
-  // Allocate with label and layout
-  template< typename Label >
-  explicit inline
-  View( const Label & arg_label
-      , typename std::enable_if<
-          Kokkos::Experimental::Impl::is_view_label<Label>::value ,
-          typename traits::array_layout >::type const & arg_layout
-      )
-    : View( Impl::ViewCtorProp< std::string >( arg_label ) , arg_layout )
-    {}
-
-  // Allocate label and layout, must disambiguate from subview constructor.
-  template< typename Label >
-  explicit inline
-  View( const Label & arg_label
-      , typename std::enable_if<
-          Kokkos::Experimental::Impl::is_view_label<Label>::value ,
-        const size_t >::type arg_N0 = 0
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0
-      )
-    : View( Impl::ViewCtorProp< std::string >( arg_label )
-          , typename traits::array_layout
-              ( arg_N0 , arg_N1 , arg_N2 , arg_N3
-              , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
-          )
-    {}
-
-  // For backward compatibility
-  explicit inline
-  View( const ViewAllocateWithoutInitializing & arg_prop
-      , const typename traits::array_layout & arg_layout
-      )
-    : View( Impl::ViewCtorProp< std::string , Kokkos::Experimental::Impl::WithoutInitializing_t >( arg_prop.label , Kokkos::Experimental::WithoutInitializing )
-          , arg_layout
-          )
-    {}
-
-  explicit inline
-  View( const ViewAllocateWithoutInitializing & arg_prop
-      , const size_t arg_N0 = 0
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0
-      )
-    : View( Impl::ViewCtorProp< std::string , Kokkos::Experimental::Impl::WithoutInitializing_t >( arg_prop.label , Kokkos::Experimental::WithoutInitializing )
-          , typename traits::array_layout
-              ( arg_N0 , arg_N1 , arg_N2 , arg_N3
-              , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
-          )
-    {}
-
-  //----------------------------------------
-  // Memory span required to wrap these dimensions.
-  static constexpr size_t memory_span( const size_t arg_N0 = 0
-                                     , const size_t arg_N1 = 0
-                                     , const size_t arg_N2 = 0
-                                     , const size_t arg_N3 = 0
-                                     , const size_t arg_N4 = 0
-                                     , const size_t arg_N5 = 0
-                                     , const size_t arg_N6 = 0
-                                     , const size_t arg_N7 = 0
-                                     )
-    {
-      return map_type::memory_span(
-        typename traits::array_layout
-          ( arg_N0 , arg_N1 , arg_N2 , arg_N3
-          , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) );
-    }
-
-  explicit KOKKOS_INLINE_FUNCTION
-  View( pointer_type arg_ptr
-      , const size_t arg_N0 = 0
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0
-      )
-    : View( Impl::ViewCtorProp<pointer_type>(arg_ptr)
-          , typename traits::array_layout
-             ( arg_N0 , arg_N1 , arg_N2 , arg_N3
-             , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
-          )
-    {}
-
-  explicit KOKKOS_INLINE_FUNCTION
-  View( pointer_type arg_ptr
-      , const typename traits::array_layout & arg_layout
-      )
-    : View( Impl::ViewCtorProp<pointer_type>(arg_ptr) , arg_layout )
-    {}
-
-  //----------------------------------------
-  // Shared scratch memory constructor
-
-  static inline
-  size_t shmem_size( const size_t arg_N0 = 0 ,
-                     const size_t arg_N1 = 0 ,
-                     const size_t arg_N2 = 0 ,
-                     const size_t arg_N3 = 0 ,
-                     const size_t arg_N4 = 0 ,
-                     const size_t arg_N5 = 0 ,
-                     const size_t arg_N6 = 0 ,
-                     const size_t arg_N7 = 0 )
-  {
-    return map_type::memory_span(
-           typename traits::array_layout
-            ( arg_N0 , arg_N1 , arg_N2 , arg_N3
-            , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) );
-  }
-
-  explicit KOKKOS_INLINE_FUNCTION
-  View( const typename traits::execution_space::scratch_memory_space & arg_space
-      , const typename traits::array_layout & arg_layout )
-    : View( Impl::ViewCtorProp<pointer_type>(
-              reinterpret_cast<pointer_type>(
-                arg_space.get_shmem( map_type::memory_span( arg_layout ) ) ) )
-         , arg_layout )
-    {}
-
-  explicit KOKKOS_INLINE_FUNCTION
-  View( const typename traits::execution_space::scratch_memory_space & arg_space
-      , const size_t arg_N0 = 0 
-      , const size_t arg_N1 = 0
-      , const size_t arg_N2 = 0
-      , const size_t arg_N3 = 0
-      , const size_t arg_N4 = 0
-      , const size_t arg_N5 = 0
-      , const size_t arg_N6 = 0
-      , const size_t arg_N7 = 0 )
-    : View( Impl::ViewCtorProp<pointer_type>(
-              reinterpret_cast<pointer_type>(
-                arg_space.get_shmem(
-                  map_type::memory_span(
-                    typename traits::array_layout
-                     ( arg_N0 , arg_N1 , arg_N2 , arg_N3
-                     , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) ) ) ) )
-          , typename traits::array_layout
-             ( arg_N0 , arg_N1 , arg_N2 , arg_N3
-             , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
-       )
-    {}
-};
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-template< class V , class ... Args >
-using Subview =
-  typename Kokkos::Experimental::Impl::ViewMapping
-    < void /* deduce subview type from source view traits */
-    , typename V::traits
-    , Args ...
-    >::type ;
-
-template< class D, class ... P , class ... Args >
-KOKKOS_INLINE_FUNCTION
-typename Kokkos::Experimental::Impl::ViewMapping
-  < void /* deduce subview type from source view traits */
-  , ViewTraits< D , P... >
-  , Args ...
-  >::type
-subview( const View< D, P... > & src , Args ... args )
-{
-  static_assert( View< D , P... >::Rank == sizeof...(Args) , 
-    "subview requires one argument for each source View rank" );
-
-  return typename
-    Kokkos::Experimental::Impl::ViewMapping
-      < void /* deduce subview type from source view traits */
-      , ViewTraits< D , P ... >
-      , Args ... >::type( src , args ... ); 
-}
-
-template< class MemoryTraits , class D, class ... P , class ... Args >
-KOKKOS_INLINE_FUNCTION
-typename Kokkos::Experimental::Impl::ViewMapping
-  < void /* deduce subview type from source view traits */
-  , ViewTraits< D , P... >
-  , Args ...
-  >::template apply< MemoryTraits >::type
-subview( const View< D, P... > & src , Args ... args )
-{
-  static_assert( View< D , P... >::Rank == sizeof...(Args) , 
-    "subview requires one argument for each source View rank" );
-
-  return typename
-    Kokkos::Experimental::Impl::ViewMapping
-      < void /* deduce subview type from source view traits */
-      , ViewTraits< D , P ... >
-      , Args ... >
-      ::template apply< MemoryTraits >
-      ::type( src , args ... ); 
-}
-
-
-
-} /* namespace Experimental */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-
-template< class LT , class ... LP , class RT , class ... RP >
-KOKKOS_INLINE_FUNCTION
-bool operator == ( const View<LT,LP...> & lhs ,
-                   const View<RT,RP...> & rhs )
-{
-  // Same data, layout, dimensions
-  typedef ViewTraits<LT,LP...>  lhs_traits ;
-  typedef ViewTraits<RT,RP...>  rhs_traits ;
-
-  return
-    std::is_same< typename lhs_traits::const_value_type ,
-                  typename rhs_traits::const_value_type >::value &&
-    std::is_same< typename lhs_traits::array_layout ,
-                  typename rhs_traits::array_layout >::value &&
-    std::is_same< typename lhs_traits::memory_space ,
-                  typename rhs_traits::memory_space >::value &&
-    unsigned(lhs_traits::rank) == unsigned(rhs_traits::rank) &&
-    lhs.data()        == rhs.data() &&
-    lhs.span()        == rhs.span() &&
-    lhs.dimension_0() == rhs.dimension_0() &&
-    lhs.dimension_1() == rhs.dimension_1() &&
-    lhs.dimension_2() == rhs.dimension_2() &&
-    lhs.dimension_3() == rhs.dimension_3() &&
-    lhs.dimension_4() == rhs.dimension_4() &&
-    lhs.dimension_5() == rhs.dimension_5() &&
-    lhs.dimension_6() == rhs.dimension_6() &&
-    lhs.dimension_7() == rhs.dimension_7();
-}
-
-template< class LT , class ... LP , class RT , class ... RP >
-KOKKOS_INLINE_FUNCTION
-bool operator != ( const View<LT,LP...> & lhs ,
-                   const View<RT,RP...> & rhs )
-{
-  return ! ( operator==(lhs,rhs) );
-}
-
-} /* namespace Experimental */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Impl {
-
-#if KOKKOS_USING_EXP_VIEW
-
-inline
-void shared_allocation_tracking_claim_and_disable()
-{ Kokkos::Experimental::Impl::SharedAllocationRecord<void,void>::tracking_claim_and_disable(); }
-
-inline
-void shared_allocation_tracking_release_and_enable()
-{ Kokkos::Experimental::Impl::SharedAllocationRecord<void,void>::tracking_release_and_enable(); }
-
-#else
-
-inline
-void shared_allocation_tracking_claim_and_disable()
-{ Kokkos::Impl::AllocationTracker::disable_tracking(); }
-
-inline
-void shared_allocation_tracking_release_and_enable()
-{ Kokkos::Impl::AllocationTracker::enable_tracking(); }
-
-#endif
-
-} /* namespace Impl */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-namespace Impl {
-
-template< class OutputView , typename Enable = void >
-struct ViewFill {
-
-  typedef typename OutputView::const_value_type  const_value_type ;
-
-  const OutputView output ;
-  const_value_type input ;
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const size_t i0 ) const
-  {
-    const size_t n1 = output.dimension_1();
-    const size_t n2 = output.dimension_2();
-    const size_t n3 = output.dimension_3();
-    const size_t n4 = output.dimension_4();
-    const size_t n5 = output.dimension_5();
-    const size_t n6 = output.dimension_6();
-    const size_t n7 = output.dimension_7();
-
-    for ( size_t i1 = 0 ; i1 < n1 ; ++i1 ) {
-    for ( size_t i2 = 0 ; i2 < n2 ; ++i2 ) {
-    for ( size_t i3 = 0 ; i3 < n3 ; ++i3 ) {
-    for ( size_t i4 = 0 ; i4 < n4 ; ++i4 ) {
-    for ( size_t i5 = 0 ; i5 < n5 ; ++i5 ) {
-    for ( size_t i6 = 0 ; i6 < n6 ; ++i6 ) {
-    for ( size_t i7 = 0 ; i7 < n7 ; ++i7 ) {
-      output(i0,i1,i2,i3,i4,i5,i6,i7) = input ;
-    }}}}}}}
-  }
-
-  ViewFill( const OutputView & arg_out , const_value_type & arg_in )
-    : output( arg_out ), input( arg_in )
-    {
-      typedef typename OutputView::execution_space  execution_space ;
-      typedef Kokkos::RangePolicy< execution_space > Policy ;
-
-      const Kokkos::Impl::ParallelFor< ViewFill , Policy > closure( *this , Policy( 0 , output.dimension_0() ) );
-
-      closure.execute();
-
-      execution_space::fence();
-    }
-};
-
-template< class OutputView >
-struct ViewFill< OutputView , typename std::enable_if< OutputView::Rank == 0 >::type > {
-  ViewFill( const OutputView & dst , const typename OutputView::const_value_type & src )
-    {
-      Kokkos::Impl::DeepCopy< typename OutputView::memory_space , Kokkos::HostSpace >
-        ( dst.data() , & src , sizeof(typename OutputView::const_value_type) );
-    }
-};
-
-template< class OutputView , class InputView >
-struct ViewRemap {
-
-  const OutputView output ;
-  const InputView  input ;
-  const size_t n0 ;
-  const size_t n1 ;
-  const size_t n2 ;
-  const size_t n3 ;
-  const size_t n4 ;
-  const size_t n5 ;
-  const size_t n6 ;
-  const size_t n7 ;
-
-  ViewRemap( const OutputView & arg_out , const InputView & arg_in )
-    : output( arg_out ), input( arg_in )
-    , n0( std::min( (size_t)arg_out.dimension_0() , (size_t)arg_in.dimension_0() ) )
-    , n1( std::min( (size_t)arg_out.dimension_1() , (size_t)arg_in.dimension_1() ) )
-    , n2( std::min( (size_t)arg_out.dimension_2() , (size_t)arg_in.dimension_2() ) )
-    , n3( std::min( (size_t)arg_out.dimension_3() , (size_t)arg_in.dimension_3() ) )
-    , n4( std::min( (size_t)arg_out.dimension_4() , (size_t)arg_in.dimension_4() ) )
-    , n5( std::min( (size_t)arg_out.dimension_5() , (size_t)arg_in.dimension_5() ) )
-    , n6( std::min( (size_t)arg_out.dimension_6() , (size_t)arg_in.dimension_6() ) )
-    , n7( std::min( (size_t)arg_out.dimension_7() , (size_t)arg_in.dimension_7() ) )
-    {
-      typedef typename OutputView::execution_space execution_space ;
-      typedef Kokkos::RangePolicy< execution_space > Policy ;
-      const Kokkos::Impl::ParallelFor< ViewRemap , Policy > closure( *this , Policy( 0 , n0 ) );
-      closure.execute();
-    }
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const size_t i0 ) const
-  {
-    for ( size_t i1 = 0 ; i1 < n1 ; ++i1 ) {
-    for ( size_t i2 = 0 ; i2 < n2 ; ++i2 ) {
-    for ( size_t i3 = 0 ; i3 < n3 ; ++i3 ) {
-    for ( size_t i4 = 0 ; i4 < n4 ; ++i4 ) {
-    for ( size_t i5 = 0 ; i5 < n5 ; ++i5 ) {
-    for ( size_t i6 = 0 ; i6 < n6 ; ++i6 ) {
-    for ( size_t i7 = 0 ; i7 < n7 ; ++i7 ) {
-      output(i0,i1,i2,i3,i4,i5,i6,i7) = input(i0,i1,i2,i3,i4,i5,i6,i7);
-    }}}}}}}
-  }
-};
-
-} /* namespace Impl */
-} /* namespace Experimental */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-
-/** \brief  Deep copy a value from Host memory into a view.  */
-template< class DT , class ... DP >
-inline
-void deep_copy
-  ( const View<DT,DP...> & dst
-  , typename ViewTraits<DT,DP...>::const_value_type & value
-  , typename std::enable_if<
-    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value
-    >::type * = 0 )
-{
-  static_assert(
-    std::is_same< typename ViewTraits<DT,DP...>::non_const_value_type ,
-                  typename ViewTraits<DT,DP...>::value_type >::value
-    , "deep_copy requires non-const type" );
-
-  Kokkos::Experimental::Impl::ViewFill< View<DT,DP...> >( dst , value );
-}
-
-/** \brief  Deep copy into a value in Host memory from a view.  */
-template< class ST , class ... SP >
-inline
-void deep_copy
-  ( typename ViewTraits<ST,SP...>::non_const_value_type & dst
-  , const View<ST,SP...> & src
-  , typename std::enable_if<
-    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value
-    >::type * = 0 )
-{
-  static_assert( ViewTraits<ST,SP...>::rank == 0 
-               , "ERROR: Non-rank-zero view in deep_copy( value , View )" );
-
-  typedef ViewTraits<ST,SP...>               src_traits ;
-  typedef typename src_traits::memory_space  src_memory_space ;
-  Kokkos::Impl::DeepCopy< HostSpace , src_memory_space >( & dst , src.data() , sizeof(ST) );
-}
-
-//----------------------------------------------------------------------------
-/** \brief  A deep copy between views of compatible type, and rank zero.  */
-template< class DT , class ... DP , class ST , class ... SP >
-inline
-void deep_copy
-  ( const View<DT,DP...> & dst
-  , const View<ST,SP...> & src
-  , typename std::enable_if<(
-    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value &&
-    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value &&
-    ( unsigned(ViewTraits<DT,DP...>::rank) == unsigned(0) &&
-      unsigned(ViewTraits<ST,SP...>::rank) == unsigned(0) )
-  )>::type * = 0 )
-{
-  static_assert(
-    std::is_same< typename ViewTraits<DT,DP...>::value_type ,
-                  typename ViewTraits<ST,SP...>::non_const_value_type >::value
-    , "deep_copy requires matching non-const destination type" );
-
-  typedef View<DT,DP...>  dst_type ;
-  typedef View<ST,SP...>  src_type ;
-
-  typedef typename dst_type::value_type    value_type ;
-  typedef typename dst_type::memory_space  dst_memory_space ;
-  typedef typename src_type::memory_space  src_memory_space ;
-
-  if ( dst.data() != src.data() ) {
-    Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.data() , src.data() , sizeof(value_type) );
-  }
-}
-
-//----------------------------------------------------------------------------
-/** \brief  A deep copy between views of the default specialization, compatible type,
- *          same non-zero rank, same contiguous layout.
- */
-template< class DT , class ... DP , class ST , class ... SP >
-inline
-void deep_copy
-  ( const View<DT,DP...> & dst
-  , const View<ST,SP...> & src
-  , typename std::enable_if<(
-    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value &&
-    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value &&
-    ( unsigned(ViewTraits<DT,DP...>::rank) != 0 ||
-      unsigned(ViewTraits<ST,SP...>::rank) != 0 )
-  )>::type * = 0 )
-{
-  static_assert(
-    std::is_same< typename ViewTraits<DT,DP...>::value_type ,
-                  typename ViewTraits<DT,DP...>::non_const_value_type >::value
-    , "deep_copy requires non-const destination type" );
-
-  static_assert(
-    ( unsigned(ViewTraits<DT,DP...>::rank) ==
-      unsigned(ViewTraits<ST,SP...>::rank) )
-    , "deep_copy requires Views of equal rank" );
-
-  typedef View<DT,DP...>  dst_type ;
-  typedef View<ST,SP...>  src_type ;
-
-  typedef typename dst_type::execution_space  dst_execution_space ;
-  typedef typename dst_type::memory_space     dst_memory_space ;
-  typedef typename src_type::memory_space     src_memory_space ;
-
-  enum { DstExecCanAccessSrc =
-   Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< typename dst_execution_space::memory_space , src_memory_space >::value };
-
-  if ( (void *) dst.data() != (void*) src.data() ) {
-
-    // Concern: If overlapping views then a parallel copy will be erroneous.
-    // ...
-
-    // If same type, equal layout, equal dimensions, equal span, and contiguous memory then can byte-wise copy
-
-    if ( std::is_same< typename ViewTraits<DT,DP...>::value_type ,
-                       typename ViewTraits<ST,SP...>::non_const_value_type >::value &&
-         (
-           std::is_same< typename ViewTraits<DT,DP...>::array_layout ,
-                         typename ViewTraits<ST,SP...>::array_layout >::value
-           ||
-           ( ViewTraits<DT,DP...>::rank == 1 &&
-             ViewTraits<ST,SP...>::rank == 1 )
-         ) &&
-         dst.span_is_contiguous() &&
-         src.span_is_contiguous() &&
-         dst.span() == src.span() &&
-         dst.dimension_0() == src.dimension_0() &&
-         dst.dimension_1() == src.dimension_1() &&
-         dst.dimension_2() == src.dimension_2() &&
-         dst.dimension_3() == src.dimension_3() &&
-         dst.dimension_4() == src.dimension_4() &&
-         dst.dimension_5() == src.dimension_5() &&
-         dst.dimension_6() == src.dimension_6() &&
-         dst.dimension_7() == src.dimension_7() ) {
-
-      const size_t nbytes = sizeof(typename dst_type::value_type) * dst.span();
-
-      Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.data() , src.data() , nbytes );
-    }
-    else if ( DstExecCanAccessSrc ) {
-      // Copying data between views in accessible memory spaces and either non-contiguous or incompatible shape.
-      Kokkos::Experimental::Impl::ViewRemap< dst_type , src_type >( dst , src );
-    }
-    else {
-      Kokkos::Impl::throw_runtime_exception("deep_copy given views that would require a temporary allocation");
-    }
-  }
-}
-
-} /* namespace Experimental */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-
-/** \brief  Deep copy a value from Host memory into a view.  */
-template< class ExecSpace ,class DT , class ... DP >
-inline
-void deep_copy
-  ( const ExecSpace &
-  , const View<DT,DP...> & dst
-  , typename ViewTraits<DT,DP...>::const_value_type & value
-  , typename std::enable_if<
-    Kokkos::Impl::is_execution_space< ExecSpace >::value &&
-    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value
-    >::type * = 0 )
-{
-  static_assert(
-    std::is_same< typename ViewTraits<DT,DP...>::non_const_value_type ,
-                  typename ViewTraits<DT,DP...>::value_type >::value
-    , "deep_copy requires non-const type" );
-
-  Kokkos::Experimental::Impl::ViewFill< View<DT,DP...> >( dst , value );
-}
-
-/** \brief  Deep copy into a value in Host memory from a view.  */
-template< class ExecSpace , class ST , class ... SP >
-inline
-void deep_copy
-  ( const ExecSpace & exec_space
-  , typename ViewTraits<ST,SP...>::non_const_value_type & dst
-  , const View<ST,SP...> & src
-  , typename std::enable_if<
-    Kokkos::Impl::is_execution_space< ExecSpace >::value &&
-    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value
-    >::type * = 0 )
-{
-  static_assert( ViewTraits<ST,SP...>::rank == 0 
-               , "ERROR: Non-rank-zero view in deep_copy( value , View )" );
-
-  typedef ViewTraits<ST,SP...>               src_traits ;
-  typedef typename src_traits::memory_space  src_memory_space ;
-  Kokkos::Impl::DeepCopy< HostSpace , src_memory_space , ExecSpace >
-    ( exec_space , & dst , src.data() , sizeof(ST) );
-}
-
-//----------------------------------------------------------------------------
-/** \brief  A deep copy between views of compatible type, and rank zero.  */
-template< class ExecSpace , class DT , class ... DP , class ST , class ... SP >
-inline
-void deep_copy
-  ( const ExecSpace & exec_space
-  , const View<DT,DP...> & dst
-  , const View<ST,SP...> & src
-  , typename std::enable_if<(
-    Kokkos::Impl::is_execution_space< ExecSpace >::value &&
-    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value &&
-    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value &&
-    ( unsigned(ViewTraits<DT,DP...>::rank) == unsigned(0) &&
-      unsigned(ViewTraits<ST,SP...>::rank) == unsigned(0) )
-  )>::type * = 0 )
-{
-  static_assert(
-    std::is_same< typename ViewTraits<DT,DP...>::value_type ,
-                  typename ViewTraits<ST,SP...>::non_const_value_type >::value
-    , "deep_copy requires matching non-const destination type" );
-
-  typedef View<DT,DP...>  dst_type ;
-  typedef View<ST,SP...>  src_type ;
-
-  typedef typename dst_type::value_type    value_type ;
-  typedef typename dst_type::memory_space  dst_memory_space ;
-  typedef typename src_type::memory_space  src_memory_space ;
-
-  if ( dst.data() != src.data() ) {
-    Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space , ExecSpace >
-      ( exec_space , dst.data() , src.data() , sizeof(value_type) );
-  }
-}
-
-//----------------------------------------------------------------------------
-/** \brief  A deep copy between views of the default specialization, compatible type,
- *          same non-zero rank, same contiguous layout.
- */
-template< class ExecSpace , class DT, class ... DP, class ST, class ... SP >
-inline
-void deep_copy
-  ( const ExecSpace & exec_space
-  , const View<DT,DP...> & dst
-  , const View<ST,SP...> & src
-  , typename std::enable_if<(
-    Kokkos::Impl::is_execution_space< ExecSpace >::value &&
-    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value &&
-    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value &&
-    ( unsigned(ViewTraits<DT,DP...>::rank) != 0 ||
-      unsigned(ViewTraits<ST,SP...>::rank) != 0 )
-  )>::type * = 0 )
-{
-  static_assert(
-    std::is_same< typename ViewTraits<DT,DP...>::value_type ,
-                  typename ViewTraits<DT,DP...>::non_const_value_type >::value
-    , "deep_copy requires non-const destination type" );
-
-  static_assert(
-    ( unsigned(ViewTraits<DT,DP...>::rank) ==
-      unsigned(ViewTraits<ST,SP...>::rank) )
-    , "deep_copy requires Views of equal rank" );
-
-  typedef View<DT,DP...>  dst_type ;
-  typedef View<ST,SP...>  src_type ;
-
-  typedef typename dst_type::execution_space  dst_execution_space ;
-  typedef typename dst_type::memory_space     dst_memory_space ;
-  typedef typename src_type::memory_space     src_memory_space ;
-
-  enum { DstExecCanAccessSrc =
-   Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< typename dst_execution_space::memory_space , src_memory_space >::value };
-
-  if ( (void *) dst.data() != (void*) src.data() ) {
-
-    // Concern: If overlapping views then a parallel copy will be erroneous.
-    // ...
-
-    // If same type, equal layout, equal dimensions, equal span, and contiguous memory then can byte-wise copy
-
-    if ( std::is_same< typename ViewTraits<DT,DP...>::value_type ,
-                       typename ViewTraits<ST,SP...>::non_const_value_type >::value &&
-         (
-           std::is_same< typename ViewTraits<DT,DP...>::array_layout ,
-                         typename ViewTraits<ST,SP...>::array_layout >::value
-           ||
-           ( ViewTraits<DT,DP...>::rank == 1 &&
-             ViewTraits<ST,SP...>::rank == 1 )
-         ) &&
-         dst.span_is_contiguous() &&
-         src.span_is_contiguous() &&
-         dst.span() == src.span() &&
-         dst.dimension_0() == src.dimension_0() &&
-         dst.dimension_1() == src.dimension_1() &&
-         dst.dimension_2() == src.dimension_2() &&
-         dst.dimension_3() == src.dimension_3() &&
-         dst.dimension_4() == src.dimension_4() &&
-         dst.dimension_5() == src.dimension_5() &&
-         dst.dimension_6() == src.dimension_6() &&
-         dst.dimension_7() == src.dimension_7() ) {
-
-      const size_t nbytes = sizeof(typename dst_type::value_type) * dst.span();
-
-      Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space , ExecSpace >
-        ( exec_space , dst.data() , src.data() , nbytes );
-    }
-    else if ( DstExecCanAccessSrc ) {
-      // Copying data between views in accessible memory spaces and either non-contiguous or incompatible shape.
-      Kokkos::Experimental::Impl::ViewRemap< dst_type , src_type >( dst , src );
-    }
-    else {
-      Kokkos::Impl::throw_runtime_exception("deep_copy given views that would require a temporary allocation");
-    }
-  }
-}
-
-} /* namespace Experimental */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-namespace Impl {
-
-// Deduce Mirror Types
-template<class Space, class T, class ... P>
-struct MirrorViewType {
-  // The incoming view_type
-  typedef typename Kokkos::Experimental::View<T,P...> src_view_type;
-  // The memory space for the mirror view
-  typedef typename Space::memory_space memory_space;
-  // Check whether it is the same memory space
-  enum { is_same_memspace = std::is_same<memory_space,typename src_view_type::memory_space>::value };
-  // The array_layout
-  typedef typename src_view_type::array_layout array_layout;
-  // The data type (we probably want it non-const since otherwise we can't even deep_copy to it.
-  typedef typename src_view_type::non_const_data_type data_type;
-  // The destination view type if it is not the same memory space
-  typedef Kokkos::Experimental::View<data_type,array_layout,Space> dest_view_type;
-  // If it is the same memory_space return the existsing view_type
-  // This will also keep the unmanaged trait if necessary
-  typedef typename std::conditional<is_same_memspace,src_view_type,dest_view_type>::type view_type;
-};
-
-template<class Space, class T, class ... P>
-struct MirrorType {
-  // The incoming view_type
-  typedef typename Kokkos::Experimental::View<T,P...> src_view_type;
-  // The memory space for the mirror view
-  typedef typename Space::memory_space memory_space;
-  // Check whether it is the same memory space
-  enum { is_same_memspace = std::is_same<memory_space,typename src_view_type::memory_space>::value };
-  // The array_layout
-  typedef typename src_view_type::array_layout array_layout;
-  // The data type (we probably want it non-const since otherwise we can't even deep_copy to it.
-  typedef typename src_view_type::non_const_data_type data_type;
-  // The destination view type if it is not the same memory space
-  typedef Kokkos::Experimental::View<data_type,array_layout,Space> view_type;
-};
-
-}
-
-template< class T , class ... P >
-inline
-typename Kokkos::Experimental::View<T,P...>::HostMirror
-create_mirror( const Kokkos::Experimental::View<T,P...> & src
-             , typename std::enable_if<
-                 ! std::is_same< typename Kokkos::Experimental::ViewTraits<T,P...>::array_layout
-                               , Kokkos::LayoutStride >::value
-               >::type * = 0
-             )
-{
-  typedef View<T,P...>                   src_type ;
-  typedef typename src_type::HostMirror  dst_type ;
-
-  return dst_type( std::string( src.label() ).append("_mirror")
-                 , src.dimension_0()
-                 , src.dimension_1()
-                 , src.dimension_2()
-                 , src.dimension_3()
-                 , src.dimension_4()
-                 , src.dimension_5()
-                 , src.dimension_6()
-                 , src.dimension_7() );
-}
-
-template< class T , class ... P >
-inline
-typename Kokkos::Experimental::View<T,P...>::HostMirror
-create_mirror( const Kokkos::Experimental::View<T,P...> & src
-             , typename std::enable_if<
-                 std::is_same< typename Kokkos::Experimental::ViewTraits<T,P...>::array_layout
-                             , Kokkos::LayoutStride >::value
-               >::type * = 0
-             )
-{
-  typedef View<T,P...>                   src_type ;
-  typedef typename src_type::HostMirror  dst_type ;
-
-  Kokkos::LayoutStride layout ;
-
-  layout.dimension[0] = src.dimension_0();
-  layout.dimension[1] = src.dimension_1();
-  layout.dimension[2] = src.dimension_2();
-  layout.dimension[3] = src.dimension_3();
-  layout.dimension[4] = src.dimension_4();
-  layout.dimension[5] = src.dimension_5();
-  layout.dimension[6] = src.dimension_6();
-  layout.dimension[7] = src.dimension_7();
-
-  layout.stride[0] = src.stride_0();
-  layout.stride[1] = src.stride_1();
-  layout.stride[2] = src.stride_2();
-  layout.stride[3] = src.stride_3();
-  layout.stride[4] = src.stride_4();
-  layout.stride[5] = src.stride_5();
-  layout.stride[6] = src.stride_6();
-  layout.stride[7] = src.stride_7();
-
-  return dst_type( std::string( src.label() ).append("_mirror") , layout );
-}
-
-
-// Create a mirror in a new space (specialization for different space)
-template<class Space, class T, class ... P>
-typename Impl::MirrorType<Space,T,P ...>::view_type create_mirror(const Space& , const Kokkos::Experimental::View<T,P...> & src) {
-  return typename Impl::MirrorType<Space,T,P ...>::view_type(src.label(),src.layout());
-}
-
-template< class T , class ... P >
-inline
-typename Kokkos::Experimental::View<T,P...>::HostMirror
-create_mirror_view( const Kokkos::Experimental::View<T,P...> & src
-                  , typename std::enable_if<(
-                      std::is_same< typename Kokkos::Experimental::View<T,P...>::memory_space
-                                  , typename Kokkos::Experimental::View<T,P...>::HostMirror::memory_space
-                                  >::value
-                      &&
-                      std::is_same< typename Kokkos::Experimental::View<T,P...>::data_type
-                                  , typename Kokkos::Experimental::View<T,P...>::HostMirror::data_type
-                                  >::value
-                    )>::type * = 0 
-                  )
-{
-  return src ;
-}
-
-template< class T , class ... P >
-inline
-typename Kokkos::Experimental::View<T,P...>::HostMirror
-create_mirror_view( const Kokkos::Experimental::View<T,P...> & src
-                  , typename std::enable_if< ! (
-                      std::is_same< typename Kokkos::Experimental::View<T,P...>::memory_space
-                                  , typename Kokkos::Experimental::View<T,P...>::HostMirror::memory_space
-                                  >::value
-                      &&
-                      std::is_same< typename Kokkos::Experimental::View<T,P...>::data_type
-                                  , typename Kokkos::Experimental::View<T,P...>::HostMirror::data_type
-                                  >::value
-                    )>::type * = 0 
-                  )
-{
-  return Kokkos::Experimental::create_mirror( src );
-}
-
-// Create a mirror view in a new space (specialization for same space)
-template<class Space, class T, class ... P>
-typename Impl::MirrorViewType<Space,T,P ...>::view_type
-create_mirror_view(const Space& , const Kokkos::Experimental::View<T,P...> & src
-  , typename std::enable_if<Impl::MirrorViewType<Space,T,P ...>::is_same_memspace>::type* = 0 ) {
-  return src;
-}
-
-// Create a mirror view in a new space (specialization for different space)
-template<class Space, class T, class ... P>
-typename Impl::MirrorViewType<Space,T,P ...>::view_type
-create_mirror_view(const Space& , const Kokkos::Experimental::View<T,P...> & src
-  , typename std::enable_if<!Impl::MirrorViewType<Space,T,P ...>::is_same_memspace>::type* = 0 ) {
-  return typename Impl::MirrorViewType<Space,T,P ...>::view_type(src.label(),src.layout());
-}
-
-} /* namespace Experimental */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-
-/** \brief  Resize a view with copying old data to new data at the corresponding indices. */
-template< class T , class ... P >
-inline
-void resize( Kokkos::Experimental::View<T,P...> & v ,
-             const size_t n0 = 0 ,
-             const size_t n1 = 0 ,
-             const size_t n2 = 0 ,
-             const size_t n3 = 0 ,
-             const size_t n4 = 0 ,
-             const size_t n5 = 0 ,
-             const size_t n6 = 0 ,
-             const size_t n7 = 0 )
-{
-  typedef Kokkos::Experimental::View<T,P...>  view_type ;
-
-  static_assert( Kokkos::Experimental::ViewTraits<T,P...>::is_managed , "Can only resize managed views" );
-
-  view_type v_resized( v.label(), n0, n1, n2, n3, n4, n5, n6, n7 );
-
-  Kokkos::Experimental::Impl::ViewRemap< view_type , view_type >( v_resized , v );
-
-  v = v_resized ;
-}
-
-/** \brief  Resize a view with copying old data to new data at the corresponding indices. */
-template< class T , class ... P >
-inline
-void realloc( Kokkos::Experimental::View<T,P...> & v ,
-              const size_t n0 = 0 ,
-              const size_t n1 = 0 ,
-              const size_t n2 = 0 ,
-              const size_t n3 = 0 ,
-              const size_t n4 = 0 ,
-              const size_t n5 = 0 ,
-              const size_t n6 = 0 ,
-              const size_t n7 = 0 )
-{
-  typedef Kokkos::Experimental::View<T,P...>  view_type ;
-
-  static_assert( Kokkos::Experimental::ViewTraits<T,P...>::is_managed , "Can only realloc managed views" );
-
-  const std::string label = v.label();
-
-  v = view_type(); // Deallocate first, if the only view to allocation
-  v = view_type( label, n0, n1, n2, n3, n4, n5, n6, n7 );
-}
-
-} /* namespace Experimental */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-#if KOKKOS_USING_EXP_VIEW
-
-namespace Kokkos {
-
-template< class D , class ... P >
-using ViewTraits = Kokkos::Experimental::ViewTraits<D,P...> ;
-
-template< class D , class ... P >
-using View = Kokkos::Experimental::View<D,P...> ;
-
-using Kokkos::Experimental::ALL ;
-using Kokkos::Experimental::deep_copy ;
-using Kokkos::Experimental::create_mirror ;
-using Kokkos::Experimental::create_mirror_view ;
-using Kokkos::Experimental::subview ;
-using Kokkos::Experimental::resize ;
-using Kokkos::Experimental::realloc ;
-using Kokkos::Experimental::is_view ;
-
-namespace Impl {
-
-using Kokkos::Experimental::is_view ;
-
-class ViewDefault {};
-
-template< class SrcViewType
-        , class Arg0Type
-        , class Arg1Type
-        , class Arg2Type
-        , class Arg3Type
-        , class Arg4Type
-        , class Arg5Type
-        , class Arg6Type
-        , class Arg7Type
-        >
-struct ViewSubview /* { typedef ... type ; } */ ;
-
-}
-
-} /* namespace Kokkos */
-
-#include <impl/Kokkos_Atomic_View.hpp>
-
-#endif /* #if KOKKOS_USING_EXP_VIEW */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-#endif
-
diff --git a/lib/kokkos/core/src/Kokkos_Complex.hpp b/lib/kokkos/core/src/Kokkos_Complex.hpp
index 11aaf96177..cdfa4429f0 100644
--- a/lib/kokkos/core/src/Kokkos_Complex.hpp
+++ b/lib/kokkos/core/src/Kokkos_Complex.hpp
@@ -121,13 +121,22 @@ public:
     return *this;
   }
 
-  //! Assignment operator.
+  /// \brief Assignment operator, for volatile <tt>*this</tt> and
+  ///   nonvolatile input.
+  ///
+  /// \param src [in] Input; right-hand side of the assignment.
+  ///
+  /// This operator returns \c void instead of <tt>volatile
+  /// complex<RealType>& </tt>.  See Kokkos Issue #177 for the
+  /// explanation.  In practice, this means that you should not chain
+  /// assignments with volatile lvalues.
   template<class InputRealType>
   KOKKOS_INLINE_FUNCTION
-  volatile complex<RealType>& operator= (const complex<InputRealType>& src) volatile {
+  void operator= (const complex<InputRealType>& src) volatile {
     re_ = src.re_;
     im_ = src.im_;
-    return *this;
+    // We deliberately do not return anything here.  See explanation
+    // in public documentation above.
   }
 
   //! Assignment operator.
diff --git a/lib/kokkos/core/src/impl/Kokkos_BasicAllocators.hpp b/lib/kokkos/core/src/Kokkos_Concepts.hpp
similarity index 56%
rename from lib/kokkos/core/src/impl/Kokkos_BasicAllocators.hpp
rename to lib/kokkos/core/src/Kokkos_Concepts.hpp
index ad3e0b35a5..82a342eec0 100644
--- a/lib/kokkos/core/src/impl/Kokkos_BasicAllocators.hpp
+++ b/lib/kokkos/core/src/Kokkos_Concepts.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,86 +36,43 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
 
-#ifndef KOKKOS_BASIC_ALLOCATORS_HPP
-#define KOKKOS_BASIC_ALLOCATORS_HPP
-
-#if ! KOKKOS_USING_EXP_VIEW
-
-namespace Kokkos { namespace Impl {
-
-/// class UnmanagedAllocator
-/// does nothing when deallocate(ptr,size) is called
-class UnmanagedAllocator
-{
-public:
-  static const char * name() { return "Unmanaged Allocator"; }
-
-  static void deallocate(void * /*ptr*/, size_t /*size*/) {}
-};
-
-
-/// class MallocAllocator
-class MallocAllocator
-{
-public:
-  static const char * name()
-  {
-    return "Malloc Allocator";
-  }
-
-  static void* allocate(size_t size);
-
-  static void deallocate(void * ptr, size_t size);
+#ifndef KOKKOS_CORE_CONCEPTS_HPP
+#define KOKKOS_CORE_CONCEPTS_HPP
 
-  static void * reallocate(void * old_ptr, size_t old_size, size_t new_size);
-};
+#include <type_traits>
 
+namespace Kokkos {
+//Schedules for Execution Policies
+struct Static {};
+struct Dynamic {};
 
-/// class AlignedAllocator
-/// memory aligned to Kokkos::Impl::MEMORY_ALIGNMENT
-class AlignedAllocator
+//Schedule Wrapper Type
+template<class T>
+struct Schedule
 {
-public:
-  static const char * name()
-  {
-    return "Aligned Allocator";
-  }
-
-  static void* allocate(size_t size);
-
-  static void deallocate(void * ptr, size_t size);
-
-  static void * reallocate(void * old_ptr, size_t old_size, size_t new_size);
+  static_assert(  std::is_same<T,Static>::value
+               || std::is_same<T,Dynamic>::value
+               , "Kokkos: Invalid Schedule<> type."
+               );
+  using schedule_type = Schedule<T>;
+  using type = T;
 };
 
-
-/// class PageAlignedAllocator
-/// memory aligned to PAGE_SIZE
-class PageAlignedAllocator
+//Specify Iteration Index Type
+template<typename T>
+struct IndexType
 {
-public:
-  static const char * name()
-  {
-    return "Page Aligned Allocator";
-  }
-
-  static void* allocate(size_t size);
-
-  static void deallocate(void * ptr, size_t size);
-
-  static void * reallocate(void * old_ptr, size_t old_size, size_t new_size);
+  static_assert(std::is_integral<T>::value,"Kokkos: Invalid IndexType<>.");
+  using index_type = IndexType<T>;
+  using type = T;
 };
 
+} // namespace Kokkos
 
-}} // namespace Kokkos::Impl
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-#endif //KOKKOS_BASIC_ALLOCATORS_HPP
-
+#endif // KOKKOS_CORE_CONCEPTS_HPP
 
diff --git a/lib/kokkos/core/src/Kokkos_Core.hpp b/lib/kokkos/core/src/Kokkos_Core.hpp
index e4a4643ce5..7cde4610ee 100644
--- a/lib/kokkos/core/src/Kokkos_Core.hpp
+++ b/lib/kokkos/core/src/Kokkos_Core.hpp
@@ -159,8 +159,6 @@ void * kokkos_realloc( void * arg_alloc , const size_t arg_alloc_size )
 } // namespace Kokkos
 
 
-#if KOKKOS_USING_EXP_VIEW
-
 namespace Kokkos {
 
 using Kokkos::Experimental::kokkos_malloc ;
@@ -169,76 +167,6 @@ using Kokkos::Experimental::kokkos_free ;
 
 }
 
-#else
-
-namespace Kokkos {
-
-namespace Impl {
-// should only by used by kokkos_malloc and kokkos_free
-struct MallocHelper
-{
-  static void increment_ref_count( AllocationTracker const & tracker )
-  {
-    tracker.increment_ref_count();
-  }
-
-  static void decrement_ref_count( AllocationTracker const & tracker )
-  {
-    tracker.decrement_ref_count();
-  }
-};
-} // namespace Impl
-
-/* Allocate memory from a memory space.
- * The allocation is tracked in Kokkos memory tracking system, so
- * leaked memory can be identified.
- */
-template< class Arg = DefaultExecutionSpace>
-void* kokkos_malloc(const std::string label, size_t count) {
-  if(count == 0) return NULL;
-  typedef typename Arg::memory_space MemorySpace;
-  Impl::AllocationTracker tracker = MemorySpace::allocate_and_track(label,count);;
-  Impl::MallocHelper::increment_ref_count( tracker );
-  return tracker.alloc_ptr();
-}
-
-template< class Arg = DefaultExecutionSpace>
-void* kokkos_malloc(const size_t& count) {
-  return kokkos_malloc<Arg>("DefaultLabel",count);
-}
-
-
-/* Free memory from a memory space.
- */
-template< class Arg = DefaultExecutionSpace>
-void kokkos_free(const void* ptr) {
-  typedef typename Arg::memory_space MemorySpace;
-  typedef typename MemorySpace::allocator allocator;
-  Impl::AllocationTracker tracker = Impl::AllocationTracker::find<allocator>(ptr);
-  if (tracker.is_valid()) {
-    Impl::MallocHelper::decrement_ref_count( tracker );
-  }
-}
-
-
-template< class Arg = DefaultExecutionSpace>
-void* kokkos_realloc(const void* old_ptr, size_t size) {
-  if(old_ptr == NULL)
-    return kokkos_malloc<Arg>(size);
-
-  typedef typename Arg::memory_space MemorySpace;
-  typedef typename MemorySpace::allocator allocator;
-  Impl::AllocationTracker tracker = Impl::AllocationTracker::find<allocator>(old_ptr);
-
-  tracker.reallocate(size);
-
-  return tracker.alloc_ptr();
-}
-
-} // namespace Kokkos
-
-#endif
-
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
diff --git a/lib/kokkos/core/src/Kokkos_Core_fwd.hpp b/lib/kokkos/core/src/Kokkos_Core_fwd.hpp
index a262864157..e9648b59b8 100644
--- a/lib/kokkos/core/src/Kokkos_Core_fwd.hpp
+++ b/lib/kokkos/core/src/Kokkos_Core_fwd.hpp
@@ -69,6 +69,9 @@ namespace {
 /**\brief Token to indicate that a parameter's value is to be automatically selected */
 constexpr AUTO_t AUTO = Kokkos::AUTO_t();
 }
+
+struct InvalidType {};
+
 }
 
 //----------------------------------------------------------------------------
@@ -205,7 +208,7 @@ namespace Impl {
 template< class Functor
         , class Policy
         , class EnableFunctor = void 
-	, class EnablePolicy = void
+	      , class EnablePolicy = void
         >
 struct FunctorPolicyExecutionSpace;
 
@@ -225,7 +228,7 @@ template< class FunctorType , class ExecPolicy , class ExecutionSpace =
 ///
 /// This is an implementation detail of parallel_reduce.  Users should
 /// skip this and go directly to the nonmember function parallel_reduce.
-template< class FunctorType , class ExecPolicy , class ExecutionSpace = 
+template< class FunctorType , class ExecPolicy , class ReducerType = InvalidType, class ExecutionSpace =
           typename Impl::FunctorPolicyExecutionSpace< FunctorType , ExecPolicy >::execution_space 
         > class ParallelReduce ;
 
diff --git a/lib/kokkos/core/src/Kokkos_Cuda.hpp b/lib/kokkos/core/src/Kokkos_Cuda.hpp
index eadcf13256..3130ee3198 100644
--- a/lib/kokkos/core/src/Kokkos_Cuda.hpp
+++ b/lib/kokkos/core/src/Kokkos_Cuda.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -56,11 +56,14 @@
 #include <Kokkos_CudaSpace.hpp>
 
 #include <Kokkos_Parallel.hpp>
+#include <Kokkos_TaskPolicy.hpp>
 #include <Kokkos_Layout.hpp>
 #include <Kokkos_ScratchSpace.hpp>
 #include <Kokkos_MemoryTraits.hpp>
 #include <impl/Kokkos_Tags.hpp>
 
+#include <KokkosExp_MDRangePolicy.hpp>
+
 /*--------------------------------------------------------------------------*/
 
 namespace Kokkos {
@@ -108,7 +111,7 @@ public:
   //! This execution space's preferred array layout.
   typedef LayoutLeft            array_layout ;
 
-  //! 
+  //!
   typedef ScratchMemorySpace< Cuda >  scratch_memory_space ;
 
   //@}
@@ -257,10 +260,10 @@ struct VerifyExecutionCanAccessMemorySpace
 #include <Cuda/Kokkos_CudaExec.hpp>
 #include <Cuda/Kokkos_Cuda_View.hpp>
 
-#include <KokkosExp_View.hpp>
 #include <Cuda/KokkosExp_Cuda_View.hpp>
 
 #include <Cuda/Kokkos_Cuda_Parallel.hpp>
+#include <Cuda/Kokkos_Cuda_Task.hpp>
 
 //----------------------------------------------------------------------------
 
diff --git a/lib/kokkos/core/src/Kokkos_CudaSpace.hpp b/lib/kokkos/core/src/Kokkos_CudaSpace.hpp
index c0223c35cf..cd728895d0 100644
--- a/lib/kokkos/core/src/Kokkos_CudaSpace.hpp
+++ b/lib/kokkos/core/src/Kokkos_CudaSpace.hpp
@@ -54,10 +54,7 @@
 
 #include <Kokkos_HostSpace.hpp>
 
-#include <impl/Kokkos_AllocationTracker.hpp>
-
 #include <Cuda/Kokkos_Cuda_abort.hpp>
-#include <Cuda/Kokkos_Cuda_BasicAllocators.hpp>
 
 /*--------------------------------------------------------------------------*/
 
@@ -77,33 +74,6 @@ public:
 
   /*--------------------------------*/
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-  typedef Impl::CudaMallocAllocator allocator;
-
-  /** \brief  Allocate a contiguous block of memory.
-   *
-   *  The input label is associated with the block of memory.
-   *  The block of memory is tracked via reference counting where
-   *  allocation gives it a reference count of one.
-   */
-  static Impl::AllocationTracker allocate_and_track( const std::string & label, const size_t size );
-
-  /*--------------------------------*/
-  /** \brief  Cuda specific function to attached texture object to an allocation.
-   *          Output the texture object, base pointer, and offset from the input pointer.
-   */
-#if defined( __CUDACC__ )
-  static void texture_object_attach(  Impl::AllocationTracker const & tracker
-                                    , unsigned type_size
-                                    , ::cudaChannelFormatDesc const & desc
-                                   );
-#endif
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-  /*--------------------------------*/
-
   CudaSpace();
   CudaSpace( CudaSpace && rhs ) = default ;
   CudaSpace( const CudaSpace & rhs ) = default ;
@@ -137,7 +107,7 @@ namespace Impl {
 /// where the hash value is derived from the address of the
 /// object for which an atomic operation is performed.
 /// This function initializes the locks to zero (unset).
-void init_lock_array_cuda_space();
+void init_lock_arrays_cuda_space();
 
 /// \brief Retrieve the pointer to the lock array for arbitrary size atomics.
 ///
@@ -146,7 +116,23 @@ void init_lock_array_cuda_space();
 /// object for which an atomic operation is performed.
 /// This function retrieves the lock array pointer.
 /// If the array is not yet allocated it will do so.
-int* lock_array_cuda_space_ptr(bool deallocate = false);
+int* atomic_lock_array_cuda_space_ptr(bool deallocate = false);
+
+/// \brief Retrieve the pointer to the scratch array for team and thread private global memory.
+///
+/// Team and Thread private scratch allocations in
+/// global memory are aquired via locks.
+/// This function retrieves the lock array pointer.
+/// If the array is not yet allocated it will do so.
+int* scratch_lock_array_cuda_space_ptr(bool deallocate = false);
+
+/// \brief Retrieve the pointer to the scratch array for unique identifiers.
+///
+/// Unique identifiers in the range 0-Cuda::concurrency
+/// are provided via locks.
+/// This function retrieves the lock array pointer.
+/// If the array is not yet allocated it will do so.
+int* threadid_lock_array_cuda_space_ptr(bool deallocate = false);
 }
 } // namespace Kokkos
 
@@ -172,33 +158,6 @@ public:
 
   /*--------------------------------*/
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-  typedef Impl::CudaUVMAllocator allocator;
-
-  /** \brief  Allocate a contiguous block of memory.
-   *
-   *  The input label is associated with the block of memory.
-   *  The block of memory is tracked via reference counting where
-   *  allocation gives it a reference count of one.
-   */
-  static Impl::AllocationTracker allocate_and_track( const std::string & label, const size_t size );
-
-
-  /** \brief  Cuda specific function to attached texture object to an allocation.
-   *          Output the texture object, base pointer, and offset from the input pointer.
-   */
-#if defined( __CUDACC__ )
-  static void texture_object_attach(  Impl::AllocationTracker const & tracker
-                                    , unsigned type_size
-                                    , ::cudaChannelFormatDesc const & desc
-                                   );
-#endif
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-  /*--------------------------------*/
-
   CudaUVMSpace();
   CudaUVMSpace( CudaUVMSpace && rhs ) = default ;
   CudaUVMSpace( const CudaUVMSpace & rhs ) = default ;
@@ -242,22 +201,6 @@ public:
 
   /*--------------------------------*/
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-  typedef Impl::CudaHostAllocator allocator ;
-
-  /** \brief  Allocate a contiguous block of memory.
-   *
-   *  The input label is associated with the block of memory.
-   *  The block of memory is tracked via reference counting where
-   *  allocation gives it a reference count of one.
-   */
-  static Impl::AllocationTracker allocate_and_track( const std::string & label, const size_t size );
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-  /*--------------------------------*/
-
   CudaHostPinnedSpace();
   CudaHostPinnedSpace( CudaHostPinnedSpace && rhs ) = default ;
   CudaHostPinnedSpace( const CudaHostPinnedSpace & rhs ) = default ;
diff --git a/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp b/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp
index 8489978f54..5834fc04db 100644
--- a/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp
+++ b/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -47,167 +47,15 @@
 #include <Kokkos_Core_fwd.hpp>
 #include <impl/Kokkos_Traits.hpp>
 #include <impl/Kokkos_StaticAssert.hpp>
+#include <impl/Kokkos_Error.hpp>
 #include <impl/Kokkos_Tags.hpp>
+#include <impl/Kokkos_AnalyzePolicy.hpp>
+#include <Kokkos_Concepts.hpp>
 #include <iostream>
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
 
-//Schedules for Execution Policies
-struct Static {
-};
-
-struct Dynamic {
-};
-
-//Schedule Wrapper Type
-template<class ScheduleType>
-struct Schedule {
-  static_assert(std::is_same<ScheduleType,Static>::value ||
-                std::is_same<ScheduleType,Dynamic>::value,
-                "Kokkos: Invalid Schedule<> type.");
-  typedef Schedule<ScheduleType> schedule_type;
-  typedef ScheduleType type;
-};
-
-//Specif Iteration Index Type
-template<typename iType>
-struct IndexType {
-  static_assert(std::is_integral<iType>::value,"Kokkos: Invalid IndexType<>.");
-  typedef IndexType<iType> index_type;
-  typedef iType type;
-};
-
-namespace Impl {
-
-template<class Arg>
-struct is_schedule_type {
-  enum { value = 0};
-};
-
-template<class ScheduleType>
-struct is_schedule_type<Schedule<ScheduleType> > {
-  enum {value = 1 };
-};
-
-template<class Arg>
-struct is_index_type {
-  enum { value = 0 };
-};
-
-template<typename iType>
-struct is_index_type<IndexType<iType> > {
-  enum { value = 1 };
-};
-
-template<typename Arg>
-struct is_tag_type {
-  enum { value = !(is_execution_space<Arg>::value ||
-                   is_schedule_type<Arg>::value ||
-                   is_index_type<Arg>::value ||
-                   std::is_integral<Arg>::value)};
-};
-
-//Policy Traits
-template<class ... Properties>
-struct PolicyTraits;
-
-template<>
-struct PolicyTraits<void> {
-  typedef void execution_space;
-  typedef void schedule_type;
-  typedef void index_type;
-  typedef void tag_type;
-};
-
-
-//Strip off ExecutionSpace
-template<class ExecutionSpace, class ... Props>
-struct PolicyTraits<typename std::enable_if<is_execution_space<ExecutionSpace>::value >::type,ExecutionSpace,Props ...> {
-  static_assert( std::is_same<typename PolicyTraits<void, Props ...>::execution_space, void>::value,
-                 "ExecutionPolicy: Only one execution space template argument may be used.");
-  typedef ExecutionSpace execution_space;
-  typedef typename PolicyTraits<void, Props ...>::schedule_type schedule_type;
-  typedef typename PolicyTraits<void, Props ...>::index_type index_type;
-  typedef typename PolicyTraits<void, Props ...>::tag_type tag_type;
-};
-
-//Strip off ScheduleType
-template<class ScheduleType, class ... Props>
-struct PolicyTraits<typename std::enable_if<is_schedule_type<Schedule<ScheduleType> >::value >::type,Schedule<ScheduleType>,Props ...> {
-  static_assert( std::is_same<typename PolicyTraits<void, Props ...>::schedule_type, void>::value,
-                 "ExecutionPolicy: Only one Schedule<..> template argument may be used.");
-  typedef typename PolicyTraits<void, Props ...>::execution_space execution_space;
-  typedef ScheduleType schedule_type;
-  typedef typename PolicyTraits<void, Props ...>::index_type index_type;
-  typedef typename PolicyTraits<void, Props ...>::tag_type tag_type;
-};
-
-//Strip off IndexType
-template<typename iType, class ... Props>
-struct PolicyTraits<void, IndexType<iType>,Props ...> {
-  static_assert( std::is_same<typename PolicyTraits<void, Props ...>::index_type, void>::value,
-                 "ExecutionPolicy: Only one IndexType<..> template argument may be used.");
-  typedef typename PolicyTraits<void, Props ...>::execution_space execution_space;
-  typedef typename PolicyTraits<void, Props ...>::schedule_type schedule_type;
-  typedef iType index_type;
-  typedef typename PolicyTraits<void, Props ...>::tag_type tag_type;
-};
-
-//Strip off raw IndexType
-template<typename iType, class ... Props>
-struct PolicyTraits<typename std::enable_if<std::is_integral<iType>::value>::type, iType,Props ...> {
-  static_assert( std::is_same<typename PolicyTraits<void, Props ...>::index_type, void>::value,
-                 "ExecutionPolicy: Only one IndexType<..> template argument may be used.");
-  typedef typename PolicyTraits<void, Props ...>::execution_space execution_space;
-  typedef typename PolicyTraits<void, Props ...>::schedule_type schedule_type;
-  typedef iType index_type;
-  typedef typename PolicyTraits<void, Props ...>::tag_type tag_type;
-};
-
-//Strip off TagType
-template<class TagType, class ... Props>
-struct PolicyTraits<typename std::enable_if<!is_schedule_type<TagType>::value &&
-                                            !is_execution_space<TagType>::value &&
-                                            !is_index_type<TagType>::value &&
-                                            !std::is_integral<TagType>::value 
-                                           >::type,
-                    TagType,Props ...> {
-  static_assert( std::is_same<typename PolicyTraits<void, Props ...>::tag_type, void>::value,
-                 "ExecutionPolicy: Only one tag type template argument may be used.");
-
-  typedef typename PolicyTraits<void, Props ...>::execution_space execution_space;
-  typedef typename PolicyTraits<void, Props ...>::schedule_type schedule_type;
-  typedef typename PolicyTraits<void, Props ...>::index_type index_type;
-  typedef TagType tag_type;
-};
-
-
-template<class ... Props>
-struct PolicyTraits {
-#ifdef KOKKOS_DIRECT_VARIADIC_EXPANSION
-  typedef typename std::conditional<std::is_same<void, typename PolicyTraits<void, Props ...>::execution_space>::value,
-    Kokkos::DefaultExecutionSpace, typename PolicyTraits<void,Props ...>::execution_space>::type execution_space;
-  typedef typename std::conditional<std::is_same<void, typename PolicyTraits<void, Props ...>::schedule_type>::value,
-    Kokkos::Static, typename PolicyTraits<void,Props ...>::schedule_type>::type schedule_type;
-  typedef typename std::conditional<std::is_same<void, typename PolicyTraits<void, Props ...>::index_type>::value,
-    typename execution_space::size_type, typename PolicyTraits<void,Props ...>::index_type>::type index_type;
-  typedef typename std::conditional<std::is_same<void, typename PolicyTraits<void, Props ...>::tag_type>::value, 
-    void, typename PolicyTraits<void,Props ...>::tag_type>::type work_tag;
-#else
-  typedef typename has_condition<Kokkos::DefaultExecutionSpace,is_execution_space,Props ...>::type execution_space;
-  typedef typename has_condition<Kokkos::Schedule<Kokkos::Static>,is_schedule_type,Props ...>::type schedule_type;
-  typedef typename has_condition<void,is_tag_type,Props ...>::type work_tag;
-  typedef typename has_condition<typename execution_space::size_type, std::is_integral, Props ... >::type default_index_type;
-  typedef typename has_condition<Kokkos::IndexType<default_index_type>,is_index_type,Props ...>::type::type index_type;
-#endif
-};
-
-}
-
-}
-
-namespace Kokkos {
 /** \brief  Execution policy for work over a range of an integral type.
  *
  * Valid template argument options:
@@ -230,7 +78,9 @@ namespace Kokkos {
  *  Blocking is the granularity of partitioning the range among threads.
  */
 template<class ... Properties>
-class RangePolicy: public Impl::PolicyTraits<Properties ... > {
+class RangePolicy
+  : public Impl::PolicyTraits<Properties ... >
+{
 private:
 
   typedef Impl::PolicyTraits<Properties ... > traits;
@@ -243,6 +93,7 @@ private:
 public:
 
   //! Tag this class as an execution policy
+  typedef RangePolicy execution_policy;
   typedef typename traits::index_type member_type ;
 
   KOKKOS_INLINE_FUNCTION const typename traits::execution_space & space() const { return m_space ; }
@@ -348,7 +199,7 @@ public:
       : m_begin(0), m_end(0)
       {
         if ( part_size ) {
-  
+
           // Split evenly among partitions, then round up to the granularity.
           const member_type work_part =
             ( ( ( ( range.end() - range.begin() ) + ( part_size - 1 ) ) / part_size )
@@ -356,7 +207,7 @@ public:
 
           m_begin = range.begin() + work_part * part_rank ;
           m_end   = m_begin       + work_part ;
-  
+
           if ( range.end() < m_begin ) m_begin = range.end() ;
           if ( range.end() < m_end )   m_end   = range.end() ;
         }
@@ -366,10 +217,11 @@ public:
      member_type m_end ;
      WorkRange();
      WorkRange & operator = ( const WorkRange & );
-   
+
   };
 };
 
+
 } // namespace Kokkos
 
 //----------------------------------------------------------------------------
@@ -377,38 +229,6 @@ public:
 
 namespace Kokkos {
 
-namespace Experimental {
-
-/** \brief Scratch memory request accepting per team and per thread value
- *
- * An instance of this class can be given as the last argument to a 
- * TeamPolicy constructor. It sets the amount of user requested shared
- * memory for the team.
- */
-
-template< class MemorySpace >
-class TeamScratchRequest {
-  size_t m_per_team;
-  size_t m_per_thread;
-  
-public:
-  TeamScratchRequest(size_t per_team_, size_t per_thread_ = 0):
-   m_per_team(per_team_), m_per_thread(per_thread_) {
-  } 
-
-  size_t per_team() const {
-    return m_per_team;
-  }
-  size_t per_thread() const {
-    return m_per_thread;
-  }
-  size_t total(const size_t team_size) const {
-    return m_per_team + m_per_thread * team_size;
-  }
-}; 
-
-}
-
 namespace Impl {
 
 
@@ -451,11 +271,9 @@ public:
 
   TeamPolicyInternal( int league_size_request , const Kokkos::AUTO_t & , int vector_length_request = 1 );
 
-  template<class MemorySpace>
-  TeamPolicyInternal( int league_size_request , int team_size_request , const Experimental::TeamScratchRequest<MemorySpace>& team_scratch_memory_request );
+/*  TeamPolicyInternal( int league_size_request , int team_size_request );
 
-  template<class MemorySpace>
-  TeamPolicyInternal( int league_size_request , const Kokkos::AUTO_t & , const Experimental::TeamScratchRequest<MemorySpace>& team_scratch_memory_request );
+  TeamPolicyInternal( int league_size_request , const Kokkos::AUTO_t & );*/
 
   /** \brief  The actual league size (number of teams) of the policy.
    *
@@ -574,12 +392,14 @@ class TeamPolicy: public
   typedef Impl::TeamPolicyInternal<
        typename Impl::PolicyTraits<Properties ... >::execution_space,
        Properties ...> internal_policy;
+
   typedef Impl::PolicyTraits<Properties ... > traits;
 
 public:
+  typedef TeamPolicy execution_policy;
 
   TeamPolicy& operator = (const TeamPolicy&) = default;
- 
+
   /** \brief  Construct policy with the given instance of the execution space */
   TeamPolicy( const typename traits::execution_space & , int league_size_request , int team_size_request , int vector_length_request = 1 )
     : internal_policy(typename traits::execution_space(),league_size_request,team_size_request, vector_length_request) {}
@@ -594,13 +414,11 @@ public:
   TeamPolicy( int league_size_request , const Kokkos::AUTO_t & , int vector_length_request = 1 )
     : internal_policy(league_size_request,Kokkos::AUTO(), vector_length_request) {}
 
-  template<class MemorySpace>
-  TeamPolicy( int league_size_request , int team_size_request , const Experimental::TeamScratchRequest<MemorySpace>& team_scratch_memory_request )
-    : internal_policy(league_size_request,team_size_request, team_scratch_memory_request) {}
+/*  TeamPolicy( int league_size_request , int team_size_request  )
+    : internal_policy(league_size_request,team_size_request) {}
 
-  template<class MemorySpace>
-  TeamPolicy( int league_size_request , const Kokkos::AUTO_t & , const Experimental::TeamScratchRequest<MemorySpace>& team_scratch_memory_request )
-    : internal_policy(league_size_request,Kokkos::AUTO(), team_scratch_memory_request) {}
+  TeamPolicy( int league_size_request , const Kokkos::AUTO_t &  )
+    : internal_policy(league_size_request,Kokkos::AUTO()) {}*/
 
 private:
   TeamPolicy(const internal_policy& p):internal_policy(p) {}
@@ -744,6 +562,7 @@ Impl::ThreadVectorRangeBoundariesStruct<iType,TeamMemberType> ThreadVectorRange(
 
 } // namespace Kokkos
 
+
 #endif /* #define KOKKOS_EXECPOLICY_HPP */
 
 //----------------------------------------------------------------------------
diff --git a/lib/kokkos/core/src/Kokkos_HBWSpace.hpp b/lib/kokkos/core/src/Kokkos_HBWSpace.hpp
index 6bef213b01..e02689b0f9 100644
--- a/lib/kokkos/core/src/Kokkos_HBWSpace.hpp
+++ b/lib/kokkos/core/src/Kokkos_HBWSpace.hpp
@@ -120,21 +120,6 @@ public:
   //! This memory space preferred device_type
   typedef Kokkos::Device<execution_space,memory_space> device_type;
 
-  /*--------------------------------*/
-#if ! KOKKOS_USING_EXP_VIEW
-
-  typedef Impl::HBWMallocAllocator allocator ;
-
-  /** \brief  Allocate a contiguous block of memory.
-   *
-   *  The input label is associated with the block of memory.
-   *  The block of memory is tracked via reference counting where
-   *  allocation gives it a reference count of one.
-   */
-  static Kokkos::Impl::AllocationTracker allocate_and_track( const std::string & label, const size_t size );
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
   /*--------------------------------*/
   /* Functions unique to the HBWSpace */
   static int in_parallel();
diff --git a/lib/kokkos/core/src/Kokkos_HostSpace.hpp b/lib/kokkos/core/src/Kokkos_HostSpace.hpp
index bea955cdd9..5fe686559a 100644
--- a/lib/kokkos/core/src/Kokkos_HostSpace.hpp
+++ b/lib/kokkos/core/src/Kokkos_HostSpace.hpp
@@ -55,9 +55,6 @@
 #include <impl/Kokkos_Traits.hpp>
 #include <impl/Kokkos_Error.hpp>
 
-#include <impl/Kokkos_AllocationTracker.hpp>
-#include <impl/Kokkos_BasicAllocators.hpp>
-
 #include <impl/KokkosExp_SharedAlloc.hpp>
 
 /*--------------------------------------------------------------------------*/
@@ -128,25 +125,6 @@ public:
   //! This memory space preferred device_type
   typedef Kokkos::Device<execution_space,memory_space> device_type;
 
-  /*--------------------------------*/
-#if ! KOKKOS_USING_EXP_VIEW
-
-#if defined( KOKKOS_USE_PAGE_ALIGNED_HOST_MEMORY )
-  typedef Impl::PageAlignedAllocator allocator ;
-#else
-  typedef Impl::AlignedAllocator allocator ;
-#endif
-
-  /** \brief  Allocate a contiguous block of memory.
-   *
-   *  The input label is associated with the block of memory.
-   *  The block of memory is tracked via reference counting where
-   *  allocation gives it a reference count of one.
-   */
-  static Impl::AllocationTracker allocate_and_track( const std::string & label, const size_t size );
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
   /*--------------------------------*/
   /* Functions unique to the HostSpace */
   static int in_parallel();
diff --git a/lib/kokkos/core/src/Kokkos_Macros.hpp b/lib/kokkos/core/src/Kokkos_Macros.hpp
index 40a46b3022..7d1e59af5e 100644
--- a/lib/kokkos/core/src/Kokkos_Macros.hpp
+++ b/lib/kokkos/core/src/Kokkos_Macros.hpp
@@ -133,11 +133,23 @@
 // still identifies as 7.0
 #error "Cuda version 7.5 or greater required for host-to-device Lambda support"
 #endif
+#if ( CUDA_VERSION < 8000 )
 #define KOKKOS_LAMBDA [=]__device__
+#else
+#define KOKKOS_LAMBDA [=]__host__ __device__
+#endif
 #define KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA 1
 #endif
 #endif /* #if defined( KOKKOS_HAVE_CUDA ) && defined( __CUDACC__ ) */
 
+
+#if defined(KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA)
+   // Cuda version 8.0 still needs the functor wrapper
+   #if (KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA /* && (CUDA_VERSION < 8000) */ )
+      #define KOKKOS_IMPL_NEED_FUNCTOR_WRAPPER
+   #endif
+#endif
+
 /*--------------------------------------------------------------------------*/
 /* Language info: C++, CUDA, OPENMP */
 
@@ -440,27 +452,16 @@
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
-/* Transitional macro to change between old and new View,
- * default to use new View.
+/* Transitional macro to change between old and new View
+ * are no longer supported.
  */
 
-#if ! defined( KOKKOS_USING_EXP_VIEW )
 #if defined( KOKKOS_USING_DEPRECATED_VIEW )
-#define KOKKOS_USING_EXP_VIEW 0
-#else
-#define KOKKOS_USING_EXP_VIEW 1
-#endif
+#error "Kokkos deprecated View has been removed"
 #endif
 
-#if KOKKOS_USING_EXP_VIEW
-#if ! defined( KOKKOS_USING_EXPERIMENTAL_VIEW )
+#define KOKKOS_USING_EXP_VIEW 1
 #define KOKKOS_USING_EXPERIMENTAL_VIEW
-#endif
-#else /* ! KOKKOS_USING_EXP_VIEW */
-#if defined( KOKKOS_USING_EXPERIMENTAL_VIEW )
-#error "KOKKOS_USING_EXP_VIEW and KOKKOS_USING_EXPERIMENAL_VIEW are both defined and are incompatible"
-#endif
-#endif
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
diff --git a/lib/kokkos/core/src/Kokkos_MemoryPool.hpp b/lib/kokkos/core/src/Kokkos_MemoryPool.hpp
index 72d2a30560..d843f7c9a1 100644
--- a/lib/kokkos/core/src/Kokkos_MemoryPool.hpp
+++ b/lib/kokkos/core/src/Kokkos_MemoryPool.hpp
@@ -44,13 +44,16 @@
 #ifndef KOKKOS_MEMORYPOOL_HPP
 #define KOKKOS_MEMORYPOOL_HPP
 
-#include <vector>
-
 #include <Kokkos_Core_fwd.hpp>
+#include <Kokkos_Parallel.hpp>
+#include <Kokkos_Atomic.hpp>
+#include <impl/Kokkos_BitOps.hpp>
 #include <impl/Kokkos_Error.hpp>
 #include <impl/KokkosExp_SharedAlloc.hpp>
-#include <Kokkos_ExecPolicy.hpp>
-#include <Kokkos_Atomic.hpp>
+
+#include <limits>
+#include <algorithm>
+#include <chrono>
 
 // How should errors be handled?  In general, production code should return a
 // value indicating failure so the user can decide how the error is handled.
@@ -60,516 +63,1431 @@
 //#define KOKKOS_MEMPOOL_PRINTERR
 
 //#define KOKKOS_MEMPOOL_PRINT_INFO
+//#define KOKKOS_MEMPOOL_PRINT_CONSTRUCTOR_INFO
+//#define KOKKOS_MEMPOOL_PRINT_BLOCKSIZE_INFO
+//#define KOKKOS_MEMPOOL_PRINT_SUPERBLOCK_INFO
+//#define KOKKOS_MEMPOOL_PRINT_ACTIVE_SUPERBLOCKS
+//#define KOKKOS_MEMPOOL_PRINT_PAGE_INFO
+//#define KOKKOS_MEMPOOL_PRINT_INDIVIDUAL_PAGE_INFO
+
+// A superblock is considered full when this percentage of its pages are full.
+#define KOKKOS_MEMPOOL_SB_FULL_FRACTION 0.80
+
+// A page is considered full when this percentage of its blocks are full.
+#define KOKKOS_MEMPOOL_PAGE_FULL_FRACTION 0.875  // 28 / 32
 
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
 namespace Experimental {
 
-template < typename Space , typename ExecSpace = typename Space::execution_space >
-class MemoryPool;
+namespace MempoolImpl {
 
-namespace Impl {
+template < typename T, typename ExecutionSpace >
+struct initialize_array {
+  typedef ExecutionSpace                      execution_space;
+  typedef typename ExecutionSpace::size_type  size_type;
 
-#ifdef KOKKOS_MEMPOOL_PRINT_INFO
-template < typename MemPool >
-struct print_mempool {
-  size_t      m_num_chunk_sizes;
-  size_t *    m_chunk_size;
-  uint64_t *  m_freelist;
-  char *      m_data;
-
-  print_mempool( size_t ncs, size_t * cs, uint64_t * f, char * d )
-    : m_num_chunk_sizes(ncs), m_chunk_size(cs), m_freelist(f), m_data(d)
-  {}
+  T *  m_data;
+  T    m_value;
 
-  KOKKOS_INLINE_FUNCTION
-  void operator()( size_t i ) const
+  initialize_array( T * d, size_t size, T v ) : m_data( d ), m_value( v )
   {
-    if ( i == 0 ) {
-      printf( "*** ON DEVICE ***\n");
-      printf( "m_chunk_size: 0x%llx\n", reinterpret_cast<uint64_t>( m_chunk_size ) );
-      printf( "  m_freelist: 0x%llx\n", reinterpret_cast<uint64_t>( m_freelist ) );
-      printf( "      m_data: 0x%llx\n", reinterpret_cast<uint64_t>( m_data ) );
-      for ( size_t l = 0; l < m_num_chunk_sizes; ++l ) {
-        printf( "%2lu    freelist: %10llu    chunk_size: %6lu\n",
-               l, get_head_offset( m_freelist[l] ), m_chunk_size[l] );
-      }
-      printf( "                              chunk_size: %6lu\n\n",
-              m_chunk_size[m_num_chunk_sizes] );
-    }
+    Kokkos::parallel_for( size, *this );
+
+    execution_space::fence();
   }
 
-  // This is only redefined here to avoid having to pass a MemPoolList object
-  // to the class.
   KOKKOS_INLINE_FUNCTION
-  uint64_t get_head_offset(uint64_t head) const
-  { return ( head >> MemPool::TAGBITS ) << MemPool::LG_MIN_CHUNKSIZE; }
+  void operator()( size_type i ) const { m_data[i] = m_value; }
 };
-#endif
 
-template < typename MemPool >
-struct initialize_mempool {
-  char *  m_data;
-  size_t  m_chunk_size;
-  size_t  m_last_chunk;
-  size_t  m_base_offset;
+template <typename Bitset>
+struct bitset_count
+{
+  typedef typename Bitset::execution_space     execution_space;
+  typedef typename execution_space::size_type  size_type;
+  typedef typename Bitset::size_type           value_type;
+  typedef typename Bitset::word_type           word_type;
+
+  word_type *   m_words;
+  value_type &  m_result;
+
+  bitset_count( word_type * w, value_type num_words, value_type & r )
+    : m_words( w ), m_result( r )
+  {
+    parallel_reduce( num_words, *this, m_result );
+  }
 
-  initialize_mempool( char * d, size_t cs, size_t lc, size_t bo )
-    : m_data(d), m_chunk_size(cs), m_last_chunk(lc), m_base_offset(bo)
-  {}
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type & v ) const
+  { v = 0; }
 
   KOKKOS_INLINE_FUNCTION
-  void operator()( size_t i ) const
+  void join( volatile value_type & dst, volatile value_type const & src ) const
+  { dst += src; }
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()( size_type i, value_type & count) const
   {
-    uint64_t * lp =
-      reinterpret_cast<uint64_t *>( m_data + m_base_offset + i * m_chunk_size );
-
-    // All entries in the list point to the next entry except the last which
-    // uses a reserved value to indicate the end of the list.  The offset from
-    // the base pointer is stored in increments of the minimum chunk size.
-    *lp = i < m_last_chunk ?
-          m_base_offset + (i + 1) * m_chunk_size :
-          MemPool::FREELIST_END;
+    count += Kokkos::Impl::bit_count( m_words[i] );
   }
 };
 
-class MemPoolList {
-private:
-
-  typedef Impl::SharedAllocationTracker  Tracker;
+template < typename Device >
+class Bitset {
+public:
+  typedef typename Device::execution_space  execution_space;
+  typedef typename Device::memory_space     memory_space;
+  typedef unsigned                          word_type;
+  typedef unsigned                          size_type;
 
-  template < typename , typename > friend class Kokkos::Experimental::MemoryPool;
-  template < typename > friend struct initialize_mempool;
-#ifdef KOKKOS_MEMPOOL_PRINT_INFO
-  template < typename > friend struct print_mempool;
-#endif
+  typedef Kokkos::Impl::DeepCopy< memory_space, Kokkos::HostSpace > raw_deep_copy;
 
   // Define some constants.
   enum {
-    // The head of a freelist is a 64 bit unsigned interger.  We divide it
-    // into 2 pieces.  The upper (64-TAGBITS) bits is the offset from the base
-    // data pointer of the allocator in increments of the minimum chunk size.
-    // The lower TAGBITS bits is the tag used to prevent ABA problems.  The
-    // largest two values that fit in the offset portion are reserved to
-    // represent the end of the freelist and that the freelist is locked.
-    //
-    // Using 32 bits for both the tag and offset and with a minimum chunk size
-    // of 128 bytes, the offset can address 549755813632 bytes (app. 512 GB)
-    // of memory.  This should be more than enough to address the whole address
-    // space of a GPU or MIC for the foreseeable future.
-    TAGBITS            = 32,
-    MIN_CHUNKSIZE      = 128,
-
-    TAGBITS_MASK       = ( uint64_t( 1 ) << TAGBITS ) - 1,
-    LG_MIN_CHUNKSIZE   = Kokkos::Impl::integral_power_of_two(MIN_CHUNKSIZE),
-
-    // The largest two values of the offset are reserved to indicate the end of a
-    // freelist (2^TAGBITS - 2) and that the freelist is locked (2^TAGBITS - 1).
-    // They are shifted so they can be compared directly to the result of
-    // get_head_offset().
-    FREELIST_END       = uint64_t( TAGBITS_MASK - 1 ) << LG_MIN_CHUNKSIZE,
-    FREELIST_LOCK      = uint64_t( TAGBITS_MASK ) << LG_MIN_CHUNKSIZE,
-
-    // This is the head value for a locked freelist.  It uses the lock value for
-    // the offset and 0 for the tagbits.
-    FREELIST_LOCK_HEAD = uint64_t( TAGBITS_MASK ) << TAGBITS
+    // Size of bitset word.  Should be 32.
+    WORD_SIZE    = sizeof(word_type) * CHAR_BIT,
+    LG_WORD_SIZE = Kokkos::Impl::integral_power_of_two( WORD_SIZE ),
+    WORD_MASK    = WORD_SIZE - 1
   };
 
-  Tracker   m_track;
+private:
+  word_type *  m_words;
+  size_type    m_size;
+  size_type    m_num_words;
+  word_type    m_last_word_mask;
 
-  // These three variables are pointers into device memory.
-  size_t *    m_chunk_size; // Array of chunk sizes of freelists.
-  uint64_t *  m_freelist;   // Array of freelist heads.
-  char *      m_data;       // Beginning memory location used for chunks.
+public:
+  ~Bitset() = default;
+  Bitset() = default;
+  Bitset( Bitset && ) = default;
+  Bitset( const Bitset & ) = default;
+  Bitset & operator = ( Bitset && ) = default;
+  Bitset & operator = ( const Bitset & ) = default;
+
+  void init( void * w, size_type s )
+  {
+    // Assumption: The size of the memory pointed to by w is a multiple of
+    //             sizeof(word_type).
 
-  size_t      m_data_size;
-  size_t      m_chunk_spacing;
+    m_words = reinterpret_cast<word_type*>( w );
+    m_size = s;
+    m_num_words = ( s + WORD_SIZE - 1 ) >> LG_WORD_SIZE;
+    m_last_word_mask = m_size & WORD_MASK ? ( word_type(1) << ( m_size & WORD_MASK ) ) - 1 : 0;
 
-#if defined(KOKKOS_MEMPOOL_PRINT_INFO) && defined(KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST)
-  static long m_count;
-#endif
+    reset();
+  }
 
-  ~MemPoolList() = default;
-  MemPoolList() = default;
-  MemPoolList( MemPoolList && ) = default;
-  MemPoolList( const MemPoolList & ) = default;
-  MemPoolList & operator = ( MemPoolList && ) = default;
-  MemPoolList & operator = ( const MemPoolList & ) = default;
+  size_type size() const { return m_size; }
 
-  template < typename MemorySpace, typename ExecutionSpace >
-  inline
-  MemPoolList( const MemorySpace & memspace, const ExecutionSpace &,
-               size_t arg_base_chunk_size, size_t arg_total_size,
-               size_t num_chunk_sizes, size_t chunk_spacing )
-    : m_track(), m_chunk_size(0), m_freelist(0), m_data(0), m_data_size(0),
-      m_chunk_spacing(chunk_spacing)
+  size_type count() const
   {
-    static_assert( sizeof(size_t) <= sizeof(void*), "" );
+    size_type val;
+    bitset_count< Bitset > bc( m_words, m_num_words, val );
+    return val;
+  }
 
-    typedef Impl::SharedAllocationRecord< MemorySpace, void >  SharedRecord;
-    typedef Kokkos::RangePolicy< ExecutionSpace >              Range;
+  void set()
+  {
+    // Set all the bits.
+    initialize_array< word_type, execution_space > ia( m_words, m_num_words, ~word_type(0) );
 
-    size_t base_chunk_size = arg_base_chunk_size;
+    if ( m_last_word_mask ) {
+      // Clear the unused bits in the last block.
+      raw_deep_copy( m_words + ( m_num_words - 1 ), &m_last_word_mask, sizeof(word_type) );
+    }
+  }
 
-    // The base chunk size must be at least MIN_CHUNKSIZE bytes as this is the
-    // cache-line size for NVIDA GPUs.
-    if ( base_chunk_size < MIN_CHUNKSIZE ) {
+  void reset()
+  {
+    initialize_array< word_type, execution_space > ia( m_words, m_num_words, word_type(0) );
+  }
 
-#ifdef KOKKOS_MEMPOOL_PRINT_INFO
-      printf( "** Chunk size must be at least %u bytes.  Setting to %u. **\n",
-              MIN_CHUNKSIZE, MIN_CHUNKSIZE);
-      fflush( stdout );
-#endif
+  KOKKOS_FORCEINLINE_FUNCTION
+  bool test( size_type i ) const
+  {
+    size_type word_pos = i >> LG_WORD_SIZE;
+    word_type word = volatile_load( &m_words[ word_pos ] );
+    word_type mask = word_type(1) << ( i & WORD_MASK );
+
+    return word & mask;
+  }
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  bool set( size_type i ) const
+  {
+    size_type word_pos = i >> LG_WORD_SIZE;
+    word_type mask = word_type(1) << ( i & WORD_MASK );
+
+    return !( atomic_fetch_or( &m_words[ word_pos ], mask ) & mask );
+  }
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  bool reset( size_type i ) const
+  {
+    size_type word_pos = i >> LG_WORD_SIZE;
+    word_type mask = word_type(1) << ( i & WORD_MASK );
+
+    return atomic_fetch_and( &m_words[ word_pos ], ~mask ) & mask;
+  }
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  Kokkos::pair< bool, word_type >
+  fetch_word_reset( size_type i ) const
+  {
+    size_type word_pos = i >> LG_WORD_SIZE;
+    word_type mask = word_type(1) << ( i & WORD_MASK );
+
+    Kokkos::pair<bool, word_type> result;
+    result.second = atomic_fetch_and( &m_words[ word_pos ], ~mask );
+    result.first = result.second & mask;
+
+    return result;
+  }
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  Kokkos::pair< bool, size_type >
+  set_any_in_word( size_type i, word_type & prev_val ) const
+  {
+    prev_val = 0;
 
-      base_chunk_size = MIN_CHUNKSIZE;
+    size_type word_pos = i >> LG_WORD_SIZE;
+    word_type word = volatile_load( &m_words[ word_pos ] );
+
+    // Loop until there are no more unset bits in the word.
+    while ( ~word ) {
+      // Find the first unset bit in the word.
+      size_type bit = Kokkos::Impl::bit_scan_forward( ~word );
+
+      // Try to set the bit.
+			word_type mask = word_type(1) << bit;
+      word = atomic_fetch_or( &m_words[ word_pos ], mask );
+
+      if ( !( word & mask ) ) {
+        // Successfully set the bit.
+        prev_val = word;
+
+        return Kokkos::pair<bool, size_type>( true, ( word_pos << LG_WORD_SIZE ) + bit );
+      }
     }
 
-    // The base chunk size must also be a multiple of MIN_CHUNKSIZE bytes for
-    // correct memory alignment of the chunks.  If it isn't a multiple of
-    // MIN_CHUNKSIZE, set it to the smallest multiple of MIN_CHUNKSIZE
-    // greater than the given chunk size.
-    if ( base_chunk_size % MIN_CHUNKSIZE != 0 ) {
-      size_t old_chunk_size = base_chunk_size;
-      base_chunk_size = ( ( old_chunk_size + MIN_CHUNKSIZE - 1 ) / MIN_CHUNKSIZE ) *
-                        MIN_CHUNKSIZE;
+    // Didn't find a free bit in this word.
+    return Kokkos::pair<bool, size_type>( false, i );
+  }
 
-#ifdef KOKKOS_MEMPOOL_PRINT_INFO
-      printf( "** Chunk size must be a multiple of %u bytes.  Given: %lu  Using: %lu. **\n",
-              MIN_CHUNKSIZE, old_chunk_size, base_chunk_size);
-      fflush( stdout );
-#endif
+  KOKKOS_FORCEINLINE_FUNCTION
+  Kokkos::pair< bool, size_type >
+  set_any_in_word( size_type i, word_type & prev_val, word_type word_mask ) const
+  {
+    prev_val = 0;
+
+    size_type word_pos = i >> LG_WORD_SIZE;
+    word_type word = volatile_load( &m_words[ word_pos ] );
+    word = ( ~word ) & word_mask;
 
+    // Loop until there are no more unset bits in the word.
+    while ( word ) {
+      // Find the first unset bit in the word.
+      size_type bit = Kokkos::Impl::bit_scan_forward( word );
+
+      // Try to set the bit.
+			word_type mask = word_type(1) << bit;
+      word = atomic_fetch_or( &m_words[ word_pos ], mask );
+
+      if ( !( word & mask ) ) {
+        // Successfully set the bit.
+        prev_val = word;
+
+        return Kokkos::pair<bool, size_type>( true, ( word_pos << LG_WORD_SIZE ) + bit );
+      }
+
+      word = ( ~word ) & word_mask;
     }
 
-    // Force total_size to be a multiple of base_chunk_size.
-    // Preserve the number of chunks originally requested.
-    size_t total_size = base_chunk_size *
-      ( ( arg_total_size + arg_base_chunk_size - 1 ) / arg_base_chunk_size );
+    // Didn't find a free bit in this word.
+    return Kokkos::pair<bool, size_type>( false, i );
+  }
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  Kokkos::pair< bool, size_type >
+  reset_any_in_word( size_type i, word_type & prev_val ) const
+  {
+    prev_val = 0;
+
+    size_type word_pos = i >> LG_WORD_SIZE;
+    word_type word = volatile_load( &m_words[ word_pos ] );
 
-    m_data_size = total_size;
+    // Loop until there are no more set bits in the word.
+    while ( word ) {
+      // Find the first unset bit in the word.
+      size_type bit = Kokkos::Impl::bit_scan_forward( word );
 
-    // Get the chunk size for the largest possible chunk.
-    //   max_chunk_size =
-    //     base_chunk_size * (m_chunk_spacing ^ (num_chunk_sizes - 1))
-    size_t max_chunk_size = base_chunk_size;
-    for (size_t i = 1; i < num_chunk_sizes; ++i) {
-      max_chunk_size *= m_chunk_spacing;
+      // Try to reset the bit.
+			word_type mask = word_type(1) << bit;
+      word = atomic_fetch_and( &m_words[ word_pos ], ~mask );
+
+      if ( word & mask ) {
+        // Successfully reset the bit.
+        prev_val = word;
+
+        return Kokkos::pair<bool, size_type>( true, ( word_pos << LG_WORD_SIZE ) + bit );
+      }
     }
 
-    // We want each chunk size to use total_size / num_chunk_sizes memory.  If
-    // the total size of the pool is not enough to accomodate this, keep making
-    // the next lower chunk size the max_chunk_size until it is.
-    while ( max_chunk_size > total_size / num_chunk_sizes ) {
-      max_chunk_size /= m_chunk_spacing;
-      --num_chunk_sizes;
+    // Didn't find a free bit in this word.
+    return Kokkos::pair<bool, size_type>( false, i );
+  }
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  Kokkos::pair< bool, size_type >
+  reset_any_in_word( size_type i, word_type & prev_val, word_type word_mask ) const
+  {
+    prev_val = 0;
+
+    size_type word_pos = i >> LG_WORD_SIZE;
+    word_type word = volatile_load( &m_words[ word_pos ] );
+    word = word & word_mask;
+
+    // Loop until there are no more set bits in the word.
+    while ( word ) {
+      // Find the first unset bit in the word.
+      size_type bit = Kokkos::Impl::bit_scan_forward( word );
+
+      // Try to reset the bit.
+			word_type mask = word_type(1) << bit;
+      word = atomic_fetch_and( &m_words[ word_pos ], ~mask );
+
+      if ( word & mask ) {
+        // Successfully reset the bit.
+        prev_val = word;
+
+        return Kokkos::pair<bool, size_type>( true, ( word_pos << LG_WORD_SIZE ) + bit );
+      }
+
+      word = word & word_mask;
     }
 
-    // We put a header at the beginnig of the device memory and use extra
-    // chunks to store the header.  The header contains:
-    //   size_t     chunk_size[num_chunk_sizes+1]
-    //   uint64_t  freelist[num_chunk_sizes]
+    // Didn't find a free bit in this word.
+    return Kokkos::pair<bool, size_type>( false, i );
+  }
+};
 
-    // Calculate the size of the header where the size is rounded up to the
-    // smallest multiple of base_chunk_size >= the needed size.  The size of the
-    // chunk size array is calculated using sizeof(void*) to guarantee alignment
-    // for the freelist array.  This assumes sizeof(size_t) <= sizeof(void*).
-    size_t header_bytes = ( 2 * num_chunk_sizes + 1 ) * sizeof(void*);
-    size_t header_size =
-      ( header_bytes + base_chunk_size - 1 ) / base_chunk_size * base_chunk_size;
+template < typename UInt32View, typename BSHeaderView, typename SBHeaderView,
+           typename MempoolBitset >
+struct create_histogram {
+  typedef typename UInt32View::execution_space  execution_space;
+  typedef typename execution_space::size_type   size_type;
+  typedef Kokkos::pair< double, uint32_t >      value_type;
+
+  size_t         m_start;
+  UInt32View     m_page_histogram;
+  BSHeaderView   m_blocksize_info;
+  SBHeaderView   m_sb_header;
+  MempoolBitset  m_sb_blocks;
+  size_t         m_lg_max_sb_blocks;
+  uint32_t       m_lg_min_block_size;
+  uint32_t       m_blocks_per_page;
+  value_type &   m_result;
+
+  create_histogram( size_t start, size_t end, UInt32View ph, BSHeaderView bsi,
+                    SBHeaderView sbh, MempoolBitset sbb, size_t lmsb,
+                    uint32_t lmbs, uint32_t bpp, value_type & r )
+    : m_start( start ), m_page_histogram( ph ), m_blocksize_info( bsi ),
+      m_sb_header( sbh ), m_sb_blocks( sbb ), m_lg_max_sb_blocks( lmsb ),
+      m_lg_min_block_size( lmbs ), m_blocks_per_page( bpp ), m_result( r )
+  {
+    Kokkos::parallel_reduce( end - start, *this, m_result );
 
-    // Allocate the memory including the header.
-    size_t alloc_size = total_size + header_size;
+    execution_space::fence();
+  }
 
-#ifdef KOKKOS_MEMPOOL_PRINT_INFO
-      printf( "** Allocating total %ld bytes\n", long(alloc_size));
-      fflush( stdout );
-#endif
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type & v ) const
+  {
+    v.first  = 0.0;
+    v.second = 0;
+  }
 
-    SharedRecord * rec =
-      SharedRecord::allocate( memspace, "mempool", alloc_size );
+  KOKKOS_INLINE_FUNCTION
+  void join( volatile value_type & dst, volatile value_type const & src ) const
+  {
+    dst.first += src.first;
+    dst.second += src.second;
+  }
 
-#ifdef KOKKOS_MEMPOOL_PRINT_INFO
-      printf( "** Allocated total %ld bytes at 0x%lx\n",
-              long(alloc_size), long(rec->data()) );
-      fflush( stdout );
-#endif
+  KOKKOS_INLINE_FUNCTION
+  void operator()( size_type i, value_type & r ) const
+  {
+    size_type i2 = i + m_start;
 
-    m_track.assign_allocated_record_to_uninitialized( rec );
+    uint32_t lg_block_size = m_sb_header(i2).m_lg_block_size;
 
-    {
-      // Get the pointers into the allocated memory.
-      char * mem = reinterpret_cast<char *>( rec->data() );
-      m_chunk_size = reinterpret_cast<size_t *>( mem );
-      m_freelist = reinterpret_cast<uint64_t *>(
-                   mem + ( num_chunk_sizes + 1 ) * sizeof(void*) );
-      m_data = mem + header_size;
+    // A superblock only has a block size of 0 when it is empty.
+    if ( lg_block_size != 0 ) {
+      uint32_t block_size_id = lg_block_size - m_lg_min_block_size;
+      uint32_t blocks_per_sb = m_blocksize_info[block_size_id].m_blocks_per_sb;
+      uint32_t pages_per_sb = m_blocksize_info[block_size_id].m_pages_per_sb;
 
-#ifdef KOKKOS_MEMPOOL_PRINT_INFO
-      printf( "** Partitioning allocation 0x%lx : m_chunk_size[0x%lx] m_freelist[0x%lx] m_data[0x%lx]\n",
-              (unsigned long) mem, (unsigned long) m_chunk_size,
-              (unsigned long) m_freelist, (unsigned long) m_data );
-      fflush( stdout );
-#endif
+      uint32_t total_allocated_blocks = 0;
+
+      for ( uint32_t j = 0; j < pages_per_sb; ++j ) {
+        unsigned start_pos = ( i2 << m_lg_max_sb_blocks ) + j * m_blocks_per_page;
+        unsigned end_pos = start_pos + m_blocks_per_page;
+        uint32_t page_allocated_blocks = 0;
+
+        for ( unsigned k = start_pos; k < end_pos; ++k ) {
+          page_allocated_blocks += m_sb_blocks.test( k );
+        }
+
+        total_allocated_blocks += page_allocated_blocks;
+
+        atomic_fetch_add( &m_page_histogram(page_allocated_blocks), 1 );
+      }
+
+      r.first += double(total_allocated_blocks) / blocks_per_sb;
+      r.second += blocks_per_sb;
     }
+  }
+};
+
+#ifdef KOKKOS_MEMPOOL_PRINT_SUPERBLOCK_INFO
+template < typename UInt32View, typename SBHeaderView, typename MempoolBitset >
+struct count_allocated_blocks {
+  typedef typename UInt32View::execution_space  execution_space;
+  typedef typename execution_space::size_type   size_type;
+
+  UInt32View     m_num_allocated_blocks;
+  SBHeaderView   m_sb_header;
+  MempoolBitset  m_sb_blocks;
+  size_t         m_sb_size;
+  size_t         m_lg_max_sb_blocks;
+
+  count_allocated_blocks( size_t num_sb, UInt32View nab, SBHeaderView sbh,
+                          MempoolBitset sbb, size_t sbs, size_t lmsb )
+    : m_num_allocated_blocks( nab ), m_sb_header( sbh ),
+      m_sb_blocks( sbb ), m_sb_size( sbs ), m_lg_max_sb_blocks( lmsb )
+  {
+    Kokkos::parallel_for( num_sb, *this );
+
+    execution_space::fence();
+  }
 
-    // Initialize the chunk sizes array.  Create num_chunk_sizes different
-    // chunk sizes where each successive chunk size is
-    // m_chunk_spacing * previous chunk size.  The last entry in the array is
-    // 0 and is used for a stopping condition.
-    m_chunk_size[0] = base_chunk_size;
-    for ( size_t i = 1; i < num_chunk_sizes; ++i ) {
-      m_chunk_size[i] = m_chunk_size[i - 1] * m_chunk_spacing;
+  KOKKOS_INLINE_FUNCTION
+  void operator()( size_type i ) const
+  {
+    uint32_t lg_block_size = m_sb_header(i).m_lg_block_size;
+
+    // A superblock only has a block size of 0 when it is empty.
+    if ( lg_block_size != 0 ) {
+      // Count the allocated blocks in the superblock.
+      uint32_t blocks_per_sb = lg_block_size > 0 ? m_sb_size >> lg_block_size : 0;
+      unsigned start_pos = i << m_lg_max_sb_blocks;
+      unsigned end_pos = start_pos + blocks_per_sb;
+      uint32_t count = 0;
+
+      for ( unsigned j = start_pos; j < end_pos; ++j ) {
+        count += m_sb_blocks.test( j );
+      }
+
+      m_num_allocated_blocks(i) = count;
     }
-    m_chunk_size[num_chunk_sizes] = 0;
+  }
+};
+#endif
 
-    std::vector<size_t> num_chunks(num_chunk_sizes);
+}
 
-    // Set the starting point in memory and get the number of chunks for each
-    // freelist.  Start with the largest chunk size to ensure usage of all the
-    // memory.  If there is leftover memory for a chunk size, it will be used
-    // by a smaller chunk size.
-    size_t used_memory = 0;
-    for ( size_t i = num_chunk_sizes; i > 0; --i ) {
-      // Set the starting position in the memory for the current chunk sizes's
-      // freelist and initialize the tag to 0.
-      m_freelist[i - 1] = create_head( used_memory, 0UL );
+/// \class MemoryPool
+/// \brief Bitset based memory manager for pools of same-sized chunks of memory.
+/// \tparam Device Kokkos device that gives the execution and memory space the
+///                allocator will be used in.
+///
+/// MemoryPool is a memory space that can be on host or device.  It provides a
+/// pool memory allocator for fast allocation of same-sized chunks of memory.
+/// The memory is only accessible on the host / device this allocator is
+/// associated with.
+///
+/// This allocator is based on ideas from the following GPU allocators:
+///   Halloc (https://github.com/canonizer/halloc).
+///   ScatterAlloc (https://github.com/ComputationalRadiationPhysics/scatteralloc)
+template < typename Device >
+class MemoryPool {
+private:
+  // The allocator uses superblocks.  A superblock is divided into pages, and a
+  // page is divided into blocks.  A block is the chunk of memory that is given
+  // out by the allocator.  A page always has a number of blocks equal to the
+  // size of the word used by the bitset.  Thus, the pagesize can vary between
+  // superblocks as it is based on the block size of the superblock.  The
+  // allocator supports all powers of 2 from MIN_BLOCK_SIZE to the size of a
+  // superblock as block sizes.
+
+  // Superblocks are divided into 4 categories:
+  //   1. empty    - is completely empty; there are no active allocations
+  //   2. partfull - partially full; there are some active allocations
+  //   3. full     - full enough with active allocations that new allocations
+  //                 will likely fail
+  //   4. active   - is currently the active superblock for a block size
+  //
+  // An inactive superblock is one that is empty, partfull, or full.
+  //
+  // New allocations occur only from an active superblock.  If a superblock is
+  // made inactive after an allocation request is made to it but before the
+  // allocation request is fulfilled, the allocation will still be attempted
+  // from that superblock.  Deallocations can  occur to partfull, full, or
+  // active superblocks.  Superblocks move between categories as allocations
+  // and deallocations happen.  Superblocks all start empty.
+  //
+  // Here are the possible moves between categories:
+  //   empty    -> active    During allocation, there is no active superblock
+  //                         or the active superblock is full.
+  //   active   -> full      During allocation, the full threshold of the
+  //                         superblock is reached when increasing the fill
+  //                         level.
+  //   full     -> partfull  During deallocation, the full threshold of the
+  //                         superblock is crossed when decreasing the fill
+  //                         level.
+  //   partfull -> empty     Deallocation of the last allocated block of an
+  //                         inactive superblock.
+  //   partfull -> active    During allocation, the active superblock is full.
+  //
+  // When a new active superblock is needed, partfull superblocks of the same
+  // block size are chosen over empty superblocks.
+  //
+  // The empty and partfull superblocks are tracked using bitsets that represent
+  // the superblocks in those repsective categories.  Empty superblocks use a
+  // single bitset, while partfull superblocks use a bitset per block size
+  // (contained sequentially in a single bitset).  Active superblocks are
+  // tracked by the active superblocks array.  Full superblocks aren't tracked
+  // at all.
+
+  typedef typename Device::execution_space    execution_space;
+  typedef typename Device::memory_space       backend_memory_space;
+  typedef Device                              device_type;
+  typedef MempoolImpl::Bitset< device_type >  MempoolBitset;
 
-      size_t mem_avail =
-        total_size - (i - 1) * ( total_size / num_chunk_sizes ) - used_memory;
+  // Define some constants.
+  enum {
+    MIN_BLOCK_SIZE     = 64,
+    LG_MIN_BLOCK_SIZE  = Kokkos::Impl::integral_power_of_two( MIN_BLOCK_SIZE ),
+    MAX_BLOCK_SIZES    = 31 - LG_MIN_BLOCK_SIZE + 1,
 
-      // Set the number of chunks for the current chunk sizes's freelist.
-      num_chunks[i - 1] = mem_avail / m_chunk_size[i - 1];
+    // Size of bitset word.
+    BLOCKS_PER_PAGE    = MempoolBitset::WORD_SIZE,
+    LG_BLOCKS_PER_PAGE = MempoolBitset::LG_WORD_SIZE,
 
-      used_memory += num_chunks[i - 1] * m_chunk_size[i - 1];
-    }
+    INVALID_SUPERBLOCK = ~uint32_t(0),
+    SUPERBLOCK_LOCK    = ~uint32_t(0) - 1,
 
-#ifdef KOKKOS_MEMPOOL_PRINT_INFO
-    printf( "\n" );
-    printf( "*** ON HOST ***\n");
-    printf( "m_chunk_size: 0x%llx\n", reinterpret_cast<uint64_t>( m_chunk_size ) );
-    printf( "  m_freelist: 0x%llx\n", reinterpret_cast<uint64_t>( m_freelist ) );
-    printf( "      m_data: 0x%llx\n", reinterpret_cast<uint64_t>( m_data ) );
-    for ( size_t i = 0; i < num_chunk_sizes; ++i ) {
-      printf( "%2lu    freelist: %10llu    chunk_size: %6lu    num_chunks: %8lu\n",
-              i, get_head_offset( m_freelist[i] ), m_chunk_size[i], num_chunks[i] );
-    }
-    printf( "                              chunk_size: %6lu\n\n",
-            m_chunk_size[num_chunk_sizes] );
-    fflush( stdout );
+    MAX_TRIES          = 32             // Cap on the number of pages searched
+                                        // before an allocation returns empty.
+  };
+
+public:
+  // Stores information about each superblock.
+  struct SuperblockHeader {
+    uint32_t  m_full_pages;
+    uint32_t  m_empty_pages;
+    uint32_t  m_lg_block_size;
+    uint32_t  m_is_active;
+
+    KOKKOS_FUNCTION
+    SuperblockHeader() :
+      m_full_pages(0), m_empty_pages(0), m_lg_block_size(0), m_is_active(false) {}
+  };
+
+  // Stores information about each block size.
+  struct BlockSizeHeader {
+    uint32_t  m_blocks_per_sb;
+    uint32_t  m_pages_per_sb;
+    uint32_t  m_sb_full_level;
+    uint32_t  m_page_full_level;
+
+    KOKKOS_FUNCTION
+    BlockSizeHeader() :
+      m_blocks_per_sb(0), m_pages_per_sb(0), m_sb_full_level(0), m_page_full_level(0) {}
+  };
+
+private:
+  typedef Impl::SharedAllocationTracker            Tracker;
+  typedef View< uint32_t *, device_type >          UInt32View;
+  typedef View< SuperblockHeader *, device_type >  SBHeaderView;
+
+  // The letters 'sb' used in any variable name mean superblock.
+
+  size_t           m_lg_sb_size;        // Log2 of superblock size.
+  size_t           m_sb_size;           // Superblock size.
+  size_t           m_lg_max_sb_blocks;  // Log2 of the number of blocks of the
+                                        // minimum block size in a superblock.
+  size_t           m_num_sb;            // Number of superblocks.
+  size_t           m_ceil_num_sb;       // Number of superblocks rounded up to the smallest
+                                        // multiple of the bitset word size.  Used by
+                                        // bitsets representing superblock categories to
+                                        // ensure different block sizes never share a word
+                                        // in the bitset.
+  size_t           m_num_block_size;    // Number of block sizes supported.
+  size_t           m_data_size;         // Amount of memory available to the allocator.
+  size_t           m_sb_blocks_size;    // Amount of memory for free / empty blocks bitset.
+  size_t           m_empty_sb_size;     // Amount of memory for empty superblocks bitset.
+  size_t           m_partfull_sb_size;  // Amount of memory for partfull superblocks bitset.
+  size_t           m_total_size;        // Total amount of memory allocated.
+  char *           m_data;              // Beginning device memory location used for
+                                        // superblocks.
+  UInt32View       m_active;            // Active superblocks IDs.
+  SBHeaderView     m_sb_header;         // Header info for superblocks.
+  MempoolBitset    m_sb_blocks;         // Bitsets representing free / allocated status
+                                        // of blocks in superblocks.
+  MempoolBitset    m_empty_sb;          // Bitset representing empty superblocks.
+  MempoolBitset    m_partfull_sb;       // Bitsets representing partially full superblocks.
+  Tracker          m_track;             // Tracker for superblock memory.
+  BlockSizeHeader  m_blocksize_info[MAX_BLOCK_SIZES];  // Header info for block sizes.
+
+  // There were several methods tried for storing the block size header info: in a View,
+  // in a View of const data, and in a RandomAccess View.  All of these were slower than
+  // storing it in a static array that is a member variable to the class.  In the latter
+  // case, the block size info gets copied into the constant memory on the GPU along with
+  // the class when it is copied there for exeucting a parallel loop.  Instead of storing
+  // the values, computing the values every time they were needed was also tried.  This
+  // method was slightly slower than storing them in the static array.
+
+public:
+  //! Tag this class as a kokkos memory space
+  typedef MemoryPool  memory_space;
+
+  ~MemoryPool() = default;
+  MemoryPool() = default;
+  MemoryPool( MemoryPool && ) = default;
+  MemoryPool( const MemoryPool & ) = default;
+  MemoryPool & operator = ( MemoryPool && ) = default;
+  MemoryPool & operator = ( const MemoryPool & ) = default;
+
+  /// \brief Initializes the memory pool.
+  /// \param memspace The memory space from which the memory pool will allocate memory.
+  /// \param total_size The requested memory amount controlled by the allocator.  The
+  ///                   actual amount is rounded up to the smallest multiple of the
+  ///                   superblock size >= the requested size.
+  /// \param log2_superblock_size Log2 of the size of superblocks used by the allocator.
+  ///                             In most use cases, the default value should work.
+  inline
+  MemoryPool( const backend_memory_space & memspace,
+              size_t total_size, size_t log2_superblock_size = 20 )
+    : m_lg_sb_size( log2_superblock_size ),
+      m_sb_size( size_t(1) << m_lg_sb_size ),
+      m_lg_max_sb_blocks( m_lg_sb_size - LG_MIN_BLOCK_SIZE ),
+      m_num_sb( ( total_size + m_sb_size - 1 ) >> m_lg_sb_size ),
+      m_ceil_num_sb( ( ( m_num_sb + BLOCKS_PER_PAGE - 1 ) >> LG_BLOCKS_PER_PAGE ) <<
+                     LG_BLOCKS_PER_PAGE ),
+      m_num_block_size( m_lg_sb_size - LG_MIN_BLOCK_SIZE + 1 ),
+      m_data_size( m_num_sb * m_sb_size ),
+      m_sb_blocks_size( ( m_num_sb << m_lg_max_sb_blocks ) / CHAR_BIT ),
+      m_empty_sb_size( m_ceil_num_sb / CHAR_BIT ),
+      m_partfull_sb_size( m_ceil_num_sb * m_num_block_size / CHAR_BIT ),
+      m_total_size( m_data_size +  m_sb_blocks_size + m_empty_sb_size + m_partfull_sb_size ),
+      m_data(0),
+      m_active( "Active superblocks" ),
+      m_sb_header( "Superblock headers" ),
+      m_track()
+  {
+    // Assumption.  The minimum block size must be a power of 2.
+    static_assert( Kokkos::Impl::is_integral_power_of_two( MIN_BLOCK_SIZE ), "" );
+
+    // Assumption.  Require a superblock be large enough so it takes at least 1
+    // whole bitset word to represent it using the minimum blocksize.
+    if ( m_sb_size < MIN_BLOCK_SIZE * BLOCKS_PER_PAGE ) {
+      printf( "\n** MemoryPool::MemoryPool() Superblock size must be >= %u **\n",
+              MIN_BLOCK_SIZE * BLOCKS_PER_PAGE );
+#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
+      fflush( stdout );
 #endif
+      Kokkos::abort( "" );
+    }
 
-#ifdef KOKKOS_MEMPOOL_PRINTERR
-    if ( used_memory != total_size ) {
-      printf( "\n** MemoryPool::MemoryPool() USED_MEMORY(%lu) != TOTAL_SIZE(%lu) **\n",
-              used_memory, total_size );
+    // Assumption.  A superblock's size can be at most 2^31.  Verify this.
+    if ( m_lg_sb_size > 31 ) {
+      printf( "\n** MemoryPool::MemoryPool() Superblock size must be < %u **\n",
+              ( uint32_t(1) << 31 ) );
 #ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
       fflush( stdout );
 #endif
       Kokkos::abort( "" );
     }
+
+    // Assumption.  The Bitset only uses unsigned for size types which limits
+    // the amount of memory the allocator can manage.  Verify the memory size
+    // is below this limit.
+    if ( m_data_size > size_t(MIN_BLOCK_SIZE) * std::numeric_limits<unsigned>::max() ) {
+      printf( "\n** MemoryPool::MemoryPool() Allocator can only manage %lu bytes of memory; requested %lu **\n",
+              size_t(MIN_BLOCK_SIZE) * std::numeric_limits<unsigned>::max(), total_size );
+#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
+      fflush( stdout );
 #endif
+      Kokkos::abort( "" );
+    }
+
+    // Allocate memory for Views.  This is done here instead of at construction
+    // so that the runtime checks can be performed before allocating memory.
+    resize(m_active, m_num_block_size );
+    resize(m_sb_header, m_num_sb );
 
-    // Create the chunks for each freelist.
-    for ( size_t i = 0; i < num_chunk_sizes; ++i ) {
-      // Initialize the next pointers to point to the next chunk for all but the
-      // last chunk which uses a reserved value to indicate the end of the list.
-      initialize_mempool<MemPoolList> im( m_data, m_chunk_size[i], num_chunks[i] - 1,
-                                          get_head_offset( m_freelist[i] ) );
+    // Allocate superblock memory.
+    typedef Impl::SharedAllocationRecord< backend_memory_space, void >  SharedRecord;
+    SharedRecord * rec =
+      SharedRecord::allocate( memspace, "mempool", m_total_size );
 
-      Kokkos::Impl::ParallelFor< initialize_mempool<MemPoolList>, Range >
-        closure( im, Range( 0, num_chunks[i] ) );
+    m_track.assign_allocated_record_to_uninitialized( rec );
+    m_data = reinterpret_cast<char *>( rec->data() );
 
-      closure.execute();
+    // Set and initialize the free / empty block bitset memory.
+    m_sb_blocks.init( m_data + m_data_size, m_num_sb << m_lg_max_sb_blocks );
 
-      ExecutionSpace::fence();
-    }
+    // Set and initialize the empty superblock block bitset memory.
+    m_empty_sb.init( m_data + m_data_size + m_sb_blocks_size, m_num_sb );
 
-#ifdef KOKKOS_MEMPOOL_PRINT_INFO
-    print_mempool<MemPoolList> pm( num_chunk_sizes, m_chunk_size, m_freelist, m_data );
+    // Start with all superblocks in the empty category.
+    m_empty_sb.set();
+
+    // Set and initialize the partfull superblock block bitset memory.
+    m_partfull_sb.init( m_data + m_data_size + m_sb_blocks_size + m_empty_sb_size,
+                        m_ceil_num_sb * m_num_block_size );
+
+    // Initialize all active superblocks to be invalid.
+    typename UInt32View::HostMirror host_active = create_mirror_view(m_active);
+    for (size_t i = 0; i < m_num_block_size; ++i) host_active(i) = INVALID_SUPERBLOCK;
+
+    deep_copy(m_active, host_active);
+
+    // Initialize the blocksize info.
+    for ( size_t i = 0; i < m_num_block_size; ++i ) {
+      uint32_t lg_block_size = i + LG_MIN_BLOCK_SIZE;
+      uint32_t blocks_per_sb = m_sb_size >> lg_block_size;
+      uint32_t pages_per_sb = ( blocks_per_sb + BLOCKS_PER_PAGE - 1 ) >> LG_BLOCKS_PER_PAGE;
+
+      m_blocksize_info[i].m_blocks_per_sb = blocks_per_sb;
+      m_blocksize_info[i].m_pages_per_sb = pages_per_sb;
+
+      // Set the full level for the superblock.
+      m_blocksize_info[i].m_sb_full_level =
+        static_cast<uint32_t>( pages_per_sb * KOKKOS_MEMPOOL_SB_FULL_FRACTION );
+
+      if ( m_blocksize_info[i].m_sb_full_level == 0 ) {
+        m_blocksize_info[i].m_sb_full_level = 1;
+      }
 
-    Kokkos::Impl::ParallelFor< print_mempool<MemPoolList>, Range >
-      closure( pm, Range( 0, 10 ) );
+      // Set the full level for the page.
+      uint32_t blocks_per_page =
+        blocks_per_sb < BLOCKS_PER_PAGE ? blocks_per_sb : BLOCKS_PER_PAGE;
 
-    closure.execute();
+      m_blocksize_info[i].m_page_full_level =
+        static_cast<uint32_t>( blocks_per_page * KOKKOS_MEMPOOL_PAGE_FULL_FRACTION );
 
-    ExecutionSpace::fence();
+      if ( m_blocksize_info[i].m_page_full_level == 0 ) {
+        m_blocksize_info[i].m_page_full_level = 1;
+      }
+    }
+
+#ifdef KOKKOS_MEMPOOL_PRINT_CONSTRUCTOR_INFO
+    printf( "\n" );
+    printf( "      m_lg_sb_size: %12lu\n", m_lg_sb_size );
+    printf( "         m_sb_size: %12lu\n", m_sb_size );
+    printf( "   m_max_sb_blocks: %12lu\n", size_t(1) << m_lg_max_sb_blocks );
+    printf( "m_lg_max_sb_blocks: %12lu\n", m_lg_max_sb_blocks );
+    printf( "          m_num_sb: %12lu\n", m_num_sb );
+    printf( "     m_ceil_num_sb: %12lu\n", m_ceil_num_sb );
+    printf( "  m_num_block_size: %12lu\n", m_num_block_size );
+    printf( "        data bytes: %12lu\n", m_data_size );
+    printf( "   sb_blocks bytes: %12lu\n", m_sb_blocks_size );
+    printf( "    empty_sb bytes: %12lu\n", m_empty_sb_size );
+    printf( " partfull_sb bytes: %12lu\n", m_partfull_sb_size );
+    printf( "       total bytes: %12lu\n", m_total_size );
+    printf( "   m_empty_sb size: %12u\n", m_empty_sb.size() );
+    printf( "m_partfull_sb size: %12u\n", m_partfull_sb.size() );
+    printf( "\n" );
+    fflush( stdout );
 #endif
-  }
 
-  /// \brief Releases a lock on a freelist.
-  KOKKOS_FUNCTION
-  uint64_t acquire_lock( volatile uint64_t * freelist ) const;
+#ifdef KOKKOS_MEMPOOL_PRINT_BLOCKSIZE_INFO
+    // Print the blocksize info for all the block sizes.
+    printf( "SIZE    BLOCKS_PER_SB    PAGES_PER_SB    SB_FULL_LEVEL    PAGE_FULL_LEVEL\n" );
+    for ( size_t i = 0; i < m_num_block_size; ++i ) {
+      printf( "%4zu    %13u    %12u    %13u    %15u\n", i + LG_MIN_BLOCK_SIZE,
+              m_blocksize_info[i].m_blocks_per_sb, m_blocksize_info[i].m_pages_per_sb,
+              m_blocksize_info[i].m_sb_full_level, m_blocksize_info[i].m_page_full_level );
+    }
+    printf( "\n" );
+#endif
+  }
 
-  /// \brief Releases a lock on a freelist.
+  /// \brief  The actual block size allocated given alloc_size.
+  KOKKOS_INLINE_FUNCTION
+  size_t allocate_block_size( const size_t alloc_size ) const
+  { return size_t(1) << ( get_block_size_index( alloc_size ) + LG_MIN_BLOCK_SIZE); }
+
+  /// \brief Allocate a chunk of memory.
+  /// \param alloc_size Size of the requested allocated in number of bytes.
+  ///
+  /// The function returns a void pointer to a memory location on success and
+  /// NULL on failure.
   KOKKOS_FUNCTION
-  void release_lock( volatile uint64_t * freelist, uint64_t new_head ) const;
+  void * allocate( size_t alloc_size ) const
+  {
+    void * p = 0;
 
-  /// \brief Tries to refill a freelist using a chunk from another freelist.
-  KOKKOS_FUNCTION
-  void * refill_freelist( size_t l_exp ) const;
+    // Only support allocations up to the superblock size.  Just return 0
+    // (failed allocation) for any size above this.
+    if (alloc_size <= m_sb_size )
+    {
+      int block_size_id = get_block_size_index( alloc_size );
+      uint32_t blocks_per_sb = m_blocksize_info[block_size_id].m_blocks_per_sb;
+      uint32_t pages_per_sb = m_blocksize_info[block_size_id].m_pages_per_sb;
+      unsigned word_size = blocks_per_sb > 32 ? 32 : blocks_per_sb;
+      unsigned word_mask = ( uint64_t(1) << word_size ) - 1;
 
-  /// \brief Claim chunks of untracked memory from the pool.
-  KOKKOS_FUNCTION
-  void * allocate( size_t alloc_size ) const;
+      uint32_t sb_id = volatile_load( &m_active(block_size_id) );
 
-  /// \brief Release claimed memory back into the pool.
-  KOKKOS_FUNCTION
-  void deallocate( void * alloc_ptr, size_t alloc_size ) const;
+      // If the active is locked, keep reading it until the lock is released.
+      while ( sb_id == SUPERBLOCK_LOCK ) {
+        sb_id = volatile_load( &m_active(block_size_id) );
+      }
 
-  // \brief Pulls the offset from a freelist head.
-  KOKKOS_INLINE_FUNCTION
-  uint64_t get_head_offset(uint64_t head) const
-  { return ( head >> TAGBITS ) << LG_MIN_CHUNKSIZE; }
+      bool allocation_done = false;
+
+      while (!allocation_done) {
+        bool need_new_sb = false;
+
+        if (sb_id != INVALID_SUPERBLOCK) {
+          // Use the value from the clock register as the hash value.
+          uint64_t hash_val = get_clock_register();
+
+          // Get the starting position for this superblock's bits in the bitset.
+          uint32_t pos_base = sb_id << m_lg_max_sb_blocks;
+
+          // Mod the hash value to choose a page in the superblock.  The
+          // initial block searched is the first block of that page.
+          uint32_t pos_rel = uint32_t( hash_val & ( pages_per_sb - 1 ) ) << LG_BLOCKS_PER_PAGE;
+
+          // Get the absolute starting position for this superblock's bits in the bitset.
+          uint32_t pos = pos_base + pos_rel;
+
+          // Keep track of the number of pages searched.  Pages in the superblock are
+          // searched linearly from the starting page.  All pages in the superblock are
+          // searched until either a location is found, or it is proven empty.
+          uint32_t pages_searched = 0;
+
+          bool search_done = false;
+
+          while (!search_done) {
+            bool success;
+            unsigned prev_val;
+
+            Kokkos::tie( success, pos ) =
+              m_sb_blocks.set_any_in_word( pos, prev_val, word_mask );
+
+            if ( !success ) {
+              if ( ++pages_searched >= pages_per_sb ) {
+                // Searched all the pages in this superblock.  Look for a new superblock.
+                //
+                // The previous method tried limiting the number of pages searched, but
+                // that caused a huge performance issue in CUDA where the outer loop
+                // executed massive numbers of times.  Threads weren't able to find a
+                // free location when the superblock wasn't full and were able to execute
+                // the outer loop many times before the superblock was switched for a new
+                // one.  Switching to an exhaustive search eliminated this possiblity and
+                // didn't slow anything down for the tests.
+                need_new_sb = true;
+                search_done = true;
+              }
+              else {
+                // Move to the next page making sure the new search position
+                // doesn't go past this superblock's bits.
+                pos += BLOCKS_PER_PAGE;
+                pos = ( pos < pos_base + blocks_per_sb ) ? pos : pos_base;
+              }
+            }
+            else {
+              // Reserved a memory location to allocate.
+              search_done = true;
+              allocation_done = true;
+
+              uint32_t lg_block_size = block_size_id + LG_MIN_BLOCK_SIZE;
+
+              p = m_data + ( size_t(sb_id) << m_lg_sb_size ) +
+                  ( ( pos - pos_base ) << lg_block_size );
+
+              uint32_t used_bits = Kokkos::Impl::bit_count( prev_val );
+
+              if ( used_bits == 0 ) {
+                // This page was empty.  Decrement the number of empty pages for
+                // the superblock.
+                atomic_fetch_sub( &m_sb_header(sb_id).m_empty_pages, 1 );
+              }
+              else if ( used_bits == m_blocksize_info[block_size_id].m_page_full_level - 1 )
+              {
+                // This page is full.  Increment the number of full pages for
+                // the superblock.
+                uint32_t full_pages = atomic_fetch_add( &m_sb_header(sb_id).m_full_pages, 1 );
+
+                // This allocation made the superblock full, so a new one needs to be found.
+                if ( full_pages == m_blocksize_info[block_size_id].m_sb_full_level - 1 ) {
+                  need_new_sb = true;
+                }
+              }
+            }
+          }
+        }
+        else {
+          // This is the first allocation for this block size.  A superblock needs
+          // to be set as the active one.  If this point is reached any other time,
+          // it is an error.
+          need_new_sb = true;
+        }
+
+        if ( need_new_sb ) {
+          uint32_t new_sb_id = find_superblock( block_size_id, sb_id );
+
+          if ( new_sb_id == sb_id ) {
+            allocation_done = true;
+#ifdef KOKKOS_MEMPOOL_PRINT_INFO
+            printf( "** No superblocks available. **\n" );
+#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
+            fflush( stdout );
+#endif
+#endif
+          }
+          else {
+            sb_id = new_sb_id;
+          }
+        }
+      }
+    }
+#ifdef KOKKOS_MEMPOOL_PRINT_INFO
+    else {
+      printf( "** Requested allocation size (%zu) larger than superblock size (%lu). **\n",
+              alloc_size, m_sb_size);
+#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
+      fflush( stdout );
+#endif
+    }
+#endif
 
-  // \brief Pulls the tag from a freelist head.
-  KOKKOS_INLINE_FUNCTION
-  uint64_t get_head_tag(uint64_t head) const { return head & TAGBITS_MASK; }
-  // \brief Creates a freelist head from a offset and tag.
-  KOKKOS_INLINE_FUNCTION
-  uint64_t create_head(uint64_t offset, uint64_t tag) const
-  { return ( ( offset >> LG_MIN_CHUNKSIZE ) << TAGBITS ) | tag; }
+    return p;
+  }
 
-  // \brief Increments a tag.
-  KOKKOS_INLINE_FUNCTION
-  uint64_t increment_tag(uint64_t tag) const { return ( tag + 1 ) & TAGBITS_MASK; }
+  /// \brief Release allocated memory back to the pool.
+  /// \param alloc_ptr Pointer to chunk of memory previously allocated by
+  ///                  the allocator.
+  /// \param alloc_size Size of the allocated memory in number of bytes.
+  KOKKOS_FUNCTION
+  void deallocate( void * alloc_ptr, size_t alloc_size ) const
+  {
+    char * ap = static_cast<char *>( alloc_ptr );
+
+    // Only deallocate memory controlled by this pool.
+    if ( ap >= m_data && ap + alloc_size <= m_data + m_data_size ) {
+      // Get the superblock for the address.  This can be calculated by math on
+      // the address since the superblocks are stored contiguously in one memory
+      // chunk.
+      uint32_t sb_id = ( ap - m_data ) >> m_lg_sb_size;
+
+      // Get the starting position for this superblock's bits in the bitset.
+      uint32_t pos_base = sb_id << m_lg_max_sb_blocks;
+
+      // Get the relative position for this memory location's bit in the bitset.
+      uint32_t offset = ( ap - m_data ) - ( size_t(sb_id) << m_lg_sb_size );
+      uint32_t lg_block_size = m_sb_header(sb_id).m_lg_block_size;
+      uint32_t block_size_id = lg_block_size - LG_MIN_BLOCK_SIZE;
+      uint32_t pos_rel = offset >> lg_block_size;
+
+      bool success;
+      unsigned prev_val;
+
+      Kokkos::tie( success, prev_val ) = m_sb_blocks.fetch_word_reset( pos_base + pos_rel );
+
+      // If the memory location was previously deallocated, do nothing.
+      if ( success ) {
+        uint32_t page_fill_level = Kokkos::Impl::bit_count( prev_val );
+
+        if ( page_fill_level == 1 ) {
+          // This page is now empty.  Increment the number of empty pages for the
+          // superblock.
+          uint32_t empty_pages = atomic_fetch_add( &m_sb_header(sb_id).m_empty_pages, 1 );
+
+          if ( !volatile_load( &m_sb_header(sb_id).m_is_active ) &&
+               empty_pages == m_blocksize_info[block_size_id].m_pages_per_sb - 1 )
+          {
+            // This deallocation caused the superblock to be empty.  Change the
+            // superblock category from partially full to empty.
+            unsigned pos = block_size_id * m_ceil_num_sb + sb_id;
+
+            if ( m_partfull_sb.reset( pos ) ) {
+              // Reset the empty pages and block size for the superblock.
+              volatile_store( &m_sb_header(sb_id).m_empty_pages, uint32_t(0) );
+              volatile_store( &m_sb_header(sb_id).m_lg_block_size, uint32_t(0) );
+
+              memory_fence();
+
+              m_empty_sb.set( sb_id );
+            }
+          }
+        }
+        else if ( page_fill_level == m_blocksize_info[block_size_id].m_page_full_level ) {
+          // This page is no longer full.  Decrement the number of full pages for
+          // the superblock.
+          uint32_t full_pages = atomic_fetch_sub( &m_sb_header(sb_id).m_full_pages, 1 );
+
+          if ( !volatile_load( &m_sb_header(sb_id).m_is_active ) &&
+               full_pages == m_blocksize_info[block_size_id].m_sb_full_level )
+          {
+            // This deallocation caused the number of full pages to decrease below
+            // the full threshold.  Change the superblock category from full to
+            // partially full.
+            unsigned pos = block_size_id * m_ceil_num_sb + sb_id;
+            m_partfull_sb.set( pos );
+          }
+        }
+      }
+    }
+#ifdef KOKKOS_MEMPOOL_PRINTERR
+    else {
+      printf( "\n** MemoryPool::deallocate() ADDRESS_OUT_OF_RANGE(0x%llx) **\n",
+              reinterpret_cast<uint64_t>( alloc_ptr ) );
+#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
+      fflush( stdout );
+#endif
+    }
+#endif
+  }
 
-  /// \brief Tests if the memory pool is empty.
+  /// \brief Tests if the memory pool has no more memory available to allocate.
   KOKKOS_INLINE_FUNCTION
   bool is_empty() const
   {
-    size_t l = 0;
-    while ( m_chunk_size[l] > 0 &&
-            get_head_offset( m_freelist[l] ) == FREELIST_END )
-    {
-      ++l;
+    // The allocator is empty if all superblocks are full.  A superblock is
+    // full if it has >= 80% of its pages allocated.
+
+    // Look at all the superblocks.  If one is not full, then the allocator
+    // isn't empty.
+    for ( size_t i = 0; i < m_num_sb; ++i ) {
+      uint32_t lg_block_size = m_sb_header(i).m_lg_block_size;
+
+      // A superblock only has a block size of 0 when it is empty.
+      if ( lg_block_size == 0 ) return false;
+
+      uint32_t block_size_id = lg_block_size - LG_MIN_BLOCK_SIZE;
+      uint32_t full_pages = volatile_load( &m_sb_header(i).m_full_pages );
+
+      if ( full_pages < m_blocksize_info[block_size_id].m_sb_full_level ) return false;
     }
 
-    return m_chunk_size[l] == 0;
+    // All the superblocks were full.  The allocator is empty.
+    return true;
   }
 
   // The following functions are used for debugging.
   void print_status() const
   {
-    for ( size_t l = 0; m_chunk_size[l] > 0; ++l ) {
-      size_t count = 0;
-      uint64_t chunk = get_head_offset( m_freelist[l] );
+    printf( "\n" );
 
-      while ( chunk != FREELIST_END ) {
-        ++count;
-        chunk = *reinterpret_cast<uint64_t *>( m_data + chunk );
-      }
+#ifdef KOKKOS_MEMPOOL_PRINT_SUPERBLOCK_INFO
+    typename SBHeaderView::HostMirror host_sb_header = create_mirror_view(m_sb_header);
+    deep_copy( host_sb_header, m_sb_header );
+
+    UInt32View num_allocated_blocks( "Allocated Blocks", m_num_sb );
 
-      printf( "chunk_size: %6lu    num_chunks: %8lu\n", m_chunk_size[l], count );
-      fflush(stdout);
+    // Count the number of allocated blocks per superblock.
+    {
+      MempoolImpl::count_allocated_blocks< UInt32View, SBHeaderView, MempoolBitset >
+        mch( m_num_sb, num_allocated_blocks, m_sb_header,
+             m_sb_blocks, m_sb_size, m_lg_max_sb_blocks );
     }
-  }
 
-  KOKKOS_INLINE_FUNCTION
-  size_t get_min_chunk_size() const { return m_chunk_size[0]; }
+    typename UInt32View::HostMirror host_num_allocated_blocks =
+      create_mirror_view(num_allocated_blocks);
+    deep_copy( host_num_allocated_blocks, num_allocated_blocks );
+
+    // Print header info of all superblocks.
+    printf( "SB_ID    SIZE    ACTIVE    EMPTY_PAGES    FULL_PAGES    USED_BLOCKS\n" );
+    for ( size_t i = 0; i < m_num_sb; ++i ) {
+      printf( "%5zu    %4u    %6d    %11u    %10u     %10u\n", i,
+              host_sb_header(i).m_lg_block_size, host_sb_header(i).m_is_active,
+              host_sb_header(i).m_empty_pages, host_sb_header(i).m_full_pages,
+              host_num_allocated_blocks(i) );
+    }
 
-  size_t get_mem_size() const { return m_data_size; }
-};
+    printf( "\n" );
+#endif
 
-} // namespace Impl
-} // namespace Experimental
-} // namespace Kokkos
+    UInt32View page_histogram( "Page Histogram", 33 );
 
-//----------------------------------------------------------------------------
-/*  Prefer to implement these functions in a separate
- *  compilation unit.  For CUDA this requires nvcc command
- *  --relocatable-device-code=true
- *  When this command is set then the macro
- *  KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
- *  is also set.
- */
-#if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA ) && \
-    ! defined( KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE )
-
-#include <impl/Kokkos_MemoryPool_Inline.hpp>
+    // Get a View version of the blocksize info.
+    typedef View< BlockSizeHeader *, device_type >  BSHeaderView;
+    BSHeaderView blocksize_info( "BlockSize Headers", MAX_BLOCK_SIZES );
 
-#endif
+    Kokkos::Impl::DeepCopy< backend_memory_space, Kokkos::HostSpace >
+      dc( blocksize_info.ptr_on_device(), m_blocksize_info,
+          sizeof(BlockSizeHeader) * m_num_block_size );
 
-//----------------------------------------------------------------------------
+    Kokkos::pair< double, uint32_t > result = Kokkos::pair< double, uint32_t >( 0.0, 0 );
 
-namespace Kokkos {
-namespace Experimental {
+    // Create the page histogram.
+    {
+      MempoolImpl::create_histogram< UInt32View, BSHeaderView, SBHeaderView, MempoolBitset >
+        mch( 0, m_num_sb, page_histogram, blocksize_info, m_sb_header, m_sb_blocks,
+             m_lg_max_sb_blocks, LG_MIN_BLOCK_SIZE, BLOCKS_PER_PAGE, result );
+    }
 
-/// \class MemoryPool
-/// \brief Memory management for pool of same-sized chunks of memory.
-///
-/// MemoryPool is a memory space that can be on host or device.  It provides a
-/// pool memory allocator for fast allocation of same-sized chunks of memory.
-/// The memory is only accessible on the host / device this allocator is
-/// associated with.
-template < typename Space , typename ExecSpace >
-class MemoryPool {
-private:
+    typename UInt32View::HostMirror host_page_histogram = create_mirror_view(page_histogram);
+    deep_copy( host_page_histogram, page_histogram );
 
-  Impl::MemPoolList  m_memory;
+    // Find the used and total pages and blocks.
+    uint32_t used_pages = 0;
+    uint32_t used_blocks = 0;
+    for ( uint32_t i = 1; i < 33; ++i ) {
+      used_pages += host_page_histogram(i);
+      used_blocks += i * host_page_histogram(i);
+    }
+    uint32_t total_pages = used_pages + host_page_histogram(0);
+
+    unsigned num_empty_sb = m_empty_sb.count();
+    unsigned num_non_empty_sb = m_num_sb - num_empty_sb;
+    unsigned num_partfull_sb = m_partfull_sb.count();
 
-  typedef ExecSpace                     execution_space;
-  typedef typename Space::memory_space  backend_memory_space;
+    uint32_t total_blocks = result.second;
+    double ave_sb_full = num_non_empty_sb == 0 ? 0.0 : result.first / num_non_empty_sb;
+    double percent_used_sb = double( m_num_sb - num_empty_sb ) / m_num_sb;
+    double percent_used_pages = total_pages == 0 ? 0.0 : double(used_pages) / total_pages;
+    double percent_used_blocks = total_blocks == 0 ? 0.0 : double(used_blocks) / total_blocks;
 
-#if defined( KOKKOS_HAVE_CUDA )
+    // Count active superblocks.
+    typename UInt32View::HostMirror host_active = create_mirror_view(m_active);
+    deep_copy(host_active, m_active);
 
-  // Current implementation requires CudaUVM memory space
-  // for Cuda memory pool.
+    unsigned num_active_sb = 0;
+    for ( size_t i = 0; i < m_num_block_size; ++i ) {
+      num_active_sb += host_active(i) != INVALID_SUPERBLOCK;
+    }
 
-  static_assert(
-    ! std::is_same< typename Space::memory_space , Kokkos::CudaSpace >::value ,
-    "Kokkos::MemoryPool currently cannot use Kokkos::CudaSpace, you must use Kokkos::CudaUVMSpace" );
+#ifdef KOKKOS_MEMPOOL_PRINT_ACTIVE_SUPERBLOCKS
+    // Print active superblocks.
+    printf( "BS_ID      SB_ID\n" );
+    for ( size_t i = 0; i < m_num_block_size; ++i ) {
+      uint32_t sb_id = host_active(i);
 
+      if ( sb_id == INVALID_SUPERBLOCK ) {
+        printf( "%5zu          I\n", i );
+      }
+      else if ( sb_id == SUPERBLOCK_LOCK ) {
+        printf( "%5zu          L\n", i );
+      }
+      else {
+        printf( "%5zu    %7u\n", i, sb_id );
+      }
+    }
+    printf( "\n" );
+    fflush( stdout );
 #endif
 
-public:
+#ifdef KOKKOS_MEMPOOL_PRINT_PAGE_INFO
+    // Print the summary page histogram.
+    printf( "USED_BLOCKS    PAGE_COUNT\n" );
+    for ( uint32_t i = 0; i < 33; ++i ) {
+      printf( "%10u    %10u\n", i, host_page_histogram[i] );
+    }
+    printf( "\n" );
+#endif
 
-  //! Tag this class as a kokkos memory space
-  typedef MemoryPool  memory_space;
+#ifdef KOKKOS_MEMPOOL_PRINT_INDIVIDUAL_PAGE_INFO
+    // Print the page histogram for a few individual superblocks.
+//    const uint32_t num_sb_id = 2;
+//    uint32_t sb_id[num_sb_id] = { 0, 10 };
+    const uint32_t num_sb_id = 1;
+    uint32_t sb_id[num_sb_id] = { 0 };
 
-  //------------------------------------
+    for ( uint32_t i = 0; i < num_sb_id; ++i ) {
+      deep_copy( page_histogram, 0 );
 
-  MemoryPool() = default;
-  MemoryPool( MemoryPool && rhs ) = default;
-  MemoryPool( const MemoryPool & rhs ) = default;
-  MemoryPool & operator = ( MemoryPool && ) = default;
-  MemoryPool & operator = ( const MemoryPool & ) = default;
-  ~MemoryPool() = default;
+      {
+        MempoolImpl::create_histogram< UInt32View, BSHeaderView, SBHeaderView, MempoolBitset >
+          mch( sb_id[i], sb_id[i] + 1, page_histogram, blocksize_info, m_sb_header,
+               m_sb_blocks, m_lg_max_sb_blocks, LG_MIN_BLOCK_SIZE, BLOCKS_PER_PAGE, result );
+      }
 
-  /// \brief Allocate memory pool
-  /// \param memspace         From where to allocate the pool.
-  /// \param base_chunk_size  Hand out memory in chunks of this size.
-  /// \param total_size       Total size of the pool.
-  MemoryPool( const backend_memory_space & memspace,
-              size_t base_chunk_size, size_t total_size,
-              size_t num_chunk_sizes = 4, size_t chunk_spacing = 4 )
-    : m_memory( memspace, execution_space(), base_chunk_size, total_size,
-                num_chunk_sizes, chunk_spacing )
-  {}
-
-  /// \brief Claim chunks of untracked memory from the pool.
-  /// Can only be called from device.
-  KOKKOS_INLINE_FUNCTION
-  void * allocate( const size_t alloc_size ) const
-  { return m_memory.allocate( alloc_size ); }
+      deep_copy( host_page_histogram, page_histogram );
 
-  /// \brief Release claimed memory back into the pool
-  /// Can only be called from device.
-  KOKKOS_INLINE_FUNCTION
-  void deallocate( void * const alloc_ptr, const size_t alloc_size ) const
-  { m_memory.deallocate( alloc_ptr, alloc_size ); }
+      printf( "SB_ID    USED_BLOCKS    PAGE_COUNT\n" );
+      for ( uint32_t j = 0; j < 33; ++j ) {
+        printf( "%5u    %10u    %10u\n", sb_id[i], j, host_page_histogram[j] );
+      }
+      printf( "\n" );
+    }
 
-  /// \brief Is out of memory at this instant
-  KOKKOS_INLINE_FUNCTION
-  bool is_empty() const { return m_memory.is_empty(); }
+/*
+    // Print the blocks used for each page of a few individual superblocks.
+    for ( uint32_t i = 0; i < num_sb_id; ++i ) {
+      uint32_t lg_block_size = host_sb_header(sb_id[i]).m_lg_block_size;
+      if ( lg_block_size != 0 ) {
+        printf( "SB_ID    BLOCK ID    USED_BLOCKS\n" );
+
+        uint32_t block_size_id = lg_block_size - LG_MIN_BLOCK_SIZE;
+        uint32_t pages_per_sb = m_blocksize_info[block_size_id].m_pages_per_sb;
+
+        for ( uint32_t j = 0; j < pages_per_sb; ++j ) {
+          unsigned start_pos = ( sb_id[i] << m_lg_max_sb_blocks ) + j * BLOCKS_PER_PAGE;
+          unsigned end_pos = start_pos + BLOCKS_PER_PAGE;
+          uint32_t num_allocated_blocks = 0;
+
+          for ( unsigned k = start_pos; k < end_pos; ++k ) {
+            num_allocated_blocks += m_sb_blocks.test( k );
+          }
+
+          printf( "%5u    %8u    %11u\n", sb_id[i], j, num_allocated_blocks );
+        }
+
+        printf( "\n" );
+      }
+    }
+*/
+#endif
+
+    printf( "   Used blocks: %10u / %10u = %10.6lf\n", used_blocks, total_blocks,
+           percent_used_blocks );
+    printf( "    Used pages: %10u / %10u = %10.6lf\n", used_pages, total_pages,
+           percent_used_pages );
+    printf( "       Used SB: %10zu / %10zu = %10.6lf\n", m_num_sb - num_empty_sb, m_num_sb,
+           percent_used_sb );
+    printf( "     Active SB: %10u\n", num_active_sb );
+    printf( "      Empty SB: %10u\n", num_empty_sb );
+    printf( "   Partfull SB: %10u\n", num_partfull_sb );
+    printf( "       Full SB: %10lu\n",
+           m_num_sb - num_active_sb - num_empty_sb - num_partfull_sb );
+    printf( "Ave. SB Full %%: %10.6lf\n", ave_sb_full );
+    printf( "\n" );
+    fflush( stdout );
+
+#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
+    fflush( stdout );
+#endif
+  }
 
-  /// \brief Minimum chunk size allocatable.
   KOKKOS_INLINE_FUNCTION
-  size_t get_min_chunk_size() const { return m_memory.get_min_chunk_size(); }
+  size_t get_min_block_size() const { return MIN_BLOCK_SIZE; }
 
-  // The following functions are used for debugging.
-  void print_status() const { m_memory.print_status(); }
-  size_t get_mem_size() const { return m_memory.get_mem_size(); }
+  size_t get_mem_size() const { return m_data_size; }
+
+private:
+  /// \brief Returns the index into the active array for the given size.
+  ///
+  /// Computes log2 of the largest power of two >= the given size
+  /// ( ie ceil( log2(size) ) ) shifted by LG_MIN_BLOCK_SIZE.
+  KOKKOS_FORCEINLINE_FUNCTION
+  int get_block_size_index( const size_t size ) const
+  {
+    // We know the size fits in a 32 bit unsigned because the size of a
+    // superblock is limited to 2^31, so casting to an unsigned is safe.
+
+    // Find the most significant nonzero bit.
+    uint32_t first_nonzero_bit =
+      Kokkos::Impl::bit_scan_reverse( static_cast<unsigned>( size ) );
+
+    // If size is an integral power of 2, ceil( log2(size) ) is equal to the
+    // most significant nonzero bit.  Otherwise, you need to add 1.  Since the
+    // minimum block size is MIN_BLOCK_SIZE, make sure ceil( log2(size) ) is at
+    // least LG_MIN_BLOCK_SIZE.
+    uint32_t lg2_size = first_nonzero_bit + !Kokkos::Impl::is_integral_power_of_two( size );
+    lg2_size = lg2_size > LG_MIN_BLOCK_SIZE ? lg2_size : LG_MIN_BLOCK_SIZE;
+
+    // Return ceil( log2(size) ) shifted so that the value for MIN_BLOCK_SIZE
+    // is 0.
+    return lg2_size - LG_MIN_BLOCK_SIZE;
+  }
+
+  /// \brief Finds a superblock with free space to become a new active superblock.
+  ///
+  /// If this function is called, the current active superblock needs to be replaced
+  /// because it is full.  Initially, only the thread that sets the active superblock
+  /// to full calls this function.  Other threads can still allocate from the "full"
+  /// active superblock because a full superblock still has locations available.  If
+  /// a thread tries to allocate from the active superblock when it has no free
+  /// locations, then that thread will call this function, too, and spin on a lock
+  /// waiting until the active superblock has been replaced.
+  KOKKOS_FUNCTION
+  uint32_t find_superblock( int block_size_id, uint32_t old_sb ) const
+  {
+    // Try to grab the lock on the head.
+    uint32_t lock_sb =
+      Kokkos::atomic_compare_exchange( &m_active(block_size_id), old_sb, SUPERBLOCK_LOCK );
+
+    // Initialize the new superblock to be the previous one so the previous
+    // superblock is returned if a new superblock can't be found.
+    uint32_t new_sb = lock_sb;
+
+    if ( lock_sb == old_sb ) {
+      // This thread has the lock.
+
+      // 1. Look for a partially filled superblock that is of the right block
+      //    size.
+
+      size_t max_tries = m_ceil_num_sb >> LG_BLOCKS_PER_PAGE;
+      size_t tries = 0;
+      bool search_done = false;
+
+      // Set the starting search position to the beginning of this block
+      // size's bitset.
+      unsigned pos = block_size_id * m_ceil_num_sb;
+
+      while (!search_done) {
+        bool success = false;
+        unsigned prev_val;
+
+        Kokkos::tie( success, pos ) = m_partfull_sb.reset_any_in_word( pos, prev_val );
+
+        if ( !success ) {
+          if ( ++tries >= max_tries ) {
+            // Exceeded number of words for this block size's bitset.
+            search_done = true;
+          }
+          else {
+            pos += BLOCKS_PER_PAGE;
+          }
+        }
+        else {
+          // Found a superblock.
+          search_done = true;
+          new_sb = pos - block_size_id * m_ceil_num_sb;
+
+          // Assertions:
+          //   1. A different superblock than the current should be found.
+#ifdef KOKKOS_MEMPOOL_PRINTERR
+          if ( new_sb == lock_sb ) {
+            printf( "\n** MemoryPool::find_superblock() FOUND_SAME_SUPERBLOCK: %u **\n",
+                    new_sb);
+#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
+            fflush( stdout );
+#endif
+            Kokkos::abort( "" );
+          }
+#endif
+
+          // Set the head status for the superblock.
+          volatile_store( &m_sb_header(new_sb).m_is_active, uint32_t(true) );
+
+          // If there was a previous active superblock, mark it as not active.
+          // It is now in the full category and as such isn't tracked.
+          if ( lock_sb != INVALID_SUPERBLOCK ) {
+            volatile_store( &m_sb_header(lock_sb).m_is_active, uint32_t(false) );
+          }
+
+          memory_fence();
+        }
+      }
+
+      // 2. Look for an empty superblock.
+      if ( new_sb == lock_sb ) {
+        tries = 0;
+        search_done = false;
+
+        // Set the starting search position to the beginning of this block
+        // size's bitset.
+        pos = 0;
+
+        while (!search_done) {
+          bool success = false;
+          unsigned prev_val;
+
+          Kokkos::tie( success, pos ) = m_empty_sb.reset_any_in_word( pos, prev_val );
+
+          if ( !success ) {
+            if ( ++tries >= max_tries ) {
+              // Exceeded number of words for this block size's bitset.
+              search_done = true;
+            }
+            else {
+              pos += BLOCKS_PER_PAGE;
+            }
+          }
+          else {
+            // Found a superblock.
+            search_done = true;
+            new_sb = pos;
+
+            // Assertions:
+            //   1. A different superblock than the current should be found.
+#ifdef KOKKOS_MEMPOOL_PRINTERR
+            if ( new_sb == lock_sb ) {
+              printf( "\n** MemoryPool::find_superblock() FOUND_SAME_SUPERBLOCK: %u **\n",
+                      new_sb);
+#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
+              fflush( stdout );
+#endif
+              Kokkos::abort( "" );
+            }
+#endif
+
+            // Set the empty pages, block size, and head status for the
+            // superblock.
+            volatile_store( &m_sb_header(new_sb).m_empty_pages,
+                            m_blocksize_info[block_size_id].m_pages_per_sb );
+            volatile_store( &m_sb_header(new_sb).m_lg_block_size,
+                            block_size_id + LG_MIN_BLOCK_SIZE );
+            volatile_store( &m_sb_header(new_sb).m_is_active, uint32_t(true) );
+
+            // If there was a previous active superblock, mark it as not active.
+            // It is now in the full category and as such isn't tracked.
+            if ( lock_sb != INVALID_SUPERBLOCK ) {
+              volatile_store( &m_sb_header(lock_sb).m_is_active, uint32_t(false) );
+            }
+
+            memory_fence();
+          }
+        }
+      }
+
+      // Write the new active superblock to release the lock.
+      atomic_exchange( &m_active(block_size_id), new_sb );
+    }
+    else {
+      // Either another thread has the lock and is switching the active superblock for
+      // this block size or another thread has already changed the active superblock
+      // since this thread read its value.  Keep reading the active superblock until
+      // it isn't locked to get the new active superblock.
+      do {
+        new_sb = volatile_load( &m_active(block_size_id) );
+      } while ( new_sb == SUPERBLOCK_LOCK );
+
+      // Assertions:
+      //   1. An invalid superblock should never be found here.
+      //   2. If the new superblock is the same as the previous superblock, the
+      //      allocator is empty.
+#ifdef KOKKOS_MEMPOOL_PRINTERR
+      if ( new_sb == INVALID_SUPERBLOCK ) {
+        printf( "\n** MemoryPool::find_superblock() FOUND_INACTIVE_SUPERBLOCK **\n" );
+#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
+        fflush( stdout );
+#endif
+        Kokkos::abort( "" );
+      }
+#endif
+    }
+
+    return new_sb;
+  }
+
+  /// Returns 64 bits from a clock register.
+  KOKKOS_FORCEINLINE_FUNCTION
+  uint64_t get_clock_register(void) const
+  {
+#if defined( __CUDA_ARCH__ )
+    // Return value of 64-bit hi-res clock register.
+	  return clock64();
+#elif defined( __i386__ ) || defined( __x86_64 )
+    // Return value of 64-bit hi-res clock register.
+    unsigned a, d;
+    __asm__ volatile("rdtsc" : "=a" (a), "=d" (d));
+    return ( (uint64_t) a) | ( ( (uint64_t) d ) << 32 );
+#else
+    const uint64_t ticks = std::chrono::high_resolution_clock::now().time_since_epoch().count();
+    return ticks;
+#endif
+  }
 };
 
 } // namespace Experimental
@@ -583,4 +1501,23 @@ public:
 #undef KOKKOS_MEMPOOL_PRINT_INFO
 #endif
 
-#endif /* #define KOKKOS_MEMORYPOOL_HPP */
+#ifdef KOKKOS_MEMPOOL_PRINT_BLOCKSIZE_INFO
+#undef KOKKOS_MEMPOOL_PRINT_BLOCKSIZE_INFO
+#endif
+
+#ifdef KOKKOS_MEMPOOL_PRINT_SUPERBLOCK_INFO
+#undef KOKKOS_MEMPOOL_PRINT_SUPERBLOCK_INFO
+#endif
+
+#ifdef KOKKOS_MEMPOOL_PRINT_PAGE_INFO
+#undef KOKKOS_MEMPOOL_PRINT_PAGE_INFO
+#endif
+
+#ifdef KOKKOS_MEMPOOL_PRINT_INDIVIDUAL_PAGE_INFO
+#undef KOKKOS_MEMPOOL_PRINT_INDIVIDUAL_PAGE_INFO
+#endif
+
+#undef KOKKOS_MEMPOOL_SB_FULL_FRACTION
+#undef KOKKOS_MEMPOOL_PAGE_FULL_FRACTION
+
+#endif // KOKKOS_MEMORYPOOL_HPP
diff --git a/lib/kokkos/core/src/Kokkos_OpenMP.hpp b/lib/kokkos/core/src/Kokkos_OpenMP.hpp
index 389ee4b2fd..7be4f8245f 100644
--- a/lib/kokkos/core/src/Kokkos_OpenMP.hpp
+++ b/lib/kokkos/core/src/Kokkos_OpenMP.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -58,9 +58,11 @@
 #endif
 #include <Kokkos_ScratchSpace.hpp>
 #include <Kokkos_Parallel.hpp>
+#include <Kokkos_TaskPolicy.hpp>
 #include <Kokkos_Layout.hpp>
 #include <impl/Kokkos_Tags.hpp>
 
+#include <KokkosExp_MDRangePolicy.hpp>
 /*--------------------------------------------------------------------------*/
 
 namespace Kokkos {
@@ -177,6 +179,7 @@ struct VerifyExecutionCanAccessMemorySpace
 
 #include <OpenMP/Kokkos_OpenMPexec.hpp>
 #include <OpenMP/Kokkos_OpenMP_Parallel.hpp>
+#include <OpenMP/Kokkos_OpenMP_Task.hpp>
 
 /*--------------------------------------------------------------------------*/
 
diff --git a/lib/kokkos/core/src/Kokkos_Pair.hpp b/lib/kokkos/core/src/Kokkos_Pair.hpp
index 7e906a4571..83436826f4 100644
--- a/lib/kokkos/core/src/Kokkos_Pair.hpp
+++ b/lib/kokkos/core/src/Kokkos_Pair.hpp
@@ -1,12 +1,12 @@
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -35,7 +35,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 
@@ -125,17 +125,26 @@ struct pair
     return *this;
   }
 
-  /// \brief Assignment operator.
+
+  /// \brief Assignment operator, for volatile <tt>*this</tt>.
   ///
-  /// This calls the assignment operators of T1 and T2.  It won't
+  /// \param p [in] Input; right-hand side of the assignment.
+  ///
+  /// This calls the assignment operators of T1 and T2.  It will not
   /// compile if the assignment operators are not defined and public.
+  ///
+  /// This operator returns \c void instead of <tt>volatile pair<T1,
+  /// T2>& </tt>.  See Kokkos Issue #177 for the explanation.  In
+  /// practice, this means that you should not chain assignments with
+  /// volatile lvalues.
   template <class U, class V>
   KOKKOS_FORCEINLINE_FUNCTION
-  volatile pair<T1, T2> & operator=(const volatile pair<U,V> &p) volatile
+  void operator=(const volatile pair<U,V> &p) volatile
   {
     first = p.first;
     second = p.second;
-    return *this;
+    // We deliberately do not return anything here.  See explanation
+    // in public documentation above.
   }
 
   // from std::pair<U,V>
diff --git a/lib/kokkos/core/src/Kokkos_Parallel.hpp b/lib/kokkos/core/src/Kokkos_Parallel.hpp
index edaced22a9..588dc90af3 100644
--- a/lib/kokkos/core/src/Kokkos_Parallel.hpp
+++ b/lib/kokkos/core/src/Kokkos_Parallel.hpp
@@ -57,7 +57,6 @@
 #include <typeinfo>
 #endif
 
-#include <impl/Kokkos_AllocationTracker.hpp>
 #include <impl/Kokkos_Tags.hpp>
 #include <impl/Kokkos_Traits.hpp>
 #include <impl/Kokkos_FunctorAdapter.hpp>
@@ -178,8 +177,8 @@ void parallel_for( const ExecPolicy  & policy
 {
 #if (KOKKOS_ENABLE_PROFILING)
     uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-     	Kokkos::Experimental::beginParallelFor("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
+     if(Kokkos::Profiling::profileLibraryLoaded()) {
+     	Kokkos::Profiling::beginParallelFor("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
      }
 #endif
 
@@ -190,8 +189,8 @@ void parallel_for( const ExecPolicy  & policy
    closure.execute();
 
 #if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-        Kokkos::Experimental::endParallelFor(kpID);
+     if(Kokkos::Profiling::profileLibraryLoaded()) {
+        Kokkos::Profiling::endParallelFor(kpID);
      }
 #endif
 }
@@ -210,8 +209,8 @@ void parallel_for( const size_t        work_count
 
 #if (KOKKOS_ENABLE_PROFILING)
   uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-  	Kokkos::Experimental::beginParallelFor("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
+     if(Kokkos::Profiling::profileLibraryLoaded()) {
+  	Kokkos::Profiling::beginParallelFor("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
      }
 #endif
     
@@ -222,8 +221,8 @@ void parallel_for( const size_t        work_count
   closure.execute();
 
 #if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelFor(kpID);
+     if(Kokkos::Profiling::profileLibraryLoaded()) {
+	Kokkos::Profiling::endParallelFor(kpID);
      }
 #endif
 }
@@ -248,405 +247,9 @@ void parallel_for( const std::string & str
   (void) str;
 }
 
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-/** \brief  Parallel reduction
- *
- * Example of a parallel_reduce functor for a POD (plain old data) value type:
- * \code
- *  class FunctorType { // For POD value type
- *  public:
- *    typedef    ...     execution_space ;
- *    typedef <podType>  value_type ;
- *    void operator()( <intType> iwork , <podType> & update ) const ;
- *    void init( <podType> & update ) const ;
- *    void join( volatile       <podType> & update ,
- *               volatile const <podType> & input ) const ;
- *
- *    typedef true_type has_final ;
- *    void final( <podType> & update ) const ;
- *  };
- * \endcode
- *
- * Example of a parallel_reduce functor for an array of POD (plain old data) values:
- * \code
- *  class FunctorType { // For array of POD value
- *  public:
- *    typedef    ...     execution_space ;
- *    typedef <podType>  value_type[] ;
- *    void operator()( <intType> , <podType> update[] ) const ;
- *    void init( <podType> update[] ) const ;
- *    void join( volatile       <podType> update[] ,
- *               volatile const <podType> input[] ) const ;
- *
- *    typedef true_type has_final ;
- *    void final( <podType> update[] ) const ;
- *  };
- * \endcode
- */
-template< class ExecPolicy , class FunctorType >
-inline
-void parallel_reduce( const ExecPolicy  & policy
-                    , const FunctorType & functor
-                    , const std::string& str = ""
-                    , typename Impl::enable_if< ! Impl::is_integral< ExecPolicy >::value >::type * = 0
-                    )
-{
-  // typedef typename
-  //   Impl::FunctorPolicyExecutionSpace< FunctorType , ExecPolicy >::execution_space
-  //     execution_space ;
-
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , typename ExecPolicy::work_tag >  ValueTraits ;
-
-  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
-                                     , typename ValueTraits::value_type
-                                     , typename ValueTraits::pointer_type
-                                     >::type value_type ;
-
-  Kokkos::View< value_type
-              , HostSpace
-              , Kokkos::MemoryUnmanaged
-              >
-    result_view ;
-
-#if (KOKKOS_ENABLE_PROFILING)
-  uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-  	Kokkos::Experimental::beginParallelReduce("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-
-    Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-    Impl::ParallelReduce< FunctorType , ExecPolicy > closure( functor , policy , result_view );
-    Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-    closure.execute();
-
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelReduce(kpID);
-     }
-#endif
-}
-
-// integral range policy
-template< class FunctorType >
-inline
-void parallel_reduce( const size_t        work_count
-                    , const FunctorType & functor
-                    , const std::string& str = ""
-                    )
-{
-  typedef typename
-    Impl::FunctorPolicyExecutionSpace< FunctorType , void >::execution_space
-      execution_space ;
-
-  typedef RangePolicy< execution_space > policy ;
-
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , void >  ValueTraits ;
-
-  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
-                                     , typename ValueTraits::value_type
-                                     , typename ValueTraits::pointer_type
-                                     >::type value_type ;
-
-  Kokkos::View< value_type
-              , HostSpace
-              , Kokkos::MemoryUnmanaged
-              >
-    result_view ;
-
-#if (KOKKOS_ENABLE_PROFILING)
-  uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-  	Kokkos::Experimental::beginParallelReduce("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-    
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType , policy > closure( functor , policy(0,work_count) , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelReduce(kpID);
-     }
-#endif
-
-}
-
-// general policy and view ouput
-template< class ExecPolicy , class FunctorType , class ViewType >
-inline
-void parallel_reduce( const ExecPolicy  & policy
-                    , const FunctorType & functor
-                    , const ViewType    & result_view
-                    , const std::string& str = ""
-                    , typename Impl::enable_if<
-                      ( Kokkos::is_view<ViewType>::value && ! Impl::is_integral< ExecPolicy >::value
-#ifdef KOKKOS_HAVE_CUDA
-                        && ! Impl::is_same<typename ExecPolicy::execution_space,Kokkos::Cuda>::value
-#endif
-                      )>::type * = 0 )
-{
-    
-#if (KOKKOS_ENABLE_PROFILING)
-  uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelReduce("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-    
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType, ExecPolicy > closure( functor , policy , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelReduce(kpID);
-     }
-#endif
-
-}
-
-// general policy and pod or array of pod output
-template< class ExecPolicy , class FunctorType >
-void parallel_reduce( const ExecPolicy  & policy
-                    , const FunctorType & functor
-#ifdef KOKKOS_HAVE_CUDA
-                    , typename Impl::enable_if<
-                      ( ! Impl::is_integral< ExecPolicy >::value &&
-                        ! Impl::is_same<typename ExecPolicy::execution_space,Kokkos::Cuda>::value )
-                      , typename Kokkos::Impl::FunctorValueTraits< FunctorType , typename ExecPolicy::work_tag >::reference_type>::type result_ref
-                      , const std::string& str = ""
-                      , typename Impl::enable_if<! Impl::is_same<typename ExecPolicy::execution_space,Kokkos::Cuda>::value >::type* = 0
-                      )
-#else
-                      , typename Impl::enable_if<
-                        ( ! Impl::is_integral< ExecPolicy >::value)
-                        , typename Kokkos::Impl::FunctorValueTraits< FunctorType , typename ExecPolicy::work_tag >::reference_type
-                        >::type result_ref
-                      , const std::string& str = ""
-                        )
-#endif
-{
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , typename ExecPolicy::work_tag >  ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueOps<    FunctorType , typename ExecPolicy::work_tag >  ValueOps ;
-
-  // Wrap the result output request in a view to inform the implementation
-  // of the type and memory space.
-
-  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
-                                     , typename ValueTraits::value_type
-                                     , typename ValueTraits::pointer_type
-                                     >::type value_type ;
-
-  Kokkos::View< value_type
-              , HostSpace
-              , Kokkos::MemoryUnmanaged
-              >
-    result_view( ValueOps::pointer( result_ref )
-               , ValueTraits::value_count( functor )
-               );
-
-#if (KOKKOS_ENABLE_PROFILING)
-  uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelReduce("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-    
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType, ExecPolicy > closure( functor , policy , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelReduce(kpID);
-     }
-#endif
-
 }
 
-// integral range policy and view ouput
-template< class FunctorType , class ViewType >
-inline
-void parallel_reduce( const size_t        work_count
-                    , const FunctorType & functor
-                    , const ViewType    & result_view
-                    , const std::string& str = ""
-                    , typename Impl::enable_if<( Kokkos::is_view<ViewType>::value
-#ifdef KOKKOS_HAVE_CUDA
-                        && ! Impl::is_same<
-                          typename Impl::FunctorPolicyExecutionSpace< FunctorType , void >::execution_space,
-                          Kokkos::Cuda>::value
-#endif
-                        )>::type * = 0 )
-{
-  typedef typename
-    Impl::FunctorPolicyExecutionSpace< FunctorType , void >::execution_space
-      execution_space ;
-
-  typedef RangePolicy< execution_space > ExecPolicy ;
-
-#if (KOKKOS_ENABLE_PROFILING)
-  uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelReduce("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType, ExecPolicy > closure( functor , ExecPolicy(0,work_count) , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-    
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelReduce(kpID);
-     }
-#endif
-
-}
-
-// integral range policy and pod or array of pod output
-template< class FunctorType >
-inline
-void parallel_reduce( const size_t        work_count
-                    , const FunctorType & functor
-                    , typename Kokkos::Impl::FunctorValueTraits<
-                         typename Impl::if_c<Impl::is_execution_policy<FunctorType>::value ||
-                                             Impl::is_integral<FunctorType>::value,
-                            void,FunctorType>::type
-                         , void >::reference_type result
-                    , const std::string& str = ""
-                    , typename Impl::enable_if< true
-#ifdef KOKKOS_HAVE_CUDA
-                              && ! Impl::is_same<
-                             typename Impl::FunctorPolicyExecutionSpace< FunctorType , void >::execution_space,
-                             Kokkos::Cuda>::value
-#endif
-                     >::type * = 0 )
-{
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , void >  ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueOps<    FunctorType , void >  ValueOps ;
-
-  typedef typename
-    Kokkos::Impl::FunctorPolicyExecutionSpace< FunctorType , void >::execution_space
-      execution_space ;
-
-  typedef Kokkos::RangePolicy< execution_space > policy ;
-
-  // Wrap the result output request in a view to inform the implementation
-  // of the type and memory space.
-
-  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
-                                     , typename ValueTraits::value_type
-                                     , typename ValueTraits::pointer_type
-                                     >::type value_type ;
-
-  Kokkos::View< value_type
-              , HostSpace
-              , Kokkos::MemoryUnmanaged
-              >
-    result_view( ValueOps::pointer( result )
-               , ValueTraits::value_count( functor )
-               );
-
-#if (KOKKOS_ENABLE_PROFILING)
-  uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelReduce("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
-     }
-#endif
-
-  Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
-  Impl::ParallelReduce< FunctorType , policy > closure( functor , policy(0,work_count) , result_view );
-  Kokkos::Impl::shared_allocation_tracking_release_and_enable();
-
-  closure.execute();
-
-#if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelReduce(kpID);
-     }
-#endif
-
-}
-#ifndef KOKKOS_HAVE_CUDA
-template< class ExecPolicy , class FunctorType , class ResultType >
-inline
-void parallel_reduce( const std::string & str
-                    , const ExecPolicy  & policy
-                    , const FunctorType & functor
-                    , ResultType * result)
-{
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG Start parallel_reduce kernel: " << str << std::endl;
-  #endif
-
-  parallel_reduce(policy,functor,result,str);
-
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG End   parallel_reduce kernel: " << str << std::endl;
-  #endif
-  (void) str;
-}
-
-template< class ExecPolicy , class FunctorType , class ResultType >
-inline
-void parallel_reduce( const std::string & str
-                    , const ExecPolicy  & policy
-                    , const FunctorType & functor
-                    , ResultType & result)
-{
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG Start parallel_reduce kernel: " << str << std::endl;
-  #endif
-
-  parallel_reduce(policy,functor,result,str);
-
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG End   parallel_reduce kernel: " << str << std::endl;
-  #endif
-  (void) str;
-}
-
-template< class ExecPolicy , class FunctorType >
-inline
-void parallel_reduce( const std::string & str
-                    , const ExecPolicy  & policy
-                    , const FunctorType & functor)
-{
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG Start parallel_reduce kernel: " << str << std::endl;
-  #endif
-
-  parallel_reduce(policy,functor,str);
-
-  #if KOKKOS_ENABLE_DEBUG_PRINT_KERNEL_NAMES
-  Kokkos::fence();
-  std::cout << "KOKKOS_DEBUG End   parallel_reduce kernel: " << str << std::endl;
-  #endif
-  (void) str;
-}
-#endif
-
-} // namespace Kokkos
-
+#include <Kokkos_Parallel_Reduce.hpp>
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
@@ -816,8 +419,8 @@ void parallel_scan( const ExecutionPolicy & policy
 {
 #if (KOKKOS_ENABLE_PROFILING)
   uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelScan("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
+     if(Kokkos::Profiling::profileLibraryLoaded()) {
+	Kokkos::Profiling::beginParallelScan("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
      }
 #endif
 
@@ -828,8 +431,8 @@ void parallel_scan( const ExecutionPolicy & policy
   closure.execute();
 
 #if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelScan(kpID);
+     if(Kokkos::Profiling::profileLibraryLoaded()) {
+	Kokkos::Profiling::endParallelScan(kpID);
      }
 #endif
 
@@ -849,8 +452,8 @@ void parallel_scan( const size_t        work_count
 
 #if (KOKKOS_ENABLE_PROFILING)
   uint64_t kpID = 0;
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::beginParallelScan("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
+     if(Kokkos::Profiling::profileLibraryLoaded()) {
+	Kokkos::Profiling::beginParallelScan("" == str ? typeid(FunctorType).name() : str, 0, &kpID);
      }
 #endif
     
@@ -861,8 +464,8 @@ void parallel_scan( const size_t        work_count
   closure.execute();
 
 #if (KOKKOS_ENABLE_PROFILING)
-     if(Kokkos::Experimental::profileLibraryLoaded()) {
-	Kokkos::Experimental::endParallelScan(kpID);
+     if(Kokkos::Profiling::profileLibraryLoaded()) {
+	Kokkos::Profiling::endParallelScan(kpID);
      }
 #endif
 
diff --git a/lib/kokkos/core/src/Kokkos_Parallel_Reduce.hpp b/lib/kokkos/core/src/Kokkos_Parallel_Reduce.hpp
new file mode 100644
index 0000000000..695bc79a1a
--- /dev/null
+++ b/lib/kokkos/core/src/Kokkos_Parallel_Reduce.hpp
@@ -0,0 +1,1240 @@
+/*
+//@HEADER
+// ************************************************************************
+//
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+//
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+//
+// ************************************************************************
+//@HEADER
+*/
+
+
+namespace Kokkos {
+
+
+template<class T, class Enable = void>
+struct is_reducer_type {
+  enum { value = 0 };
+};
+
+
+template<class T>
+struct is_reducer_type<T,typename std::enable_if<
+                       std::is_same<T,typename T::reducer_type>::value
+                      >::type> {
+  enum { value = 1 };
+};
+
+namespace Experimental {
+
+
+template<class Scalar,class Space = HostSpace>
+struct Sum {
+public:
+  //Required
+  typedef Sum reducer_type;
+  typedef Scalar value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+  value_type init_value;
+
+private:
+  result_view_type result;
+
+  template<class ValueType, bool is_arithmetic = std::is_arithmetic<ValueType>::value >
+  struct InitWrapper;
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,true> {
+    static ValueType value() {
+      return static_cast<value_type>(0);
+    }
+  };
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,false> {
+    static ValueType value() {
+      return value_type();
+    }
+  };
+
+public:
+
+  Sum(value_type& result_):
+    init_value(InitWrapper<value_type>::value()),result(&result_) {}
+  Sum(const result_view_type& result_):
+    init_value(InitWrapper<value_type>::value()),result(result_) {}
+  Sum(value_type& result_, const value_type& init_value_):
+    init_value(init_value_),result(&result_) {}
+  Sum(const result_view_type& result_, const value_type& init_value_):
+    init_value(init_value_),result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    dest += src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    dest += src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = init_value;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar,class Space = HostSpace>
+struct Prod {
+public:
+  //Required
+  typedef Prod reducer_type;
+  typedef Scalar value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+  value_type init_value;
+
+private:
+  result_view_type result;
+
+  template<class ValueType, bool is_arithmetic = std::is_arithmetic<ValueType>::value >
+  struct InitWrapper;
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,true> {
+    static ValueType value() {
+      return static_cast<value_type>(1);
+    }
+  };
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,false> {
+    static ValueType value() {
+      return value_type();
+    }
+  };
+
+public:
+
+  Prod(value_type& result_):
+    init_value(InitWrapper<value_type>::value()),result(&result_) {}
+  Prod(const result_view_type& result_):
+    init_value(InitWrapper<value_type>::value()),result(result_) {}
+  Prod(value_type& result_, const value_type& init_value_):
+    init_value(init_value_),result(&result_) {}
+  Prod(const result_view_type& result_, const value_type& init_value_):
+    init_value(init_value_),result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    dest *= src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    dest *= src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = init_value;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Space = HostSpace>
+struct Min {
+public:
+  //Required
+  typedef Min reducer_type;
+  typedef typename std::remove_cv<Scalar>::type value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+  value_type init_value;
+
+private:
+  result_view_type result;
+
+  template<class ValueType, bool is_arithmetic = std::is_arithmetic<ValueType>::value >
+  struct InitWrapper;
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,true> {
+    static ValueType value() {
+      return std::numeric_limits<value_type>::max();
+    }
+  };
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,false> {
+    static ValueType value() {
+      return value_type();
+    }
+  };
+
+public:
+
+  Min(value_type& result_):
+    init_value(InitWrapper<value_type>::value()),result(&result_) {}
+  Min(const result_view_type& result_):
+    init_value(InitWrapper<value_type>::value()),result(result_) {}
+  Min(value_type& result_, const value_type& init_value_):
+    init_value(init_value_),result(&result_) {}
+  Min(const result_view_type& result_, const value_type& init_value_):
+    init_value(init_value_),result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    if ( src < dest )
+      dest = src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    if ( src < dest )
+      dest = src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = init_value;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Space = HostSpace>
+struct Max {
+public:
+  //Required
+  typedef Max reducer_type;
+  typedef typename std::remove_cv<Scalar>::type value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+  value_type init_value;
+
+private:
+  result_view_type result;
+
+  template<class ValueType, bool is_arithmetic = std::is_arithmetic<ValueType>::value >
+  struct InitWrapper;
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,true> {
+    static ValueType value() {
+      return std::numeric_limits<value_type>::min();
+    }
+  };
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,false> {
+    static ValueType value() {
+      return value_type();
+    }
+  };
+
+public:
+
+  Max(value_type& result_):
+    init_value(InitWrapper<value_type>::value()),result(&result_) {}
+  Max(const result_view_type& result_):
+    init_value(InitWrapper<value_type>::value()),result(result_) {}
+  Max(value_type& result_, const value_type& init_value_):
+    init_value(init_value_),result(&result_) {}
+  Max(const result_view_type& result_, const value_type& init_value_):
+    init_value(init_value_),result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    if ( src > dest )
+      dest = src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    if ( src > dest )
+      dest = src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = init_value;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Space = HostSpace>
+struct LAnd {
+public:
+  //Required
+  typedef LAnd reducer_type;
+  typedef Scalar value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+private:
+  result_view_type result;
+
+public:
+
+  LAnd(value_type& result_):result(&result_) {}
+  LAnd(const result_view_type& result_):result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    dest = dest && src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    dest = dest && src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = 1;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Space = HostSpace>
+struct LOr {
+public:
+  //Required
+  typedef LOr reducer_type;
+  typedef Scalar value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+private:
+  result_view_type result;
+
+public:
+
+  LOr(value_type& result_):result(&result_) {}
+  LOr(const result_view_type& result_):result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    dest = dest || src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    dest = dest || src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = 0;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Space = HostSpace>
+struct LXor {
+public:
+  //Required
+  typedef LXor reducer_type;
+  typedef Scalar value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+private:
+  result_view_type result;
+
+public:
+
+  LXor(value_type& result_):result(&result_) {}
+  LXor(const result_view_type& result_):result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    dest = dest? (!src) : src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    dest = dest? (!src) : src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = 0;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Space = HostSpace>
+struct BAnd {
+public:
+  //Required
+  typedef BAnd reducer_type;
+  typedef typename std::remove_cv<Scalar>::type value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+  value_type init_value;
+
+private:
+  result_view_type result;
+
+public:
+
+  BAnd(value_type& result_):
+    init_value(value_type() | (~value_type())),result(&result_) {}
+  BAnd(const result_view_type& result_):
+    init_value(value_type() | (~value_type())),result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+      dest = dest & src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    dest = dest & src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = init_value;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Space = HostSpace>
+struct BOr {
+public:
+  //Required
+  typedef BOr reducer_type;
+  typedef typename std::remove_cv<Scalar>::type value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+  value_type init_value;
+
+private:
+  result_view_type result;
+
+public:
+
+  BOr(value_type& result_):
+    init_value(value_type() & (~value_type())),result(&result_) {}
+  BOr(const result_view_type& result_):
+    init_value(value_type() & (~value_type())),result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+      dest = dest | src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    dest = dest | src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = init_value;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Space = HostSpace>
+struct BXor {
+public:
+  //Required
+  typedef BXor reducer_type;
+  typedef typename std::remove_cv<Scalar>::type value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+  value_type init_value;
+
+private:
+  result_view_type result;
+
+public:
+
+  BXor(value_type& result_):
+    init_value(value_type() & (~value_type())),result(&result_) {}
+  BXor(const result_view_type& result_):
+    init_value(value_type() & (~value_type())),result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+      dest = dest ^ src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    dest = dest ^ src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = init_value;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Index>
+struct ValLocScalar {
+  Scalar val;
+  Index loc;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator = (const ValLocScalar& rhs) {
+    val = rhs.val;
+    loc = rhs.loc;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void operator = (const volatile ValLocScalar& rhs) volatile {
+    val = rhs.val;
+    loc = rhs.loc;
+  }
+};
+
+template<class Scalar, class Index, class Space = HostSpace>
+struct MinLoc {
+private:
+  typedef typename std::remove_cv<Scalar>::type scalar_type;
+  typedef typename std::remove_cv<Index>::type index_type;
+
+public:
+  //Required
+  typedef MinLoc reducer_type;
+  typedef ValLocScalar<scalar_type,index_type> value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+  scalar_type init_value;
+
+private:
+  result_view_type result;
+
+  template<class ValueType, bool is_arithmetic = std::is_arithmetic<ValueType>::value >
+  struct InitWrapper;
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,true> {
+    static ValueType value() {
+      return std::numeric_limits<scalar_type>::max();
+    }
+  };
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,false> {
+    static ValueType value() {
+      return scalar_type();
+    }
+  };
+
+public:
+
+  MinLoc(value_type& result_):
+    init_value(InitWrapper<scalar_type>::value()),result(&result_) {}
+  MinLoc(const result_view_type& result_):
+    init_value(InitWrapper<scalar_type>::value()),result(result_) {}
+  MinLoc(value_type& result_, const scalar_type& init_value_):
+    init_value(init_value_),result(&result_) {}
+  MinLoc(const result_view_type& result_, const scalar_type& init_value_):
+    init_value(init_value_),result(result_) {}
+
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    if ( src.val < dest.val )
+      dest = src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    if ( src.val < dest.val )
+      dest = src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val.val = init_value;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Index, class Space = HostSpace>
+struct MaxLoc {
+private:
+  typedef typename std::remove_cv<Scalar>::type scalar_type;
+  typedef typename std::remove_cv<Index>::type index_type;
+
+public:
+  //Required
+  typedef MaxLoc reducer_type;
+  typedef ValLocScalar<scalar_type,index_type> value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+  scalar_type init_value;
+
+private:
+  result_view_type result;
+
+  template<class ValueType, bool is_arithmetic = std::is_arithmetic<ValueType>::value >
+  struct InitWrapper;
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,true> {
+    static ValueType value() {
+      return std::numeric_limits<scalar_type>::min();
+    }
+  };
+
+  template<class ValueType >
+  struct InitWrapper<ValueType,false> {
+    static ValueType value() {
+      return scalar_type();
+    }
+  };
+
+public:
+
+  MaxLoc(value_type& result_):
+    init_value(InitWrapper<scalar_type>::value()),result(&result_) {}
+  MaxLoc(const result_view_type& result_):
+    init_value(InitWrapper<scalar_type>::value()),result(result_) {}
+  MaxLoc(value_type& result_, const scalar_type& init_value_):
+    init_value(init_value_),result(&result_) {}
+  MaxLoc(const result_view_type& result_, const scalar_type& init_value_):
+    init_value(init_value_),result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    if ( src.val > dest.val )
+      dest = src;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    if ( src.val > dest.val )
+      dest = src;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val.val = init_value;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<class Scalar, class Index>
+struct MinMaxLocScalar {
+  Scalar min_val,max_val;
+  Index min_loc,max_loc;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator = (const MinMaxLocScalar& rhs) {
+    min_val = rhs.min_val;
+    min_loc = rhs.min_loc;
+    max_val = rhs.max_val;
+    max_loc = rhs.max_loc;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void operator = (const volatile MinMaxLocScalar& rhs) volatile {
+    min_val = rhs.min_val;
+    min_loc = rhs.min_loc;
+    max_val = rhs.max_val;
+    max_loc = rhs.max_loc;
+  }
+};
+
+template<class Scalar, class Index, class Space = HostSpace>
+struct MinMaxLoc {
+private:
+  typedef typename std::remove_cv<Scalar>::type scalar_type;
+  typedef typename std::remove_cv<Index>::type index_type;
+
+public:
+  //Required
+  typedef MinMaxLoc reducer_type;
+  typedef MinMaxLocScalar<scalar_type,index_type> value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+  scalar_type min_init_value;
+  scalar_type max_init_value;
+
+private:
+  result_view_type result;
+
+  template<class ValueType, bool is_arithmetic = std::is_arithmetic<ValueType>::value >
+  struct MinInitWrapper;
+
+  template<class ValueType >
+  struct MinInitWrapper<ValueType,true> {
+    static ValueType value() {
+      return std::numeric_limits<scalar_type>::max();
+    }
+  };
+
+  template<class ValueType >
+  struct MinInitWrapper<ValueType,false> {
+    static ValueType value() {
+      return scalar_type();
+    }
+  };
+
+  template<class ValueType, bool is_arithmetic = std::is_arithmetic<ValueType>::value >
+  struct MaxInitWrapper;
+
+  template<class ValueType >
+  struct MaxInitWrapper<ValueType,true> {
+    static ValueType value() {
+      return std::numeric_limits<scalar_type>::min();
+    }
+  };
+
+  template<class ValueType >
+  struct MaxInitWrapper<ValueType,false> {
+    static ValueType value() {
+      return scalar_type();
+    }
+  };
+
+public:
+
+  MinMaxLoc(value_type& result_):
+    min_init_value(MinInitWrapper<scalar_type>::value()),max_init_value(MaxInitWrapper<scalar_type>::value()),result(&result_) {}
+  MinMaxLoc(const result_view_type& result_):
+    min_init_value(MinInitWrapper<scalar_type>::value()),max_init_value(MaxInitWrapper<scalar_type>::value()),result(result_) {}
+  MinMaxLoc(value_type& result_, const scalar_type& min_init_value_, const scalar_type& max_init_value_):
+    min_init_value(min_init_value_),max_init_value(max_init_value_),result(&result_) {}
+  MinMaxLoc(const result_view_type& result_, const scalar_type& min_init_value_, const scalar_type& max_init_value_):
+    min_init_value(min_init_value_),max_init_value(max_init_value_),result(result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    if ( src.min_val < dest.min_val ) {
+      dest.min_val = src.min_val;
+      dest.min_loc = src.min_loc;
+    }
+    if ( src.max_val > dest.max_val ) {
+      dest.max_val = src.max_val;
+      dest.max_loc = src.max_loc;
+    }
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    if ( src.min_val < dest.min_val ) {
+      dest.min_val = src.min_val;
+      dest.min_loc = src.min_loc;
+    }
+    if ( src.max_val > dest.max_val ) {
+      dest.max_val = src.max_val;
+      dest.max_loc = src.max_loc;
+    }
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val.min_val = min_init_value;
+    val.max_val = max_init_value;
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+}
+}
+
+
+namespace Kokkos {
+namespace Impl {
+
+template< class T, class ReturnType , class ValueTraits>
+struct ParallelReduceReturnValue;
+
+template< class ReturnType , class FunctorType >
+struct ParallelReduceReturnValue<typename std::enable_if<Kokkos::is_view<ReturnType>::value>::type, ReturnType, FunctorType> {
+  typedef ReturnType return_type;
+  typedef InvalidType reducer_type;
+
+  typedef typename return_type::value_type value_type_scalar;
+  typedef typename return_type::value_type value_type_array[];
+
+  typedef typename if_c<return_type::rank==0,value_type_scalar,value_type_array>::type value_type;
+
+  static return_type& return_value(ReturnType& return_val, const FunctorType&) {
+    return return_val;
+  }
+};
+
+template< class ReturnType , class FunctorType>
+struct ParallelReduceReturnValue<typename std::enable_if<
+                                   !Kokkos::is_view<ReturnType>::value &&
+                                  (!std::is_array<ReturnType>::value && !std::is_pointer<ReturnType>::value) &&
+                                   !Kokkos::is_reducer_type<ReturnType>::value
+                                 >::type, ReturnType, FunctorType> {
+  typedef Kokkos::View<  ReturnType
+                       , Kokkos::HostSpace
+                       , Kokkos::MemoryUnmanaged
+      > return_type;
+
+  typedef InvalidType reducer_type;
+
+  typedef typename return_type::value_type value_type;
+
+  static return_type return_value(ReturnType& return_val, const FunctorType&) {
+    return return_type(&return_val);
+  }
+};
+
+template< class ReturnType , class FunctorType>
+struct ParallelReduceReturnValue<typename std::enable_if<
+                                  (is_array<ReturnType>::value || std::is_pointer<ReturnType>::value)
+                                >::type, ReturnType, FunctorType> {
+  typedef Kokkos::View<  typename std::remove_const<ReturnType>::type
+                       , Kokkos::HostSpace
+                       , Kokkos::MemoryUnmanaged
+      > return_type;
+
+  typedef InvalidType reducer_type;
+
+  typedef typename return_type::value_type value_type[];
+
+  static return_type return_value(ReturnType& return_val,
+                                  const FunctorType& functor) {
+    return return_type(return_val,functor.value_count);
+  }
+};
+
+template< class ReturnType , class FunctorType>
+struct ParallelReduceReturnValue<typename std::enable_if<
+                                   Kokkos::is_reducer_type<ReturnType>::value
+                                >::type, ReturnType, FunctorType> {
+  typedef ReturnType return_type;
+  typedef ReturnType reducer_type;
+  typedef typename return_type::value_type value_type;
+
+  static return_type return_value(ReturnType& return_val,
+                                  const FunctorType& functor) {
+    return return_val;
+  }
+};
+}
+
+namespace Impl {
+template< class T, class ReturnType , class FunctorType>
+struct ParallelReducePolicyType;
+
+template< class PolicyType , class FunctorType >
+struct ParallelReducePolicyType<typename std::enable_if<Kokkos::Impl::is_execution_policy<PolicyType>::value>::type, PolicyType,FunctorType> {
+
+  typedef PolicyType policy_type;
+  static PolicyType policy(const PolicyType& policy_) {
+    return policy_;
+  }
+};
+
+template< class PolicyType , class FunctorType >
+struct ParallelReducePolicyType<typename std::enable_if<std::is_integral<PolicyType>::value>::type, PolicyType,FunctorType> {
+  typedef typename
+    Impl::FunctorPolicyExecutionSpace< FunctorType , void >::execution_space
+      execution_space ;
+
+  typedef Kokkos::RangePolicy<execution_space> policy_type;
+
+  static policy_type policy(const PolicyType& policy_) {
+    return policy_type(0,policy_);
+  }
+};
+
+}
+
+namespace Impl {
+  template< class FunctorType, class ExecPolicy, class ValueType, class ExecutionSpace>
+  struct ParallelReduceFunctorType {
+    typedef FunctorType functor_type;
+    static const functor_type& functor(const functor_type& functor) {
+      return functor;
+    }
+  };
+}
+
+namespace Impl {
+
+  template< class PolicyType, class FunctorType, class ReturnType >
+  struct ParallelReduceAdaptor {
+    typedef Impl::ParallelReduceReturnValue<void,ReturnType,FunctorType> return_value_adapter;
+    #ifdef KOKKOS_IMPL_NEED_FUNCTOR_WRAPPER
+    typedef Impl::ParallelReduceFunctorType<FunctorType,PolicyType,
+                                            typename return_value_adapter::value_type,
+                                            typename PolicyType::execution_space> functor_adaptor;
+    #endif
+    static inline
+    void execute(const std::string& label,
+        const PolicyType& policy,
+        const FunctorType& functor,
+        ReturnType& return_value) {
+          #if (KOKKOS_ENABLE_PROFILING)
+            uint64_t kpID = 0;
+            if(Kokkos::Profiling::profileLibraryLoaded()) {
+              Kokkos::Profiling::beginParallelReduce("" == label ? typeid(FunctorType).name() : label, 0, &kpID);
+            }
+          #endif
+
+          Kokkos::Impl::shared_allocation_tracking_claim_and_disable();
+          #ifdef KOKKOS_IMPL_NEED_FUNCTOR_WRAPPER
+          Impl::ParallelReduce<typename functor_adaptor::functor_type, PolicyType, typename return_value_adapter::reducer_type >
+             closure(functor_adaptor::functor(functor),
+                     policy,
+                     return_value_adapter::return_value(return_value,functor));
+          #else
+          Impl::ParallelReduce<FunctorType, PolicyType, typename return_value_adapter::reducer_type >
+             closure(functor,
+                     policy,
+                     return_value_adapter::return_value(return_value,functor));
+          #endif
+          Kokkos::Impl::shared_allocation_tracking_release_and_enable();
+          closure.execute();
+
+          #if (KOKKOS_ENABLE_PROFILING)
+            if(Kokkos::Profiling::profileLibraryLoaded()) {
+              Kokkos::Profiling::endParallelReduce(kpID);
+            }
+          #endif
+        }
+
+  };
+}
+/*! \fn void parallel_reduce(label,policy,functor,return_argument)
+    \brief Perform a parallel reduction.
+    \param label An optional Label giving the call name. Must be able to construct a std::string from the argument.
+    \param policy A Kokkos Execution Policy, such as an integer, a RangePolicy or a TeamPolicy.
+    \param functor A functor with a reduction operator, and optional init, join and final functions.
+    \param return_argument A return argument which can be a scalar, a View, or a ReducerStruct. This argument can be left out if the functor has a final function.
+*/
+
+/** \brief  Parallel reduction
+ *
+ * parallel_reduce performs parallel reductions with arbitrary functions - i.e.
+ * it is not solely data based. The call expects up to 4 arguments:
+ *
+ *
+ * Example of a parallel_reduce functor for a POD (plain old data) value type:
+ * \code
+ *  class FunctorType { // For POD value type
+ *  public:
+ *    typedef    ...     execution_space ;
+ *    typedef <podType>  value_type ;
+ *    void operator()( <intType> iwork , <podType> & update ) const ;
+ *    void init( <podType> & update ) const ;
+ *    void join( volatile       <podType> & update ,
+ *               volatile const <podType> & input ) const ;
+ *
+ *    typedef true_type has_final ;
+ *    void final( <podType> & update ) const ;
+ *  };
+ * \endcode
+ *
+ * Example of a parallel_reduce functor for an array of POD (plain old data) values:
+ * \code
+ *  class FunctorType { // For array of POD value
+ *  public:
+ *    typedef    ...     execution_space ;
+ *    typedef <podType>  value_type[] ;
+ *    void operator()( <intType> , <podType> update[] ) const ;
+ *    void init( <podType> update[] ) const ;
+ *    void join( volatile       <podType> update[] ,
+ *               volatile const <podType> input[] ) const ;
+ *
+ *    typedef true_type has_final ;
+ *    void final( <podType> update[] ) const ;
+ *  };
+ * \endcode
+ */
+
+// ReturnValue is scalar or array: take by reference
+
+template< class PolicyType, class FunctorType, class ReturnType >
+inline
+void parallel_reduce(const std::string& label,
+                     const PolicyType& policy,
+                     const FunctorType& functor,
+                     ReturnType& return_value,
+                     typename Impl::enable_if<
+                       Kokkos::Impl::is_execution_policy<PolicyType>::value
+                     >::type * = 0) {
+  Impl::ParallelReduceAdaptor<PolicyType,FunctorType,ReturnType>::execute(label,policy,functor,return_value);
+}
+
+template< class PolicyType, class FunctorType, class ReturnType >
+inline
+void parallel_reduce(const PolicyType& policy,
+                     const FunctorType& functor,
+                     ReturnType& return_value,
+                     typename Impl::enable_if<
+                       Kokkos::Impl::is_execution_policy<PolicyType>::value
+                     >::type * = 0) {
+  Impl::ParallelReduceAdaptor<PolicyType,FunctorType,ReturnType>::execute("",policy,functor,return_value);
+}
+
+template< class FunctorType, class ReturnType >
+inline
+void parallel_reduce(const size_t& policy,
+                     const FunctorType& functor,
+                     ReturnType& return_value) {
+  typedef typename Impl::ParallelReducePolicyType<void,size_t,FunctorType>::policy_type policy_type;
+  Impl::ParallelReduceAdaptor<policy_type,FunctorType,ReturnType>::execute("",policy_type(0,policy),functor,return_value);
+}
+
+template< class FunctorType, class ReturnType >
+inline
+void parallel_reduce(const std::string& label,
+                     const size_t& policy,
+                     const FunctorType& functor,
+                     ReturnType& return_value) {
+  typedef typename Impl::ParallelReducePolicyType<void,size_t,FunctorType>::policy_type policy_type;
+  Impl::ParallelReduceAdaptor<policy_type,FunctorType,ReturnType>::execute(label,policy_type(0,policy),functor,return_value);
+}
+
+// ReturnValue as View or Reducer: take by copy to allow for inline construction
+
+template< class PolicyType, class FunctorType, class ReturnType >
+inline
+void parallel_reduce(const std::string& label,
+                     const PolicyType& policy,
+                     const FunctorType& functor,
+                     const ReturnType& return_value,
+                     typename Impl::enable_if<
+                       Kokkos::Impl::is_execution_policy<PolicyType>::value
+                     >::type * = 0) {
+  Impl::ParallelReduceAdaptor<PolicyType,FunctorType,const ReturnType>::execute(label,policy,functor,return_value);
+}
+
+template< class PolicyType, class FunctorType, class ReturnType >
+inline
+void parallel_reduce(const PolicyType& policy,
+                     const FunctorType& functor,
+                     const ReturnType& return_value,
+                     typename Impl::enable_if<
+                       Kokkos::Impl::is_execution_policy<PolicyType>::value
+                     >::type * = 0) {
+  Impl::ParallelReduceAdaptor<PolicyType,FunctorType,const ReturnType>::execute("",policy,functor,return_value);
+}
+
+template< class FunctorType, class ReturnType >
+inline
+void parallel_reduce(const size_t& policy,
+                     const FunctorType& functor,
+                     const ReturnType& return_value) {
+  typedef typename Impl::ParallelReducePolicyType<void,size_t,FunctorType>::policy_type policy_type;
+
+  Impl::ParallelReduceAdaptor<policy_type,FunctorType,const ReturnType>::execute("",policy_type(0,policy),functor,return_value);
+}
+
+template< class FunctorType, class ReturnType >
+inline
+void parallel_reduce(const std::string& label,
+                     const size_t& policy,
+                     const FunctorType& functor,
+                     const ReturnType& return_value) {
+  typedef typename Impl::ParallelReducePolicyType<void,size_t,FunctorType>::policy_type policy_type;
+  Impl::ParallelReduceAdaptor<policy_type,FunctorType,const ReturnType>::execute(label,policy_type(0,policy),functor,return_value);
+}
+
+// No Return Argument
+
+template< class PolicyType, class FunctorType>
+inline
+void parallel_reduce(const std::string& label,
+                     const PolicyType& policy,
+                     const FunctorType& functor,
+                     typename Impl::enable_if<
+                       Kokkos::Impl::is_execution_policy<PolicyType>::value
+                     >::type * = 0) {
+  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , void >  ValueTraits ;
+  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
+                                     , typename ValueTraits::value_type
+                                     , typename ValueTraits::pointer_type
+                                     >::type value_type ;
+
+  typedef Kokkos::View< value_type
+              , Kokkos::HostSpace
+              , Kokkos::MemoryUnmanaged
+              > result_view_type;
+  result_view_type result_view ;
+
+  Impl::ParallelReduceAdaptor<PolicyType,FunctorType,result_view_type>::execute(label,policy,functor,result_view);
+}
+
+template< class PolicyType, class FunctorType >
+inline
+void parallel_reduce(const PolicyType& policy,
+                     const FunctorType& functor,
+                     typename Impl::enable_if<
+                       Kokkos::Impl::is_execution_policy<PolicyType>::value
+                     >::type * = 0) {
+  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , void >  ValueTraits ;
+  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
+                                     , typename ValueTraits::value_type
+                                     , typename ValueTraits::pointer_type
+                                     >::type value_type ;
+
+  typedef Kokkos::View< value_type
+              , Kokkos::HostSpace
+              , Kokkos::MemoryUnmanaged
+              > result_view_type;
+  result_view_type result_view ;
+
+  Impl::ParallelReduceAdaptor<PolicyType,FunctorType,result_view_type>::execute("",policy,functor,result_view);
+}
+
+template< class FunctorType >
+inline
+void parallel_reduce(const size_t& policy,
+                     const FunctorType& functor) {
+  typedef typename Impl::ParallelReducePolicyType<void,size_t,FunctorType>::policy_type policy_type;
+  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , void >  ValueTraits ;
+  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
+                                     , typename ValueTraits::value_type
+                                     , typename ValueTraits::pointer_type
+                                     >::type value_type ;
+
+  typedef Kokkos::View< value_type
+              , Kokkos::HostSpace
+              , Kokkos::MemoryUnmanaged
+              > result_view_type;
+  result_view_type result_view ;
+
+  Impl::ParallelReduceAdaptor<policy_type,FunctorType,result_view_type>::execute("",policy_type(0,policy),functor,result_view);
+}
+
+template< class FunctorType>
+inline
+void parallel_reduce(const std::string& label,
+                     const size_t& policy,
+                     const FunctorType& functor) {
+  typedef typename Impl::ParallelReducePolicyType<void,size_t,FunctorType>::policy_type policy_type;
+  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , void >  ValueTraits ;
+  typedef typename Kokkos::Impl::if_c< (ValueTraits::StaticValueSize != 0)
+                                     , typename ValueTraits::value_type
+                                     , typename ValueTraits::pointer_type
+                                     >::type value_type ;
+
+  typedef Kokkos::View< value_type
+              , Kokkos::HostSpace
+              , Kokkos::MemoryUnmanaged
+              > result_view_type;
+  result_view_type result_view ;
+
+  Impl::ParallelReduceAdaptor<policy_type,FunctorType,result_view_type>::execute(label,policy_type(0,policy),functor,result_view);
+}
+
+
+
+} //namespace Kokkos
diff --git a/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp b/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp
index 17654170ed..09a5993863 100644
--- a/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp
+++ b/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp
@@ -66,11 +66,15 @@ public:
 
 private:
 
-  mutable char * m_iter ;
-  char *         m_end ;
+  mutable char * m_iter_L0 ;
+  char *         m_end_L0 ;
+  mutable char * m_iter_L1 ;
+  char *         m_end_L1 ;
+
 
   mutable int m_multiplier;
   mutable int m_offset;
+  mutable int m_default_level;
 
   ScratchMemorySpace();
   ScratchMemorySpace & operator = ( const ScratchMemorySpace & );
@@ -95,34 +99,58 @@ public:
 
   template< typename IntType >
   KOKKOS_INLINE_FUNCTION
-  void* get_shmem (const IntType& size) const {
-    void* tmp = m_iter + m_offset * align (size);
-    if (m_end < (m_iter += align (size) * m_multiplier)) {
-      m_iter -= align (size) * m_multiplier; // put it back like it was
-  #ifdef KOKKOS_HAVE_DEBUG
-      // mfh 23 Jun 2015: printf call consumes 25 registers
-      // in a CUDA build, so only print in debug mode.  The
-      // function still returns NULL if not enough memory.
-      printf ("ScratchMemorySpace<...>::get_shmem: Failed to allocate "
-              "%ld byte(s); remaining capacity is %ld byte(s)\n", long(size),
-              long(m_end-m_iter));
-  #endif // KOKKOS_HAVE_DEBUG
-      tmp = 0;
+  void* get_shmem (const IntType& size, int level = -1) const {
+    if(level == -1)
+      level = m_default_level;
+    if(level == 0) {
+      void* tmp = m_iter_L0 + m_offset * align (size);
+      if (m_end_L0 < (m_iter_L0 += align (size) * m_multiplier)) {
+        m_iter_L0 -= align (size) * m_multiplier; // put it back like it was
+        #ifdef KOKKOS_HAVE_DEBUG
+        // mfh 23 Jun 2015: printf call consumes 25 registers
+        // in a CUDA build, so only print in debug mode.  The
+        // function still returns NULL if not enough memory.
+        printf ("ScratchMemorySpace<...>::get_shmem: Failed to allocate "
+                "%ld byte(s); remaining capacity is %ld byte(s)\n", long(size),
+                long(m_end_L0-m_iter_L0));
+        #endif // KOKKOS_HAVE_DEBUG
+        tmp = 0;
+      }
+      return tmp;
+    } else {
+      void* tmp = m_iter_L1 + m_offset * align (size);
+      if (m_end_L1 < (m_iter_L1 += align (size) * m_multiplier)) {
+        m_iter_L1 -= align (size) * m_multiplier; // put it back like it was
+        #ifdef KOKKOS_HAVE_DEBUG
+        // mfh 23 Jun 2015: printf call consumes 25 registers
+        // in a CUDA build, so only print in debug mode.  The
+        // function still returns NULL if not enough memory.
+        printf ("ScratchMemorySpace<...>::get_shmem: Failed to allocate "
+                "%ld byte(s); remaining capacity is %ld byte(s)\n", long(size),
+                long(m_end_L1-m_iter_L1));
+        #endif // KOKKOS_HAVE_DEBUG
+        tmp = 0;
+      }
+      return tmp;
+
     }
-    return tmp;
   }
 
   template< typename IntType >
   KOKKOS_INLINE_FUNCTION
-  ScratchMemorySpace( void * ptr , const IntType & size )
-    : m_iter( (char *) ptr )
-    , m_end(  m_iter + size )
+  ScratchMemorySpace( void * ptr_L0 , const IntType & size_L0 , void * ptr_L1 = NULL , const IntType & size_L1 = 0)
+    : m_iter_L0( (char *) ptr_L0 )
+    , m_end_L0(  m_iter_L0 + size_L0 )
+    , m_iter_L1( (char *) ptr_L1 )
+    , m_end_L1(  m_iter_L1 + size_L1 )
     , m_multiplier( 1 )
     , m_offset( 0 )
+    , m_default_level( 0 )
     {}
 
   KOKKOS_INLINE_FUNCTION
-  const ScratchMemorySpace& set_team_thread_mode(const int& multiplier, const int& offset) const {
+  const ScratchMemorySpace& set_team_thread_mode(const int& level, const int& multiplier, const int& offset) const {
+    m_default_level = level;
     m_multiplier = multiplier;
     m_offset = offset;
     return *this;
diff --git a/lib/kokkos/core/src/Kokkos_Serial.hpp b/lib/kokkos/core/src/Kokkos_Serial.hpp
index 656be5d09f..233b56c939 100644
--- a/lib/kokkos/core/src/Kokkos_Serial.hpp
+++ b/lib/kokkos/core/src/Kokkos_Serial.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -50,12 +50,17 @@
 #include <cstddef>
 #include <iosfwd>
 #include <Kokkos_Parallel.hpp>
+#include <Kokkos_TaskPolicy.hpp>
 #include <Kokkos_Layout.hpp>
 #include <Kokkos_HostSpace.hpp>
 #include <Kokkos_ScratchSpace.hpp>
 #include <Kokkos_MemoryTraits.hpp>
 #include <impl/Kokkos_Tags.hpp>
 #include <impl/Kokkos_FunctorAdapter.hpp>
+#include <impl/Kokkos_Profiling_Interface.hpp>
+
+
+#include <KokkosExp_MDRangePolicy.hpp>
 
 #if defined( KOKKOS_HAVE_SERIAL )
 
@@ -142,7 +147,9 @@ public:
 
     // Init the array of locks used for arbitrarily sized atomics
     Impl::init_lock_array_host_space();
-
+    #if (KOKKOS_ENABLE_PROFILING)
+      Kokkos::Profiling::initialize();
+    #endif
   }
 
   static int is_initialized() { return 1 ; }
@@ -151,7 +158,11 @@ public:
   static int concurrency() {return 1;};
 
   //! Free any resources being consumed by the device.
-  static void finalize() {}
+  static void finalize() {
+    #if (KOKKOS_ENABLE_PROFILING)
+      Kokkos::Profiling::finalize();
+    #endif
+  }
 
   //! Print configuration information to the given output stream.
   static void print_configuration( std::ostream & , const bool /* detail */ = false ) {}
@@ -307,8 +318,8 @@ class TeamPolicyInternal< Kokkos::Serial , Properties ... >:public PolicyTraits<
 {
 private:
 
-  size_t m_team_scratch_size ;
-  size_t m_thread_scratch_size ;
+  size_t m_team_scratch_size[2] ;
+  size_t m_thread_scratch_size[2] ;
   int    m_league_size ;
   int    m_chunk_size;
 
@@ -324,8 +335,10 @@ public:
 
   TeamPolicyInternal& operator = (const TeamPolicyInternal& p) {
     m_league_size = p.m_league_size;
-    m_team_scratch_size = p.m_team_scratch_size;
-    m_thread_scratch_size = p.m_thread_scratch_size;
+    m_team_scratch_size[0] = p.m_team_scratch_size[0];
+    m_thread_scratch_size[0] = p.m_thread_scratch_size[0];
+    m_team_scratch_size[1] = p.m_team_scratch_size[1];
+    m_thread_scratch_size[1] = p.m_thread_scratch_size[1];
     m_chunk_size = p.m_chunk_size;
     return *this;
   }
@@ -348,15 +361,15 @@ public:
 
   inline int team_size() const { return 1 ; }
   inline int league_size() const { return m_league_size ; }
-  inline size_t scratch_size() const { return m_team_scratch_size + m_thread_scratch_size; }
+  inline size_t scratch_size(const int& level, int = 0) const { return m_team_scratch_size[level] + m_thread_scratch_size[level]; }
 
   /** \brief  Specify league size, request team size */
   TeamPolicyInternal( execution_space &
             , int league_size_request
             , int /* team_size_request */
             , int /* vector_length_request */ = 1 )
-    : m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    : m_team_scratch_size { 0 , 0 }
+    , m_thread_scratch_size { 0 , 0 }
     , m_league_size( league_size_request )
     , m_chunk_size ( 32 )
     {}
@@ -365,8 +378,8 @@ public:
             , int league_size_request
             , const Kokkos::AUTO_t & /* team_size_request */
             , int /* vector_length_request */ = 1 )
-    : m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    : m_team_scratch_size { 0 , 0 }
+    , m_thread_scratch_size { 0 , 0 }
     , m_league_size( league_size_request )
     , m_chunk_size ( 32 )
     {}
@@ -374,8 +387,8 @@ public:
   TeamPolicyInternal( int league_size_request
             , int /* team_size_request */
             , int /* vector_length_request */ = 1 )
-    : m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    : m_team_scratch_size { 0 , 0 }
+    , m_thread_scratch_size { 0 , 0 }
     , m_league_size( league_size_request )
     , m_chunk_size ( 32 )
     {}
@@ -383,8 +396,8 @@ public:
   TeamPolicyInternal( int league_size_request
             , const Kokkos::AUTO_t & /* team_size_request */
             , int /* vector_length_request */ = 1 )
-    : m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    : m_team_scratch_size { 0 , 0 }
+    , m_thread_scratch_size { 0 , 0 }
     , m_league_size( league_size_request )
     , m_chunk_size ( 32 )
     {}
@@ -401,26 +414,23 @@ public:
 
   /** \brief set per team scratch size for a specific level of the scratch hierarchy */
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerTeamValue& per_team) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_team_scratch_size = per_team.value;
+    p.m_team_scratch_size[level] = per_team.value;
     return p;
   };
 
   /** \brief set per thread scratch size for a specific level of the scratch hierarchy */
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerThreadValue& per_thread) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_thread_scratch_size = per_thread.value;
+    p.m_thread_scratch_size[level] = per_thread.value;
     return p;
   };
 
   /** \brief set per thread and per team scratch size for a specific level of the scratch hierarchy */
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerTeamValue& per_team, const PerThreadValue& per_thread) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_team_scratch_size = per_team.value;
-    p.m_thread_scratch_size = per_thread.value;
+    p.m_team_scratch_size[level] = per_team.value;
+    p.m_thread_scratch_size[level] = per_thread.value;
     return p;
   };
 
@@ -440,7 +450,7 @@ namespace Kokkos {
 namespace Impl {
 
 template< class FunctorType , class ... Traits >
-class ParallelFor< FunctorType , 
+class ParallelFor< FunctorType ,
                    Kokkos::RangePolicy< Traits ... > ,
                    Kokkos::Serial
                  >
@@ -489,9 +499,10 @@ public:
 
 /*--------------------------------------------------------------------------*/
 
-template< class FunctorType , class ... Traits >
+template< class FunctorType , class ReducerType , class ... Traits >
 class ParallelReduce< FunctorType
                     , Kokkos::RangePolicy< Traits ... >
+                    , ReducerType
                     , Kokkos::Serial
                     >
 {
@@ -499,14 +510,19 @@ private:
 
   typedef Kokkos::RangePolicy< Traits ... > Policy ;
   typedef typename Policy::work_tag                                  WorkTag ;
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , WorkTag >  ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueInit<   FunctorType , WorkTag >  ValueInit ;
+
+  typedef Kokkos::Impl::if_c< std::is_same<InvalidType,ReducerType>::value, FunctorType, ReducerType> ReducerConditional;
+  typedef typename ReducerConditional::type ReducerTypeFwd;
+
+  typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd , WorkTag >  ValueTraits ;
+  typedef Kokkos::Impl::FunctorValueInit<   ReducerTypeFwd , WorkTag >  ValueInit ;
 
   typedef typename ValueTraits::pointer_type    pointer_type ;
   typedef typename ValueTraits::reference_type  reference_type ;
 
   const FunctorType   m_functor ;
   const Policy        m_policy ;
+  const ReducerType   m_reducer ;
   const pointer_type  m_result_ptr ;
 
 
@@ -515,15 +531,15 @@ private:
   typename std::enable_if< std::is_same< TagType , void >::value >::type
   exec( pointer_type ptr ) const
     {
-      reference_type update = ValueInit::init( m_functor , ptr );
+      reference_type update = ValueInit::init(  ReducerConditional::select(m_functor , m_reducer) , ptr );
 
       const typename Policy::member_type e = m_policy.end();
       for ( typename Policy::member_type i = m_policy.begin() ; i < e ; ++i ) {
         m_functor( i , update );
       }
 
-      Kokkos::Impl::FunctorFinal< FunctorType , TagType >::
-        final( m_functor , ptr );
+      Kokkos::Impl::FunctorFinal< ReducerTypeFwd , TagType >::
+        final(  ReducerConditional::select(m_functor , m_reducer) , ptr );
     }
 
   template< class TagType >
@@ -532,15 +548,15 @@ private:
   exec( pointer_type ptr ) const
     {
       const TagType t{} ;
-      reference_type update = ValueInit::init( m_functor , ptr );
+      reference_type update = ValueInit::init(  ReducerConditional::select(m_functor , m_reducer) , ptr );
 
       const typename Policy::member_type e = m_policy.end();
       for ( typename Policy::member_type i = m_policy.begin() ; i < e ; ++i ) {
         m_functor( t , i , update );
       }
 
-      Kokkos::Impl::FunctorFinal< FunctorType , TagType >::
-        final( m_functor , ptr );
+      Kokkos::Impl::FunctorFinal< ReducerTypeFwd , TagType >::
+        final(  ReducerConditional::select(m_functor , m_reducer) , ptr );
     }
 
 public:
@@ -549,25 +565,43 @@ public:
   void execute() const
     {
       pointer_type ptr = (pointer_type) Kokkos::Serial::scratch_memory_resize
-           ( ValueTraits::value_size( m_functor ) , 0 );
+           ( ValueTraits::value_size(  ReducerConditional::select(m_functor , m_reducer) ) , 0 );
 
       this-> template exec< WorkTag >( m_result_ptr ? m_result_ptr : ptr );
     }
 
-  template< class ViewType >
+  template< class HostViewType >
+  ParallelReduce( const FunctorType  & arg_functor ,
+                  const Policy       & arg_policy ,
+                  const HostViewType & arg_result_view ,
+                  typename std::enable_if<
+                               Kokkos::is_view< HostViewType >::value &&
+                              !Kokkos::is_reducer_type<ReducerType>::value
+                  ,void*>::type = NULL)
+    : m_functor( arg_functor )
+    , m_policy( arg_policy )
+    , m_reducer( InvalidType() )
+    , m_result_ptr( arg_result_view.ptr_on_device() )
+    {
+      static_assert( Kokkos::is_view< HostViewType >::value
+        , "Kokkos::Serial reduce result must be a View" );
+
+      static_assert( std::is_same< typename HostViewType::memory_space , HostSpace >::value
+        , "Kokkos::Serial reduce result must be a View in HostSpace" );
+    }
+
+  inline
   ParallelReduce( const FunctorType & arg_functor
-                , const Policy      & arg_policy
-                , const ViewType    & arg_result )
+                , Policy       arg_policy
+                , const ReducerType& reducer )
     : m_functor( arg_functor )
     , m_policy(  arg_policy )
-    , m_result_ptr( arg_result.ptr_on_device() )
+    , m_reducer( reducer )
+    , m_result_ptr(  reducer.result_view().data() )
     {
-      static_assert( Kokkos::is_view< ViewType >::value
-        , "Reduction result on Kokkos::Serial must be a Kokkos::View" );
-
-      static_assert( std::is_same< typename ViewType::memory_space
+      /*static_assert( std::is_same< typename ViewType::memory_space
                                       , Kokkos::HostSpace >::value
-        , "Reduction result on Kokkos::Serial must be a Kokkos::View in HostSpace" );
+        , "Reduction result on Kokkos::OpenMP must be a Kokkos::View in HostSpace" );*/
     }
 };
 
@@ -697,15 +731,16 @@ public:
              , const Policy      & arg_policy )
     : m_functor( arg_functor )
     , m_league(  arg_policy.league_size() )
-    , m_shared( arg_policy.scratch_size() + FunctorTeamShmemSize< FunctorType >::value( arg_functor , 1 ) )
+    , m_shared( arg_policy.scratch_size(0) + arg_policy.scratch_size(1) + FunctorTeamShmemSize< FunctorType >::value( arg_functor , 1 ) )
     { }
 };
 
 /*--------------------------------------------------------------------------*/
 
-template< class FunctorType , class ... Properties >
+template< class FunctorType , class ReducerType , class ... Properties >
 class ParallelReduce< FunctorType
                     , Kokkos::TeamPolicy< Properties ... >
+                    , ReducerType
                     , Kokkos::Serial
                     >
 {
@@ -714,30 +749,35 @@ private:
   typedef TeamPolicyInternal< Kokkos::Serial, Properties ... > Policy ;
   typedef typename Policy::member_type                       Member ;
   typedef typename Policy::work_tag                          WorkTag ;
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , WorkTag > ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueInit<   FunctorType , WorkTag > ValueInit ;
+
+  typedef Kokkos::Impl::if_c< std::is_same<InvalidType,ReducerType>::value, FunctorType, ReducerType> ReducerConditional;
+  typedef typename ReducerConditional::type ReducerTypeFwd;
+
+  typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd , WorkTag >  ValueTraits ;
+  typedef Kokkos::Impl::FunctorValueInit<   ReducerTypeFwd , WorkTag >  ValueInit ;
 
   typedef typename ValueTraits::pointer_type    pointer_type ;
   typedef typename ValueTraits::reference_type  reference_type ;
 
   const FunctorType  m_functor ;
   const int          m_league ;
-  const int          m_shared ;
+  const ReducerType  m_reducer ;
         pointer_type m_result_ptr ;
+  const int          m_shared ;
 
   template< class TagType >
   inline
   typename std::enable_if< std::is_same< TagType , void >::value >::type
   exec( pointer_type ptr ) const
     {
-      reference_type update = ValueInit::init( m_functor , ptr );
+      reference_type update = ValueInit::init(  ReducerConditional::select(m_functor , m_reducer) , ptr );
 
       for ( int ileague = 0 ; ileague < m_league ; ++ileague ) {
         m_functor( Member(ileague,m_league,m_shared) , update );
       }
 
-      Kokkos::Impl::FunctorFinal< FunctorType , TagType >::
-        final( m_functor , ptr );
+      Kokkos::Impl::FunctorFinal< ReducerTypeFwd , TagType >::
+        final(  ReducerConditional::select(m_functor , m_reducer) , ptr );
     }
 
   template< class TagType >
@@ -747,14 +787,14 @@ private:
     {
       const TagType t{} ;
 
-      reference_type update = ValueInit::init( m_functor , ptr );
+      reference_type update = ValueInit::init(  ReducerConditional::select(m_functor , m_reducer) , ptr );
 
       for ( int ileague = 0 ; ileague < m_league ; ++ileague ) {
         m_functor( t , Member(ileague,m_league,m_shared) , update );
       }
 
-      Kokkos::Impl::FunctorFinal< FunctorType , TagType >::
-        final( m_functor , ptr );
+      Kokkos::Impl::FunctorFinal< ReducerTypeFwd , TagType >::
+        final(  ReducerConditional::select(m_functor , m_reducer) , ptr );
     }
 
 public:
@@ -763,7 +803,7 @@ public:
   void execute() const
     {
       pointer_type ptr = (pointer_type) Kokkos::Serial::scratch_memory_resize
-           ( ValueTraits::value_size( m_functor ) , m_shared );
+           ( ValueTraits::value_size(  ReducerConditional::select(m_functor , m_reducer) ) , m_shared );
 
       this-> template exec< WorkTag >( m_result_ptr ? m_result_ptr : ptr );
     }
@@ -771,12 +811,16 @@ public:
   template< class ViewType >
   ParallelReduce( const FunctorType  & arg_functor
                 , const Policy       & arg_policy
-                , const ViewType     & arg_result
-                )
+                , const ViewType     & arg_result ,
+                typename std::enable_if<
+                  Kokkos::is_view< ViewType >::value &&
+                  !Kokkos::is_reducer_type<ReducerType>::value
+                  ,void*>::type = NULL)
     : m_functor( arg_functor )
     , m_league( arg_policy.league_size() )
-    , m_shared( arg_policy.scratch_size() + FunctorTeamShmemSize< FunctorType >::value( m_functor , 1 ) )
+    , m_reducer( InvalidType() )
     , m_result_ptr( arg_result.ptr_on_device() )
+    , m_shared( arg_policy.scratch_size(0) + arg_policy.scratch_size(1) + FunctorTeamShmemSize< FunctorType >::value( m_functor , 1 ) )
     {
       static_assert( Kokkos::is_view< ViewType >::value
         , "Reduction result on Kokkos::Serial must be a Kokkos::View" );
@@ -786,6 +830,21 @@ public:
         , "Reduction result on Kokkos::Serial must be a Kokkos::View in HostSpace" );
     }
 
+  inline
+  ParallelReduce( const FunctorType & arg_functor
+    , Policy       arg_policy
+    , const ReducerType& reducer )
+  : m_functor( arg_functor )
+  , m_league(  arg_policy.league_size() )
+  , m_reducer( reducer )
+  , m_result_ptr(  reducer.result_view().data() )
+  , m_shared( arg_policy.scratch_size(0) + arg_policy.scratch_size(1) + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
+  {
+  /*static_assert( std::is_same< typename ViewType::memory_space
+                          , Kokkos::HostSpace >::value
+  , "Reduction result on Kokkos::OpenMP must be a Kokkos::View in HostSpace" );*/
+  }
+
 };
 
 } // namespace Impl
@@ -1045,6 +1104,10 @@ void single(const Impl::ThreadSingleStruct<Impl::SerialTeamMember>& , const Func
 }
 }
 
+//----------------------------------------------------------------------------
+
+#include <impl/Kokkos_Serial_Task.hpp>
+
 #endif // defined( KOKKOS_HAVE_SERIAL )
 #endif /* #define KOKKOS_SERIAL_HPP */
 
diff --git a/lib/kokkos/core/src/Kokkos_TaskPolicy.hpp b/lib/kokkos/core/src/Kokkos_TaskPolicy.hpp
index 5f999e9a34..fc9113b750 100644
--- a/lib/kokkos/core/src/Kokkos_TaskPolicy.hpp
+++ b/lib/kokkos/core/src/Kokkos_TaskPolicy.hpp
@@ -1,4 +1,3 @@
-
 /*
 //@HEADER
 // ************************************************************************
@@ -47,13 +46,655 @@
 #ifndef KOKKOS_TASKPOLICY_HPP
 #define KOKKOS_TASKPOLICY_HPP
 
+//----------------------------------------------------------------------------
+
 #include <Kokkos_Core_fwd.hpp>
+
+// If compiling with CUDA then must be using CUDA 8 or better
+// and use relocateable device code to enable the task policy.
+// nvcc relocatable device code option: --relocatable-device-code=true
+
+#if ( defined( KOKKOS_COMPILER_NVCC ) )
+  #if ( 8000 <= CUDA_VERSION ) && \
+      defined( KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE )
+
+  #define KOKKOS_ENABLE_TASKPOLICY
+
+  #endif
+#else
+
+#define KOKKOS_ENABLE_TASKPOLICY
+
+#endif
+
+
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
+//----------------------------------------------------------------------------
+
 #include <Kokkos_MemoryPool.hpp>
-#include <impl/Kokkos_Traits.hpp>
 #include <impl/Kokkos_Tags.hpp>
-#include <impl/Kokkos_StaticAssert.hpp>
-#include <impl/Kokkos_AllocationTracker.hpp>
+#include <impl/Kokkos_TaskQueue.hpp>
+
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+
+enum TaskType { TaskTeam   = Impl::TaskBase<void,void,void>::TaskTeam
+              , TaskSingle = Impl::TaskBase<void,void,void>::TaskSingle };
+
+enum TaskPriority { TaskHighPriority    = 0
+                  , TaskRegularPriority = 1
+                  , TaskLowPriority     = 2 };
+
+template< typename Space >
+class TaskPolicy ;
+
+template< typename Space >
+void wait( TaskPolicy< Space > const & );
+
+} // namespace Kokkos
+
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+namespace Impl {
+
+/*\brief  Implementation data for task data management, access, and execution.
+ *
+ *  CRTP Inheritance structure to allow static_cast from the
+ *  task root type and a task's FunctorType.
+ *
+ *    TaskBase< Space , ResultType , FunctorType >
+ *      : TaskBase< Space , ResultType , void >
+ *      , FunctorType
+ *      { ... };
+ *
+ *    TaskBase< Space , ResultType , void >
+ *      : TaskBase< Space , void , void >
+ *      { ... };
+ */
+template< typename Space , typename ResultType , typename FunctorType >
+class TaskBase ;
+
+template< typename Space >
+class TaskExec ;
+
+}} // namespace Kokkos::Impl
+
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+
+/**
+ *
+ *  Future< space >  // value_type == void
+ *  Future< value >  // space == Default
+ *  Future< value , space >
+ *
+ */
+template< typename Arg1 /* = void */ , typename Arg2 /* = void */ >
+class Future {
+private:
+
+  template< typename > friend class TaskPolicy ;
+  template< typename , typename > friend class Future ;
+  template< typename , typename , typename > friend class Impl::TaskBase ;
+
+  enum { Arg1_is_space  = Kokkos::Impl::is_space< Arg1 >::value };
+  enum { Arg2_is_space  = Kokkos::Impl::is_space< Arg2 >::value };
+  enum { Arg1_is_value  = ! Arg1_is_space &&
+                          ! std::is_same< Arg1 , void >::value };
+  enum { Arg2_is_value  = ! Arg2_is_space &&
+                          ! std::is_same< Arg2 , void >::value };
+
+  static_assert( ! ( Arg1_is_space && Arg2_is_space )
+               , "Future cannot be given two spaces" );
+
+  static_assert( ! ( Arg1_is_value && Arg2_is_value )
+               , "Future cannot be given two value types" );
+
+  using ValueType =
+    typename std::conditional< Arg1_is_value , Arg1 ,
+    typename std::conditional< Arg2_is_value , Arg2 , void
+    >::type >::type ;
+
+  using Space =
+    typename std::conditional< Arg1_is_space , Arg1 ,
+    typename std::conditional< Arg2_is_space , Arg2 , void
+    >::type >::type ;
+
+  using task_base  = Impl::TaskBase< Space , ValueType , void > ;
+  using queue_type = Impl::TaskQueue< Space > ;
+
+  task_base * m_task ;
+
+  KOKKOS_INLINE_FUNCTION explicit
+  Future( task_base * task ) : m_task(0)
+    { if ( task ) queue_type::assign( & m_task , task ); }
+
+  //----------------------------------------
+
+public:
+
+  using execution_space = typename Space::execution_space ;
+  using value_type      = ValueType ;
+
+  //----------------------------------------
+
+  KOKKOS_INLINE_FUNCTION
+  bool is_null() const { return 0 == m_task ; }
+
+  KOKKOS_INLINE_FUNCTION
+  int reference_count() const
+    { return 0 != m_task ? m_task->reference_count() : 0 ; }
+
+  //----------------------------------------
+
+  KOKKOS_INLINE_FUNCTION
+  ~Future() { if ( m_task ) queue_type::assign( & m_task , (task_base*)0 ); }
+
+  //----------------------------------------
+
+  KOKKOS_INLINE_FUNCTION
+  constexpr Future() noexcept : m_task(0) {}
+
+  KOKKOS_INLINE_FUNCTION
+  Future( Future && rhs )
+    : m_task( rhs.m_task ) { rhs.m_task = 0 ; }
+
+  KOKKOS_INLINE_FUNCTION
+  Future( const Future & rhs )
+    : m_task(0)
+    { if ( rhs.m_task ) queue_type::assign( & m_task , rhs.m_task ); }
+
+  KOKKOS_INLINE_FUNCTION
+  Future & operator = ( Future && rhs )
+    {
+      if ( m_task ) queue_type::assign( & m_task , (task_base*)0 );
+      m_task = rhs.m_task ;
+      rhs.m_task = 0 ;
+      return *this ;
+    }
+
+  KOKKOS_INLINE_FUNCTION
+  Future & operator = ( const Future & rhs )
+    {
+      if ( m_task || rhs.m_task ) queue_type::assign( & m_task , rhs.m_task );
+      return *this ;
+    }
+
+  //----------------------------------------
+
+  template< class A1 , class A2 >
+  KOKKOS_INLINE_FUNCTION
+  Future( Future<A1,A2> && rhs )
+    : m_task( rhs.m_task )
+    {
+      static_assert
+        ( std::is_same< Space , void >::value ||
+          std::is_same< Space , typename Future<A1,A2>::Space >::value
+        , "Assigned Futures must have the same space" );
+
+      static_assert
+        ( std::is_same< value_type , void >::value ||
+          std::is_same< value_type , typename Future<A1,A2>::value_type >::value
+        , "Assigned Futures must have the same value_type" );
+
+      rhs.m_task = 0 ;
+    }
+
+  template< class A1 , class A2 >
+  KOKKOS_INLINE_FUNCTION
+  Future( const Future<A1,A2> & rhs )
+    : m_task(0)
+    {
+      static_assert
+        ( std::is_same< Space , void >::value ||
+          std::is_same< Space , typename Future<A1,A2>::Space >::value
+        , "Assigned Futures must have the same space" );
+
+      static_assert
+        ( std::is_same< value_type , void >::value ||
+          std::is_same< value_type , typename Future<A1,A2>::value_type >::value
+        , "Assigned Futures must have the same value_type" );
+
+      if ( rhs.m_task ) queue_type::assign( & m_task , rhs.m_task );
+    }
+
+  template< class A1 , class A2 >
+  KOKKOS_INLINE_FUNCTION
+  Future & operator = ( const Future<A1,A2> & rhs )
+    {
+      static_assert
+        ( std::is_same< Space , void >::value ||
+          std::is_same< Space , typename Future<A1,A2>::Space >::value
+        , "Assigned Futures must have the same space" );
+
+      static_assert
+        ( std::is_same< value_type , void >::value ||
+          std::is_same< value_type , typename Future<A1,A2>::value_type >::value
+        , "Assigned Futures must have the same value_type" );
+
+      if ( m_task || rhs.m_task ) queue_type::assign( & m_task , rhs.m_task );
+      return *this ;
+    }
+
+  template< class A1 , class A2 >
+  KOKKOS_INLINE_FUNCTION
+  Future & operator = ( Future<A1,A2> && rhs )
+    {
+      static_assert
+        ( std::is_same< Space , void >::value ||
+          std::is_same< Space , typename Future<A1,A2>::Space >::value
+        , "Assigned Futures must have the same space" );
+
+      static_assert
+        ( std::is_same< value_type , void >::value ||
+          std::is_same< value_type , typename Future<A1,A2>::value_type >::value
+        , "Assigned Futures must have the same value_type" );
+
+      if ( m_task ) queue_type::assign( & m_task , (task_base*) 0 );
+      m_task = rhs.m_task ;
+      rhs.m_task = 0 ;
+      return *this ;
+    }
+
+  //----------------------------------------
+
+  KOKKOS_INLINE_FUNCTION
+  typename task_base::get_return_type
+  get() const
+    {
+      if ( 0 == m_task ) {
+        Kokkos::abort( "Kokkos:::Future::get ERROR: is_null()");
+      }
+      return m_task->get();
+    }
+};
+
+} // namespace Kokkos
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+
+template< typename ExecSpace >
+class TaskPolicy
+{
+private:
+
+  using track_type = Kokkos::Experimental::Impl::SharedAllocationTracker ;
+  using queue_type = Kokkos::Impl::TaskQueue< ExecSpace > ;
+  using task_base  = Impl::TaskBase< ExecSpace , void , void > ;
+
+  track_type   m_track ;
+  queue_type * m_queue ;
+
+  //----------------------------------------
+  // Process optional arguments to spawn and respawn functions
+
+  KOKKOS_INLINE_FUNCTION static
+  void assign( task_base * const ) {}
+
+  // TaskTeam or TaskSingle
+  template< typename ... Options >
+  KOKKOS_INLINE_FUNCTION static
+  void assign( task_base * const task
+             , TaskType const & arg
+             , Options const & ... opts )
+    {
+      task->m_task_type = arg ;
+      assign( task , opts ... );
+    }
+
+  // TaskHighPriority or TaskRegularPriority or TaskLowPriority
+  template< typename ... Options >
+  KOKKOS_INLINE_FUNCTION static
+  void assign( task_base * const task
+             , TaskPriority const & arg
+             , Options const & ... opts )
+    {
+      task->m_priority = arg ;
+      assign( task , opts ... );
+    }
+
+  // Future for a dependence
+  template< typename A1 , typename A2 , typename ... Options >
+  KOKKOS_INLINE_FUNCTION static
+  void assign( task_base * const task
+             , Future< A1 , A2 > const & arg 
+             , Options const & ... opts )
+    {
+      // Assign dependence to task->m_next
+      // which will be processed within subsequent call to schedule.
+      // Error if the dependence is reset.
+
+      if ( 0 != Kokkos::atomic_exchange(& task->m_next, arg.m_task) ) {
+        Kokkos::abort("TaskPolicy ERROR: resetting task dependence");
+      }
+
+      if ( 0 != arg.m_task ) {
+        // The future may be destroyed upon returning from this call
+        // so increment reference count to track this assignment.
+        Kokkos::atomic_fetch_add( &(arg.m_task->m_ref_count) , 1 );
+      }
+
+      assign( task , opts ... );
+    }
+
+  //----------------------------------------
+
+public:
+
+  using execution_policy = TaskPolicy ;
+  using execution_space  = ExecSpace ;
+  using memory_space     = typename queue_type::memory_space ;
+  using member_type      = Kokkos::Impl::TaskExec< ExecSpace > ;
+
+  KOKKOS_INLINE_FUNCTION
+  TaskPolicy() : m_track(), m_queue(0) {}
+
+  KOKKOS_INLINE_FUNCTION
+  TaskPolicy( TaskPolicy && rhs ) = default ;
+
+  KOKKOS_INLINE_FUNCTION
+  TaskPolicy( TaskPolicy const & rhs ) = default ;
+
+  KOKKOS_INLINE_FUNCTION
+  TaskPolicy & operator = ( TaskPolicy && rhs ) = default ;
+
+  KOKKOS_INLINE_FUNCTION
+  TaskPolicy & operator = ( TaskPolicy const & rhs ) = default ;
+
+  TaskPolicy( memory_space const & arg_memory_space
+            , unsigned const arg_memory_pool_capacity
+            , unsigned const arg_memory_pool_log2_superblock = 12 )
+    : m_track()
+    , m_queue(0)
+    {
+      typedef Kokkos::Experimental::Impl::SharedAllocationRecord
+        < memory_space , typename queue_type::Destroy >
+          record_type ;
+
+      record_type * record =
+        record_type::allocate( arg_memory_space
+                             , "TaskQueue"
+                             , sizeof(queue_type)
+                             );
+
+      m_queue = new( record->data() )
+        queue_type( arg_memory_space
+                  , arg_memory_pool_capacity
+                  , arg_memory_pool_log2_superblock );
+
+      record->m_destroy.m_queue = m_queue ;
+
+      m_track.assign_allocated_record_to_uninitialized( record );
+    }
+
+  //----------------------------------------
+  /**\brief  Allocation size for a spawned task */
+  template< typename FunctorType >
+  KOKKOS_FUNCTION
+  size_t spawn_allocation_size() const
+    {
+      using task_type  = Impl::TaskBase< execution_space
+                                       , typename FunctorType::value_type
+                                       , FunctorType > ;
+
+      return m_queue->allocate_block_size( sizeof(task_type) );
+    }
+
+  /**\brief  Allocation size for a when_all aggregate */
+  KOKKOS_FUNCTION
+  size_t when_all_allocation_size( int narg ) const
+    {
+      using task_base  = Kokkos::Impl::TaskBase< ExecSpace , void , void > ;
+
+      return m_queue->allocate_block_size( sizeof(task_base) + narg * sizeof(task_base*) );
+    }
+
+  //----------------------------------------
+
+  /**\brief  A task spawns a task with options
+   *
+   *  1) High, Normal, or Low priority
+   *  2) With or without dependence
+   *  3) Team or Serial
+   */
+  template< typename FunctorType , typename ... Options >
+  KOKKOS_FUNCTION
+  Future< typename FunctorType::value_type , ExecSpace >
+  task_spawn( FunctorType const & arg_functor 
+            , Options const & ... arg_options
+            ) const
+    {
+      using value_type  = typename FunctorType::value_type ;
+      using future_type = Future< value_type , execution_space > ;
+      using task_type   = Impl::TaskBase< execution_space
+                                        , value_type
+                                        , FunctorType > ;
+
+      //----------------------------------------
+      // Give single-thread back-ends an opportunity to clear
+      // queue of ready tasks before allocating a new task
+
+      m_queue->iff_single_thread_recursive_execute();
+
+      //----------------------------------------
+
+      future_type f ;
+
+      // Allocate task from memory pool
+      f.m_task =
+        reinterpret_cast< task_type * >(m_queue->allocate(sizeof(task_type)));
 
+      if ( f.m_task ) {
+
+        // Placement new construction
+        new ( f.m_task ) task_type( arg_functor );
+
+        // Reference count starts at two
+        // +1 for matching decrement when task is complete
+        // +1 for future
+        f.m_task->m_queue      = m_queue ;
+        f.m_task->m_ref_count  = 2 ;
+        f.m_task->m_alloc_size = sizeof(task_type);
+
+        assign( f.m_task , arg_options... );
+
+        // Spawning from within the execution space so the
+        // apply function pointer is guaranteed to be valid
+        f.m_task->m_apply = task_type::apply ;
+
+        m_queue->schedule( f.m_task );
+        // this task may be updated or executed at any moment
+      }
+
+      return f ;
+    }
+
+  /**\brief  The host process spawns a task with options
+   *
+   *  1) High, Normal, or Low priority
+   *  2) With or without dependence
+   *  3) Team or Serial
+   */
+  template< typename FunctorType , typename ... Options >
+  inline
+  Future< typename FunctorType::value_type , ExecSpace >
+  host_spawn( FunctorType const & arg_functor 
+            , Options const & ... arg_options
+            ) const
+    {
+      using value_type  = typename FunctorType::value_type ;
+      using future_type = Future< value_type , execution_space > ;
+      using task_type   = Impl::TaskBase< execution_space
+                                        , value_type
+                                        , FunctorType > ;
+
+      future_type f ;
+
+      // Allocate task from memory pool
+      f.m_task = 
+        reinterpret_cast<task_type*>( m_queue->allocate(sizeof(task_type)) );
+
+      if ( f.m_task ) {
+
+        // Placement new construction
+        new( f.m_task ) task_type( arg_functor );
+
+        // Reference count starts at two:
+        // +1 to match decrement when task completes
+        // +1 for the future
+        f.m_task->m_queue      = m_queue ;
+        f.m_task->m_ref_count  = 2 ;
+        f.m_task->m_alloc_size = sizeof(task_type);
+
+        assign( f.m_task , arg_options... );
+
+        // Potentially spawning outside execution space so the
+        // apply function pointer must be obtained from execution space.
+        // Required for Cuda execution space function pointer.
+        queue_type::specialization::template
+          proc_set_apply< FunctorType >( & f.m_task->m_apply );
+
+        m_queue->schedule( f.m_task );
+      }
+      return f ;
+    }
+
+  /**\brief  Return a future that is complete
+   *         when all input futures are complete.
+   */
+  template< typename A1 , typename A2 >
+  KOKKOS_FUNCTION
+  Future< ExecSpace >
+  when_all( int narg , Future< A1 , A2 > const * const arg ) const
+    {
+      static_assert
+        ( std::is_same< execution_space
+                      , typename Future< A1 , A2 >::execution_space
+                      >::value
+        , "Future must have same execution space" );
+
+      using future_type = Future< ExecSpace > ;
+      using task_base   = Kokkos::Impl::TaskBase< ExecSpace , void , void > ;
+
+      future_type f ;
+
+      size_t const size  = sizeof(task_base) + narg * sizeof(task_base*);
+
+      f.m_task =
+        reinterpret_cast< task_base * >( m_queue->allocate( size ) );
+
+      if ( f.m_task ) {
+
+        new( f.m_task ) task_base();
+
+        // Reference count starts at two:
+        // +1 to match decrement when task completes
+        // +1 for the future
+        f.m_task->m_queue      = m_queue ;
+        f.m_task->m_ref_count  = 2 ;
+        f.m_task->m_alloc_size = size ;
+        f.m_task->m_dep_count  = narg ;
+        f.m_task->m_task_type  = task_base::Aggregate ;
+
+        task_base ** const dep = f.m_task->aggregate_dependences();
+
+        // Assign dependences to increment their reference count
+        // The futures may be destroyed upon returning from this call
+        // so increment reference count to track this assignment.
+
+        for ( int i = 0 ; i < narg ; ++i ) {
+          task_base * const t = dep[i] = arg[i].m_task ;
+          if ( 0 != t ) {
+            Kokkos::atomic_fetch_add( &(t->m_ref_count) , 1 );
+          }
+        }
+
+        m_queue->schedule( f.m_task );
+        // this when_all may be processed at any moment
+      }
+
+      return f ;
+    }
+
+  /**\brief  An executing task respawns itself with options
+   *
+   *  1) High, Normal, or Low priority
+   *  2) With or without dependence
+   */
+  template< class FunctorType , typename ... Options >
+  KOKKOS_FUNCTION
+  void respawn( FunctorType * task_self
+              , Options const & ... arg_options ) const
+    {
+      using value_type  = typename FunctorType::value_type ;
+      using task_type   = Impl::TaskBase< execution_space
+                                        , value_type
+                                        , FunctorType > ;
+
+      task_base * const zero = (task_base *) 0 ;
+      task_base * const lock = (task_base *) task_base::LockTag ;
+      task_type * const task = static_cast< task_type * >( task_self );
+
+      // Precondition:
+      //   task is in Executing state
+      //   therefore  m_next == LockTag
+      //
+      // Change to m_next == 0 for no dependence
+
+      if ( lock != Kokkos::atomic_exchange( & task->m_next, zero ) ) {
+        Kokkos::abort("TaskPolicy::respawn ERROR: already respawned");
+      }
+
+      assign( task , arg_options... );
+
+      // Postcondition:
+      //   task is in Executing-Respawn state
+      //   therefore  m_next == dependece or 0
+    }
+
+  //----------------------------------------
+
+  template< typename S >
+  friend
+  void Kokkos::wait( Kokkos::TaskPolicy< S > const & );
+
+  //----------------------------------------
+
+  inline
+  int allocation_capacity() const noexcept
+    { return m_queue->m_memory.get_mem_size(); }
+
+  KOKKOS_INLINE_FUNCTION
+  int allocated_task_count() const noexcept
+    { return m_queue->m_count_alloc ; }
+
+  KOKKOS_INLINE_FUNCTION
+  int allocated_task_count_max() const noexcept
+    { return m_queue->m_max_alloc ; }
+
+  KOKKOS_INLINE_FUNCTION
+  long allocated_task_count_accum() const noexcept
+    { return m_queue->m_accum_alloc ; }
+
+};
+
+template< typename ExecSpace >
+inline
+void wait( TaskPolicy< ExecSpace > const & policy )
+{ policy.m_queue->execute(); }
+
+} // namespace Kokkos
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
@@ -463,5 +1104,6 @@ void wait( TaskPolicy< ExecSpace > & );
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
-#endif /* #define KOKKOS_TASKPOLICY_HPP */
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
+#endif /* #ifndef KOKKOS_TASKPOLICY_HPP */
 
diff --git a/lib/kokkos/core/src/Kokkos_Threads.hpp b/lib/kokkos/core/src/Kokkos_Threads.hpp
index 23efefce34..c9ebbf9265 100644
--- a/lib/kokkos/core/src/Kokkos_Threads.hpp
+++ b/lib/kokkos/core/src/Kokkos_Threads.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -211,6 +211,8 @@ struct VerifyExecutionCanAccessMemorySpace
 #include <Threads/Kokkos_ThreadsTeam.hpp>
 #include <Threads/Kokkos_Threads_Parallel.hpp>
 
+#include <KokkosExp_MDRangePolicy.hpp>
+
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
diff --git a/lib/kokkos/core/src/Kokkos_View.hpp b/lib/kokkos/core/src/Kokkos_View.hpp
index 2f98b4dfa5..1cc8b03381 100644
--- a/lib/kokkos/core/src/Kokkos_View.hpp
+++ b/lib/kokkos/core/src/Kokkos_View.hpp
@@ -46,69 +46,61 @@
 
 #include <type_traits>
 #include <string>
-#include <Kokkos_Core_fwd.hpp>
-
-#if ! KOKKOS_USING_EXP_VIEW
+#include <algorithm>
+#include <initializer_list>
 
+#include <Kokkos_Core_fwd.hpp>
 #include <Kokkos_HostSpace.hpp>
 #include <Kokkos_MemoryTraits.hpp>
-
-#include <impl/Kokkos_StaticAssert.hpp>
-#include <impl/Kokkos_Traits.hpp>
-#include <impl/Kokkos_Shape.hpp>
-#include <impl/Kokkos_AnalyzeShape.hpp>
-#include <impl/Kokkos_Tags.hpp>
-
-// Must define before includng <impl/Kokkos_ViewOffset.hpp>
-namespace Kokkos { struct ALL ; }
-
-#include <impl/Kokkos_ViewOffset.hpp>
-#include <impl/Kokkos_ViewSupport.hpp>
+#include <Kokkos_ExecPolicy.hpp>
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
+namespace Experimental {
 namespace Impl {
 
-/** \brief  View specialization mapping of view traits to a specialization tag */
-template< class ValueType ,
-          class ArraySpecialize ,
-          class ArrayLayout ,
-          class MemorySpace ,
-          class MemoryTraits >
-struct ViewSpecialize ;
-
-/** \brief  Defines the type of a subview given a source view type
- *          and subview argument types.
- */
-template< class SrcViewType
-        , class Arg0Type
-        , class Arg1Type
-        , class Arg2Type
-        , class Arg3Type
-        , class Arg4Type
-        , class Arg5Type
-        , class Arg6Type
-        , class Arg7Type
-        >
-struct ViewSubview /* { typedef ... type ; } */ ;
+template< class DstMemorySpace , class SrcMemorySpace >
+struct DeepCopy ;
 
-template< class DstViewSpecialize ,
-          class SrcViewSpecialize = void ,
-          class Enable = void >
-struct ViewAssignment ;
+template< class DataType >
+struct ViewArrayAnalysis ;
 
-template< class DstMemorySpace , class SrcMemorySpace , class ExecutionSpace>
-struct DeepCopy ;
+template< class DataType , class ArrayLayout
+        , typename ValueType =
+          typename ViewArrayAnalysis< DataType >::non_const_value_type
+        >
+struct ViewDataAnalysis ;
+
+template< class , class ... >
+class ViewMapping { public: enum { is_assignable = false }; };
+
+template< class MemorySpace >
+struct ViewOperatorBoundsErrorAbort ;
+
+template<>
+struct ViewOperatorBoundsErrorAbort< Kokkos::HostSpace > {
+  static void apply( const size_t rank
+                   , const size_t n0 , const size_t n1
+                   , const size_t n2 , const size_t n3
+                   , const size_t n4 , const size_t n5
+                   , const size_t n6 , const size_t n7
+                   , const size_t i0 , const size_t i1
+                   , const size_t i2 , const size_t i3
+                   , const size_t i4 , const size_t i5
+                   , const size_t i6 , const size_t i7 );
+};
 
 } /* namespace Impl */
-} // namespace Kokkos
+} /* namespace Experimental */
+} /* namespace Kokkos */
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
+namespace Experimental {
 
 /** \class ViewTraits
  *  \brief Traits class for accessing attributes of a View.
@@ -116,247 +108,189 @@ namespace Kokkos {
  * This is an implementation detail of View.  It is only of interest
  * to developers implementing a new specialization of View.
  *
- * Template argument permutations:
- *   - View< DataType , void         , void         , void >
- *   - View< DataType , Space        , void         , void >
- *   - View< DataType , Space        , MemoryTraits , void >
- *   - View< DataType , Space        , void         , MemoryTraits >
- *   - View< DataType , ArrayLayout  , void         , void >
- *   - View< DataType , ArrayLayout  , Space        , void >
- *   - View< DataType , ArrayLayout  , MemoryTraits , void   >
- *   - View< DataType , ArrayLayout  , Space        , MemoryTraits >
- *   - View< DataType , MemoryTraits , void         , void  >
+ * Template argument options:
+ *   - View< DataType >
+ *   - View< DataType , Space >
+ *   - View< DataType , Space , MemoryTraits >
+ *   - View< DataType , ArrayLayout >
+ *   - View< DataType , ArrayLayout , Space >
+ *   - View< DataType , ArrayLayout , MemoryTraits >
+ *   - View< DataType , ArrayLayout , Space , MemoryTraits >
+ *   - View< DataType , MemoryTraits >
  */
 
-template< class DataType ,
-          class Arg1 = void ,
-          class Arg2 = void ,
-          class Arg3 = void >
-class ViewTraits {
-private:
+template< class DataType , class ... Properties >
+struct ViewTraits ;
+
+template<>
+struct ViewTraits< void >
+{
+  typedef void  execution_space ;
+  typedef void  memory_space ;
+  typedef void  HostMirrorSpace ;
+  typedef void  array_layout ;
+  typedef void  memory_traits ;
+};
+
+template< class ... Prop >
+struct ViewTraits< void , void , Prop ... >
+{
+  // Ignore an extraneous 'void'
+  typedef typename ViewTraits<void,Prop...>::execution_space  execution_space ;
+  typedef typename ViewTraits<void,Prop...>::memory_space     memory_space ;
+  typedef typename ViewTraits<void,Prop...>::HostMirrorSpace  HostMirrorSpace ;
+  typedef typename ViewTraits<void,Prop...>::array_layout     array_layout ;
+  typedef typename ViewTraits<void,Prop...>::memory_traits    memory_traits ;
+};
+
+template< class ArrayLayout , class ... Prop >
+struct ViewTraits< typename std::enable_if< Kokkos::Impl::is_array_layout<ArrayLayout>::value >::type , ArrayLayout , Prop ... >
+{
+  // Specify layout, keep subsequent space and memory traits arguments
+
+  typedef typename ViewTraits<void,Prop...>::execution_space  execution_space ;
+  typedef typename ViewTraits<void,Prop...>::memory_space     memory_space ;
+  typedef typename ViewTraits<void,Prop...>::HostMirrorSpace  HostMirrorSpace ;
+  typedef          ArrayLayout                                array_layout ;
+  typedef typename ViewTraits<void,Prop...>::memory_traits    memory_traits ;
+};
+
+template< class Space , class ... Prop >
+struct ViewTraits< typename std::enable_if< Kokkos::Impl::is_space<Space>::value >::type , Space , Prop ... >
+{
+  // Specify Space, memory traits should be the only subsequent argument.
+
+  static_assert( std::is_same< typename ViewTraits<void,Prop...>::execution_space , void >::value &&
+                 std::is_same< typename ViewTraits<void,Prop...>::memory_space    , void >::value &&
+                 std::is_same< typename ViewTraits<void,Prop...>::HostMirrorSpace , void >::value &&
+                 std::is_same< typename ViewTraits<void,Prop...>::array_layout    , void >::value
+               , "Only one View Execution or Memory Space template argument" );
+
+  typedef typename Space::execution_space                   execution_space ;
+  typedef typename Space::memory_space                      memory_space ;
+  typedef typename Kokkos::Impl::is_space< Space >::host_mirror_space
+      HostMirrorSpace ;
+  typedef typename execution_space::array_layout            array_layout ;
+  typedef typename ViewTraits<void,Prop...>::memory_traits  memory_traits ;
+};
+
+template< class MemoryTraits , class ... Prop >
+struct ViewTraits< typename std::enable_if< Kokkos::Impl::is_memory_traits<MemoryTraits>::value >::type , MemoryTraits , Prop ... >
+{
+  // Specify memory trait, should not be any subsequent arguments
+
+  static_assert( std::is_same< typename ViewTraits<void,Prop...>::execution_space , void >::value &&
+                 std::is_same< typename ViewTraits<void,Prop...>::memory_space    , void >::value &&
+                 std::is_same< typename ViewTraits<void,Prop...>::array_layout    , void >::value &&
+                 std::is_same< typename ViewTraits<void,Prop...>::memory_traits   , void >::value
+               , "MemoryTrait is the final optional template argument for a View" );
+
+  typedef void          execution_space ;
+  typedef void          memory_space ;
+  typedef void          HostMirrorSpace ;
+  typedef void          array_layout ;
+  typedef MemoryTraits  memory_traits ;
+};
 
-  // Layout, Space, and MemoryTraits are optional
-  // but need to appear in that order. That means Layout
-  // can only be Arg1, Space can be Arg1 or Arg2, and
-  // MemoryTraits can be Arg1, Arg2 or Arg3
 
-  enum { Arg1IsLayout = Impl::is_array_layout<Arg1>::value };
+template< class DataType , class ... Properties >
+struct ViewTraits {
+private:
 
-  enum { Arg1IsSpace = Impl::is_space<Arg1>::value };
-  enum { Arg2IsSpace = Impl::is_space<Arg2>::value };
+  // Unpack the properties arguments
+  typedef ViewTraits< void , Properties ... >  prop ;
 
-  enum { Arg1IsMemoryTraits = Impl::is_memory_traits<Arg1>::value };
-  enum { Arg2IsMemoryTraits = Impl::is_memory_traits<Arg2>::value };
-  enum { Arg3IsMemoryTraits = Impl::is_memory_traits<Arg3>::value };
+  typedef typename
+    std::conditional< ! std::is_same< typename prop::execution_space , void >::value
+                    , typename prop::execution_space
+                    , Kokkos::DefaultExecutionSpace
+                    >::type
+      ExecutionSpace ;
 
-  enum { Arg1IsVoid = Impl::is_same< Arg1 , void >::value };
-  enum { Arg2IsVoid = Impl::is_same< Arg2 , void >::value };
-  enum { Arg3IsVoid = Impl::is_same< Arg3 , void >::value };
+  typedef typename
+    std::conditional< ! std::is_same< typename prop::memory_space , void >::value
+                    , typename prop::memory_space
+                    , typename ExecutionSpace::memory_space
+                    >::type
+      MemorySpace ;
 
-  // Arg1 is Layout, Space, MemoryTraits, or void
   typedef typename
-    Impl::StaticAssert<
-      ( 1 == Arg1IsLayout + Arg1IsSpace + Arg1IsMemoryTraits + Arg1IsVoid )
-      , Arg1 >::type Arg1Verified ;
-
-  // If Arg1 is Layout       then Arg2 is Space, MemoryTraits, or void
-  // If Arg1 is Space        then Arg2 is MemoryTraits or void
-  // If Arg1 is MemoryTraits then Arg2 is void
-  // If Arg1 is Void         then Arg2 is void
+    std::conditional< ! std::is_same< typename prop::array_layout , void >::value
+                    , typename prop::array_layout
+                    , typename ExecutionSpace::array_layout
+                    >::type
+      ArrayLayout ;
+
   typedef typename
-    Impl::StaticAssert<
-      ( Arg1IsLayout       && ( 1 == Arg2IsSpace + Arg2IsMemoryTraits + Arg2IsVoid ) ) ||
-      ( Arg1IsSpace        && ( 0 == Arg2IsSpace ) && ( 1 == Arg2IsMemoryTraits + Arg2IsVoid ) ) ||
-      ( Arg1IsMemoryTraits && Arg2IsVoid ) ||
-      ( Arg1IsVoid         && Arg2IsVoid )
-      , Arg2 >::type Arg2Verified ;
-
-  // Arg3 is MemoryTraits or void and at most one argument is MemoryTraits
+    std::conditional
+      < ! std::is_same< typename prop::HostMirrorSpace , void >::value
+      , typename prop::HostMirrorSpace
+      , typename Kokkos::Impl::is_space< ExecutionSpace >::host_mirror_space
+      >::type
+      HostMirrorSpace ;
+
   typedef typename
-    Impl::StaticAssert<
-      ( 1 == Arg3IsMemoryTraits + Arg3IsVoid ) &&
-      ( Arg1IsMemoryTraits + Arg2IsMemoryTraits + Arg3IsMemoryTraits <= 1 )
-      , Arg3 >::type Arg3Verified ;
-
-  // Arg1 or Arg2 may have execution and memory spaces
-  typedef typename Impl::if_c<( Arg1IsSpace ), Arg1Verified ,
-          typename Impl::if_c<( Arg2IsSpace ), Arg2Verified ,
-          Kokkos::DefaultExecutionSpace
-          >::type >::type::execution_space  ExecutionSpace ;
-
-  typedef typename Impl::if_c<( Arg1IsSpace ), Arg1Verified ,
-          typename Impl::if_c<( Arg2IsSpace ), Arg2Verified ,
-          Kokkos::DefaultExecutionSpace
-          >::type >::type::memory_space  MemorySpace ;
-
-  typedef typename Impl::is_space<
-    typename Impl::if_c<( Arg1IsSpace ), Arg1Verified ,
-    typename Impl::if_c<( Arg2IsSpace ), Arg2Verified ,
-    Kokkos::DefaultExecutionSpace
-    >::type >::type >::host_mirror_space  HostMirrorSpace ;
-
-  // Arg1 may be array layout
-  typedef typename Impl::if_c< Arg1IsLayout , Arg1Verified ,
-          typename ExecutionSpace::array_layout
-          >::type ArrayLayout ;
-
-  // Arg1, Arg2, or Arg3 may be memory traits
-  typedef typename Impl::if_c< Arg1IsMemoryTraits , Arg1Verified ,
-          typename Impl::if_c< Arg2IsMemoryTraits , Arg2Verified ,
-          typename Impl::if_c< Arg3IsMemoryTraits , Arg3Verified ,
-          MemoryManaged
-          >::type >::type >::type  MemoryTraits ;
-
-  typedef Impl::AnalyzeShape<DataType> analysis ;
+    std::conditional< ! std::is_same< typename prop::memory_traits , void >::value
+                    , typename prop::memory_traits
+                    , typename Kokkos::MemoryManaged
+                    >::type
+      MemoryTraits ;
+
+  // Analyze data type's properties,
+  // May be specialized based upon the layout and value type
+  typedef Kokkos::Experimental::Impl::ViewDataAnalysis< DataType , ArrayLayout > data_analysis ;
 
 public:
 
   //------------------------------------
   // Data type traits:
 
-  typedef DataType                            data_type ;
-  typedef typename analysis::const_type       const_data_type ;
-  typedef typename analysis::non_const_type   non_const_data_type ;
+  typedef typename data_analysis::type            data_type ;
+  typedef typename data_analysis::const_type      const_data_type ;
+  typedef typename data_analysis::non_const_type  non_const_data_type ;
 
   //------------------------------------
-  // Array of intrinsic scalar type traits:
+  // Compatible array of trivial type traits:
 
-  typedef typename analysis::array_intrinsic_type            array_intrinsic_type ;
-  typedef typename analysis::const_array_intrinsic_type      const_array_intrinsic_type ;
-  typedef typename analysis::non_const_array_intrinsic_type  non_const_array_intrinsic_type ;
+  typedef typename data_analysis::scalar_array_type            scalar_array_type ;
+  typedef typename data_analysis::const_scalar_array_type      const_scalar_array_type ;
+  typedef typename data_analysis::non_const_scalar_array_type  non_const_scalar_array_type ;
 
   //------------------------------------
   // Value type traits:
 
-  typedef typename analysis::value_type            value_type ;
-  typedef typename analysis::const_value_type      const_value_type ;
-  typedef typename analysis::non_const_value_type  non_const_value_type ;
+  typedef typename data_analysis::value_type            value_type ;
+  typedef typename data_analysis::const_value_type      const_value_type ;
+  typedef typename data_analysis::non_const_value_type  non_const_value_type ;
 
   //------------------------------------
-  // Layout and shape traits:
+  // Mapping traits:
 
-  typedef ArrayLayout                array_layout ;
-  typedef typename analysis::shape   shape_type ;
+  typedef ArrayLayout                         array_layout ;
+  typedef typename data_analysis::dimension   dimension ;
+  typedef typename data_analysis::specialize  specialize /* mapping specialization tag */ ;
 
-  enum { rank         = shape_type::rank };
-  enum { rank_dynamic = shape_type::rank_dynamic };
+  enum { rank         = dimension::rank };
+  enum { rank_dynamic = dimension::rank_dynamic };
 
   //------------------------------------
   // Execution space, memory space, memory access traits, and host mirror space.
 
-  typedef ExecutionSpace   execution_space ;
-  typedef MemorySpace      memory_space ;
-  typedef Device<ExecutionSpace,MemorySpace>  device_type ;
-  typedef MemoryTraits     memory_traits ;
-  typedef HostMirrorSpace  host_mirror_space ;
+  typedef ExecutionSpace                              execution_space ;
+  typedef MemorySpace                                 memory_space ;
+  typedef Kokkos::Device<ExecutionSpace,MemorySpace>  device_type ;
+  typedef MemoryTraits                                memory_traits ;
+  typedef HostMirrorSpace                             host_mirror_space ;
 
-  typedef typename memory_space::size_type  size_type ;
+  typedef typename MemorySpace::size_type  size_type ;
 
-  enum { is_hostspace      = Impl::is_same< memory_space , HostSpace >::value };
-  enum { is_managed        = memory_traits::Unmanaged == 0 };
-  enum { is_random_access  = memory_traits::RandomAccess == 1 };
+  enum { is_hostspace      = std::is_same< MemorySpace , HostSpace >::value };
+  enum { is_managed        = MemoryTraits::Unmanaged    == 0 };
+  enum { is_random_access  = MemoryTraits::RandomAccess == 1 };
 
   //------------------------------------
-
-
-  //------------------------------------
-  // Specialization tag:
-
-  typedef typename
-    Impl::ViewSpecialize< value_type
-                        , typename analysis::specialize
-                        , array_layout
-                        , memory_space
-                        , memory_traits
-                        >::type specialize ;
-};
-
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Impl {
-
-class ViewDefault {};
-
-/** \brief  Default view specialization has LayoutLeft, LayoutRight, or LayoutStride.
- */
-template< class ValueType , class MemorySpace , class MemoryTraits >
-struct ViewSpecialize< ValueType , void , LayoutLeft , MemorySpace , MemoryTraits >
-{ typedef ViewDefault type ; };
-
-template< class ValueType , class MemorySpace , class MemoryTraits >
-struct ViewSpecialize< ValueType , void , LayoutRight , MemorySpace , MemoryTraits >
-{ typedef ViewDefault type ; };
-
-template< class ValueType , class MemorySpace , class MemoryTraits >
-struct ViewSpecialize< ValueType , void , LayoutStride , MemorySpace , MemoryTraits >
-{ typedef ViewDefault type ; };
-
-} /* namespace Impl */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Impl {
-
-/** \brief Types for compile-time detection of View usage errors */
-namespace ViewError {
-
-struct allocation_constructor_requires_managed {};
-struct allocation_constructor_requires_nonconst {};
-struct user_pointer_constructor_requires_unmanaged {};
-struct device_shmem_constructor_requires_unmanaged {};
-
-struct scalar_operator_called_from_non_scalar_view {};
-
-} /* namespace ViewError */
-
-//----------------------------------------------------------------------------
-/** \brief  Enable view parentheses operator for
- *          match of layout and integral arguments.
- *          If correct rank define type from traits,
- *          otherwise define type as an error message.
- */
-template< class ReturnType , class Traits , class Layout , unsigned Rank ,
-          typename iType0 = int , typename iType1 = int ,
-          typename iType2 = int , typename iType3 = int ,
-          typename iType4 = int , typename iType5 = int ,
-          typename iType6 = int , typename iType7 = int ,
-          class Enable = void >
-struct ViewEnableArrayOper ;
-
-template< class ReturnType , class Traits , class Layout , unsigned Rank ,
-          typename iType0 , typename iType1 ,
-          typename iType2 , typename iType3 ,
-          typename iType4 , typename iType5 ,
-          typename iType6 , typename iType7 >
-struct ViewEnableArrayOper<
-   ReturnType , Traits , Layout , Rank ,
-   iType0 , iType1 , iType2 , iType3 ,
-   iType4 , iType5 , iType6 , iType7 ,
-   typename enable_if<
-     iType0(0) == 0 && iType1(0) == 0 && iType2(0) == 0 && iType3(0) == 0 &&
-     iType4(0) == 0 && iType5(0) == 0 && iType6(0) == 0 && iType7(0) == 0 &&
-     is_same< typename Traits::array_layout , Layout >::value &&
-     ( unsigned(Traits::rank) == Rank )
-   >::type >
-{
-  typedef ReturnType type ;
 };
 
-} /* namespace Impl */
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-
 /** \class View
  *  \brief View to an array of data.
  *
@@ -376,11 +310,13 @@ namespace Kokkos {
  * they may occur.
  *
  * Valid ways in which template arguments may be specified:
- *   - View< DataType , Space >
- *   - View< DataType , Space  ,         MemoryTraits >
- *   - View< DataType , Space  , void  , MemoryTraits >
+ *   - View< DataType >
+ *   - View< DataType , Layout >
  *   - View< DataType , Layout , Space >
  *   - View< DataType , Layout , Space , MemoryTraits >
+ *   - View< DataType , Space >
+ *   - View< DataType , Space , MemoryTraits >
+ *   - View< DataType , MemoryTraits >
  *
  * \tparam DataType (required) This indicates both the type of each
  *   entry of the array, and the combination of compile-time and
@@ -437,1194 +373,1425 @@ namespace Kokkos {
  * }
  * \endcode
  */
-template< class DataType ,
-          class Arg1Type = void , /* ArrayLayout, SpaceType, or MemoryTraits */
-          class Arg2Type = void , /* SpaceType or MemoryTraits */
-          class Arg3Type = void , /* MemoryTraits */
-          class Specialize =
-            typename ViewTraits<DataType,Arg1Type,Arg2Type,Arg3Type>::specialize >
+template< class DataType , class ... Properties >
 class View ;
 
-template< class C >
-struct is_view : public Impl::bool_< false > {};
-
-template< class D , class A1 , class A2 , class A3 , class S >
-struct is_view< View< D , A1 , A2 , A3 , S > > : public Impl::bool_< true > {};
-
-namespace Impl {
-using Kokkos::is_view ;
-}
+} /* namespace Experimental */
+} /* namespace Kokkos */
 
+//----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
-template< class DataType ,
-          class Arg1Type ,
-          class Arg2Type ,
-          class Arg3Type >
-class View< DataType , Arg1Type , Arg2Type , Arg3Type , Impl::ViewDefault >
-  : public ViewTraits< DataType , Arg1Type , Arg2Type, Arg3Type >
-{
-public:
+#include <impl/KokkosExp_ViewMapping.hpp>
+#include <impl/KokkosExp_ViewArray.hpp>
 
-  typedef ViewTraits< DataType , Arg1Type , Arg2Type, Arg3Type > traits ;
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
 
-private:
+namespace Kokkos {
+namespace Experimental {
 
-  // Assignment of compatible views requirement:
-  template< class , class , class , class , class > friend class View ;
+namespace {
 
-  // Assignment of compatible subview requirement:
-  template< class , class , class > friend struct Impl::ViewAssignment ;
+constexpr Kokkos::Experimental::Impl::ALL_t
+  ALL = Kokkos::Experimental::Impl::ALL_t();
 
-  // Dimensions, cardinality, capacity, and offset computation for
-  // multidimensional array view of contiguous memory.
-  // Inherits from Impl::Shape
-  typedef Impl::ViewOffset< typename traits::shape_type
-                          , typename traits::array_layout
-                          > offset_map_type ;
+constexpr Kokkos::Experimental::Impl::WithoutInitializing_t
+  WithoutInitializing = Kokkos::Experimental::Impl::WithoutInitializing_t();
 
-  // Intermediary class for data management and access
-  typedef Impl::ViewDataManagement< traits > view_data_management ;
+constexpr Kokkos::Experimental::Impl::AllowPadding_t
+  AllowPadding        = Kokkos::Experimental::Impl::AllowPadding_t();
 
-  //----------------------------------------
-  // Data members:
+}
 
-  typename view_data_management::handle_type  m_ptr_on_device ;
-  offset_map_type                             m_offset_map ;
-  view_data_management                        m_management ;
-  Impl::AllocationTracker                     m_tracker ;
+/** \brief  Create View allocation parameter bundle from argument list.
+ *
+ *  Valid argument list members are:
+ *    1) label as a "string" or std::string
+ *    2) memory space instance of the View::memory_space type
+ *    3) execution space instance compatible with the View::memory_space
+ *    4) Kokkos::WithoutInitializing to bypass initialization
+ *    4) Kokkos::AllowPadding to allow allocation to pad dimensions for memory alignment
+ */
+template< class ... Args >
+inline
+Impl::ViewCtorProp< typename Impl::ViewCtorProp< void , Args >::type ... >
+view_alloc( Args const & ... args )
+{
+  typedef
+    Impl::ViewCtorProp< typename Impl::ViewCtorProp< void , Args >::type ... >
+      return_type ;
 
-  //----------------------------------------
+  static_assert( ! return_type::has_pointer
+               , "Cannot give pointer-to-memory for view allocation" );
 
-public:
+  return return_type( args... );
+}
 
-  /** return type for all indexing operators */
-  typedef typename view_data_management::return_type reference_type ;
+template< class ... Args >
+inline
+Impl::ViewCtorProp< typename Impl::ViewCtorProp< void , Args >::type ... >
+view_wrap( Args const & ... args )
+{
+  typedef
+    Impl::ViewCtorProp< typename Impl::ViewCtorProp< void , Args >::type ... >
+      return_type ;
 
-  enum { reference_type_is_lvalue = view_data_management::ReturnTypeIsReference };
+  static_assert( ! return_type::has_memory_space &&
+                 ! return_type::has_execution_space &&
+                 ! return_type::has_label &&
+                 return_type::has_pointer
+               , "Must only give pointer-to-memory for view wrapping" );
 
-  typedef View< typename traits::array_intrinsic_type ,
-                typename traits::array_layout ,
-                typename traits::device_type ,
-                typename traits::memory_traits > array_type ;
+  return return_type( args... );
+}
 
-  typedef View< typename traits::const_data_type ,
-                typename traits::array_layout ,
-                typename traits::device_type ,
-                typename traits::memory_traits > const_type ;
+} /* namespace Experimental */
+} /* namespace Kokkos */
 
-  typedef View< typename traits::non_const_data_type ,
-                typename traits::array_layout ,
-                typename traits::device_type ,
-                typename traits::memory_traits > non_const_type ;
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
 
-  typedef View< typename traits::non_const_data_type ,
-                typename traits::array_layout ,
-                typename traits::host_mirror_space ,
-                void > HostMirror ;
+namespace Kokkos {
+namespace Experimental {
 
-  //------------------------------------
-  // Shape
+template< class DataType , class ... Properties >
+class View ;
 
-  enum { Rank = traits::rank };
+template< class > struct is_view : public std::false_type {};
 
-  KOKKOS_INLINE_FUNCTION offset_map_type shape() const { return m_offset_map ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_0() const { return m_offset_map.N0 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_1() const { return m_offset_map.N1 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_2() const { return m_offset_map.N2 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_3() const { return m_offset_map.N3 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_4() const { return m_offset_map.N4 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_5() const { return m_offset_map.N5 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_6() const { return m_offset_map.N6 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_7() const { return m_offset_map.N7 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type size() const { return m_offset_map.cardinality(); }
+template< class D, class ... P >
+struct is_view< View<D,P...> > : public std::true_type {};
 
-  template< typename iType >
-  KOKKOS_INLINE_FUNCTION
-  typename traits::size_type dimension( const iType & i ) const
-    { return Impl::dimension( m_offset_map , i ); }
+template< class D, class ... P >
+struct is_view< const View<D,P...> > : public std::true_type {};
 
-  //------------------------------------
-  // Destructor, constructors, assignment operators:
+template< class DataType , class ... Properties >
+class View : public ViewTraits< DataType , Properties ... > {
+private:
 
-  KOKKOS_INLINE_FUNCTION
-  ~View() {}
+  template< class , class ... > friend class View ;
+  template< class , class ... > friend class Impl::ViewMapping ;
 
-  KOKKOS_INLINE_FUNCTION
-  View()
-    : m_ptr_on_device()
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-    { m_offset_map.assign(0, 0,0,0,0,0,0,0,0); }
+public:
 
-  KOKKOS_INLINE_FUNCTION
-  View( const View & rhs )
-    : m_ptr_on_device()
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-    {
-      (void) Impl::ViewAssignment<
-         typename traits::specialize ,
-         typename traits::specialize >( *this , rhs );
-    }
+  typedef ViewTraits< DataType , Properties ... > traits ;
 
-  KOKKOS_INLINE_FUNCTION
-  View & operator = ( const View & rhs )
-    {
-      (void) Impl::ViewAssignment<
-         typename traits::specialize ,
-         typename traits::specialize >( *this , rhs );
-      return *this ;
-    }
+private:
 
-  //------------------------------------
-  // Construct or assign compatible view:
+  typedef Kokkos::Experimental::Impl::ViewMapping< traits , void > map_type ;
+  typedef Kokkos::Experimental::Impl::SharedAllocationTracker      track_type ;
 
-  template< class RT , class RL , class RD , class RM , class RS >
-  KOKKOS_INLINE_FUNCTION
-  View( const View<RT,RL,RD,RM,RS> & rhs )
-    : m_ptr_on_device()
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-    {
-      (void) Impl::ViewAssignment<
-         typename traits::specialize , RS >( *this , rhs );
-    }
+  track_type  m_track ;
+  map_type    m_map ;
 
-  template< class RT , class RL , class RD , class RM , class RS >
-  KOKKOS_INLINE_FUNCTION
-  View & operator = ( const View<RT,RL,RD,RM,RS> & rhs )
-    {
-      (void) Impl::ViewAssignment<
-         typename traits::specialize , RS >( *this , rhs );
-      return *this ;
-    }
+public:
 
-  //------------------------------------
-  /**\brief Allocation of a managed view with possible alignment padding.
-   *
-   *  Allocation properties for allocating and initializing to the default value_type:
-   *    Kokkos::ViewAllocate()
-   *    Kokkos::ViewAllocate("label")  OR  "label"
-   *    Kokkos::ViewAllocate(std::string("label"))  OR  std::string("label")
-   *
-   *  Allocation properties for allocating and bypassing initialization:
-   *    Kokkos::ViewAllocateWithoutInitializing()
-   *    Kokkos::ViewAllocateWithoutInitializing("label")
-   */
+  //----------------------------------------
+  /** \brief  Compatible view of array of scalar types */
+  typedef View< typename traits::scalar_array_type ,
+                typename traits::array_layout ,
+                typename traits::device_type ,
+                typename traits::memory_traits >
+    array_type ;
 
-  template< class AllocationProperties >
-  explicit inline
-  View( const AllocationProperties & prop ,
-        // Impl::ViewAllocProp::size_type exists when the traits and allocation properties
-        // are valid for allocating viewed memory.
-        const typename Impl::ViewAllocProp< traits , AllocationProperties >::size_type n0 = 0 ,
-        const size_t n1 = 0 ,
-        const size_t n2 = 0 ,
-        const size_t n3 = 0 ,
-        const size_t n4 = 0 ,
-        const size_t n5 = 0 ,
-        const size_t n6 = 0 ,
-        const size_t n7 = 0 ,
-        const size_t n8 = 0 )
-    : m_ptr_on_device()
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-    {
-      typedef Impl::ViewAllocProp< traits , AllocationProperties > Alloc ;
+  /** \brief  Compatible view of const data type */
+  typedef View< typename traits::const_data_type ,
+                typename traits::array_layout ,
+                typename traits::device_type ,
+                typename traits::memory_traits >
+    const_type ;
 
-      static_assert(!std::is_same<typename traits::array_layout, LayoutStride>::value,
-                         "LayoutStride does not support View constructor which takes dimensions directly!");
+  /** \brief  Compatible view of non-const data type */
+  typedef View< typename traits::non_const_data_type ,
+                typename traits::array_layout ,
+                typename traits::device_type ,
+                typename traits::memory_traits >
+    non_const_type ;
 
-      m_offset_map.assign( n0, n1, n2, n3, n4, n5, n6, n7, n8 );
-      if(Alloc::AllowPadding)
-        m_offset_map.set_padding();
+  /** \brief  Compatible HostMirror view */
+  typedef View< typename traits::non_const_data_type ,
+                typename traits::array_layout ,
+                typename traits::host_mirror_space >
+    HostMirror ;
 
-      m_ptr_on_device = view_data_management::template allocate< Alloc::Initialize >( Alloc::label(prop) , m_offset_map, m_tracker );
+  //----------------------------------------
+  // Domain rank and extents
 
-    }
+  enum { Rank = map_type::Rank };
 
-  template< class AllocationProperties >
-  explicit inline
-  View( const AllocationProperties & prop ,
-        const typename traits::array_layout & layout ,
-        // Impl::ViewAllocProp::size_type exists when the traits and allocation properties
-        // are valid for allocating viewed memory.
-        const typename Impl::ViewAllocProp< traits , AllocationProperties >::size_type = 0 )
-    : m_ptr_on_device()
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-    {
-      typedef Impl::ViewAllocProp< traits , AllocationProperties > Alloc ;
+ /** \brief rank() to be implemented
+  */
+  //KOKKOS_INLINE_FUNCTION
+  //static
+  //constexpr unsigned rank() { return map_type::Rank; }
 
-      m_offset_map.assign( layout );
-      if(Alloc::AllowPadding)
-        m_offset_map.set_padding();
+  template< typename iType >
+  KOKKOS_INLINE_FUNCTION constexpr
+  typename std::enable_if< std::is_integral<iType>::value , size_t >::type
+  extent( const iType & r ) const
+    { return m_map.extent(r); }
 
-      m_ptr_on_device = view_data_management::template allocate< Alloc::Initialize >( Alloc::label(prop) , m_offset_map, m_tracker );
+  template< typename iType >
+  KOKKOS_INLINE_FUNCTION constexpr
+  typename std::enable_if< std::is_integral<iType>::value , int >::type
+  extent_int( const iType & r ) const
+    { return static_cast<int>(m_map.extent(r)); }
 
-      m_management.set_noncontiguous();
-    }
+  KOKKOS_INLINE_FUNCTION constexpr
+  typename traits::array_layout layout() const
+    { return m_map.layout(); }
 
-  //------------------------------------
-  // Assign an unmanaged View from pointer, can be called in functors.
-  // No alignment padding is performed.
+  //----------------------------------------
+  /*  Deprecate all 'dimension' functions in favor of
+   *  ISO/C++ vocabulary 'extent'.
+   */
 
-  template< class Type >
-  explicit KOKKOS_INLINE_FUNCTION
-  View( Type * ptr ,
-        typename Impl::ViewRawPointerProp< traits , Type >::size_type n0 = 0 ,
-        const size_t n1 = 0 ,
-        const size_t n2 = 0 ,
-        const size_t n3 = 0 ,
-        const size_t n4 = 0 ,
-        const size_t n5 = 0 ,
-        const size_t n6 = 0 ,
-        const size_t n7 = 0 ,
-        const size_t n8 = 0 )
-    : m_ptr_on_device(ptr)
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-    {
-      m_offset_map.assign( n0, n1, n2, n3, n4, n5, n6, n7, n8 );
-      m_management.set_unmanaged();
-    }
+  template< typename iType >
+  KOKKOS_INLINE_FUNCTION constexpr
+  typename std::enable_if< std::is_integral<iType>::value , size_t >::type
+  dimension( const iType & r ) const { return extent( r ); }
+
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_0() const { return m_map.dimension_0(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_1() const { return m_map.dimension_1(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_2() const { return m_map.dimension_2(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_3() const { return m_map.dimension_3(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_4() const { return m_map.dimension_4(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_5() const { return m_map.dimension_5(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_6() const { return m_map.dimension_6(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t dimension_7() const { return m_map.dimension_7(); }
 
-  template< class Type >
-  explicit KOKKOS_INLINE_FUNCTION
-  View( Type * ptr ,
-        typename traits::array_layout const & layout ,
-        typename Impl::ViewRawPointerProp< traits , Type >::size_type = 0 )
-    : m_ptr_on_device(ptr)
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-    {
-      m_offset_map.assign( layout );
-      m_management.set_unmanaged();
-      m_management.set_noncontiguous();
-    }
+  //----------------------------------------
 
+  KOKKOS_INLINE_FUNCTION constexpr size_t size() const { return m_map.dimension_0() *
+                                                                m_map.dimension_1() *
+                                                                m_map.dimension_2() *
+                                                                m_map.dimension_3() *
+                                                                m_map.dimension_4() *
+                                                                m_map.dimension_5() *
+                                                                m_map.dimension_6() *
+                                                                m_map.dimension_7(); }
+
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_0() const { return m_map.stride_0(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_1() const { return m_map.stride_1(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_2() const { return m_map.stride_2(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_3() const { return m_map.stride_3(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_4() const { return m_map.stride_4(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_5() const { return m_map.stride_5(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_6() const { return m_map.stride_6(); }
+  KOKKOS_INLINE_FUNCTION constexpr size_t stride_7() const { return m_map.stride_7(); }
 
+  template< typename iType >
+  KOKKOS_INLINE_FUNCTION void stride( iType * const s ) const { m_map.stride(s); }
 
-  //------------------------------------
-  // Assign a View from an AllocationTracker,
-  // The allocator used must be compatiable with the memory space of the view
-  // No alignment padding is performed.
-  // TODO: Should these allow padding??? DJS 01/15/15
-  explicit
-  View( Impl::AllocationTracker const &arg_tracker ,
-        const size_t n0 = 0 ,
-        const size_t n1 = 0 ,
-        const size_t n2 = 0 ,
-        const size_t n3 = 0 ,
-        const size_t n4 = 0 ,
-        const size_t n5 = 0 ,
-        const size_t n6 = 0 ,
-        const size_t n7 = 0 ,
-        const size_t n8 = 0 )
-    : m_ptr_on_device(reinterpret_cast<typename traits::value_type*>(arg_tracker.alloc_ptr()))
-    , m_offset_map()
-    , m_management()
-    , m_tracker(arg_tracker)
-    {
-      m_offset_map.assign( n0, n1, n2, n3, n4, n5, n6, n7, n8 );
+  //----------------------------------------
+  // Range span is the span which contains all members.
 
-      const size_t req_size = m_offset_map.capacity() * sizeof(typename traits::value_type);
-      if ( m_tracker.alloc_size() < req_size ) {
-        Impl::throw_runtime_exception("Error: tracker.alloc_size() < req_size");
-      }
-    }
+  typedef typename map_type::reference_type  reference_type ;
+  typedef typename map_type::pointer_type    pointer_type ;
 
-  explicit
-  View( Impl::AllocationTracker const & arg_tracker
-      , typename traits::array_layout const & layout )
-    : m_ptr_on_device(reinterpret_cast<typename traits::value_type*>(arg_tracker.alloc_ptr()))
-    , m_offset_map()
-    , m_management()
-    , m_tracker(arg_tracker)
-    {
-      m_offset_map.assign( layout );
+  enum { reference_type_is_lvalue_reference = std::is_lvalue_reference< reference_type >::value };
 
-      const size_t req_size = m_offset_map.capacity() * sizeof(typename traits::value_type);
-      if ( m_tracker.alloc_size() < req_size ) {
-        Impl::throw_runtime_exception("Error: tracker.alloc_size() < req_size");
-      }
+  KOKKOS_INLINE_FUNCTION constexpr size_t span() const { return m_map.span(); }
+  // Deprecated, use 'span()' instead
+  KOKKOS_INLINE_FUNCTION constexpr size_t capacity() const { return m_map.span(); }
+  KOKKOS_INLINE_FUNCTION constexpr bool   span_is_contiguous() const { return m_map.span_is_contiguous(); }
+  KOKKOS_INLINE_FUNCTION constexpr pointer_type data() const { return m_map.data(); }
 
-      m_management.set_noncontiguous();
-    }
+  // Deprecated, use 'span_is_contigous()' instead
+  KOKKOS_INLINE_FUNCTION constexpr bool   is_contiguous() const { return m_map.span_is_contiguous(); }
+  // Deprecated, use 'data()' instead
+  KOKKOS_INLINE_FUNCTION constexpr pointer_type ptr_on_device() const { return m_map.data(); }
 
-  //------------------------------------
-  /** \brief  Constructors for subviews requires following
-   *          type-compatibility condition, enforce via StaticAssert.
-   *
-   *  Impl::is_same< View ,
-   *                 typename Impl::ViewSubview< View<D,A1,A2,A3,Impl::ViewDefault>
-   *                                           , ArgType0 , ArgType1 , ArgType2 , ArgType3
-   *                                           , ArgType4 , ArgType5 , ArgType6 , ArgType7
-   *                 >::type >::value
-   */
-  template< class D , class A1 , class A2 , class A3
-          , class SubArg0_type , class SubArg1_type , class SubArg2_type , class SubArg3_type
-          , class SubArg4_type , class SubArg5_type , class SubArg6_type , class SubArg7_type
-          >
-  KOKKOS_INLINE_FUNCTION
-  View( const View<D,A1,A2,A3,Impl::ViewDefault> & src
-      , const SubArg0_type & arg0 , const SubArg1_type & arg1
-      , const SubArg2_type & arg2 , const SubArg3_type & arg3
-      , const SubArg4_type & arg4 , const SubArg5_type & arg5
-      , const SubArg6_type & arg6 , const SubArg7_type & arg7
-      );
-
-  template< class D , class A1 , class A2 , class A3
-          , class SubArg0_type , class SubArg1_type , class SubArg2_type , class SubArg3_type
-          , class SubArg4_type , class SubArg5_type , class SubArg6_type
-          >
-  KOKKOS_INLINE_FUNCTION
-  View( const View<D,A1,A2,A3,Impl::ViewDefault> & src
-      , const SubArg0_type & arg0 , const SubArg1_type & arg1
-      , const SubArg2_type & arg2 , const SubArg3_type & arg3
-      , const SubArg4_type & arg4 , const SubArg5_type & arg5
-      , const SubArg6_type & arg6
-      );
-
-  template< class D , class A1 , class A2 , class A3
-          , class SubArg0_type , class SubArg1_type , class SubArg2_type , class SubArg3_type
-          , class SubArg4_type , class SubArg5_type
-          >
-  KOKKOS_INLINE_FUNCTION
-  View( const View<D,A1,A2,A3,Impl::ViewDefault> & src
-      , const SubArg0_type & arg0 , const SubArg1_type & arg1
-      , const SubArg2_type & arg2 , const SubArg3_type & arg3
-      , const SubArg4_type & arg4 , const SubArg5_type & arg5
-      );
-
-  template< class D , class A1 , class A2 , class A3
-          , class SubArg0_type , class SubArg1_type , class SubArg2_type , class SubArg3_type
-          , class SubArg4_type
-          >
-  KOKKOS_INLINE_FUNCTION
-  View( const View<D,A1,A2,A3,Impl::ViewDefault> & src
-      , const SubArg0_type & arg0 , const SubArg1_type & arg1
-      , const SubArg2_type & arg2 , const SubArg3_type & arg3
-      , const SubArg4_type & arg4
-      );
-
-  template< class D , class A1 , class A2 , class A3
-          , class SubArg0_type , class SubArg1_type , class SubArg2_type , class SubArg3_type
-          >
-  KOKKOS_INLINE_FUNCTION
-  View( const View<D,A1,A2,A3,Impl::ViewDefault> & src
-      , const SubArg0_type & arg0 , const SubArg1_type & arg1
-      , const SubArg2_type & arg2 , const SubArg3_type & arg3
-      );
-
-  template< class D , class A1 , class A2 , class A3
-          , class SubArg0_type , class SubArg1_type , class SubArg2_type
-          >
-  KOKKOS_INLINE_FUNCTION
-  View( const View<D,A1,A2,A3,Impl::ViewDefault> & src
-      , const SubArg0_type & arg0 , const SubArg1_type & arg1
-      , const SubArg2_type & arg2
-      );
-
-  template< class D , class A1 , class A2 , class A3
-          , class SubArg0_type , class SubArg1_type
-          >
-  KOKKOS_INLINE_FUNCTION
-  View( const View<D,A1,A2,A3,Impl::ViewDefault> & src
-      , const SubArg0_type & arg0 , const SubArg1_type & arg1
-      );
+  //----------------------------------------
+  // Allow specializations to query their specialized map
 
-  template< class D , class A1 , class A2 , class A3
-          , class SubArg0_type
-          >
   KOKKOS_INLINE_FUNCTION
-  View( const View<D,A1,A2,A3,Impl::ViewDefault> & src
-      , const SubArg0_type & arg0
-      );
-
-  //------------------------------------
-  // Assign unmanaged View to portion of execution space's shared memory
-
-  typedef Impl::if_c< ! traits::is_managed ,
-                      const typename traits::execution_space::scratch_memory_space & ,
-                      Impl::ViewError::device_shmem_constructor_requires_unmanaged >
-      if_scratch_memory_constructor ;
-
-  explicit KOKKOS_INLINE_FUNCTION
-  View( typename if_scratch_memory_constructor::type space ,
-        const unsigned n0 = 0 ,
-        const unsigned n1 = 0 ,
-        const unsigned n2 = 0 ,
-        const unsigned n3 = 0 ,
-        const unsigned n4 = 0 ,
-        const unsigned n5 = 0 ,
-        const unsigned n6 = 0 ,
-        const unsigned n7 = 0 )
-    : m_ptr_on_device()
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-    {
-      typedef typename traits::value_type  value_type_ ;
-
-      enum { align = 8 };
-      enum { mask  = align - 1 };
-
-      m_offset_map.assign( n0, n1, n2, n3, n4, n5, n6, n7 );
+  const Kokkos::Experimental::Impl::ViewMapping< traits , void > &
+  implementation_map() const { return m_map ; }
 
-      typedef Impl::if_c< ! traits::is_managed ,
-                          value_type_ * ,
-                          Impl::ViewError::device_shmem_constructor_requires_unmanaged >
-        if_device_shmem_pointer ;
+  //----------------------------------------
 
-      // Select the first argument:
-      m_ptr_on_device = if_device_shmem_pointer::select(
-       (value_type_*) space.get_shmem( unsigned( sizeof(value_type_) * m_offset_map.capacity() + unsigned(mask) ) & ~unsigned(mask) ) );
-    }
+private:
 
-  explicit KOKKOS_INLINE_FUNCTION
-  View( typename if_scratch_memory_constructor::type space ,
-        typename traits::array_layout const & layout)
-    : m_ptr_on_device()
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-    {
-      typedef typename traits::value_type  value_type_ ;
+  enum {
+    is_layout_left = std::is_same< typename traits::array_layout
+                                  , Kokkos::LayoutLeft >::value ,
 
-      typedef Impl::if_c< ! traits::is_managed ,
-                          value_type_ * ,
-                          Impl::ViewError::device_shmem_constructor_requires_unmanaged >
-        if_device_shmem_pointer ;
+    is_layout_right = std::is_same< typename traits::array_layout
+                                  , Kokkos::LayoutRight >::value ,
 
-      m_offset_map.assign( layout );
-      m_management.set_unmanaged();
-      m_management.set_noncontiguous();
+    is_layout_stride = std::is_same< typename traits::array_layout
+                                   , Kokkos::LayoutStride >::value ,
 
-      enum { align = 8 };
-      enum { mask  = align - 1 };
+    is_default_map =
+      std::is_same< typename traits::specialize , void >::value &&
+      ( is_layout_left || is_layout_right || is_layout_stride )
+  };
 
-      // Select the first argument:
-      m_ptr_on_device = if_device_shmem_pointer::select(
-       (value_type_*) space.get_shmem( unsigned( sizeof(value_type_) * m_offset_map.capacity() + unsigned(mask) ) & ~unsigned(mask) ) );
-    }
+#if defined( KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK )
 
-  static inline
-  unsigned shmem_size( const unsigned n0 = 0 ,
-                       const unsigned n1 = 0 ,
-                       const unsigned n2 = 0 ,
-                       const unsigned n3 = 0 ,
-                       const unsigned n4 = 0 ,
-                       const unsigned n5 = 0 ,
-                       const unsigned n6 = 0 ,
-                       const unsigned n7 = 0 )
-  {
-    enum { align = 8 };
-    enum { mask  = align - 1 };
+#define KOKKOS_VIEW_OPERATOR_VERIFY( ARG ) \
+  Kokkos::Impl::VerifyExecutionCanAccessMemorySpace \
+    < Kokkos::Impl::ActiveExecutionMemorySpace , typename traits::memory_space >::verify(); \
+  Kokkos::Experimental::Impl::view_verify_operator_bounds ARG ;
 
-    typedef typename traits::value_type  value_type_ ;
+#else
 
-    offset_map_type offset_map ;
+#define KOKKOS_VIEW_OPERATOR_VERIFY( ARG ) \
+  Kokkos::Impl::VerifyExecutionCanAccessMemorySpace \
+    < Kokkos::Impl::ActiveExecutionMemorySpace , typename traits::memory_space >::verify();
 
-    offset_map.assign( n0, n1, n2, n3, n4, n5, n6, n7 );
+#endif
 
-    return unsigned( sizeof(value_type_) * offset_map.capacity() + unsigned(mask) ) & ~unsigned(mask) ;
-  }
+public:
 
-  //------------------------------------
-  // Is not allocated
+  //------------------------------
+  // Rank 0 operator()
 
+  template< class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  bool is_null() const { return 0 == ptr_on_device() ; }
-
-  //------------------------------------
-  // Operators for scalar (rank zero) views.
-
-  typedef Impl::if_c< traits::rank == 0 ,
-                      typename traits::value_type ,
-                      Impl::ViewError::scalar_operator_called_from_non_scalar_view >
-    if_scalar_operator ;
-
-  typedef Impl::if_c< traits::rank == 0 ,
-                      reference_type ,
-                      Impl::ViewError::scalar_operator_called_from_non_scalar_view >
-    if_scalar_operator_return ;
-  KOKKOS_INLINE_FUNCTION
-  const View & operator = ( const typename if_scalar_operator::type & rhs ) const
+  typename std::enable_if<( Kokkos::Impl::are_integral<Args...>::value
+                            && ( 0 == Rank )
+                          ), reference_type >::type
+  operator()( Args ... args ) const
     {
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
-      m_ptr_on_device[ 0 ] = if_scalar_operator::select( rhs );
-      return *this ;
-    }
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,args...) )
 
-  KOKKOS_FORCEINLINE_FUNCTION
-  operator typename if_scalar_operator_return::type () const
-    {
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
-      return if_scalar_operator_return::select( m_ptr_on_device[ 0 ] );
+      return m_map.reference();
     }
 
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename if_scalar_operator_return::type operator()() const
-    {
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
-      return if_scalar_operator_return::select( m_ptr_on_device[ 0 ] );
-    }
+  //------------------------------
+  // Rank 1 operator()
 
+  template< typename I0
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename if_scalar_operator_return::type operator*() const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,Args...>::value
+      && ( 1 == Rank )
+      && ! is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0
+            , Args ... args ) const
     {
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
-      return if_scalar_operator_return::select( m_ptr_on_device[ 0 ] );
-    }
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,args...) )
 
-  //------------------------------------
-  // Array member access operators enabled if
-  // (1) a zero value of all argument types are compile-time comparable to zero
-  // (2) the rank matches the number of arguments
-  // (3) the memory space is valid for the access
-  //------------------------------------
-  // rank 1:
-  // Specialisation for LayoutLeft and LayoutRight since we know its stride 1
+      return m_map.reference(i0);
+    }
 
-  template< typename iType0 >
+  template< typename I0
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type , traits, LayoutLeft, 1, iType0 >::type
-    operator[] ( const iType0 & i0 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,Args...>::value
+      && ( 1 == Rank )
+      && is_default_map
+      && ! is_layout_stride
+    ), reference_type >::type
+  operator()( const I0 & i0
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_1( m_offset_map, i0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,args...) )
 
-      return m_ptr_on_device[ i0 ];
+      return m_map.m_handle[ i0 ];
     }
 
-  template< typename iType0 >
+  template< typename I0
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type , traits,  LayoutLeft, 1, iType0 >::type
-    operator() ( const iType0 & i0 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,Args...>::value
+      && ( 1 == Rank )
+      && is_default_map
+      && is_layout_stride
+    ), reference_type >::type
+  operator()( const I0 & i0
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_1( m_offset_map, i0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,args...) )
 
-      return m_ptr_on_device[ i0 ];
+      return m_map.m_handle[ m_map.m_offset.m_stride.S0 * i0 ];
     }
 
-  template< typename iType0 >
+  //------------------------------
+  // Rank 1 operator[]
+
+  template< typename I0 >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type , traits, LayoutLeft, 1, iType0 >::type
-    at( const iType0 & i0 , const int , const int , const int ,
-        const int , const int , const int , const int ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0>::value
+      && ( 1 == Rank )
+      && ! is_default_map
+    ), reference_type >::type
+  operator[]( const I0 & i0 ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_1( m_offset_map, i0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0) )
 
-      return m_ptr_on_device[ i0 ];
+      return m_map.reference(i0);
     }
 
-  template< typename iType0 >
+  template< typename I0 >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type , traits, LayoutRight, 1, iType0 >::type
-    operator[] ( const iType0 & i0 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0>::value
+      && ( 1 == Rank )
+      && is_default_map
+      && ! is_layout_stride
+    ), reference_type >::type
+  operator[]( const I0 & i0 ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_1( m_offset_map, i0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0) )
 
-      return m_ptr_on_device[ i0 ];
+      return m_map.m_handle[ i0 ];
     }
 
-  template< typename iType0 >
+  template< typename I0 >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type , traits,  LayoutRight, 1, iType0 >::type
-    operator() ( const iType0 & i0 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0>::value
+      && ( 1 == Rank )
+      && is_default_map
+      && is_layout_stride
+    ), reference_type >::type
+  operator[]( const I0 & i0 ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_1( m_offset_map, i0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0) )
 
-      return m_ptr_on_device[ i0 ];
+      return m_map.m_handle[ m_map.m_offset.m_stride.S0 * i0 ];
     }
 
-  template< typename iType0 >
+  //------------------------------
+  // Rank 2
+
+  template< typename I0 , typename I1
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type , traits, LayoutRight, 1, iType0 >::type
-    at( const iType0 & i0 , const int , const int , const int ,
-        const int , const int , const int , const int ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
+      && ( 2 == Rank )
+      && ! is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_1( m_offset_map, i0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
 
-      return m_ptr_on_device[ i0 ];
+      return m_map.reference(i0,i1);
     }
 
-  template< typename iType0 >
+  template< typename I0 , typename I1
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type , traits,
-                 typename Impl::if_c<
-                   Impl::is_same<typename traits::array_layout, LayoutRight>::value ||
-                   Impl::is_same<typename traits::array_layout, LayoutLeft>::value ,
-                   void, typename traits::array_layout>::type,
-                 1, iType0 >::type
-    operator[] ( const iType0 & i0 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
+      && ( 2 == Rank )
+      && is_default_map
+      && is_layout_left && ( traits::rank_dynamic == 0 )
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_1( m_offset_map, i0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0) ];
+      return m_map.m_handle[ i0 + m_map.m_offset.m_dim.N0 * i1 ];
     }
 
-  template< typename iType0 >
+  template< typename I0 , typename I1
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type , traits,
-                 typename Impl::if_c<
-                   Impl::is_same<typename traits::array_layout, LayoutRight>::value ||
-                   Impl::is_same<typename traits::array_layout, LayoutLeft>::value ,
-                   void, typename traits::array_layout>::type,
-                 1, iType0 >::type
-    operator() ( const iType0 & i0 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
+      && ( 2 == Rank )
+      && is_default_map
+      && is_layout_left && ( traits::rank_dynamic != 0 )
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_1( m_offset_map, i0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0) ];
+      return m_map.m_handle[ i0 + m_map.m_offset.m_stride * i1 ];
     }
 
-  template< typename iType0 >
+  template< typename I0 , typename I1
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type , traits,
-                 typename Impl::if_c<
-                   Impl::is_same<typename traits::array_layout, LayoutRight>::value ||
-                   Impl::is_same<typename traits::array_layout, LayoutLeft>::value ,
-                   void, typename traits::array_layout>::type,
-                 1, iType0 >::type
-    at( const iType0 & i0 , const int , const int , const int ,
-        const int , const int , const int , const int ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
+      && ( 2 == Rank )
+      && is_default_map
+      && is_layout_right && ( traits::rank_dynamic == 0 )
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_1( m_offset_map, i0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0) ];
+      return m_map.m_handle[ i1 + m_map.m_offset.m_dim.N1 * i0 ];
     }
 
-  // rank 2:
-
-  template< typename iType0 , typename iType1 >
+  template< typename I0 , typename I1
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 2, iType0, iType1 >::type
-    operator() ( const iType0 & i0 , const iType1 & i1 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
+      && ( 2 == Rank )
+      && is_default_map
+      && is_layout_right && ( traits::rank_dynamic != 0 )
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_2( m_offset_map, i0,i1 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1) ];
+      return m_map.m_handle[ i1 + m_map.m_offset.m_stride * i0 ];
     }
 
-  template< typename iType0 , typename iType1 >
+  template< typename I0 , typename I1
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 2, iType0, iType1 >::type
-    at( const iType0 & i0 , const iType1 & i1 , const int , const int ,
-        const int , const int , const int , const int ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,Args...>::value
+      && ( 2 == Rank )
+      && is_default_map
+      && is_layout_stride
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_2( m_offset_map, i0,i1 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1) ];
+      return m_map.m_handle[ i0 * m_map.m_offset.m_stride.S0 +
+                             i1 * m_map.m_offset.m_stride.S1 ];
     }
 
-  // rank 3:
+  //------------------------------
+  // Rank 3
 
-  template< typename iType0 , typename iType1 , typename iType2 >
+  template< typename I0 , typename I1 , typename I2
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 3, iType0, iType1, iType2 >::type
-    operator() ( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,Args...>::value
+      && ( 3 == Rank )
+      && is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_3( m_offset_map, i0,i1,i2 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2) ];
+      return m_map.m_handle[ m_map.m_offset(i0,i1,i2) ];
     }
 
-  template< typename iType0 , typename iType1 , typename iType2 >
+  template< typename I0 , typename I1 , typename I2
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 3, iType0, iType1, iType2 >::type
-    at( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const int ,
-        const int , const int , const int , const int ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,Args...>::value
+      && ( 3 == Rank )
+      && ! is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_3( m_offset_map, i0,i1,i2 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2) ];
+      return m_map.reference(i0,i1,i2);
     }
 
-  // rank 4:
+  //------------------------------
+  // Rank 4
 
-  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 >
+  template< typename I0 , typename I1 , typename I2 , typename I3
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 4, iType0, iType1, iType2, iType3 >::type
-    operator() ( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,Args...>::value
+      && ( 4 == Rank )
+      && is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_4( m_offset_map, i0,i1,i2,i3 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2,i3) ];
+      return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3) ];
     }
 
-  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 >
+  template< typename I0 , typename I1 , typename I2 , typename I3
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 4, iType0, iType1, iType2, iType3 >::type
-    at( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ,
-        const int , const int , const int , const int ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,Args...>::value
+      && ( 4 == Rank )
+      && ! is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_4( m_offset_map, i0,i1,i2,i3 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2,i3) ];
+      return m_map.reference(i0,i1,i2,i3);
     }
 
-  // rank 5:
+  //------------------------------
+  // Rank 5
 
-  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 ,
-            typename iType4 >
+  template< typename I0 , typename I1 , typename I2 , typename I3
+          , typename I4
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 5, iType0, iType1, iType2, iType3 , iType4 >::type
-    operator() ( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ,
-                 const iType4 & i4 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,Args...>::value
+      && ( 5 == Rank )
+      && is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
+            , const I4 & i4
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_5( m_offset_map, i0,i1,i2,i3,i4 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2,i3,i4) ];
+      return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4) ];
     }
 
-  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 ,
-            typename iType4 >
+  template< typename I0 , typename I1 , typename I2 , typename I3
+          , typename I4
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 5, iType0, iType1, iType2, iType3 , iType4 >::type
-    at( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ,
-        const iType4 & i4 , const int , const int , const int ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,Args...>::value
+      && ( 5 == Rank )
+      && ! is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
+            , const I4 & i4
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_5( m_offset_map, i0,i1,i2,i3,i4 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2,i3,i4) ];
+      return m_map.reference(i0,i1,i2,i3,i4);
     }
 
-  // rank 6:
+  //------------------------------
+  // Rank 6
 
-  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 ,
-            typename iType4 , typename iType5 >
+  template< typename I0 , typename I1 , typename I2 , typename I3
+          , typename I4 , typename I5
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 6,
-                                      iType0, iType1, iType2, iType3 , iType4, iType5 >::type
-    operator() ( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ,
-                 const iType4 & i4 , const iType5 & i5 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,Args...>::value
+      && ( 6 == Rank )
+      && is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
+            , const I4 & i4 , const I5 & i5
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_6( m_offset_map, i0,i1,i2,i3,i4,i5 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2,i3,i4,i5) ];
+      return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5) ];
     }
 
-  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 ,
-            typename iType4 , typename iType5 >
+  template< typename I0 , typename I1 , typename I2 , typename I3
+          , typename I4 , typename I5
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 6,
-                                      iType0, iType1, iType2, iType3 , iType4, iType5 >::type
-    at( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ,
-        const iType4 & i4 , const iType5 & i5 , const int , const int ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,Args...>::value
+      && ( 6 == Rank )
+      && ! is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
+            , const I4 & i4 , const I5 & i5
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_6( m_offset_map, i0,i1,i2,i3,i4,i5 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2,i3,i4,i5) ];
+      return m_map.reference(i0,i1,i2,i3,i4,i5);
     }
 
-  // rank 7:
+  //------------------------------
+  // Rank 7
 
-  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 ,
-            typename iType4 , typename iType5 , typename iType6 >
+  template< typename I0 , typename I1 , typename I2 , typename I3
+          , typename I4 , typename I5 , typename I6
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 7,
-                                      iType0, iType1, iType2, iType3 , iType4, iType5, iType6 >::type
-    operator() ( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ,
-                 const iType4 & i4 , const iType5 & i5 , const iType6 & i6 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,I6,Args...>::value
+      && ( 7 == Rank )
+      && is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
+            , const I4 & i4 , const I5 & i5 , const I6 & i6
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_7( m_offset_map, i0,i1,i2,i3,i4,i5,i6 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,i6,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2,i3,i4,i5,i6) ];
+      return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5,i6) ];
     }
 
-  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 ,
-            typename iType4 , typename iType5 , typename iType6 >
+  template< typename I0 , typename I1 , typename I2 , typename I3
+          , typename I4 , typename I5 , typename I6
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 7,
-                                      iType0, iType1, iType2, iType3 , iType4, iType5, iType6 >::type
-    at( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ,
-        const iType4 & i4 , const iType5 & i5 , const iType6 & i6 , const int ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,I6,Args...>::value
+      && ( 7 == Rank )
+      && ! is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
+            , const I4 & i4 , const I5 & i5 , const I6 & i6
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_7( m_offset_map, i0,i1,i2,i3,i4,i5,i6 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,i6,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2,i3,i4,i5,i6) ];
+      return m_map.reference(i0,i1,i2,i3,i4,i5,i6);
     }
 
-  // rank 8:
+  //------------------------------
+  // Rank 8
 
-  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 ,
-            typename iType4 , typename iType5 , typename iType6 , typename iType7 >
+  template< typename I0 , typename I1 , typename I2 , typename I3
+          , typename I4 , typename I5 , typename I6 , typename I7
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 8,
-                                      iType0, iType1, iType2, iType3 , iType4, iType5, iType6, iType7 >::type
-    operator() ( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ,
-                 const iType4 & i4 , const iType5 & i5 , const iType6 & i6 , const iType7 & i7 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,I6,I7,Args...>::value
+      && ( 8 == Rank )
+      && is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
+            , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_8( m_offset_map, i0,i1,i2,i3,i4,i5,i6,i7 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,i6,i7,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2,i3,i4,i5,i6,i7) ];
+      return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5,i6,i7) ];
     }
 
-  template< typename iType0 , typename iType1 , typename iType2 , typename iType3 ,
-            typename iType4 , typename iType5 , typename iType6 , typename iType7 >
+  template< typename I0 , typename I1 , typename I2 , typename I3
+          , typename I4 , typename I5 , typename I6 , typename I7
+          , class ... Args >
   KOKKOS_FORCEINLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< reference_type ,
-                                      traits, typename traits::array_layout, 8,
-                                      iType0, iType1, iType2, iType3 , iType4, iType5, iType6, iType7 >::type
-    at( const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ,
-        const iType4 & i4 , const iType5 & i5 , const iType6 & i6 , const iType7 & i7 ) const
+  typename std::enable_if<
+    ( Kokkos::Impl::are_integral<I0,I1,I2,I3,I4,I5,I6,I7,Args...>::value
+      && ( 8 == Rank )
+      && ! is_default_map
+    ), reference_type >::type
+  operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3
+            , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7
+            , Args ... args ) const
     {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_8( m_offset_map, i0,i1,i2,i3,i4,i5,i6,i7 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , ptr_on_device() );
+      KOKKOS_VIEW_OPERATOR_VERIFY( (m_map,i0,i1,i2,i3,i4,i5,i6,i7,args...) )
 
-      return m_ptr_on_device[ m_offset_map(i0,i1,i2,i3,i4,i5,i6,i7) ];
+      return m_map.reference(i0,i1,i2,i3,i4,i5,i6,i7);
     }
 
-  //------------------------------------
-  // Access to the underlying contiguous storage of this view specialization.
-  // These methods are specific to specialization of a view.
+#undef KOKKOS_VIEW_OPERATOR_VERIFY
 
-  KOKKOS_FORCEINLINE_FUNCTION
-  typename traits::value_type * ptr_on_device() const
-    { return (typename traits::value_type *) m_ptr_on_device ; }
+  //----------------------------------------
+  // Standard destructor, constructors, and assignment operators
 
-  // Stride of physical storage, dimensioned to at least Rank
-  template< typename iType >
   KOKKOS_INLINE_FUNCTION
-  void stride( iType * const s ) const
-  { m_offset_map.stride(s); }
+  ~View() {}
 
-  // Count of contiguously allocated data members including padding.
   KOKKOS_INLINE_FUNCTION
-  typename traits::size_type capacity() const
-  { return m_offset_map.capacity(); }
+  View() : m_track(), m_map() {}
 
-  // If the view data can be treated (deep copied)
-  // as a contiguous block of memory.
   KOKKOS_INLINE_FUNCTION
-  bool is_contiguous() const
-  { return m_management.is_contiguous(); }
+  View( const View & rhs ) : m_track( rhs.m_track ), m_map( rhs.m_map ) {}
 
-  const Impl::AllocationTracker & tracker() const { return m_tracker; }
+  KOKKOS_INLINE_FUNCTION
+  View( View && rhs ) : m_track( rhs.m_track ), m_map( rhs.m_map ) {}
+
+  KOKKOS_INLINE_FUNCTION
+  View & operator = ( const View & rhs ) { m_track = rhs.m_track ; m_map = rhs.m_map ; return *this ; }
+
+  KOKKOS_INLINE_FUNCTION
+  View & operator = ( View && rhs ) { m_track = rhs.m_track ; m_map = rhs.m_map ; return *this ; }
+
+  //----------------------------------------
+  // Compatible view copy constructor and assignment
+  // may assign unmanaged from managed.
+
+  template< class RT , class ... RP >
+  KOKKOS_INLINE_FUNCTION
+  View( const View<RT,RP...> & rhs )
+    : m_track( rhs.m_track , traits::is_managed )
+    , m_map()
+    {
+      typedef typename View<RT,RP...>::traits  SrcTraits ;
+      typedef Kokkos::Experimental::Impl::ViewMapping< traits , SrcTraits , void >  Mapping ;
+      static_assert( Mapping::is_assignable , "Incompatible View copy construction" );
+      Mapping::assign( m_map , rhs.m_map , rhs.m_track );
+    }
+
+  template< class RT , class ... RP >
+  KOKKOS_INLINE_FUNCTION
+  View & operator = ( const View<RT,RP...> & rhs )
+    {
+      typedef typename View<RT,RP...>::traits  SrcTraits ;
+      typedef Kokkos::Experimental::Impl::ViewMapping< traits , SrcTraits , void >  Mapping ;
+      static_assert( Mapping::is_assignable , "Incompatible View copy assignment" );
+      Mapping::assign( m_map , rhs.m_map , rhs.m_track );
+      m_track.assign( rhs.m_track , traits::is_managed );
+      return *this ;
+    }
+
+  //----------------------------------------
+  // Compatible subview constructor
+  // may assign unmanaged from managed.
+
+  template< class RT , class ... RP , class Arg0 , class ... Args >
+  KOKKOS_INLINE_FUNCTION
+  View( const View< RT , RP... > & src_view
+      , const Arg0 & arg0 , Args ... args )
+    : m_track( src_view.m_track , traits::is_managed )
+    , m_map()
+    {
+      typedef View< RT , RP... > SrcType ;
+
+      typedef Kokkos::Experimental::Impl::ViewMapping
+        < void /* deduce destination view type from source view traits */
+        , typename SrcType::traits
+        , Arg0 , Args... > Mapping ;
+
+      typedef typename Mapping::type DstType ;
+
+      static_assert( Kokkos::Experimental::Impl::ViewMapping< traits , typename DstType::traits , void >::is_assignable
+        , "Subview construction requires compatible view and subview arguments" );
+
+      Mapping::assign( m_map, src_view.m_map, arg0 , args... );
+    }
+
+  //----------------------------------------
+  // Allocation tracking properties
+
+  KOKKOS_INLINE_FUNCTION
+  int use_count() const
+    { return m_track.use_count(); }
+
+  inline
+  const std::string label() const
+    { return m_track.template get_label< typename traits::memory_space >(); }
+
+  //----------------------------------------
+  // Allocation according to allocation properties and array layout
+
+  template< class ... P >
+  explicit inline
+  View( const Impl::ViewCtorProp< P ... > & arg_prop
+      , typename std::enable_if< ! Impl::ViewCtorProp< P... >::has_pointer
+                               , typename traits::array_layout
+                               >::type const & arg_layout
+      )
+    : m_track()
+    , m_map()
+    {
+      // Append layout and spaces if not input
+      typedef Impl::ViewCtorProp< P ... > alloc_prop_input ;
+
+      // use 'std::integral_constant<unsigned,I>' for non-types
+      // to avoid duplicate class error.
+      typedef Impl::ViewCtorProp
+        < P ...
+        , typename std::conditional
+            < alloc_prop_input::has_label
+            , std::integral_constant<unsigned,0>
+            , typename std::string
+            >::type
+        , typename std::conditional
+            < alloc_prop_input::has_memory_space
+            , std::integral_constant<unsigned,1>
+            , typename traits::device_type::memory_space
+            >::type
+        , typename std::conditional
+            < alloc_prop_input::has_execution_space
+            , std::integral_constant<unsigned,2>
+            , typename traits::device_type::execution_space
+            >::type
+        > alloc_prop ;
+
+      static_assert( traits::is_managed
+                   , "View allocation constructor requires managed memory" );
+
+      if ( alloc_prop::initialize &&
+           ! alloc_prop::execution_space::is_initialized() ) {
+        // If initializing view data then
+        // the execution space must be initialized.
+        Kokkos::Impl::throw_runtime_exception("Constructing View and initializing data with uninitialized execution space");
+      }
+
+      // Copy the input allocation properties with possibly defaulted properties
+      alloc_prop prop( arg_prop );
+
+//------------------------------------------------------------
+#if defined( KOKKOS_HAVE_CUDA )
+      // If allocating in CudaUVMSpace must fence before and after
+      // the allocation to protect against possible concurrent access
+      // on the CPU and the GPU.
+      // Fence using the trait's executon space (which will be Kokkos::Cuda)
+      // to avoid incomplete type errors from usng Kokkos::Cuda directly.
+      if ( std::is_same< Kokkos::CudaUVMSpace , typename traits::device_type::memory_space >::value ) {
+        traits::device_type::memory_space::execution_space::fence();
+      }
+#endif
+//------------------------------------------------------------
+
+      Kokkos::Experimental::Impl::SharedAllocationRecord<> *
+        record = m_map.allocate_shared( prop , arg_layout );
+
+//------------------------------------------------------------
+#if defined( KOKKOS_HAVE_CUDA )
+      if ( std::is_same< Kokkos::CudaUVMSpace , typename traits::device_type::memory_space >::value ) {
+        traits::device_type::memory_space::execution_space::fence();
+      }
+#endif
+//------------------------------------------------------------
+
+      // Setup and initialization complete, start tracking
+      m_track.assign_allocated_record_to_uninitialized( record );
+    }
+
+  // Wrap memory according to properties and array layout
+  template< class ... P >
+  explicit KOKKOS_INLINE_FUNCTION
+  View( const Impl::ViewCtorProp< P ... > & arg_prop
+      , typename std::enable_if< Impl::ViewCtorProp< P... >::has_pointer
+                               , typename traits::array_layout
+                               >::type const & arg_layout
+      )
+    : m_track() // No memory tracking
+    , m_map( arg_prop , arg_layout )
+    {
+      static_assert(
+        std::is_same< pointer_type
+                    , typename Impl::ViewCtorProp< P... >::pointer_type
+                    >::value ,
+        "Constructing View to wrap user memory must supply matching pointer type" );
+    }
+
+  // Simple dimension-only layout
+  template< class ... P >
+  explicit inline
+  View( const Impl::ViewCtorProp< P ... > & arg_prop
+      , typename std::enable_if< ! Impl::ViewCtorProp< P... >::has_pointer
+                               , size_t
+                               >::type const arg_N0 = 0
+      , const size_t arg_N1 = 0
+      , const size_t arg_N2 = 0
+      , const size_t arg_N3 = 0
+      , const size_t arg_N4 = 0
+      , const size_t arg_N5 = 0
+      , const size_t arg_N6 = 0
+      , const size_t arg_N7 = 0
+      )
+    : View( arg_prop
+          , typename traits::array_layout
+              ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+              , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
+          )
+    {}
+
+  template< class ... P >
+  explicit KOKKOS_INLINE_FUNCTION
+  View( const Impl::ViewCtorProp< P ... > & arg_prop
+      , typename std::enable_if< Impl::ViewCtorProp< P... >::has_pointer
+                               , size_t
+                               >::type const arg_N0 = 0
+      , const size_t arg_N1 = 0
+      , const size_t arg_N2 = 0
+      , const size_t arg_N3 = 0
+      , const size_t arg_N4 = 0
+      , const size_t arg_N5 = 0
+      , const size_t arg_N6 = 0
+      , const size_t arg_N7 = 0
+      )
+    : View( arg_prop
+          , typename traits::array_layout
+              ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+              , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
+          )
+    {}
+
+  // Allocate with label and layout
+  template< typename Label >
+  explicit inline
+  View( const Label & arg_label
+      , typename std::enable_if<
+          Kokkos::Experimental::Impl::is_view_label<Label>::value ,
+          typename traits::array_layout >::type const & arg_layout
+      )
+    : View( Impl::ViewCtorProp< std::string >( arg_label ) , arg_layout )
+    {}
+
+  // Allocate label and layout, must disambiguate from subview constructor.
+  template< typename Label >
+  explicit inline
+  View( const Label & arg_label
+      , typename std::enable_if<
+          Kokkos::Experimental::Impl::is_view_label<Label>::value ,
+        const size_t >::type arg_N0 = 0
+      , const size_t arg_N1 = 0
+      , const size_t arg_N2 = 0
+      , const size_t arg_N3 = 0
+      , const size_t arg_N4 = 0
+      , const size_t arg_N5 = 0
+      , const size_t arg_N6 = 0
+      , const size_t arg_N7 = 0
+      )
+    : View( Impl::ViewCtorProp< std::string >( arg_label )
+          , typename traits::array_layout
+              ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+              , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
+          )
+    {}
+
+  // For backward compatibility
+  explicit inline
+  View( const ViewAllocateWithoutInitializing & arg_prop
+      , const typename traits::array_layout & arg_layout
+      )
+    : View( Impl::ViewCtorProp< std::string , Kokkos::Experimental::Impl::WithoutInitializing_t >( arg_prop.label , Kokkos::Experimental::WithoutInitializing )
+          , arg_layout
+          )
+    {}
+
+  explicit inline
+  View( const ViewAllocateWithoutInitializing & arg_prop
+      , const size_t arg_N0 = 0
+      , const size_t arg_N1 = 0
+      , const size_t arg_N2 = 0
+      , const size_t arg_N3 = 0
+      , const size_t arg_N4 = 0
+      , const size_t arg_N5 = 0
+      , const size_t arg_N6 = 0
+      , const size_t arg_N7 = 0
+      )
+    : View( Impl::ViewCtorProp< std::string , Kokkos::Experimental::Impl::WithoutInitializing_t >( arg_prop.label , Kokkos::Experimental::WithoutInitializing )
+          , typename traits::array_layout
+              ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+              , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
+          )
+    {}
+
+  //----------------------------------------
+  // Memory span required to wrap these dimensions.
+  static constexpr size_t required_allocation_size(
+                                       const size_t arg_N0 = 0
+                                     , const size_t arg_N1 = 0
+                                     , const size_t arg_N2 = 0
+                                     , const size_t arg_N3 = 0
+                                     , const size_t arg_N4 = 0
+                                     , const size_t arg_N5 = 0
+                                     , const size_t arg_N6 = 0
+                                     , const size_t arg_N7 = 0
+                                     )
+    {
+      return map_type::memory_span(
+        typename traits::array_layout
+          ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+          , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) );
+    }
+
+  explicit KOKKOS_INLINE_FUNCTION
+  View( pointer_type arg_ptr
+      , const size_t arg_N0 = 0
+      , const size_t arg_N1 = 0
+      , const size_t arg_N2 = 0
+      , const size_t arg_N3 = 0
+      , const size_t arg_N4 = 0
+      , const size_t arg_N5 = 0
+      , const size_t arg_N6 = 0
+      , const size_t arg_N7 = 0
+      )
+    : View( Impl::ViewCtorProp<pointer_type>(arg_ptr)
+          , typename traits::array_layout
+             ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+             , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
+          )
+    {}
+
+  explicit KOKKOS_INLINE_FUNCTION
+  View( pointer_type arg_ptr
+      , const typename traits::array_layout & arg_layout
+      )
+    : View( Impl::ViewCtorProp<pointer_type>(arg_ptr) , arg_layout )
+    {}
+
+  //----------------------------------------
+  // Shared scratch memory constructor
+
+  static inline
+  size_t shmem_size( const size_t arg_N0 = ~size_t(0) ,
+                     const size_t arg_N1 = ~size_t(0) ,
+                     const size_t arg_N2 = ~size_t(0) ,
+                     const size_t arg_N3 = ~size_t(0) ,
+                     const size_t arg_N4 = ~size_t(0) ,
+                     const size_t arg_N5 = ~size_t(0) ,
+                     const size_t arg_N6 = ~size_t(0) ,
+                     const size_t arg_N7 = ~size_t(0) )
+  {
+    const size_t num_passed_args =
+      ( arg_N0 != ~size_t(0) ) + ( arg_N1 != ~size_t(0) ) + ( arg_N2 != ~size_t(0) ) +
+      ( arg_N3 != ~size_t(0) ) + ( arg_N4 != ~size_t(0) ) + ( arg_N5 != ~size_t(0) ) +
+      ( arg_N6 != ~size_t(0) ) + ( arg_N7 != ~size_t(0) );
+
+    if ( std::is_same<typename traits::specialize,void>::value && num_passed_args != traits::rank_dynamic ) {
+      Kokkos::abort( "Kokkos::View::shmem_size() rank_dynamic != number of arguments.\n" );
+    }
+
+    return map_type::memory_span(
+           typename traits::array_layout
+            ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+            , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) );
+  }
+
+  explicit KOKKOS_INLINE_FUNCTION
+  View( const typename traits::execution_space::scratch_memory_space & arg_space
+      , const typename traits::array_layout & arg_layout )
+    : View( Impl::ViewCtorProp<pointer_type>(
+              reinterpret_cast<pointer_type>(
+                arg_space.get_shmem( map_type::memory_span( arg_layout ) ) ) )
+         , arg_layout )
+    {}
+
+  explicit KOKKOS_INLINE_FUNCTION
+  View( const typename traits::execution_space::scratch_memory_space & arg_space
+      , const size_t arg_N0 = 0
+      , const size_t arg_N1 = 0
+      , const size_t arg_N2 = 0
+      , const size_t arg_N3 = 0
+      , const size_t arg_N4 = 0
+      , const size_t arg_N5 = 0
+      , const size_t arg_N6 = 0
+      , const size_t arg_N7 = 0 )
+    : View( Impl::ViewCtorProp<pointer_type>(
+              reinterpret_cast<pointer_type>(
+                arg_space.get_shmem(
+                  map_type::memory_span(
+                    typename traits::array_layout
+                     ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+                     , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) ) ) ) )
+          , typename traits::array_layout
+             ( arg_N0 , arg_N1 , arg_N2 , arg_N3
+             , arg_N4 , arg_N5 , arg_N6 , arg_N7 )
+       )
+    {}
 };
 
-} /* namespace Kokkos */
+
+ /** \brief Temporary free function rank()
+  *         until rank() is implemented
+  *         in the View
+  */
+  template < typename D , class ... P >
+  KOKKOS_INLINE_FUNCTION
+  constexpr unsigned rank( const View<D , P...> & V ) { return V.Rank; } //Temporary until added to view
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
-namespace Kokkos {
+template< class V , class ... Args >
+using Subview =
+  typename Kokkos::Experimental::Impl::ViewMapping
+    < void /* deduce subview type from source view traits */
+    , typename V::traits
+    , Args ...
+    >::type ;
 
-template< class LT , class LL , class LD , class LM , class LS ,
-          class RT , class RL , class RD , class RM , class RS >
+template< class D, class ... P , class ... Args >
 KOKKOS_INLINE_FUNCTION
-typename Impl::enable_if<( Impl::is_same< LS , RS >::value ), bool >::type
-operator == ( const View<LT,LL,LD,LM,LS> & lhs ,
-              const View<RT,RL,RD,RM,RS> & rhs )
+typename Kokkos::Experimental::Impl::ViewMapping
+  < void /* deduce subview type from source view traits */
+  , ViewTraits< D , P... >
+  , Args ...
+  >::type
+subview( const View< D, P... > & src , Args ... args )
 {
-  // Same data, layout, dimensions
-  typedef ViewTraits<LT,LL,LD,LM> lhs_traits ;
-  typedef ViewTraits<RT,RL,RD,RM> rhs_traits ;
-
-  return
-    Impl::is_same< typename lhs_traits::const_data_type ,
-                   typename rhs_traits::const_data_type >::value &&
-    Impl::is_same< typename lhs_traits::array_layout ,
-                   typename rhs_traits::array_layout >::value &&
-    Impl::is_same< typename lhs_traits::memory_space ,
-                   typename rhs_traits::memory_space >::value &&
-    Impl::is_same< typename lhs_traits::specialize ,
-                   typename rhs_traits::specialize >::value &&
-    lhs.ptr_on_device() == rhs.ptr_on_device() &&
-    lhs.shape()         == rhs.shape() ;
+  static_assert( View< D , P... >::Rank == sizeof...(Args) ,
+    "subview requires one argument for each source View rank" );
+
+  return typename
+    Kokkos::Experimental::Impl::ViewMapping
+      < void /* deduce subview type from source view traits */
+      , ViewTraits< D , P ... >
+      , Args ... >::type( src , args ... );
 }
 
-template< class LT , class LL , class LD , class LM , class LS ,
-          class RT , class RL , class RD , class RM , class RS >
+template< class MemoryTraits , class D, class ... P , class ... Args >
 KOKKOS_INLINE_FUNCTION
-bool operator != ( const View<LT,LL,LD,LM,LS> & lhs ,
-                   const View<RT,RL,RD,RM,RS> & rhs )
+typename Kokkos::Experimental::Impl::ViewMapping
+  < void /* deduce subview type from source view traits */
+  , ViewTraits< D , P... >
+  , Args ...
+  >::template apply< MemoryTraits >::type
+subview( const View< D, P... > & src , Args ... args )
 {
-  return ! operator==( lhs , rhs );
+  static_assert( View< D , P... >::Rank == sizeof...(Args) ,
+    "subview requires one argument for each source View rank" );
+
+  return typename
+    Kokkos::Experimental::Impl::ViewMapping
+      < void /* deduce subview type from source view traits */
+      , ViewTraits< D , P ... >
+      , Args ... >
+      ::template apply< MemoryTraits >
+      ::type( src , args ... );
 }
 
-//----------------------------------------------------------------------------
 
 
-} // namespace Kokkos
+} /* namespace Experimental */
+} /* namespace Kokkos */
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
+namespace Experimental {
 
-//----------------------------------------------------------------------------
-/** \brief  Deep copy a value into a view.
- */
-template< class DT , class DL , class DD , class DM , class DS >
-inline
-void deep_copy( const View<DT,DL,DD,DM,DS> & dst ,
-                typename Impl::enable_if<(
-                  Impl::is_same< typename ViewTraits<DT,DL,DD,DM>::non_const_value_type ,
-                                 typename ViewTraits<DT,DL,DD,DM>::value_type >::value
-                ), typename ViewTraits<DT,DL,DD,DM>::const_value_type >::type & value )
+template< class LT , class ... LP , class RT , class ... RP >
+KOKKOS_INLINE_FUNCTION
+bool operator == ( const View<LT,LP...> & lhs ,
+                   const View<RT,RP...> & rhs )
 {
-  Impl::ViewFill< View<DT,DL,DD,DM,DS> >( dst , value );
+  // Same data, layout, dimensions
+  typedef ViewTraits<LT,LP...>  lhs_traits ;
+  typedef ViewTraits<RT,RP...>  rhs_traits ;
+
+  return
+    std::is_same< typename lhs_traits::const_value_type ,
+                  typename rhs_traits::const_value_type >::value &&
+    std::is_same< typename lhs_traits::array_layout ,
+                  typename rhs_traits::array_layout >::value &&
+    std::is_same< typename lhs_traits::memory_space ,
+                  typename rhs_traits::memory_space >::value &&
+    unsigned(lhs_traits::rank) == unsigned(rhs_traits::rank) &&
+    lhs.data()        == rhs.data() &&
+    lhs.span()        == rhs.span() &&
+    lhs.dimension_0() == rhs.dimension_0() &&
+    lhs.dimension_1() == rhs.dimension_1() &&
+    lhs.dimension_2() == rhs.dimension_2() &&
+    lhs.dimension_3() == rhs.dimension_3() &&
+    lhs.dimension_4() == rhs.dimension_4() &&
+    lhs.dimension_5() == rhs.dimension_5() &&
+    lhs.dimension_6() == rhs.dimension_6() &&
+    lhs.dimension_7() == rhs.dimension_7();
 }
 
-template< class ST , class SL , class SD , class SM , class SS >
-inline
-typename Impl::enable_if<( ViewTraits<ST,SL,SD,SM>::rank == 0 )>::type
-deep_copy( ST & dst , const View<ST,SL,SD,SM,SS> & src )
+template< class LT , class ... LP , class RT , class ... RP >
+KOKKOS_INLINE_FUNCTION
+bool operator != ( const View<LT,LP...> & lhs ,
+                   const View<RT,RP...> & rhs )
 {
-  typedef  ViewTraits<ST,SL,SD,SM>  src_traits ;
-  typedef typename src_traits::memory_space  src_memory_space ;
-  Impl::DeepCopy< HostSpace , src_memory_space >( & dst , src.ptr_on_device() , sizeof(ST) );
+  return ! ( operator==(lhs,rhs) );
 }
 
+} /* namespace Experimental */
+} /* namespace Kokkos */
+
+//----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
-/** \brief  A deep copy between views of compatible type, and rank zero.
- */
-template< class DT , class DL , class DD , class DM , class DS ,
-          class ST , class SL , class SD , class SM , class SS >
-inline
-void deep_copy( const View<DT,DL,DD,DM,DS> & dst ,
-                const View<ST,SL,SD,SM,SS> & src ,
-                typename Impl::enable_if<(
-                  // Same type and destination is not constant:
-                  Impl::is_same< typename View<DT,DL,DD,DM,DS>::value_type ,
-                                 typename View<ST,SL,SD,SM,SS>::non_const_value_type >::value
-                  &&
-                  // Rank zero:
-                  ( unsigned(View<DT,DL,DD,DM,DS>::rank) == unsigned(0) ) &&
-                  ( unsigned(View<ST,SL,SD,SM,SS>::rank) == unsigned(0) )
-                )>::type * = 0 )
-{
-  typedef  View<DT,DL,DD,DM,DS>  dst_type ;
-  typedef  View<ST,SL,SD,SM,SS>  src_type ;
 
-  typedef typename dst_type::memory_space  dst_memory_space ;
-  typedef typename src_type::memory_space  src_memory_space ;
-  typedef typename src_type::value_type    value_type ;
+namespace Kokkos {
+namespace Impl {
 
-  if ( dst.ptr_on_device() != src.ptr_on_device() ) {
-    Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.ptr_on_device() , src.ptr_on_device() , sizeof(value_type) );
-  }
-}
+inline
+void shared_allocation_tracking_claim_and_disable()
+{ Kokkos::Experimental::Impl::SharedAllocationRecord<void,void>::tracking_claim_and_disable(); }
 
-//----------------------------------------------------------------------------
-/** \brief  A deep copy between views of the default specialization, compatible type,
- *          same non-zero rank, same contiguous layout.
- */
-template< class DT , class DL , class DD , class DM ,
-          class ST , class SL , class SD , class SM >
 inline
-void deep_copy( const View<DT,DL,DD,DM,Impl::ViewDefault> & dst ,
-                const View<ST,SL,SD,SM,Impl::ViewDefault> & src ,
-                typename Impl::enable_if<(
-                  // Same type and destination is not constant:
-                  Impl::is_same< typename View<DT,DL,DD,DM,Impl::ViewDefault>::value_type ,
-                                 typename View<ST,SL,SD,SM,Impl::ViewDefault>::non_const_value_type >::value
-                  &&
-                  // Same non-zero rank:
-                  ( unsigned(View<DT,DL,DD,DM,Impl::ViewDefault>::rank) ==
-                    unsigned(View<ST,SL,SD,SM,Impl::ViewDefault>::rank) )
-                  &&
-                  ( 0 < unsigned(View<DT,DL,DD,DM,Impl::ViewDefault>::rank) )
-                  &&
-                  // Same layout:
-                  Impl::is_same< typename View<DT,DL,DD,DM,Impl::ViewDefault>::array_layout ,
-                                 typename View<ST,SL,SD,SM,Impl::ViewDefault>::array_layout >::value
-                )>::type * = 0 )
-{
-  typedef  View<DT,DL,DD,DM,Impl::ViewDefault>  dst_type ;
-  typedef  View<ST,SL,SD,SM,Impl::ViewDefault>  src_type ;
+void shared_allocation_tracking_release_and_enable()
+{ Kokkos::Experimental::Impl::SharedAllocationRecord<void,void>::tracking_release_and_enable(); }
 
-  typedef typename dst_type::memory_space  dst_memory_space ;
-  typedef typename src_type::memory_space  src_memory_space ;
+} /* namespace Impl */
+} /* namespace Kokkos */
 
-  enum { is_contiguous = // Contiguous (e.g., non-strided, non-tiled) layout
-           Impl::is_same< typename View<DT,DL,DD,DM,Impl::ViewDefault>::array_layout , LayoutLeft >::value ||
-           Impl::is_same< typename View<DT,DL,DD,DM,Impl::ViewDefault>::array_layout , LayoutRight >::value };
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
 
-  if ( dst.ptr_on_device() != src.ptr_on_device() ) {
+namespace Kokkos {
+namespace Experimental {
+namespace Impl {
 
-    // Same shape (dimensions)
+template< class OutputView , typename Enable = void >
+struct ViewFill {
 
-    const bool shapes_are_equal = dst.shape() == src.shape();
+  typedef typename OutputView::const_value_type  const_value_type ;
 
-    if ( shapes_are_equal && is_contiguous && dst.capacity() == src.capacity() ) {
+  const OutputView output ;
+  const_value_type input ;
 
-      // Views span equal length contiguous range.
-      // Assuming can perform a straight memory copy over this range.
+  KOKKOS_INLINE_FUNCTION
+  void operator()( const size_t i0 ) const
+  {
+    const size_t n1 = output.dimension_1();
+    const size_t n2 = output.dimension_2();
+    const size_t n3 = output.dimension_3();
+    const size_t n4 = output.dimension_4();
+    const size_t n5 = output.dimension_5();
+    const size_t n6 = output.dimension_6();
+    const size_t n7 = output.dimension_7();
+
+    for ( size_t i1 = 0 ; i1 < n1 ; ++i1 ) {
+    for ( size_t i2 = 0 ; i2 < n2 ; ++i2 ) {
+    for ( size_t i3 = 0 ; i3 < n3 ; ++i3 ) {
+    for ( size_t i4 = 0 ; i4 < n4 ; ++i4 ) {
+    for ( size_t i5 = 0 ; i5 < n5 ; ++i5 ) {
+    for ( size_t i6 = 0 ; i6 < n6 ; ++i6 ) {
+    for ( size_t i7 = 0 ; i7 < n7 ; ++i7 ) {
+      output(i0,i1,i2,i3,i4,i5,i6,i7) = input ;
+    }}}}}}}
+  }
 
-      const size_t nbytes = sizeof(typename dst_type::value_type) * dst.capacity();
+  ViewFill( const OutputView & arg_out , const_value_type & arg_in )
+    : output( arg_out ), input( arg_in )
+    {
+      typedef typename OutputView::execution_space  execution_space ;
+      typedef Kokkos::RangePolicy< execution_space > Policy ;
 
-      Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.ptr_on_device() , src.ptr_on_device() , nbytes );
-    }
-    else {
-      // Destination view's execution space must be able to directly access source memory space
-      // in order for the ViewRemap functor run in the destination memory space's execution space.
-      size_t stride[8];
-      src.stride(stride);
-      size_t size_stride = stride[0]*src.dimension_0();
-      size_t size_dim = src.dimension_0();
-      for(int i = 1; i<src.rank; i++) {
-        if(stride[i]*src.dimension(i)>size_stride)
-          size_stride = stride[i]*src.dimension(i);
-        size_dim*=src.dimension(i);
-      }
+      const Kokkos::Impl::ParallelFor< ViewFill , Policy > closure( *this , Policy( 0 , output.dimension_0() ) );
 
-      if( shapes_are_equal && size_stride == size_dim) {
-        const size_t nbytes = sizeof(typename dst_type::value_type) * dst.capacity();
+      closure.execute();
 
-        Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.ptr_on_device() , src.ptr_on_device() , nbytes );
-      } else {
-        Impl::ViewRemap< dst_type , src_type >( dst , src );
-      }
+      execution_space::fence();
     }
-  }
-}
-
+};
 
-/** \brief Deep copy equal dimension arrays in the same space which
- *         have different layouts or specializations.
- */
-template< class DT , class DL , class DD , class DM , class DS ,
-          class ST , class SL , class SD , class SM , class SS >
-inline
-void deep_copy( const View< DT, DL, DD, DM, DS > & dst ,
-                const View< ST, SL, SD, SM, SS > & src ,
-                const typename Impl::enable_if<(
-                  // Same type and destination is not constant:
-                  Impl::is_same< typename View<DT,DL,DD,DM,DS>::value_type ,
-                                 typename View<DT,DL,DD,DM,DS>::non_const_value_type >::value
-                  &&
-                  // Source memory space is accessible to destination memory space
-                  Impl::VerifyExecutionCanAccessMemorySpace< typename View<DT,DL,DD,DM,DS>::memory_space
-                                                           , typename View<ST,SL,SD,SM,SS>::memory_space >::value
-                  &&
-                  // Same non-zero rank
-                  ( unsigned( View<DT,DL,DD,DM,DS>::rank ) ==
-                    unsigned( View<ST,SL,SD,SM,SS>::rank ) )
-                  &&
-                  ( 0 < unsigned( View<DT,DL,DD,DM,DS>::rank ) )
-                  &&
-                  // Different layout or different specialization:
-                  ( ( ! Impl::is_same< typename View<DT,DL,DD,DM,DS>::array_layout ,
-                                       typename View<ST,SL,SD,SM,SS>::array_layout >::value )
-                    ||
-                    ( ! Impl::is_same< DS , SS >::value )
-                  )
-                )>::type * = 0 )
-{
-  typedef View< DT, DL, DD, DM, DS > dst_type ;
-  typedef View< ST, SL, SD, SM, SS > src_type ;
+template< class OutputView >
+struct ViewFill< OutputView , typename std::enable_if< OutputView::Rank == 0 >::type > {
+  ViewFill( const OutputView & dst , const typename OutputView::const_value_type & src )
+    {
+      Kokkos::Impl::DeepCopy< typename OutputView::memory_space , Kokkos::HostSpace >
+        ( dst.data() , & src , sizeof(typename OutputView::const_value_type) );
+    }
+};
 
-  assert_shapes_equal_dimension( dst.shape() , src.shape() );
+template< class OutputView , class InputView , class ExecSpace = typename OutputView::execution_space >
+struct ViewRemap {
+
+  const OutputView output ;
+  const InputView  input ;
+  const size_t n0 ;
+  const size_t n1 ;
+  const size_t n2 ;
+  const size_t n3 ;
+  const size_t n4 ;
+  const size_t n5 ;
+  const size_t n6 ;
+  const size_t n7 ;
+
+  ViewRemap( const OutputView & arg_out , const InputView & arg_in )
+    : output( arg_out ), input( arg_in )
+    , n0( std::min( (size_t)arg_out.dimension_0() , (size_t)arg_in.dimension_0() ) )
+    , n1( std::min( (size_t)arg_out.dimension_1() , (size_t)arg_in.dimension_1() ) )
+    , n2( std::min( (size_t)arg_out.dimension_2() , (size_t)arg_in.dimension_2() ) )
+    , n3( std::min( (size_t)arg_out.dimension_3() , (size_t)arg_in.dimension_3() ) )
+    , n4( std::min( (size_t)arg_out.dimension_4() , (size_t)arg_in.dimension_4() ) )
+    , n5( std::min( (size_t)arg_out.dimension_5() , (size_t)arg_in.dimension_5() ) )
+    , n6( std::min( (size_t)arg_out.dimension_6() , (size_t)arg_in.dimension_6() ) )
+    , n7( std::min( (size_t)arg_out.dimension_7() , (size_t)arg_in.dimension_7() ) )
+    {
+      typedef Kokkos::RangePolicy< ExecSpace > Policy ;
+      const Kokkos::Impl::ParallelFor< ViewRemap , Policy > closure( *this , Policy( 0 , n0 ) );
+      closure.execute();
+    }
 
-  Impl::ViewRemap< dst_type , src_type >( dst , src );
-}
+  KOKKOS_INLINE_FUNCTION
+  void operator()( const size_t i0 ) const
+  {
+    for ( size_t i1 = 0 ; i1 < n1 ; ++i1 ) {
+    for ( size_t i2 = 0 ; i2 < n2 ; ++i2 ) {
+    for ( size_t i3 = 0 ; i3 < n3 ; ++i3 ) {
+    for ( size_t i4 = 0 ; i4 < n4 ; ++i4 ) {
+    for ( size_t i5 = 0 ; i5 < n5 ; ++i5 ) {
+    for ( size_t i6 = 0 ; i6 < n6 ; ++i6 ) {
+    for ( size_t i7 = 0 ; i7 < n7 ; ++i7 ) {
+      output(i0,i1,i2,i3,i4,i5,i6,i7) = input(i0,i1,i2,i3,i4,i5,i6,i7);
+    }}}}}}}
+  }
+};
 
-}
+} /* namespace Impl */
+} /* namespace Experimental */
+} /* namespace Kokkos */
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
+namespace Experimental {
 
-//----------------------------------------------------------------------------
-/** \brief  Deep copy a value into a view.
- */
-template< class ExecSpace, class DT , class DL , class DD , class DM , class DS >
+/** \brief  Deep copy a value from Host memory into a view.  */
+template< class DT , class ... DP >
 inline
-void deep_copy( const ExecSpace&, const View<DT,DL,DD,DM,DS> & dst ,
-                typename Impl::enable_if<(
-                  Impl::is_same< typename ViewTraits<DT,DL,DD,DM>::non_const_value_type ,
-                                 typename ViewTraits<DT,DL,DD,DM>::value_type >::value
-                ), typename ViewTraits<DT,DL,DD,DM>::const_value_type >::type & value )
+void deep_copy
+  ( const View<DT,DP...> & dst
+  , typename ViewTraits<DT,DP...>::const_value_type & value
+  , typename std::enable_if<
+    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value
+    >::type * = 0 )
 {
-  Impl::ViewFill< View<DT,DL,DD,DM,DS> >( dst , value );
+  static_assert(
+    std::is_same< typename ViewTraits<DT,DP...>::non_const_value_type ,
+                  typename ViewTraits<DT,DP...>::value_type >::value
+    , "deep_copy requires non-const type" );
+
+  Kokkos::Experimental::Impl::ViewFill< View<DT,DP...> >( dst , value );
 }
 
-template< class ExecSpace, class ST , class SL , class SD , class SM , class SS >
+/** \brief  Deep copy into a value in Host memory from a view.  */
+template< class ST , class ... SP >
 inline
-typename Impl::enable_if<( ViewTraits<ST,SL,SD,SM>::rank == 0 )>::type
-deep_copy( const ExecSpace& exec,  ST & dst , const View<ST,SL,SD,SM,SS> & src )
+void deep_copy
+  ( typename ViewTraits<ST,SP...>::non_const_value_type & dst
+  , const View<ST,SP...> & src
+  , typename std::enable_if<
+    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value
+    >::type * = 0 )
 {
-  typedef  ViewTraits<ST,SL,SD,SM>  src_traits ;
+  static_assert( ViewTraits<ST,SP...>::rank == 0
+               , "ERROR: Non-rank-zero view in deep_copy( value , View )" );
+
+  typedef ViewTraits<ST,SP...>               src_traits ;
   typedef typename src_traits::memory_space  src_memory_space ;
-  Impl::DeepCopy< HostSpace , src_memory_space , ExecSpace >( exec , & dst , src.ptr_on_device() , sizeof(ST) );
+  Kokkos::Impl::DeepCopy< HostSpace , src_memory_space >( & dst , src.data() , sizeof(ST) );
 }
 
 //----------------------------------------------------------------------------
-/** \brief  A deep copy between views of compatible type, and rank zero.
- */
-template< class ExecSpace ,
-          class DT , class DL , class DD , class DM , class DS ,
-          class ST , class SL , class SD , class SM , class SS >
+/** \brief  A deep copy between views of compatible type, and rank zero.  */
+template< class DT , class ... DP , class ST , class ... SP >
 inline
-void deep_copy( const ExecSpace& exec,
-                const View<DT,DL,DD,DM,DS> & dst ,
-                const View<ST,SL,SD,SM,SS> & src ,
-                typename Impl::enable_if<(
-                  // Same type and destination is not constant:
-                  Impl::is_same< typename View<DT,DL,DD,DM,DS>::value_type ,
-                                 typename View<ST,SL,SD,SM,SS>::non_const_value_type >::value
-                  &&
-                  // Rank zero:
-                  ( unsigned(View<DT,DL,DD,DM,DS>::rank) == unsigned(0) ) &&
-                  ( unsigned(View<ST,SL,SD,SM,SS>::rank) == unsigned(0) )
-                )>::type * = 0 )
+void deep_copy
+  ( const View<DT,DP...> & dst
+  , const View<ST,SP...> & src
+  , typename std::enable_if<(
+    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value &&
+    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value &&
+    ( unsigned(ViewTraits<DT,DP...>::rank) == unsigned(0) &&
+      unsigned(ViewTraits<ST,SP...>::rank) == unsigned(0) )
+  )>::type * = 0 )
 {
-  typedef  View<DT,DL,DD,DM,DS>  dst_type ;
-  typedef  View<ST,SL,SD,SM,SS>  src_type ;
+  static_assert(
+    std::is_same< typename ViewTraits<DT,DP...>::value_type ,
+                  typename ViewTraits<ST,SP...>::non_const_value_type >::value
+    , "deep_copy requires matching non-const destination type" );
+
+  typedef View<DT,DP...>  dst_type ;
+  typedef View<ST,SP...>  src_type ;
 
+  typedef typename dst_type::value_type    value_type ;
   typedef typename dst_type::memory_space  dst_memory_space ;
   typedef typename src_type::memory_space  src_memory_space ;
-  typedef typename src_type::value_type    value_type ;
 
-  if ( dst.ptr_on_device() != src.ptr_on_device() ) {
-    Impl::DeepCopy< dst_memory_space , src_memory_space , ExecSpace >( exec , dst.ptr_on_device() , src.ptr_on_device() , sizeof(value_type) );
+  if ( dst.data() != src.data() ) {
+    Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.data() , src.data() , sizeof(value_type) );
   }
 }
 
@@ -1632,172 +1799,395 @@ void deep_copy( const ExecSpace& exec,
 /** \brief  A deep copy between views of the default specialization, compatible type,
  *          same non-zero rank, same contiguous layout.
  */
-template< class ExecSpace ,
-          class DT , class DL , class DD , class DM ,
-          class ST , class SL , class SD , class SM >
+template< class DT , class ... DP , class ST , class ... SP >
 inline
-void deep_copy( const ExecSpace & exec,
-                const View<DT,DL,DD,DM,Impl::ViewDefault> & dst ,
-                const View<ST,SL,SD,SM,Impl::ViewDefault> & src ,
-                typename Impl::enable_if<(
-                  // Same type and destination is not constant:
-                  Impl::is_same< typename View<DT,DL,DD,DM,Impl::ViewDefault>::value_type ,
-                                 typename View<ST,SL,SD,SM,Impl::ViewDefault>::non_const_value_type >::value
-                  &&
-                  // Same non-zero rank:
-                  ( unsigned(View<DT,DL,DD,DM,Impl::ViewDefault>::rank) ==
-                    unsigned(View<ST,SL,SD,SM,Impl::ViewDefault>::rank) )
-                  &&
-                  ( 0 < unsigned(View<DT,DL,DD,DM,Impl::ViewDefault>::rank) )
-                  &&
-                  // Same layout:
-                  Impl::is_same< typename View<DT,DL,DD,DM,Impl::ViewDefault>::array_layout ,
-                                 typename View<ST,SL,SD,SM,Impl::ViewDefault>::array_layout >::value
-                )>::type * = 0 )
+void deep_copy
+  ( const View<DT,DP...> & dst
+  , const View<ST,SP...> & src
+  , typename std::enable_if<(
+    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value &&
+    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value &&
+    ( unsigned(ViewTraits<DT,DP...>::rank) != 0 ||
+      unsigned(ViewTraits<ST,SP...>::rank) != 0 )
+  )>::type * = 0 )
 {
-  typedef  View<DT,DL,DD,DM,Impl::ViewDefault>  dst_type ;
-  typedef  View<ST,SL,SD,SM,Impl::ViewDefault>  src_type ;
+  static_assert(
+    std::is_same< typename ViewTraits<DT,DP...>::value_type ,
+                  typename ViewTraits<DT,DP...>::non_const_value_type >::value
+    , "deep_copy requires non-const destination type" );
+
+  static_assert(
+    ( unsigned(ViewTraits<DT,DP...>::rank) ==
+      unsigned(ViewTraits<ST,SP...>::rank) )
+    , "deep_copy requires Views of equal rank" );
+
+  typedef View<DT,DP...>  dst_type ;
+  typedef View<ST,SP...>  src_type ;
+
+  typedef typename dst_type::execution_space  dst_execution_space ;
+  typedef typename src_type::execution_space  src_execution_space ;
+  typedef typename dst_type::memory_space     dst_memory_space ;
+  typedef typename src_type::memory_space     src_memory_space ;
+
+  enum { DstExecCanAccessSrc =
+   Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< typename dst_execution_space::memory_space , src_memory_space >::value };
+
+  enum { SrcExecCanAccessDst =
+   Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< typename src_execution_space::memory_space , dst_memory_space >::value };
+
+
+  if ( (void *) dst.data() != (void*) src.data() ) {
+
+    // Concern: If overlapping views then a parallel copy will be erroneous.
+    // ...
+
+    // If same type, equal layout, equal dimensions, equal span, and contiguous memory then can byte-wise copy
+
+    if ( std::is_same< typename ViewTraits<DT,DP...>::value_type ,
+                       typename ViewTraits<ST,SP...>::non_const_value_type >::value &&
+         (
+           ( std::is_same< typename ViewTraits<DT,DP...>::array_layout ,
+                           typename ViewTraits<ST,SP...>::array_layout >::value
+             &&
+             ( std::is_same< typename ViewTraits<DT,DP...>::array_layout ,
+                             typename Kokkos::LayoutLeft>::value
+             ||
+               std::is_same< typename ViewTraits<DT,DP...>::array_layout ,
+                             typename Kokkos::LayoutRight>::value
+             )
+           )
+           ||
+           ( ViewTraits<DT,DP...>::rank == 1 &&
+             ViewTraits<ST,SP...>::rank == 1 )
+         ) &&
+         dst.span_is_contiguous() &&
+         src.span_is_contiguous() &&
+         dst.span() == src.span() &&
+         dst.dimension_0() == src.dimension_0() &&
+         dst.dimension_1() == src.dimension_1() &&
+         dst.dimension_2() == src.dimension_2() &&
+         dst.dimension_3() == src.dimension_3() &&
+         dst.dimension_4() == src.dimension_4() &&
+         dst.dimension_5() == src.dimension_5() &&
+         dst.dimension_6() == src.dimension_6() &&
+         dst.dimension_7() == src.dimension_7() ) {
+
+      const size_t nbytes = sizeof(typename dst_type::value_type) * dst.span();
+
+      Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.data() , src.data() , nbytes );
+    }
+    else if ( std::is_same< typename ViewTraits<DT,DP...>::value_type ,
+                            typename ViewTraits<ST,SP...>::non_const_value_type >::value &&
+         (
+           ( std::is_same< typename ViewTraits<DT,DP...>::array_layout ,
+                           typename ViewTraits<ST,SP...>::array_layout >::value
+             &&
+             std::is_same< typename ViewTraits<DT,DP...>::array_layout ,
+                          typename Kokkos::LayoutStride>::value
+           )
+           ||
+           ( ViewTraits<DT,DP...>::rank == 1 &&
+             ViewTraits<ST,SP...>::rank == 1 )
+         ) &&
+         dst.span_is_contiguous() &&
+         src.span_is_contiguous() &&
+         dst.span() == src.span() &&
+         dst.dimension_0() == src.dimension_0() &&
+         dst.dimension_1() == src.dimension_1() &&
+         dst.dimension_2() == src.dimension_2() &&
+         dst.dimension_3() == src.dimension_3() &&
+         dst.dimension_4() == src.dimension_4() &&
+         dst.dimension_5() == src.dimension_5() &&
+         dst.dimension_6() == src.dimension_6() &&
+         dst.dimension_7() == src.dimension_7() &&
+         dst.stride_0() == src.stride_0() &&
+         dst.stride_1() == src.stride_1() &&
+         dst.stride_2() == src.stride_2() &&
+         dst.stride_3() == src.stride_3() &&
+         dst.stride_4() == src.stride_4() &&
+         dst.stride_5() == src.stride_5() &&
+         dst.stride_6() == src.stride_6() &&
+         dst.stride_7() == src.stride_7()
+         ) {
+
+      const size_t nbytes = sizeof(typename dst_type::value_type) * dst.span();
+
+      Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space >( dst.data() , src.data() , nbytes );
+    }
+    else if ( DstExecCanAccessSrc ) {
+      // Copying data between views in accessible memory spaces and either non-contiguous or incompatible shape.
+      Kokkos::Experimental::Impl::ViewRemap< dst_type , src_type >( dst , src );
+    }
+    else if ( SrcExecCanAccessDst ) {
+      // Copying data between views in accessible memory spaces and either non-contiguous or incompatible shape.
+      Kokkos::Experimental::Impl::ViewRemap< dst_type , src_type , src_execution_space >( dst , src );
+    }
+    else {
+      Kokkos::Impl::throw_runtime_exception("deep_copy given views that would require a temporary allocation");
+    }
+  }
+}
 
-  typedef typename dst_type::memory_space  dst_memory_space ;
-  typedef typename src_type::memory_space  src_memory_space ;
+} /* namespace Experimental */
+} /* namespace Kokkos */
 
-  enum { is_contiguous = // Contiguous (e.g., non-strided, non-tiled) layout
-           Impl::is_same< typename View<DT,DL,DD,DM,Impl::ViewDefault>::array_layout , LayoutLeft >::value ||
-           Impl::is_same< typename View<DT,DL,DD,DM,Impl::ViewDefault>::array_layout , LayoutRight >::value };
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
 
-  if ( dst.ptr_on_device() != src.ptr_on_device() ) {
+namespace Kokkos {
+namespace Experimental {
 
-    // Same shape (dimensions)
+/** \brief  Deep copy a value from Host memory into a view.  */
+template< class ExecSpace ,class DT , class ... DP >
+inline
+void deep_copy
+  ( const ExecSpace &
+  , const View<DT,DP...> & dst
+  , typename ViewTraits<DT,DP...>::const_value_type & value
+  , typename std::enable_if<
+    Kokkos::Impl::is_execution_space< ExecSpace >::value &&
+    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value
+    >::type * = 0 )
+{
+  static_assert(
+    std::is_same< typename ViewTraits<DT,DP...>::non_const_value_type ,
+                  typename ViewTraits<DT,DP...>::value_type >::value
+    , "deep_copy requires non-const type" );
 
-    const bool shapes_are_equal = dst.shape() == src.shape();
+  Kokkos::Experimental::Impl::ViewFill< View<DT,DP...> >( dst , value );
+}
 
-    if ( shapes_are_equal && is_contiguous && dst.capacity() == src.capacity() ) {
+/** \brief  Deep copy into a value in Host memory from a view.  */
+template< class ExecSpace , class ST , class ... SP >
+inline
+void deep_copy
+  ( const ExecSpace & exec_space
+  , typename ViewTraits<ST,SP...>::non_const_value_type & dst
+  , const View<ST,SP...> & src
+  , typename std::enable_if<
+    Kokkos::Impl::is_execution_space< ExecSpace >::value &&
+    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value
+    >::type * = 0 )
+{
+  static_assert( ViewTraits<ST,SP...>::rank == 0
+               , "ERROR: Non-rank-zero view in deep_copy( value , View )" );
 
-      // Views span equal length contiguous range.
-      // Assuming can perform a straight memory copy over this range.
+  typedef ViewTraits<ST,SP...>               src_traits ;
+  typedef typename src_traits::memory_space  src_memory_space ;
+  Kokkos::Impl::DeepCopy< HostSpace , src_memory_space , ExecSpace >
+    ( exec_space , & dst , src.data() , sizeof(ST) );
+}
 
-      const size_t nbytes = sizeof(typename dst_type::value_type) * dst.capacity();
+//----------------------------------------------------------------------------
+/** \brief  A deep copy between views of compatible type, and rank zero.  */
+template< class ExecSpace , class DT , class ... DP , class ST , class ... SP >
+inline
+void deep_copy
+  ( const ExecSpace & exec_space
+  , const View<DT,DP...> & dst
+  , const View<ST,SP...> & src
+  , typename std::enable_if<(
+    Kokkos::Impl::is_execution_space< ExecSpace >::value &&
+    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value &&
+    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value &&
+    ( unsigned(ViewTraits<DT,DP...>::rank) == unsigned(0) &&
+      unsigned(ViewTraits<ST,SP...>::rank) == unsigned(0) )
+  )>::type * = 0 )
+{
+  static_assert(
+    std::is_same< typename ViewTraits<DT,DP...>::value_type ,
+                  typename ViewTraits<ST,SP...>::non_const_value_type >::value
+    , "deep_copy requires matching non-const destination type" );
 
-      Impl::DeepCopy< dst_memory_space , src_memory_space , ExecSpace >( exec , dst.ptr_on_device() , src.ptr_on_device() , nbytes );
-    }
-    else {
-      // Destination view's execution space must be able to directly access source memory space
-      // in order for the ViewRemap functor run in the destination memory space's execution space.
-      size_t stride[8];
-      src.stride(stride);
-      size_t size_stride = stride[0]*src.dimension_0();
-      size_t size_dim = src.dimension_0();
-      for(int i = 1; i<src.rank; i++) {
-        if(stride[i]*src.dimension(i)>size_stride)
-          size_stride = stride[i]*src.dimension(i);
-        size_dim*=src.dimension(i);
-      }
+  typedef View<DT,DP...>  dst_type ;
+  typedef View<ST,SP...>  src_type ;
 
-      if( shapes_are_equal && size_stride == size_dim) {
-        const size_t nbytes = sizeof(typename dst_type::value_type) * dst.capacity();
+  typedef typename dst_type::value_type    value_type ;
+  typedef typename dst_type::memory_space  dst_memory_space ;
+  typedef typename src_type::memory_space  src_memory_space ;
 
-        Impl::DeepCopy< dst_memory_space , src_memory_space , ExecSpace >( exec , dst.ptr_on_device() , src.ptr_on_device() , nbytes );
-      } else {
-        Impl::ViewRemap< dst_type , src_type >( dst , src );
-      }
-    }
+  if ( dst.data() != src.data() ) {
+    Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space , ExecSpace >
+      ( exec_space , dst.data() , src.data() , sizeof(value_type) );
   }
 }
 
-
-/** \brief Deep copy equal dimension arrays in the same space which
- *         have different layouts or specializations.
+//----------------------------------------------------------------------------
+/** \brief  A deep copy between views of the default specialization, compatible type,
+ *          same non-zero rank, same contiguous layout.
  */
-template< class ExecSpace ,
-          class DT , class DL , class DD , class DM , class DS ,
-          class ST , class SL , class SD , class SM , class SS >
+template< class ExecSpace , class DT, class ... DP, class ST, class ... SP >
 inline
-void deep_copy( const ExecSpace& ,
-                const View< DT, DL, DD, DM, DS > & dst ,
-                const View< ST, SL, SD, SM, SS > & src ,
-                const typename Impl::enable_if<(
-                  // Same type and destination is not constant:
-                  Impl::is_same< typename View<DT,DL,DD,DM,DS>::value_type ,
-                                 typename View<DT,DL,DD,DM,DS>::non_const_value_type >::value
-                  &&
-                  // Source memory space is accessible to destination memory space
-                  Impl::VerifyExecutionCanAccessMemorySpace< typename View<DT,DL,DD,DM,DS>::memory_space
-                                                           , typename View<ST,SL,SD,SM,SS>::memory_space >::value
-                  &&
-                  // Same non-zero rank
-                  ( unsigned( View<DT,DL,DD,DM,DS>::rank ) ==
-                    unsigned( View<ST,SL,SD,SM,SS>::rank ) )
-                  &&
-                  ( 0 < unsigned( View<DT,DL,DD,DM,DS>::rank ) )
-                  &&
-                  // Different layout or different specialization:
-                  ( ( ! Impl::is_same< typename View<DT,DL,DD,DM,DS>::array_layout ,
-                                       typename View<ST,SL,SD,SM,SS>::array_layout >::value )
-                    ||
-                    ( ! Impl::is_same< DS , SS >::value )
-                  )
-                )>::type * = 0 )
+void deep_copy
+  ( const ExecSpace & exec_space
+  , const View<DT,DP...> & dst
+  , const View<ST,SP...> & src
+  , typename std::enable_if<(
+    Kokkos::Impl::is_execution_space< ExecSpace >::value &&
+    std::is_same< typename ViewTraits<DT,DP...>::specialize , void >::value &&
+    std::is_same< typename ViewTraits<ST,SP...>::specialize , void >::value &&
+    ( unsigned(ViewTraits<DT,DP...>::rank) != 0 ||
+      unsigned(ViewTraits<ST,SP...>::rank) != 0 )
+  )>::type * = 0 )
 {
-  typedef View< DT, DL, DD, DM, DS > dst_type ;
-  typedef View< ST, SL, SD, SM, SS > src_type ;
-
-  assert_shapes_equal_dimension( dst.shape() , src.shape() );
-
-  Impl::ViewRemap< dst_type , src_type >( dst , src );
+  static_assert(
+    std::is_same< typename ViewTraits<DT,DP...>::value_type ,
+                  typename ViewTraits<DT,DP...>::non_const_value_type >::value
+    , "deep_copy requires non-const destination type" );
+
+  static_assert(
+    ( unsigned(ViewTraits<DT,DP...>::rank) ==
+      unsigned(ViewTraits<ST,SP...>::rank) )
+    , "deep_copy requires Views of equal rank" );
+
+  typedef View<DT,DP...>  dst_type ;
+  typedef View<ST,SP...>  src_type ;
+
+  typedef typename dst_type::execution_space  dst_execution_space ;
+  typedef typename src_type::execution_space  src_execution_space ;
+  typedef typename dst_type::memory_space     dst_memory_space ;
+  typedef typename src_type::memory_space     src_memory_space ;
+
+  enum { DstExecCanAccessSrc =
+   Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< typename dst_execution_space::memory_space , src_memory_space >::value };
+
+  enum { SrcExecCanAccessDst =
+   Kokkos::Impl::VerifyExecutionCanAccessMemorySpace< typename src_execution_space::memory_space , dst_memory_space >::value };
+
+  if ( (void *) dst.data() != (void*) src.data() ) {
+
+    // Concern: If overlapping views then a parallel copy will be erroneous.
+    // ...
+
+    // If same type, equal layout, equal dimensions, equal span, and contiguous memory then can byte-wise copy
+
+    if ( std::is_same< typename ViewTraits<DT,DP...>::value_type ,
+                       typename ViewTraits<ST,SP...>::non_const_value_type >::value &&
+         (
+           std::is_same< typename ViewTraits<DT,DP...>::array_layout ,
+                         typename ViewTraits<ST,SP...>::array_layout >::value
+           ||
+           ( ViewTraits<DT,DP...>::rank == 1 &&
+             ViewTraits<ST,SP...>::rank == 1 )
+         ) &&
+         dst.span_is_contiguous() &&
+         src.span_is_contiguous() &&
+         dst.span() == src.span() &&
+         dst.dimension_0() == src.dimension_0() &&
+         dst.dimension_1() == src.dimension_1() &&
+         dst.dimension_2() == src.dimension_2() &&
+         dst.dimension_3() == src.dimension_3() &&
+         dst.dimension_4() == src.dimension_4() &&
+         dst.dimension_5() == src.dimension_5() &&
+         dst.dimension_6() == src.dimension_6() &&
+         dst.dimension_7() == src.dimension_7() ) {
+
+      const size_t nbytes = sizeof(typename dst_type::value_type) * dst.span();
+
+      Kokkos::Impl::DeepCopy< dst_memory_space , src_memory_space , ExecSpace >
+        ( exec_space , dst.data() , src.data() , nbytes );
+    }
+    else if ( DstExecCanAccessSrc ) {
+      // Copying data between views in accessible memory spaces and either non-contiguous or incompatible shape.
+      Kokkos::Experimental::Impl::ViewRemap< dst_type , src_type >( dst , src );
+    }
+    else if ( SrcExecCanAccessDst ) {
+      // Copying data between views in accessible memory spaces and either non-contiguous or incompatible shape.
+      Kokkos::Experimental::Impl::ViewRemap< dst_type , src_type , src_execution_space >( dst , src );
+    }
+    else {
+      Kokkos::Impl::throw_runtime_exception("deep_copy given views that would require a temporary allocation");
+    }
+  }
 }
 
-}
+} /* namespace Experimental */
+} /* namespace Kokkos */
+
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
+namespace Experimental {
+namespace Impl {
+
+// Deduce Mirror Types
+template<class Space, class T, class ... P>
+struct MirrorViewType {
+  // The incoming view_type
+  typedef typename Kokkos::Experimental::View<T,P...> src_view_type;
+  // The memory space for the mirror view
+  typedef typename Space::memory_space memory_space;
+  // Check whether it is the same memory space
+  enum { is_same_memspace = std::is_same<memory_space,typename src_view_type::memory_space>::value };
+  // The array_layout
+  typedef typename src_view_type::array_layout array_layout;
+  // The data type (we probably want it non-const since otherwise we can't even deep_copy to it.
+  typedef typename src_view_type::non_const_data_type data_type;
+  // The destination view type if it is not the same memory space
+  typedef Kokkos::Experimental::View<data_type,array_layout,Space> dest_view_type;
+  // If it is the same memory_space return the existsing view_type
+  // This will also keep the unmanaged trait if necessary
+  typedef typename std::conditional<is_same_memspace,src_view_type,dest_view_type>::type view_type;
+};
+
+template<class Space, class T, class ... P>
+struct MirrorType {
+  // The incoming view_type
+  typedef typename Kokkos::Experimental::View<T,P...> src_view_type;
+  // The memory space for the mirror view
+  typedef typename Space::memory_space memory_space;
+  // Check whether it is the same memory space
+  enum { is_same_memspace = std::is_same<memory_space,typename src_view_type::memory_space>::value };
+  // The array_layout
+  typedef typename src_view_type::array_layout array_layout;
+  // The data type (we probably want it non-const since otherwise we can't even deep_copy to it.
+  typedef typename src_view_type::non_const_data_type data_type;
+  // The destination view type if it is not the same memory space
+  typedef Kokkos::Experimental::View<data_type,array_layout,Space> view_type;
+};
 
-template< class T , class L , class D , class M , class S >
-typename Impl::enable_if<(
-    View<T,L,D,M,S>::is_managed &&
-    !Impl::is_same<L,LayoutStride>::value
-  ), typename View<T,L,D,M,S>::HostMirror >::type
+}
+
+template< class T , class ... P >
 inline
-create_mirror( const View<T,L,D,M,S> & src )
+typename Kokkos::Experimental::View<T,P...>::HostMirror
+create_mirror( const Kokkos::Experimental::View<T,P...> & src
+             , typename std::enable_if<
+                 ! std::is_same< typename Kokkos::Experimental::ViewTraits<T,P...>::array_layout
+                               , Kokkos::LayoutStride >::value
+               >::type * = 0
+             )
 {
-  typedef View<T,L,D,M,S>                  view_type ;
-  typedef typename view_type::HostMirror    host_view_type ;
-
-  // 'view' is managed therefore we can allocate a
-  // compatible host_view through the ordinary constructor.
-
-  std::string label = src.tracker().label();
-  label.append("_mirror");
-
-  return host_view_type( label ,
-                         src.dimension_0() ,
-                         src.dimension_1() ,
-                         src.dimension_2() ,
-                         src.dimension_3() ,
-                         src.dimension_4() ,
-                         src.dimension_5() ,
-                         src.dimension_6() ,
-                         src.dimension_7() );
+  typedef View<T,P...>                   src_type ;
+  typedef typename src_type::HostMirror  dst_type ;
+
+  return dst_type( std::string( src.label() ).append("_mirror")
+                 , src.dimension_0()
+                 , src.dimension_1()
+                 , src.dimension_2()
+                 , src.dimension_3()
+                 , src.dimension_4()
+                 , src.dimension_5()
+                 , src.dimension_6()
+                 , src.dimension_7() );
 }
 
-template< class T , class L , class D , class M , class S >
-typename Impl::enable_if<(
-    View<T,L,D,M,S>::is_managed &&
-    Impl::is_same<L,LayoutStride>::value
-  ), typename View<T,L,D,M,S>::HostMirror >::type
+template< class T , class ... P >
 inline
-create_mirror( const View<T,L,D,M,S> & src )
+typename Kokkos::Experimental::View<T,P...>::HostMirror
+create_mirror( const Kokkos::Experimental::View<T,P...> & src
+             , typename std::enable_if<
+                 std::is_same< typename Kokkos::Experimental::ViewTraits<T,P...>::array_layout
+                             , Kokkos::LayoutStride >::value
+               >::type * = 0
+             )
 {
-  typedef View<T,L,D,M,S>                  view_type ;
-  typedef typename view_type::HostMirror    host_view_type ;
+  typedef View<T,P...>                   src_type ;
+  typedef typename src_type::HostMirror  dst_type ;
 
-  // 'view' is managed therefore we can allocate a
-  // compatible host_view through the ordinary constructor.
+  Kokkos::LayoutStride layout ;
 
-  std::string label = src.tracker().label();
-  label.append("_mirror");
-  LayoutStride layout;
-  src.stride(layout.stride);
   layout.dimension[0] = src.dimension_0();
   layout.dimension[1] = src.dimension_1();
   layout.dimension[2] = src.dimension_2();
@@ -1807,37 +2197,91 @@ create_mirror( const View<T,L,D,M,S> & src )
   layout.dimension[6] = src.dimension_6();
   layout.dimension[7] = src.dimension_7();
 
-  return host_view_type( label , layout );
+  layout.stride[0] = src.stride_0();
+  layout.stride[1] = src.stride_1();
+  layout.stride[2] = src.stride_2();
+  layout.stride[3] = src.stride_3();
+  layout.stride[4] = src.stride_4();
+  layout.stride[5] = src.stride_5();
+  layout.stride[6] = src.stride_6();
+  layout.stride[7] = src.stride_7();
+
+  return dst_type( std::string( src.label() ).append("_mirror") , layout );
+}
+
+
+// Create a mirror in a new space (specialization for different space)
+template<class Space, class T, class ... P>
+typename Impl::MirrorType<Space,T,P ...>::view_type create_mirror(const Space& , const Kokkos::Experimental::View<T,P...> & src) {
+  return typename Impl::MirrorType<Space,T,P ...>::view_type(src.label(),src.layout());
 }
-template< class T , class L , class D , class M , class S >
-typename Impl::enable_if<(
-    View<T,L,D,M,S>::is_managed &&
-    Impl::ViewAssignable< typename View<T,L,D,M,S>::HostMirror , View<T,L,D,M,S> >::value
-  ), typename View<T,L,D,M,S>::HostMirror >::type
+
+template< class T , class ... P >
 inline
-create_mirror_view( const View<T,L,D,M,S> & src )
+typename Kokkos::Experimental::View<T,P...>::HostMirror
+create_mirror_view( const Kokkos::Experimental::View<T,P...> & src
+                  , typename std::enable_if<(
+                      std::is_same< typename Kokkos::Experimental::View<T,P...>::memory_space
+                                  , typename Kokkos::Experimental::View<T,P...>::HostMirror::memory_space
+                                  >::value
+                      &&
+                      std::is_same< typename Kokkos::Experimental::View<T,P...>::data_type
+                                  , typename Kokkos::Experimental::View<T,P...>::HostMirror::data_type
+                                  >::value
+                    )>::type * = 0
+                  )
 {
   return src ;
 }
 
-template< class T , class L , class D , class M , class S >
-typename Impl::enable_if<(
-    View<T,L,D,M,S>::is_managed &&
-    ! Impl::ViewAssignable< typename View<T,L,D,M,S>::HostMirror , View<T,L,D,M,S> >::value
-  ), typename View<T,L,D,M,S>::HostMirror >::type
+template< class T , class ... P >
 inline
-create_mirror_view( const View<T,L,D,M,S> & src )
+typename Kokkos::Experimental::View<T,P...>::HostMirror
+create_mirror_view( const Kokkos::Experimental::View<T,P...> & src
+                  , typename std::enable_if< ! (
+                      std::is_same< typename Kokkos::Experimental::View<T,P...>::memory_space
+                                  , typename Kokkos::Experimental::View<T,P...>::HostMirror::memory_space
+                                  >::value
+                      &&
+                      std::is_same< typename Kokkos::Experimental::View<T,P...>::data_type
+                                  , typename Kokkos::Experimental::View<T,P...>::HostMirror::data_type
+                                  >::value
+                    )>::type * = 0
+                  )
 {
-  return create_mirror( src );
+  return Kokkos::Experimental::create_mirror( src );
+}
+
+// Create a mirror view in a new space (specialization for same space)
+template<class Space, class T, class ... P>
+typename Impl::MirrorViewType<Space,T,P ...>::view_type
+create_mirror_view(const Space& , const Kokkos::Experimental::View<T,P...> & src
+  , typename std::enable_if<Impl::MirrorViewType<Space,T,P ...>::is_same_memspace>::type* = 0 ) {
+  return src;
+}
+
+// Create a mirror view in a new space (specialization for different space)
+template<class Space, class T, class ... P>
+typename Impl::MirrorViewType<Space,T,P ...>::view_type
+create_mirror_view(const Space& , const Kokkos::Experimental::View<T,P...> & src
+  , typename std::enable_if<!Impl::MirrorViewType<Space,T,P ...>::is_same_memspace>::type* = 0 ) {
+  return typename Impl::MirrorViewType<Space,T,P ...>::view_type(src.label(),src.layout());
 }
 
+} /* namespace Experimental */
+} /* namespace Kokkos */
+
+//----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
+namespace Kokkos {
+namespace Experimental {
+
 /** \brief  Resize a view with copying old data to new data at the corresponding indices. */
-template< class T , class L , class D , class M , class S >
+template< class T , class ... P >
 inline
-void resize( View<T,L,D,M,S> & v ,
-             const typename Impl::enable_if< ViewTraits<T,L,D,M>::is_managed , size_t >::type n0 ,
+void resize( Kokkos::Experimental::View<T,P...> & v ,
+             const size_t n0 = 0 ,
              const size_t n1 = 0 ,
              const size_t n2 = 0 ,
              const size_t n3 = 0 ,
@@ -1846,24 +2290,22 @@ void resize( View<T,L,D,M,S> & v ,
              const size_t n6 = 0 ,
              const size_t n7 = 0 )
 {
-  typedef View<T,L,D,M,S> view_type ;
+  typedef Kokkos::Experimental::View<T,P...>  view_type ;
 
-  const std::string label = v.tracker().label();
+  static_assert( Kokkos::Experimental::ViewTraits<T,P...>::is_managed , "Can only resize managed views" );
 
-  view_type v_resized( label, n0, n1, n2, n3, n4, n5, n6, n7 );
+  view_type v_resized( v.label(), n0, n1, n2, n3, n4, n5, n6, n7 );
 
-  Impl::ViewRemap< view_type , view_type >( v_resized , v );
-
-  view_type::execution_space::fence();
+  Kokkos::Experimental::Impl::ViewRemap< view_type , view_type >( v_resized , v );
 
   v = v_resized ;
 }
 
-/** \brief  Reallocate a view without copying old data to new data */
-template< class T , class L , class D , class M , class S >
+/** \brief  Resize a view with copying old data to new data at the corresponding indices. */
+template< class T , class ... P >
 inline
-void realloc( View<T,L,D,M,S> & v ,
-              const typename Impl::enable_if< ViewTraits<T,L,D,M>::is_managed , size_t >::type n0 ,
+void realloc( Kokkos::Experimental::View<T,P...> & v ,
+              const size_t n0 = 0 ,
               const size_t n1 = 0 ,
               const size_t n2 = 0 ,
               const size_t n3 = 0 ,
@@ -1872,239 +2314,71 @@ void realloc( View<T,L,D,M,S> & v ,
               const size_t n6 = 0 ,
               const size_t n7 = 0 )
 {
-  typedef View<T,L,D,M,S> view_type ;
+  typedef Kokkos::Experimental::View<T,P...>  view_type ;
+
+  static_assert( Kokkos::Experimental::ViewTraits<T,P...>::is_managed , "Can only realloc managed views" );
 
-  // Query the current label and reuse it.
-  const std::string label = v.tracker().label();
+  const std::string label = v.label();
 
-  v = view_type(); // deallocate first, if the only view to memory.
+  v = view_type(); // Deallocate first, if the only view to allocation
   v = view_type( label, n0, n1, n2, n3, n4, n5, n6, n7 );
 }
 
-} // namespace Kokkos
+} /* namespace Experimental */
+} /* namespace Kokkos */
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
 
-template< class D , class A1 , class A2 , class A3 , class S ,
-          class ArgType0 , class ArgType1 , class ArgType2 , class ArgType3 ,
-          class ArgType4 , class ArgType5 , class ArgType6 , class ArgType7 >
-KOKKOS_INLINE_FUNCTION
-typename Impl::ViewSubview< View<D,A1,A2,A3,S>
-                          , ArgType0 , ArgType1 , ArgType2 , ArgType3
-                          , ArgType4 , ArgType5 , ArgType6 , ArgType7
-                          >::type
-subview( const View<D,A1,A2,A3,S> & src ,
-         const ArgType0 & arg0 ,
-         const ArgType1 & arg1 ,
-         const ArgType2 & arg2 ,
-         const ArgType3 & arg3 ,
-         const ArgType4 & arg4 ,
-         const ArgType5 & arg5 ,
-         const ArgType6 & arg6 ,
-         const ArgType7 & arg7 )
-{
-  typedef typename
-    Impl::ViewSubview< View<D,A1,A2,A3,S>
-                 , ArgType0 , ArgType1 , ArgType2 , ArgType3
-                 , ArgType4 , ArgType5 , ArgType6 , ArgType7
-                 >::type
-      DstViewType ;
+template< class D , class ... P >
+using ViewTraits = Kokkos::Experimental::ViewTraits<D,P...> ;
 
-  return DstViewType( src, arg0, arg1, arg2, arg3, arg4, arg5, arg6, arg7 );
-}
+using Experimental::View ; //modified due to gcc parser bug 
+//template< class D , class ... P >
+//using View = Kokkos::Experimental::View<D,P...> ;
 
-template< class D , class A1 , class A2 , class A3 , class S ,
-          class ArgType0 , class ArgType1 , class ArgType2 , class ArgType3 ,
-          class ArgType4 , class ArgType5 , class ArgType6 >
-KOKKOS_INLINE_FUNCTION
-typename Impl::ViewSubview< View<D,A1,A2,A3,S>
-                          , ArgType0 , ArgType1 , ArgType2 , ArgType3
-                          , ArgType4 , ArgType5 , ArgType6 , void
-                          >::type
-subview( const View<D,A1,A2,A3,S> & src ,
-         const ArgType0 & arg0 ,
-         const ArgType1 & arg1 ,
-         const ArgType2 & arg2 ,
-         const ArgType3 & arg3 ,
-         const ArgType4 & arg4 ,
-         const ArgType5 & arg5 ,
-         const ArgType6 & arg6 )
-{
-  typedef typename
-    Impl::ViewSubview< View<D,A1,A2,A3,S>
-                 , ArgType0 , ArgType1 , ArgType2 , ArgType3
-                 , ArgType4 , ArgType5 , ArgType6 , void
-                 >::type
-      DstViewType ;
-
-  return DstViewType( src, arg0, arg1, arg2, arg3, arg4, arg5, arg6 );
-}
+using Kokkos::Experimental::ALL ;
+using Kokkos::Experimental::WithoutInitializing ;
+using Kokkos::Experimental::AllowPadding ;
+using Kokkos::Experimental::view_alloc ;
+using Kokkos::Experimental::view_wrap ;
 
-template< class D , class A1 , class A2 , class A3 , class S ,
-          class ArgType0 , class ArgType1 , class ArgType2 , class ArgType3 ,
-          class ArgType4 , class ArgType5 >
-KOKKOS_INLINE_FUNCTION
-typename Impl::ViewSubview< View<D,A1,A2,A3,S>
-                          , ArgType0 , ArgType1 , ArgType2 , ArgType3
-                          , ArgType4 , ArgType5 , void , void
-                          >::type
-subview( const View<D,A1,A2,A3,S> & src ,
-         const ArgType0 & arg0 ,
-         const ArgType1 & arg1 ,
-         const ArgType2 & arg2 ,
-         const ArgType3 & arg3 ,
-         const ArgType4 & arg4 ,
-         const ArgType5 & arg5 )
-{
-  typedef typename
-    Impl::ViewSubview< View<D,A1,A2,A3,S>
-                 , ArgType0 , ArgType1 , ArgType2 , ArgType3
-                 , ArgType4 , ArgType5 , void , void
-                 >::type
-      DstViewType ;
-
-  return DstViewType( src, arg0, arg1, arg2, arg3, arg4, arg5 );
-}
-
-template< class D , class A1 , class A2 , class A3 , class S ,
-          class ArgType0 , class ArgType1 , class ArgType2 , class ArgType3 ,
-          class ArgType4 >
-KOKKOS_INLINE_FUNCTION
-typename Impl::ViewSubview< View<D,A1,A2,A3,S>
-                          , ArgType0 , ArgType1 , ArgType2 , ArgType3
-                          , ArgType4 , void , void , void
-                          >::type
-subview( const View<D,A1,A2,A3,S> & src ,
-         const ArgType0 & arg0 ,
-         const ArgType1 & arg1 ,
-         const ArgType2 & arg2 ,
-         const ArgType3 & arg3 ,
-         const ArgType4 & arg4 )
-{
-  typedef typename
-    Impl::ViewSubview< View<D,A1,A2,A3,S>
-                 , ArgType0 , ArgType1 , ArgType2 , ArgType3
-                 , ArgType4 , void , void , void
-                 >::type
-      DstViewType ;
-
-  return DstViewType( src, arg0, arg1, arg2, arg3, arg4 );
-}
-
-template< class D , class A1 , class A2 , class A3 , class S ,
-          class ArgType0 , class ArgType1 , class ArgType2 , class ArgType3 >
-KOKKOS_INLINE_FUNCTION
-typename Impl::ViewSubview< View<D,A1,A2,A3,S>
-                          , ArgType0 , ArgType1 , ArgType2 , ArgType3
-                          , void , void , void , void
-                          >::type
-subview( const View<D,A1,A2,A3,S> & src ,
-         const ArgType0 & arg0 ,
-         const ArgType1 & arg1 ,
-         const ArgType2 & arg2 ,
-         const ArgType3 & arg3 )
-{
-  typedef typename
-    Impl::ViewSubview< View<D,A1,A2,A3,S>
-                 , ArgType0 , ArgType1 , ArgType2 , ArgType3
-                 , void , void , void , void
-                 >::type
-      DstViewType ;
-
-  return DstViewType( src, arg0, arg1, arg2, arg3 );
-}
-
-template< class D , class A1 , class A2 , class A3 , class S ,
-          class ArgType0 , class ArgType1 , class ArgType2 >
-KOKKOS_INLINE_FUNCTION
-typename Impl::ViewSubview< View<D,A1,A2,A3,S>
-                          , ArgType0 , ArgType1 , ArgType2 , void
-                          , void , void , void , void
-                          >::type
-subview( const View<D,A1,A2,A3,S> & src ,
-         const ArgType0 & arg0 ,
-         const ArgType1 & arg1 ,
-         const ArgType2 & arg2 )
-{
-  typedef typename
-    Impl::ViewSubview< View<D,A1,A2,A3,S>
-                 , ArgType0 , ArgType1 , ArgType2 , void
-                 , void , void , void , void
-                 >::type
-      DstViewType ;
+using Kokkos::Experimental::deep_copy ;
+using Kokkos::Experimental::create_mirror ;
+using Kokkos::Experimental::create_mirror_view ;
+using Kokkos::Experimental::subview ;
+using Kokkos::Experimental::resize ;
+using Kokkos::Experimental::realloc ;
+using Kokkos::Experimental::is_view ;
 
-  return DstViewType( src, arg0, arg1, arg2 );
-}
+namespace Impl {
 
-template< class D , class A1 , class A2 , class A3 , class S ,
-          class ArgType0 , class ArgType1 >
-KOKKOS_INLINE_FUNCTION
-typename Impl::ViewSubview< View<D,A1,A2,A3,S>
-                          , ArgType0 , ArgType1 , void , void
-                          , void , void , void , void
-                          >::type
-subview( const View<D,A1,A2,A3,S> & src ,
-         const ArgType0 & arg0 ,
-         const ArgType1 & arg1 )
-{
-  typedef typename
-    Impl::ViewSubview< View<D,A1,A2,A3,S>
-                 , ArgType0 , ArgType1 , void , void
-                 , void , void , void , void
-                 >::type
-      DstViewType ;
+using Kokkos::Experimental::is_view ;
 
-  return DstViewType( src, arg0, arg1 );
-}
+class ViewDefault {};
 
-template< class D , class A1 , class A2 , class A3 , class S ,
-          class ArgType0 >
-KOKKOS_INLINE_FUNCTION
-typename Impl::ViewSubview< View<D,A1,A2,A3,S>
-                          , ArgType0 , void , void , void
-                          , void , void , void , void
-                          >::type
-subview( const View<D,A1,A2,A3,S> & src ,
-         const ArgType0 & arg0 )
-{
-  typedef typename
-    Impl::ViewSubview< View<D,A1,A2,A3,S>
-                 , ArgType0 , void , void , void
-                 , void , void , void , void
-                 >::type
-      DstViewType ;
+template< class SrcViewType
+        , class Arg0Type
+        , class Arg1Type
+        , class Arg2Type
+        , class Arg3Type
+        , class Arg4Type
+        , class Arg5Type
+        , class Arg6Type
+        , class Arg7Type
+        >
+struct ViewSubview /* { typedef ... type ; } */ ;
 
-  return DstViewType( src, arg0 );
 }
 
-} // namespace Kokkos
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
+} /* namespace Kokkos */
 
-#include <impl/Kokkos_ViewDefault.hpp>
 #include <impl/Kokkos_Atomic_View.hpp>
 
-#include <impl/Kokkos_ViewOffset.hpp>
-#include <impl/Kokkos_ViewSupport.hpp>
-
-namespace Kokkos {
-/** \brief  Tag denoting that a subview should capture all of a dimension */
-struct ALL { KOKKOS_INLINE_FUNCTION ALL(){} };
-}
-
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-#include <KokkosExp_View.hpp>
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-#endif
+#endif /* #ifndef KOKKOS_VIEW_HPP */
 
diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel.hpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel.hpp
index c58706bbaa..27ae5803ce 100644
--- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel.hpp
+++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Parallel.hpp
@@ -178,9 +178,10 @@ public:
 namespace Kokkos {
 namespace Impl {
 
-template< class FunctorType , class ... Traits >
+template< class FunctorType , class ReducerType, class ... Traits >
 class ParallelReduce< FunctorType
                     , Kokkos::RangePolicy< Traits ...>
+                    , ReducerType
                     , Kokkos::OpenMP
                     >
 {
@@ -192,15 +193,21 @@ private:
   typedef typename Policy::WorkRange    WorkRange ;
   typedef typename Policy::member_type  Member ;
 
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType, WorkTag > ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueInit<   FunctorType, WorkTag > ValueInit ;
-  typedef Kokkos::Impl::FunctorValueJoin<   FunctorType, WorkTag > ValueJoin ;
+  typedef Kokkos::Impl::if_c< std::is_same<InvalidType,ReducerType>::value, FunctorType, ReducerType> ReducerConditional;
+  typedef typename ReducerConditional::type ReducerTypeFwd;
+
+  // Static Assert WorkTag void if ReducerType not InvalidType
+
+  typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd, WorkTag > ValueTraits ;
+  typedef Kokkos::Impl::FunctorValueInit<   ReducerTypeFwd, WorkTag > ValueInit ;
+  typedef Kokkos::Impl::FunctorValueJoin<   ReducerTypeFwd, WorkTag > ValueJoin ;
 
   typedef typename ValueTraits::pointer_type    pointer_type ;
   typedef typename ValueTraits::reference_type  reference_type ;
 
   const FunctorType   m_functor ;
   const Policy        m_policy ;
+  const ReducerType   m_reducer ;
   const pointer_type  m_result_ptr ;
 
   template< class TagType >
@@ -252,7 +259,7 @@ public:
       OpenMPexec::verify_is_process("Kokkos::OpenMP parallel_reduce");
       OpenMPexec::verify_initialized("Kokkos::OpenMP parallel_reduce");
 
-      OpenMPexec::resize_scratch( ValueTraits::value_size( m_functor ) , 0 );
+      OpenMPexec::resize_scratch( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) , 0 );
 
 #pragma omp parallel
       {
@@ -260,7 +267,7 @@ public:
         const WorkRange range( m_policy, exec.pool_rank(), exec.pool_size() );
         ParallelReduce::template exec_range< WorkTag >
           ( m_functor , range.begin() , range.end()
-          , ValueInit::init( m_functor , exec.scratch_reduce() ) );
+          , ValueInit::init( ReducerConditional::select(m_functor , m_reducer), exec.scratch_reduce() ) );
       }
 /* END #pragma omp parallel */
 
@@ -269,13 +276,13 @@ public:
       const pointer_type ptr = pointer_type( OpenMPexec::pool_rev(0)->scratch_reduce() );
 
       for ( int i = 1 ; i < OpenMPexec::pool_size() ; ++i ) {
-        ValueJoin::join( m_functor , ptr , OpenMPexec::pool_rev(i)->scratch_reduce() );
+        ValueJoin::join( ReducerConditional::select(m_functor , m_reducer) , ptr , OpenMPexec::pool_rev(i)->scratch_reduce() );
       }
 
-      Kokkos::Impl::FunctorFinal<  FunctorType , WorkTag >::final( m_functor , ptr );
+      Kokkos::Impl::FunctorFinal<  ReducerTypeFwd , WorkTag >::final( ReducerConditional::select(m_functor , m_reducer) , ptr );
 
       if ( m_result_ptr ) {
-        const int n = ValueTraits::value_count( m_functor );
+        const int n = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) );
 
         for ( int j = 0 ; j < n ; ++j ) { m_result_ptr[j] = ptr[j] ; }
       }
@@ -289,7 +296,7 @@ public:
       OpenMPexec::verify_is_process("Kokkos::OpenMP parallel_reduce");
       OpenMPexec::verify_initialized("Kokkos::OpenMP parallel_reduce");
 
-      OpenMPexec::resize_scratch( ValueTraits::value_size( m_functor ) , 0 );
+      OpenMPexec::resize_scratch( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) , 0 );
 
 #pragma omp parallel
       {
@@ -302,7 +309,7 @@ public:
 
         long work_index = exec.get_work_index();
 
-        reference_type update = ValueInit::init( m_functor , exec.scratch_reduce() );
+        reference_type update = ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , exec.scratch_reduce() );
         while(work_index != -1) {
           const Member begin = static_cast<Member>(work_index) * m_policy.chunk_size();
           const Member end = begin + m_policy.chunk_size() < m_policy.end()?begin+m_policy.chunk_size():m_policy.end();
@@ -319,13 +326,13 @@ public:
       const pointer_type ptr = pointer_type( OpenMPexec::pool_rev(0)->scratch_reduce() );
 
       for ( int i = 1 ; i < OpenMPexec::pool_size() ; ++i ) {
-        ValueJoin::join( m_functor , ptr , OpenMPexec::pool_rev(i)->scratch_reduce() );
+        ValueJoin::join( ReducerConditional::select(m_functor , m_reducer) , ptr , OpenMPexec::pool_rev(i)->scratch_reduce() );
       }
 
-      Kokkos::Impl::FunctorFinal<  FunctorType , WorkTag >::final( m_functor , ptr );
+      Kokkos::Impl::FunctorFinal<  ReducerTypeFwd , WorkTag >::final( ReducerConditional::select(m_functor , m_reducer) , ptr );
 
       if ( m_result_ptr ) {
-        const int n = ValueTraits::value_count( m_functor );
+        const int n = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) );
 
         for ( int j = 0 ; j < n ; ++j ) { m_result_ptr[j] = ptr[j] ; }
       }
@@ -337,18 +344,35 @@ public:
   inline
   ParallelReduce( const FunctorType & arg_functor
                 , Policy       arg_policy
-                , const ViewType    & arg_result_view )
+                , const ViewType    & arg_result_view
+                , typename std::enable_if<
+                           Kokkos::is_view< ViewType >::value &&
+                           !Kokkos::is_reducer_type<ReducerType>::value
+                  ,void*>::type = NULL)
     : m_functor( arg_functor )
     , m_policy(  arg_policy )
-    , m_result_ptr(  arg_result_view.ptr_on_device() )
+    , m_reducer( InvalidType() )
+    , m_result_ptr(  arg_result_view.data() )
     {
-      static_assert( Kokkos::is_view< ViewType >::value
-        , "Reduction result on Kokkos::OpenMP must be a Kokkos::View" );
+      /*static_assert( std::is_same< typename ViewType::memory_space
+                                      , Kokkos::HostSpace >::value
+        , "Reduction result on Kokkos::OpenMP must be a Kokkos::View in HostSpace" );*/
+    }
 
-      static_assert( std::is_same< typename ViewType::memory_space
+  inline
+  ParallelReduce( const FunctorType & arg_functor
+                , Policy       arg_policy
+                , const ReducerType& reducer )
+    : m_functor( arg_functor )
+    , m_policy(  arg_policy )
+    , m_reducer( reducer )
+    , m_result_ptr(  reducer.result_view().data() )
+    {
+      /*static_assert( std::is_same< typename ViewType::memory_space
                                       , Kokkos::HostSpace >::value
-        , "Reduction result on Kokkos::OpenMP must be a Kokkos::View in HostSpace" );
+        , "Reduction result on Kokkos::OpenMP must be a Kokkos::View in HostSpace" );*/
     }
+
 };
 
 } // namespace Impl
@@ -568,13 +592,13 @@ public:
 
       const size_t team_reduce_size = Policy::member_type::team_reduce_size();
 
-      OpenMPexec::resize_scratch( 0 , team_reduce_size + m_shmem_size );
+      OpenMPexec::resize_scratch( 0 , team_reduce_size + m_shmem_size + m_policy.scratch_size(1));
 
 #pragma omp parallel
       {
         ParallelFor::template exec_team< WorkTag, typename Policy::schedule_type::type>
           ( m_functor
-          , Member( * OpenMPexec::get_thread_omp(), m_policy, m_shmem_size) );
+          , Member( * OpenMPexec::get_thread_omp(), m_policy, m_shmem_size, 0) );
       }
 /* END #pragma omp parallel */
     }
@@ -584,14 +608,15 @@ public:
                const Policy      & arg_policy )
     : m_functor( arg_functor )
     , m_policy(  arg_policy )
-    , m_shmem_size( arg_policy.scratch_size() + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
+    , m_shmem_size( arg_policy.scratch_size(0) + arg_policy.scratch_size(1) + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
     {}
 };
 
 
-template< class FunctorType , class ... Properties >
+template< class FunctorType , class ReducerType, class ... Properties >
 class ParallelReduce< FunctorType
                     , Kokkos::TeamPolicy< Properties ... >
+                    , ReducerType
                     , Kokkos::OpenMP
                     >
 {
@@ -602,15 +627,19 @@ private:
   typedef typename Policy::work_tag     WorkTag ;
   typedef typename Policy::member_type  Member ;
 
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType , WorkTag >  ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueInit<   FunctorType , WorkTag >  ValueInit ;
-  typedef Kokkos::Impl::FunctorValueJoin<   FunctorType , WorkTag >  ValueJoin ;
+  typedef Kokkos::Impl::if_c< std::is_same<InvalidType,ReducerType>::value, FunctorType, ReducerType> ReducerConditional;
+  typedef typename ReducerConditional::type ReducerTypeFwd;
+
+  typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd , WorkTag >  ValueTraits ;
+  typedef Kokkos::Impl::FunctorValueInit<   ReducerTypeFwd , WorkTag >  ValueInit ;
+  typedef Kokkos::Impl::FunctorValueJoin<   ReducerTypeFwd , WorkTag >  ValueJoin ;
 
   typedef typename ValueTraits::pointer_type    pointer_type ;
   typedef typename ValueTraits::reference_type  reference_type ;
 
   const FunctorType  m_functor ;
   const Policy       m_policy ;
+  const ReducerType  m_reducer ;
   const pointer_type m_result_ptr ;
   const int          m_shmem_size ;
 
@@ -644,7 +673,7 @@ public:
 
       const size_t team_reduce_size = Policy::member_type::team_reduce_size();
 
-      OpenMPexec::resize_scratch( ValueTraits::value_size( m_functor ) , team_reduce_size + m_shmem_size );
+      OpenMPexec::resize_scratch( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) , team_reduce_size + m_shmem_size );
 
 #pragma omp parallel
       {
@@ -652,8 +681,8 @@ public:
 
         ParallelReduce::template exec_team< WorkTag >
           ( m_functor
-          , Member( exec , m_policy , m_shmem_size )
-          , ValueInit::init( m_functor , exec.scratch_reduce() ) );
+          , Member( exec , m_policy , m_shmem_size, 0 )
+          , ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , exec.scratch_reduce() ) );
       }
 /* END #pragma omp parallel */
 
@@ -665,13 +694,13 @@ public:
           max_active_threads = m_policy.league_size()* m_policy.team_size();
 
         for ( int i = 1 ; i < max_active_threads ; ++i ) {
-          ValueJoin::join( m_functor , ptr , OpenMPexec::pool_rev(i)->scratch_reduce() );
+          ValueJoin::join( ReducerConditional::select(m_functor , m_reducer) , ptr , OpenMPexec::pool_rev(i)->scratch_reduce() );
         }
 
-        Kokkos::Impl::FunctorFinal< FunctorType , WorkTag >::final( m_functor , ptr );
+        Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTag >::final( ReducerConditional::select(m_functor , m_reducer) , ptr );
 
         if ( m_result_ptr ) {
-          const int n = ValueTraits::value_count( m_functor );
+          const int n = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) );
 
           for ( int j = 0 ; j < n ; ++j ) { m_result_ptr[j] = ptr[j] ; }
         }
@@ -682,12 +711,33 @@ public:
   inline
   ParallelReduce( const FunctorType  & arg_functor ,
                   const Policy       & arg_policy ,
-                  const ViewType     & arg_result )
+                  const ViewType     & arg_result ,
+                  typename std::enable_if<
+                    Kokkos::is_view< ViewType >::value &&
+                    !Kokkos::is_reducer_type<ReducerType>::value
+                    ,void*>::type = NULL)
     : m_functor( arg_functor )
     , m_policy(  arg_policy )
+    , m_reducer( InvalidType() )
     , m_result_ptr( arg_result.ptr_on_device() )
-    , m_shmem_size( arg_policy.scratch_size() + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
+    , m_shmem_size( arg_policy.scratch_size(0) + arg_policy.scratch_size(1) + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
     {}
+
+  inline
+  ParallelReduce( const FunctorType & arg_functor
+    , Policy       arg_policy
+    , const ReducerType& reducer )
+  : m_functor( arg_functor )
+  , m_policy(  arg_policy )
+  , m_reducer( reducer )
+  , m_result_ptr(  reducer.result_view().data() )
+  , m_shmem_size( arg_policy.scratch_size(0) + arg_policy.scratch_size(1) + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
+  {
+  /*static_assert( std::is_same< typename ViewType::memory_space
+                          , Kokkos::HostSpace >::value
+  , "Reduction result on Kokkos::OpenMP must be a Kokkos::View in HostSpace" );*/
+  }
+
 };
 
 } // namespace Impl
diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.cpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.cpp
new file mode 100644
index 0000000000..3e22033f7c
--- /dev/null
+++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.cpp
@@ -0,0 +1,329 @@
+/*
+//@HEADER
+// ************************************************************************
+// 
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+// 
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+// 
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+// 
+// ************************************************************************
+//@HEADER
+*/
+
+#include <Kokkos_Core.hpp>
+
+#if defined( KOKKOS_HAVE_OPENMP ) && defined( KOKKOS_ENABLE_TASKPOLICY )
+
+#include <impl/Kokkos_TaskQueue_impl.hpp>
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+namespace Impl {
+
+template class TaskQueue< Kokkos::OpenMP > ;
+
+//----------------------------------------------------------------------------
+
+TaskExec< Kokkos::OpenMP >::
+TaskExec()
+  : m_self_exec( 0 )
+  , m_team_exec( 0 )
+  , m_sync_mask( 0 )
+  , m_sync_value( 0 )
+  , m_sync_step( 0 )
+  , m_group_rank( 0 )
+  , m_team_rank( 0 )
+  , m_team_size( 1 )
+{
+}
+
+TaskExec< Kokkos::OpenMP >::
+TaskExec( Kokkos::Impl::OpenMPexec & arg_exec , int const arg_team_size )
+  : m_self_exec( & arg_exec )
+  , m_team_exec( arg_exec.pool_rev(arg_exec.pool_rank_rev() / arg_team_size) )
+  , m_sync_mask( 0 )
+  , m_sync_value( 0 )
+  , m_sync_step( 0 )
+  , m_group_rank( arg_exec.pool_rank_rev() / arg_team_size )
+  , m_team_rank(  arg_exec.pool_rank_rev() % arg_team_size )
+  , m_team_size(  arg_team_size )
+{
+  // This team spans
+  //    m_self_exec->pool_rev( team_size * group_rank )
+  //    m_self_exec->pool_rev( team_size * ( group_rank + 1 ) - 1 )
+
+  int64_t volatile * const sync = (int64_t *) m_self_exec->scratch_reduce();
+
+  sync[0] = int64_t(0) ;
+  sync[1] = int64_t(0) ;
+
+  for ( int i = 0 ; i < m_team_size ; ++i ) {
+    m_sync_value |= int64_t(1) << (8*i);
+    m_sync_mask  |= int64_t(3) << (8*i);
+  }
+
+  Kokkos::memory_fence();
+}
+
+#if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST )
+
+void TaskExec< Kokkos::OpenMP >::team_barrier_impl() const
+{
+  if ( m_team_exec->scratch_reduce_size() < int(2 * sizeof(int64_t)) ) {
+    Kokkos::abort("TaskQueue<OpenMP> scratch_reduce memory too small");
+  }
+
+  // Use team shared memory to synchronize.
+  // Alternate memory locations between barriers to avoid a sequence
+  // of barriers overtaking one another.
+
+  int64_t volatile * const sync =
+    ((int64_t *) m_team_exec->scratch_reduce()) + ( m_sync_step & 0x01 );
+
+  // This team member sets one byte within the sync variable
+  int8_t volatile * const sync_self =
+   ((int8_t *) sync) + m_team_rank ;
+
+#if 0
+fprintf( stdout
+       , "barrier group(%d) member(%d) step(%d) wait(%lx) : before(%lx)\n"
+       , m_group_rank
+       , m_team_rank
+       , m_sync_step
+       , m_sync_value
+       , *sync
+       );
+fflush(stdout);
+#endif
+
+  *sync_self = int8_t( m_sync_value & 0x03 ); // signal arrival
+
+  while ( m_sync_value != *sync ); // wait for team to arrive
+
+#if 0
+fprintf( stdout
+       , "barrier group(%d) member(%d) step(%d) wait(%lx) : after(%lx)\n"
+       , m_group_rank
+       , m_team_rank
+       , m_sync_step
+       , m_sync_value
+       , *sync
+       );
+fflush(stdout);
+#endif
+
+  ++m_sync_step ;
+
+  if ( 0 == ( 0x01 & m_sync_step ) ) { // Every other step
+    m_sync_value ^= m_sync_mask ;
+    if ( 1000 < m_sync_step ) m_sync_step = 0 ;
+  }
+}
+
+#endif
+
+//----------------------------------------------------------------------------
+
+void TaskQueueSpecialization< Kokkos::OpenMP >::execute
+  ( TaskQueue< Kokkos::OpenMP > * const queue )
+{
+  using execution_space = Kokkos::OpenMP ;
+  using queue_type      = TaskQueue< execution_space > ;
+  using task_root_type  = TaskBase< execution_space , void , void > ;
+  using PoolExec        = Kokkos::Impl::OpenMPexec ;
+  using Member          = TaskExec< execution_space > ;
+
+  task_root_type * const end = (task_root_type *) task_root_type::EndTag ;
+
+  // Required:  team_size <= 8
+
+  const int team_size = PoolExec::pool_size(2); // Threads per core
+  // const int team_size = PoolExec::pool_size(1); // Threads per NUMA
+
+  if ( 8 < team_size ) {
+    Kokkos::abort("TaskQueue<OpenMP> unsupported team size");
+  }
+
+#pragma omp parallel
+  {
+    PoolExec & self = *PoolExec::get_thread_omp();
+
+    Member single_exec ;
+    Member team_exec( self , team_size );
+
+    // Team shared memory
+    task_root_type * volatile * const task_shared =
+      (task_root_type **) team_exec.m_team_exec->scratch_thread();
+
+// Barrier across entire OpenMP thread pool to insure initialization
+#pragma omp barrier
+
+    // Loop until all queues are empty and no tasks in flight
+
+    do {
+
+      task_root_type * task = 0 ;
+
+      // Each team lead attempts to acquire either a thread team task
+      // or a single thread task for the team.
+
+      if ( 0 == team_exec.team_rank() ) {
+
+        task = 0 < *((volatile int *) & queue->m_ready_count) ? end : 0 ;
+
+        // Loop by priority and then type
+        for ( int i = 0 ; i < queue_type::NumQueue && end == task ; ++i ) {
+          for ( int j = 0 ; j < 2 && end == task ; ++j ) {
+            task = queue_type::pop_task( & queue->m_ready[i][j] );
+          }
+        }
+      }
+
+      // Team lead broadcast acquired task to team members:
+
+      if ( 1 < team_exec.team_size() ) {
+
+        if ( 0 == team_exec.team_rank() ) *task_shared = task ;
+
+        // Fence to be sure task_shared is stored before the barrier
+        Kokkos::memory_fence();
+
+        // Whole team waits for every team member to reach this statement
+        team_exec.team_barrier();
+
+        // Fence to be sure task_shared is stored
+        Kokkos::memory_fence();
+
+        task = *task_shared ;
+      }
+
+#if 0
+fprintf( stdout
+       , "\nexecute group(%d) member(%d) task_shared(0x%lx) task(0x%lx)\n"
+       , team_exec.m_group_rank
+       , team_exec.m_team_rank
+       , uintptr_t(task_shared)
+       , uintptr_t(task)
+       );
+fflush(stdout);
+#endif
+
+      if ( 0 == task ) break ; // 0 == m_ready_count
+
+      if ( end == task ) {
+        // All team members wait for whole team to reach this statement.
+        // Is necessary to prevent task_shared from being updated
+        // before it is read by all threads.
+        team_exec.team_barrier();
+      }
+      else if ( task_root_type::TaskTeam == task->m_task_type ) {
+        // Thread Team Task
+        (*task->m_apply)( task , & team_exec );
+
+        // The m_apply function performs a barrier
+
+        if ( 0 == team_exec.team_rank() ) {
+          // team member #0 completes the task, which may delete the task
+          queue->complete( task ); 
+        }
+      }
+      else {
+        // Single Thread Task
+
+        if ( 0 == team_exec.team_rank() ) {
+
+          (*task->m_apply)( task , & single_exec );
+
+          queue->complete( task ); 
+        }
+
+        // All team members wait for whole team to reach this statement.
+        // Not necessary to complete the task.
+        // Is necessary to prevent task_shared from being updated
+        // before it is read by all threads.
+        team_exec.team_barrier();
+      }
+    } while(1);
+  }
+// END #pragma omp parallel
+
+}
+
+void TaskQueueSpecialization< Kokkos::OpenMP >::
+  iff_single_thread_recursive_execute
+    ( TaskQueue< Kokkos::OpenMP > * const queue )
+{
+  using execution_space = Kokkos::OpenMP ;
+  using queue_type      = TaskQueue< execution_space > ;
+  using task_root_type  = TaskBase< execution_space , void , void > ;
+  using Member          = TaskExec< execution_space > ;
+
+  if ( 1 == omp_get_num_threads() ) {
+
+    task_root_type * const end = (task_root_type *) task_root_type::EndTag ;
+
+    Member single_exec ;
+
+    task_root_type * task = end ;
+
+    do {
+
+      task = end ;
+
+      // Loop by priority and then type
+      for ( int i = 0 ; i < queue_type::NumQueue && end == task ; ++i ) {
+        for ( int j = 0 ; j < 2 && end == task ; ++j ) {
+          task = queue_type::pop_task( & queue->m_ready[i][j] );
+        }
+      }
+
+      if ( end == task ) break ;
+
+      (*task->m_apply)( task , & single_exec );
+
+      queue->complete( task ); 
+
+    } while(1);
+  }
+}
+
+}} /* namespace Kokkos::Impl */
+
+//----------------------------------------------------------------------------
+
+#endif /* #if defined( KOKKOS_HAVE_OPENMP ) && defined( KOKKOS_ENABLE_TASKPOLICY ) */
+
+
diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.hpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.hpp
new file mode 100644
index 0000000000..2761247c40
--- /dev/null
+++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.hpp
@@ -0,0 +1,356 @@
+/*
+//@HEADER
+// ************************************************************************
+// 
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+// 
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+// 
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+// 
+// ************************************************************************
+//@HEADER
+*/
+
+#ifndef KOKKOS_IMPL_OPENMP_TASK_HPP
+#define KOKKOS_IMPL_OPENMP_TASK_HPP
+
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+namespace Impl {
+
+template<>
+class TaskQueueSpecialization< Kokkos::OpenMP >
+{
+public:
+
+  using execution_space = Kokkos::OpenMP ;
+  using queue_type      = Kokkos::Impl::TaskQueue< execution_space > ;
+  using task_base_type  = Kokkos::Impl::TaskBase< execution_space , void , void > ;
+
+  // Must specify memory space
+  using memory_space = Kokkos::HostSpace ;
+
+  static
+  void iff_single_thread_recursive_execute( queue_type * const );
+
+  // Must provide task queue execution function
+  static void execute( queue_type * const );
+
+  // Must provide mechanism to set function pointer in
+  // execution space from the host process.
+  template< typename FunctorType >
+  static
+  void proc_set_apply( task_base_type::function_type * ptr )
+    {
+      using TaskType = TaskBase< Kokkos::OpenMP
+                               , typename FunctorType::value_type
+                               , FunctorType
+                               > ;
+       *ptr = TaskType::apply ;
+    }
+};
+
+extern template class TaskQueue< Kokkos::OpenMP > ;
+
+//----------------------------------------------------------------------------
+
+template<>
+class TaskExec< Kokkos::OpenMP >
+{
+private:
+
+  TaskExec( TaskExec && ) = delete ;
+  TaskExec( TaskExec const & ) = delete ;
+  TaskExec & operator = ( TaskExec && ) = delete ;
+  TaskExec & operator = ( TaskExec const & ) = delete ;
+
+
+  using PoolExec = Kokkos::Impl::OpenMPexec ;
+
+  friend class Kokkos::Impl::TaskQueue< Kokkos::OpenMP > ;
+  friend class Kokkos::Impl::TaskQueueSpecialization< Kokkos::OpenMP > ;
+
+  PoolExec * const m_self_exec ;  ///< This thread's thread pool data structure 
+  PoolExec * const m_team_exec ;  ///< Team thread's thread pool data structure
+  int64_t          m_sync_mask ;
+  int64_t mutable  m_sync_value ;
+  int     mutable  m_sync_step ;
+  int              m_group_rank ; ///< Which "team" subset of thread pool
+  int              m_team_rank ;  ///< Which thread within a team
+  int              m_team_size ;
+
+  TaskExec();
+  TaskExec( PoolExec & arg_exec , int arg_team_size );
+
+  void team_barrier_impl() const ;
+
+public:
+
+#if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST )
+  void * team_shared() const
+    { return m_team_exec ? m_team_exec->scratch_thread() : (void*) 0 ; }
+
+  int team_shared_size() const
+    { return m_team_exec ? m_team_exec->scratch_thread_size() : 0 ; }
+
+  /**\brief  Whole team enters this function call
+   *         before any teeam member returns from
+   *         this function call.
+   */
+  void team_barrier() const { if ( 1 < m_team_size ) team_barrier_impl(); }
+#else
+  KOKKOS_INLINE_FUNCTION void team_barrier() const {}
+  KOKKOS_INLINE_FUNCTION void * team_shared() const { return 0 ; }
+  KOKKOS_INLINE_FUNCTION int team_shared_size() const { return 0 ; }
+#endif
+
+  KOKKOS_INLINE_FUNCTION
+  int team_rank() const { return m_team_rank ; }
+
+  KOKKOS_INLINE_FUNCTION
+  int team_size() const { return m_team_size ; }
+};
+
+}} /* namespace Kokkos::Impl */
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+
+template<typename iType>
+KOKKOS_INLINE_FUNCTION
+Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::OpenMP > >
+TeamThreadRange
+  ( Impl::TaskExec< Kokkos::OpenMP > & thread
+  , const iType & count )
+{
+  return Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::OpenMP > >(thread,count);
+}
+
+template<typename iType>
+KOKKOS_INLINE_FUNCTION
+Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::OpenMP > >
+TeamThreadRange
+  ( Impl:: TaskExec< Kokkos::OpenMP > & thread
+  , const iType & start
+  , const iType & end )
+{
+  return Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::OpenMP > >(thread,start,end);
+}
+
+/** \brief  Inter-thread parallel_for. Executes lambda(iType i) for each i=0..N-1.
+ *
+ * The range i=0..N-1 is mapped to all threads of the the calling thread team.
+ * This functionality requires C++11 support.
+*/
+template<typename iType, class Lambda>
+KOKKOS_INLINE_FUNCTION
+void parallel_for
+  ( const Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::OpenMP > >& loop_boundaries
+  , const Lambda& lambda
+  )
+{
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    lambda(i);
+  }
+}
+
+template<typename iType, class Lambda, typename ValueType>
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  ( const Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::OpenMP > >& loop_boundaries
+  , const Lambda& lambda
+  , ValueType& initialized_result)
+{
+  int team_rank = loop_boundaries.thread.team_rank(); // member num within the team
+  ValueType result = initialized_result;
+
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    lambda(i, result);
+  }
+
+  if ( 1 < loop_boundaries.thread.team_size() ) {
+
+    ValueType *shared = (ValueType*) loop_boundaries.thread.team_shared();
+
+    loop_boundaries.thread.team_barrier();
+    shared[team_rank] = result;
+
+    loop_boundaries.thread.team_barrier();
+
+    // reduce across threads to thread 0
+    if (team_rank == 0) {
+      for (int i = 1; i < loop_boundaries.thread.team_size(); i++) {
+        shared[0] += shared[i];
+      }
+    }
+
+    loop_boundaries.thread.team_barrier();
+
+    // broadcast result
+    initialized_result = shared[0];
+  }
+  else {
+    initialized_result = result ;
+  }
+}
+
+template< typename iType, class Lambda, typename ValueType, class JoinType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::OpenMP > >& loop_boundaries,
+   const Lambda & lambda,
+   const JoinType & join,
+   ValueType& initialized_result)
+{
+  int team_rank = loop_boundaries.thread.team_rank(); // member num within the team
+  ValueType result = initialized_result;
+
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    lambda(i, result);
+  }
+
+  if ( 1 < loop_boundaries.thread.team_size() ) {
+    ValueType *shared = (ValueType*) loop_boundaries.thread.team_shared();
+
+    loop_boundaries.thread.team_barrier();
+    shared[team_rank] = result;
+
+    loop_boundaries.thread.team_barrier();
+
+    // reduce across threads to thread 0
+    if (team_rank == 0) {
+      for (int i = 1; i < loop_boundaries.thread.team_size(); i++) {
+        join(shared[0], shared[i]);
+      }
+    }
+
+    loop_boundaries.thread.team_barrier();
+
+    // broadcast result
+    initialized_result = shared[0];
+  }
+  else {
+    initialized_result = result ;
+  }
+}
+
+// placeholder for future function
+template< typename iType, class Lambda, typename ValueType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::OpenMP > >& loop_boundaries,
+   const Lambda & lambda,
+   ValueType& initialized_result)
+{
+}
+
+// placeholder for future function
+template< typename iType, class Lambda, typename ValueType, class JoinType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::OpenMP > >& loop_boundaries,
+   const Lambda & lambda,
+   const JoinType & join,
+   ValueType& initialized_result)
+{
+}
+
+template< typename ValueType, typename iType, class Lambda >
+KOKKOS_INLINE_FUNCTION
+void parallel_scan
+  (const Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::OpenMP > >& loop_boundaries,
+   const Lambda & lambda)
+{
+  ValueType accum = 0 ;
+  ValueType val, local_total;
+  ValueType *shared = (ValueType*) loop_boundaries.thread.team_shared();
+  int team_size = loop_boundaries.thread.team_size();
+  int team_rank = loop_boundaries.thread.team_rank(); // member num within the team
+
+  // Intra-member scan
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    local_total = 0;
+    lambda(i,local_total,false);
+    val = accum;
+    lambda(i,val,true);
+    accum += local_total;
+  }
+
+  shared[team_rank] = accum;
+  loop_boundaries.thread.team_barrier();
+
+  // Member 0 do scan on accumulated totals
+  if (team_rank == 0) {
+    for( iType i = 1; i < team_size; i+=1) {
+      shared[i] += shared[i-1];
+    }
+    accum = 0; // Member 0 set accum to 0 in preparation for inter-member scan
+  }
+
+  loop_boundaries.thread.team_barrier();
+
+  // Inter-member scan adding in accumulated totals
+  if (team_rank != 0) { accum = shared[team_rank-1]; }
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    local_total = 0;
+    lambda(i,local_total,false);
+    val = accum;
+    lambda(i,val,true);
+    accum += local_total;
+  }
+}
+
+// placeholder for future function
+template< typename iType, class Lambda, typename ValueType >
+KOKKOS_INLINE_FUNCTION
+void parallel_scan
+  (const Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::OpenMP > >& loop_boundaries,
+   const Lambda & lambda)
+{
+}
+
+
+} /* namespace Kokkos */
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
+#endif /* #ifndef KOKKOS_IMPL_OPENMP_TASK_HPP */
+
diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.cpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.cpp
index f73f1e932a..7d06a2f661 100644
--- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.cpp
+++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.cpp
@@ -49,6 +49,7 @@
 #include <impl/Kokkos_Error.hpp>
 #include <iostream>
 #include <impl/Kokkos_CPUDiscovery.hpp>
+#include <impl/Kokkos_Profiling_Interface.hpp>
 
 #ifdef KOKKOS_HAVE_OPENMP
 
@@ -85,16 +86,8 @@ int OpenMPexec::m_map_rank[ OpenMPexec::MAX_THREAD_COUNT ] = { 0 };
 
 int OpenMPexec::m_pool_topo[ 4 ] = { 0 };
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-OpenMPexec::Pool OpenMPexec::m_pool;
-
-#else
-
 OpenMPexec * OpenMPexec::m_pool[ OpenMPexec::MAX_THREAD_COUNT ] = { 0 };
 
-#endif
-
 void OpenMPexec::verify_is_process( const char * const label )
 {
   if ( omp_in_parallel() ) {
@@ -125,16 +118,12 @@ void OpenMPexec::clear_scratch()
 #pragma omp parallel
   {
     const int rank_rev = m_map_rank[ omp_get_thread_num() ];
-#if KOKKOS_USING_EXP_VIEW
     typedef Kokkos::Experimental::Impl::SharedAllocationRecord< Kokkos::HostSpace , void > Record ;
     if ( m_pool[ rank_rev ] ) {
       Record * const r = Record::get_record( m_pool[ rank_rev ] );
       m_pool[ rank_rev ] = 0 ;
       Record::decrement( r );
     }
-#else
-    m_pool.at(rank_rev).clear();
-#endif
   }
 /* END #pragma omp parallel */
 }
@@ -172,8 +161,6 @@ void OpenMPexec::resize_scratch( size_t reduce_size , size_t thread_size )
       const int rank_rev = m_map_rank[ omp_get_thread_num() ];
       const int rank     = pool_size - ( rank_rev + 1 );
 
-#if KOKKOS_USING_EXP_VIEW
-
       typedef Kokkos::Experimental::Impl::SharedAllocationRecord< Kokkos::HostSpace , void > Record ;
 
       Record * const r = Record::allocate( Kokkos::HostSpace()
@@ -184,15 +171,6 @@ void OpenMPexec::resize_scratch( size_t reduce_size , size_t thread_size )
 
       m_pool[ rank_rev ] = reinterpret_cast<OpenMPexec*>( r->data() );
 
-#else
-
-      #pragma omp critical
-      {
-        m_pool.at(rank_rev) = HostSpace::allocate_and_track( "openmp_scratch", alloc_size );
-      }
-
-#endif
-
       new ( m_pool[ rank_rev ] ) OpenMPexec( rank , ALLOC_EXEC , reduce_size , thread_size );
     }
 /* END #pragma omp parallel */
@@ -330,6 +308,10 @@ void OpenMP::initialize( unsigned thread_count ,
   }
   // Init the array for used for arbitrarily sized atomics
   Impl::init_lock_array_host_space();
+
+  #if (KOKKOS_ENABLE_PROFILING)
+    Kokkos::Profiling::initialize();
+  #endif
 }
 
 //----------------------------------------------------------------------------
@@ -350,6 +332,10 @@ void OpenMP::finalize()
   if ( Impl::s_using_hwloc && Kokkos::hwloc::can_bind_threads() ) {
     hwloc::unbind_this_thread();
   }
+
+  #if (KOKKOS_ENABLE_PROFILING)
+    Kokkos::Profiling::finalize();
+  #endif
 }
 
 //----------------------------------------------------------------------------
diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.hpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.hpp
index 723b2f9429..a01c9cb644 100644
--- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.hpp
+++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.hpp
@@ -46,7 +46,6 @@
 
 #include <impl/Kokkos_Traits.hpp>
 #include <impl/Kokkos_spinwait.hpp>
-#include <impl/Kokkos_AllocationTracker.hpp>
 
 #include <Kokkos_Atomic.hpp>
 #include <iostream>
@@ -63,38 +62,10 @@ public:
 
   enum { MAX_THREAD_COUNT = 4096 };
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-  struct Pool
-  {
-    Pool() : m_trackers() {}
-
-    AllocationTracker m_trackers[ MAX_THREAD_COUNT ];
-
-    OpenMPexec * operator[](int i)
-    {
-      return reinterpret_cast<OpenMPexec *>(m_trackers[i].alloc_ptr());
-    }
-
-    AllocationTracker & at(int i)
-    {
-      return m_trackers[i];
-    }
-  };
-
-
-private:
-
-  static Pool         m_pool; // Indexed by: m_pool_rank_rev
-
-#else
-
 private:
 
   static OpenMPexec * m_pool[ MAX_THREAD_COUNT ]; // Indexed by: m_pool_rank_rev
 
-#endif
-
   static int          m_pool_topo[ 4 ];
   static int          m_map_rank[ MAX_THREAD_COUNT ];
 
@@ -145,6 +116,12 @@ public:
 
   inline long team_work_index() const { return m_team_work_index ; }
 
+  inline int scratch_reduce_size() const
+    { return m_scratch_reduce_end - m_scratch_exec_end ; }
+
+  inline int scratch_thread_size() const
+    { return m_scratch_thread_end - m_scratch_reduce_end ; }
+
   inline void * scratch_reduce() const { return ((char *) this) + m_scratch_exec_end ; }
   inline void * scratch_thread() const { return ((char *) this) + m_scratch_reduce_end ; }
 
@@ -157,15 +134,15 @@ public:
 
   ~OpenMPexec() {}
 
-  OpenMPexec( const int poolRank
-            , const int scratch_exec_size
-            , const int scratch_reduce_size
-            , const int scratch_thread_size )
-    : m_pool_rank( poolRank )
-    , m_pool_rank_rev( pool_size() - ( poolRank + 1 ) )
-    , m_scratch_exec_end( scratch_exec_size )
-    , m_scratch_reduce_end( m_scratch_exec_end   + scratch_reduce_size )
-    , m_scratch_thread_end( m_scratch_reduce_end + scratch_thread_size )
+  OpenMPexec( const int arg_poolRank
+            , const int arg_scratch_exec_size
+            , const int arg_scratch_reduce_size
+            , const int arg_scratch_thread_size )
+    : m_pool_rank( arg_poolRank )
+    , m_pool_rank_rev( pool_size() - ( arg_poolRank + 1 ) )
+    , m_scratch_exec_end( arg_scratch_exec_size )
+    , m_scratch_reduce_end( m_scratch_exec_end   + arg_scratch_reduce_size )
+    , m_scratch_thread_end( m_scratch_reduce_end + arg_scratch_thread_size )
     , m_barrier_state(0)
     {}
 
@@ -330,7 +307,7 @@ public:
 
   Impl::OpenMPexec    & m_exec ;
   scratch_memory_space  m_team_shared ;
-  int                   m_team_shmem ;
+  int                   m_team_scratch_size[2] ;
   int                   m_team_base_rev ;
   int                   m_team_rank_rev ;
   int                   m_team_rank ;
@@ -378,15 +355,15 @@ public:
 
   KOKKOS_INLINE_FUNCTION
   const execution_space::scratch_memory_space& team_shmem() const
-    { return m_team_shared.set_team_thread_mode(1,0) ; }
+    { return m_team_shared.set_team_thread_mode(0,1,0) ; }
 
   KOKKOS_INLINE_FUNCTION
   const execution_space::scratch_memory_space& team_scratch(int) const
-    { return m_team_shared.set_team_thread_mode(1,0) ; }
+    { return m_team_shared.set_team_thread_mode(0,1,0) ; }
 
   KOKKOS_INLINE_FUNCTION
   const execution_space::scratch_memory_space& thread_scratch(int) const
-    { return m_team_shared.set_team_thread_mode(team_size(),team_rank()) ; }
+    { return m_team_shared.set_team_thread_mode(0,team_size(),team_rank()) ; }
 
   KOKKOS_INLINE_FUNCTION int league_rank() const { return m_league_rank ; }
   KOKKOS_INLINE_FUNCTION int league_size() const { return m_league_size ; }
@@ -568,11 +545,12 @@ public:
   inline
   OpenMPexecTeamMember( Impl::OpenMPexec & exec
                       , const TeamPolicyInternal< OpenMP, Properties ...> & team
-                      , const int shmem_size
+                      , const int shmem_size_L1
+                      , const int shmem_size_L2
                       )
     : m_exec( exec )
     , m_team_shared(0,0)
-    , m_team_shmem( shmem_size )
+    , m_team_scratch_size{ shmem_size_L1 , shmem_size_L2 }
     , m_team_base_rev(0)
     , m_team_rank_rev(0)
     , m_team_rank(0)
@@ -580,7 +558,7 @@ public:
     , m_league_rank(0)
     , m_league_end(0)
     , m_league_size( team.league_size() )
-    , m_chunk_size( team.chunk_size() )
+    , m_chunk_size( team.chunk_size()>0?team.chunk_size():team.team_iter() )
     , m_league_chunk_end(0)
     , m_team_lead_exec( *exec.pool_rev( team.team_alloc() * (m_exec.pool_rank_rev()/team.team_alloc()) ))
     , m_team_alloc( team.team_alloc())
@@ -589,10 +567,9 @@ public:
       const int pool_team_rank_rev   = pool_rank_rev % team.team_alloc();
       const int pool_league_rank_rev = pool_rank_rev / team.team_alloc();
       const int pool_num_teams       = OpenMP::thread_pool_size(0)/team.team_alloc();
-      const int chunk_size           = team.chunk_size()>0?team.chunk_size():team.team_iter();
-      const int chunks_per_team      = ( team.league_size() + chunk_size*pool_num_teams-1 ) / (chunk_size*pool_num_teams);
-            int league_iter_end      = team.league_size() - pool_league_rank_rev * chunks_per_team * chunk_size;
-            int league_iter_begin    = league_iter_end - chunks_per_team * chunk_size;
+      const int chunks_per_team      = ( team.league_size() + m_chunk_size*pool_num_teams-1 ) / (m_chunk_size*pool_num_teams);
+            int league_iter_end      = team.league_size() - pool_league_rank_rev * chunks_per_team * m_chunk_size;
+            int league_iter_begin    = league_iter_end - chunks_per_team * m_chunk_size;
       if (league_iter_begin < 0)     league_iter_begin = 0;
       if (league_iter_end>team.league_size()) league_iter_end = team.league_size();
 
@@ -611,7 +588,9 @@ public:
         m_team_rank      = m_team_size - ( m_team_rank_rev + 1 );
         m_league_end     = league_iter_end ;
         m_league_rank    = league_iter_begin ;
-        new( (void*) &m_team_shared ) space( ( (char*) m_exec.pool_rev(m_team_base_rev)->scratch_thread() ) + TEAM_REDUCE_SIZE , m_team_shmem );
+        new( (void*) &m_team_shared ) space( ( (char*) m_exec.pool_rev(m_team_base_rev)->scratch_thread() ) + TEAM_REDUCE_SIZE , m_team_scratch_size[0] ,
+                                             ( (char*) m_exec.pool_rev(m_team_base_rev)->scratch_thread() ) + TEAM_REDUCE_SIZE + m_team_scratch_size[0],
+                                               0 );
       }
 
       if ( (m_team_rank_rev == 0) && (m_invalid_thread == 0) ) {
@@ -627,10 +606,13 @@ public:
 
   void next_static()
     {
-      if ( ++m_league_rank < m_league_end ) {
+      if ( m_league_rank < m_league_end ) {
         team_barrier();
-        new( (void*) &m_team_shared ) space( ( (char*) m_exec.pool_rev(m_team_base_rev)->scratch_thread() ) + TEAM_REDUCE_SIZE , m_team_shmem );
+        new( (void*) &m_team_shared ) space( ( (char*) m_exec.pool_rev(m_team_base_rev)->scratch_thread() ) + TEAM_REDUCE_SIZE , m_team_scratch_size[0] ,
+                                             ( (char*) m_exec.pool_rev(m_team_base_rev)->scratch_thread() ) + TEAM_REDUCE_SIZE + m_team_scratch_size[0],
+                                               0);
       }
+      m_league_rank++;
     }
 
   bool valid_dynamic() {
@@ -661,10 +643,13 @@ public:
     if(m_invalid_thread)
       return;
 
-    team_barrier();
-    if ( ++m_league_rank < m_league_chunk_end ) {
-      new( (void*) &m_team_shared ) space( ( (char*) m_exec.pool_rev(m_team_base_rev)->scratch_thread() ) + TEAM_REDUCE_SIZE , m_team_shmem );
+    if ( m_league_rank < m_league_chunk_end ) {
+      team_barrier();
+      new( (void*) &m_team_shared ) space( ( (char*) m_exec.pool_rev(m_team_base_rev)->scratch_thread() ) + TEAM_REDUCE_SIZE , m_team_scratch_size[0] ,
+                                           ( (char*) m_exec.pool_rev(m_team_base_rev)->scratch_thread() ) + TEAM_REDUCE_SIZE + m_team_scratch_size[0],
+                                             0);
     }
+    m_league_rank++;
   }
 
   static inline int team_reduce_size() { return TEAM_REDUCE_SIZE ; }
@@ -687,8 +672,10 @@ public:
     m_team_size = p.m_team_size;
     m_team_alloc = p.m_team_alloc;
     m_team_iter = p.m_team_iter;
-    m_team_scratch_size = p.m_team_scratch_size;
-    m_thread_scratch_size = p.m_thread_scratch_size;
+    m_team_scratch_size[0] = p.m_team_scratch_size[0];
+    m_thread_scratch_size[0] = p.m_thread_scratch_size[0];
+    m_team_scratch_size[1] = p.m_team_scratch_size[1];
+    m_thread_scratch_size[1] = p.m_thread_scratch_size[1];
     m_chunk_size = p.m_chunk_size;
     return *this;
   }
@@ -719,8 +706,8 @@ private:
   int m_team_alloc ;
   int m_team_iter ;
 
-  size_t m_team_scratch_size;
-  size_t m_thread_scratch_size;
+  size_t m_team_scratch_size[2];
+  size_t m_thread_scratch_size[2];
 
   int m_chunk_size;
 
@@ -753,15 +740,19 @@ public:
 
   inline int team_size()   const { return m_team_size ; }
   inline int league_size() const { return m_league_size ; }
-  inline size_t scratch_size() const { return m_team_scratch_size + m_team_size*m_thread_scratch_size ; }
+  inline size_t scratch_size(const int& level, int team_size_ = -1) const {
+    if(team_size_ < 0)
+      team_size_ = m_team_size;
+    return m_team_scratch_size[level] + team_size_*m_thread_scratch_size[level] ;
+  }
 
   /** \brief  Specify league size, request team size */
   TeamPolicyInternal( typename traits::execution_space &
             , int league_size_request
             , int team_size_request
             , int /* vector_length_request */ = 1 )
-            : m_team_scratch_size ( 0 )
-            , m_thread_scratch_size ( 0 )
+            : m_team_scratch_size { 0 , 0 }
+            , m_thread_scratch_size { 0 , 0 }
             , m_chunk_size(0)
     { init( league_size_request , team_size_request ); }
 
@@ -769,24 +760,24 @@ public:
             , int league_size_request
             , const Kokkos::AUTO_t & /* team_size_request */
             , int /* vector_length_request */ = 1)
-            : m_team_scratch_size ( 0 )
-            , m_thread_scratch_size ( 0 )
+            : m_team_scratch_size { 0 , 0 }
+            , m_thread_scratch_size { 0 , 0 }
             , m_chunk_size(0)
     { init( league_size_request , traits::execution_space::thread_pool_size(2) ); }
 
   TeamPolicyInternal( int league_size_request
             , int team_size_request
             , int /* vector_length_request */ = 1 )
-            : m_team_scratch_size ( 0 )
-            , m_thread_scratch_size ( 0 )
+            : m_team_scratch_size { 0 , 0 }
+            , m_thread_scratch_size { 0 , 0 }
             , m_chunk_size(0)
     { init( league_size_request , team_size_request ); }
 
   TeamPolicyInternal( int league_size_request
             , const Kokkos::AUTO_t & /* team_size_request */
             , int /* vector_length_request */ = 1 )
-            : m_team_scratch_size ( 0 )
-            , m_thread_scratch_size ( 0 )
+            : m_team_scratch_size { 0 , 0 }
+            , m_thread_scratch_size { 0 , 0 }
             , m_chunk_size(0)
     { init( league_size_request , traits::execution_space::thread_pool_size(2) ); }
 
@@ -803,24 +794,21 @@ public:
   }
 
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerTeamValue& per_team) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_team_scratch_size = per_team.value;
+    p.m_team_scratch_size[level] = per_team.value;
     return p;
   };
 
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerThreadValue& per_thread) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_thread_scratch_size = per_thread.value;
+    p.m_thread_scratch_size[level] = per_thread.value;
     return p;
   };
 
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerTeamValue& per_team, const PerThreadValue& per_thread) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_team_scratch_size = per_team.value;
-    p.m_thread_scratch_size = per_thread.value;
+    p.m_team_scratch_size[level] = per_team.value;
+    p.m_thread_scratch_size[level] = per_thread.value;
     return p;
   };
 
diff --git a/lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.cpp b/lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.cpp
index 92c5b97b9a..3123a297c4 100644
--- a/lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.cpp
+++ b/lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.cpp
@@ -104,7 +104,7 @@ namespace Kokkos {
 
 int Qthread::is_initialized()
 {
-  Impl::s_number_workers != 0 ;
+  return Impl::s_number_workers != 0 ;
 }
 
 int Qthread::concurrency()
diff --git a/lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.hpp b/lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.hpp
index a1f533b232..f948eb2903 100644
--- a/lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.hpp
+++ b/lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -113,7 +113,7 @@ public:
         m_worker_state = QthreadExec::Inactive ;
         Impl::spinwait( m_worker_state , QthreadExec::Inactive );
       }
-    
+
       for ( n = 1 ; ( ! ( rev_rank & n ) ) && ( ( j = rev_rank + n ) < m_worker_size ) ; n <<= 1 ) {
         m_worker_base[j]->m_worker_state = QthreadExec::Active ;
       }
@@ -136,7 +136,7 @@ public:
           m_worker_state = QthreadExec::Inactive ;
           Impl::spinwait( m_worker_state , QthreadExec::Inactive );
         }
-    
+
         for ( n = 1 ; ( ! ( rev_rank & n ) ) && ( ( j = rev_rank + n ) < team_size ) ; n <<= 1 ) {
           m_shepherd_base[j]->m_worker_state = QthreadExec::Active ;
         }
@@ -145,11 +145,13 @@ public:
 
   //----------------------------------------
   /** Reduce across all workers participating in the 'exec_all' */
-  template< class FunctorType , class ArgTag >
+  template< class FunctorType , class ReducerType , class ArgTag >
   inline
-  void exec_all_reduce( const FunctorType & func ) const
+  void exec_all_reduce( const FunctorType & func, const ReducerType & reduce ) const
     {
-      typedef Kokkos::Impl::FunctorValueJoin< FunctorType , ArgTag > ValueJoin ;
+      typedef Kokkos::Impl::if_c< std::is_same<InvalidType, ReducerType>::value, FunctorType, ReducerType > ReducerConditional;
+      typedef typename ReducerConditional::type ReducerTypeFwd;
+      typedef Kokkos::Impl::FunctorValueJoin< ReducerTypeFwd, ArgTag > ValueJoin ;
 
       const int rev_rank = m_worker_size - ( m_worker_rank + 1 );
 
@@ -160,14 +162,14 @@ public:
 
         Impl::spinwait( fan.m_worker_state , QthreadExec::Active );
 
-        ValueJoin::join( func , m_scratch_alloc , fan.m_scratch_alloc );
+        ValueJoin::join( ReducerConditional::select(func , reduce) , m_scratch_alloc , fan.m_scratch_alloc );
       }
 
       if ( rev_rank ) {
         m_worker_state = QthreadExec::Inactive ;
         Impl::spinwait( m_worker_state , QthreadExec::Inactive );
       }
-    
+
       for ( n = 1 ; ( ! ( rev_rank & n ) ) && ( ( j = rev_rank + n ) < m_worker_size ) ; n <<= 1 ) {
         m_worker_base[j]->m_worker_state = QthreadExec::Active ;
       }
@@ -197,7 +199,7 @@ public:
       }
       else {
         // Root thread scans across values before releasing threads
-        // Worker data is in reverse order, so m_worker_base[0] is the 
+        // Worker data is in reverse order, so m_worker_base[0] is the
         // highest ranking thread.
 
         // Copy from lower ranking to higher ranking worker.
@@ -216,7 +218,7 @@ public:
           ValueJoin::join( func , m_worker_base[i-1]->m_scratch_alloc , m_worker_base[i]->m_scratch_alloc );
         }
       }
-    
+
       for ( n = 1 ; ( ! ( rev_rank & n ) ) && ( ( j = rev_rank + n ) < m_worker_size ) ; n <<= 1 ) {
         m_worker_base[j]->m_worker_state = QthreadExec::Active ;
       }
@@ -349,7 +351,7 @@ public:
       }
       else {
         // Root thread scans across values before releasing threads
-        // Worker data is in reverse order, so m_shepherd_base[0] is the 
+        // Worker data is in reverse order, so m_shepherd_base[0] is the
         // highest ranking thread.
 
         // Copy from lower ranking to higher ranking worker.
@@ -371,7 +373,7 @@ public:
 
         memory_fence();
       }
-    
+
       for ( n = 1 ; ( ! ( rev_rank & n ) ) && ( ( j = rev_rank + n ) < team_size ) ; n <<= 1 ) {
         m_shepherd_base[j]->m_worker_state = QthreadExec::Active ;
       }
diff --git a/lib/kokkos/core/src/Qthread/Kokkos_Qthread_Parallel.hpp b/lib/kokkos/core/src/Qthread/Kokkos_Qthread_Parallel.hpp
index 2e3cdce562..5b6419289f 100644
--- a/lib/kokkos/core/src/Qthread/Kokkos_Qthread_Parallel.hpp
+++ b/lib/kokkos/core/src/Qthread/Kokkos_Qthread_Parallel.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -130,9 +130,10 @@ public:
 
 //----------------------------------------------------------------------------
 
-template< class FunctorType , class ... Traits >
+template< class FunctorType , class ReducerType , class ... Traits >
 class ParallelReduce< FunctorType
                     , Kokkos::RangePolicy< Traits ... >
+                    , ReducerType
                     , Kokkos::Qthread
                     >
 {
@@ -141,18 +142,24 @@ private:
   typedef Kokkos::RangePolicy< Traits ... >  Policy ;
 
   typedef typename Policy::work_tag     WorkTag ;
-  typedef typename Policy::member_type  Member ;
   typedef typename Policy::WorkRange    WorkRange ;
+  typedef typename Policy::member_type  Member ;
 
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType, WorkTag > ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueInit<   FunctorType, WorkTag > ValueInit ;
+  typedef Kokkos::Impl::if_c< std::is_same<InvalidType, ReducerType>::value, FunctorType, ReducerType > ReducerConditional;
+  typedef typename ReducerConditional::type ReducerTypeFwd;
+
+  // Static Assert WorkTag void if ReducerType not InvalidType
+
+  typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd, WorkTag > ValueTraits ;
+  typedef Kokkos::Impl::FunctorValueInit<   ReducerTypeFwd, WorkTag > ValueInit ;
 
   typedef typename ValueTraits::pointer_type    pointer_type ;
   typedef typename ValueTraits::reference_type  reference_type ;
 
-  const FunctorType  m_functor ;
-  const Policy       m_policy ;
-  const pointer_type m_result_ptr ;
+  const FunctorType   m_functor ;
+  const Policy        m_policy ;
+  const ReducerType   m_reducer ;
+  const pointer_type  m_result_ptr ;
 
   template< class TagType >
   inline static
@@ -187,9 +194,10 @@ private:
 
     ParallelReduce::template exec_range< WorkTag >(
       self.m_functor, range.begin(), range.end(),
-      ValueInit::init( self.m_functor , exec.exec_all_reduce_value() ) );
+      ValueInit::init( ReducerConditional::select(self.m_functor , self.m_reducer)
+                     , exec.exec_all_reduce_value() ) );
 
-    exec.template exec_all_reduce<FunctorType, WorkTag >( self.m_functor );
+    exec.template exec_all_reduce< FunctorType, ReducerType, WorkTag >( self.m_functor, self.m_reducer );
   }
 
 public:
@@ -197,26 +205,39 @@ public:
   inline
   void execute() const
     {
-      QthreadExec::resize_worker_scratch( ValueTraits::value_size( m_functor ) , 0 );
+      QthreadExec::resize_worker_scratch( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) , 0 );
       Impl::QthreadExec::exec_all( Qthread::instance() , & ParallelReduce::exec , this );
 
       const pointer_type data = (pointer_type) QthreadExec::exec_all_reduce_result();
 
-      Kokkos::Impl::FunctorFinal< FunctorType , typename Policy::work_tag >::final( m_functor , data );
+      Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTag >::final( ReducerConditional::select(m_functor , m_reducer) , data );
 
       if ( m_result_ptr ) {
-        const unsigned n = ValueTraits::value_count( m_functor );
+        const unsigned n = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) );
         for ( unsigned i = 0 ; i < n ; ++i ) { m_result_ptr[i] = data[i]; }
       }
     }
 
-  template< class HostViewType >
+  template< class ViewType >
   ParallelReduce( const FunctorType  & arg_functor
                 , const Policy       & arg_policy
-                , const HostViewType & arg_result_view )
+                , const ViewType & arg_result_view
+                , typename std::enable_if<Kokkos::is_view< ViewType >::value &&
+                                          !Kokkos::is_reducer_type< ReducerType >::value
+                                          , void*>::type = NULL)
     : m_functor( arg_functor )
-    , m_policy(  arg_policy )
-    , m_result_ptr( arg_result_view.ptr_on_device() )
+    , m_policy( arg_policy )
+    , m_reducer( InvalidType() )
+    , m_result_ptr( arg_result_view.data() )
+    { }
+
+  ParallelReduce( const FunctorType & arg_functor
+                , Policy       arg_policy
+                , const ReducerType& reducer )
+    : m_functor( arg_functor )
+    , m_policy( arg_policy )
+    , m_reducer( reducer )
+    , m_result_ptr( reducer.result_view().data() )
     { }
 };
 
@@ -291,10 +312,12 @@ public:
 
 //----------------------------------------------------------------------------
 
-template< class FunctorType , class ... Properties >
+template< class FunctorType , class ReducerType , class ... Properties >
 class ParallelReduce< FunctorType
                     , TeamPolicy< Properties... >
-                    , Kokkos::Qthread >
+                    , ReducerType
+                    , Kokkos::Qthread
+                    >
 {
 private:
 
@@ -303,14 +326,18 @@ private:
   typedef typename Policy::work_tag     WorkTag ;
   typedef typename Policy::member_type  Member ;
 
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType, WorkTag > ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueInit<   FunctorType, WorkTag > ValueInit ;
+  typedef Kokkos::Impl::if_c< std::is_same<InvalidType,ReducerType>::value, FunctorType, ReducerType> ReducerConditional;
+  typedef typename ReducerConditional::type ReducerTypeFwd;
+
+  typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd , WorkTag >  ValueTraits ;
+  typedef Kokkos::Impl::FunctorValueInit<   ReducerTypeFwd , WorkTag >  ValueInit ;
 
   typedef typename ValueTraits::pointer_type    pointer_type ;
   typedef typename ValueTraits::reference_type  reference_type ;
 
   const FunctorType  m_functor ;
   const Policy       m_policy ;
+  const ReducerType  m_reducer ;
   const pointer_type m_result_ptr ;
 
   template< class TagType >
@@ -345,9 +372,10 @@ private:
     ParallelReduce::template exec_team< WorkTag >
       ( self.m_functor
       , Member( exec , self.m_policy )
-      , ValueInit::init( self.m_functor , exec.exec_all_reduce_value() ) );
+      , ValueInit::init( ReducerConditional::select( self.m_functor , self.m_reducer )
+                       , exec.exec_all_reduce_value() ) );
 
-    exec.template exec_all_reduce< FunctorType , WorkTag >( self.m_functor );
+    exec.template exec_all_reduce< FunctorType, ReducerType, WorkTag >( self.m_functor, self.m_reducer );
   }
 
 public:
@@ -356,29 +384,43 @@ public:
   void execute() const
     {
       QthreadExec::resize_worker_scratch
-        ( /* reduction   memory */ ValueTraits::value_size( m_functor )
+        ( /* reduction   memory */ ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) )
         , /* team shared memory */ FunctorTeamShmemSize< FunctorType >::value( m_functor , m_policy.team_size() ) );
 
       Impl::QthreadExec::exec_all( Qthread::instance() , & ParallelReduce::exec , this );
 
       const pointer_type data = (pointer_type) QthreadExec::exec_all_reduce_result();
 
-      Kokkos::Impl::FunctorFinal< FunctorType , typename Policy::work_tag >::final( m_functor , data );
+      Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTag >::final( ReducerConditional::select(m_functor , m_reducer), data );
 
       if ( m_result_ptr ) {
-        const unsigned n = ValueTraits::value_count( m_functor );
+        const unsigned n = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) );
         for ( unsigned i = 0 ; i < n ; ++i ) { m_result_ptr[i] = data[i]; }
       }
     }
 
   template< class ViewType >
-  ParallelReduce( const FunctorType & arg_functor ,
-                  const Policy      & arg_policy ,
-                  const ViewType    & arg_result )
+  ParallelReduce( const FunctorType & arg_functor
+                , const Policy      & arg_policy
+                , const ViewType    & arg_result
+                , typename std::enable_if<Kokkos::is_view< ViewType >::value &&
+                                          !Kokkos::is_reducer_type< ReducerType >::value
+                                          , void*>::type = NULL)
     : m_functor( arg_functor )
-    , m_policy(  arg_policy )
+    , m_policy( arg_policy )
+    , m_reducer( InvalidType() )
     , m_result_ptr( arg_result.ptr_on_device() )
     { }
+
+  inline
+  ParallelReduce( const FunctorType & arg_functor
+                , Policy       arg_policy
+                , const ReducerType& reducer )
+  : m_functor( arg_functor )
+  , m_policy( arg_policy )
+  , m_reducer( reducer )
+  , m_result_ptr( reducer.result_view().data() )
+  { }
 };
 
 //----------------------------------------------------------------------------
@@ -395,8 +437,8 @@ private:
   typedef Kokkos::RangePolicy< Traits ... >  Policy ;
 
   typedef typename Policy::work_tag     WorkTag ;
-  typedef typename Policy::member_type  Member ;
   typedef typename Policy::WorkRange    WorkRange ;
+  typedef typename Policy::member_type  Member ;
 
   typedef Kokkos::Impl::FunctorValueTraits< FunctorType, WorkTag > ValueTraits ;
   typedef Kokkos::Impl::FunctorValueInit<   FunctorType, WorkTag > ValueInit ;
diff --git a/lib/kokkos/core/src/Qthread/Kokkos_Qthread_TaskPolicy.cpp b/lib/kokkos/core/src/Qthread/Kokkos_Qthread_TaskPolicy.cpp
index 0765072030..8cc39d277c 100644
--- a/lib/kokkos/core/src/Qthread/Kokkos_Qthread_TaskPolicy.cpp
+++ b/lib/kokkos/core/src/Qthread/Kokkos_Qthread_TaskPolicy.cpp
@@ -58,6 +58,8 @@
 #include <Kokkos_Atomic.hpp>
 #include <Qthread/Kokkos_Qthread_TaskPolicy.hpp>
 
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
@@ -120,13 +122,13 @@ Task::~TaskMember()
 }
 
 
-Task::TaskMember( const function_verify_type        arg_verify
-                , const function_dealloc_type       arg_dealloc
-                , const function_apply_single_type  arg_apply_single
-                , const function_apply_team_type    arg_apply_team
-                , volatile int &                    arg_active_count
-                , const unsigned                    arg_sizeof_derived
-                , const unsigned                    arg_dependence_capacity
+Task::TaskMember( const function_verify_type   arg_verify
+                , const function_dealloc_type  arg_dealloc
+                , const function_single_type   arg_apply_single
+                , const function_team_type     arg_apply_team
+                , volatile int &               arg_active_count
+                , const unsigned               arg_sizeof_derived
+                , const unsigned               arg_dependence_capacity
                 )
   : m_dealloc( arg_dealloc )
   , m_verify(  arg_verify )
@@ -144,12 +146,12 @@ Task::TaskMember( const function_verify_type        arg_verify
   for ( unsigned i = 0 ; i < arg_dependence_capacity ; ++i ) m_dep[i] = 0 ;
 }
 
-Task::TaskMember( const function_dealloc_type       arg_dealloc
-                , const function_apply_single_type  arg_apply_single
-                , const function_apply_team_type    arg_apply_team
-                , volatile int &                    arg_active_count
-                , const unsigned                    arg_sizeof_derived
-                , const unsigned                    arg_dependence_capacity
+Task::TaskMember( const function_dealloc_type  arg_dealloc
+                , const function_single_type   arg_apply_single
+                , const function_team_type     arg_apply_team
+                , volatile int &               arg_active_count
+                , const unsigned               arg_sizeof_derived
+                , const unsigned               arg_dependence_capacity
                 )
   : m_dealloc( arg_dealloc )
   , m_verify(  & Task::verify_type<void> )
@@ -316,12 +318,8 @@ aligned_t Task::qthread_func( void * arg )
                                         , int(Kokkos::Experimental::TASK_STATE_EXECUTING)
                                         );
 
-  // It is a single thread's responsibility to close out
-  // this task's execution.
-  bool close_out = false ;
-
   if ( task->m_apply_team && ! task->m_apply_single ) {
-    const Kokkos::Impl::QthreadTeamPolicyMember::TaskTeam task_team_tag ;
+    Kokkos::Impl::QthreadTeamPolicyMember::TaskTeam task_team_tag ;
 
     // Initialize team size and rank with shephered info
     Kokkos::Impl::QthreadTeamPolicyMember member( task_team_tag );
@@ -344,7 +342,7 @@ fflush(stdout);
     if ( member.team_rank() == 0 ) task->closeout();
     member.team_barrier();
   }
-  else if ( task->m_apply_team && task->m_apply_single == reinterpret_cast<function_apply_single_type>(1) ) {
+  else if ( task->m_apply_team && task->m_apply_single == reinterpret_cast<function_single_type>(1) ) {
     // Team hard-wired to one, no cloning
     Kokkos::Impl::QthreadTeamPolicyMember member ;
     (*task->m_apply_team)( task , member );
@@ -488,5 +486,6 @@ void wait( Kokkos::Experimental::TaskPolicy< Kokkos::Qthread > & policy )
 } // namespace Experimental
 } // namespace Kokkos
 
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
 #endif /* #if defined( KOKKOS_HAVE_QTHREAD ) */
 
diff --git a/lib/kokkos/core/src/Qthread/Kokkos_Qthread_TaskPolicy.hpp b/lib/kokkos/core/src/Qthread/Kokkos_Qthread_TaskPolicy.hpp
index 118f13d9f1..22a565503d 100644
--- a/lib/kokkos/core/src/Qthread/Kokkos_Qthread_TaskPolicy.hpp
+++ b/lib/kokkos/core/src/Qthread/Kokkos_Qthread_TaskPolicy.hpp
@@ -69,6 +69,8 @@
 
 #include <impl/Kokkos_FunctorAdapter.hpp>
 
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
 //----------------------------------------------------------------------------
 
 namespace Kokkos {
@@ -80,24 +82,24 @@ class TaskMember< Kokkos::Qthread , void , void >
 {
 public:
 
-  typedef void         (* function_apply_single_type) ( TaskMember * );
-  typedef void         (* function_apply_team_type)   ( TaskMember * , Kokkos::Impl::QthreadTeamPolicyMember & );
-  typedef void         (* function_dealloc_type)( TaskMember * );
   typedef TaskMember * (* function_verify_type) ( TaskMember * );
+  typedef void         (* function_single_type) ( TaskMember * );
+  typedef void         (* function_team_type)   ( TaskMember * , Kokkos::Impl::QthreadTeamPolicyMember & );
+  typedef void         (* function_dealloc_type)( TaskMember * );
 
 private:
 
-  const function_dealloc_type       m_dealloc ;       ///< Deallocation
-  const function_verify_type        m_verify ;        ///< Result type verification
-  const function_apply_single_type  m_apply_single ;  ///< Apply function
-  const function_apply_team_type    m_apply_team ;    ///< Apply function
-  int volatile * const              m_active_count ;  ///< Count of active tasks on this policy
-  aligned_t                         m_qfeb ;          ///< Qthread full/empty bit
-  TaskMember ** const               m_dep ;           ///< Dependences
-  const int                         m_dep_capacity ;  ///< Capacity of dependences
-  int                               m_dep_size ;      ///< Actual count of dependences
-  int                               m_ref_count ;     ///< Reference count
-  int                               m_state ;         ///< State of the task
+  const function_dealloc_type  m_dealloc ;       ///< Deallocation
+  const function_verify_type   m_verify ;        ///< Result type verification
+  const function_single_type   m_apply_single ;  ///< Apply function
+  const function_team_type     m_apply_team ;    ///< Apply function
+  int volatile * const         m_active_count ;  ///< Count of active tasks on this policy
+  aligned_t                    m_qfeb ;          ///< Qthread full/empty bit
+  TaskMember ** const          m_dep ;           ///< Dependences
+  const int                    m_dep_capacity ;  ///< Capacity of dependences
+  int                          m_dep_size ;      ///< Actual count of dependences
+  int                          m_ref_count ;     ///< Reference count
+  int                          m_state ;         ///< State of the task
 
   TaskMember() /* = delete */ ;
   TaskMember( const TaskMember & ) /* = delete */ ;
@@ -128,22 +130,22 @@ protected :
   ~TaskMember();
 
   // Used by TaskMember< Qthread , ResultType , void >
-  TaskMember( const function_verify_type        arg_verify
-            , const function_dealloc_type       arg_dealloc
-            , const function_apply_single_type  arg_apply_single
-            , const function_apply_team_type    arg_apply_team
-            , volatile int &                    arg_active_count
-            , const unsigned                    arg_sizeof_derived
-            , const unsigned                    arg_dependence_capacity
+  TaskMember( const function_verify_type   arg_verify
+            , const function_dealloc_type  arg_dealloc
+            , const function_single_type   arg_apply_single
+            , const function_team_type     arg_apply_team
+            , volatile int &               arg_active_count
+            , const unsigned               arg_sizeof_derived
+            , const unsigned               arg_dependence_capacity
             );
 
   // Used for TaskMember< Qthread , void , void >
-  TaskMember( const function_dealloc_type       arg_dealloc
-            , const function_apply_single_type  arg_apply_single
-            , const function_apply_team_type    arg_apply_team
-            , volatile int &                    arg_active_count
-            , const unsigned                    arg_sizeof_derived
-            , const unsigned                    arg_dependence_capacity
+  TaskMember( const function_dealloc_type  arg_dealloc
+            , const function_single_type   arg_apply_single
+            , const function_team_type     arg_apply_team
+            , volatile int &               arg_active_count
+            , const unsigned               arg_sizeof_derived
+            , const unsigned               arg_dependence_capacity
             );
 
 public:
@@ -221,7 +223,7 @@ public:
       typedef typename DerivedTaskType::functor_type  functor_type ;
       typedef typename functor_type::value_type       value_type ;
 
-      const function_apply_single_type flag = reinterpret_cast<function_apply_single_type>( arg_is_team ? 0 : 1 );
+      const function_single_type flag = reinterpret_cast<function_single_type>( arg_is_team ? 0 : 1 );
 
       DerivedTaskType * const task =
         new( allocate( sizeof(DerivedTaskType) , arg_dependence_capacity ) )
@@ -379,16 +381,16 @@ protected:
 
   typedef TaskMember< Kokkos::Qthread , void , void >  task_root_type ;
   typedef task_root_type::function_dealloc_type        function_dealloc_type ;
-  typedef task_root_type::function_apply_single_type   function_apply_single_type ;
-  typedef task_root_type::function_apply_team_type     function_apply_team_type ;
+  typedef task_root_type::function_single_type         function_single_type ;
+  typedef task_root_type::function_team_type           function_team_type ;
 
   inline
-  TaskMember( const function_dealloc_type       arg_dealloc
-            , const function_apply_single_type  arg_apply_single
-            , const function_apply_team_type    arg_apply_team
-            , volatile int &                    arg_active_count
-            , const unsigned                    arg_sizeof_derived
-            , const unsigned                    arg_dependence_capacity
+  TaskMember( const function_dealloc_type  arg_dealloc
+            , const function_single_type   arg_apply_single
+            , const function_team_type     arg_apply_team
+            , volatile int &               arg_active_count
+            , const unsigned               arg_sizeof_derived
+            , const unsigned               arg_dependence_capacity
             )
     : task_root_type( & task_root_type::template verify_type< ResultType >
                     , arg_dealloc
@@ -413,17 +415,17 @@ public:
   typedef TaskMember< Kokkos::Qthread , void , void >        task_root_type ;
   typedef TaskMember< Kokkos::Qthread , ResultType , void >  task_base_type ;
   typedef task_root_type::function_dealloc_type              function_dealloc_type ;
-  typedef task_root_type::function_apply_single_type         function_apply_single_type ;
-  typedef task_root_type::function_apply_team_type           function_apply_team_type ;
+  typedef task_root_type::function_single_type               function_single_type ;
+  typedef task_root_type::function_team_type                 function_team_type ;
 
   inline
-  TaskMember( const function_dealloc_type       arg_dealloc
-            , const function_apply_single_type  arg_apply_single
-            , const function_apply_team_type    arg_apply_team
-            , volatile int &                    arg_active_count
-            , const unsigned                    arg_sizeof_derived
-            , const unsigned                    arg_dependence_capacity
-            , const functor_type &              arg_functor
+  TaskMember( const function_dealloc_type  arg_dealloc
+            , const function_single_type   arg_apply_single
+            , const function_team_type     arg_apply_team
+            , volatile int &               arg_active_count
+            , const unsigned               arg_sizeof_derived
+            , const unsigned               arg_dependence_capacity
+            , const functor_type &         arg_functor
             )
     : task_base_type( arg_dealloc
                     , arg_apply_single
@@ -453,6 +455,7 @@ class TaskPolicy< Kokkos::Qthread >
 public:
 
   typedef Kokkos::Qthread                        execution_space ;
+  typedef TaskPolicy                             execution_policy ;
   typedef Kokkos::Impl::QthreadTeamPolicyMember  member_type ;
 
 private:
@@ -489,14 +492,17 @@ public:
     , const unsigned arg_task_team_size = 0 /* choose default */
     );
 
-  TaskPolicy() = default ;
-  TaskPolicy( TaskPolicy && rhs ) = default ;
-  TaskPolicy( const TaskPolicy & rhs ) = default ;
-  TaskPolicy & operator = ( TaskPolicy && rhs ) = default ;
-  TaskPolicy & operator = ( const TaskPolicy & rhs ) = default ;
+  KOKKOS_FUNCTION TaskPolicy() = default ;
+  KOKKOS_FUNCTION TaskPolicy( TaskPolicy && rhs ) = default ;
+  KOKKOS_FUNCTION TaskPolicy( const TaskPolicy & rhs ) = default ;
+  KOKKOS_FUNCTION TaskPolicy & operator = ( TaskPolicy && rhs ) = default ;
+  KOKKOS_FUNCTION TaskPolicy & operator = ( const TaskPolicy & rhs ) = default ;
 
   //----------------------------------------
 
+  KOKKOS_INLINE_FUNCTION
+  int allocated_task_count() const { return m_active_count ; }
+
   template< class ValueType >
   const Future< ValueType , execution_space > &
     spawn( const Future< ValueType , execution_space > & f 
@@ -653,5 +659,6 @@ public:
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
 #endif /* #define KOKKOS_QTHREAD_TASK_HPP */
 
diff --git a/lib/kokkos/core/src/Qthread/README b/lib/kokkos/core/src/Qthread/README
index 5d8f29a4ee..6e6c86a9ef 100644
--- a/lib/kokkos/core/src/Qthread/README
+++ b/lib/kokkos/core/src/Qthread/README
@@ -3,26 +3,23 @@
 
 # Cloning repository and branch:
 
-git clone https://github.com/stelleg/qthreads qthreads-with-clone
+git clone git@github.com:Qthreads/qthreads.git qthreads
 
-cd qthreads-with-clone
+cd qthreads
 
-# Added to ./git/config
-#
-# [branch "cloned_tasks"]
-#        remote = origin
-#        merge = refs/heads/cloned_tasks
-#
+# checkout branch with "cloned tasks"
 
-git branch cloned_tasks
-git checkout cloned_tasks
-git pull
+git checkout dev-kokkos
+
+# Configure/autogen
 
 sh autogen.sh
 
-# configurure with 'hwloc' installation:
+# configure with 'hwloc' installation:
 
 ./configure CFLAGS="-DCLONED_TASKS -DQTHREAD_LOCAL_PRIORITY" --with-hwloc=${HWLOCDIR} --prefix=${INSTALLDIR}
 
+# install
 
+make install
 
diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp
index e1d3fe06e6..5f0b8f70cd 100644
--- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp
+++ b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp
@@ -53,6 +53,7 @@
 #include <Kokkos_Core.hpp>
 #include <impl/Kokkos_Error.hpp>
 #include <impl/Kokkos_CPUDiscovery.hpp>
+#include <impl/Kokkos_Profiling_Interface.hpp>
 
 
 //----------------------------------------------------------------------------
@@ -134,11 +135,7 @@ void ThreadsExec::driver(void)
 
 ThreadsExec::ThreadsExec()
   : m_pool_base(0)
-#if ! KOKKOS_USING_EXP_VIEW
-  , m_scratch()
-#else
   , m_scratch(0)
-#endif
   , m_scratch_reduce_end(0)
   , m_scratch_thread_end(0)
   , m_numa_rank(0)
@@ -198,8 +195,6 @@ ThreadsExec::~ThreadsExec()
 {
   const unsigned entry = m_pool_size - ( m_pool_rank + 1 );
 
-#if KOKKOS_USING_EXP_VIEW
-
   typedef Kokkos::Experimental::Impl::SharedAllocationRecord< Kokkos::HostSpace , void > Record ;
 
   if ( m_scratch ) {
@@ -210,12 +205,6 @@ ThreadsExec::~ThreadsExec()
     Record::decrement( r );
   }
 
-#else
-
-  m_scratch.clear();
-
-#endif
-
   m_pool_base   = 0 ;
   m_scratch_reduce_end = 0 ;
   m_scratch_thread_end = 0 ;
@@ -439,8 +428,6 @@ void * ThreadsExec::root_reduce_scratch()
 
 void ThreadsExec::execute_resize_scratch( ThreadsExec & exec , const void * )
 {
-#if KOKKOS_USING_EXP_VIEW
-
   typedef Kokkos::Experimental::Impl::SharedAllocationRecord< Kokkos::HostSpace , void > Record ;
 
   if ( exec.m_scratch ) {
@@ -451,19 +438,11 @@ void ThreadsExec::execute_resize_scratch( ThreadsExec & exec , const void * )
     Record::decrement( r );
   }
 
-#else
-
-  exec.m_scratch.clear();
-
-#endif
-
   exec.m_scratch_reduce_end = s_threads_process.m_scratch_reduce_end ;
   exec.m_scratch_thread_end = s_threads_process.m_scratch_thread_end ;
 
   if ( s_threads_process.m_scratch_thread_end ) {
 
-#if KOKKOS_USING_EXP_VIEW
-
     // Allocate tracked memory:
     {
       Record * const r = Record::allocate( Kokkos::HostSpace() , "thread_scratch" , s_threads_process.m_scratch_thread_end );
@@ -475,15 +454,6 @@ void ThreadsExec::execute_resize_scratch( ThreadsExec & exec , const void * )
 
     unsigned * ptr = reinterpret_cast<unsigned *>( exec.m_scratch );
 
-#else
-
-    exec.m_scratch =
-      HostSpace::allocate_and_track( "thread_scratch" , s_threads_process.m_scratch_thread_end );
-
-    unsigned * ptr = reinterpret_cast<unsigned *>( exec.m_scratch.alloc_ptr() );
-
-#endif
-
     unsigned * const end = ptr + s_threads_process.m_scratch_thread_end / sizeof(unsigned);
 
     // touch on this thread
@@ -520,11 +490,7 @@ void * ThreadsExec::resize_scratch( size_t reduce_size , size_t thread_size )
     s_threads_process.m_scratch = s_threads_exec[0]->m_scratch ;
   }
 
-#if KOKKOS_USING_EXP_VIEW
   return s_threads_process.m_scratch ;
-#else
-  return s_threads_process.m_scratch.alloc_ptr() ;
-#endif
 }
 
 //----------------------------------------------------------------------------
@@ -758,6 +724,9 @@ void ThreadsExec::initialize( unsigned thread_count ,
   // Init the array for used for arbitrarily sized atomics
   Impl::init_lock_array_host_space();
 
+  #if (KOKKOS_ENABLE_PROFILING)
+    Kokkos::Profiling::initialize();
+  #endif
 }
 
 //----------------------------------------------------------------------------
@@ -807,6 +776,10 @@ void ThreadsExec::finalize()
   s_threads_process.m_pool_size       = 1 ;
   s_threads_process.m_pool_fan_size   = 0 ;
   s_threads_process.m_pool_state = ThreadsExec::Inactive ;
+
+  #if (KOKKOS_ENABLE_PROFILING)
+    Kokkos::Profiling::finalize();
+  #endif
 }
 
 //----------------------------------------------------------------------------
diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp
index b2019aaf77..4ec1450d0f 100644
--- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp
+++ b/lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp
@@ -49,7 +49,6 @@
 #include <utility>
 #include <impl/Kokkos_spinwait.hpp>
 #include <impl/Kokkos_FunctorAdapter.hpp>
-#include <impl/Kokkos_AllocationTracker.hpp>
 
 #include <Kokkos_Atomic.hpp>
 
@@ -89,11 +88,7 @@ private:
 
   ThreadsExec * const * m_pool_base ; ///< Base for pool fan-in
 
-#if ! KOKKOS_USING_EXP_VIEW
-  Impl::AllocationTracker m_scratch ;
-#else
   void *        m_scratch ;
-#endif
   int           m_scratch_reduce_end ;
   int           m_scratch_thread_end ;
   int           m_numa_rank ;
@@ -138,19 +133,10 @@ public:
   static int get_thread_count();
   static ThreadsExec * get_thread( const int init_thread_rank );
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-  inline void * reduce_memory() const { return reinterpret_cast<unsigned char *>(m_scratch.alloc_ptr()); }
-  KOKKOS_INLINE_FUNCTION  void * scratch_memory() const { return reinterpret_cast<unsigned char *>(m_scratch.alloc_ptr()) + m_scratch_reduce_end ; }
-
-#else
-
   inline void * reduce_memory() const { return m_scratch ; }
   KOKKOS_INLINE_FUNCTION  void * scratch_memory() const
     { return reinterpret_cast<unsigned char *>(m_scratch) + m_scratch_reduce_end ; }
 
-#endif
-
   KOKKOS_INLINE_FUNCTION  int volatile & state() { return m_pool_state ; }
   KOKKOS_INLINE_FUNCTION  ThreadsExec * const * pool_base() const { return m_pool_base ; }
 
diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp b/lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp
index b425ac4773..3407ffaa54 100644
--- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp
+++ b/lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp
@@ -129,15 +129,15 @@ public:
 
   KOKKOS_INLINE_FUNCTION
   const execution_space::scratch_memory_space & team_shmem() const
-    { return m_team_shared.set_team_thread_mode(1,0) ; }
+    { return m_team_shared.set_team_thread_mode(0,1,0) ; }
 
   KOKKOS_INLINE_FUNCTION
   const execution_space::scratch_memory_space & team_scratch(int) const
-    { return m_team_shared.set_team_thread_mode(1,0) ; }
+    { return m_team_shared.set_team_thread_mode(0,1,0) ; }
 
   KOKKOS_INLINE_FUNCTION
   const execution_space::scratch_memory_space & thread_scratch(int) const
-    { return m_team_shared.set_team_thread_mode(team_size(),team_rank()) ; }
+    { return m_team_shared.set_team_thread_mode(0,team_size(),team_rank()) ; }
 
   KOKKOS_INLINE_FUNCTION int league_rank() const { return m_league_rank ; }
   KOKKOS_INLINE_FUNCTION int league_size() const { return m_league_size ; }
@@ -433,10 +433,11 @@ public:
 
   void next_static()
     {
-      if ( ++m_league_rank < m_league_end ) {
+      if ( m_league_rank < m_league_end ) {
         team_barrier();
         set_team_shared();
       }
+      m_league_rank++;
     }
 
   bool valid_dynamic() {
@@ -468,10 +469,11 @@ public:
     if(m_invalid_thread)
       return;
 
-    team_barrier();
-    if ( ++m_league_rank < m_league_chunk_end ) {
+    if ( m_league_rank < m_league_chunk_end ) {
+      team_barrier();
       set_team_shared();
     }
+    m_league_rank++;
   }
 
   void set_league_shmem( const int arg_league_rank
@@ -504,8 +506,8 @@ private:
   int m_team_alloc ;
   int m_team_iter ;
 
-  size_t m_team_scratch_size;
-  size_t m_thread_scratch_size;
+  size_t m_team_scratch_size[2];
+  size_t m_thread_scratch_size[2];
 
   int m_chunk_size;
 
@@ -549,8 +551,10 @@ public:
     m_team_size = p.m_team_size;
     m_team_alloc = p.m_team_alloc;
     m_team_iter = p.m_team_iter;
-    m_team_scratch_size = p.m_team_scratch_size;
-    m_thread_scratch_size = p.m_thread_scratch_size;
+    m_team_scratch_size[0] = p.m_team_scratch_size[0];
+    m_thread_scratch_size[0] = p.m_thread_scratch_size[0];
+    m_team_scratch_size[1] = p.m_team_scratch_size[1];
+    m_thread_scratch_size[1] = p.m_thread_scratch_size[1];
     m_chunk_size = p.m_chunk_size;
     return *this;
   }
@@ -577,7 +581,12 @@ public:
   inline int team_size() const { return m_team_size ; }
   inline int team_alloc() const { return m_team_alloc ; }
   inline int league_size() const { return m_league_size ; }
-  inline size_t scratch_size() const { return m_team_scratch_size + m_team_size*m_thread_scratch_size ; }
+  inline size_t scratch_size(const int& level, int team_size_ = -1 ) const {
+    if(team_size_ < 0)
+      team_size_ = m_team_size;
+    return m_team_scratch_size[level] + team_size_*m_thread_scratch_size[level] ;
+  }
+
   inline int team_iter() const { return m_team_iter ; }
 
   /** \brief  Specify league size, request team size */
@@ -588,8 +597,8 @@ public:
     : m_league_size(0)
     , m_team_size(0)
     , m_team_alloc(0)
-    , m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    , m_team_scratch_size { 0 , 0 }
+    , m_thread_scratch_size { 0 , 0 }
     , m_chunk_size(0)
     { init(league_size_request,team_size_request); (void) vector_length_request; }
 
@@ -601,8 +610,8 @@ public:
     : m_league_size(0)
     , m_team_size(0)
     , m_team_alloc(0)
-    , m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    , m_team_scratch_size { 0 , 0 }
+    , m_thread_scratch_size { 0 , 0 }
     , m_chunk_size(0)
     { init(league_size_request,traits::execution_space::thread_pool_size(2)); }
 
@@ -612,8 +621,8 @@ public:
     : m_league_size(0)
     , m_team_size(0)
     , m_team_alloc(0)
-    , m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    , m_team_scratch_size { 0 , 0 }
+    , m_thread_scratch_size { 0 , 0 }
     , m_chunk_size(0)
     { init(league_size_request,team_size_request); }
 
@@ -623,8 +632,8 @@ public:
     : m_league_size(0)
     , m_team_size(0)
     , m_team_alloc(0)
-    , m_team_scratch_size ( 0 )
-    , m_thread_scratch_size ( 0 )
+    , m_team_scratch_size { 0 , 0 }
+    , m_thread_scratch_size { 0 , 0 }
     , m_chunk_size(0)
     { init(league_size_request,traits::execution_space::thread_pool_size(2)); }
 
@@ -639,26 +648,23 @@ public:
 
   /** \brief set per team scratch size for a specific level of the scratch hierarchy */
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerTeamValue& per_team) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_team_scratch_size = per_team.value;
+    p.m_team_scratch_size[level] = per_team.value;
     return p;
   };
 
   /** \brief set per thread scratch size for a specific level of the scratch hierarchy */
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerThreadValue& per_thread) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_thread_scratch_size = per_thread.value;
+    p.m_thread_scratch_size[level] = per_thread.value;
     return p;
   };
 
   /** \brief set per thread and per team scratch size for a specific level of the scratch hierarchy */
   inline TeamPolicyInternal set_scratch_size(const int& level, const PerTeamValue& per_team, const PerThreadValue& per_thread) const {
-    (void) level;
     TeamPolicyInternal p = *this;
-    p.m_team_scratch_size = per_team.value;
-    p.m_thread_scratch_size = per_thread.value;
+    p.m_team_scratch_size[level] = per_team.value;
+    p.m_thread_scratch_size[level] = per_thread.value;
     return p;
   };
 
diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_Parallel.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_Parallel.hpp
index 55ddecf87f..1aba00c94b 100644
--- a/lib/kokkos/core/src/Threads/Kokkos_Threads_Parallel.hpp
+++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_Parallel.hpp
@@ -264,7 +264,7 @@ public:
              , const Policy      & arg_policy )
     : m_functor( arg_functor )
     , m_policy(  arg_policy )
-    , m_shared( arg_policy.scratch_size() + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
+    , m_shared( arg_policy.scratch_size(0) + arg_policy.scratch_size(1) + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
     { }
 };
 
@@ -272,9 +272,10 @@ public:
 //----------------------------------------------------------------------------
 /* ParallelReduce with Kokkos::Threads and RangePolicy */
 
-template< class FunctorType , class ... Traits >
+template< class FunctorType , class ReducerType, class ... Traits >
 class ParallelReduce< FunctorType
                     , Kokkos::RangePolicy< Traits ... >
+                    , ReducerType
                     , Kokkos::Threads
                     >
 {
@@ -286,14 +287,18 @@ private:
   typedef typename Policy::WorkRange   WorkRange ;
   typedef typename Policy::member_type Member ;
 
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType, WorkTag > ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueInit<   FunctorType, WorkTag > ValueInit ;
+  typedef Kokkos::Impl::if_c< std::is_same<InvalidType,ReducerType>::value, FunctorType, ReducerType> ReducerConditional;
+  typedef typename ReducerConditional::type ReducerTypeFwd;
+
+  typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd, WorkTag > ValueTraits ;
+  typedef Kokkos::Impl::FunctorValueInit<   ReducerTypeFwd, WorkTag > ValueInit ;
 
   typedef typename ValueTraits::pointer_type    pointer_type ;
   typedef typename ValueTraits::reference_type  reference_type ;
 
   const FunctorType  m_functor ;
   const Policy       m_policy ;
+  const ReducerType   m_reducer ;
   const pointer_type m_result_ptr ;
 
   template< class TagType >
@@ -344,9 +349,9 @@ private:
 
     ParallelReduce::template exec_range< WorkTag >
       ( self.m_functor , range.begin() , range.end() 
-      , ValueInit::init( self.m_functor , exec.reduce_memory() ) );
+      , ValueInit::init( ReducerConditional::select(self.m_functor , self.m_reducer) , exec.reduce_memory() ) );
 
-    exec.template fan_in_reduce< FunctorType , WorkTag >( self.m_functor );
+    exec.template fan_in_reduce< ReducerTypeFwd , WorkTag >( ReducerConditional::select(self.m_functor , self.m_reducer) );
   }
 
   template<class Schedule>
@@ -362,7 +367,7 @@ private:
     exec.barrier();
 
     long work_index = exec.get_work_index();
-    reference_type update = ValueInit::init( self.m_functor , exec.reduce_memory() );
+    reference_type update = ValueInit::init( ReducerConditional::select(self.m_functor , self.m_reducer) , exec.reduce_memory() );
     while(work_index != -1) {
       const Member begin = static_cast<Member>(work_index) * self.m_policy.chunk_size();
       const Member end = begin + self.m_policy.chunk_size() < self.m_policy.end()?begin+self.m_policy.chunk_size():self.m_policy.end();
@@ -372,7 +377,7 @@ private:
       work_index = exec.get_work_index();
     }
 
-    exec.template fan_in_reduce< FunctorType , WorkTag >( self.m_functor );
+    exec.template fan_in_reduce< ReducerTypeFwd , WorkTag >( ReducerConditional::select(self.m_functor , self.m_reducer) );
   }
 
 public:
@@ -380,7 +385,7 @@ public:
   inline
   void execute() const
     {
-      ThreadsExec::resize_scratch( ValueTraits::value_size( m_functor ) , 0 );
+      ThreadsExec::resize_scratch( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) , 0 );
 
       ThreadsExec::start( & ParallelReduce::exec , this );
 
@@ -391,7 +396,7 @@ public:
         const pointer_type data =
           (pointer_type) ThreadsExec::root_reduce_scratch();
 
-        const unsigned n = ValueTraits::value_count( m_functor );
+        const unsigned n = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) );
         for ( unsigned i = 0 ; i < n ; ++i ) { m_result_ptr[i] = data[i]; }
       }
     }
@@ -399,9 +404,14 @@ public:
   template< class HostViewType >
   ParallelReduce( const FunctorType  & arg_functor ,
                   const Policy       & arg_policy ,
-                  const HostViewType & arg_result_view )
+                  const HostViewType & arg_result_view ,
+                  typename std::enable_if<
+                               Kokkos::is_view< HostViewType >::value &&
+                              !Kokkos::is_reducer_type<ReducerType>::value
+                  ,void*>::type = NULL)
     : m_functor( arg_functor )
     , m_policy( arg_policy )
+    , m_reducer( InvalidType() )
     , m_result_ptr( arg_result_view.ptr_on_device() )
     {
       static_assert( Kokkos::is_view< HostViewType >::value
@@ -410,14 +420,30 @@ public:
       static_assert( std::is_same< typename HostViewType::memory_space , HostSpace >::value
         , "Kokkos::Threads reduce result must be a View in HostSpace" );
     }
+
+  inline
+  ParallelReduce( const FunctorType & arg_functor
+                , Policy       arg_policy
+                , const ReducerType& reducer )
+    : m_functor( arg_functor )
+    , m_policy(  arg_policy )
+    , m_reducer( reducer )
+    , m_result_ptr(  reducer.result_view().data() )
+    {
+      /*static_assert( std::is_same< typename ViewType::memory_space
+                                      , Kokkos::HostSpace >::value
+        , "Reduction result on Kokkos::OpenMP must be a Kokkos::View in HostSpace" );*/
+    }
+
 };
 
 //----------------------------------------------------------------------------
 /* ParallelReduce with Kokkos::Threads and TeamPolicy */
 
-template< class FunctorType , class ... Properties >
+template< class FunctorType , class ReducerType, class ... Properties >
 class ParallelReduce< FunctorType
                     , Kokkos::TeamPolicy< Properties ... >
+                    , ReducerType
                     , Kokkos::Threads
                     >
 {
@@ -426,14 +452,19 @@ private:
   typedef Kokkos::Impl::TeamPolicyInternal< Kokkos::Threads, Properties ... >              Policy ;
   typedef typename Policy::work_tag                                WorkTag ;
   typedef typename Policy::member_type                             Member ;
-  typedef Kokkos::Impl::FunctorValueTraits< FunctorType, WorkTag > ValueTraits ;
-  typedef Kokkos::Impl::FunctorValueInit<   FunctorType, WorkTag > ValueInit ;
+
+  typedef Kokkos::Impl::if_c< std::is_same<InvalidType,ReducerType>::value, FunctorType, ReducerType> ReducerConditional;
+  typedef typename ReducerConditional::type ReducerTypeFwd;
+
+  typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd, WorkTag > ValueTraits ;
+  typedef Kokkos::Impl::FunctorValueInit<   ReducerTypeFwd, WorkTag > ValueInit ;
 
   typedef typename ValueTraits::pointer_type    pointer_type ;
   typedef typename ValueTraits::reference_type  reference_type ;
 
   const FunctorType  m_functor ;
   const Policy       m_policy ;
+  const ReducerType  m_reducer ;
   const pointer_type m_result_ptr ;
   const int          m_shared ;
 
@@ -464,9 +495,9 @@ private:
 
     ParallelReduce::template exec_team< WorkTag >
       ( self.m_functor , Member( & exec , self.m_policy , self.m_shared )
-      , ValueInit::init( self.m_functor , exec.reduce_memory() ) );
+      , ValueInit::init( ReducerConditional::select(self.m_functor , self.m_reducer) , exec.reduce_memory() ) );
 
-    exec.template fan_in_reduce< FunctorType , WorkTag >( self.m_functor );
+    exec.template fan_in_reduce< ReducerTypeFwd , WorkTag >( ReducerConditional::select(self.m_functor , self.m_reducer) );
   }
 
 public:
@@ -474,7 +505,7 @@ public:
   inline
   void execute() const
     {
-      ThreadsExec::resize_scratch( ValueTraits::value_size( m_functor ) , Policy::member_type::team_reduce_size() + m_shared );
+      ThreadsExec::resize_scratch( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) , Policy::member_type::team_reduce_size() + m_shared );
 
       ThreadsExec::start( & ParallelReduce::exec , this );
 
@@ -484,20 +515,41 @@ public:
 
         const pointer_type data = (pointer_type) ThreadsExec::root_reduce_scratch();
 
-        const unsigned n = ValueTraits::value_count( m_functor );
+        const unsigned n = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) );
         for ( unsigned i = 0 ; i < n ; ++i ) { m_result_ptr[i] = data[i]; }
       }
     }
 
   template< class ViewType >
-  ParallelReduce( const FunctorType & arg_functor
-                , const Policy      & arg_policy
-                , const ViewType    & arg_result )
+  inline
+  ParallelReduce( const FunctorType  & arg_functor ,
+                  const Policy       & arg_policy ,
+                  const ViewType     & arg_result ,
+                  typename std::enable_if<
+                    Kokkos::is_view< ViewType >::value &&
+                    !Kokkos::is_reducer_type<ReducerType>::value
+                    ,void*>::type = NULL)
     : m_functor( arg_functor )
-    , m_policy( arg_policy )
+    , m_policy(  arg_policy )
+    , m_reducer( InvalidType() )
     , m_result_ptr( arg_result.ptr_on_device() )
-    , m_shared( arg_policy.scratch_size() + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
-    { }
+    , m_shared( arg_policy.scratch_size(0) + arg_policy.scratch_size(1) + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
+    {}
+
+  inline
+  ParallelReduce( const FunctorType & arg_functor
+    , Policy       arg_policy
+    , const ReducerType& reducer )
+  : m_functor( arg_functor )
+  , m_policy(  arg_policy )
+  , m_reducer( reducer )
+  , m_result_ptr(  reducer.result_view().data() )
+  , m_shared( arg_policy.scratch_size(0) + arg_policy.scratch_size(1) + FunctorTeamShmemSize< FunctorType >::value( arg_functor , arg_policy.team_size() ) )
+  {
+  /*static_assert( std::is_same< typename ViewType::memory_space
+                          , Kokkos::HostSpace >::value
+  , "Reduction result on Kokkos::OpenMP must be a Kokkos::View in HostSpace" );*/
+  }
 };
 
 //----------------------------------------------------------------------------
diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_TaskPolicy.cpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_TaskPolicy.cpp
index 258e683a4f..e1599284b2 100644
--- a/lib/kokkos/core/src/Threads/Kokkos_Threads_TaskPolicy.cpp
+++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_TaskPolicy.cpp
@@ -46,9 +46,10 @@
 #include <stdio.h>
 #include <iostream>
 #include <sstream>
+#include <Kokkos_Core.hpp>
 #include <Threads/Kokkos_Threads_TaskPolicy.hpp>
 
-#if defined( KOKKOS_HAVE_PTHREAD )
+#if defined( KOKKOS_HAVE_PTHREAD ) && defined( KOKKOS_ENABLE_TASKPOLICY )
 
 #define QLOCK   (reinterpret_cast<void*>( ~((uintptr_t)0) ))
 #define QDENIED (reinterpret_cast<void*>( ~((uintptr_t)0) - 1 ))
@@ -87,9 +88,8 @@ ThreadsTaskPolicyQueue::ThreadsTaskPolicyQueue
   , const unsigned arg_task_team_size
   )
   : m_space( Kokkos::Threads::memory_space()
-           , arg_task_max_size
-           , arg_task_max_size * arg_task_max_count
-           , 1 /* only one level of memory pool */
+           , arg_task_max_size * arg_task_max_count * 1.2
+           , 16 /* log2(superblock size) */
            )
   , m_team { 0 , 0 , 0 }
   , m_serial { 0 , 0 , 0 }
@@ -624,10 +624,10 @@ ThreadsTaskPolicyQueue::allocate_task
   // User created task memory pool with an estimate,
   // if estimate is to low then report and throw exception.
 
-  if ( m_space.get_min_chunk_size() < size_alloc ) {
+  if ( m_space.get_min_block_size() < size_alloc ) {
     fprintf(stderr,"TaskPolicy<Threads> task allocation requires %d bytes on memory pool with %d byte chunk size\n"
            , int(size_alloc)
-           , int(m_space.get_min_chunk_size())
+           , int(m_space.get_min_block_size())
            );
     fflush(stderr);
     Kokkos::Impl::throw_runtime_exception("TaskMember< Threads >::task_allocate");
@@ -926,5 +926,5 @@ void Task::clear_dependence()
 } /* namespace Experimental */
 } /* namespace Kokkos */
 
-#endif /* #if defined( KOKKOS_HAVE_PTHREAD ) */
+#endif /* #if defined( KOKKOS_HAVE_PTHREAD ) && defined( KOKKOS_ENABLE_TASKPOLICY ) */
 
diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_TaskPolicy.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_TaskPolicy.hpp
index a0c28afd0c..116d32e4fc 100644
--- a/lib/kokkos/core/src/Threads/Kokkos_Threads_TaskPolicy.hpp
+++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_TaskPolicy.hpp
@@ -50,7 +50,7 @@
 #include <Kokkos_Threads.hpp>
 #include <Kokkos_TaskPolicy.hpp>
 
-#if defined( KOKKOS_HAVE_PTHREAD )
+#if defined( KOKKOS_HAVE_PTHREAD ) && defined( KOKKOS_ENABLE_TASKPOLICY )
 
 //----------------------------------------------------------------------------
 
@@ -737,10 +737,9 @@ public:
 } /* namespace Experimental */
 } /* namespace Kokkos */
 
-#endif /* #if defined( KOKKOS_HAVE_PTHREAD ) */
-
 //----------------------------------------------------------------------------
 
+#endif /* #if defined( KOKKOS_HAVE_PTHREAD ) && defined( KOKKOS_ENABLE_TASKPOLICY ) */
 #endif /* #ifndef KOKKOS_THREADS_TASKPOLICY_HPP */
 
 
diff --git a/lib/kokkos/core/src/impl/KokkosExp_SharedAlloc.hpp b/lib/kokkos/core/src/impl/KokkosExp_SharedAlloc.hpp
index feb3632d43..1498eafb00 100644
--- a/lib/kokkos/core/src/impl/KokkosExp_SharedAlloc.hpp
+++ b/lib/kokkos/core/src/impl/KokkosExp_SharedAlloc.hpp
@@ -246,8 +246,8 @@ private:
   enum : uintptr_t { DO_NOT_DEREF_FLAG = 0x01ul };
 
   // The allocation record resides in Host memory space
-  Record  * m_record ;
   uintptr_t m_record_bits ;
+  Record  * m_record ;
 
 public:
 
diff --git a/lib/kokkos/core/src/impl/KokkosExp_ViewCtor.hpp b/lib/kokkos/core/src/impl/KokkosExp_ViewCtor.hpp
index 9ace88dfb1..6525fed0a5 100644
--- a/lib/kokkos/core/src/impl/KokkosExp_ViewCtor.hpp
+++ b/lib/kokkos/core/src/impl/KokkosExp_ViewCtor.hpp
@@ -47,8 +47,6 @@
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
-#if KOKKOS_USING_EXP_VIEW
-
 namespace Kokkos {
 
 /* For backward compatibility */
@@ -68,8 +66,6 @@ struct ViewAllocateWithoutInitializing {
 
 } /* namespace Kokkos */
 
-#endif
-
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
diff --git a/lib/kokkos/core/src/impl/KokkosExp_ViewMapping.hpp b/lib/kokkos/core/src/impl/KokkosExp_ViewMapping.hpp
index 39339185e7..ed56536cd9 100644
--- a/lib/kokkos/core/src/impl/KokkosExp_ViewMapping.hpp
+++ b/lib/kokkos/core/src/impl/KokkosExp_ViewMapping.hpp
@@ -2604,18 +2604,24 @@ class ViewMapping< DstTraits , SrcTraits ,
     &&
     std::is_same< typename DstTraits::specialize , void >::value
     &&
-    (
-      std::is_same< typename DstTraits::array_layout , Kokkos::LayoutLeft >::value ||
-      std::is_same< typename DstTraits::array_layout , Kokkos::LayoutRight >::value ||
-      std::is_same< typename DstTraits::array_layout , Kokkos::LayoutStride >::value
-    )
-    &&
     std::is_same< typename SrcTraits::specialize , void >::value
     &&
     (
-      std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutLeft >::value ||
-      std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutRight >::value ||
-      std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutStride >::value
+      std::is_same< typename DstTraits::array_layout , typename SrcTraits::array_layout >::value
+      ||
+      (
+        (
+          std::is_same< typename DstTraits::array_layout , Kokkos::LayoutLeft >::value ||
+          std::is_same< typename DstTraits::array_layout , Kokkos::LayoutRight >::value ||
+          std::is_same< typename DstTraits::array_layout , Kokkos::LayoutStride >::value
+        )
+        &&
+        (
+          std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutLeft >::value ||
+          std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutRight >::value ||
+          std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutStride >::value
+        )
+      )
     )
   )>::type >
 {
diff --git a/lib/kokkos/core/src/impl/Kokkos_AllocationTracker.cpp b/lib/kokkos/core/src/impl/Kokkos_AllocationTracker.cpp
deleted file mode 100644
index c95557793a..0000000000
--- a/lib/kokkos/core/src/impl/Kokkos_AllocationTracker.cpp
+++ /dev/null
@@ -1,848 +0,0 @@
-/*
-//@HEADER
-// ************************************************************************
-// 
-//                        Kokkos v. 2.0
-//              Copyright (2014) Sandia Corporation
-// 
-// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
-// the U.S. Government retains certain rights in this software.
-// 
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are
-// met:
-//
-// 1. Redistributions of source code must retain the above copyright
-// notice, this list of conditions and the following disclaimer.
-//
-// 2. Redistributions in binary form must reproduce the above copyright
-// notice, this list of conditions and the following disclaimer in the
-// documentation and/or other materials provided with the distribution.
-//
-// 3. Neither the name of the Corporation nor the names of the
-// contributors may be used to endorse or promote products derived from
-// this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
-// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
-// ************************************************************************
-//@HEADER
-*/
-
-#include <Kokkos_Core_fwd.hpp>
-
-#if ! KOKKOS_USING_EXP_VIEW
-
-#if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST )
-
-#include <Kokkos_Atomic.hpp>
-
-#include <impl/Kokkos_Singleton.hpp>
-#include <impl/Kokkos_AllocationTracker.hpp>
-#include <impl/Kokkos_Error.hpp>
-
-
-#include <string>
-#include <vector>
-#include <sstream>
-#include <algorithm>
-#include <utility>
-#include <cstdlib>
-#include <cstring>
-#include <iostream>
-#include <iomanip>
-
-/* Enable clean up of memory leaks */
-#define CLEAN_UP_MEMORY_LEAKS 0
-
-namespace Kokkos { namespace Impl {
-
-namespace {
-
-
-//-----------------------------------------------------------------------------
-// AllocationRecord
-//-----------------------------------------------------------------------------
-//
-// Used to track details about an allocation and provide a ref count
-// sizeof(AllocationRecord) == 128
-struct AllocationRecord
-{
-  enum {
-     OFFSET = sizeof(AllocatorBase*)          // allocator
-            + sizeof(void*)                   // alloc_ptr
-            + sizeof(uint64_t)                // alloc_size
-            + sizeof(AllocatorAttributeBase*) // attribute
-            + sizeof(uint32_t)                // node_index
-            + sizeof(uint32_t)                // ref_count
-   , LABEL_LENGTH = 128 - OFFSET
-  };
-
-  AllocatorBase * const          allocator;
-  void * const                   alloc_ptr;
-  const uint64_t                 alloc_size;
-  AllocatorAttributeBase * const attribute;
-  const int32_t                  node_index;
-  volatile uint32_t              ref_count;
-  const char                     label[LABEL_LENGTH];
-
-
-  AllocationRecord(  AllocatorBase * const arg_allocator
-                   , void *   arg_alloc_ptr
-                   , uint64_t arg_alloc_size
-                   , int32_t  arg_node_index
-                   , const std::string & arg_label
-                  )
-    : allocator(arg_allocator)
-    , alloc_ptr(arg_alloc_ptr)
-    , alloc_size(arg_alloc_size)
-    , attribute(NULL)
-    , node_index(arg_node_index)
-    , ref_count(1)
-    , label() // zero fill
-  {
-    const size_t length = static_cast<size_t>(LABEL_LENGTH-1u) < arg_label.size() ? static_cast<size_t>(LABEL_LENGTH-1u) : arg_label.size();
-    strncpy( const_cast<char *>(label), arg_label.c_str(), length );
-  }
-
-  ~AllocationRecord()
-  {
-    if (attribute) {
-      delete attribute;
-    }
-  }
-
-  uint32_t increment_ref_count()
-  {
-    uint32_t old_value = atomic_fetch_add( &ref_count, static_cast<uint32_t>(1) );
-    return old_value + 1u;
-  }
-
-  uint32_t decrement_ref_count()
-  {
-    uint32_t old_value = atomic_fetch_sub( &ref_count, static_cast<uint32_t>(1) );
-    return old_value - 1u;
-  }
-
-  void print( std::ostream & oss ) const
-  {
-    oss << "{ " << allocator->name()
-        << " } : \"" << label
-        << "\" ref_count(" << ref_count
-        << ") memory[ " << alloc_ptr
-        << " + " << alloc_size
-        << " ]" ;
-  }
-
-  bool set_attribute( AllocatorAttributeBase * attr )
-  {
-    bool result = false;
-    if (attribute == NULL) {
-      result = NULL == atomic_compare_exchange(  const_cast<AllocatorAttributeBase **>(&attribute)
-                                               , reinterpret_cast<AllocatorAttributeBase *>(NULL)
-                                               , attr );
-    }
-
-    return result;
-  }
-
-  // disallow copy and assignment
-  AllocationRecord( const AllocationRecord & );
-  AllocationRecord & operator=(const AllocationRecord &);
-};
-
-template <int NumBlocks>
-struct Bitset
-{
-  enum { blocks = NumBlocks };
-  enum { size = blocks * 64 };
-  enum { block_mask = 63u };
-  enum { block_shift = 6 };
-
-  // used to find free bits in a bitset
-  static int count_trailing_zeros(uint64_t x)
-  {
-    #if defined( KOKKOS_COMPILER_GNU ) || defined( KOKKOS_COMPILER_CLANG ) || defined( KOKKOS_COMPILER_APPLECC )
-      return x ? __builtin_ctzll(x) : 64;
-    #elif defined( KOKKOS_COMPILER_INTEL )
-      enum { shift = 32 };
-      enum { mask = (static_cast<uint64_t>(1) << shift) - 1u };
-      return (x & mask) ? _bit_scan_forward(static_cast<int>(x & mask)) :
-             (x >> shift) ? shift + _bit_scan_forward(static_cast<int>(x >> shift)) :
-             64 ;
-    #elif defined( KOKKOS_COMPILER_IBM )
-      return x ? __cnttz8(x) : 64;
-    #else
-      int i = 0;
-      for (; ((x & (static_cast<uint64_t>(1) << i)) == 0u) && i < 64; ++i ) {}
-      return i;
-    #endif
-  }
-
-  Bitset()
-    : m_bits()
-  {
-    for (int i=0; i < blocks; ++i) {
-      m_bits[i] = 0u;
-    }
-  }
-
-  bool set( int i )
-  {
-    const uint64_t bit = static_cast<uint64_t>(1) << ( i & block_mask );
-    return !( atomic_fetch_or( m_bits + (i >> block_shift), bit ) & bit );
-  }
-
-  bool reset( int i )
-  {
-    const uint64_t bit = static_cast<uint64_t>(1) << ( i & block_mask );
-    return atomic_fetch_and( m_bits + (i >> block_shift), ~bit ) & bit;
-  }
-
-  bool test( int i )
-  {
-    const uint64_t block = m_bits[ i >> block_shift ];
-    const uint64_t bit = static_cast<uint64_t>(1) << ( i & block_mask );
-    return block & bit;
-  }
-
-  int find_first_unset() const
-  {
-    for (int i=0; i < blocks; ++i) {
-      const uint64_t block = m_bits[i];
-      int b = count_trailing_zeros( ~block );
-
-      if ( b < 64 ) {
-        return (i << block_shift) + b;
-      }
-    }
-    return size;
-  }
-
-  volatile uint64_t m_bits[blocks];
-};
-
-//-----------------------------------------------------------------------------
-// AllocationRecordPool -- singleton class
-//
-// global_alloc_rec_pool is the ONLY instance of this class
-//
-//-----------------------------------------------------------------------------
-// Record AllocationRecords in a lock-free circular list.
-// Each node in the list has a buffer with space for 959 ((15*64)-1) records
-// managed by a bitset.  Atomics are used to set and reset bits in the bit set.
-// The head of the list is atomically updated to the last node found with
-// unused space.
-//
-// Cost time to create an allocation record: amortized O(1), worst case O(num nodes)
-// Cost to destroy an allocation recored: O(1)
-//
-// Singleton allocations are pushed onto a lock-free stack that is destroyed
-// after the circular list of allocation records.
-struct AllocationRecordPool
-{
-  enum { BITSET_BLOCKS = 15 };
-
-  typedef Bitset<BITSET_BLOCKS> bitset_type;
-
-  enum { BUFFER_SIZE = (bitset_type::size - 1) * sizeof(AllocationRecord) };
-
-  struct AllocationNode
-  {
-    AllocationNode()
-      : next()
-      , bitset()
-      , buffer()
-    {
-      // set the first bit to used
-      bitset.set(0);
-    }
-
-    void * get_buffer( int32_t node_index )
-    {
-      return buffer + (node_index-1) * sizeof(AllocationRecord);
-    }
-
-    // return 0 if no space is available in the node
-    int32_t get_node_index()
-    {
-      int32_t node_index = 0;
-      do {
-        node_index = bitset.find_first_unset();
-
-        // successfully claimed a bit
-        if ( node_index != bitset.size && bitset.set(node_index) )
-        {
-          return node_index;
-        }
-      } while ( node_index != bitset.size );
-      return 0;
-    }
-
-    void clear_node_index( int32_t node_index )
-    {
-      bitset.reset(node_index);
-    }
-
-    AllocationNode * next;
-    bitset_type      bitset;
-    char             buffer[BUFFER_SIZE];
-  };
-
-  struct SingletonNode
-  {
-    void * buffer;
-    SingletonNode * next;
-    Impl::singleton_destroy_function_type destroy;
-
-    SingletonNode( size_t size, Impl::singleton_create_function_type create_func, Impl::singleton_destroy_function_type destroy_func  )
-      : buffer(NULL)
-      , next(NULL)
-      , destroy(destroy_func)
-    {
-      if (size) {
-        buffer = malloc(size);
-        create_func(buffer);
-      }
-    }
-
-    ~SingletonNode()
-    {
-      if (buffer) {
-        try {
-          destroy(buffer);
-        } catch(...) {}
-        free(buffer);
-      }
-    }
-  };
-
-  AllocationRecordPool()
-    : head( new AllocationNode() )
-    , singleton_head(NULL)
-  {
-    // setup ring
-    head->next = head;
-  }
-
-  ~AllocationRecordPool()
-  {
-    // delete allocation records
-    {
-      AllocationNode * start = head;
-
-      AllocationNode * curr = start;
-
-      std::vector< std::string > string_vec;
-
-      do {
-        AllocationNode * next = curr->next;
-
-        #if defined( KOKKOS_DEBUG_PRINT_ALLOCATION_BITSET )
-        // print node bitset
-        for (int i=0; i < bitset_type::blocks; ++i ) {
-          std::cout << std::hex << std::showbase << curr->bitset.m_bits[i] << "   ";
-        }
-        std::cout << std::endl;
-        #endif
-
-        // bit zero does not map to an AllocationRecord
-        for ( int32_t i=1; i < bitset_type::size; ++i )
-        {
-          if (curr->bitset.test(i)) {
-            AllocationRecord * alloc_rec = reinterpret_cast<AllocationRecord *>( curr->get_buffer(i) );
-
-            std::ostringstream oss;
-            alloc_rec->print( oss );
-            string_vec.push_back( oss.str() );
-
-#if CLEAN_UP_MEMORY_LEAKS
-/* Cleaning up memory leaks prevents memory error detection tools
- * from reporting the original source of allocation, which can
- * impede debugging with such tools.
- */
-            try {
-              destroy(alloc_rec);
-            }
-            catch(...) {}
-#endif
-          }
-        }
-
-        curr->next = NULL;
-
-        delete curr;
-
-        curr = next;
-      } while ( curr != start );
-
-      //if ( !string_vec.empty() ) {
-      //  std::sort( string_vec.begin(), string_vec.end() );
-      //
-      //  std::ostringstream oss;
-      //  oss << "Error: Allocation pool destroyed with the following memory leak(s):\n";
-      //  for (size_t i=0; i< string_vec.size(); ++i)
-      //  {
-      //    oss << "   " << string_vec[i] << std::endl;
-      //  }
-      //
-      //  std::cerr << oss.str() << std::endl;
-      //}
-    }
-
-    // delete singletons
-    {
-      SingletonNode * curr = singleton_head;
-
-      while (curr) {
-        SingletonNode * next = curr->next;
-        delete curr;
-        curr = next;
-      }
-    }
-  }
-
-  AllocationRecord * create(  AllocatorBase * arg_allocator
-                            , void * arg_alloc_ptr
-                            , size_t arg_alloc_size
-                            , const std::string & arg_label
-                           )
-  {
-    AllocationNode * start = volatile_load(&head);
-
-    AllocationNode * curr = start;
-
-
-    int32_t node_index = curr->get_node_index();
-
-    if (node_index == 0) {
-      curr = volatile_load(&curr->next);
-    }
-
-    while (node_index == 0 && curr != start)
-    {
-      node_index = curr->get_node_index();
-      if (node_index == 0) {
-        curr = volatile_load(&curr->next);
-      }
-    }
-
-    // Need to allocate and insert a new node
-    if (node_index == 0 && curr == start)
-    {
-      AllocationNode * new_node = new AllocationNode();
-
-      node_index = new_node->get_node_index();
-
-      AllocationNode * next = NULL;
-      do {
-        next = volatile_load(&curr->next);
-        new_node->next = next;
-        memory_fence();
-      } while ( next != atomic_compare_exchange( &(curr->next), next, new_node ) );
-
-      curr = new_node;
-    }
-
-    void * buffer = curr->get_buffer(node_index);
-
-    // try to set head to curr
-    if ( start != curr )
-    {
-      atomic_compare_exchange( & head, start, curr );
-    }
-
-    return new (buffer) AllocationRecord(  arg_allocator
-                                         , arg_alloc_ptr
-                                         , arg_alloc_size
-                                         , node_index
-                                         , arg_label
-                                        );
-  }
-
-  void destroy( AllocationRecord * alloc_rec )
-  {
-    if (alloc_rec) {
-      const int32_t node_index = alloc_rec->node_index;
-      AllocationNode * node = get_node( alloc_rec );
-
-      // deallocate memory
-      alloc_rec->allocator->deallocate( alloc_rec->alloc_ptr, alloc_rec->alloc_size );
-
-      // call destructor
-      alloc_rec->~AllocationRecord();
-
-      // wait for writes to complete
-      memory_fence();
-
-      // clear node index
-      node->clear_node_index( node_index );
-    }
-  }
-
-  void * create_singleton( size_t size, Impl::singleton_create_function_type create_func, Impl::singleton_destroy_function_type destroy_func )
-  {
-    SingletonNode * node = new SingletonNode( size, create_func, destroy_func );
-    SingletonNode * next;
-
-    // insert new node at the head of the list
-    do {
-      next = volatile_load(&singleton_head);
-      node->next = next;
-    } while ( next != atomic_compare_exchange( &singleton_head, next, node ) );
-
-    return node->buffer;
-  }
-
-  void print_memory( std::ostream & out ) const
-  {
-    AllocationNode * start = head;
-
-    AllocationNode * curr = start;
-
-    std::vector< std::string > string_vec;
-
-    do {
-      AllocationNode * next = curr->next;
-
-      // bit zero does not map to an AllocationRecord
-      for ( int32_t i=1; i < bitset_type::size; ++i )
-      {
-        if (curr->bitset.test(i)) {
-          AllocationRecord * alloc_rec = reinterpret_cast<AllocationRecord *>( curr->get_buffer(i) );
-
-          std::ostringstream oss;
-          alloc_rec->print( oss );
-          string_vec.push_back( oss.str() );
-        }
-      }
-      curr = next;
-    } while ( curr != start );
-
-    if ( !string_vec.empty() ) {
-      std::sort( string_vec.begin(), string_vec.end() );
-
-      std::ostringstream oss;
-      oss << "Tracked Memory:" << std::endl;
-      for (size_t i=0; i< string_vec.size(); ++i)
-      {
-        oss << "   " << string_vec[i] << std::endl;
-      }
-      out << oss.str() << std::endl;
-    }
-    else {
-      out << "No Tracked Memory" << std::endl;
-    }
-  }
-
-  // find an AllocationRecord such that
-  // alloc_ptr <= ptr < alloc_ptr + alloc_size
-  // otherwise return NULL
-  AllocationRecord * find( void const * ptr, AllocatorBase const * allocator ) const
-  {
-    AllocationNode * start = head;
-
-    AllocationNode * curr = start;
-
-    char const * const char_ptr = reinterpret_cast<const char *>(ptr);
-
-    do {
-      AllocationNode * next = curr->next;
-
-      // bit zero does not map to an AllocationRecord
-      for ( int32_t i=1; i < bitset_type::size; ++i )
-      {
-        if (curr->bitset.test(i)) {
-          AllocationRecord * alloc_rec = reinterpret_cast<AllocationRecord *>( curr->get_buffer(i) );
-
-          char const * const alloc_ptr = reinterpret_cast<char const *>(alloc_rec->alloc_ptr);
-
-          if (   (allocator == alloc_rec->allocator)
-              && (alloc_ptr <= char_ptr)
-              && (char_ptr < (alloc_ptr + alloc_rec->alloc_size)) )
-          {
-            return alloc_rec;
-          }
-        }
-      }
-      curr = next;
-    } while ( curr != start );
-
-    return NULL;
-  }
-
-private:
-
-  AllocationNode * get_node( AllocationRecord * alloc_rec )
-  {
-    return reinterpret_cast<AllocationNode *>( alloc_rec - alloc_rec->node_index);
-  }
-
-  AllocationNode * head;
-  SingletonNode * singleton_head;
-};
-
-// create the global pool for allocation records
-AllocationRecordPool global_alloc_rec_pool;
-
-
-
-// convert a uintptr_t to an AllocationRecord pointer
-inline
-AllocationRecord * to_alloc_rec( uintptr_t alloc_rec )
-{
-  return reinterpret_cast<AllocationRecord *>( alloc_rec & ~static_cast<uintptr_t>(1) );
-}
-
-} // unnamed namespace
-
-//-----------------------------------------------------------------------------
-// Allocation Tracker methods
-//-----------------------------------------------------------------------------
-
-// Create a reference counted AllocationTracker
-void AllocationTracker::initalize(  AllocatorBase * arg_allocator
-                                  , void * arg_alloc_ptr
-                                  , size_t arg_alloc_size
-                                  , const std::string & arg_label
-                                 )
-{
-  if ( arg_allocator && arg_alloc_ptr && arg_alloc_size) {
-    // create record
-    AllocationRecord * alloc_rec = global_alloc_rec_pool.create(  arg_allocator
-                                                                , arg_alloc_ptr
-                                                                , arg_alloc_size
-                                                                , arg_label
-                                                               );
-
-    m_alloc_rec = reinterpret_cast<uintptr_t>(alloc_rec) | REF_COUNT_BIT;
-  }
-}
-
-void AllocationTracker::reallocate( size_t size ) const
-{
-  AllocationRecord * rec = to_alloc_rec( m_alloc_rec );
-
-  void * the_alloc_ptr = rec->allocator->reallocate( rec->alloc_ptr, rec->alloc_size, size );
-
-  if ( NULL != the_alloc_ptr )
-  {
-    *const_cast<void **>(&rec->alloc_ptr) = the_alloc_ptr;
-    *const_cast<uint64_t *>(&rec->alloc_size) = size;
-  }
-  else {
-    Impl::throw_runtime_exception( "Error: unable to reallocate allocation tracker");
-  }
-}
-
-
-void AllocationTracker::increment_ref_count() const
-{
-  to_alloc_rec( m_alloc_rec )->increment_ref_count();
-}
-
-
-void AllocationTracker::decrement_ref_count() const
-{
-  AllocationRecord * alloc_rec = to_alloc_rec( m_alloc_rec );
-  uint32_t the_ref_count = alloc_rec->decrement_ref_count();
-  if (the_ref_count == 0u) {
-    try {
-      global_alloc_rec_pool.destroy( alloc_rec );
-    }
-    catch(...) {}
-  }
-}
-
-namespace {
-
-struct NullAllocator { static const char * name() { return "Null Allocator"; } };
-
-}
-
-AllocatorBase * AllocationTracker::allocator() const
-{
-  if (m_alloc_rec & REF_COUNT_MASK) {
-    return to_alloc_rec(m_alloc_rec)->allocator;
-  }
-  return Allocator<NullAllocator>::singleton();
-}
-
-void * AllocationTracker::alloc_ptr()  const
-{
-  if (m_alloc_rec & REF_COUNT_MASK) {
-    return to_alloc_rec(m_alloc_rec)->alloc_ptr;
-  }
-  return NULL;
-}
-
-size_t AllocationTracker::alloc_size() const
-{
-  if (m_alloc_rec & REF_COUNT_MASK) {
-    return to_alloc_rec(m_alloc_rec)->alloc_size;
-  }
-  return 0u;
-}
-
-size_t AllocationTracker::ref_count()  const
-{
-  if (m_alloc_rec & REF_COUNT_MASK) {
-    return to_alloc_rec(m_alloc_rec)->ref_count;
-  }
-  return 0u;
-}
-
-char const * AllocationTracker::label() const
-{
-  if (m_alloc_rec & REF_COUNT_MASK) {
-    return to_alloc_rec(m_alloc_rec)->label;
-  }
-  return "[Empty Allocation Tracker]";
-}
-
-void AllocationTracker::print( std::ostream & oss) const
-{
-  if (m_alloc_rec & REF_COUNT_MASK) {
-    to_alloc_rec(m_alloc_rec)->print(oss);
-  }
-  else {
-    oss << label();
-  }
-}
-
-bool AllocationTracker::set_attribute( AllocatorAttributeBase * attr ) const
-{
-  bool result = false;
-  if (m_alloc_rec & REF_COUNT_MASK) {
-    result = to_alloc_rec(m_alloc_rec)->set_attribute(attr);
-  }
-  return result;
-}
-
-AllocatorAttributeBase * AllocationTracker::attribute() const
-{
-  if (m_alloc_rec & REF_COUNT_MASK) {
-    return to_alloc_rec(m_alloc_rec)->attribute;
-  }
-  return NULL;
-}
-
-void AllocationTracker::print_tracked_memory( std::ostream & out )
-{
-  global_alloc_rec_pool.print_memory( out );
-}
-
-
-AllocationTracker AllocationTracker::find( void const * ptr, AllocatorBase const * arg_allocator )
-{
-  AllocationRecord * alloc_rec = global_alloc_rec_pool.find(ptr, arg_allocator);
-
-  AllocationTracker tracker;
-
-  if ( alloc_rec != NULL )
-  {
-    if ( tracking_enabled() ) {
-      alloc_rec->increment_ref_count();
-      tracker.m_alloc_rec = reinterpret_cast<uintptr_t>(alloc_rec) | REF_COUNT_BIT;
-    }
-    else {
-      tracker.m_alloc_rec = reinterpret_cast<uintptr_t>(alloc_rec);
-    }
-  }
-
-  return tracker ;
-}
-
-
-
-//-----------------------------------------------------------------------------
-// static AllocationTracker
-//-----------------------------------------------------------------------------
-#if defined( KOKKOS_USE_DECENTRALIZED_HOST )
-namespace {
-
-  // TODO : Detect compiler support for thread local variables
-  #if defined( KOKKOS_HAVE_DEFAULT_DEVICE_TYPE_OPENMP )
-    bool g_thread_local_tracking_enabled = true;
-    #pragma omp threadprivate(g_thread_local_tracking_enabled)
-  #elif defined( KOKKOS_HAVE_DEFAULT_DEVICE_TYPE_THREADS )
-    __thread bool g_thread_local_tracking_enabled = true;
-  #elif defined( KOKKOS_HAVE_OPENMP )
-    bool g_thread_local_tracking_enabled = true;
-    #pragma omp threadprivate(g_thread_local_tracking_enabled)
-  #elif defined( KOKKOS_HAVE_PTHREAD )
-    __thread bool g_thread_local_tracking_enabled = true;
-  #elif defined( KOKKOS_HAVE_SERIAL )
-      bool g_thread_local_tracking_enabled = true;
-  #endif
-} // unnamed namespace
-
-void AllocationTracker::disable_tracking()
-{
-  g_thread_local_tracking_enabled = false;
-}
-
-void AllocationTracker::enable_tracking()
-{
-  g_thread_local_tracking_enabled = true;
-}
-
-bool AllocationTracker::tracking_enabled()
-{
-  return g_thread_local_tracking_enabled;
-}
-#else
-namespace {
-enum TrackingEnum { TRACKING_ENABLED, TRACKING_DISABLED };
-volatile TrackingEnum g_tracking_enabled = TRACKING_ENABLED;
-}
-
-void AllocationTracker::disable_tracking()
-{
-  if ( TRACKING_ENABLED != atomic_compare_exchange( &g_tracking_enabled, TRACKING_ENABLED, TRACKING_DISABLED ) ) {
-    Impl::throw_runtime_exception("Error: Tracking already disabled");
-  }
-}
-
-void AllocationTracker::enable_tracking()
-{
-  if ( TRACKING_DISABLED != atomic_compare_exchange( &g_tracking_enabled, TRACKING_DISABLED, TRACKING_ENABLED ) ) {
-    Impl::throw_runtime_exception("Error: Tracking already enabled");
-  }
-}
-
-bool AllocationTracker::tracking_enabled()
-{
-  return g_tracking_enabled == TRACKING_ENABLED;
-}
-#endif
-
-
-//-----------------------------------------------------------------------------
-// create singleton free function
-//-----------------------------------------------------------------------------
-void * create_singleton(  size_t size
-                        , Impl::singleton_create_function_type create_func
-                        , Impl::singleton_destroy_function_type destroy_func )
-{
-  return global_alloc_rec_pool.create_singleton( size, create_func, destroy_func );
-}
-
-}} // namespace Kokkos::Impl
-
-#endif /* #if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST ) */
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
diff --git a/lib/kokkos/core/src/impl/Kokkos_AllocationTracker.hpp b/lib/kokkos/core/src/impl/Kokkos_AllocationTracker.hpp
deleted file mode 100644
index 738a9d7908..0000000000
--- a/lib/kokkos/core/src/impl/Kokkos_AllocationTracker.hpp
+++ /dev/null
@@ -1,574 +0,0 @@
-/*
-//@HEADER
-// ************************************************************************
-// 
-//                        Kokkos v. 2.0
-//              Copyright (2014) Sandia Corporation
-// 
-// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
-// the U.S. Government retains certain rights in this software.
-// 
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are
-// met:
-//
-// 1. Redistributions of source code must retain the above copyright
-// notice, this list of conditions and the following disclaimer.
-//
-// 2. Redistributions in binary form must reproduce the above copyright
-// notice, this list of conditions and the following disclaimer in the
-// documentation and/or other materials provided with the distribution.
-//
-// 3. Neither the name of the Corporation nor the names of the
-// contributors may be used to endorse or promote products derived from
-// this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
-// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
-// ************************************************************************
-//@HEADER
-*/
-
-#ifndef KOKKOS_ALLOCATION_TRACKER_HPP
-#define KOKKOS_ALLOCATION_TRACKER_HPP
-
-#include <Kokkos_Macros.hpp>
-
-#if ! KOKKOS_USING_EXP_VIEW
-
-#include <impl/Kokkos_Traits.hpp>
-#include <impl/Kokkos_Error.hpp>
-
-#include <stdint.h>
-#include <cstdlib>
-#include <string>
-#include <iosfwd>
-
-namespace Kokkos { namespace Impl {
-
-//-----------------------------------------------------------------------------
-// Create Singleton objects
-//-----------------------------------------------------------------------------
-
-typedef void * (*singleton_create_function_type)(void * buffer);
-typedef void (*singleton_destroy_function_type)(void *);
-
-void * create_singleton(  size_t size
-                        , singleton_create_function_type create_func
-                        , singleton_destroy_function_type destroy_func
-                       );
-
-
-
-/// class Singleton
-///
-/// Default construct a singleton type.  This method is used to circumvent
-/// order of construction issues.  Singleton objects are destroyed after all
-/// other allocations in the reverse order of their creation.
-template <typename Type>
-class Singleton
-{
-public:
-  /// Get a pointer to the Singleton. Default construct the singleton if it does not already exist
-  static Type * get()
-  {
-    static Type * singleton = NULL;
-    if (singleton == NULL) {
-      Impl::singleton_create_function_type  create_func = &create;
-      Impl::singleton_destroy_function_type destroy_func = &destroy;
-      singleton = reinterpret_cast<Type*>( Impl::create_singleton( sizeof(Type), create_func, destroy_func ) );
-    }
-    return singleton;
-  }
-
-private:
-
-  /// Call the Type constructor
-  static void destroy(void * ptr)
-  {
-    reinterpret_cast<Type*>(ptr)->~Type();
-  }
-
-  /// placement new the Type in buffer
-  static void * create(void * buffer)
-  {
-    return new (buffer) Type();
-  }
-};
-
-
-//-----------------------------------------------------------------------------
-// AllocatorBase
-//-----------------------------------------------------------------------------
-
-/// class AllocatorBase
-///
-/// Abstract base class for all Allocators.
-/// Allocators should be singleton objects, use Singleton<Allocator>::get to create
-/// to avoid order of destruction issues
-class AllocatorBase
-{
-public:
-  /// name of the allocator
-  /// used to report memory leaks
-  virtual const char * name() const = 0;
-
-  /// Allocate a buffer of size number of bytes
-  virtual void* allocate(size_t size) const = 0;
-
-  /// Deallocate a buffer with size number of bytes
-  /// The pointer must have been allocated with a call to corresponding allocate
-  virtual void deallocate(void * ptr, size_t size) const = 0;
-
-  /// Changes the size of the memory block pointed to by ptr.
-  /// Ptr must have been allocated with the corresponding allocate call
-  /// The function may move the memory block to a new location
-  /// (whose address is returned by the function).
-  ///
-  /// The content of the memory block is preserved up to the lesser of the new and
-  /// old sizes, even if the block is moved to a new location. If the new size is larger,
-  /// the value of the newly allocated portion is indeterminate.
-  ///
-  /// In case that ptr is a null pointer, the function behaves like allocate, assigning a
-  /// new block of size bytes and returning a pointer to its beginning.
-  virtual void * reallocate(void * old_ptr, size_t old_size, size_t new_size) const = 0;
-
-  /// can a texture object be bound to the allocated memory
-  virtual bool support_texture_binding() const = 0;
-
-  /// virtual destructor
-  virtual ~AllocatorBase() {}
-};
-
-/// class AllocatorAttributeBase
-class AllocatorAttributeBase
-{
-public:
-  virtual ~AllocatorAttributeBase() {}
-};
-
-//-----------------------------------------------------------------------------
-// Allocator< StaticAllocator > : public AllocatorBase
-//-----------------------------------------------------------------------------
-
-// HasStaticName
-template<typename T>
-class HasStaticName
-{
-  typedef const char * (*static_method)();
-  template<typename U, static_method> struct SFINAE {};
-  template<typename U> static char Test(SFINAE<U, &U::name>*);
-  template<typename U> static int Test(...);
-public:
-  enum { value = sizeof(Test<T>(0)) == sizeof(char) };
-};
-
-
-template <typename T>
-inline
-typename enable_if<HasStaticName<T>::value, const char *>::type
-allocator_name()
-{
-  return T::name();
-}
-
-template <typename T>
-inline
-typename enable_if<!HasStaticName<T>::value, const char *>::type
-allocator_name()
-{
-  return "Unnamed Allocator";
-}
-
-
-// HasStaticAllocate
-template<typename T>
-class HasStaticAllocate
-{
-  typedef void * (*static_method)(size_t);
-  template<typename U, static_method> struct SFINAE {};
-  template<typename U> static char Test(SFINAE<U, &U::allocate>*);
-  template<typename U> static int Test(...);
-public:
-  enum { value = sizeof(Test<T>(0)) == sizeof(char) };
-};
-
-template <typename T>
-inline
-typename enable_if<HasStaticAllocate<T>::value, void *>::type
-allocator_allocate(size_t size)
-{
-  return T::allocate(size);
-}
-
-template <typename T>
-inline
-typename enable_if<!HasStaticAllocate<T>::value, void *>::type
-allocator_allocate(size_t)
-{
-  throw_runtime_exception(  std::string("Error: ")
-                          + std::string(allocator_name<T>())
-                          + std::string(" cannot allocate memory!") );
-  return NULL;
-}
-
-// HasStaticDeallocate
-template<typename T>
-class HasStaticDeallocate
-{
-  typedef void (*static_method)(void *, size_t);
-  template<typename U, static_method> struct SFINAE {};
-  template<typename U> static char Test(SFINAE<U, &U::deallocate>*);
-  template<typename U> static int Test(...);
-public:
-  enum { value = sizeof(Test<T>(0)) == sizeof(char) };
-};
-
-template <typename T>
-inline
-typename enable_if<HasStaticDeallocate<T>::value, void>::type
-allocator_deallocate(void * ptr, size_t size)
-{
-  T::deallocate(ptr,size);
-}
-
-template <typename T>
-inline
-typename enable_if<!HasStaticDeallocate<T>::value, void>::type
-allocator_deallocate(void *, size_t)
-{
-  throw_runtime_exception(  std::string("Error: ")
-                          + std::string(allocator_name<T>())
-                          + std::string(" cannot deallocate memory!") );
-}
-
-// HasStaticReallocate
-template<typename T>
-class HasStaticReallocate
-{
-  typedef void * (*static_method)(void *, size_t, size_t);
-  template<typename U, static_method> struct SFINAE {};
-  template<typename U> static char Test(SFINAE<U, &U::reallocate>*);
-  template<typename U> static int Test(...);
-public:
-  enum { value = sizeof(Test<T>(0)) == sizeof(char) };
-};
-
-template <typename T>
-inline
-typename enable_if<HasStaticReallocate<T>::value, void *>::type
-allocator_reallocate(void * old_ptr, size_t old_size, size_t new_size)
-{
-  return T::reallocate(old_ptr, old_size, new_size);
-}
-
-template <typename T>
-inline
-typename enable_if<!HasStaticReallocate<T>::value, void *>::type
-allocator_reallocate(void *, size_t, size_t)
-{
-  throw_runtime_exception(  std::string("Error: ")
-                          + std::string(allocator_name<T>())
-                          + std::string(" cannot reallocate memory!") );
-  return NULL;
-}
-
-// HasStaticReallocate
-template<typename T>
-class HasStaticSupportTextureBinding
-{
-  typedef bool (*static_method)();
-  template<typename U, static_method> struct SFINAE {};
-  template<typename U> static char Test(SFINAE<U, &U::support_texture_binding>*);
-  template<typename U> static int Test(...);
-public:
-  enum { value = sizeof(Test<T>(0)) == sizeof(char) };
-};
-
-template <typename T>
-inline
-typename enable_if<HasStaticSupportTextureBinding<T>::value, bool>::type
-allocator_support_texture_binding()
-{
-  return T::support_texture_binding();
-}
-
-template <typename T>
-inline
-typename enable_if<!HasStaticSupportTextureBinding<T>::value, bool>::type
-allocator_support_texture_binding()
-{
-  return false;
-}
-
-template <typename T>
-class Allocator : public AllocatorBase
-{
-public:
-  virtual const char * name() const
-  {
-    return allocator_name<T>();
-  }
-
-  virtual void* allocate(size_t size) const
-  {
-    return allocator_allocate<T>(size);
-  }
-
-  virtual void deallocate(void * ptr, size_t size) const
-  {
-    allocator_deallocate<T>(ptr,size);
-  }
-
-  virtual void * reallocate(void * old_ptr, size_t old_size, size_t new_size) const
-  {
-    return allocator_reallocate<T>(old_ptr, old_size, new_size);
-  }
-
-  virtual bool support_texture_binding() const
-  {
-    return allocator_support_texture_binding<T>();
-  }
-
-  static AllocatorBase * singleton()
-  {
-    return Singleton< Allocator<T> >::get();
-  }
-};
-
-//-----------------------------------------------------------------------------
-// AllocationTracker
-//-----------------------------------------------------------------------------
-
-// forward declaration for friend classes
-struct MallocHelper;
-
-/// class AllocationTracker
-/// Will call deallocate from the AllocatorBase when the reference count reaches 0.
-/// Reference counting is disabled when the host is in parallel.
-class AllocationTracker
-{
-  // use the least significant bit of the AllocationRecord pointer to indicate if the
-  // AllocationTracker should reference count
-  enum {
-     REF_COUNT_BIT = static_cast<uintptr_t>(1)
-   , REF_COUNT_MASK = ~static_cast<uintptr_t>(1)
-  };
-
-public:
-
-  /// Find an AllocationTracker such that
-  /// alloc_ptr <= ptr < alloc_ptr + alloc_size
-  /// O(n) where n is the number of tracked allocations.
-  template <typename StaticAllocator>
-  static AllocationTracker find( void const * ptr )
-  {
-    return find( ptr, Allocator<StaticAllocator>::singleton() );
-  }
-
-
-  /// Pretty print all the currently tracked memory
-  static void print_tracked_memory( std::ostream & out );
-
-  /// Default constructor
-  KOKKOS_INLINE_FUNCTION
-  AllocationTracker()
-    : m_alloc_rec(0)
-  {}
-
-  /// Create a AllocationTracker
-  ///
-  /// Start reference counting the alloc_ptr.
-  /// When the reference count reachs 0 the allocator deallocate method
-  /// will be call with the given size.  The alloc_ptr should have been
-  /// allocated with the allocator's allocate method.
-  ///
-  /// If arg_allocator == NULL OR arg_alloc_ptr == NULL OR size == 0
-  /// do nothing
-  template <typename StaticAllocator>
-  AllocationTracker(  StaticAllocator const &
-                    , void * arg_alloc_ptr
-                    , size_t arg_alloc_size
-                    , const std::string & arg_label = std::string("") )
-    : m_alloc_rec(0)
-  {
-    AllocatorBase * arg_allocator = Allocator<StaticAllocator>::singleton();
-    initalize( arg_allocator, arg_alloc_ptr, arg_alloc_size, arg_label);
-  }
-
-  /// Create a AllocationTracker
-  ///
-  /// Start reference counting the alloc_ptr.
-  /// When the reference count reachs 0 the allocator deallocate method
-  /// will be call with the given size.  The alloc_ptr should have been
-  /// allocated with the allocator's allocate method.
-  ///
-  /// If arg_allocator == NULL OR arg_alloc_ptr == NULL OR size == 0
-  /// do nothing
-  template <typename StaticAllocator>
-  AllocationTracker(  StaticAllocator const &
-                    , size_t arg_alloc_size
-                    , const std::string & arg_label = std::string("")
-                   )
-    : m_alloc_rec(0)
-  {
-    AllocatorBase * arg_allocator = Allocator<StaticAllocator>::singleton();
-    void * arg_alloc_ptr = arg_allocator->allocate( arg_alloc_size );
-
-    initalize( arg_allocator, arg_alloc_ptr, arg_alloc_size, arg_label);
-  }
-
-  /// Copy an AllocatorTracker
-  KOKKOS_INLINE_FUNCTION
-  AllocationTracker( const AllocationTracker & rhs )
-    : m_alloc_rec( rhs.m_alloc_rec)
-  {
-#if !defined( __CUDA_ARCH__ )
-    if ( rhs.ref_counting() && tracking_enabled() ) {
-      increment_ref_count();
-    }
-    else {
-      m_alloc_rec = m_alloc_rec & REF_COUNT_MASK;
-    }
-#else
-    m_alloc_rec = m_alloc_rec & REF_COUNT_MASK;
-#endif
-  }
-
-  /// Copy an AllocatorTracker
-  /// Decrement the reference count of the current tracker if necessary
-  KOKKOS_INLINE_FUNCTION
-  AllocationTracker & operator=( const AllocationTracker & rhs )
-  {
-    if (this != &rhs) {
-#if !defined( __CUDA_ARCH__ )
-      if ( ref_counting() ) {
-        decrement_ref_count();
-      }
-
-      m_alloc_rec = rhs.m_alloc_rec;
-
-      if ( rhs.ref_counting() && tracking_enabled() ) {
-        increment_ref_count();
-      }
-      else {
-        m_alloc_rec = m_alloc_rec & REF_COUNT_MASK;
-      }
-#else
-      m_alloc_rec = rhs.m_alloc_rec & REF_COUNT_MASK;
-#endif
-    }
-
-    return * this;
-  }
-
-  /// Destructor
-  /// Decrement the reference count if necessary
-  KOKKOS_INLINE_FUNCTION
-  ~AllocationTracker()
-  {
-#if !defined( __CUDA_ARCH__ )
-    if ( ref_counting() ) {
-      decrement_ref_count();
-    }
-#endif
-  }
-
-  /// Is the tracker valid?
-  KOKKOS_INLINE_FUNCTION
-  bool is_valid() const
-  {
-    return (m_alloc_rec & REF_COUNT_MASK);
-  }
-
-
-
-  /// clear the tracker
-  KOKKOS_INLINE_FUNCTION
-  void clear()
-  {
-#if !defined( __CUDA_ARCH__ )
-    if ( ref_counting() ) {
-      decrement_ref_count();
-    }
-#endif
-    m_alloc_rec = 0;
-  }
-
-  /// is this tracker currently counting allocations?
-  KOKKOS_INLINE_FUNCTION
-  bool ref_counting() const
-  {
-    return (m_alloc_rec & REF_COUNT_BIT);
-  }
-
-  AllocatorBase * allocator() const;
-
-  /// pointer to the allocated memory
-  void * alloc_ptr()  const;
-
-  /// size in bytes of the allocated memory
-  size_t alloc_size() const;
-
-  /// the current reference count
-  size_t ref_count()  const;
-
-  /// the label given to the allocation
-  char const * label() const;
-
-  /// pretty print all the tracker's information to the std::ostream
-  void print( std::ostream & oss) const;
-
-
-  /// set an attribute ptr on the allocation record
-  /// the arg_attribute pointer will be deleted when the record is destroyed
-  /// the attribute ptr can only be set once
-  bool set_attribute( AllocatorAttributeBase * arg_attribute) const;
-
-  /// get the attribute ptr from the allocation record
-  AllocatorAttributeBase * attribute() const;
-
-
-  /// reallocate the memory tracked by this allocation
-  /// NOT thread-safe
-  void reallocate( size_t size ) const;
-
-  static void disable_tracking();
-  static void enable_tracking();
-  static bool tracking_enabled();
-
-private:
-
-  static AllocationTracker find( void const * ptr, AllocatorBase const * arg_allocator );
-
-  void initalize(  AllocatorBase * arg_allocator
-                 , void * arg_alloc_ptr
-                 , size_t arg_alloc_size
-                 , std::string const & label );
-
-  void increment_ref_count() const;
-  void decrement_ref_count() const;
-
-  friend struct Impl::MallocHelper;
-
-  uintptr_t m_alloc_rec;
-};
-
-}} // namespace Kokkos::Impl
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-#endif //KOKKOS_ALLOCATION_TRACKER_HPP
-
diff --git a/lib/kokkos/core/src/impl/Kokkos_AnalyzePolicy.hpp b/lib/kokkos/core/src/impl/Kokkos_AnalyzePolicy.hpp
new file mode 100644
index 0000000000..0246a7b9af
--- /dev/null
+++ b/lib/kokkos/core/src/impl/Kokkos_AnalyzePolicy.hpp
@@ -0,0 +1,197 @@
+/*
+//@HEADER
+// ************************************************************************
+//
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+//
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+//
+// ************************************************************************
+//@HEADER
+*/
+
+#ifndef KOKKOS_IMPL_ANALYZE_POLICY_HPP
+#define KOKKOS_IMPL_ANALYZE_POLICY_HPP
+
+#include <Kokkos_Core_fwd.hpp>
+#include <Kokkos_Concepts.hpp>
+#include <impl/Kokkos_Tags.hpp>
+
+namespace Kokkos { namespace Impl {
+
+template < typename ExecutionSpace   = void
+         , typename Schedule         = void
+         , typename WorkTag          = void
+         , typename IndexType        = void
+         , typename IterationPattern = void
+         >
+struct PolicyTraitsBase
+{
+  using type = PolicyTraitsBase< ExecutionSpace, Schedule, WorkTag, IndexType, IterationPattern>;
+
+  using execution_space   = ExecutionSpace;
+  using schedule_type     = Schedule;
+  using work_tag          = WorkTag;
+  using index_type        = IndexType;
+  using iteration_pattern = IterationPattern;
+};
+
+
+template <typename PolicyBase, typename ExecutionSpace>
+struct SetExecutionSpace
+{
+  static_assert( is_void<typename PolicyBase::execution_space>::value
+               , "Kokkos Error: More than one execution space given" );
+  using type = PolicyTraitsBase< ExecutionSpace
+                               , typename PolicyBase::schedule_type
+                               , typename PolicyBase::work_tag
+                               , typename PolicyBase::index_type
+                               , typename PolicyBase::iteration_pattern
+                               >;
+};
+
+template <typename PolicyBase, typename Schedule>
+struct SetSchedule
+{
+  static_assert( is_void<typename PolicyBase::schedule_type>::value
+               , "Kokkos Error: More than one schedule type given" );
+  using type = PolicyTraitsBase< typename PolicyBase::execution_space
+                               , Schedule
+                               , typename PolicyBase::work_tag
+                               , typename PolicyBase::index_type
+                               , typename PolicyBase::iteration_pattern
+                               >;
+};
+
+template <typename PolicyBase, typename WorkTag>
+struct SetWorkTag
+{
+  static_assert( is_void<typename PolicyBase::work_tag>::value
+               , "Kokkos Error: More than one work tag given" );
+  using type = PolicyTraitsBase< typename PolicyBase::execution_space
+                               , typename PolicyBase::schedule_type
+                               , WorkTag
+                               , typename PolicyBase::index_type
+                               , typename PolicyBase::iteration_pattern
+                               >;
+};
+
+template <typename PolicyBase, typename IndexType>
+struct SetIndexType
+{
+  static_assert( is_void<typename PolicyBase::index_type>::value
+               , "Kokkos Error: More than one index type given" );
+  using type = PolicyTraitsBase< typename PolicyBase::execution_space
+                               , typename PolicyBase::schedule_type
+                               , typename PolicyBase::work_tag
+                               , IndexType
+                               , typename PolicyBase::iteration_pattern
+                               >;
+};
+
+
+template <typename PolicyBase, typename IterationPattern>
+struct SetIterationPattern
+{
+  static_assert( is_void<typename PolicyBase::iteration_pattern>::value
+               , "Kokkos Error: More than one iteration_pattern given" );
+  using type = PolicyTraitsBase< typename PolicyBase::execution_space
+                               , typename PolicyBase::schedule_type
+                               , typename PolicyBase::work_tag
+                               , typename PolicyBase::index_type
+                               , IterationPattern
+                               >;
+};
+
+
+template <typename Base, typename... Traits>
+struct AnalyzePolicy;
+
+template <typename Base, typename T, typename... Traits>
+struct AnalyzePolicy<Base, T, Traits...> : public
+  AnalyzePolicy<
+      typename std::conditional< is_execution_space<T>::value  , SetExecutionSpace<Base,T>
+    , typename std::conditional< is_schedule_type<T>::value    , SetSchedule<Base,T>
+    , typename std::conditional< is_index_type<T>::value       , SetIndexType<Base,T>
+    , typename std::conditional< std::is_integral<T>::value    , SetIndexType<Base, IndexType<T> >
+    , typename std::conditional< is_iteration_pattern<T>::value, SetIterationPattern<Base,T>
+    , SetWorkTag<Base,T>
+    >::type >::type >::type >::type>::type::type
+  , Traits...
+  >
+{};
+
+template <typename Base>
+struct AnalyzePolicy<Base>
+{
+  using execution_space = typename std::conditional< is_void< typename Base::execution_space >::value
+                                                   , DefaultExecutionSpace
+                                                   , typename Base::execution_space
+                                                   >::type;
+
+  using schedule_type = typename std::conditional< is_void< typename Base::schedule_type >::value
+                                                 , Schedule< Static >
+                                                 , typename Base::schedule_type
+                                                 >::type;
+
+  using work_tag = typename Base::work_tag;
+
+  using index_type = typename std::conditional< is_void< typename Base::index_type >::value
+                                              , IndexType< typename execution_space::size_type >
+                                              , typename Base::index_type
+                                              >::type
+                                               ::type // nasty hack to make index_type into an integral_type
+                                              ;       // instead of the wrapped IndexType<T> for backwards compatibility
+
+  using iteration_pattern = typename std::conditional< is_void< typename Base::iteration_pattern >::value
+                                                     , void // TODO set default iteration pattern
+                                                     , typename Base::iteration_pattern
+                                                     >::type;
+  using type = PolicyTraitsBase< execution_space
+                               , schedule_type
+                               , work_tag
+                               , index_type
+                               , iteration_pattern
+                               >;
+};
+
+template <typename... Traits>
+struct PolicyTraits
+  : public AnalyzePolicy< PolicyTraitsBase<>, Traits... >::type
+{};
+
+}} // namespace Kokkos::Impl
+
+
+#endif //KOKKOS_IMPL_ANALYZE_POLICY_HPP
diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp
index 8a27ce6f22..fd7ea845e7 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -218,7 +218,17 @@ T atomic_compare_exchange( volatile T * const dest , const T compare ,
   while( !Impl::lock_address_host_space( (void*) dest ) );
   T return_val = *dest;
   if( return_val == compare ) {
-    const T tmp = *dest = val;
+    // Don't use the following line of code here:
+    //
+    //const T tmp = *dest = val;
+    //
+    // Instead, put each assignment in its own statement.  This is
+    // because the overload of T::operator= for volatile *this should
+    // return void, not volatile T&.  See Kokkos #177:
+    //
+    // https://github.com/kokkos/kokkos/issues/177
+    *dest = val;
+    const T tmp = *dest;
     #ifndef KOKKOS_COMPILER_CLANG
     (void) tmp;
     #endif
@@ -239,7 +249,7 @@ T atomic_compare_exchange( volatile T * const dest, const T compare, const T val
   {
     retval = dest[0];
     if ( retval == compare )
-  	dest[0] = val;
+        dest[0] = val;
   }
   return retval;
 }
diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Exchange.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Exchange.hpp
index 8990604674..e8cac4ba3b 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Exchange.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Exchange.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -228,7 +228,17 @@ T atomic_exchange( volatile T * const dest ,
 {
   while( !Impl::lock_address_host_space( (void*) dest ) );
   T return_val = *dest;
-  const T tmp = *dest = val;
+  // Don't use the following line of code here:
+  //
+  //const T tmp = *dest = val;
+  //
+  // Instead, put each assignment in its own statement.  This is
+  // because the overload of T::operator= for volatile *this should
+  // return void, not volatile T&.  See Kokkos #177:
+  //
+  // https://github.com/kokkos/kokkos/issues/177
+  *dest = val;
+  const T tmp = *dest;
   #ifndef KOKKOS_COMPILER_CLANG
   (void) tmp;
   #endif
@@ -305,7 +315,9 @@ void atomic_assign( volatile T * const dest ,
   // member.  The volatile return value implicitly defines a
   // dereference that some compilers (gcc 4.7.2) warn is being ignored.
   // Suppress warning by casting return to void.
-  (void)( *dest = val );
+  //(void)( *dest = val );
+  *dest = val;
+
   Impl::unlock_address_host_space( (void*) dest );
 }
 //----------------------------------------------------------------------------
diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Add.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Add.hpp
index 239bbf7cbb..62dfcdd2f8 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Add.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Add.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -93,7 +93,7 @@ T atomic_fetch_add( volatile T * const dest ,
     assume.i = oldval.i ;
     newval.t = assume.t + val ;
     oldval.i = atomicCAS( (int*)dest , assume.i , newval.i );
-  } while ( assumed.i != oldval.i );
+  } while ( assume.i != oldval.i );
 
   return oldval.t ;
 }
@@ -156,9 +156,26 @@ T atomic_fetch_add( volatile T * const dest ,
 
 #elif defined(KOKKOS_ATOMICS_USE_GCC) || defined(KOKKOS_ATOMICS_USE_INTEL)
 
+#if defined( KOKKOS_ENABLE_ASM ) && defined ( KOKKOS_USE_ISA_X86_64 )
+KOKKOS_INLINE_FUNCTION
+int atomic_fetch_add( volatile int * dest , const int val )
+{
+        int original = val;
+
+        __asm__ __volatile__(
+                "lock xadd %1, %0"
+                : "+m" (*dest), "+r" (original)
+                : "m" (*dest), "r" (original)
+                : "memory"
+        );
+
+        return original;
+}
+#else
 KOKKOS_INLINE_FUNCTION
 int atomic_fetch_add( volatile int * const dest , const int val )
-{ return __sync_fetch_and_add(dest,val); }
+{ return __sync_fetch_and_add(dest, val); }
+#endif
 
 KOKKOS_INLINE_FUNCTION
 long int atomic_fetch_add( volatile long int * const dest , const long int val )
@@ -276,7 +293,17 @@ T atomic_fetch_add( volatile T * const dest ,
 {
   while( !Impl::lock_address_host_space( (void*) dest ) );
   T return_val = *dest;
-  const T tmp = *dest = return_val + val;
+  // Don't use the following line of code here:
+  //
+  //const T tmp = *dest = return_val + val;
+  //
+  // Instead, put each assignment in its own statement.  This is
+  // because the overload of T::operator= for volatile *this should
+  // return void, not volatile T&.  See Kokkos #177:
+  //
+  // https://github.com/kokkos/kokkos/issues/177
+  *dest = return_val + val;
+  const T tmp = *dest;
   (void) tmp;
   Impl::unlock_address_host_space( (void*) dest );
   return return_val;
diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp
index 647b3ad4e1..a3a57aa81c 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp
@@ -73,7 +73,7 @@ T atomic_fetch_sub( volatile T * const dest ,
     assume.i = oldval.i ;
     newval.t = assume.t - val ;
     oldval.i = atomicCAS( (int*)dest , assume.i , newval.i );
-  } while ( assumed.i != oldval.i );
+  } while ( assume.i != oldval.i );
 
   return oldval.t ;
 }
diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp
index 76f3ccac73..343e9bf4c4 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp
@@ -48,6 +48,22 @@
 namespace Kokkos {
 namespace Impl {
 
+template<class Scalar1, class Scalar2>
+struct MaxOper {
+  KOKKOS_FORCEINLINE_FUNCTION
+  static Scalar1 apply(const Scalar1& val1, const Scalar2& val2) {
+    return (val1 > val2 ? val1 : val2);
+  }
+};
+
+template<class Scalar1, class Scalar2>
+struct MinOper {
+  KOKKOS_FORCEINLINE_FUNCTION
+  static Scalar1 apply(const Scalar1& val1, const Scalar2& val2) {
+    return (val1 < val2 ? val1 : val2);
+  }
+};
+
 template<class Scalar1, class Scalar2>
 struct AddOper {
   KOKKOS_FORCEINLINE_FUNCTION
@@ -276,6 +292,18 @@ T atomic_oper_fetch( const Oper& op, volatile T * const dest ,
 namespace Kokkos {
 
 // Fetch_Oper atomics: return value before operation
+template < typename T >
+KOKKOS_INLINE_FUNCTION
+T atomic_fetch_max(volatile T * const dest, const T val) {
+  return Impl::atomic_fetch_oper(Impl::MaxOper<T,const T>(),dest,val);
+}
+
+template < typename T >
+KOKKOS_INLINE_FUNCTION
+T atomic_fetch_min(volatile T * const dest, const T val) {
+  return Impl::atomic_fetch_oper(Impl::MinOper<T,const T>(),dest,val);
+}
+
 template < typename T >
 KOKKOS_INLINE_FUNCTION
 T atomic_fetch_mul(volatile T * const dest, const T val) {
@@ -326,6 +354,18 @@ T atomic_fetch_rshift(volatile T * const dest, const unsigned int val) {
 
 
 // Oper Fetch atomics: return value after operation
+template < typename T >
+KOKKOS_INLINE_FUNCTION
+T atomic_max_fetch(volatile T * const dest, const T val) {
+  return Impl::atomic_oper_fetch(Impl::MaxOper<T,const T>(),dest,val);
+}
+
+template < typename T >
+KOKKOS_INLINE_FUNCTION
+T atomic_min_fetch(volatile T * const dest, const T val) {
+  return Impl::atomic_oper_fetch(Impl::MinOper<T,const T>(),dest,val);
+}
+
 template < typename T >
 KOKKOS_INLINE_FUNCTION
 T atomic_mul_fetch(volatile T * const dest, const T val) {
diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_View.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_View.hpp
index 4a2a408273..6e48faa694 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Atomic_View.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_View.hpp
@@ -425,42 +425,6 @@ struct Kokkos_Atomic_is_only_allowed_with_32bit_and_64bit_scalars<8> {
   typedef int64_t type;
 };
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-class AllocationTracker;
-
-// Must be non-const, atomic access trait, and 32 or 64 bit type for true atomics.
-template<class ViewTraits>
-class ViewDataHandle<
-  ViewTraits ,
-  typename enable_if<
-    ( ! is_same<typename ViewTraits::const_value_type,typename ViewTraits::value_type>::value) &&
-    ( ViewTraits::memory_traits::Atomic )
-  >::type >
-{
-private:
-//  typedef typename if_c<(sizeof(typename ViewTraits::const_value_type)==4) ||
-//                        (sizeof(typename ViewTraits::const_value_type)==8),
-//                         int, Kokkos_Atomic_is_only_allowed_with_32bit_and_64bit_scalars >::type
-//                   atomic_view_possible;
-  typedef typename Kokkos_Atomic_is_only_allowed_with_32bit_and_64bit_scalars<sizeof(typename ViewTraits::const_value_type)>::type enable_atomic_type;
-  typedef ViewDataHandle self_type;
-
-public:
-  enum {  ReturnTypeIsReference = false };
-
-  typedef Impl::AtomicViewDataHandle<ViewTraits> handle_type;
-  typedef Impl::AtomicDataElement<ViewTraits>    return_type;
-
-  KOKKOS_INLINE_FUNCTION
-  static handle_type create_handle( typename ViewTraits::value_type * arg_data_ptr, AllocationTracker const & /*arg_tracker*/ )
-  {
-    return handle_type(arg_data_ptr);
-  }
-};
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
 }} // namespace Kokkos::Impl
 
 #endif
diff --git a/lib/kokkos/core/src/impl/Kokkos_BasicAllocators.cpp b/lib/kokkos/core/src/impl/Kokkos_BasicAllocators.cpp
deleted file mode 100644
index 7cf233c689..0000000000
--- a/lib/kokkos/core/src/impl/Kokkos_BasicAllocators.cpp
+++ /dev/null
@@ -1,287 +0,0 @@
-/*
-//@HEADER
-// ************************************************************************
-// 
-//                        Kokkos v. 2.0
-//              Copyright (2014) Sandia Corporation
-// 
-// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
-// the U.S. Government retains certain rights in this software.
-// 
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are
-// met:
-//
-// 1. Redistributions of source code must retain the above copyright
-// notice, this list of conditions and the following disclaimer.
-//
-// 2. Redistributions in binary form must reproduce the above copyright
-// notice, this list of conditions and the following disclaimer in the
-// documentation and/or other materials provided with the distribution.
-//
-// 3. Neither the name of the Corporation nor the names of the
-// contributors may be used to endorse or promote products derived from
-// this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
-// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
-// ************************************************************************
-//@HEADER
-*/
-
-#include <Kokkos_HostSpace.hpp>
-
-#if ! KOKKOS_USING_EXP_VIEW
-
-#include <impl/Kokkos_BasicAllocators.hpp>
-#include <impl/Kokkos_Error.hpp>
-
-
-#include <stdint.h>    // uintptr_t
-#include <cstdlib>     // for malloc, realloc, and free
-#include <cstring>     // for memcpy
-
-#if defined(KOKKOS_POSIX_MEMALIGN_AVAILABLE)
-#include <sys/mman.h>  // for mmap, munmap, MAP_ANON, etc
-#include <unistd.h>    // for sysconf, _SC_PAGE_SIZE, _SC_PHYS_PAGES
-#endif
-
-#include <sstream>
-
-namespace Kokkos { namespace Impl {
-
-/*--------------------------------------------------------------------------*/
-
-void* MallocAllocator::allocate( size_t size )
-{
-  void * ptr = NULL;
-  if (size) {
-    ptr = malloc(size);
-
-    if (!ptr)
-    {
-      std::ostringstream msg ;
-      msg << name() << ": allocate(" << size << ") FAILED";
-      throw_runtime_exception( msg.str() );
-    }
-  }
-  return ptr;
-}
-
-void MallocAllocator::deallocate( void * ptr, size_t /*size*/ )
-{
-  if (ptr) {
-    free(ptr);
-  }
-}
-
-void * MallocAllocator::reallocate(void * old_ptr, size_t /*old_size*/, size_t new_size)
-{
-  void * ptr = realloc(old_ptr, new_size);
-
-  if (new_size > 0u && ptr == NULL) {
-    throw_runtime_exception("Error: Malloc Allocator could not reallocate memory");
-  }
-  return ptr;
-}
-
-/*--------------------------------------------------------------------------*/
-
-namespace {
-
-void * raw_aligned_allocate( size_t size, size_t alignment )
-{
-  void * ptr = NULL;
-  if ( size ) {
-#if defined( __INTEL_COMPILER ) && !defined ( KOKKOS_HAVE_CUDA )
-    ptr = _mm_malloc( size , alignment );
-
-#elif defined(KOKKOS_POSIX_MEMALIGN_AVAILABLE)
-
-    posix_memalign( & ptr, alignment , size );
-
-#else
-    // Over-allocate to and round up to guarantee proper alignment.
-    size_t size_padded = size + alignment + sizeof(void *);
-    void * alloc_ptr = malloc( size_padded );
-
-    if (alloc_ptr) {
-      uintptr_t address = reinterpret_cast<uintptr_t>(alloc_ptr);
-      // offset enough to record the alloc_ptr
-      address += sizeof(void *);
-      uintptr_t rem = address % alignment;
-      uintptr_t offset = rem ? (alignment - rem) : 0u;
-      address += offset;
-      ptr = reinterpret_cast<void *>(address);
-      // record the alloc'd pointer
-      address -= sizeof(void *);
-      *reinterpret_cast<void **>(address) = alloc_ptr;
-    }
-#endif
-  }
-  return ptr;
-}
-
-void raw_aligned_deallocate( void * ptr, size_t /*size*/ )
-{
-  if ( ptr ) {
-#if defined( __INTEL_COMPILER ) && !defined ( KOKKOS_HAVE_CUDA )
-    _mm_free( ptr );
-
-#elif defined(KOKKOS_POSIX_MEMALIGN_AVAILABLE)
-    free( ptr );
-#else
-    // get the alloc'd pointer
-    void * alloc_ptr = *(reinterpret_cast<void **>(ptr) -1);
-    free( alloc_ptr );
-#endif
-  }
-
-}
-
-}
-
-void* AlignedAllocator::allocate( size_t size )
-{
-  void * ptr = 0 ;
-
-  if ( size ) {
-    ptr = raw_aligned_allocate(size, MEMORY_ALIGNMENT);
-
-    if (!ptr)
-    {
-      std::ostringstream msg ;
-      msg << name() << ": allocate(" << size << ") FAILED";
-      throw_runtime_exception( msg.str() );
-    }
-  }
-  return ptr;
-}
-
-void AlignedAllocator::deallocate( void * ptr, size_t size )
-{
-  raw_aligned_deallocate( ptr, size);
-}
-
-void * AlignedAllocator::reallocate(void * old_ptr, size_t old_size, size_t new_size)
-{
-  void * ptr = old_ptr;;
-
-  if (old_size < new_size) {
-    ptr = allocate( new_size );
-
-    memcpy(ptr, old_ptr, old_size );
-
-    deallocate( old_ptr, old_size );
-  }
-
-  return ptr;
-}
-
-/*--------------------------------------------------------------------------*/
-
-// mmap flags for private anonymous memory allocation
-#if defined( MAP_ANONYMOUS ) && defined( MAP_PRIVATE )
-  #define MMAP_FLAGS (MAP_PRIVATE | MAP_ANONYMOUS)
-#elif defined( MAP_ANON) && defined( MAP_PRIVATE )
-  #define MMAP_FLAGS (MAP_PRIVATE | MAP_ANON)
-#else
-  #define NO_MMAP
-#endif
-
-// huge page tables
-#if !defined( NO_MMAP )
-  #if defined( MAP_HUGETLB )
-    #define MMAP_FLAGS_HUGE (MMAP_FLAGS | MAP_HUGETLB )
-  #elif defined( MMAP_FLAGS )
-    #define MMAP_FLAGS_HUGE MMAP_FLAGS
-  #endif
-  // threshold to use huge pages
-  #define MMAP_USE_HUGE_PAGES (1u << 27)
-#endif
-
-// read write access to private memory
-#if !defined( NO_MMAP )
-  #define MMAP_PROTECTION (PROT_READ | PROT_WRITE)
-#endif
-
-
-void* PageAlignedAllocator::allocate( size_t size )
-{
-  void *ptr = NULL;
-  if (size) {
-#if !defined NO_MMAP
-    if ( size < MMAP_USE_HUGE_PAGES ) {
-      ptr = mmap( NULL, size, MMAP_PROTECTION, MMAP_FLAGS, -1 /*file descriptor*/, 0 /*offset*/);
-    } else {
-      ptr = mmap( NULL, size, MMAP_PROTECTION, MMAP_FLAGS_HUGE, -1 /*file descriptor*/, 0 /*offset*/);
-    }
-    if (ptr == MAP_FAILED) {
-      ptr = NULL;
-    }
-#else
-    static const size_t page_size = 4096; // TODO: read in from sysconf( _SC_PAGE_SIZE )
-
-    ptr = raw_aligned_allocate( size, page_size);
-#endif
-    if (!ptr)
-    {
-      std::ostringstream msg ;
-      msg << name() << ": allocate(" << size << ") FAILED";
-      throw_runtime_exception( msg.str() );
-    }
-  }
-  return ptr;
-}
-
-void PageAlignedAllocator::deallocate( void * ptr, size_t size )
-{
-#if !defined( NO_MMAP )
-  munmap(ptr, size);
-#else
-  raw_aligned_deallocate(ptr, size);
-#endif
-}
-
-void * PageAlignedAllocator::reallocate(void * old_ptr, size_t old_size, size_t new_size)
-{
-  void * ptr = NULL;
-#if defined( NO_MMAP ) || defined( __APPLE__ ) || defined( __CYGWIN__ )
-
-  if (old_size != new_size) {
-    ptr = allocate( new_size );
-
-    memcpy(ptr, old_ptr, (old_size < new_size ? old_size : new_size) );
-
-    deallocate( old_ptr, old_size );
-  }
-  else {
-    ptr = old_ptr;
-  }
-#else
-  ptr = mremap( old_ptr, old_size, new_size, MREMAP_MAYMOVE );
-
-  if (ptr == MAP_FAILED) {
-    throw_runtime_exception("Error: Page Aligned Allocator could not reallocate memory");
-  }
-#endif
-
-  return ptr;
-}
-
-}} // namespace Kokkos::Impl
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
diff --git a/lib/kokkos/core/src/impl/Kokkos_BitOps.hpp b/lib/kokkos/core/src/impl/Kokkos_BitOps.hpp
new file mode 100644
index 0000000000..0ffbc0548a
--- /dev/null
+++ b/lib/kokkos/core/src/impl/Kokkos_BitOps.hpp
@@ -0,0 +1,122 @@
+/*
+//@HEADER
+// ************************************************************************
+//
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+//
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+//
+// ************************************************************************
+//@HEADER
+*/
+
+#ifndef KOKKOS_BITOPS_HPP
+#define KOKKOS_BITOPS_HPP
+
+#include <Kokkos_Macros.hpp>
+#include <stdint.h>
+#include <climits>
+
+namespace Kokkos {
+namespace Impl {
+
+KOKKOS_FORCEINLINE_FUNCTION
+int bit_scan_forward( unsigned i )
+{
+#if defined( __CUDA_ARCH__ )
+  return __ffs(i) - 1;
+#elif defined( __GNUC__ ) || defined( __GNUG__ )
+  return __builtin_ffs(i) - 1;
+#elif defined( __INTEL_COMPILER )
+  return _bit_scan_forward(i);
+#else
+
+  unsigned t = 1u;
+  int r = 0;
+  while ( i && ( i & t == 0 ) )
+  {
+    t = t << 1;
+    ++r;
+  }
+  return r;
+#endif
+}
+
+KOKKOS_FORCEINLINE_FUNCTION
+int bit_scan_reverse( unsigned i )
+{
+  enum { shift = static_cast<int>( sizeof(unsigned) * CHAR_BIT - 1 ) };
+#if defined( __CUDA_ARCH__ )
+  return shift - __clz(i);
+#elif defined( __GNUC__ ) || defined( __GNUG__ )
+  return shift - __builtin_clz(i);
+#elif defined( __INTEL_COMPILER )
+  return _bit_scan_reverse(i);
+#else
+  unsigned t = 1u << shift;
+  int r = 0;
+  while ( i && ( i & t == 0 ) )
+  {
+    t = t >> 1;
+    ++r;
+  }
+  return r;
+#endif
+}
+
+/// Count the number of bits set.
+KOKKOS_FORCEINLINE_FUNCTION
+int bit_count( unsigned i )
+{
+#if defined( __CUDA_ARCH__ )
+  return __popc(i);
+#elif defined( __GNUC__ ) || defined( __GNUG__ )
+  return __builtin_popcount(i);
+#elif defined ( __INTEL_COMPILER )
+  return _popcnt32(i);
+#else
+  // http://graphics.stanford.edu/~seander/bithacks.html#CountBitsSetNaive
+  i = i - ( ( i >> 1 ) & ~0u / 3u );                             // temp
+  i = ( i & ~0u / 15u * 3u ) + ( ( i >> 2 ) & ~0u / 15u * 3u );  // temp
+  i = ( i + ( i >> 4 ) ) & ~0u / 255u * 15u;                     // temp
+
+  // count
+  return (int)( ( i * ( ~0u / 255u ) ) >> ( sizeof(unsigned) - 1 ) * CHAR_BIT );
+#endif
+}
+
+} // namespace Impl
+} // namespace Kokkos
+
+#endif // KOKKOS_BITOPS_HPP
diff --git a/lib/kokkos/core/src/impl/Kokkos_Core.cpp b/lib/kokkos/core/src/impl/Kokkos_Core.cpp
index 94db15d96f..567a214140 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Core.cpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Core.cpp
@@ -148,7 +148,7 @@ setenv("MEMKIND_HBW_NODES", "1", 0);
 #endif
 
 #if (KOKKOS_ENABLE_PROFILING)
-    Kokkos::Experimental::initialize();
+    Kokkos::Profiling::initialize();
 #endif
 }
 
@@ -190,7 +190,7 @@ void finalize_internal( const bool all_spaces = false )
 #endif
 
 #if (KOKKOS_ENABLE_PROFILING)
-    Kokkos::Experimental::finalize();
+    Kokkos::Profiling::finalize();
 #endif
 
 }
diff --git a/lib/kokkos/core/src/impl/Kokkos_FunctorAdapter.hpp b/lib/kokkos/core/src/impl/Kokkos_FunctorAdapter.hpp
index 43a1b2afbd..78b6794491 100644
--- a/lib/kokkos/core/src/impl/Kokkos_FunctorAdapter.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_FunctorAdapter.hpp
@@ -75,6 +75,7 @@ struct FunctorValueTraits
   typedef void value_type ;
   typedef void pointer_type ;
   typedef void reference_type ;
+  typedef void functor_type ;
 
   enum { StaticValueSize = 0 };
 
@@ -88,7 +89,10 @@ struct FunctorValueTraits
 template<class ArgTag>
 struct FunctorValueTraits<void, ArgTag,false>
 {
-  typedef void reference_type;
+  typedef void value_type ;
+  typedef void pointer_type ;
+  typedef void reference_type ;
+  typedef void functor_type ;
 };
 
 /** \brief  FunctorType::value_type is explicitly declared so use it.
@@ -106,6 +110,7 @@ template< class FunctorType , class ArgTag >
 struct FunctorValueTraits< FunctorType , ArgTag , true /* == exists FunctorType::value_type */ >
 {
   typedef typename Impl::remove_extent< typename FunctorType::value_type >::type  value_type ;
+  typedef FunctorType functor_type;
 
   static_assert( 0 == ( sizeof(value_type) % sizeof(int) ) ,
     "Reduction functor's declared value_type requires: 0 == sizeof(value_type) % sizeof(int)" );
@@ -342,6 +347,7 @@ public:
   typedef typename Impl::if_c< IS_VOID || IS_REJECT , void , ValueType   >::type  value_type ;
   typedef typename Impl::if_c< IS_VOID || IS_REJECT , void , ValueType * >::type  pointer_type ;
   typedef typename Impl::if_c< IS_VOID || IS_REJECT , void , ValueType & >::type  reference_type ;
+  typedef FunctorType functor_type;
 
   static_assert( IS_VOID || IS_REJECT || 0 == ( sizeof(ValueType) % sizeof(int) ) ,
     "Reduction functor's value_type deduced from functor::operator() requires: 0 == sizeof(value_type) % sizeof(int)" );
@@ -568,24 +574,56 @@ struct FunctorValueJoin ;
 template< class FunctorType , class ArgTag , class T , class Enable >
 struct FunctorValueJoin< FunctorType , ArgTag , T & , Enable >
 {
+  KOKKOS_FORCEINLINE_FUNCTION
+  FunctorValueJoin(const FunctorType& ){}
+
   KOKKOS_FORCEINLINE_FUNCTION static
   void join( const FunctorType & f , volatile void * const lhs , const volatile void * const rhs )
     {
       *((volatile T*)lhs) += *((const volatile T*)rhs);
     }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator()( volatile T& lhs , const volatile T& rhs ) const
+    {
+      lhs += rhs;
+    }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator() ( T& lhs , const T& rhs ) const
+    {
+      lhs += rhs;
+    }
 };
 
 /* No 'join' function provided, array of values */
 template< class FunctorType , class ArgTag , class T , class Enable >
 struct FunctorValueJoin< FunctorType , ArgTag , T * , Enable >
 {
+  const FunctorType& f;
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  FunctorValueJoin(const FunctorType& f_):f(f_){}
+
   KOKKOS_FORCEINLINE_FUNCTION static
-  void join( const FunctorType & f , volatile void * const lhs , const volatile void * const rhs )
+  void join( const FunctorType & f_ , volatile void * const lhs , const volatile void * const rhs )
     {
-      const int n = FunctorValueTraits<FunctorType,ArgTag>::value_count(f);
+      const int n = FunctorValueTraits<FunctorType,ArgTag>::value_count(f_);
 
       for ( int i = 0 ; i < n ; ++i ) { ((volatile T*)lhs)[i] += ((const volatile T*)rhs)[i]; }
     }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator()( volatile T* const lhs , const volatile T* const rhs ) const
+    {
+      const int n = FunctorValueTraits<FunctorType,ArgTag>::value_count(f);
+
+      for ( int i = 0 ; i < n ; ++i ) { lhs[i] += rhs[i]; }
+    }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator() ( T* lhs , const T* rhs ) const
+    {
+      const int n = FunctorValueTraits<FunctorType,ArgTag>::value_count(f);
+
+      for ( int i = 0 ; i < n ; ++i ) { lhs[i] += rhs[i]; }
+    }
 };
 
 /* 'join' function provided, single value */
@@ -599,10 +637,25 @@ struct FunctorValueJoin
   , decltype( FunctorValueJoinFunction< FunctorType , ArgTag >::enable_if( & FunctorType::join ) )
   >
 {
+  const FunctorType& f;
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  FunctorValueJoin(const FunctorType& f_):f(f_){}
+
   KOKKOS_FORCEINLINE_FUNCTION static
-  void join( const FunctorType & f , volatile void * const lhs , const volatile void * const rhs )
+  void join( const FunctorType & f_ , volatile void * const lhs , const volatile void * const rhs )
+    {
+      f_.join( ArgTag() , *((volatile T *)lhs) , *((const volatile T *)rhs) );
+    }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator()( volatile T& lhs , const volatile T& rhs ) const
+    {
+      f.join( ArgTag() , lhs , rhs );
+    }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator() ( T& lhs , const T& rhs ) const
     {
-      f.join( ArgTag() , *((volatile T *)lhs) , *((const volatile T *)rhs) );
+      f.join( ArgTag(), lhs , rhs );
     }
 };
 
@@ -617,10 +670,25 @@ struct FunctorValueJoin
   , decltype( FunctorValueJoinFunction< FunctorType , void >::enable_if( & FunctorType::join ) )
   >
 {
+  const FunctorType& f;
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  FunctorValueJoin(const FunctorType& f_):f(f_){}
+
   KOKKOS_FORCEINLINE_FUNCTION static
-  void join( const FunctorType & f , volatile void * const lhs , const volatile void * const rhs )
+  void join( const FunctorType & f_ , volatile void * const lhs , const volatile void * const rhs )
     {
-      f.join( *((volatile T *)lhs) , *((const volatile T *)rhs) );
+      f_.join( *((volatile T *)lhs) , *((const volatile T *)rhs) );
+    }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator()( volatile T& lhs , const volatile T& rhs ) const
+    {
+      f.join( lhs , rhs );
+    }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator() ( T& lhs , const T& rhs ) const
+    {
+      f.join( lhs , rhs );
     }
 };
 
@@ -635,10 +703,25 @@ struct FunctorValueJoin
   , decltype( FunctorValueJoinFunction< FunctorType , ArgTag >::enable_if( & FunctorType::join ) )
   >
 {
+  const FunctorType& f;
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  FunctorValueJoin(const FunctorType& f_):f(f_){}
+
   KOKKOS_FORCEINLINE_FUNCTION static
-  void join( const FunctorType & f , volatile void * const lhs , const volatile void * const rhs )
+  void join( const FunctorType & f_ , volatile void * const lhs , const volatile void * const rhs )
+    {
+      f_.join( ArgTag() , (volatile T *)lhs , (const volatile T *)rhs );
+    }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator()( volatile T* const lhs , const volatile T* const rhs ) const
     {
-      f.join( ArgTag() , (volatile T *)lhs , (const volatile T *)rhs );
+      f.join( ArgTag() , lhs , rhs );
+    }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator() ( T* lhs , const T* rhs ) const
+    {
+      f.join( ArgTag(), lhs , rhs );
     }
 };
 
@@ -653,10 +736,25 @@ struct FunctorValueJoin
   , decltype( FunctorValueJoinFunction< FunctorType , void >::enable_if( & FunctorType::join ) )
   >
 {
+  const FunctorType& f;
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  FunctorValueJoin(const FunctorType& f_):f(f_){}
+
   KOKKOS_FORCEINLINE_FUNCTION static
-  void join( const FunctorType & f , volatile void * const lhs , const volatile void * const rhs )
+  void join( const FunctorType & f_ , volatile void * const lhs , const volatile void * const rhs )
+    {
+      f_.join( (volatile T *)lhs , (const volatile T *)rhs );
+    }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator() ( volatile T* const lhs , const volatile T* const rhs ) const
+    {
+      f.join( lhs , rhs );
+    }
+  KOKKOS_FORCEINLINE_FUNCTION
+  void operator() ( T* lhs , const T* rhs ) const
     {
-      f.join( (volatile T *)lhs , (const volatile T *)rhs );
+      f.join( lhs , rhs );
     }
 };
 
diff --git a/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp b/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp
index 20956ce593..11cc120212 100644
--- a/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp
+++ b/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp
@@ -56,7 +56,6 @@
 #include <algorithm>
 
 #include <Kokkos_HBWSpace.hpp>
-#include <impl/Kokkos_BasicAllocators.hpp>
 #include <impl/Kokkos_Error.hpp>
 #include <Kokkos_Atomic.hpp>
 #ifdef KOKKOS_HAVE_HBWSPACE
@@ -126,23 +125,6 @@ int HBWSpace::in_parallel()
 
 /*--------------------------------------------------------------------------*/
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-namespace Kokkos {
-namespace Experimental {
-
-Kokkos::Impl::AllocationTracker HBWSpace::allocate_and_track( const std::string & label, const size_t size )
-{
-  return Kokkos::Impl::AllocationTracker( allocator(), size, label );
-}
-
-} // namespace Experimental
-} // namespace Kokkos
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-/*--------------------------------------------------------------------------*/
-
 namespace Kokkos {
 namespace Experimental {
 
diff --git a/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp b/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp
index 9dc774cdeb..b52f4591ef 100644
--- a/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp
+++ b/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp
@@ -93,7 +93,6 @@
 #include <cstring>
 
 #include <Kokkos_HostSpace.hpp>
-#include <impl/Kokkos_BasicAllocators.hpp>
 #include <impl/Kokkos_Error.hpp>
 #include <Kokkos_Atomic.hpp>
 
@@ -156,21 +155,6 @@ int HostSpace::in_parallel()
 
 /*--------------------------------------------------------------------------*/
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-namespace Kokkos {
-
-Impl::AllocationTracker HostSpace::allocate_and_track( const std::string & label, const size_t size )
-{
-  return Impl::AllocationTracker( allocator(), size, label );
-}
-
-} // namespace Kokkos
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-/*--------------------------------------------------------------------------*/
-
 namespace Kokkos {
 
 /* Default allocation mechanism */
diff --git a/lib/kokkos/core/src/impl/Kokkos_MemoryPool_Inline.hpp b/lib/kokkos/core/src/impl/Kokkos_MemoryPool_Inline.hpp
deleted file mode 100644
index bb858d8d9e..0000000000
--- a/lib/kokkos/core/src/impl/Kokkos_MemoryPool_Inline.hpp
+++ /dev/null
@@ -1,446 +0,0 @@
-/*
-//@HEADER
-// ************************************************************************
-//
-//                        Kokkos v. 2.0
-//              Copyright (2014) Sandia Corporation
-//
-// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
-// the U.S. Government retains certain rights in this software.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are
-// met:
-//
-// 1. Redistributions of source code must retain the above copyright
-// notice, this list of conditions and the following disclaimer.
-//
-// 2. Redistributions in binary form must reproduce the above copyright
-// notice, this list of conditions and the following disclaimer in the
-// documentation and/or other materials provided with the distribution.
-//
-// 3. Neither the name of the Corporation nor the names of the
-// contributors may be used to endorse or promote products derived from
-// this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
-// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-//
-// ************************************************************************
-//@HEADER
-*/
-
-#ifndef KOKKOS_MEMORYPOOL_CPP
-#define KOKKOS_MEMORYPOOL_CPP
-
-// How should errors be handled?  In general, production code should return a
-// value indicating failure so the user can decide how the error is handled.
-// While experimental, code can abort instead.  If KOKKOS_MEMPOOLLIST_PRINTERR
-// is defined, the code will abort with an error message.  Otherwise, the code
-// will return with a value indicating failure when possible, or do nothing
-// instead.
-//#define KOKKOS_MEMPOOLLIST_PRINTERR
-
-//#define KOKKOS_MEMPOOLLIST_PRINT_INFO
-
-//----------------------------------------------------------------------------
-
-#if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_CUDA )
-
-/* This '.cpp' is being included by the header file
- * to inline these functions for Cuda.
- *
- *  Prefer to implement these functions in a separate
- *  compilation unit.  However, the 'nvcc' linker
- *  has an internal error when attempting separate compilation
- *  (--relocatable-device-code=true)
- *  of Kokkos unit tests.
- */
-
-#define KOKKOS_MEMPOOLLIST_INLINE inline
-
-#else
-
-/*  This '.cpp' file is being separately compiled for the Host */
-
-#include <Kokkos_MemoryPool.hpp>
-#include <Kokkos_Atomic.hpp>
-
-#define KOKKOS_MEMPOOLLIST_INLINE /* */
-
-#endif
-
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Experimental {
-namespace Impl {
-
-#if defined(KOKKOS_MEMPOOLLIST_PRINT_INFO) && defined(KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST)
-long MemPoolList::m_count = 0;
-#endif
-
-KOKKOS_FUNCTION
-KOKKOS_MEMPOOLLIST_INLINE
-uint64_t
-MemPoolList::acquire_lock( volatile uint64_t * freelist ) const
-{
-  uint64_t old_head;
-  bool locked = false;
-
-  while ( !locked ) {
-    old_head = *freelist;
-
-    if ( old_head != FREELIST_LOCK_HEAD ) {
-      // In the initial look at the head, the freelist wasn't locked.
-      // Attempt to lock the head of list.  If the list was changed (including
-      // being locked) between the initial look and now, head will be different
-      // than old_head.  This means the lock can't proceed and has to be
-      // tried again.
-      uint64_t head =
-        atomic_compare_exchange( freelist, old_head, uint64_t(FREELIST_LOCK_HEAD) );
-
-      if ( head == old_head ) locked = true;
-    }
-  }
-
-  return old_head;
-}
-
-KOKKOS_FUNCTION
-KOKKOS_MEMPOOLLIST_INLINE
-void
-MemPoolList::release_lock( volatile uint64_t * freelist, uint64_t new_head ) const
-{
-  // This function is only intended to be called if acquire_lock() has already
-  // been called to acquire a lock on freelist.  Thus, we know that the value
-  // pointed to by freelist is FREELIST_LOCK_HEAD.
-#ifdef KOKKOS_MEMPOOLLIST_PRINTERR
-  uint64_t head =
-#endif
-    atomic_compare_exchange( freelist, uint64_t(FREELIST_LOCK_HEAD), new_head );
-
-#ifdef KOKKOS_MEMPOOLLIST_PRINTERR
-  if ( head != FREELIST_LOCK_HEAD ) {
-    // We shouldn't get here, but this check is here for sanity.
-    printf( "\n** MemoryPool::allocate() UNLOCK_ERROR(0x%llx) **\n",
-            reinterpret_cast<uint64_t>( freelist ) );
-#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-    fflush( stdout );
-#endif
-    Kokkos::abort( "" );
-  }
-#endif
-}
-
-KOKKOS_FUNCTION
-KOKKOS_MEMPOOLLIST_INLINE
-void *
-MemPoolList::refill_freelist( size_t l_exp ) const
-{
-  void * p = 0;
-  volatile uint64_t * l_exp_freelist = m_freelist + l_exp;
-
-  // The l_exp freelist is empty. Grab a lock on the freelist.
-  uint64_t l_exp_old_head = acquire_lock( l_exp_freelist );
-
-  uint64_t l_exp_old_head_off = get_head_offset( l_exp_old_head );
-
-  if ( l_exp_old_head_off != FREELIST_END ) {
-    // Another thread put some more entries on the freelist between when
-    // this thread saw it empty and acquired the lock.  Just return an entry.
-    uint64_t l_exp_old_head_tag = get_head_tag( l_exp_old_head );
-    uint64_t new_head_tag = increment_tag( l_exp_old_head_tag );
-    uint64_t new_head_off = *reinterpret_cast<uint64_t *>( m_data + l_exp_old_head_off );
-    uint64_t new_head = create_head( new_head_off, new_head_tag );
-
-    // Release the lock, replacing the head with the next entry on the list.
-    release_lock( l_exp_freelist, new_head );
-
-    // Set the chunk to return.
-    p = m_data + l_exp_old_head_off;
-  }
-  else {
-    // The l_exp freelist is empty.
-
-    size_t l = l_exp + 1;
-    bool done = false;
-
-    while ( !done ) {
-      // Find the next freelist that is either locked or not empty.  A locked
-      // freelist will probably have memory available when the lock is
-      // released.
-      while ( m_chunk_size[l] > 0 &&
-              get_head_offset( m_freelist[l] ) == FREELIST_END ) ++l;
-
-      if ( m_chunk_size[l] == 0 ) {
-        // We got to the end of the list of freelists without finding any
-        // available memory which means the pool is empty.  Release the lock
-        // on the l_exp freelist.
-        release_lock( l_exp_freelist, l_exp_old_head );
-
-        // Exit out of the loop.
-        done = true;
-      }
-      else {
-        volatile uint64_t * l_freelist = m_freelist + l;
-
-        // Grab a lock on the l freelist.
-        uint64_t l_old_head = acquire_lock( l_freelist );
-        uint64_t l_old_head_off = get_head_offset( l_old_head );
-
-        if ( l_old_head_off != FREELIST_END ) {
-          // The l freelist has chunks.  Grab one to divide.
-
-          // Create a new head for the l_freelist by using the second entry
-          // in the list and incrementing the current tag.
-          uint64_t l_old_head_tag = get_head_tag( l_old_head );
-          uint64_t new_head_tag = increment_tag( l_old_head_tag );
-          uint64_t new_head_off =
-            *reinterpret_cast<volatile uint64_t *>( m_data + l_old_head_off );
-          uint64_t new_head = create_head( new_head_off, new_head_tag );
-
-          // Release the lock on the l freelist.
-          release_lock( l_freelist, new_head );
-
-          // Subdivide the chunk into smaller chunks.  The first chunk will
-          // be returned to satisfy the allocaiton request.  The remainder
-          // of the chunks will be inserted onto the appropriate freelist.
-          size_t num_chunks = m_chunk_size[l] / m_chunk_size[l_exp];
-
-          // Link the chunks following the first chunk to form a list.
-          uint64_t lp_head = l_old_head_off + m_chunk_size[l_exp];
-          uint64_t lp_tail = l_old_head_off + (num_chunks - 1) * m_chunk_size[l_exp];
-
-          for ( uint64_t offset = lp_head; offset < lp_tail;
-                offset += m_chunk_size[l_exp] )
-          {
-            *reinterpret_cast<uint64_t *>( m_data + offset ) =
-              offset + m_chunk_size[l_exp];
-          }
-
-          // Set the tail entry to be the end of the list.
-          *reinterpret_cast<volatile uint64_t *>( m_data + lp_tail ) = FREELIST_END;
-
-          memory_fence();
-
-          // Create a new head for the l_exp_freelist.
-          new_head = create_head( lp_head, get_head_tag( l_exp_old_head ) );
-
-          // This thread already has the lock on the l_exp freelist, so just
-          // release the lock placing the divided memory on the list.
-          release_lock( l_exp_freelist, new_head );
-
-          // Set the chunk to return.
-          p = m_data + l_old_head_off;
-          done = true;
-        }
-        else {
-          // Release the lock on the l freelist.  Put the old head back on.
-          release_lock( l_freelist, l_old_head );
-        }
-      }
-    }
-  }
-
-  return p;
-}
-
-KOKKOS_FUNCTION
-KOKKOS_MEMPOOLLIST_INLINE
-void *
-MemPoolList::allocate( size_t alloc_size ) const
-{
-  void * p = 0;
-
-  // Find the first freelist whose chunk size is big enough for allocation.
-  size_t l_exp = 0;
-  while ( m_chunk_size[l_exp] > 0 && alloc_size > m_chunk_size[l_exp] ) ++l_exp;
-
-#ifdef KOKKOS_MEMPOOLLIST_PRINTERR
-  if ( m_chunk_size[l_exp] == 0 ) {
-    Kokkos::abort( "\n** MemoryPool::allocate() REQUESTED_SIZE_TOO_LARGE **\n" );
-  }
-#endif
-
-  // Do a fast fail test for an empty list.  This checks for l_exp and all
-  // higher freelists being empty.
-  size_t l = l_exp;
-  while ( m_chunk_size[l] > 0 &&
-          get_head_offset( m_freelist[l] ) == FREELIST_END ) ++l;
-
-  if ( m_chunk_size[l] != 0 ) {
-    // Try to grab a chunk from the l_exp list.
-    volatile uint64_t * l_exp_freelist = m_freelist + l_exp;
-
-    bool done = false;
-
-    while ( !done ) {
-      uint64_t old_head = *l_exp_freelist;
-      uint64_t old_head_off = get_head_offset( old_head );
-
-      if ( old_head_off == FREELIST_END ) {
-        // The list is empty.  Try to refill it and grab a chunk.
-        p = refill_freelist(l_exp);
-
-        done = true;
-      }
-      else if ( old_head_off != FREELIST_LOCK ) {
-        // The freelist wasn't empty or locked, so try to pop off the head.
-        uint64_t old_head_tag = get_head_tag( old_head );
-
-        // Increment the tag by 1, wrapping around to 0 after 2^32-1.
-        uint64_t new_head_tag = increment_tag( old_head_tag );
-        uint64_t new_head_off = *reinterpret_cast<uint64_t *>( m_data + old_head_off );
-        uint64_t new_head = create_head( new_head_off, new_head_tag );
-
-        // Attempt to pull off the head of the list and put the next entry in
-        // its place.  If the list was changed
-        // (including being locked) between the initial look and now, head will
-        // be different than old_head.  This means the insert can't proceed and
-        // has to be tried again.
-        uint64_t head = atomic_compare_exchange( l_exp_freelist, old_head, new_head );
-
-        if ( head == old_head ) {
-          done = true;
-          p = m_data + old_head_off;
-        }
-      }
-    }
-  }
-
-#ifdef KOKKOS_MEMPOOLLIST_PRINT_INFO
-#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-  long val = p == 0 ?
-             *reinterpret_cast<volatile long *>( &m_count ) :
-             Kokkos::atomic_fetch_add( &m_count, 1 );
-
-  printf( "  allocate(): %6ld   size: %6lu    l: %2lu  %2lu   0x%llx\n", val,
-          alloc_size, l_exp, l, reinterpret_cast<uint64_t>( p ) );
-  fflush( stdout );
-#else
-  printf( "  allocate()   size: %6lu    l: %2lu  %2lu   0x%lx\n", alloc_size,
-          l_exp, l, reinterpret_cast<uint64_t>( p ) );
-#endif
-#endif
-
-#ifdef KOKKOS_MEMPOOLLIST_PRINTERR
-  if ( p == 0 ) {
-    printf( "** MemoryPool::allocate() NO_CHUNKS_BIG_ENOUGH **\n" );
-#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-    fflush( stdout );
-#endif
-  }
-#endif
-
-  return p;
-}
-
-KOKKOS_FUNCTION
-KOKKOS_MEMPOOLLIST_INLINE
-void
-MemPoolList::deallocate( void * alloc_ptr, size_t alloc_size ) const
-{
-#ifdef KOKKOS_MEMPOOLLIST_PRINTERR
-  // Verify that the pointer is controlled by this pool.
-  {
-    char * ap = static_cast<char *>( alloc_ptr );
-
-    if ( ap < m_data || ap + alloc_size > m_data + m_data_size ) {
-      printf( "\n** MemoryPool::deallocate() ADDRESS_OUT_OF_RANGE(0x%llx) **\n",
-              reinterpret_cast<uint64_t>( alloc_ptr ) );
-#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-      fflush( stdout );
-#endif
-      Kokkos::abort( "" );
-    }
-  }
-#endif
-
-  // Determine which freelist to place deallocated memory on.
-  size_t l = 0;
-  while ( m_chunk_size[l] > 0 && alloc_size > m_chunk_size[l] ) ++l;
-
-#ifdef KOKKOS_MEMPOOLLIST_PRINTERR
-  if ( m_chunk_size[l] == 0 ) {
-    printf( "\n** MemoryPool::deallocate() CHUNK_TOO_LARGE(%lu) **\n", alloc_size );
-#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-    fflush( stdout );
-#endif
-    Kokkos::abort( "" );
-  }
-#endif
-
-  uint64_t offset = static_cast<char *>( alloc_ptr ) - m_data;
-
-  // Insert a single chunk at the head of the freelist.
-  volatile uint64_t * freelist = m_freelist + l;
-
-  bool inserted = false;
-
-  while ( !inserted ) {
-    uint64_t old_head = *freelist;
-
-    if ( old_head != FREELIST_LOCK_HEAD ) {
-      // In the initial look at the head, the freelist wasn't locked.
-
-      uint64_t old_head_off = get_head_offset(old_head);
-      uint64_t old_head_tag = get_head_tag(old_head);
-      uint64_t new_head = create_head( offset, old_head_tag );
-
-      // Proactively point the new head to the old head assuming a successful
-      // insertion into the list.
-      *reinterpret_cast<volatile uint64_t *>( alloc_ptr ) = old_head_off;
-
-      memory_fence();
-
-      // Attempt to insert at head of list.  If the list was changed
-      // (including being locked) between the initial look and now, head will
-      // be different than old_head.  This means the insert can't proceed and
-      // has to be tried again.
-      uint64_t head = atomic_compare_exchange( freelist, old_head, new_head );
-
-      if ( head == old_head ) inserted = true;
-    }
-  }
-
-#ifdef KOKKOS_MEMPOOLLIST_PRINT_INFO
-#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-  long val = Kokkos::atomic_fetch_add( &m_count, -1 ) - 1;
-  printf( "deallocate(): %6ld   size: %6lu    l: %2lu       0x%llx\n", val,
-          alloc_size, l, reinterpret_cast<uint64_t>( alloc_ptr ) );
-  fflush( stdout );
-#else
-  printf( "deallocate()   size: %6lu    l: %2lu       0x%lx\n", alloc_size, l,
-          reinterpret_cast<uint64_t>( alloc_ptr ) );
-#endif
-#endif
-}
-
-
-} // namespace Impl
-} // namespace Experimental
-} // namespace Kokkos
-
-#undef KOKKOS_MEMPOOLLIST_INLINE
-
-#ifdef KOKKOS_MEMPOOLLIST_PRINTERR
-#undef KOKKOS_MEMPOOLLIST_PRINTERR
-#endif
-
-#ifdef KOKKOS_MEMPOOLLIST_PRINT_INFO
-#undef KOKKOS_MEMPOOLLIST_PRINT_INFO
-#endif
-
-#endif /* #ifndef KOKKOS_MEMORYPOOL_CPP */
diff --git a/lib/kokkos/core/src/impl/Kokkos_PhysicalLayout.hpp b/lib/kokkos/core/src/impl/Kokkos_PhysicalLayout.hpp
index 0e87c63e44..556c96d863 100644
--- a/lib/kokkos/core/src/impl/Kokkos_PhysicalLayout.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_PhysicalLayout.hpp
@@ -58,7 +58,7 @@ struct PhysicalLayout {
   long long int stride[8]; //distance between two neighboring elements in a given dimension
 
   template< class T , class L , class D , class M >
-  PhysicalLayout( const View<T,L,D,M,ViewDefault> & view )
+  PhysicalLayout( const View<T,L,D,M> & view )
     : layout_type( is_same< typename View<T,L,D,M>::array_layout , LayoutLeft  >::value ? Left : (
                    is_same< typename View<T,L,D,M>::array_layout , LayoutRight >::value ? Right : Error ))
     , rank( view.Rank )
@@ -66,17 +66,6 @@ struct PhysicalLayout {
       for(int i=0;i<8;i++) stride[i] = 0;
       view.stride( stride );
     }
-  #ifdef KOKKOS_HAVE_CUDA
-  template< class T , class L , class D , class M >
-  PhysicalLayout( const View<T,L,D,M,ViewCudaTexture> & view )
-    : layout_type( is_same< typename View<T,L,D,M>::array_layout , LayoutLeft  >::value ? Left : (
-                   is_same< typename View<T,L,D,M>::array_layout , LayoutRight >::value ? Right : Error ))
-    , rank( view.Rank )
-    {
-      for(int i=0;i<8;i++) stride[i] = 0;
-      view.stride( stride );
-    }
-  #endif
 };
 
 }
diff --git a/lib/kokkos/core/src/impl/Kokkos_Profiling_DeviceInfo.hpp b/lib/kokkos/core/src/impl/Kokkos_Profiling_DeviceInfo.hpp
index 5da60841d4..8ea1e816cd 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Profiling_DeviceInfo.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Profiling_DeviceInfo.hpp
@@ -45,7 +45,7 @@
 #define KOKKOSP_DEVICE_INFO_HPP
 
 namespace Kokkos {
-namespace Experimental {
+namespace Profiling {
 
     struct KokkosPDeviceInfo {
         uint32_t deviceID;
diff --git a/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.cpp b/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.cpp
index f499cc63a7..91faed170a 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.cpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.cpp
@@ -47,7 +47,7 @@
 #include <string.h>
 
 namespace Kokkos {
-  namespace Experimental {
+  namespace Profiling {
     bool profileLibraryLoaded() {
        	return (NULL != initProfileLibrary);
     }
@@ -95,6 +95,12 @@ namespace Kokkos {
     }
     
     void initialize() {
+
+        // Make sure initialize calls happens only once
+        static int is_initialized = 0;
+        if(is_initialized) return;
+        is_initialized = 1;
+
         void* firstProfileLibrary;
 
         char* envProfileLibrary  = getenv("KOKKOS_PROFILE_LIBRARY");
@@ -153,6 +159,11 @@ namespace Kokkos {
     }
 
     void finalize() {
+      // Make sure finalize calls happens only once
+      static int is_finalized = 0;
+      if(is_finalized) return;
+      is_finalized = 1;
+
       if(NULL != finalizeProfileLibrary) {
         (*finalizeProfileLibrary)();
 
diff --git a/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp b/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp
index 919c4f619e..4f01256335 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp
@@ -60,7 +60,7 @@
 
 #if (KOKKOS_ENABLE_PROFILING)
 namespace Kokkos {
-  namespace Experimental {
+  namespace Profiling {
 
     typedef void (*initFunction)(const int,
 	const uint64_t,
diff --git a/lib/kokkos/core/src/impl/Kokkos_Serial_Task.cpp b/lib/kokkos/core/src/impl/Kokkos_Serial_Task.cpp
new file mode 100644
index 0000000000..e8bdbde6c6
--- /dev/null
+++ b/lib/kokkos/core/src/impl/Kokkos_Serial_Task.cpp
@@ -0,0 +1,147 @@
+/*
+//@HEADER
+// ************************************************************************
+// 
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+// 
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+// 
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+// 
+// ************************************************************************
+//@HEADER
+*/
+
+#include <Kokkos_Core.hpp>
+
+#if defined( KOKKOS_HAVE_SERIAL ) && defined( KOKKOS_ENABLE_TASKPOLICY )
+
+#include <impl/Kokkos_TaskQueue_impl.hpp>
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+namespace Impl {
+
+template class TaskQueue< Kokkos::Serial > ;
+
+void TaskQueueSpecialization< Kokkos::Serial >::execute
+  ( TaskQueue< Kokkos::Serial > * const queue )
+{
+  using execution_space = Kokkos::Serial ;
+  using queue_type      = TaskQueue< execution_space > ;
+  using task_root_type  = TaskBase< execution_space , void , void > ;
+  using Member          = TaskExec< execution_space > ;
+
+  task_root_type * const end = (task_root_type *) task_root_type::EndTag ;
+
+  Member exec ;
+
+  // Loop until all queues are empty
+  while ( 0 < queue->m_ready_count ) {
+
+    task_root_type * task = end ;
+
+    for ( int i = 0 ; i < queue_type::NumQueue && end == task ; ++i ) {
+      for ( int j = 0 ; j < 2 && end == task ; ++j ) {
+        task = queue_type::pop_task( & queue->m_ready[i][j] );
+      }
+    }
+
+    if ( end != task ) {
+
+      // pop_task resulted in lock == task->m_next
+      // In the executing state
+
+      (*task->m_apply)( task , & exec );
+
+#if 0
+  printf( "TaskQueue<Serial>::executed: 0x%lx { 0x%lx 0x%lx %d %d %d }\n"
+        , uintptr_t(task)
+        , uintptr_t(task->m_wait)
+        , uintptr_t(task->m_next)
+        , task->m_task_type
+        , task->m_priority
+        , task->m_ref_count );
+#endif
+
+      // If a respawn then re-enqueue otherwise the task is complete
+      // and all tasks waiting on this task are updated.
+      queue->complete( task );
+    }
+    else if ( 0 != queue->m_ready_count ) {
+      Kokkos::abort("TaskQueue<Serial>::execute ERROR: ready_count");
+    }
+  }
+}
+
+void TaskQueueSpecialization< Kokkos::Serial > ::
+  iff_single_thread_recursive_execute(
+    TaskQueue< Kokkos::Serial > * const queue )
+{
+  using execution_space = Kokkos::Serial ;
+  using queue_type      = TaskQueue< execution_space > ;
+  using task_root_type  = TaskBase< execution_space , void , void > ;
+  using Member          = TaskExec< execution_space > ;
+
+  task_root_type * const end = (task_root_type *) task_root_type::EndTag ;
+
+  Member exec ;
+
+  // Loop until no runnable task
+
+  task_root_type * task = end ;
+  
+  do {
+
+    task = end ;
+
+    for ( int i = 0 ; i < queue_type::NumQueue && end == task ; ++i ) {
+      for ( int j = 0 ; j < 2 && end == task ; ++j ) {
+        task = queue_type::pop_task( & queue->m_ready[i][j] );
+      }
+    }
+
+    if ( end == task ) break ;
+
+    (*task->m_apply)( task , & exec );
+
+    queue->complete( task );
+
+  } while(1);
+}
+
+}} /* namespace Kokkos::Impl */
+
+#endif /* #if defined( KOKKOS_HAVE_SERIAL ) && defined( KOKKOS_ENABLE_TASKPOLICY ) */
+
diff --git a/lib/kokkos/core/src/impl/Kokkos_Serial_Task.hpp b/lib/kokkos/core/src/impl/Kokkos_Serial_Task.hpp
new file mode 100644
index 0000000000..48a110c5f1
--- /dev/null
+++ b/lib/kokkos/core/src/impl/Kokkos_Serial_Task.hpp
@@ -0,0 +1,271 @@
+/*
+//@HEADER
+// ************************************************************************
+// 
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+// 
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+// 
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+// 
+// ************************************************************************
+//@HEADER
+*/
+
+#ifndef KOKKOS_IMPL_SERIAL_TASK_HPP
+#define KOKKOS_IMPL_SERIAL_TASK_HPP
+
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+namespace Impl {
+
+//----------------------------------------------------------------------------
+
+template<>
+class TaskQueueSpecialization< Kokkos::Serial >
+{
+public:
+
+  using execution_space = Kokkos::Serial ;
+  using memory_space    = Kokkos::HostSpace ;
+  using queue_type      = Kokkos::Impl::TaskQueue< execution_space > ;
+  using task_base_type  = Kokkos::Impl::TaskBase< execution_space , void , void > ;
+
+  static
+  void iff_single_thread_recursive_execute( queue_type * const );
+
+  static
+  void execute( queue_type * const );
+
+  template< typename FunctorType >
+  static
+  void proc_set_apply( task_base_type::function_type * ptr )
+    {
+      using TaskType = TaskBase< Kokkos::Serial
+                               , typename FunctorType::value_type
+                               , FunctorType
+                               > ;
+       *ptr = TaskType::apply ;
+    }
+};
+
+extern template class TaskQueue< Kokkos::Serial > ;
+
+//----------------------------------------------------------------------------
+
+template<>
+class TaskExec< Kokkos::Serial >
+{
+public:
+
+  KOKKOS_INLINE_FUNCTION void team_barrier() const {}
+  KOKKOS_INLINE_FUNCTION int team_rank() const { return 0 ; }
+  KOKKOS_INLINE_FUNCTION int team_size() const { return 1 ; }
+};
+
+template<typename iType>
+struct TeamThreadRangeBoundariesStruct<iType, TaskExec< Kokkos::Serial > >
+{
+  typedef iType index_type;
+  const iType start ;
+  const iType end ;
+  enum {increment = 1};
+  //const  TaskExec< Kokkos::Serial > & thread;
+  TaskExec< Kokkos::Serial > & thread;
+
+  KOKKOS_INLINE_FUNCTION
+  TeamThreadRangeBoundariesStruct
+    //( const TaskExec< Kokkos::Serial > & arg_thread, const iType& arg_count)
+    ( TaskExec< Kokkos::Serial > & arg_thread, const iType& arg_count)
+    : start(0)
+    , end(arg_count)
+    , thread(arg_thread)
+    {}
+
+  KOKKOS_INLINE_FUNCTION
+  TeamThreadRangeBoundariesStruct
+    //( const TaskExec< Kokkos::Serial > & arg_thread
+    ( TaskExec< Kokkos::Serial > & arg_thread
+    , const iType& arg_start
+    , const iType & arg_end
+    )
+    : start( arg_start )
+    , end(   arg_end)
+    , thread( arg_thread )
+    {}
+};
+
+}} /* namespace Kokkos::Impl */
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+/*
+template<typename iType>
+KOKKOS_INLINE_FUNCTION
+Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Serial > >
+TeamThreadRange( const Impl::TaskExec< Kokkos::Serial > & thread
+               , const iType & count )
+{
+  return Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Serial > >(thread,count);
+}
+*/
+//TODO const issue omp
+template<typename iType>
+KOKKOS_INLINE_FUNCTION
+Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Serial > >
+TeamThreadRange( Impl::TaskExec< Kokkos::Serial > & thread
+               , const iType & count )
+{
+  return Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Serial > >(thread,count);
+}
+/*
+template<typename iType>
+KOKKOS_INLINE_FUNCTION
+Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::Serial > >
+TeamThreadRange( const Impl:: TaskExec< Kokkos::Serial > & thread, const iType & start , const iType & end )
+{
+  return Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::Serial > >(thread,start,end);
+}
+*/
+//TODO const issue omp
+template<typename iType>
+KOKKOS_INLINE_FUNCTION
+Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::Serial > >
+TeamThreadRange( Impl:: TaskExec< Kokkos::Serial > & thread, const iType & start , const iType & end )
+{
+  return Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::Serial > >(thread,start,end);
+}
+
+  /** \brief  Inter-thread parallel_for. Executes lambda(iType i) for each i=0..N-1.
+   *
+   * The range i=0..N-1 is mapped to all threads of the the calling thread team.
+   * This functionality requires C++11 support.*/
+template<typename iType, class Lambda>
+KOKKOS_INLINE_FUNCTION
+void parallel_for(const Impl::TeamThreadRangeBoundariesStruct<iType,Impl:: TaskExec< Kokkos::Serial > >& loop_boundaries, const Lambda& lambda) {
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment)
+    lambda(i);
+}
+
+template< typename iType, class Lambda, typename ValueType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Serial > >& loop_boundaries,
+   const Lambda & lambda,
+   ValueType& initialized_result)
+{
+
+  ValueType result = initialized_result;
+
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment)
+    lambda(i, result);
+
+  initialized_result = result;
+}
+
+template< typename iType, class Lambda, typename ValueType, class JoinType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Serial > >& loop_boundaries,
+   const Lambda & lambda,
+   const JoinType & join,
+   ValueType& initialized_result)
+{
+  ValueType result = initialized_result;
+
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment)
+    lambda(i, result);
+
+  initialized_result = result;
+}
+// placeholder for future function
+template< typename iType, class Lambda, typename ValueType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Serial > >& loop_boundaries,
+   const Lambda & lambda,
+   ValueType& initialized_result)
+{
+}
+// placeholder for future function
+template< typename iType, class Lambda, typename ValueType, class JoinType >
+KOKKOS_INLINE_FUNCTION
+void parallel_reduce
+  (const Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Serial > >& loop_boundaries,
+   const Lambda & lambda,
+   const JoinType & join,
+   ValueType& initialized_result)
+{
+}
+
+template< typename ValueType, typename iType, class Lambda >
+KOKKOS_INLINE_FUNCTION
+void parallel_scan
+  (const Impl::TeamThreadRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Serial > >& loop_boundaries,
+   const Lambda & lambda)
+{
+  ValueType accum = 0 ;
+  ValueType val, local_total;
+
+  for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) {
+    local_total = 0;
+    lambda(i,local_total,false);
+    val = accum;
+    lambda(i,val,true);
+    accum += local_total;
+  }
+
+}
+
+// placeholder for future function
+template< typename iType, class Lambda, typename ValueType >
+KOKKOS_INLINE_FUNCTION
+void parallel_scan
+  (const Impl::ThreadVectorRangeBoundariesStruct<iType,Impl::TaskExec< Kokkos::Serial > >& loop_boundaries,
+   const Lambda & lambda)
+{
+}
+
+} /* namespace Kokkos */
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
+#endif /* #ifndef KOKKOS_IMPL_SERIAL_TASK_HPP */
+
diff --git a/lib/kokkos/core/src/impl/Kokkos_Serial_TaskPolicy.cpp b/lib/kokkos/core/src/impl/Kokkos_Serial_TaskPolicy.cpp
index 5f3e65b327..1577df07cd 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Serial_TaskPolicy.cpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Serial_TaskPolicy.cpp
@@ -45,7 +45,8 @@
 
 #include <impl/Kokkos_Serial_TaskPolicy.hpp>
 
-#if defined( KOKKOS_HAVE_SERIAL )
+#if defined( KOKKOS_HAVE_SERIAL ) && defined( KOKKOS_ENABLE_TASKPOLICY )
+
 #include <stdlib.h>
 #include <stdexcept>
 #include <iostream>
@@ -252,6 +253,12 @@ void Task::schedule()
 
   if ( ok_state && ok_list ) {
 
+    if ( TASK_STATE_CONSTRUCTING == m_state ) {
+      // Initial scheduling increment,
+      // matched by decrement when task is complete.
+      ++m_ref_count ;
+    }
+
     // Will be waiting for execution upon return from this function
 
     m_state = Kokkos::Experimental::TASK_STATE_WAITING ;
@@ -286,7 +293,8 @@ void Task::execute_ready_tasks()
     // Task * task ;
     // while ( ! CAS( & s_ready , task = s_ready , s_ready->m_next ) );
 
-    Task * const task = s_ready ;
+    Task * task = s_ready ;
+
     s_ready = task->m_next ;
 
     task->m_next = 0 ;
@@ -325,6 +333,9 @@ void Task::execute_ready_tasks()
 
         x = next ;
       }
+
+      // Decrement to match the initial scheduling increment
+      assign( & task , 0 );
     }
   }
 }
@@ -333,4 +344,5 @@ void Task::execute_ready_tasks()
 } // namespace Experimental
 } // namespace Kokkos
 
-#endif // defined( KOKKOS_HAVE_SERIAL )
+#endif /* #if defined( KOKKOS_HAVE_SERIAL ) && defined( KOKKOS_ENABLE_TASKPOLICY ) */
+
diff --git a/lib/kokkos/core/src/impl/Kokkos_Serial_TaskPolicy.hpp b/lib/kokkos/core/src/impl/Kokkos_Serial_TaskPolicy.hpp
index 3171449c16..a333f948ae 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Serial_TaskPolicy.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Serial_TaskPolicy.hpp
@@ -43,10 +43,11 @@
 
 // Experimental unified task-data parallel manycore LDRD
 
-#ifndef KOKKOS_SERIAL_TASKPOLICY_HPP
-#define KOKKOS_SERIAL_TASKPOLICY_HPP
+#ifndef KOKKOS_EXPERIMENTAL_SERIAL_TASKPOLICY_HPP
+#define KOKKOS_EXPERIMENTAL_SERIAL_TASKPOLICY_HPP
 
 #include <Kokkos_Macros.hpp>
+
 #if defined( KOKKOS_HAVE_SERIAL )
 
 #include <string>
@@ -57,6 +58,8 @@
 #include <Kokkos_TaskPolicy.hpp>
 #include <Kokkos_View.hpp>
 
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
 #include <impl/Kokkos_FunctorAdapter.hpp>
 
 //----------------------------------------------------------------------------
@@ -668,6 +671,7 @@ void wait( TaskPolicy< Kokkos::Serial > & )
 
 //----------------------------------------------------------------------------
 
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
 #endif /* defined( KOKKOS_HAVE_SERIAL ) */
-#endif /* #define KOKKOS_SERIAL_TASK_HPP */
+#endif /* #define KOKKOS_EXPERIMENTAL_SERIAL_TASK_HPP */
 
diff --git a/lib/kokkos/core/src/impl/Kokkos_Tags.hpp b/lib/kokkos/core/src/impl/Kokkos_Tags.hpp
index 399b633be9..0bc2864ff1 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Tags.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Tags.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -46,93 +46,84 @@
 
 #include <impl/Kokkos_Traits.hpp>
 #include <Kokkos_Core_fwd.hpp>
+#include <type_traits>
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Impl {
-
-template< class C , class Enable = void >
-struct is_memory_space_enable
-{ typedef std::false_type type ; };
-
-template< class C >
-struct is_memory_space_enable< C ,
-  typename std::enable_if<
-    std::is_same< C , typename C::memory_space >::value
-  >::type >
-{ typedef std::true_type type ; };
-
-
-template< class C , class Enable = void >
-struct is_execution_space_enable
-{ typedef std::false_type type ; };
-
-template< class C >
-struct is_execution_space_enable< C ,
-  typename std::enable_if<
-    std::is_same< C , typename C::execution_space >::value
-  >::type >
-{ typedef std::true_type type ; };
-
-
-template< class C , class Enable = void >
-struct is_execution_policy_enable
-{ typedef std::false_type type ; };
+/** KOKKOS_HAVE_TYPE( Type )
+ *
+ * defines a meta-function that check if a type expose an internal typedef or
+ * type alias which matches Type
+ *
+ * e.g.
+ *   KOKKOS_HAVE_TYPE( array_layout );
+ *   struct Foo { using array_layout = void; };
+ *   have_array_layout<Foo>::value == 1;
+ */
+#define KOKKOS_HAVE_TYPE( Type )                                                \
+template <typename T>                                                           \
+struct have_##Type {                                                            \
+  template <typename U> static std::false_type have_type(...);                  \
+  template <typename U> static std::true_type  have_type( typename U::Type* );  \
+  using type = decltype(have_type<T>(nullptr));                                 \
+  static constexpr bool value = type::value;                                    \
+}
 
-template< class C >
-struct is_execution_policy_enable< C ,
-  typename std::enable_if<
-    std::is_same< C , typename C::execution_policy >::value
-  >::type >
-{ typedef std::true_type type ; };
+/** KOKKOS_IS_CONCEPT( Concept )
+ *
+ * defines a meta-function that check if a type match the given Kokkos concept
+ * type alias which matches Type
+ *
+ * e.g.
+ *   KOKKOS_IS_CONCEPT( array_layout );
+ *   struct Foo { using array_layout = Foo; };
+ *   is_array_layout<Foo>::value == 1;
+ */
+#define KOKKOS_IS_CONCEPT( Concept )                                            \
+template <typename T>                                                           \
+struct is_##Concept {                                                           \
+  template <typename U> static std::false_type have_concept(...);               \
+  template <typename U> static auto have_concept( typename U::Concept* )        \
+                          ->typename std::is_same<T, typename U::Concept>::type;\
+  using type = decltype(have_concept<T>(nullptr));                              \
+  static constexpr bool value = type::value;                                    \
+}
 
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
 
-template< class C , class Enable = void >
-struct is_array_layout_enable
-{ typedef std::false_type type ; };
+namespace Kokkos { namespace Impl {
 
-template< class C >
-struct is_array_layout_enable< C ,
-  typename std::enable_if<
-    std::is_same< C , typename C::array_layout >::value
-  >::type >
-{ typedef std::true_type type ; };
+template <typename T>
+using is_void = std::is_same<void,T>;
 
+// is_memory_space<T>::value
+KOKKOS_IS_CONCEPT( memory_space );
 
-template< class C , class Enable = void >
-struct is_memory_traits_enable
-{ typedef std::false_type type ; };
+// is_memory_traits<T>::value
+KOKKOS_IS_CONCEPT( memory_traits );
 
-template< class C >
-struct is_memory_traits_enable< C ,
-  typename std::enable_if<
-    std::is_same< C , typename C::memory_traits >::value
-  >::type >
-{ typedef std::true_type type ; };
+// is_execution_space<T>::value
+KOKKOS_IS_CONCEPT( execution_space );
 
+// is_execution_policy<T>::value
+KOKKOS_IS_CONCEPT( execution_policy );
 
-template< class C >
-using is_memory_space = typename is_memory_space_enable<C>::type ;
+// is_array_layout<T>::value
+KOKKOS_IS_CONCEPT( array_layout );
 
-template< class C >
-using is_execution_space = typename is_execution_space_enable<C>::type ;
+// is_iteration_pattern<T>::value
+KOKKOS_IS_CONCEPT( iteration_pattern );
 
-template< class C >
-using is_execution_policy = typename is_execution_policy_enable<C>::type ;
+// is_schedule_type<T>::value
+KOKKOS_IS_CONCEPT( schedule_type );
 
-template< class C >
-using is_array_layout = typename is_array_layout_enable<C>::type ;
+// is_index_type<T>::value
+KOKKOS_IS_CONCEPT( index_type );
 
-template< class C >
-using is_memory_traits = typename is_memory_traits_enable<C>::type ;
+}} // namespace Kokkos::Impl
 
-}
-}
 
 //----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
diff --git a/lib/kokkos/core/src/impl/Kokkos_TaskQueue.hpp b/lib/kokkos/core/src/impl/Kokkos_TaskQueue.hpp
new file mode 100644
index 0000000000..663bb1985d
--- /dev/null
+++ b/lib/kokkos/core/src/impl/Kokkos_TaskQueue.hpp
@@ -0,0 +1,499 @@
+/*
+//@HEADER
+// ************************************************************************
+// 
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+// 
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+// 
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+// 
+// ************************************************************************
+//@HEADER
+*/
+
+// Experimental unified task-data parallel manycore LDRD
+
+#ifndef KOKKOS_IMPL_TASKQUEUE_HPP
+#define KOKKOS_IMPL_TASKQUEUE_HPP
+
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
+#include <string>
+#include <typeinfo>
+#include <stdexcept>
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+
+template< typename > class TaskPolicy ;
+
+template< typename Arg1 = void , typename Arg2 = void > class Future ;
+
+} /* namespace Kokkos */
+
+namespace Kokkos {
+namespace Impl {
+
+template< typename , typename , typename > class TaskBase ;
+template< typename > class TaskExec ;
+
+} /* namespace Impl */
+} /* namespace Kokkos */
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+namespace Impl {
+
+template< typename Space >
+class TaskQueueSpecialization ;
+
+/** \brief  Manage task allocation, deallocation, and scheduling.
+ *
+ *  Task execution is deferred to the TaskQueueSpecialization.
+ *  All other aspects of task management have shared implementation.
+ */
+template< typename ExecSpace >
+class TaskQueue {
+private:
+
+  friend class TaskQueueSpecialization< ExecSpace > ;
+  friend class Kokkos::TaskPolicy< ExecSpace > ;
+
+  using execution_space = ExecSpace ;
+  using specialization  = TaskQueueSpecialization< execution_space > ;
+  using memory_space    = typename specialization::memory_space ;
+  using device_type     = Kokkos::Device< execution_space , memory_space > ;
+  using memory_pool     = Kokkos::Experimental::MemoryPool< device_type > ;
+  using task_root_type  = Kokkos::Impl::TaskBase<execution_space,void,void> ;
+
+  struct Destroy {
+    TaskQueue * m_queue ;
+    void destroy_shared_allocation();
+  };
+
+  //----------------------------------------
+
+  enum : int { NumQueue = 3 };
+
+  // Queue is organized as [ priority ][ type ]
+
+  memory_pool               m_memory ;
+  task_root_type * volatile m_ready[ NumQueue ][ 2 ];
+  long                      m_accum_alloc ; // Accumulated number of allocations
+  int                       m_count_alloc ; // Current number of allocations
+  int                       m_max_alloc ;   // Maximum number of allocations
+  int                       m_ready_count ; // Number of ready or executing
+
+  //----------------------------------------
+
+  ~TaskQueue();
+  TaskQueue() = delete ;
+  TaskQueue( TaskQueue && ) = delete ;
+  TaskQueue( TaskQueue const & ) = delete ;
+  TaskQueue & operator = ( TaskQueue && ) = delete ;
+  TaskQueue & operator = ( TaskQueue const & ) = delete ;
+
+  TaskQueue
+    ( const memory_space & arg_space
+    , unsigned const arg_memory_pool_capacity
+    , unsigned const arg_memory_pool_superblock_capacity_log2
+    );
+
+  // Schedule a task
+  //   Precondition:
+  //     task is not executing
+  //     task->m_next is the dependence or zero
+  //   Postcondition:
+  //     task->m_next is linked list membership
+  KOKKOS_FUNCTION
+  void schedule( task_root_type * const );
+
+  // Complete a task
+  //   Precondition:
+  //     task is not executing
+  //     task->m_next == LockTag  =>  task is complete
+  //     task->m_next != LockTag  =>  task is respawn
+  //   Postcondition:
+  //     task->m_wait == LockTag  =>  task is complete
+  //     task->m_wait != LockTag  =>  task is waiting
+  KOKKOS_FUNCTION
+  void complete( task_root_type * );
+
+  KOKKOS_FUNCTION
+  static bool push_task( task_root_type * volatile * const
+                       , task_root_type * const );
+
+  KOKKOS_FUNCTION
+  static task_root_type * pop_task( task_root_type * volatile * const );
+
+  KOKKOS_FUNCTION static
+  void decrement( task_root_type * task );
+
+public:
+
+  // If and only if the execution space is a single thread
+  // then execute ready tasks.
+  KOKKOS_INLINE_FUNCTION
+  void iff_single_thread_recursive_execute()
+    {
+#if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST )
+      specialization::iff_single_thread_recursive_execute( this );
+#endif
+    }
+
+  void execute() { specialization::execute( this ); }
+
+  // Assign task pointer with reference counting of assigned tasks
+  template< typename LV , typename RV >
+  KOKKOS_FUNCTION static
+  void assign( TaskBase< execution_space,LV,void> ** const lhs
+             , TaskBase< execution_space,RV,void> *  const rhs )
+    {
+      using task_lhs = TaskBase< execution_space,LV,void> ;
+#if 0
+  {
+    printf( "assign( 0x%lx { 0x%lx %d %d } , 0x%lx { 0x%lx %d %d } )\n"
+          , uintptr_t( lhs ? *lhs : 0 )
+          , uintptr_t( lhs && *lhs ? (*lhs)->m_next : 0 )
+          , int( lhs && *lhs ? (*lhs)->m_task_type : 0 )
+          , int( lhs && *lhs ? (*lhs)->m_ref_count : 0 )
+          , uintptr_t(rhs)
+          , uintptr_t( rhs ? rhs->m_next : 0 )
+          , int( rhs ? rhs->m_task_type : 0 )
+          , int( rhs ? rhs->m_ref_count : 0 )
+          );
+    fflush( stdout );
+  }
+#endif
+
+      if ( *lhs ) decrement( *lhs );
+      if ( rhs ) { Kokkos::atomic_fetch_add( &(rhs->m_ref_count) , 1 ); }
+
+      // Force write of *lhs
+
+      *static_cast< task_lhs * volatile * >(lhs) = rhs ;
+
+      Kokkos::memory_fence();
+    }
+
+  KOKKOS_FUNCTION
+  size_t allocate_block_size( size_t n ); ///< Actual block size allocated
+
+  KOKKOS_FUNCTION
+  void * allocate( size_t n ); ///< Allocate from the memory pool
+
+  KOKKOS_FUNCTION
+  void deallocate( void * p , size_t n ); ///< Deallocate to the memory pool
+};
+
+} /* namespace Impl */
+} /* namespace Kokkos */
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace Kokkos {
+namespace Impl {
+
+template<>
+class TaskBase< void , void , void > {
+public:
+  enum : int16_t   { TaskTeam = 0 , TaskSingle = 1 , Aggregate = 2 };
+  enum : uintptr_t { LockTag = ~uintptr_t(0) , EndTag = ~uintptr_t(1) };
+};
+
+/** \brief  Base class for task management, access, and execution.
+ *
+ *  Inheritance structure to allow static_cast from the task root type
+ *  and a task's FunctorType.
+ *
+ *    // Enable a Future to access result data
+ *    TaskBase< Space , ResultType , void >
+ *      : TaskBase< void , void , void >
+ *      { ... };
+ *
+ *    // Enable a functor to access the base class
+ *    TaskBase< Space , ResultType , FunctorType >
+ *      : TaskBase< Space , ResultType , void >
+ *      , FunctorType
+ *      { ... };
+ *
+ *
+ *  States of a task:
+ *
+ *    Constructing State, NOT IN a linked list
+ *      m_wait == 0
+ *      m_next == 0
+ *
+ *    Scheduling transition : Constructing -> Waiting
+ *      before:
+ *        m_wait == 0
+ *        m_next == this task's initial dependence, 0 if none
+ *      after:
+ *        m_wait == EndTag
+ *        m_next == EndTag
+ *
+ *    Waiting State, IN a linked list
+ *      m_apply != 0
+ *      m_queue != 0
+ *      m_ref_count > 0
+ *      m_wait == head of linked list of tasks waiting on this task
+ *      m_next == next of linked list of tasks
+ *
+ *    transition : Waiting -> Executing
+ *      before:
+ *        m_next == EndTag
+ *      after::
+ *        m_next == LockTag
+ *
+ *    Executing State, NOT IN a linked list
+ *      m_apply != 0
+ *      m_queue != 0
+ *      m_ref_count > 0
+ *      m_wait == head of linked list of tasks waiting on this task
+ *      m_next == LockTag
+ *
+ *    Respawn transition : Executing -> Executing-Respawn
+ *      before:
+ *        m_next == LockTag
+ *      after:
+ *        m_next == this task's updated dependence, 0 if none
+ *
+ *    Executing-Respawn State, NOT IN a linked list
+ *      m_apply != 0
+ *      m_queue != 0
+ *      m_ref_count > 0
+ *      m_wait == head of linked list of tasks waiting on this task
+ *      m_next == this task's updated dependence, 0 if none
+ *
+ *    transition : Executing -> Complete
+ *      before:
+ *        m_wait == head of linked list
+ *      after:
+ *        m_wait == LockTag
+ *
+ *    Complete State, NOT IN a linked list
+ *      m_wait == LockTag: cannot add dependence
+ *      m_next == LockTag: not a member of a wait queue
+ *
+ */
+template< typename ExecSpace >
+class TaskBase< ExecSpace , void , void >
+{
+public:
+
+  enum : int16_t   { TaskTeam   = TaskBase<void,void,void>::TaskTeam
+                   , TaskSingle = TaskBase<void,void,void>::TaskSingle
+                   , Aggregate  = TaskBase<void,void,void>::Aggregate };
+
+  enum : uintptr_t { LockTag = TaskBase<void,void,void>::LockTag
+                   , EndTag  = TaskBase<void,void,void>::EndTag };
+
+  using execution_space = ExecSpace ;
+  using queue_type      = TaskQueue< execution_space > ;
+
+  template< typename > friend class Kokkos::TaskPolicy ;
+
+  typedef void (* function_type) ( TaskBase * , void * );
+
+  // sizeof(TaskBase) == 48
+
+  function_type  m_apply ;     ///< Apply function pointer
+  queue_type   * m_queue ;     ///< Queue in which this task resides
+  TaskBase     * m_wait ;      ///< Linked list of tasks waiting on this
+  TaskBase     * m_next ;      ///< Waiting linked-list next
+  int32_t        m_ref_count ; ///< Reference count
+  int32_t        m_alloc_size ;///< Allocation size
+  int32_t        m_dep_count ; ///< Aggregate's number of dependences
+  int16_t        m_task_type ; ///< Type of task
+  int16_t        m_priority ;  ///< Priority of runnable task
+
+  TaskBase( TaskBase && ) = delete ;
+  TaskBase( const TaskBase & ) = delete ;
+  TaskBase & operator = ( TaskBase && ) = delete ;
+  TaskBase & operator = ( const TaskBase & ) = delete ;
+
+  KOKKOS_INLINE_FUNCTION ~TaskBase() = default ;
+
+  KOKKOS_INLINE_FUNCTION
+  constexpr TaskBase() noexcept
+    : m_apply(0)
+    , m_queue(0)
+    , m_wait(0)
+    , m_next(0)
+    , m_ref_count(0)
+    , m_alloc_size(0)
+    , m_dep_count(0)
+    , m_task_type( TaskSingle )
+    , m_priority( 1 /* TaskRegularPriority */ )
+    {}
+
+  //----------------------------------------
+
+  KOKKOS_INLINE_FUNCTION
+  TaskBase ** aggregate_dependences()
+    { return reinterpret_cast<TaskBase**>( this + 1 ); }
+
+  using get_return_type = void ;
+
+  KOKKOS_INLINE_FUNCTION
+  get_return_type get() const {}
+};
+
+template < typename ExecSpace , typename ResultType >
+class TaskBase< ExecSpace , ResultType , void >
+  : public TaskBase< ExecSpace , void , void >
+{
+private:
+
+  static_assert( sizeof(TaskBase<ExecSpace,void,void>) == 48 , "" );
+
+  TaskBase( TaskBase && ) = delete ;
+  TaskBase( const TaskBase & ) = delete ;
+  TaskBase & operator = ( TaskBase && ) = delete ;
+  TaskBase & operator = ( const TaskBase & ) = delete ;
+
+public:
+
+  ResultType   m_result ;
+
+  KOKKOS_INLINE_FUNCTION ~TaskBase() = default ;
+
+  KOKKOS_INLINE_FUNCTION
+  TaskBase()
+    : TaskBase< ExecSpace , void , void >()
+    , m_result()
+    {}
+
+  using get_return_type = ResultType const & ;
+
+  KOKKOS_INLINE_FUNCTION
+  get_return_type get() const { return m_result ; }
+};
+
+
+template< typename ExecSpace , typename ResultType , typename FunctorType >
+class TaskBase
+  : public TaskBase< ExecSpace , ResultType , void >
+  , public FunctorType
+{
+private:
+
+  TaskBase() = delete ;
+  TaskBase( TaskBase && ) = delete ;
+  TaskBase( const TaskBase & ) = delete ;
+  TaskBase & operator = ( TaskBase && ) = delete ;
+  TaskBase & operator = ( const TaskBase & ) = delete ;
+
+public:
+
+  using root_type    = TaskBase< ExecSpace , void , void > ;
+  using base_type    = TaskBase< ExecSpace , ResultType , void > ;
+  using member_type  = TaskExec< ExecSpace > ;
+  using functor_type = FunctorType ;
+  using result_type  = ResultType ;
+
+  template< typename Type >
+  KOKKOS_INLINE_FUNCTION static
+  void apply_functor
+    ( Type * const task
+    , typename std::enable_if
+        < std::is_same< typename Type::result_type , void >::value
+        , member_type * const 
+        >::type member
+    )
+    {
+      using fType = typename Type::functor_type ;
+      static_cast<fType*>(task)->operator()( *member );
+    }
+
+  template< typename Type >
+  KOKKOS_INLINE_FUNCTION static
+  void apply_functor
+    ( Type * const task
+    , typename std::enable_if
+        < ! std::is_same< typename Type::result_type , void >::value
+        , member_type * const 
+        >::type member
+    )
+    {
+      using fType = typename Type::functor_type ;
+      static_cast<fType*>(task)->operator()( *member , task->m_result );
+    }
+
+  KOKKOS_FUNCTION static
+  void apply( root_type * root , void * exec )
+    {
+      TaskBase    * const lock   = reinterpret_cast< TaskBase * >( root_type::LockTag );
+      TaskBase    * const task   = static_cast< TaskBase * >( root );
+      member_type * const member = reinterpret_cast< member_type * >( exec );
+
+      TaskBase::template apply_functor( task , member );
+
+      // Task may be serial or team.
+      // If team then must synchronize before querying task->m_next.
+      // If team then only one thread calls destructor.
+
+      member->team_barrier();
+
+      if ( 0 == member->team_rank() && lock == task->m_next ) {
+        // Did not respawn, destroy the functor to free memory
+        static_cast<functor_type*>(task)->~functor_type();
+        // Cannot destroy the task until its dependences
+        // have been processed.
+      }
+    }
+
+  KOKKOS_INLINE_FUNCTION
+  TaskBase( FunctorType const & arg_functor )
+    : base_type()
+    , FunctorType( arg_functor )
+    {}
+
+  KOKKOS_INLINE_FUNCTION
+  ~TaskBase() {}
+};
+
+} /* namespace Impl */
+} /* namespace Kokkos */
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
+#endif /* #ifndef KOKKOS_IMPL_TASKQUEUE_HPP */
+
diff --git a/lib/kokkos/core/src/impl/Kokkos_TaskQueue_impl.hpp b/lib/kokkos/core/src/impl/Kokkos_TaskQueue_impl.hpp
new file mode 100644
index 0000000000..70a880d4a2
--- /dev/null
+++ b/lib/kokkos/core/src/impl/Kokkos_TaskQueue_impl.hpp
@@ -0,0 +1,569 @@
+/*
+//@HEADER
+// ************************************************************************
+// 
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+// 
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+// 
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+// 
+// ************************************************************************
+//@HEADER
+*/
+
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
+namespace Kokkos {
+namespace Impl {
+
+//----------------------------------------------------------------------------
+
+template< typename ExecSpace >
+void TaskQueue< ExecSpace >::Destroy::destroy_shared_allocation()
+{
+  m_queue->~TaskQueue();
+}
+
+//----------------------------------------------------------------------------
+
+template< typename ExecSpace >
+TaskQueue< ExecSpace >::TaskQueue
+  ( const TaskQueue< ExecSpace >::memory_space & arg_space
+  , unsigned const arg_memory_pool_capacity
+  , unsigned const arg_memory_pool_superblock_capacity_log2
+  )
+  : m_memory( arg_space
+            , arg_memory_pool_capacity
+            , arg_memory_pool_superblock_capacity_log2 )
+  , m_ready()
+  , m_accum_alloc(0)
+  , m_max_alloc(0)
+  , m_ready_count(0)
+{
+  for ( int i = 0 ; i < NumQueue ; ++i ) {
+    m_ready[i][0] = (task_root_type *) task_root_type::EndTag ;
+    m_ready[i][1] = (task_root_type *) task_root_type::EndTag ;
+  }
+}
+
+//----------------------------------------------------------------------------
+
+template< typename ExecSpace >
+TaskQueue< ExecSpace >::~TaskQueue()
+{
+  // Verify that queues are empty and ready count is zero
+
+  for ( int i = 0 ; i < NumQueue ; ++i ) {
+    for ( int j = 0 ; j < 2 ; ++j ) {
+      if ( m_ready[i][j] != (task_root_type *) task_root_type::EndTag ) {
+        Kokkos::abort("TaskQueue::~TaskQueue ERROR: has ready tasks");
+      }
+    }
+  }
+
+  if ( 0 != m_ready_count ) {
+    Kokkos::abort("TaskQueue::~TaskQueue ERROR: has ready or executing tasks");
+  }
+}
+
+//----------------------------------------------------------------------------
+
+template< typename ExecSpace >
+KOKKOS_FUNCTION
+void TaskQueue< ExecSpace >::decrement
+  ( TaskQueue< ExecSpace >::task_root_type * task )
+{
+  const int count = Kokkos::atomic_fetch_add(&(task->m_ref_count),-1);
+
+#if 0
+  if ( 1 == count ) {
+    printf( "decrement-destroy( 0x%lx { 0x%lx %d %d } )\n"
+          , uintptr_t( task )
+          , uintptr_t( task->m_next )
+          , int( task->m_task_type )
+          , int( task->m_ref_count )
+          );
+  }
+#endif
+
+  if ( ( 1 == count ) && 
+       ( task->m_next == (task_root_type *) task_root_type::LockTag ) ) {
+    // Reference count is zero and task is complete, deallocate.
+    task->m_queue->deallocate( task , task->m_alloc_size );
+  }   
+  else if ( count <= 1 ) { 
+    Kokkos::abort("TaskPolicy task has negative reference count or is incomplete" );
+  }   
+}
+
+//----------------------------------------------------------------------------
+
+template< typename ExecSpace >
+KOKKOS_FUNCTION
+size_t TaskQueue< ExecSpace >::allocate_block_size( size_t n )
+{
+  return m_memory.allocate_block_size( n );
+}
+
+template< typename ExecSpace >
+KOKKOS_FUNCTION
+void * TaskQueue< ExecSpace >::allocate( size_t n )
+{
+  void * const p = m_memory.allocate(n);
+
+  if ( p ) {
+    Kokkos::atomic_increment( & m_accum_alloc );
+    Kokkos::atomic_increment( & m_count_alloc );
+
+    if ( m_max_alloc < m_count_alloc ) m_max_alloc = m_count_alloc ;
+  }
+
+  return p ;
+}
+
+template< typename ExecSpace >
+KOKKOS_FUNCTION
+void TaskQueue< ExecSpace >::deallocate( void * p , size_t n )
+{
+  m_memory.deallocate( p , n );
+  Kokkos::atomic_decrement( & m_count_alloc );
+}
+
+//----------------------------------------------------------------------------
+
+template< typename ExecSpace >
+KOKKOS_FUNCTION
+bool TaskQueue< ExecSpace >::push_task
+  ( TaskQueue< ExecSpace >::task_root_type * volatile * const queue
+  , TaskQueue< ExecSpace >::task_root_type * const task
+  )
+{
+  // Push task into a concurrently pushed and popped queue.
+  // The queue is a linked list where 'task->m_next' form the links.
+  // Fail the push attempt if the queue is locked;
+  // otherwise retry until the push succeeds.
+
+#if 0
+  printf( "push_task( 0x%lx { 0x%lx } 0x%lx { 0x%lx 0x%lx %d %d %d } )\n"
+        , uintptr_t(queue)
+        , uintptr_t(*queue)
+        , uintptr_t(task)
+        , uintptr_t(task->m_wait)
+        , uintptr_t(task->m_next)
+        , task->m_task_type
+        , task->m_priority
+        , task->m_ref_count );
+#endif
+
+  task_root_type * const zero = (task_root_type *) 0 ;
+  task_root_type * const lock = (task_root_type *) task_root_type::LockTag ;
+
+  task_root_type * volatile * const next = & task->m_next ;
+
+  if ( zero != *next ) {
+    Kokkos::abort("TaskQueue::push_task ERROR: already a member of another queue" );
+  }
+
+  task_root_type * y = *queue ;
+
+  while ( lock != y ) {
+
+    *next = y ;
+
+    // Do not proceed until '*next' has been stored.
+    Kokkos::memory_fence();
+
+    task_root_type * const x = y ;
+
+    y = Kokkos::atomic_compare_exchange(queue,y,task);
+
+    if ( x == y ) return true ;
+  }
+
+  // Failed, replace 'task->m_next' value since 'task' remains
+  // not a member of a queue.
+
+  *next = zero ;
+
+  // Do not proceed until '*next' has been stored.
+  Kokkos::memory_fence();
+
+  return false ;
+}
+
+//----------------------------------------------------------------------------
+
+template< typename ExecSpace >
+KOKKOS_FUNCTION
+typename TaskQueue< ExecSpace >::task_root_type *
+TaskQueue< ExecSpace >::pop_task
+  ( TaskQueue< ExecSpace >::task_root_type * volatile * const queue )
+{
+  // Pop task from a concurrently pushed and popped queue.
+  // The queue is a linked list where 'task->m_next' form the links.
+
+  task_root_type * const zero = (task_root_type *) 0 ;
+  task_root_type * const lock = (task_root_type *) task_root_type::LockTag ;
+  task_root_type * const end  = (task_root_type *) task_root_type::EndTag ;
+
+  // *queue is
+  //   end   => an empty queue
+  //   lock  => a locked queue
+  //   valid
+
+  // Retry until the lock is acquired or the queue is empty.
+
+  task_root_type * task = *queue ;
+
+  while ( end != task ) {
+
+    // The only possible values for the queue are
+    // (1) lock, (2) end, or (3) a valid task.
+    // Thus zero will never appear in the queue.
+    //
+    // If queue is locked then just read by guaranteeing
+    // the CAS will fail.
+
+    if ( lock == task ) task = 0 ;
+
+    task_root_type * const x = task ;
+
+    task = Kokkos::atomic_compare_exchange(queue,task,lock);
+
+    if ( x == task ) break ; // CAS succeeded and queue is locked
+  }
+
+  if ( end != task ) {
+
+    // This thread has locked the queue and removed 'task' from the queue.
+    // Extract the next entry of the queue from 'task->m_next'
+    // and mark 'task' as popped from a queue by setting
+    // 'task->m_next = lock'.
+
+    task_root_type * const next =
+      Kokkos::atomic_exchange( & task->m_next , lock );
+
+    // Place the next entry in the head of the queue,
+    // which also unlocks the queue.
+
+    task_root_type * const unlock =
+      Kokkos::atomic_exchange( queue , next );
+
+    if ( next == zero || next == lock || lock != unlock ) {
+      Kokkos::abort("TaskQueue::pop_task ERROR");
+    }
+  }
+
+#if 0
+  if ( end != task ) {
+    printf( "pop_task( 0x%lx 0x%lx { 0x%lx 0x%lx %d %d %d } )\n"
+          , uintptr_t(queue)
+          , uintptr_t(task)
+          , uintptr_t(task->m_wait)
+          , uintptr_t(task->m_next)
+          , int(task->m_task_type)
+          , int(task->m_priority)
+          , int(task->m_ref_count) );
+  }
+#endif
+
+  return task ;
+}
+
+//----------------------------------------------------------------------------
+
+template< typename ExecSpace >
+KOKKOS_FUNCTION
+void TaskQueue< ExecSpace >::schedule
+  ( TaskQueue< ExecSpace >::task_root_type * const task )
+{
+  // Schedule a runnable or when_all task upon construction / spawn
+  // and upon completion of other tasks that 'task' is waiting on.
+
+  // Precondition on runnable task state:
+  //   task is either constructing or executing
+  //
+  //   Constructing state:
+  //     task->m_wait == 0
+  //     task->m_next == dependence
+  //   Executing-respawn state:
+  //     task->m_wait == head of linked list
+  //     task->m_next == dependence
+  //
+  //  Task state transition:
+  //     Constructing      ->  Waiting
+  //     Executing-respawn ->  Waiting
+  //
+  //  Postcondition on task state:
+  //     task->m_wait == head of linked list
+  //     task->m_next == member of linked list
+
+#if 0
+  printf( "schedule( 0x%lx { 0x%lx 0x%lx %d %d %d }\n"
+        , uintptr_t(task)
+        , uintptr_t(task->m_wait)
+        , uintptr_t(task->m_next)
+        , task->m_task_type
+        , task->m_priority
+        , task->m_ref_count );
+#endif
+
+  task_root_type * const zero = (task_root_type *) 0 ;
+  task_root_type * const lock = (task_root_type *) task_root_type::LockTag ;
+  task_root_type * const end  = (task_root_type *) task_root_type::EndTag ;
+
+  //----------------------------------------
+  {
+    // If Constructing then task->m_wait == 0
+    // Change to waiting by task->m_wait = EndTag
+
+    task_root_type * const init =
+      Kokkos::atomic_compare_exchange( & task->m_wait , zero , end );
+
+    // Precondition
+
+    if ( lock == init ) {
+      Kokkos::abort("TaskQueue::schedule ERROR: task is complete");
+    }
+
+    // if ( init == 0 ) Constructing       ->  Waiting
+    // else             Executing-Respawn  ->  Waiting
+  }
+  //----------------------------------------
+
+  if ( task_root_type::Aggregate != task->m_task_type ) {
+
+    // Scheduling a runnable task which may have a depencency 'dep'.
+    // Extract dependence, if any, from task->m_next.
+    // If 'dep' is not null then attempt to push 'task'
+    // into the wait queue of 'dep'.
+    // If the push succeeds then 'task' may be
+    // processed or executed by another thread at any time.
+    // If the push fails then 'dep' is complete and 'task'
+    // is ready to execute.
+
+    task_root_type * dep = Kokkos::atomic_exchange( & task->m_next , zero );
+
+    const bool is_ready = 
+      ( 0 == dep ) || ( ! push_task( & dep->m_wait , task ) );
+
+    // Reference count for dep was incremented when assigned
+    // to task->m_next so that if it completed prior to the
+    // above push_task dep would not be destroyed.
+    // dep reference count can now be decremented,
+    // which may deallocate the task.
+    TaskQueue::assign( & dep , (task_root_type *)0 );
+
+    if ( is_ready ) {
+
+      // No dependence or 'dep' is complete so push task into ready queue.
+      // Increment the ready count before pushing into ready queue
+      // to track number of ready + executing tasks.
+      // The ready count will be decremented when the task is complete.
+
+      Kokkos::atomic_increment( & m_ready_count );
+
+      task_root_type * volatile * const queue =
+        & m_ready[ task->m_priority ][ task->m_task_type ];
+
+      // A push_task fails if the ready queue is locked.
+      // A ready queue is only locked during a push or pop;
+      // i.e., it is never permanently locked.
+      // Retry push to ready queue until it succeeds.
+      // When the push succeeds then 'task' may be
+      // processed or executed by another thread at any time.
+
+      while ( ! push_task( queue , task ) );
+    }
+  }
+  //----------------------------------------
+  else {
+    // Scheduling a 'when_all' task with multiple dependences.
+    // This scheduling may be called when the 'when_all' is
+    // (1) created or
+    // (2) being removed from a completed task's wait list.
+
+    task_root_type ** const aggr = task->aggregate_dependences();
+
+    // Assume the 'when_all' is complete until a dependence is
+    // found that is not complete.
+
+    bool is_complete = true ;
+
+    for ( int i = task->m_dep_count ; 0 < i && is_complete ; ) {
+
+      --i ;
+
+      // Loop dependences looking for an incomplete task.
+      // Add this task to the incomplete task's wait queue.
+
+      // Remove a task 'x' from the dependence list.
+      // The reference count of 'x' was incremented when
+      // it was assigned into the dependence list.
+
+      task_root_type * x = Kokkos::atomic_exchange( aggr + i , zero );
+
+      if ( x ) {
+
+        // If x->m_wait is not locked then push succeeds
+        // and the aggregate is not complete.
+        // If the push succeeds then this when_all 'task' may be
+        // processed by another thread at any time.
+        // For example, 'x' may be completeed by another
+        // thread and then re-schedule this when_all 'task'.
+
+        is_complete = ! push_task( & x->m_wait , task );
+
+        // Decrement reference count which had been incremented
+        // when 'x' was added to the dependence list.
+
+        TaskQueue::assign( & x , zero );
+      }
+    }
+
+    if ( is_complete ) {
+      // The when_all 'task' was not added to a wait queue because
+      // all dependences were complete so this aggregate is complete.
+      // Complete the when_all 'task' to schedule other tasks
+      // that are waiting for the when_all 'task' to complete.
+
+      task->m_next = lock ;
+
+      complete( task );
+
+      // '*task' may have been deleted upon completion
+    }
+  }
+  //----------------------------------------
+  // Postcondition:
+  //   A runnable 'task' was pushed into a wait or ready queue.
+  //   An aggregate 'task' was either pushed to a wait queue
+  //   or completed.
+  // Concurrent execution may have already popped 'task'
+  // from a queue and processed it as appropriate.
+}
+
+//----------------------------------------------------------------------------
+
+template< typename ExecSpace >
+KOKKOS_FUNCTION
+void TaskQueue< ExecSpace >::complete
+  ( TaskQueue< ExecSpace >::task_root_type * task )
+{
+  // Complete a runnable task that has finished executing
+  // or a when_all task when all of its dependeneces are complete.
+
+  task_root_type * const zero = (task_root_type *) 0 ;
+  task_root_type * const lock = (task_root_type *) task_root_type::LockTag ;
+  task_root_type * const end  = (task_root_type *) task_root_type::EndTag ;
+
+#if 0
+  printf( "complete( 0x%lx { 0x%lx 0x%lx %d %d %d }\n"
+        , uintptr_t(task)
+        , uintptr_t(task->m_wait)
+        , uintptr_t(task->m_next)
+        , task->m_task_type
+        , task->m_priority
+        , task->m_ref_count );
+  fflush( stdout );
+#endif
+
+  const bool runnable = task_root_type::Aggregate != task->m_task_type ;
+
+  //----------------------------------------
+
+  if ( runnable && lock != task->m_next ) {
+    // Is a runnable task has finished executing and requested respawn.
+    // Schedule the task for subsequent execution.
+
+    schedule( task );
+  }
+  //----------------------------------------
+  else {
+    // Is either an aggregate or a runnable task that executed
+    // and did not respawn.  Transition this task to complete.
+
+    // If 'task' is an aggregate then any of the runnable tasks that
+    // it depends upon may be attempting to complete this 'task'.
+    // Must only transition a task once to complete status.
+    // This is controled by atomically locking the wait queue.
+
+    // Stop other tasks from adding themselves to this task's wait queue
+    // by locking the head of this task's wait queue.
+
+    task_root_type * x = Kokkos::atomic_exchange( & task->m_wait , lock );
+
+    if ( x != (task_root_type *) lock ) {
+
+      // This thread has transitioned this 'task' to complete.
+      // 'task' is no longer in a queue and is not executing
+      // so decrement the reference count from 'task's creation.
+      // If no other references to this 'task' then it will be deleted.
+
+      TaskQueue::assign( & task , zero );
+
+      // This thread has exclusive access to the wait list so
+      // the concurrency-safe pop_task function is not needed.
+      // Schedule the tasks that have been waiting on the input 'task',
+      // which may have been deleted.
+
+      while ( x != end ) {
+
+        // Set x->m_next = zero  <=  no dependence
+
+        task_root_type * const next =
+          (task_root_type *) Kokkos::atomic_exchange( & x->m_next , zero );
+
+        schedule( x );
+
+        x = next ;
+      }
+    }
+  }
+
+  if ( runnable ) {
+    // A runnable task was popped from a ready queue and executed.
+    // If respawned into a ready queue then the ready count was incremented
+    // so decrement whether respawned or not.
+    Kokkos::atomic_decrement( & m_ready_count );
+  }
+}
+
+//----------------------------------------------------------------------------
+
+} /* namespace Impl */
+} /* namespace Kokkos */
+
+
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
+
diff --git a/lib/kokkos/core/src/impl/Kokkos_Timer.hpp b/lib/kokkos/core/src/impl/Kokkos_Timer.hpp
index 80a326f080..1f14e42874 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Timer.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Timer.hpp
@@ -109,6 +109,9 @@ public:
 };
 
 } // namespace Impl
+
+  using Kokkos::Impl::Timer ;
+
 } // namespace Kokkos
 
 #endif /* #ifndef KOKKOS_IMPLWALLTIME_HPP */
diff --git a/lib/kokkos/core/src/impl/Kokkos_Traits.hpp b/lib/kokkos/core/src/impl/Kokkos_Traits.hpp
index b9e07a82de..278f715bc9 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Traits.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Traits.hpp
@@ -47,6 +47,7 @@
 #include <stddef.h>
 #include <stdint.h>
 #include <Kokkos_Macros.hpp>
+#include <string>
 #include <type_traits>
 
 namespace Kokkos {
@@ -357,9 +358,31 @@ struct is_integral : public integral_constant< bool ,
     std::is_same< T , uint64_t >::value 
   )>
 {};
-
 //----------------------------------------------------------------------------
 
+template<typename T>
+struct is_label : public false_type {};
+
+template<>
+struct is_label<const char*> : public true_type {};
+
+template<>
+struct is_label<char*> : public true_type {};
+
+
+template<int N>
+struct is_label<const char[N]> : public true_type {};
+
+template<int N>
+struct is_label<char[N]> : public true_type {};
+
+
+template<>
+struct is_label<const std::string> : public true_type {};
+
+template<>
+struct is_label<std::string> : public true_type {};
+
 // These 'constexpr'functions can be used as
 // both regular functions and meta-function.
 
diff --git a/lib/kokkos/core/src/impl/Kokkos_ViewSupport.hpp b/lib/kokkos/core/src/impl/Kokkos_ViewSupport.hpp
index 452af66cde..8b63039f57 100644
--- a/lib/kokkos/core/src/impl/Kokkos_ViewSupport.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_ViewSupport.hpp
@@ -115,135 +115,6 @@ template< class ExecSpace , class Type , bool Initialize >
 struct ViewDefaultConstruct
 { ViewDefaultConstruct( Type * , size_t ) {} };
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-/** \brief  ViewDataHandle provides the type of the 'data handle' which the view
- *          uses to access data with the [] operator. It also provides
- *          an allocate function and a function to extract a raw ptr from the
- *          data handle. ViewDataHandle also defines an enum ReferenceAble which
- *          specifies whether references/pointers to elements can be taken and a
- *          'return_type' which is what the view operators will give back.
- *          Specialisation of this object allows three things depending
- *          on ViewTraits and compiler options:
- *          (i)   Use special allocator (e.g. huge pages/small pages and pinned memory)
- *          (ii)  Use special data handle type (e.g. add Cuda Texture Object)
- *          (iii) Use special access intrinsics (e.g. texture fetch and non-caching loads)
- */
-template< class StaticViewTraits , class Enable = void >
-struct ViewDataHandle {
-
-  enum { ReturnTypeIsReference = true };
-
-  typedef typename StaticViewTraits::value_type * handle_type;
-  typedef typename StaticViewTraits::value_type & return_type;
-
-  KOKKOS_INLINE_FUNCTION
-  static handle_type create_handle( typename StaticViewTraits::value_type * arg_data_ptr, AllocationTracker const & /*arg_tracker*/ )
-  {
-    return handle_type(arg_data_ptr);
-  }
-};
-
-template< class StaticViewTraits , class Enable = void >
-class ViewDataManagement : public ViewDataHandle< StaticViewTraits > {
-private:
-
-  template< class , class > friend class ViewDataManagement ;
-
-  struct PotentiallyManaged  {};
-  struct StaticallyUnmanaged {};
-
-  /* Statically unmanaged if traits or not executing in host-accessible memory space */
-  typedef typename
-    Impl::if_c< StaticViewTraits::is_managed &&
-                Impl::is_same< Kokkos::HostSpace
-                             , Kokkos::Impl::ActiveExecutionMemorySpace >::value
-              , PotentiallyManaged
-              , StaticallyUnmanaged
-              >::type StaticManagementTag ;
-
-  enum { Unmanaged     = 0x01
-       , Noncontiguous = 0x02
-       };
-
-  enum { DefaultTraits = Impl::is_same< StaticManagementTag , StaticallyUnmanaged >::value ? Unmanaged : 0 };
-
-  unsigned m_traits ; ///< Runtime traits
-
-
-  template< class T >
-  inline static
-  unsigned assign( const ViewDataManagement<T> & rhs , const PotentiallyManaged & )
-    { return rhs.m_traits | ( rhs.is_managed() && Kokkos::HostSpace::in_parallel() ? unsigned(Unmanaged) : 0u ); }
-
-  template< class T >
-  KOKKOS_INLINE_FUNCTION static
-  unsigned assign( const ViewDataManagement<T> & rhs , const StaticallyUnmanaged & )
-    { return rhs.m_traits | Unmanaged ; }
-
-public:
-
-  typedef typename ViewDataHandle< StaticViewTraits >::handle_type handle_type;
-
-  KOKKOS_INLINE_FUNCTION
-  ViewDataManagement() : m_traits( DefaultTraits ) {}
-
-  KOKKOS_INLINE_FUNCTION
-  ViewDataManagement( const ViewDataManagement & rhs )
-    : m_traits( assign( rhs , StaticManagementTag() ) ) {}
-
-  KOKKOS_INLINE_FUNCTION
-  ViewDataManagement & operator = ( const ViewDataManagement & rhs )
-    { m_traits = assign( rhs , StaticManagementTag() ); return *this ; }
-
-  template< class SVT >
-  KOKKOS_INLINE_FUNCTION
-  ViewDataManagement( const ViewDataManagement<SVT> & rhs )
-    : m_traits( assign( rhs , StaticManagementTag() ) ) {}
-
-  template< class SVT >
-  KOKKOS_INLINE_FUNCTION
-  ViewDataManagement & operator = ( const ViewDataManagement<SVT> & rhs )
-    { m_traits = assign( rhs , StaticManagementTag() ); return *this ; }
-
-  KOKKOS_INLINE_FUNCTION
-  bool is_managed() const { return ! ( m_traits & Unmanaged ); }
-
-  KOKKOS_INLINE_FUNCTION
-  bool is_contiguous() const { return ! ( m_traits & Noncontiguous ); }
-
-  KOKKOS_INLINE_FUNCTION
-  void set_unmanaged() { m_traits |= Unmanaged ; }
-
-  KOKKOS_INLINE_FUNCTION
-  void set_noncontiguous() { m_traits |= Noncontiguous ; }
-
-  template< bool Initialize >
-  static
-  handle_type allocate(  const std::string & label
-                       , const Impl::ViewOffset< typename StaticViewTraits::shape_type, typename StaticViewTraits::array_layout > & offset_map
-                       , AllocationTracker & tracker
-               )
-    {
-      typedef typename StaticViewTraits::execution_space  execution_space ;
-      typedef typename StaticViewTraits::memory_space     memory_space ;
-      typedef typename StaticViewTraits::value_type       value_type ;
-
-      const size_t count = offset_map.capacity();
-
-      tracker = memory_space::allocate_and_track( label, sizeof(value_type) * count );
-
-      value_type * ptr = reinterpret_cast<value_type *>(tracker.alloc_ptr());
-
-      // Default construct within the view's execution space.
-      (void) ViewDefaultConstruct< execution_space , value_type , Initialize >( ptr , count );
-
-      return ViewDataHandle< StaticViewTraits >::create_handle(ptr, tracker);
-    }
-};
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
 } // namespace Impl
 } // namespace Kokkos
 
diff --git a/lib/kokkos/core/src/impl/Kokkos_ViewTileLeft.hpp b/lib/kokkos/core/src/impl/Kokkos_ViewTileLeft.hpp
index 0fc3e22b9e..61d2e35702 100644
--- a/lib/kokkos/core/src/impl/Kokkos_ViewTileLeft.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_ViewTileLeft.hpp
@@ -46,164 +46,11 @@
 
 #include <impl/KokkosExp_ViewTile.hpp>
 
-#if KOKKOS_USING_EXP_VIEW
-
 namespace Kokkos {
 
 using Kokkos::Experimental::tile_subview ;
 
 }
 
-#else
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-namespace Kokkos {
-namespace Impl {
-
-template< class T , unsigned N0 , unsigned N1 , class MemorySpace , class MemoryTraits >
-struct ViewSpecialize< T , void , LayoutTileLeft<N0,N1> , MemorySpace , MemoryTraits >
-{
-  typedef ViewDefault type ;
-};
-
-struct ViewTile {};
-
-template< class ShapeType , unsigned N0 , unsigned N1 >
-struct ViewOffset< ShapeType
-                 , LayoutTileLeft<N0,N1,true> /* Only accept properly shaped tiles */
-                 , typename Impl::enable_if<( 2 == ShapeType::rank
-                                              &&
-                                              2 == ShapeType::rank_dynamic
-                                            )>::type >
-  : public ShapeType
-{
-  enum { SHIFT_0 = Impl::integral_power_of_two(N0) };
-  enum { SHIFT_1 = Impl::integral_power_of_two(N1) };
-  enum { MASK_0  = N0 - 1 };
-  enum { MASK_1  = N1 - 1 };
-
-  typedef size_t                      size_type ;
-  typedef ShapeType                   shape_type ;
-  typedef LayoutTileLeft<N0,N1,true>  array_layout ;
-
-  enum { has_padding = true };
-
-  size_type tile_N0 ;
-
-  KOKKOS_INLINE_FUNCTION
-  void assign( const ViewOffset & rhs )
-    {
-      shape_type::N0 = rhs.N0 ;
-      shape_type::N1 = rhs.N1 ;
-      tile_N0 = ( rhs.N0 + MASK_0 ) >> SHIFT_0 ; // number of tiles in first dimension
-    }
-
-  KOKKOS_INLINE_FUNCTION
-  void assign( size_t n0 , size_t n1
-             , int = 0 , int = 0
-             , int = 0 , int = 0
-             , int = 0 , int = 0
-             , int = 0
-             )
-    {
-      shape_type::N0 = n0 ;
-      shape_type::N1 = n1 ;
-      tile_N0 = ( n0 + MASK_0 ) >> SHIFT_0 ; // number of tiles in first dimension
-    }
-
-
-  KOKKOS_INLINE_FUNCTION
-  void set_padding() {}
-
-
-  template< typename I0 , typename I1 >
-  KOKKOS_INLINE_FUNCTION
-  size_type operator()( I0 const & i0 , I1 const & i1
-                      , int = 0 , int = 0
-                      , int = 0 , int = 0
-                      , int = 0 , int = 0
-                      ) const
-    {
-      return /* ( ( Tile offset                             ) *  ( Tile size       ) ) */
-                ( ( (i0>>SHIFT_0) + tile_N0 * (i1>>SHIFT_1) ) << (SHIFT_0 + SHIFT_1) ) +
-             /* ( Offset within tile                       ) */
-                ( (i0 & MASK_0) + ((i1 & MASK_1)<<SHIFT_0) ) ;
-    }
-
-  template< typename I0 , typename I1 >
-  KOKKOS_INLINE_FUNCTION
-  size_type tile_begin( I0 const & i_tile0 , I1 const & i_tile1 ) const
-    {
-      return ( i_tile0 + tile_N0 * i_tile1 ) << ( SHIFT_0 + SHIFT_1 );
-    }
-
-
-  KOKKOS_INLINE_FUNCTION
-  size_type capacity() const
-    {
-      // ( TileDim0 * ( TileDim1 ) ) * TileSize
-      return ( tile_N0 * ( ( shape_type::N1 + MASK_1 ) >> SHIFT_1 ) ) << ( SHIFT_0 + SHIFT_1 );
-    }
-};
-
-template<>
-struct ViewAssignment< ViewTile , void , void >
-{
-  // Some compilers have type-matching issues on the integer values when using:
-  //   template< class T , unsigned N0 , unsigned N1 , class A2 , class A3 >
-  template< class T , unsigned dN0 , unsigned dN1
-          , class A2 , class A3
-          , unsigned sN0 , unsigned sN1 >
-  KOKKOS_INLINE_FUNCTION
-  ViewAssignment( View< T[dN0][dN1], LayoutLeft, A2, A3, Impl::ViewDefault > & dst
-                , View< T** , LayoutTileLeft<sN0,sN1,true>, A2, A3, Impl::ViewDefault > const & src
-                , size_t const i_tile0
-                , typename Impl::enable_if< unsigned(dN0) == unsigned(sN0) &&
-                                            unsigned(dN1) == unsigned(sN1)
-                                          , size_t const
-                                          >::type i_tile1
-                )
-   {
-     // Destination is always contiguous but source may be non-contiguous
-     // so don't assign the whole view management object.
-     // Just query and appropriately set the reference-count state.
-
-     if ( ! src.m_management.is_managed() ) dst.m_management.set_unmanaged();
-
-     dst.m_ptr_on_device = src.m_ptr_on_device + src.m_offset_map.tile_begin(i_tile0,i_tile1);
-
-     dst.m_tracker = src.m_tracker;
-   }
-};
-
-} /* namespace Impl */
-} /* namespace Kokkos */
-
-namespace Kokkos {
-
-template< class T , unsigned N0, unsigned N1, class A2, class A3 >
-KOKKOS_INLINE_FUNCTION
-View< T[N0][N1], LayoutLeft, A2, A3, Impl::ViewDefault >
-tile_subview( const View<T**,LayoutTileLeft<N0,N1,true>,A2,A3,Impl::ViewDefault> & src
-            , const size_t i_tile0
-            , const size_t i_tile1
-            )
-{
-  View< T[N0][N1], LayoutLeft, A2, A3, Impl::ViewDefault > dst ;
-
-  (void) Impl::ViewAssignment< Impl::ViewTile , void , void >( dst , src , i_tile0 , i_tile1 );
-
-  return dst ;
-}
-
-} /* namespace Kokkos */
-
-//----------------------------------------------------------------------------
-//----------------------------------------------------------------------------
-
-#endif
-
 #endif /* #ifndef KOKKOS_VIEWTILELEFT_HPP */
 
diff --git a/lib/kokkos/core/unit_test/CMakeLists.txt b/lib/kokkos/core/unit_test/CMakeLists.txt
index e835245e25..5bb2b672e1 100644
--- a/lib/kokkos/core/unit_test/CMakeLists.txt
+++ b/lib/kokkos/core/unit_test/CMakeLists.txt
@@ -44,7 +44,7 @@ ENDIF()
 IF(Kokkos_ENABLE_OpenMP)
   TRIBITS_ADD_EXECUTABLE_AND_TEST(
     UnitTest_OpenMP
-    SOURCES UnitTestMain.cpp TestOpenMP.cpp
+    SOURCES UnitTestMain.cpp TestOpenMP.cpp TestOpenMP_a.cpp TestOpenMP_b.cpp TestOpenMP_c.cpp
     COMM serial mpi
     NUM_MPI_PROCS 1
     FAIL_REGULAR_EXPRESSION "  FAILED  "
@@ -66,7 +66,7 @@ ENDIF()
 IF(Kokkos_ENABLE_Cuda)
   TRIBITS_ADD_EXECUTABLE_AND_TEST(
     UnitTest_Cuda
-    SOURCES UnitTestMain.cpp TestCuda.cpp
+    SOURCES UnitTestMain.cpp TestCuda.cpp TestCuda_a.cpp TestCuda_b.cpp TestCuda_c.cpp
     COMM serial mpi
     NUM_MPI_PROCS 1
     FAIL_REGULAR_EXPRESSION "  FAILED  "
@@ -76,27 +76,30 @@ ENDIF()
 
 TRIBITS_ADD_EXECUTABLE_AND_TEST(
   UnitTest_Default
-  SOURCES UnitTestMain.cpp TestDefaultDeviceType.cpp TestDefaultDeviceTypeInit.cpp
+  SOURCES UnitTestMain.cpp TestDefaultDeviceType.cpp TestDefaultDeviceType_a.cpp
   COMM serial mpi
   NUM_MPI_PROCS 1
   FAIL_REGULAR_EXPRESSION "  FAILED  "
     TESTONLYLIBS kokkos_gtest
 )
 
+foreach(INITTESTS_NUM RANGE 1 16)
 TRIBITS_ADD_EXECUTABLE_AND_TEST(
-  UnitTest_HWLOC
-  SOURCES UnitTestMain.cpp  TestHWLOC.cpp
+  UnitTest_DefaultInit_${INITTESTS_NUM}
+  SOURCES UnitTestMain.cpp TestDefaultDeviceTypeInit_${INITTESTS_NUM}.cpp
   COMM serial mpi
   NUM_MPI_PROCS 1
   FAIL_REGULAR_EXPRESSION "  FAILED  "
     TESTONLYLIBS kokkos_gtest
 )
+endforeach(INITTESTS_NUM)
 
 TRIBITS_ADD_EXECUTABLE_AND_TEST(
-  UnitTest_AllocationTracker
-  SOURCES UnitTestMain.cpp  TestAllocationTracker.cpp
+  UnitTest_HWLOC
+  SOURCES UnitTestMain.cpp  TestHWLOC.cpp
   COMM serial mpi
   NUM_MPI_PROCS 1
   FAIL_REGULAR_EXPRESSION "  FAILED  "
-  TESTONLYLIBS kokkos_gtest
+    TESTONLYLIBS kokkos_gtest
 )
+
diff --git a/lib/kokkos/core/unit_test/Makefile b/lib/kokkos/core/unit_test/Makefile
index 6e0f56a62c..3d9d212c1e 100644
--- a/lib/kokkos/core/unit_test/Makefile
+++ b/lib/kokkos/core/unit_test/Makefile
@@ -61,17 +61,16 @@ OBJ_HWLOC = TestHWLOC.o UnitTestMain.o gtest-all.o
 TARGETS += KokkosCore_UnitTest_HWLOC
 TEST_TARGETS += test-hwloc
 
-OBJ_ALLOCATIONTRACKER = TestAllocationTracker.o UnitTestMain.o gtest-all.o
-TARGETS += KokkosCore_UnitTest_AllocationTracker
-TEST_TARGETS += test-allocationtracker
-
-OBJ_DEFAULT = TestDefaultDeviceType.o UnitTestMain.o gtest-all.o
+OBJ_DEFAULT = TestDefaultDeviceType.o TestDefaultDeviceType_a.o UnitTestMain.o gtest-all.o
 TARGETS += KokkosCore_UnitTest_Default
 TEST_TARGETS += test-default
 
-OBJ_DEFAULTINIT = TestDefaultDeviceTypeInit.o UnitTestMain.o gtest-all.o
-TARGETS += KokkosCore_UnitTest_DefaultInit
-TEST_TARGETS += test-default-init
+NUM_INITTESTS = 16
+INITTESTS_NUMBERS := $(shell seq 1 ${NUM_INITTESTS})
+INITTESTS_TARGETS := $(addprefix KokkosCore_UnitTest_DefaultDeviceTypeInit_,${INITTESTS_NUMBERS})
+TARGETS += ${INITTESTS_TARGETS}
+INITTESTS_TEST_TARGETS := $(addprefix test-default-init-,${INITTESTS_NUMBERS})
+TEST_TARGETS += ${INITTESTS_TEST_TARGETS}
 
 OBJ_SYNCHRONIC = TestSynchronic.o UnitTestMain.o gtest-all.o
 TARGETS += KokkosCore_UnitTest_Synchronic
@@ -101,8 +100,8 @@ KokkosCore_UnitTest_AllocationTracker: $(OBJ_ALLOCATIONTRACKER) $(KOKKOS_LINK_DE
 KokkosCore_UnitTest_Default: $(OBJ_DEFAULT) $(KOKKOS_LINK_DEPENDS)
 	$(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_DEFAULT) $(KOKKOS_LIBS) $(LIB) -o KokkosCore_UnitTest_Default
 
-KokkosCore_UnitTest_DefaultInit: $(OBJ_DEFAULTINIT) $(KOKKOS_LINK_DEPENDS)
-	$(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_DEFAULTINIT) $(KOKKOS_LIBS) $(LIB) -o KokkosCore_UnitTest_DefaultInit
+${INITTESTS_TARGETS}: KokkosCore_UnitTest_DefaultDeviceTypeInit_%: TestDefaultDeviceTypeInit_%.o UnitTestMain.o gtest-all.o $(KOKKOS_LINK_DEPENDS)
+	$(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) TestDefaultDeviceTypeInit_$*.o UnitTestMain.o gtest-all.o $(KOKKOS_LIBS) $(LIB) -o KokkosCore_UnitTest_DefaultDeviceTypeInit_$*
 
 KokkosCore_UnitTest_Synchronic: $(OBJ_SYNCHRONIC) $(KOKKOS_LINK_DEPENDS)
 	$(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_SYNCHRONIC) $(KOKKOS_LIBS) $(LIB) -o KokkosCore_UnitTest_Synchronic
@@ -131,8 +130,8 @@ test-allocationtracker: KokkosCore_UnitTest_AllocationTracker
 test-default: KokkosCore_UnitTest_Default
 	./KokkosCore_UnitTest_Default
 
-test-default-init: KokkosCore_UnitTest_DefaultInit
-	./KokkosCore_UnitTest_DefaultInit
+${INITTESTS_TEST_TARGETS}: test-default-init-%: KokkosCore_UnitTest_DefaultDeviceTypeInit_%
+	./KokkosCore_UnitTest_DefaultDeviceTypeInit_$*
 
 test-synchronic: KokkosCore_UnitTest_Synchronic
 	./KokkosCore_UnitTest_Synchronic
diff --git a/lib/kokkos/core/unit_test/TestAggregate.hpp b/lib/kokkos/core/unit_test/TestAggregate.hpp
index 1fbb4bf4b1..5388a60787 100644
--- a/lib/kokkos/core/unit_test/TestAggregate.hpp
+++ b/lib/kokkos/core/unit_test/TestAggregate.hpp
@@ -52,665 +52,6 @@
 
 /*--------------------------------------------------------------------------*/
 
-#if ! KOKKOS_USING_EXP_VIEW
-
-namespace Test {
-
-struct EmbedArray {};
-
-struct ArrayProxyContiguous {};
-struct ArrayProxyStrided {};
-
-template< typename T , unsigned N = 0 , class Proxy = void >
-struct Array ;
-
-template< typename T >
-struct Array<T,0,ArrayProxyContiguous>
-{
-public:
-  typedef T value_type ;
-
-  enum { StaticLength = 0 };
-  T * const value ;
-  const unsigned count ;
-
-  KOKKOS_INLINE_FUNCTION
-  Array( T * v , unsigned n ) : value(v), count(n) {}
-
-  template< class Proxy >
-  KOKKOS_INLINE_FUNCTION
-  Array & operator = ( const Array<T,0,Proxy> & rhs ) { return *this ; }
-};
-
-template< typename T , unsigned N >
-struct Array<T,N,ArrayProxyContiguous>
-{
-public:
-  typedef T value_type ;
-
-  enum { StaticLength = N };
-  T * const value ;
-
-  KOKKOS_INLINE_FUNCTION
-  Array( T * v , unsigned ) : value(v) {}
-
-  template< class Proxy >
-  KOKKOS_INLINE_FUNCTION
-  Array & operator = ( const Array<T,N,Proxy> & rhs ) { return *this ; }
-};
-
-template< typename T , unsigned N >
-struct Array<T,N,ArrayProxyStrided>
-{
-public:
-  typedef T value_type ;
-
-  enum { StaticLength = N };
-  T * const value ;
-  const unsigned stride ;
-
-  KOKKOS_INLINE_FUNCTION
-  Array( T * v , unsigned , unsigned s ) : value(v), stride(s) {}
-
-  template< class Proxy >
-  KOKKOS_INLINE_FUNCTION
-  Array & operator = ( const Array<T,N,Proxy> & rhs ) { return *this ; }
-};
-
-template< typename T >
-struct Array<T,0,ArrayProxyStrided>
-{
-public:
-  typedef T value_type ;
-
-  enum { StaticLength = 0 };
-  T * const value ;
-  const unsigned count ;
-  const unsigned stride ;
-
-  KOKKOS_INLINE_FUNCTION
-  Array( T * v , unsigned n , unsigned s ) : value(v), count(n), stride(s) {}
-
-  template< class Proxy >
-  KOKKOS_INLINE_FUNCTION
-  Array & operator = ( const Array<T,0,Proxy> & rhs ) { return *this ; }
-};
-
-template< typename T >
-struct Array<T,0,void>
-{
-public:
-  typedef T value_type ;
-
-  enum { StaticLength = 0 };
-  T * value ;
-  const unsigned count ;
-
-  KOKKOS_INLINE_FUNCTION
-  Array() : value(0) , count(0) {}
-
-  template< unsigned N , class Proxy >
-  KOKKOS_INLINE_FUNCTION
-  Array( const Array<T,N,Proxy> & rhs ) : value(rhs.value), count(N) {}
-};
-
-template< typename T , unsigned N >
-struct Array<T,N,void>
-{
-public:
-  typedef T value_type ;
-
-  enum { StaticLength = N };
-  T value[N] ;
-
-  template< class Proxy >
-  KOKKOS_INLINE_FUNCTION
-  Array & operator = ( const Array<T,N,Proxy> & ) { return *this ; }
-};
-
-} // namespace Test
-
-/*--------------------------------------------------------------------------*/
-/*--------------------------------------------------------------------------*/
-
-namespace Kokkos {
-namespace Impl {
-
-template< typename T , unsigned N >
-struct AnalyzeShape< Test::Array< T , N > >
-  : public ShapeInsert< typename AnalyzeShape< T >::shape , N >::type
-{
-private:
-  typedef AnalyzeShape< T > nested ;
-public:
-
-  typedef Test::EmbedArray specialize ;
-
-  typedef typename ShapeInsert< typename nested::shape , N >::type shape ;
-
-  typedef typename nested::array_intrinsic_type   array_intrinsic_type[ N ];
-  typedef Test::Array< T , N >          value_type ;
-  typedef Test::Array< T , N >          type ;
-
-  typedef const array_intrinsic_type  const_array_intrinsic_type ;
-  typedef const value_type  const_value_type ;
-  typedef const type        const_type ;
-
-  typedef typename nested::non_const_array_intrinsic_type          non_const_array_intrinsic_type[ N ];
-  typedef Test::Array< typename nested::non_const_value_type , N > non_const_value_type ;
-  typedef Test::Array< typename nested::non_const_value_type , N > non_const_type ;
-};
-
-template< typename T >
-struct AnalyzeShape< Test::Array< T , 0 > >
-  : public ShapeInsert< typename AnalyzeShape< T >::shape , 0 >::type
-{
-private:
-  typedef AnalyzeShape< T > nested ;
-public:
-
-  typedef Test::EmbedArray specialize ;
-
-  typedef typename ShapeInsert< typename nested::shape , 0 >::type shape ;
-
-  typedef typename nested::array_intrinsic_type * array_intrinsic_type ;
-  typedef Test::Array< T , 0 >          value_type ;
-  typedef Test::Array< T , 0 >          type ;
-
-  typedef const array_intrinsic_type  const_array_intrinsic_type ;
-  typedef const value_type  const_value_type ;
-  typedef const type        const_type ;
-
-  typedef typename nested::non_const_array_intrinsic_type  * non_const_array_intrinsic_type ;
-  typedef Test::Array< typename nested::non_const_value_type , 0 > non_const_value_type ;
-  typedef Test::Array< typename nested::non_const_value_type , 0 > non_const_type ;
-};
-
-/*--------------------------------------------------------------------------*/
-
-template< class ValueType , class MemorySpace , class MemoryTraits >
-struct ViewSpecialize< ValueType
-                     , Test::EmbedArray
-                     , LayoutLeft
-                     , MemorySpace
-                     , MemoryTraits >
-{ typedef Test::EmbedArray type ; };
-
-template< class ValueType , class MemorySpace , class MemoryTraits >
-struct ViewSpecialize< ValueType
-                     , Test::EmbedArray
-                     , LayoutRight
-                     , MemorySpace
-                     , MemoryTraits >
-{ typedef Test::EmbedArray type ; };
-
-/*--------------------------------------------------------------------------*/
-
-template<>
-struct ViewAssignment< Test::EmbedArray , Test::EmbedArray , void >
-{
-  //------------------------------------
-  /** \brief  Compatible value and shape */
-
-  template< class DT , class DL , class DD , class DM ,
-            class ST , class SL , class SD , class SM >
-  KOKKOS_INLINE_FUNCTION
-  ViewAssignment(       View<DT,DL,DD,DM,Test::EmbedArray> & dst
-                , const View<ST,SL,SD,SM,Test::EmbedArray> & src
-                , const typename enable_if<(
-                    ViewAssignable< ViewTraits<DT,DL,DD,DM> ,
-                                    ViewTraits<ST,SL,SD,SM> >::value
-                    )>::type * = 0
-                  )
-  {
-    dst.m_offset_map.assign( src.m_offset_map );
-
-    dst.m_ptr_on_device = src.m_ptr_on_device ;
-
-    dst.m_tracker = src.m_tracker;
-  }
-};
-
-template<>
-struct ViewAssignment< ViewDefault , Test::EmbedArray , void >
-{
-  //------------------------------------
-  /** \brief  Compatible value and shape */
-
-  template< class ST , class SL , class SD , class SM >
-  KOKKOS_INLINE_FUNCTION
-  ViewAssignment( typename View<ST,SL,SD,SM,Test::EmbedArray>::array_type & dst
-                , const View<ST,SL,SD,SM,Test::EmbedArray> & src
-                )
-  {
-    dst.m_offset_map.assign( src.m_offset_map );
-
-    dst.m_ptr_on_device = src.m_ptr_on_device ;
-
-    dst.m_tracker = src.m_tracker;
-  }
-};
-
-
-} // namespace Impl
-} // namespace Kokkos
-
-/*--------------------------------------------------------------------------*/
-/*--------------------------------------------------------------------------*/
-
-namespace Kokkos {
-
-template< class DataType ,
-          class Arg1Type ,
-          class Arg2Type ,
-          class Arg3Type >
-class View< DataType , Arg1Type , Arg2Type , Arg3Type , Test::EmbedArray >
-  : public ViewTraits< DataType , Arg1Type , Arg2Type, Arg3Type >
-{
-public:
-
-  typedef ViewTraits< DataType , Arg1Type , Arg2Type, Arg3Type > traits ;
-
-private:
-
-  // Assignment of compatible views requirement:
-  template< class , class , class , class , class > friend class View ;
-
-  // Assignment of compatible subview requirement:
-  template< class , class , class > friend struct Impl::ViewAssignment ;
-
-  typedef Impl::ViewOffset< typename traits::shape_type ,
-                            typename traits::array_layout > offset_map_type ;
-
-  typedef Impl::ViewDataManagement< traits > view_data_management ;
-
-  // traits::value_type = Test::Array< T , N >
-
-  typename traits::value_type::value_type * m_ptr_on_device ;
-  offset_map_type                           m_offset_map ;
-  view_data_management                      m_management ;
-  Impl::AllocationTracker                   m_tracker ;
-
-public:
-
-  typedef View< typename traits::array_intrinsic_type ,
-                typename traits::array_layout ,
-                typename traits::execution_space ,
-                typename traits::memory_traits > array_type ;
-
-  typedef View< typename traits::non_const_data_type ,
-                typename traits::array_layout ,
-                typename traits::execution_space ,
-                typename traits::memory_traits > non_const_type ;
-
-  typedef View< typename traits::const_data_type ,
-                typename traits::array_layout ,
-                typename traits::execution_space ,
-                typename traits::memory_traits > const_type ;
-
-  typedef View< typename traits::non_const_data_type ,
-                typename traits::array_layout ,
-                typename traits::host_mirror_space ,
-                void > HostMirror ;
-
-  //------------------------------------
-  // Shape
-
-  enum { Rank = traits::rank - 1 };
-
-  KOKKOS_INLINE_FUNCTION typename traits::shape_type shape() const { return m_offset_map ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_0() const { return m_offset_map.N0 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_1() const { return m_offset_map.N1 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_2() const { return m_offset_map.N2 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_3() const { return m_offset_map.N3 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_4() const { return m_offset_map.N4 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_5() const { return m_offset_map.N5 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_6() const { return m_offset_map.N6 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type dimension_7() const { return m_offset_map.N7 ; }
-  KOKKOS_INLINE_FUNCTION typename traits::size_type size() const
-  {
-    return   m_offset_map.N0
-           * m_offset_map.N1
-           * m_offset_map.N2
-           * m_offset_map.N3
-           * m_offset_map.N4
-           * m_offset_map.N5
-           * m_offset_map.N6
-           * m_offset_map.N7
-           ;
-  }
-
-  template< typename iType >
-  KOKKOS_INLINE_FUNCTION
-  typename traits::size_type dimension( const iType & i ) const
-    { return Impl::dimension( m_offset_map , i ); }
-
-  //------------------------------------
-  // Destructor, constructors, assignment operators:
-
-  KOKKOS_INLINE_FUNCTION
-  ~View() {}
-
-  KOKKOS_INLINE_FUNCTION
-  View()
-    : m_ptr_on_device(0)
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-  { m_offset_map.assing(0,0,0,0,0,0,0,0); }
-
-  KOKKOS_INLINE_FUNCTION
-  View( const View & rhs )
-    : m_ptr_on_device(0)
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-  {
-    (void) Impl::ViewAssignment<
-      typename traits::specialize ,
-      typename traits::specialize >( *this , rhs );
-  }
-
-  KOKKOS_INLINE_FUNCTION
-  View & operator = ( const View & rhs )
-    {
-      (void) Impl::ViewAssignment<
-        typename traits::specialize ,
-        typename traits::specialize >( *this , rhs );
-      return *this ;
-    }
-
-  //------------------------------------
-  // Construct or assign compatible view:
-
-  template< class RT , class RL , class RD , class RM , class RS >
-  KOKKOS_INLINE_FUNCTION
-  View( const View<RT,RL,RD,RM,RS> & rhs )
-    : m_ptr_on_device(0)
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-  {
-    (void) Impl::ViewAssignment<
-      typename traits::specialize , RS >( *this , rhs );
-  }
-
-  template< class RT , class RL , class RD , class RM , class RS >
-  KOKKOS_INLINE_FUNCTION
-  View & operator = ( const View<RT,RL,RD,RM,RS> & rhs )
-    {
-      (void) Impl::ViewAssignment<
-        typename traits::specialize , RS >( *this , rhs );
-      return *this ;
-    }
-
-  //------------------------------------
-  // Allocation of a managed view with possible alignment padding.
-
-  template< class AllocationProperties >
-  explicit inline
-  View( const AllocationProperties & prop ,
-        const typename Impl::ViewAllocProp< traits , AllocationProperties >::size_type n0 = 0 ,
-        const size_t n1 = 0 ,
-        const size_t n2 = 0 ,
-        const size_t n3 = 0 ,
-        const size_t n4 = 0 ,
-        const size_t n5 = 0 ,
-        const size_t n6 = 0 ,
-        const size_t n7 = 0 )
-    : m_ptr_on_device(0)
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-  {
-    typedef Impl::ViewAllocProp< traits , AllocationProperties > Alloc ;
-
-    typedef typename traits::memory_space  memory_space ;
-    typedef typename traits::value_type::value_type   scalar_type ;
-
-    m_offset_map.assign( n0, n1, n2, n3, n4, n5, n6, n7 );
-    m_offset_map.set_padding();
-
-    m_tracker = memory_space::allocate_and_track( Alloc::label( prop ), sizeof(scalar_type) * m_offset_map.capacity() );
-
-    m_ptr_on_device = reinterpret_cast<scalar_type *>(m_tracker.alloc_ptr());
-
-    (void) Impl::ViewDefaultConstruct< typename traits::execution_space , scalar_type , Alloc::Initialize >( m_ptr_on_device , m_offset_map.capacity() );
-  }
-
-  //------------------------------------
-  // Assign an unmanaged View from pointer, can be called in functors.
-  // No alignment padding is performed.
-
-  typedef Impl::if_c< ! traits::is_managed ,
-                      typename traits::value_type::value_type * ,
-                      Impl::ViewError::user_pointer_constructor_requires_unmanaged >
-    if_user_pointer_constructor ;
-
-  View( typename if_user_pointer_constructor::type ptr ,
-        const size_t n0 = 0 ,
-        const size_t n1 = 0 ,
-        const size_t n2 = 0 ,
-        const size_t n3 = 0 ,
-        const size_t n4 = 0 ,
-        const size_t n5 = 0 ,
-        const size_t n6 = 0 ,
-        const size_t n7 = 0 )
-    : m_ptr_on_device(0)
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-  {
-    m_offset_map.assign( n0, n1, n2, n3, n4, n5, n6, n7 );
-    m_ptr_on_device = if_user_pointer_constructor::select( ptr );
-    m_management.set_unmanaged();
-  }
-
-  //------------------------------------
-  // Assign unmanaged View to portion of Device shared memory
-
-  typedef Impl::if_c< ! traits::is_managed ,
-                      typename traits::execution_space ,
-                      Impl::ViewError::device_shmem_constructor_requires_unmanaged >
-      if_device_shmem_constructor ;
-
-  explicit KOKKOS_INLINE_FUNCTION
-  View( typename if_device_shmem_constructor::type & dev ,
-        const unsigned n0 = 0 ,
-        const unsigned n1 = 0 ,
-        const unsigned n2 = 0 ,
-        const unsigned n3 = 0 ,
-        const unsigned n4 = 0 ,
-        const unsigned n5 = 0 ,
-        const unsigned n6 = 0 ,
-        const unsigned n7 = 0 )
-    : m_ptr_on_device(0)
-    , m_offset_map()
-    , m_management()
-    , m_tracker()
-  {
-    typedef typename traits::value_type::value_type   scalar_type ;
-
-    enum { align = 8 };
-    enum { mask  = align - 1 };
-
-    typedef Impl::if_c< ! traits::is_managed ,
-                        scalar_type * ,
-                        Impl::ViewError::device_shmem_constructor_requires_unmanaged >
-      if_device_shmem_pointer ;
-
-    m_offset_map.assign( n0, n1, n2, n3, n4, n5, n6, n7 );
-
-    // Select the first argument:
-    m_ptr_on_device = if_device_shmem_pointer::select(
-     (scalar_type *) dev.get_shmem( unsigned( sizeof(scalar_type) * m_offset_map.capacity() + unsigned(mask) ) & ~unsigned(mask) ) );
-  }
-
-  static inline
-  unsigned shmem_size( const unsigned n0 = 0 ,
-                       const unsigned n1 = 0 ,
-                       const unsigned n2 = 0 ,
-                       const unsigned n3 = 0 ,
-                       const unsigned n4 = 0 ,
-                       const unsigned n5 = 0 ,
-                       const unsigned n6 = 0 ,
-                       const unsigned n7 = 0 )
-  {
-    enum { align = 8 };
-    enum { mask  = align - 1 };
-
-    typedef typename traits::value_type::value_type   scalar_type ;
-
-    offset_map_type offset_map ;
-
-    offset_map.assign( n0, n1, n2, n3, n4, n5, n6, n7 );
-
-    return unsigned( sizeof(scalar_type) * offset_map.capacity() + unsigned(mask) ) & ~unsigned(mask) ;
-  }
-
-  //------------------------------------
-  // Is not allocated
-
-  KOKKOS_INLINE_FUNCTION
-  bool is_null() const { return 0 == m_ptr_on_device ; }
-
-  //------------------------------------
-  // LayoutLeft, rank 2:
-
-  typedef Test::Array< typename traits::value_type::value_type ,
-                       traits::value_type::StaticLength ,
-                       Test::ArrayProxyStrided > LeftValue ;
-
-  template< typename iType0 >
-  KOKKOS_INLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< LeftValue , traits, LayoutLeft, 2, iType0 >::type
-    operator[] ( const iType0 & i0 ) const
-    {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_2( m_offset_map, i0, 0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , m_ptr_on_device );
-
-      return LeftValue( m_ptr_on_device + i0 , m_offset_map.N1 , m_offset_map.S0 );
-    }
-
-  template< typename iType0 >
-  KOKKOS_INLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< LeftValue , traits, LayoutLeft, 2, iType0 >::type
-    operator() ( const iType0 & i0 ) const
-    {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_2( m_offset_map, i0, 0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , m_ptr_on_device );
-
-      return LeftValue( m_ptr_on_device + i0 , m_offset_map.N1 , m_offset_map.S0 );
-    }
-
-  template< typename iType0 >
-  KOKKOS_INLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< LeftValue , traits, LayoutLeft, 2, iType0 >::type
-    at( const iType0 & i0 , const int , const int , const int ,
-        const int , const int , const int , const int ) const
-    {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_2( m_offset_map, i0, 0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , m_ptr_on_device );
-
-      return LeftValue( m_ptr_on_device + i0 , m_offset_map.N1 , m_offset_map.S0 );
-    }
-
-  //------------------------------------
-  // LayoutRight, rank 2:
-
-  typedef Test::Array< typename traits::value_type::value_type ,
-                       traits::value_type::StaticLength ,
-                       Test::ArrayProxyContiguous > RightValue ;
-
-  template< typename iType0 >
-  KOKKOS_INLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< RightValue , traits, LayoutRight, 2, iType0 >::type
-    operator[] ( const iType0 & i0 ) const
-    {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_2( m_offset_map, i0, 0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , m_ptr_on_device );
-
-      return RightValue( m_ptr_on_device + i0 , m_offset_map.N1 );
-    }
-
-  template< typename iType0 >
-  KOKKOS_INLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< RightValue , traits, LayoutRight, 2, iType0 >::type
-    operator() ( const iType0 & i0 ) const
-    {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_2( m_offset_map, i0, 0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , m_ptr_on_device );
-
-      return RightValue( m_ptr_on_device + i0 , m_offset_map.N1 );
-    }
-
-  template< typename iType0 >
-  KOKKOS_INLINE_FUNCTION
-  typename Impl::ViewEnableArrayOper< RightValue , traits, LayoutRight, 2, iType0 >::type
-    at( const iType0 & i0 , const int , const int , const int ,
-        const int , const int , const int , const int ) const
-    {
-      KOKKOS_ASSERT_SHAPE_BOUNDS_2( m_offset_map, i0, 0 );
-      KOKKOS_RESTRICT_EXECUTION_TO_DATA( typename traits::memory_space , m_ptr_on_device );
-
-      return RightValue( m_ptr_on_device + i0 , m_offset_map.N1 );
-    }
-
-  //------------------------------------
-  // Access to the underlying contiguous storage of this view specialization.
-  // These methods are specific to specialization of a view.
-
-  KOKKOS_INLINE_FUNCTION
-  typename traits::value_type::value_type * ptr_on_device() const { return m_ptr_on_device ; }
-
-  // Stride of physical storage, dimensioned to at least Rank
-  template< typename iType >
-  KOKKOS_INLINE_FUNCTION
-  void stride( iType * const s ) const
-    { m_offset_map.stride( s ); }
-
-  // Count of contiguously allocated data members including padding.
-  KOKKOS_INLINE_FUNCTION
-  typename traits::size_type capacity() const
-    { return m_offset_map.capacity(); }
-};
-
-} // namespace Kokkos
-
-/*--------------------------------------------------------------------------*/
-/*--------------------------------------------------------------------------*/
-
-namespace Test {
-
-template< class DeviceType >
-int TestViewAggregate()
-{
-  typedef Kokkos::View< Test::Array<double,32> * , DeviceType > a32_type ;
-  typedef typename a32_type::array_type a32_base_type ;
-
-  typedef Kokkos::View< Test::Array<double> * , DeviceType > a0_type ;
-  typedef typename a0_type::array_type a0_base_type ;
-
-  a32_type      a32("a32",100);
-  a32_base_type a32_base ;
-
-  a0_type       a0("a0",100,32);
-  a0_base_type  a0_base ;
-
-  a32_base = a32 ;
-  a0_base = a0 ;
-
-
-  return 0 ;
-}
-
-}
-
-/*--------------------------------------------------------------------------*/
-/*--------------------------------------------------------------------------*/
-
-#else /* #if ! KOKKOS_USING_EXP_VIEW */
-
 #include <impl/KokkosExp_ViewArray.hpp>
 
 namespace Test {
@@ -762,8 +103,6 @@ void TestViewAggregate()
 
 }
 
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
 /*--------------------------------------------------------------------------*/
 /*--------------------------------------------------------------------------*/
 
diff --git a/lib/kokkos/core/unit_test/TestAggregateReduction.hpp b/lib/kokkos/core/unit_test/TestAggregateReduction.hpp
index b0b3747087..bd05cd347b 100644
--- a/lib/kokkos/core/unit_test/TestAggregateReduction.hpp
+++ b/lib/kokkos/core/unit_test/TestAggregateReduction.hpp
@@ -57,12 +57,10 @@ struct StaticArray {
   T value[N] ;
 
   KOKKOS_INLINE_FUNCTION
-  StaticArray()
-    { for ( unsigned i = 0 ; i < N ; ++i ) value[i] = T(); }
+  StaticArray() = default;
 
   KOKKOS_INLINE_FUNCTION
-  StaticArray( const StaticArray & rhs )
-    { for ( unsigned i = 0 ; i < N ; ++i ) value[i] = rhs.value[i]; }
+  StaticArray( const StaticArray & rhs ) = default;
 
   KOKKOS_INLINE_FUNCTION
   operator T () { return value[0]; }
@@ -75,11 +73,7 @@ struct StaticArray {
     }
 
   KOKKOS_INLINE_FUNCTION
-  StaticArray & operator = ( const StaticArray & rhs )
-    {
-      for ( unsigned i = 0 ; i < N ; ++i ) value[i] = rhs.value[i] ;
-      return *this ;
-    }
+  StaticArray & operator = ( const StaticArray & rhs ) = default;
 
   KOKKOS_INLINE_FUNCTION
   StaticArray operator * ( const StaticArray & rhs )
@@ -111,6 +105,8 @@ struct StaticArray {
     }
 };
 
+static_assert(std::is_trivial<StaticArray<int, 4>>::value, "Not trivial");
+
 template< typename T , class Space >
 struct DOT {
   typedef T      value_type ;
diff --git a/lib/kokkos/core/unit_test/TestAllocationTracker.cpp b/lib/kokkos/core/unit_test/TestAllocationTracker.cpp
deleted file mode 100644
index b3a7fe9803..0000000000
--- a/lib/kokkos/core/unit_test/TestAllocationTracker.cpp
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
-//@HEADER
-// ************************************************************************
-// 
-//                        Kokkos v. 2.0
-//              Copyright (2014) Sandia Corporation
-// 
-// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
-// the U.S. Government retains certain rights in this software.
-// 
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted provided that the following conditions are
-// met:
-//
-// 1. Redistributions of source code must retain the above copyright
-// notice, this list of conditions and the following disclaimer.
-//
-// 2. Redistributions in binary form must reproduce the above copyright
-// notice, this list of conditions and the following disclaimer in the
-// documentation and/or other materials provided with the distribution.
-//
-// 3. Neither the name of the Corporation nor the names of the
-// contributors may be used to endorse or promote products derived from
-// this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
-// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
-// ************************************************************************
-//@HEADER
-*/
-
-#include <gtest/gtest.h>
-
-#include <iostream>
-#include <vector>
-
-#include <Kokkos_Core.hpp>
-
-#include <impl/Kokkos_AllocationTracker.hpp>
-#include <impl/Kokkos_BasicAllocators.hpp>
-
-namespace Test {
-
-class alocation_tracker : public ::testing::Test {
-protected:
-  static void SetUpTestCase()
-  {
-    Kokkos::initialize();
-  }
-
-  static void TearDownTestCase()
-  {
-    Kokkos::finalize();
-  }
-};
-
-TEST_F( alocation_tracker, simple)
-{
-
-#if ! KOKKOS_USING_EXP_VIEW
-
-  using namespace Kokkos::Impl;
-
-  {
-    AllocationTracker tracker;
-    EXPECT_FALSE( tracker.is_valid() );
-  }
-
-  // test ref count and label
-  {
-    int size = 100;
-    std::vector<AllocationTracker> trackers(size);
-
-    trackers[0] = AllocationTracker( MallocAllocator(), 128,"Test");
-
-    for (int i=0; i<size; ++i) {
-      trackers[i] = trackers[0];
-    }
-
-    EXPECT_EQ(100u, trackers[0].ref_count());
-    EXPECT_EQ(std::string("Test"), std::string(trackers[0].label()));
-  }
-
-
-  // test circular list
-  {
-    int num_allocs = 3000;
-    unsigned ref_count = 100;
-
-    std::vector<AllocationTracker> trackers(num_allocs);
-
-    for (int i=0; i<num_allocs; ++i) {
-      trackers[i] = AllocationTracker( MallocAllocator(), 128, "Test");
-      std::vector<AllocationTracker> ref_trackers(ref_count);
-      for (unsigned j=0; j<ref_count; ++j) {
-        ref_trackers[j] = trackers[i];
-      }
-      EXPECT_EQ( ref_count + 1u, trackers[i].ref_count() );
-    }
-
-    for (int i=0; i<num_allocs; ++i) {
-      EXPECT_EQ( 1u, trackers[i].ref_count() );
-    }
-  }
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-}
-
-TEST_F( alocation_tracker, force_leaks)
-{
-// uncomment to force memory leaks
-#if 0
-  using namespace Kokkos::Impl;
-  Kokkos::kokkos_malloc("Forced Leak", 4096*10);
-  Kokkos::kokkos_malloc<Kokkos::HostSpace>("Forced Leak", 4096*10);
-#endif
-}
-
-TEST_F( alocation_tracker, disable_reference_counting)
-{
-
-#if ! KOKKOS_USING_EXP_VIEW
-
-  using namespace Kokkos::Impl;
-  // test ref count and label
-  {
-    int size = 100;
-    std::vector<AllocationTracker> trackers(size);
-
-    trackers[0] = AllocationTracker( MallocAllocator(), 128,"Test");
-
-    for (int i=1; i<size; ++i) {
-      Kokkos::Impl::AllocationTracker::disable_tracking();
-      trackers[i] = trackers[0] ;
-      Kokkos::Impl::AllocationTracker::enable_tracking();
-    }
-
-    EXPECT_EQ(1u, trackers[0].ref_count());
-    EXPECT_EQ(std::string("Test"), std::string(trackers[0].label()));
-  }
-
-#endif /* #if ! KOKKOS_USING_EXP_VIEW */
-
-}
-
-} // namespace Test
diff --git a/lib/kokkos/core/unit_test/TestAtomic.hpp b/lib/kokkos/core/unit_test/TestAtomic.hpp
index 7b3ab14c06..e948723574 100644
--- a/lib/kokkos/core/unit_test/TestAtomic.hpp
+++ b/lib/kokkos/core/unit_test/TestAtomic.hpp
@@ -84,10 +84,9 @@ struct SuperScalar {
   }
 
   KOKKOS_INLINE_FUNCTION
-  volatile SuperScalar& operator = (const SuperScalar& src) volatile  {
+  void operator = (const SuperScalar& src) volatile  {
     for(int i=0; i<N; i++)
       val[i] = src.val[i];
-    return *this;
   }
 
   KOKKOS_INLINE_FUNCTION
@@ -208,6 +207,10 @@ T AddLoopSerial(int loop) {
   return val;
 }
 
+//------------------------------------------------------
+//--------------atomic_compare_exchange-----------------
+//------------------------------------------------------
+
 template<class T,class DEVICE_TYPE>
 struct CASFunctor{
   typedef DEVICE_TYPE execution_space;
@@ -270,6 +273,10 @@ T CASLoopSerial(int loop) {
   return val;
 }
 
+//----------------------------------------------
+//--------------atomic_exchange-----------------
+//----------------------------------------------
+
 template<class T,class DEVICE_TYPE>
 struct ExchFunctor{
   typedef DEVICE_TYPE execution_space;
diff --git a/lib/kokkos/core/unit_test/TestAtomicOperations.hpp b/lib/kokkos/core/unit_test/TestAtomicOperations.hpp
new file mode 100644
index 0000000000..aee4bda06c
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestAtomicOperations.hpp
@@ -0,0 +1,841 @@
+/*
+//@HEADER
+// ************************************************************************
+//
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+//
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+//
+// ************************************************************************
+//@HEADER
+*/
+
+#include <Kokkos_Core.hpp>
+
+namespace TestAtomicOperations {
+
+//-----------------------------------------------
+//--------------zero_functor---------------------
+//-----------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct ZeroFunctor {
+  typedef DEVICE_TYPE execution_space;
+  typedef typename Kokkos::View<T,execution_space> type;
+  typedef typename Kokkos::View<T,execution_space>::HostMirror h_type;
+  type data;
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    data() = 0;
+  }
+};
+
+//-----------------------------------------------
+//--------------init_functor---------------------
+//-----------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct InitFunctor {
+  typedef DEVICE_TYPE execution_space;
+  typedef typename Kokkos::View<T,execution_space> type;
+  typedef typename Kokkos::View<T,execution_space>::HostMirror h_type;
+  type data;
+  T init_value ;
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    data() = init_value;
+  }
+
+  InitFunctor(T _init_value) : init_value(_init_value) {}
+};
+
+
+//---------------------------------------------------
+//--------------atomic_fetch_max---------------------
+//---------------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct MaxFunctor{
+  typedef DEVICE_TYPE execution_space;
+  typedef Kokkos::View<T,execution_space> type;
+  type data;
+  T i0;
+  T i1;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    //Kokkos::atomic_fetch_max(&data(),(T)1);
+    Kokkos::atomic_fetch_max(&data(),(T)i1);
+  }
+  MaxFunctor( T _i0 , T _i1 ) : i0(_i0) , i1(_i1) {}
+};
+
+template<class T, class execution_space >
+T MaxAtomic(T i0 , T i1) {
+  struct InitFunctor<T,execution_space> f_init(i0);
+  typename InitFunctor<T,execution_space>::type data("Data");
+  typename InitFunctor<T,execution_space>::h_type h_data("HData");
+  f_init.data = data;
+  Kokkos::parallel_for(1,f_init);
+  execution_space::fence();
+
+  struct MaxFunctor<T,execution_space> f(i0,i1);
+  f.data = data;
+  Kokkos::parallel_for(1,f);
+  execution_space::fence();
+
+  Kokkos::deep_copy(h_data,data);
+  T val = h_data();
+  return val;
+}
+
+template<class T>
+T MaxAtomicCheck(T i0 , T i1) {
+  T* data = new T[1];
+  data[0] = 0;
+
+  *data = (i0 > i1 ? i0 : i1) ;
+
+  T val = *data;
+  delete [] data;
+  return val;
+}
+
+template<class T,class DeviceType>
+bool MaxAtomicTest(T i0, T i1)
+{
+  T res       = MaxAtomic<T,DeviceType>(i0,i1);
+  T resSerial = MaxAtomicCheck<T>(i0,i1);
+
+  bool passed = true;
+
+  if ( resSerial != res ) {
+    passed = false;
+
+    std::cout << "Loop<"
+              << typeid(T).name()
+              << ">( test = MaxAtomicTest"
+              << " FAILED : "
+              << resSerial << " != " << res
+              << std::endl ;
+  }
+
+  return passed ;
+}
+
+//---------------------------------------------------
+//--------------atomic_fetch_min---------------------
+//---------------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct MinFunctor{
+  typedef DEVICE_TYPE execution_space;
+  typedef Kokkos::View<T,execution_space> type;
+  type data;
+  T i0;
+  T i1;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    Kokkos::atomic_fetch_min(&data(),(T)i1);
+  }
+  MinFunctor( T _i0 , T _i1 ) : i0(_i0) , i1(_i1) {}
+};
+
+template<class T, class execution_space >
+T MinAtomic(T i0 , T i1) {
+  struct InitFunctor<T,execution_space> f_init(i0);
+  typename InitFunctor<T,execution_space>::type data("Data");
+  typename InitFunctor<T,execution_space>::h_type h_data("HData");
+  f_init.data = data;
+  Kokkos::parallel_for(1,f_init);
+  execution_space::fence();
+
+  struct MinFunctor<T,execution_space> f(i0,i1);
+  f.data = data;
+  Kokkos::parallel_for(1,f);
+  execution_space::fence();
+
+  Kokkos::deep_copy(h_data,data);
+  T val = h_data();
+  return val;
+}
+
+template<class T>
+T MinAtomicCheck(T i0 , T i1) {
+  T* data = new T[1];
+  data[0] = 0;
+
+  *data = (i0 < i1 ? i0 : i1) ;
+
+  T val = *data;
+  delete [] data;
+  return val;
+}
+
+template<class T,class DeviceType>
+bool MinAtomicTest(T i0, T i1)
+{
+  T res       = MinAtomic<T,DeviceType>(i0,i1);
+  T resSerial = MinAtomicCheck<T>(i0,i1);
+
+  bool passed = true;
+
+  if ( resSerial != res ) {
+    passed = false;
+
+    std::cout << "Loop<"
+              << typeid(T).name()
+              << ">( test = MinAtomicTest"
+              << " FAILED : "
+              << resSerial << " != " << res
+              << std::endl ;
+  }
+
+  return passed ;
+}
+
+//---------------------------------------------------
+//--------------atomic_fetch_mul---------------------
+//---------------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct MulFunctor{
+  typedef DEVICE_TYPE execution_space;
+  typedef Kokkos::View<T,execution_space> type;
+  type data;
+  T i0;
+  T i1;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    Kokkos::atomic_fetch_mul(&data(),(T)i1);
+  }
+  MulFunctor( T _i0 , T _i1 ) : i0(_i0) , i1(_i1) {}
+};
+
+template<class T, class execution_space >
+T MulAtomic(T i0 , T i1) {
+  struct InitFunctor<T,execution_space> f_init(i0);
+  typename InitFunctor<T,execution_space>::type data("Data");
+  typename InitFunctor<T,execution_space>::h_type h_data("HData");
+  f_init.data = data;
+  Kokkos::parallel_for(1,f_init);
+  execution_space::fence();
+
+  struct MulFunctor<T,execution_space> f(i0,i1);
+  f.data = data;
+  Kokkos::parallel_for(1,f);
+  execution_space::fence();
+
+  Kokkos::deep_copy(h_data,data);
+  T val = h_data();
+  return val;
+}
+
+template<class T>
+T MulAtomicCheck(T i0 , T i1) {
+  T* data = new T[1];
+  data[0] = 0;
+
+  *data = i0*i1 ;
+
+  T val = *data;
+  delete [] data;
+  return val;
+}
+
+template<class T,class DeviceType>
+bool MulAtomicTest(T i0, T i1)
+{
+  T res       = MulAtomic<T,DeviceType>(i0,i1);
+  T resSerial = MulAtomicCheck<T>(i0,i1);
+
+  bool passed = true;
+
+  if ( resSerial != res ) {
+    passed = false;
+
+    std::cout << "Loop<"
+              << typeid(T).name()
+              << ">( test = MulAtomicTest"
+              << " FAILED : "
+              << resSerial << " != " << res
+              << std::endl ;
+  }
+
+  return passed ;
+}
+
+//---------------------------------------------------
+//--------------atomic_fetch_div---------------------
+//---------------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct DivFunctor{
+  typedef DEVICE_TYPE execution_space;
+  typedef Kokkos::View<T,execution_space> type;
+  type data;
+  T i0;
+  T i1;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    Kokkos::atomic_fetch_div(&data(),(T)i1);
+  }
+  DivFunctor( T _i0 , T _i1 ) : i0(_i0) , i1(_i1) {}
+};
+
+template<class T, class execution_space >
+T DivAtomic(T i0 , T i1) {
+  struct InitFunctor<T,execution_space> f_init(i0);
+  typename InitFunctor<T,execution_space>::type data("Data");
+  typename InitFunctor<T,execution_space>::h_type h_data("HData");
+  f_init.data = data;
+  Kokkos::parallel_for(1,f_init);
+  execution_space::fence();
+
+  struct DivFunctor<T,execution_space> f(i0,i1);
+  f.data = data;
+  Kokkos::parallel_for(1,f);
+  execution_space::fence();
+
+  Kokkos::deep_copy(h_data,data);
+  T val = h_data();
+  return val;
+}
+
+template<class T>
+T DivAtomicCheck(T i0 , T i1) {
+  T* data = new T[1];
+  data[0] = 0;
+
+  *data = i0/i1 ;
+
+  T val = *data;
+  delete [] data;
+  return val;
+}
+
+template<class T,class DeviceType>
+bool DivAtomicTest(T i0, T i1)
+{
+  T res       = DivAtomic<T,DeviceType>(i0,i1);
+  T resSerial = DivAtomicCheck<T>(i0,i1);
+
+  bool passed = true;
+
+  if ( resSerial != res ) {
+    passed = false;
+
+    std::cout << "Loop<"
+              << typeid(T).name()
+              << ">( test = DivAtomicTest"
+              << " FAILED : "
+              << resSerial << " != " << res
+              << std::endl ;
+  }
+
+  return passed ;
+}
+
+//---------------------------------------------------
+//--------------atomic_fetch_mod---------------------
+//---------------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct ModFunctor{
+  typedef DEVICE_TYPE execution_space;
+  typedef Kokkos::View<T,execution_space> type;
+  type data;
+  T i0;
+  T i1;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    Kokkos::atomic_fetch_mod(&data(),(T)i1);
+  }
+  ModFunctor( T _i0 , T _i1 ) : i0(_i0) , i1(_i1) {}
+};
+
+template<class T, class execution_space >
+T ModAtomic(T i0 , T i1) {
+  struct InitFunctor<T,execution_space> f_init(i0);
+  typename InitFunctor<T,execution_space>::type data("Data");
+  typename InitFunctor<T,execution_space>::h_type h_data("HData");
+  f_init.data = data;
+  Kokkos::parallel_for(1,f_init);
+  execution_space::fence();
+
+  struct ModFunctor<T,execution_space> f(i0,i1);
+  f.data = data;
+  Kokkos::parallel_for(1,f);
+  execution_space::fence();
+
+  Kokkos::deep_copy(h_data,data);
+  T val = h_data();
+  return val;
+}
+
+template<class T>
+T ModAtomicCheck(T i0 , T i1) {
+  T* data = new T[1];
+  data[0] = 0;
+
+  *data = i0%i1 ;
+
+  T val = *data;
+  delete [] data;
+  return val;
+}
+
+template<class T,class DeviceType>
+bool ModAtomicTest(T i0, T i1)
+{
+  T res       = ModAtomic<T,DeviceType>(i0,i1);
+  T resSerial = ModAtomicCheck<T>(i0,i1);
+
+  bool passed = true;
+
+  if ( resSerial != res ) {
+    passed = false;
+
+    std::cout << "Loop<"
+              << typeid(T).name()
+              << ">( test = ModAtomicTest"
+              << " FAILED : "
+              << resSerial << " != " << res
+              << std::endl ;
+  }
+
+  return passed ;
+}
+
+//---------------------------------------------------
+//--------------atomic_fetch_and---------------------
+//---------------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct AndFunctor{
+  typedef DEVICE_TYPE execution_space;
+  typedef Kokkos::View<T,execution_space> type;
+  type data;
+  T i0;
+  T i1;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    Kokkos::atomic_fetch_and(&data(),(T)i1);
+  }
+  AndFunctor( T _i0 , T _i1 ) : i0(_i0) , i1(_i1) {}
+};
+
+template<class T, class execution_space >
+T AndAtomic(T i0 , T i1) {
+  struct InitFunctor<T,execution_space> f_init(i0);
+  typename InitFunctor<T,execution_space>::type data("Data");
+  typename InitFunctor<T,execution_space>::h_type h_data("HData");
+  f_init.data = data;
+  Kokkos::parallel_for(1,f_init);
+  execution_space::fence();
+
+  struct AndFunctor<T,execution_space> f(i0,i1);
+  f.data = data;
+  Kokkos::parallel_for(1,f);
+  execution_space::fence();
+
+  Kokkos::deep_copy(h_data,data);
+  T val = h_data();
+  return val;
+}
+
+template<class T>
+T AndAtomicCheck(T i0 , T i1) {
+  T* data = new T[1];
+  data[0] = 0;
+
+  *data = i0&i1 ;
+
+  T val = *data;
+  delete [] data;
+  return val;
+}
+
+template<class T,class DeviceType>
+bool AndAtomicTest(T i0, T i1)
+{
+  T res       = AndAtomic<T,DeviceType>(i0,i1);
+  T resSerial = AndAtomicCheck<T>(i0,i1);
+
+  bool passed = true;
+
+  if ( resSerial != res ) {
+    passed = false;
+
+    std::cout << "Loop<"
+              << typeid(T).name()
+              << ">( test = AndAtomicTest"
+              << " FAILED : "
+              << resSerial << " != " << res
+              << std::endl ;
+  }
+
+  return passed ;
+}
+
+//---------------------------------------------------
+//--------------atomic_fetch_or----------------------
+//---------------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct OrFunctor{
+  typedef DEVICE_TYPE execution_space;
+  typedef Kokkos::View<T,execution_space> type;
+  type data;
+  T i0;
+  T i1;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    Kokkos::atomic_fetch_or(&data(),(T)i1);
+  }
+  OrFunctor( T _i0 , T _i1 ) : i0(_i0) , i1(_i1) {}
+};
+
+template<class T, class execution_space >
+T OrAtomic(T i0 , T i1) {
+  struct InitFunctor<T,execution_space> f_init(i0);
+  typename InitFunctor<T,execution_space>::type data("Data");
+  typename InitFunctor<T,execution_space>::h_type h_data("HData");
+  f_init.data = data;
+  Kokkos::parallel_for(1,f_init);
+  execution_space::fence();
+
+  struct OrFunctor<T,execution_space> f(i0,i1);
+  f.data = data;
+  Kokkos::parallel_for(1,f);
+  execution_space::fence();
+
+  Kokkos::deep_copy(h_data,data);
+  T val = h_data();
+  return val;
+}
+
+template<class T>
+T OrAtomicCheck(T i0 , T i1) {
+  T* data = new T[1];
+  data[0] = 0;
+
+  *data = i0|i1 ;
+
+  T val = *data;
+  delete [] data;
+  return val;
+}
+
+template<class T,class DeviceType>
+bool OrAtomicTest(T i0, T i1)
+{
+  T res       = OrAtomic<T,DeviceType>(i0,i1);
+  T resSerial = OrAtomicCheck<T>(i0,i1);
+
+  bool passed = true;
+
+  if ( resSerial != res ) {
+    passed = false;
+
+    std::cout << "Loop<"
+              << typeid(T).name()
+              << ">( test = OrAtomicTest"
+              << " FAILED : "
+              << resSerial << " != " << res
+              << std::endl ;
+  }
+
+  return passed ;
+}
+
+//---------------------------------------------------
+//--------------atomic_fetch_xor---------------------
+//---------------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct XorFunctor{
+  typedef DEVICE_TYPE execution_space;
+  typedef Kokkos::View<T,execution_space> type;
+  type data;
+  T i0;
+  T i1;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    Kokkos::atomic_fetch_xor(&data(),(T)i1);
+  }
+  XorFunctor( T _i0 , T _i1 ) : i0(_i0) , i1(_i1) {}
+};
+
+template<class T, class execution_space >
+T XorAtomic(T i0 , T i1) {
+  struct InitFunctor<T,execution_space> f_init(i0);
+  typename InitFunctor<T,execution_space>::type data("Data");
+  typename InitFunctor<T,execution_space>::h_type h_data("HData");
+  f_init.data = data;
+  Kokkos::parallel_for(1,f_init);
+  execution_space::fence();
+
+  struct XorFunctor<T,execution_space> f(i0,i1);
+  f.data = data;
+  Kokkos::parallel_for(1,f);
+  execution_space::fence();
+
+  Kokkos::deep_copy(h_data,data);
+  T val = h_data();
+  return val;
+}
+
+template<class T>
+T XorAtomicCheck(T i0 , T i1) {
+  T* data = new T[1];
+  data[0] = 0;
+
+  *data = i0^i1 ;
+
+  T val = *data;
+  delete [] data;
+  return val;
+}
+
+template<class T,class DeviceType>
+bool XorAtomicTest(T i0, T i1)
+{
+  T res       = XorAtomic<T,DeviceType>(i0,i1);
+  T resSerial = XorAtomicCheck<T>(i0,i1);
+
+  bool passed = true;
+
+  if ( resSerial != res ) {
+    passed = false;
+
+    std::cout << "Loop<"
+              << typeid(T).name()
+              << ">( test = XorAtomicTest"
+              << " FAILED : "
+              << resSerial << " != " << res
+              << std::endl ;
+  }
+
+  return passed ;
+}
+
+//---------------------------------------------------
+//--------------atomic_fetch_lshift---------------------
+//---------------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct LShiftFunctor{
+  typedef DEVICE_TYPE execution_space;
+  typedef Kokkos::View<T,execution_space> type;
+  type data;
+  T i0;
+  T i1;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    Kokkos::atomic_fetch_lshift(&data(),(T)i1);
+  }
+  LShiftFunctor( T _i0 , T _i1 ) : i0(_i0) , i1(_i1) {}
+};
+
+template<class T, class execution_space >
+T LShiftAtomic(T i0 , T i1) {
+  struct InitFunctor<T,execution_space> f_init(i0);
+  typename InitFunctor<T,execution_space>::type data("Data");
+  typename InitFunctor<T,execution_space>::h_type h_data("HData");
+  f_init.data = data;
+  Kokkos::parallel_for(1,f_init);
+  execution_space::fence();
+
+  struct LShiftFunctor<T,execution_space> f(i0,i1);
+  f.data = data;
+  Kokkos::parallel_for(1,f);
+  execution_space::fence();
+
+  Kokkos::deep_copy(h_data,data);
+  T val = h_data();
+  return val;
+}
+
+template<class T>
+T LShiftAtomicCheck(T i0 , T i1) {
+  T* data = new T[1];
+  data[0] = 0;
+
+  *data = i0<<i1 ;
+
+  T val = *data;
+  delete [] data;
+  return val;
+}
+
+template<class T,class DeviceType>
+bool LShiftAtomicTest(T i0, T i1)
+{
+  T res       = LShiftAtomic<T,DeviceType>(i0,i1);
+  T resSerial = LShiftAtomicCheck<T>(i0,i1);
+
+  bool passed = true;
+
+  if ( resSerial != res ) {
+    passed = false;
+
+    std::cout << "Loop<"
+              << typeid(T).name()
+              << ">( test = LShiftAtomicTest"
+              << " FAILED : "
+              << resSerial << " != " << res
+              << std::endl ;
+  }
+
+  return passed ;
+}
+
+//---------------------------------------------------
+//--------------atomic_fetch_rshift---------------------
+//---------------------------------------------------
+
+template<class T,class DEVICE_TYPE>
+struct RShiftFunctor{
+  typedef DEVICE_TYPE execution_space;
+  typedef Kokkos::View<T,execution_space> type;
+  type data;
+  T i0;
+  T i1;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(int) const {
+    Kokkos::atomic_fetch_rshift(&data(),(T)i1);
+  }
+  RShiftFunctor( T _i0 , T _i1 ) : i0(_i0) , i1(_i1) {}
+};
+
+template<class T, class execution_space >
+T RShiftAtomic(T i0 , T i1) {
+  struct InitFunctor<T,execution_space> f_init(i0);
+  typename InitFunctor<T,execution_space>::type data("Data");
+  typename InitFunctor<T,execution_space>::h_type h_data("HData");
+  f_init.data = data;
+  Kokkos::parallel_for(1,f_init);
+  execution_space::fence();
+
+  struct RShiftFunctor<T,execution_space> f(i0,i1);
+  f.data = data;
+  Kokkos::parallel_for(1,f);
+  execution_space::fence();
+
+  Kokkos::deep_copy(h_data,data);
+  T val = h_data();
+  return val;
+}
+
+template<class T>
+T RShiftAtomicCheck(T i0 , T i1) {
+  T* data = new T[1];
+  data[0] = 0;
+
+  *data = i0>>i1 ;
+
+  T val = *data;
+  delete [] data;
+  return val;
+}
+
+template<class T,class DeviceType>
+bool RShiftAtomicTest(T i0, T i1)
+{
+  T res       = RShiftAtomic<T,DeviceType>(i0,i1);
+  T resSerial = RShiftAtomicCheck<T>(i0,i1);
+
+  bool passed = true;
+
+  if ( resSerial != res ) {
+    passed = false;
+
+    std::cout << "Loop<"
+              << typeid(T).name()
+              << ">( test = RShiftAtomicTest"
+              << " FAILED : "
+              << resSerial << " != " << res
+              << std::endl ;
+  }
+
+  return passed ;
+}
+
+
+//---------------------------------------------------
+//--------------atomic_test_control------------------
+//---------------------------------------------------
+
+template<class T,class DeviceType>
+bool AtomicOperationsTestIntegralType( int i0 , int i1 , int test )
+{
+  switch (test) {
+    case 1: return MaxAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 2: return MinAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 3: return MulAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 4: return DivAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 5: return ModAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 6: return AndAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 7: return OrAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 8: return XorAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 9: return LShiftAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 10: return RShiftAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+  }
+  return 0;
+}
+
+template<class T,class DeviceType>
+bool AtomicOperationsTestNonIntegralType( int i0 , int i1 , int test )
+{
+  switch (test) {
+    case 1: return MaxAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 2: return MinAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 3: return MulAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+    case 4: return DivAtomicTest<T,DeviceType>( (T)i0 , (T)i1 );
+  }
+  return 0;
+}
+
+} // namespace
+
diff --git a/lib/kokkos/core/unit_test/TestCuda.cpp b/lib/kokkos/core/unit_test/TestCuda.cpp
index 3958c1a344..e615566252 100644
--- a/lib/kokkos/core/unit_test/TestCuda.cpp
+++ b/lib/kokkos/core/unit_test/TestCuda.cpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -81,24 +81,31 @@
 #include <TestTaskPolicy.hpp>
 #include <TestPolicyConstruction.hpp>
 
+#include <TestMDRange.hpp>
+
 //----------------------------------------------------------------------------
 
 class cuda : public ::testing::Test {
 protected:
-  static void SetUpTestCase()
+  static void SetUpTestCase();
+  static void TearDownTestCase();
+};
+
+void cuda::SetUpTestCase()
   {
     Kokkos::Cuda::print_configuration( std::cout );
     Kokkos::HostSpace::execution_space::initialize();
     Kokkos::Cuda::initialize( Kokkos::Cuda::SelectDevice(0) );
   }
-  static void TearDownTestCase()
+
+void cuda::TearDownTestCase()
   {
     Kokkos::Cuda::finalize();
     Kokkos::HostSpace::execution_space::finalize();
   }
-};
 
 //----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
 
 namespace Test {
 
@@ -116,6 +123,11 @@ void test_cuda_spaces_int_value( int * ptr )
   if ( *ptr == 42 ) { *ptr = 2 * 42 ; }
 }
 
+TEST_F( cuda , md_range ) {
+  TestMDRange_2D< Kokkos::Cuda >::test_for2(100,100);
+
+  TestMDRange_3D< Kokkos::Cuda >::test_for3(100,100,100);
+}
 
 TEST_F( cuda , compiler_macros )
 {
@@ -223,7 +235,6 @@ struct TestViewCudaTexture {
     }
 };
 
-
 TEST_F( cuda , impl_view_texture )
 {
   TestViewCudaTexture< Kokkos::CudaSpace >::run();
@@ -265,7 +276,6 @@ struct TestViewCudaAccessible {
     }
 };
 
-
 TEST_F( cuda , impl_view_accessible )
 {
   TestViewCudaAccessible< Kokkos::CudaSpace , Kokkos::Cuda >::run();
@@ -276,338 +286,5 @@ TEST_F( cuda , impl_view_accessible )
   TestViewCudaAccessible< Kokkos::CudaHostPinnedSpace , Kokkos::Cuda >::run();
   TestViewCudaAccessible< Kokkos::CudaHostPinnedSpace , Kokkos::HostSpace::execution_space >::run();
 }
-/*
-//----------------------------------------------------------------------------
-
-TEST_F( cuda, view_impl )
-{
-  // test_abort<<<32,32>>>(); // Aborts the kernel with CUDA version 4.1 or greater
-
-  test_view_impl< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_api )
-{
-  typedef Kokkos::View< const int * , Kokkos::Cuda , Kokkos::MemoryTraits< Kokkos::RandomAccess > > view_texture_managed ;
-  typedef Kokkos::View< const int * , Kokkos::Cuda , Kokkos::MemoryTraits< Kokkos::RandomAccess | Kokkos::Unmanaged > > view_texture_unmanaged ;
-
-  TestViewAPI< double , Kokkos::Cuda >();
-  TestViewAPI< double , Kokkos::CudaUVMSpace >();
-
-#if 0
-  Kokkos::View<double, Kokkos::Cuda > x("x");
-  Kokkos::View<double[1], Kokkos::Cuda > y("y");
-  // *x = 10 ;
-  // x() = 10 ;
-  // y[0] = 10 ;
-  // y(0) = 10 ;
-#endif
-}
-
-
-TEST_F( cuda , view_nested_view )
-{
-  ::Test::view_nested_view< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_auto_1d_left ) {
-  TestViewSubview::test_auto_1d< Kokkos::LayoutLeft,Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_auto_1d_right ) {
-  TestViewSubview::test_auto_1d< Kokkos::LayoutRight,Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_auto_1d_stride ) {
-  TestViewSubview::test_auto_1d< Kokkos::LayoutStride,Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_assign_strided ) {
-  TestViewSubview::test_1d_strided_assignment< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_left_0 ) {
-  TestViewSubview::test_left_0< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_left_1 ) {
-  TestViewSubview::test_left_1< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_left_2 ) {
-  TestViewSubview::test_left_2< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_left_3 ) {
-  TestViewSubview::test_left_3< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_right_0 ) {
-  TestViewSubview::test_right_0< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_right_1 ) {
-  TestViewSubview::test_right_1< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_right_3 ) {
-  TestViewSubview::test_right_3< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_1d_assign ) {
-  TestViewSubview::test_1d_assign< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_2d_from_3d ) {
-  TestViewSubview::test_2d_subview_3d< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_2d_from_5d ) {
-  TestViewSubview::test_2d_subview_5d< Kokkos::CudaUVMSpace >();
-}
-
-
-TEST_F( cuda, range_tag )
-{
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_scan(1000);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(1001);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(1001);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_scan(1001);
-  //TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_dynamic_policy(1000);
-}
-
-TEST_F( cuda, team_tag )
-{
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(1000);
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(1000);
-}
-
-TEST_F( cuda, reduce )
-{
-  TestReduce< long ,   Kokkos::Cuda >( 10000000 );
-  TestReduce< double , Kokkos::Cuda >( 1000000 );
-  TestReduce< int , Kokkos::Cuda >( 0 );
-}
-
-TEST_F( cuda, reduce_team )
-{
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 3 );
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 3 );
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 100000 );
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 100000 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 3 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 3 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 100000 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 100000 );
-}
-
-TEST_F( cuda, shared_team )
-{
-  TestSharedTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >();
-  TestSharedTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >();
-}
-
-
-#if defined (KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA)
-TEST_F( cuda, lambda_shared_team )
-{
-  TestLambdaSharedTeam< Kokkos::CudaSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Static> >();
-  TestLambdaSharedTeam< Kokkos::CudaUVMSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Static> >();
-  TestLambdaSharedTeam< Kokkos::CudaHostPinnedSpace, Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static>  >();
-  TestLambdaSharedTeam< Kokkos::CudaSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Dynamic> >();
-  TestLambdaSharedTeam< Kokkos::CudaUVMSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Dynamic> >();
-  TestLambdaSharedTeam< Kokkos::CudaHostPinnedSpace, Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic>  >();
-}
-#endif
-
-
-TEST_F( cuda, reduce_dynamic )
-{
-  TestReduceDynamic< long ,   Kokkos::Cuda >( 10000000 );
-  TestReduceDynamic< double , Kokkos::Cuda >( 1000000 );
-}
-
-TEST_F( cuda, reduce_dynamic_view )
-{
-  TestReduceDynamicView< long ,   Kokkos::Cuda >( 10000000 );
-  TestReduceDynamicView< double , Kokkos::Cuda >( 1000000 );
-}
-
-TEST_F( cuda, atomic )
-{
-  const int loop_count = 1e3 ;
-
-  ASSERT_TRUE( ( TestAtomic::Loop<int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<long int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned long int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned long int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned long int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<long long int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long long int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long long int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<double,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<double,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<double,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<float,Kokkos::Cuda>(100,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<float,Kokkos::Cuda>(100,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<float,Kokkos::Cuda>(100,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<Kokkos::complex<double> ,Kokkos::Cuda>(100,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<Kokkos::complex<double> ,Kokkos::Cuda>(100,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<Kokkos::complex<double> ,Kokkos::Cuda>(100,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::Cuda>(100,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::Cuda>(100,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::Cuda>(100,3) ) );
-
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda, tile_layout)
-{
-  TestTile::test< Kokkos::Cuda , 1 , 1 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 1 , 1 >( 2 , 3 );
-  TestTile::test< Kokkos::Cuda , 1 , 1 >( 9 , 10 );
-
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 2 , 3 );
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 4 , 4 );
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 9 , 9 );
-
-  TestTile::test< Kokkos::Cuda , 2 , 4 >( 9 , 9 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 9 , 9 );
-
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 4 , 4 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 9 , 9 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 9 , 11 );
-
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 4 , 4 );
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 9 , 9 );
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 9 , 11 );
-}
-
-TEST_F( cuda , view_aggregate )
-{
-  TestViewAggregate< Kokkos::Cuda >();
-  TestViewAggregateReduction< Kokkos::Cuda >();
-}
-
-
-TEST_F( cuda , scan )
-{
-  TestScan< Kokkos::Cuda >::test_range( 1 , 1000 );
-  TestScan< Kokkos::Cuda >( 1000000 );
-  TestScan< Kokkos::Cuda >( 10000000 );
-
-  TestScan< Kokkos::Cuda >( 0 );
-  TestScan< Kokkos::Cuda >( 0 , 0 );
-
-  Kokkos::Cuda::fence();
-}
-
-TEST_F( cuda , team_scan )
-{
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 10 );
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 10 );
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 10000 );
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 10000 );
-}
-
-TEST_F( cuda , memory_pool )
-{
-  bool val_uvm = TestMemoryPool::test_mempool< Kokkos::Cuda, Kokkos::CudaUVMSpace >( 128, 128000 );
-  ASSERT_TRUE( val_uvm );
-
-  Kokkos::Cuda::fence();
-
-  TestMemoryPool::test_mempool2< Kokkos::Cuda, Kokkos::CudaUVMSpace >( 128, 2560000 );
-
-  Kokkos::Cuda::fence();
-}
-
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda , template_meta_functions )
-{
-  TestTemplateMetaFunctions<int, Kokkos::Cuda >();
-}
-
-//----------------------------------------------------------------------------
-
-namespace Test {
-
-TEST_F( cuda , reduction_deduction )
-{
-  TestCXX11::test_reduction_deduction< Kokkos::Cuda >();
-}
-
-TEST_F( cuda , team_vector )
-{
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(0) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(1) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(2) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(3) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(4) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(5) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(6) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(7) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(8) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(9) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(10) ) );
-}
-*/
-}
-
-//----------------------------------------------------------------------------
-/*
-#if defined( KOKKOS_ENABLE_CUDA_TASK_POLICY )
 
-TEST_F( cuda , task_policy )
-{
-  TestTaskPolicy::test_task_dep< Kokkos::Cuda >( 10 );
-
-  for ( long i = 0 ; i < 15 ; ++i ) {
-      // printf("TestTaskPolicy::test_fib< Kokkos::Cuda >(%d);\n",i);
-    TestTaskPolicy::test_fib< Kokkos::Cuda >(i,4096);
-  }
-  for ( long i = 0 ; i < 35 ; ++i ) {
-      // printf("TestTaskPolicy::test_fib2< Kokkos::Cuda >(%d);\n",i);
-    TestTaskPolicy::test_fib2< Kokkos::Cuda >(i,4096);
-  }
 }
-
-TEST_F( cuda , task_team )
-{
-  TestTaskPolicy::test_task_team< Kokkos::Cuda >(1000);
-}
-
-TEST_F( cuda , task_latch )
-{
-  TestTaskPolicy::test_latch< Kokkos::Cuda >(10);
-  TestTaskPolicy::test_latch< Kokkos::Cuda >(1000);
-}
-
-#endif /* #if defined( KOKKOS_ENABLE_CUDA_TASK_POLICY ) */
-
diff --git a/lib/kokkos/core/unit_test/TestCuda_a.cpp b/lib/kokkos/core/unit_test/TestCuda_a.cpp
index 05716153d1..4680c33386 100644
--- a/lib/kokkos/core/unit_test/TestCuda_a.cpp
+++ b/lib/kokkos/core/unit_test/TestCuda_a.cpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -85,199 +85,13 @@
 
 class cuda : public ::testing::Test {
 protected:
-  static void SetUpTestCase()
-  {
-    Kokkos::Cuda::print_configuration( std::cout );
-    Kokkos::HostSpace::execution_space::initialize();
-    Kokkos::Cuda::initialize( Kokkos::Cuda::SelectDevice(0) );
-  }
-  static void TearDownTestCase()
-  {
-    Kokkos::Cuda::finalize();
-    Kokkos::HostSpace::execution_space::finalize();
-  }
+  static void SetUpTestCase();
+  static void TearDownTestCase();
 };
 
 //----------------------------------------------------------------------------
 
 namespace Test {
-/*
-__global__
-void test_abort()
-{
-  Kokkos::Impl::VerifyExecutionCanAccessMemorySpace<
-    Kokkos::CudaSpace ,
-    Kokkos::HostSpace >::verify();
-}
-
-__global__
-void test_cuda_spaces_int_value( int * ptr )
-{
-  if ( *ptr == 42 ) { *ptr = 2 * 42 ; }
-}
-
-
-TEST_F( cuda , compiler_macros )
-{
-  ASSERT_TRUE( ( TestCompilerMacros::Test< Kokkos::Cuda >() ) );
-}
-
-TEST_F( cuda , memory_space )
-{
-  TestMemorySpace< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, uvm )
-{
-  if ( Kokkos::CudaUVMSpace::available() ) {
-
-    int * uvm_ptr = (int*) Kokkos::kokkos_malloc< Kokkos::CudaUVMSpace >("uvm_ptr",sizeof(int));
-
-    *uvm_ptr = 42 ;
-
-    Kokkos::Cuda::fence();
-    test_cuda_spaces_int_value<<<1,1>>>(uvm_ptr);
-    Kokkos::Cuda::fence();
-
-    EXPECT_EQ( *uvm_ptr, int(2*42) );
-
-    Kokkos::kokkos_free< Kokkos::CudaUVMSpace >(uvm_ptr );
-  }
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda , impl_shared_alloc )
-{
-  test_shared_alloc< Kokkos::CudaSpace , Kokkos::HostSpace::execution_space >();
-  test_shared_alloc< Kokkos::CudaUVMSpace , Kokkos::HostSpace::execution_space >();
-  test_shared_alloc< Kokkos::CudaHostPinnedSpace , Kokkos::HostSpace::execution_space >();
-}
-
-TEST_F( cuda, policy_construction) {
-  TestRangePolicyConstruction< Kokkos::Cuda >();
-  TestTeamPolicyConstruction< Kokkos::Cuda >();
-}
-
-TEST_F( cuda , impl_view_mapping )
-{
-  test_view_mapping< Kokkos::Cuda >();
-  test_view_mapping< Kokkos::CudaUVMSpace >();
-  test_view_mapping_subview< Kokkos::Cuda >();
-  test_view_mapping_subview< Kokkos::CudaUVMSpace >();
-  test_view_mapping_operator< Kokkos::Cuda >();
-  test_view_mapping_operator< Kokkos::CudaUVMSpace >();
-  TestViewMappingAtomic< Kokkos::Cuda >::run();
-}
-
-TEST_F( cuda , view_of_class )
-{
-  TestViewMappingClassValue< Kokkos::CudaSpace >::run();
-  TestViewMappingClassValue< Kokkos::CudaUVMSpace >::run();
-}
-
-template< class MemSpace >
-struct TestViewCudaTexture {
-
-  enum { N = 1000 };
-
-  using V = Kokkos::Experimental::View<double*,MemSpace> ;
-  using T = Kokkos::Experimental::View<const double*, MemSpace, Kokkos::MemoryRandomAccess > ;
-
-  V m_base ;
-  T m_tex ;
-
-  struct TagInit {};
-  struct TagTest {};
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagInit & , const int i ) const { m_base[i] = i + 1 ; }
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagTest & , const int i , long & error_count ) const
-    { if ( m_tex[i] != i + 1 ) ++error_count ; }
-
-  TestViewCudaTexture()
-    : m_base("base",N)
-    , m_tex( m_base )
-    {}
-
-  static void run()
-    {
-      EXPECT_TRUE( ( std::is_same< typename V::reference_type
-                                 , double &
-                                 >::value ) );
-
-      EXPECT_TRUE( ( std::is_same< typename T::reference_type
-                                 , const double
-                                 >::value ) );
-
-      EXPECT_TRUE(  V::reference_type_is_lvalue_reference ); // An ordinary view
-      EXPECT_FALSE( T::reference_type_is_lvalue_reference ); // Texture fetch returns by value
-
-      TestViewCudaTexture self ;
-      Kokkos::parallel_for( Kokkos::RangePolicy< Kokkos::Cuda , TagInit >(0,N) , self );
-      long error_count = -1 ;
-      Kokkos::parallel_reduce( Kokkos::RangePolicy< Kokkos::Cuda , TagTest >(0,N) , self , error_count );
-      EXPECT_EQ( error_count , 0 );
-    }
-};
-
-
-TEST_F( cuda , impl_view_texture )
-{
-  TestViewCudaTexture< Kokkos::CudaSpace >::run();
-  TestViewCudaTexture< Kokkos::CudaUVMSpace >::run();
-}
-
-template< class MemSpace , class ExecSpace >
-struct TestViewCudaAccessible {
-
-  enum { N = 1000 };
-
-  using V = Kokkos::Experimental::View<double*,MemSpace> ;
-
-  V m_base ;
-
-  struct TagInit {};
-  struct TagTest {};
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagInit & , const int i ) const { m_base[i] = i + 1 ; }
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagTest & , const int i , long & error_count ) const
-    { if ( m_base[i] != i + 1 ) ++error_count ; }
-
-  TestViewCudaAccessible()
-    : m_base("base",N)
-    {}
-
-  static void run()
-    {
-      TestViewCudaAccessible self ;
-      Kokkos::parallel_for( Kokkos::RangePolicy< typename MemSpace::execution_space , TagInit >(0,N) , self );
-      MemSpace::execution_space::fence();
-      // Next access is a different execution space, must complete prior kernel.
-      long error_count = -1 ;
-      Kokkos::parallel_reduce( Kokkos::RangePolicy< ExecSpace , TagTest >(0,N) , self , error_count );
-      EXPECT_EQ( error_count , 0 );
-    }
-};
-
-
-TEST_F( cuda , impl_view_accessible )
-{
-  TestViewCudaAccessible< Kokkos::CudaSpace , Kokkos::Cuda >::run();
-
-  TestViewCudaAccessible< Kokkos::CudaUVMSpace , Kokkos::Cuda >::run();
-  TestViewCudaAccessible< Kokkos::CudaUVMSpace , Kokkos::HostSpace::execution_space >::run();
-
-  TestViewCudaAccessible< Kokkos::CudaHostPinnedSpace , Kokkos::Cuda >::run();
-  TestViewCudaAccessible< Kokkos::CudaHostPinnedSpace , Kokkos::HostSpace::execution_space >::run();
-}
-*/
-//----------------------------------------------------------------------------
 
 TEST_F( cuda, view_impl )
 {
@@ -304,7 +118,6 @@ TEST_F( cuda, view_api )
 #endif
 }
 
-
 TEST_F( cuda , view_nested_view )
 {
   ::Test::view_nested_view< Kokkos::Cuda >();
@@ -366,248 +179,4 @@ TEST_F( cuda, view_subview_2d_from_5d ) {
   TestViewSubview::test_2d_subview_5d< Kokkos::CudaUVMSpace >();
 }
 
-/*
-TEST_F( cuda, range_tag )
-{
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_scan(1000);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(1001);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(1001);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_scan(1001);
-  //TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_dynamic_policy(1000);
-}
-
-TEST_F( cuda, team_tag )
-{
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(1000);
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(1000);
-}
-
-TEST_F( cuda, reduce )
-{
-  TestReduce< long ,   Kokkos::Cuda >( 10000000 );
-  TestReduce< double , Kokkos::Cuda >( 1000000 );
-  TestReduce< int , Kokkos::Cuda >( 0 );
-}
-
-TEST_F( cuda, reduce_team )
-{
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 3 );
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 3 );
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 100000 );
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 100000 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 3 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 3 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 100000 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 100000 );
 }
-
-TEST_F( cuda, shared_team )
-{
-  TestSharedTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >();
-  TestSharedTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >();
-}
-
-
-#if defined (KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA)
-TEST_F( cuda, lambda_shared_team )
-{
-  TestLambdaSharedTeam< Kokkos::CudaSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Static> >();
-  TestLambdaSharedTeam< Kokkos::CudaUVMSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Static> >();
-  TestLambdaSharedTeam< Kokkos::CudaHostPinnedSpace, Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static>  >();
-  TestLambdaSharedTeam< Kokkos::CudaSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Dynamic> >();
-  TestLambdaSharedTeam< Kokkos::CudaUVMSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Dynamic> >();
-  TestLambdaSharedTeam< Kokkos::CudaHostPinnedSpace, Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic>  >();
-}
-#endif
-
-
-TEST_F( cuda, reduce_dynamic )
-{
-  TestReduceDynamic< long ,   Kokkos::Cuda >( 10000000 );
-  TestReduceDynamic< double , Kokkos::Cuda >( 1000000 );
-}
-
-TEST_F( cuda, reduce_dynamic_view )
-{
-  TestReduceDynamicView< long ,   Kokkos::Cuda >( 10000000 );
-  TestReduceDynamicView< double , Kokkos::Cuda >( 1000000 );
-}
-
-TEST_F( cuda, atomic )
-{
-  const int loop_count = 1e3 ;
-
-  ASSERT_TRUE( ( TestAtomic::Loop<int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<long int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned long int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned long int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned long int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<long long int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long long int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long long int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<double,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<double,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<double,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<float,Kokkos::Cuda>(100,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<float,Kokkos::Cuda>(100,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<float,Kokkos::Cuda>(100,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<Kokkos::complex<double> ,Kokkos::Cuda>(100,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<Kokkos::complex<double> ,Kokkos::Cuda>(100,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<Kokkos::complex<double> ,Kokkos::Cuda>(100,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::Cuda>(100,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::Cuda>(100,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::Cuda>(100,3) ) );
-
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda, tile_layout)
-{
-  TestTile::test< Kokkos::Cuda , 1 , 1 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 1 , 1 >( 2 , 3 );
-  TestTile::test< Kokkos::Cuda , 1 , 1 >( 9 , 10 );
-
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 2 , 3 );
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 4 , 4 );
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 9 , 9 );
-
-  TestTile::test< Kokkos::Cuda , 2 , 4 >( 9 , 9 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 9 , 9 );
-
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 4 , 4 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 9 , 9 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 9 , 11 );
-
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 4 , 4 );
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 9 , 9 );
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 9 , 11 );
-}
-
-TEST_F( cuda , view_aggregate )
-{
-  TestViewAggregate< Kokkos::Cuda >();
-  TestViewAggregateReduction< Kokkos::Cuda >();
-}
-
-
-TEST_F( cuda , scan )
-{
-  TestScan< Kokkos::Cuda >::test_range( 1 , 1000 );
-  TestScan< Kokkos::Cuda >( 1000000 );
-  TestScan< Kokkos::Cuda >( 10000000 );
-
-  TestScan< Kokkos::Cuda >( 0 );
-  TestScan< Kokkos::Cuda >( 0 , 0 );
-
-  Kokkos::Cuda::fence();
-}
-
-TEST_F( cuda , team_scan )
-{
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 10 );
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 10 );
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 10000 );
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 10000 );
-}
-
-TEST_F( cuda , memory_pool )
-{
-  bool val_uvm = TestMemoryPool::test_mempool< Kokkos::Cuda, Kokkos::CudaUVMSpace >( 128, 128000 );
-  ASSERT_TRUE( val_uvm );
-
-  Kokkos::Cuda::fence();
-
-  TestMemoryPool::test_mempool2< Kokkos::Cuda, Kokkos::CudaUVMSpace >( 128, 2560000 );
-
-  Kokkos::Cuda::fence();
-}
-
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda , template_meta_functions )
-{
-  TestTemplateMetaFunctions<int, Kokkos::Cuda >();
-}
-
-//----------------------------------------------------------------------------
-
-namespace Test {
-
-TEST_F( cuda , reduction_deduction )
-{
-  TestCXX11::test_reduction_deduction< Kokkos::Cuda >();
-}
-
-TEST_F( cuda , team_vector )
-{
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(0) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(1) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(2) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(3) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(4) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(5) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(6) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(7) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(8) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(9) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(10) ) );
-}
-*/
-}
-
-//----------------------------------------------------------------------------
-/*
-#if defined( KOKKOS_ENABLE_CUDA_TASK_POLICY )
-
-TEST_F( cuda , task_policy )
-{
-  TestTaskPolicy::test_task_dep< Kokkos::Cuda >( 10 );
-
-  for ( long i = 0 ; i < 15 ; ++i ) {
-      // printf("TestTaskPolicy::test_fib< Kokkos::Cuda >(%d);\n",i);
-    TestTaskPolicy::test_fib< Kokkos::Cuda >(i,4096);
-  }
-  for ( long i = 0 ; i < 35 ; ++i ) {
-      // printf("TestTaskPolicy::test_fib2< Kokkos::Cuda >(%d);\n",i);
-    TestTaskPolicy::test_fib2< Kokkos::Cuda >(i,4096);
-  }
-}
-
-TEST_F( cuda , task_team )
-{
-  TestTaskPolicy::test_task_team< Kokkos::Cuda >(1000);
-}
-
-TEST_F( cuda , task_latch )
-{
-  TestTaskPolicy::test_latch< Kokkos::Cuda >(10);
-  TestTaskPolicy::test_latch< Kokkos::Cuda >(1000);
-}
-
-#endif /* #if defined( KOKKOS_ENABLE_CUDA_TASK_POLICY ) */
-
diff --git a/lib/kokkos/core/unit_test/TestCuda_b.cpp b/lib/kokkos/core/unit_test/TestCuda_b.cpp
index 3d57347bb8..d4ca949e57 100644
--- a/lib/kokkos/core/unit_test/TestCuda_b.cpp
+++ b/lib/kokkos/core/unit_test/TestCuda_b.cpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -85,290 +85,22 @@
 
 class cuda : public ::testing::Test {
 protected:
-  static void SetUpTestCase()
-  {
-    Kokkos::Cuda::print_configuration( std::cout );
-    Kokkos::HostSpace::execution_space::initialize();
-    Kokkos::Cuda::initialize( Kokkos::Cuda::SelectDevice(0) );
-  }
-  static void TearDownTestCase()
-  {
-    Kokkos::Cuda::finalize();
-    Kokkos::HostSpace::execution_space::finalize();
-  }
+  static void SetUpTestCase();
+  static void TearDownTestCase();
 };
 
 //----------------------------------------------------------------------------
 
 namespace Test {
-/*
-__global__
-void test_abort()
-{
-  Kokkos::Impl::VerifyExecutionCanAccessMemorySpace<
-    Kokkos::CudaSpace ,
-    Kokkos::HostSpace >::verify();
-}
-
-__global__
-void test_cuda_spaces_int_value( int * ptr )
-{
-  if ( *ptr == 42 ) { *ptr = 2 * 42 ; }
-}
-
-
-TEST_F( cuda , compiler_macros )
-{
-  ASSERT_TRUE( ( TestCompilerMacros::Test< Kokkos::Cuda >() ) );
-}
-
-TEST_F( cuda , memory_space )
-{
-  TestMemorySpace< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, uvm )
-{
-  if ( Kokkos::CudaUVMSpace::available() ) {
-
-    int * uvm_ptr = (int*) Kokkos::kokkos_malloc< Kokkos::CudaUVMSpace >("uvm_ptr",sizeof(int));
-
-    *uvm_ptr = 42 ;
-
-    Kokkos::Cuda::fence();
-    test_cuda_spaces_int_value<<<1,1>>>(uvm_ptr);
-    Kokkos::Cuda::fence();
-
-    EXPECT_EQ( *uvm_ptr, int(2*42) );
-
-    Kokkos::kokkos_free< Kokkos::CudaUVMSpace >(uvm_ptr );
-  }
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda , impl_shared_alloc )
-{
-  test_shared_alloc< Kokkos::CudaSpace , Kokkos::HostSpace::execution_space >();
-  test_shared_alloc< Kokkos::CudaUVMSpace , Kokkos::HostSpace::execution_space >();
-  test_shared_alloc< Kokkos::CudaHostPinnedSpace , Kokkos::HostSpace::execution_space >();
-}
-
-TEST_F( cuda, policy_construction) {
-  TestRangePolicyConstruction< Kokkos::Cuda >();
-  TestTeamPolicyConstruction< Kokkos::Cuda >();
-}
-
-TEST_F( cuda , impl_view_mapping )
-{
-  test_view_mapping< Kokkos::Cuda >();
-  test_view_mapping< Kokkos::CudaUVMSpace >();
-  test_view_mapping_subview< Kokkos::Cuda >();
-  test_view_mapping_subview< Kokkos::CudaUVMSpace >();
-  test_view_mapping_operator< Kokkos::Cuda >();
-  test_view_mapping_operator< Kokkos::CudaUVMSpace >();
-  TestViewMappingAtomic< Kokkos::Cuda >::run();
-}
-
-TEST_F( cuda , view_of_class )
-{
-  TestViewMappingClassValue< Kokkos::CudaSpace >::run();
-  TestViewMappingClassValue< Kokkos::CudaUVMSpace >::run();
-}
-
-template< class MemSpace >
-struct TestViewCudaTexture {
-
-  enum { N = 1000 };
-
-  using V = Kokkos::Experimental::View<double*,MemSpace> ;
-  using T = Kokkos::Experimental::View<const double*, MemSpace, Kokkos::MemoryRandomAccess > ;
-
-  V m_base ;
-  T m_tex ;
-
-  struct TagInit {};
-  struct TagTest {};
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagInit & , const int i ) const { m_base[i] = i + 1 ; }
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagTest & , const int i , long & error_count ) const
-    { if ( m_tex[i] != i + 1 ) ++error_count ; }
-
-  TestViewCudaTexture()
-    : m_base("base",N)
-    , m_tex( m_base )
-    {}
-
-  static void run()
-    {
-      EXPECT_TRUE( ( std::is_same< typename V::reference_type
-                                 , double &
-                                 >::value ) );
-
-      EXPECT_TRUE( ( std::is_same< typename T::reference_type
-                                 , const double
-                                 >::value ) );
-
-      EXPECT_TRUE(  V::reference_type_is_lvalue_reference ); // An ordinary view
-      EXPECT_FALSE( T::reference_type_is_lvalue_reference ); // Texture fetch returns by value
-
-      TestViewCudaTexture self ;
-      Kokkos::parallel_for( Kokkos::RangePolicy< Kokkos::Cuda , TagInit >(0,N) , self );
-      long error_count = -1 ;
-      Kokkos::parallel_reduce( Kokkos::RangePolicy< Kokkos::Cuda , TagTest >(0,N) , self , error_count );
-      EXPECT_EQ( error_count , 0 );
-    }
-};
-
-
-TEST_F( cuda , impl_view_texture )
-{
-  TestViewCudaTexture< Kokkos::CudaSpace >::run();
-  TestViewCudaTexture< Kokkos::CudaUVMSpace >::run();
-}
-
-template< class MemSpace , class ExecSpace >
-struct TestViewCudaAccessible {
-
-  enum { N = 1000 };
-
-  using V = Kokkos::Experimental::View<double*,MemSpace> ;
-
-  V m_base ;
-
-  struct TagInit {};
-  struct TagTest {};
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagInit & , const int i ) const { m_base[i] = i + 1 ; }
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagTest & , const int i , long & error_count ) const
-    { if ( m_base[i] != i + 1 ) ++error_count ; }
-
-  TestViewCudaAccessible()
-    : m_base("base",N)
-    {}
-
-  static void run()
-    {
-      TestViewCudaAccessible self ;
-      Kokkos::parallel_for( Kokkos::RangePolicy< typename MemSpace::execution_space , TagInit >(0,N) , self );
-      MemSpace::execution_space::fence();
-      // Next access is a different execution space, must complete prior kernel.
-      long error_count = -1 ;
-      Kokkos::parallel_reduce( Kokkos::RangePolicy< ExecSpace , TagTest >(0,N) , self , error_count );
-      EXPECT_EQ( error_count , 0 );
-    }
-};
-
-
-TEST_F( cuda , impl_view_accessible )
-{
-  TestViewCudaAccessible< Kokkos::CudaSpace , Kokkos::Cuda >::run();
-
-  TestViewCudaAccessible< Kokkos::CudaUVMSpace , Kokkos::Cuda >::run();
-  TestViewCudaAccessible< Kokkos::CudaUVMSpace , Kokkos::HostSpace::execution_space >::run();
-
-  TestViewCudaAccessible< Kokkos::CudaHostPinnedSpace , Kokkos::Cuda >::run();
-  TestViewCudaAccessible< Kokkos::CudaHostPinnedSpace , Kokkos::HostSpace::execution_space >::run();
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda, view_impl )
-{
-  // test_abort<<<32,32>>>(); // Aborts the kernel with CUDA version 4.1 or greater
-
-  test_view_impl< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_api )
-{
-  typedef Kokkos::View< const int * , Kokkos::Cuda , Kokkos::MemoryTraits< Kokkos::RandomAccess > > view_texture_managed ;
-  typedef Kokkos::View< const int * , Kokkos::Cuda , Kokkos::MemoryTraits< Kokkos::RandomAccess | Kokkos::Unmanaged > > view_texture_unmanaged ;
-
-  TestViewAPI< double , Kokkos::Cuda >();
-  TestViewAPI< double , Kokkos::CudaUVMSpace >();
-
-#if 0
-  Kokkos::View<double, Kokkos::Cuda > x("x");
-  Kokkos::View<double[1], Kokkos::Cuda > y("y");
-  // *x = 10 ;
-  // x() = 10 ;
-  // y[0] = 10 ;
-  // y(0) = 10 ;
-#endif
-}
-
-
-TEST_F( cuda , view_nested_view )
-{
-  ::Test::view_nested_view< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_auto_1d_left ) {
-  TestViewSubview::test_auto_1d< Kokkos::LayoutLeft,Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_auto_1d_right ) {
-  TestViewSubview::test_auto_1d< Kokkos::LayoutRight,Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_auto_1d_stride ) {
-  TestViewSubview::test_auto_1d< Kokkos::LayoutStride,Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_assign_strided ) {
-  TestViewSubview::test_1d_strided_assignment< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_left_0 ) {
-  TestViewSubview::test_left_0< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_left_1 ) {
-  TestViewSubview::test_left_1< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_left_2 ) {
-  TestViewSubview::test_left_2< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_left_3 ) {
-  TestViewSubview::test_left_3< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_right_0 ) {
-  TestViewSubview::test_right_0< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_right_1 ) {
-  TestViewSubview::test_right_1< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_right_3 ) {
-  TestViewSubview::test_right_3< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_1d_assign ) {
-  TestViewSubview::test_1d_assign< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_2d_from_3d ) {
-  TestViewSubview::test_2d_subview_3d< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_2d_from_5d ) {
-  TestViewSubview::test_2d_subview_5d< Kokkos::CudaUVMSpace >();
-}
-*/
 
 TEST_F( cuda, range_tag )
 {
+  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_for(3);
+  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_reduce(3);
+  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_scan(3);
+  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(3);
+  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(3);
+  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_scan(3);
   TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
   TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
   TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_scan(1000);
@@ -380,6 +112,10 @@ TEST_F( cuda, range_tag )
 
 TEST_F( cuda, team_tag )
 {
+  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_for(3);
+  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_reduce(3);
+  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(3);
+  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(3);
   TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
   TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
   TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(1000);
@@ -393,6 +129,14 @@ TEST_F( cuda, reduce )
   TestReduce< int , Kokkos::Cuda >( 0 );
 }
 
+TEST_F( cuda , reducers )
+{
+  TestReducers<int, Kokkos::Cuda>::execute_integer();
+  TestReducers<size_t, Kokkos::Cuda>::execute_integer();
+  TestReducers<double, Kokkos::Cuda>::execute_float();
+  TestReducers<Kokkos::complex<double>, Kokkos::Cuda>::execute_basic();
+}
+
 TEST_F( cuda, reduce_team )
 {
   TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 3 );
@@ -411,7 +155,6 @@ TEST_F( cuda, shared_team )
   TestSharedTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >();
 }
 
-
 #if defined (KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA)
 TEST_F( cuda, lambda_shared_team )
 {
@@ -424,6 +167,14 @@ TEST_F( cuda, lambda_shared_team )
 }
 #endif
 
+TEST_F( cuda, shmem_size) {
+  TestShmemSize< Kokkos::Cuda >();
+}
+
+TEST_F( cuda, multi_level_scratch) {
+  TestMultiLevelScratchTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >();
+  TestMultiLevelScratchTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >();
+}
 
 TEST_F( cuda, reduce_dynamic )
 {
@@ -436,178 +187,5 @@ TEST_F( cuda, reduce_dynamic_view )
   TestReduceDynamicView< long ,   Kokkos::Cuda >( 10000000 );
   TestReduceDynamicView< double , Kokkos::Cuda >( 1000000 );
 }
-/*
-TEST_F( cuda, atomic )
-{
-  const int loop_count = 1e3 ;
-
-  ASSERT_TRUE( ( TestAtomic::Loop<int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<long int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned long int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned long int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<unsigned long int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<long long int,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long long int,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<long long int,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<double,Kokkos::Cuda>(loop_count,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<double,Kokkos::Cuda>(loop_count,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<double,Kokkos::Cuda>(loop_count,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<float,Kokkos::Cuda>(100,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<float,Kokkos::Cuda>(100,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<float,Kokkos::Cuda>(100,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<Kokkos::complex<double> ,Kokkos::Cuda>(100,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<Kokkos::complex<double> ,Kokkos::Cuda>(100,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<Kokkos::complex<double> ,Kokkos::Cuda>(100,3) ) );
-
-  ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::Cuda>(100,1) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::Cuda>(100,2) ) );
-  ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::Cuda>(100,3) ) );
-
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda, tile_layout)
-{
-  TestTile::test< Kokkos::Cuda , 1 , 1 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 1 , 1 >( 2 , 3 );
-  TestTile::test< Kokkos::Cuda , 1 , 1 >( 9 , 10 );
-
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 2 , 3 );
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 4 , 4 );
-  TestTile::test< Kokkos::Cuda , 2 , 2 >( 9 , 9 );
 
-  TestTile::test< Kokkos::Cuda , 2 , 4 >( 9 , 9 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 9 , 9 );
-
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 4 , 4 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 9 , 9 );
-  TestTile::test< Kokkos::Cuda , 4 , 4 >( 9 , 11 );
-
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 1 , 1 );
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 4 , 4 );
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 9 , 9 );
-  TestTile::test< Kokkos::Cuda , 8 , 8 >( 9 , 11 );
-}
-
-TEST_F( cuda , view_aggregate )
-{
-  TestViewAggregate< Kokkos::Cuda >();
-  TestViewAggregateReduction< Kokkos::Cuda >();
 }
-
-
-TEST_F( cuda , scan )
-{
-  TestScan< Kokkos::Cuda >::test_range( 1 , 1000 );
-  TestScan< Kokkos::Cuda >( 1000000 );
-  TestScan< Kokkos::Cuda >( 10000000 );
-
-  TestScan< Kokkos::Cuda >( 0 );
-  TestScan< Kokkos::Cuda >( 0 , 0 );
-
-  Kokkos::Cuda::fence();
-}
-
-TEST_F( cuda , team_scan )
-{
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 10 );
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 10 );
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 10000 );
-  TestScanTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 10000 );
-}
-
-TEST_F( cuda , memory_pool )
-{
-  bool val_uvm = TestMemoryPool::test_mempool< Kokkos::Cuda, Kokkos::CudaUVMSpace >( 128, 128000 );
-  ASSERT_TRUE( val_uvm );
-
-  Kokkos::Cuda::fence();
-
-  TestMemoryPool::test_mempool2< Kokkos::Cuda, Kokkos::CudaUVMSpace >( 128, 2560000 );
-
-  Kokkos::Cuda::fence();
-}
-
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda , template_meta_functions )
-{
-  TestTemplateMetaFunctions<int, Kokkos::Cuda >();
-}
-
-//----------------------------------------------------------------------------
-
-namespace Test {
-
-TEST_F( cuda , reduction_deduction )
-{
-  TestCXX11::test_reduction_deduction< Kokkos::Cuda >();
-}
-
-TEST_F( cuda , team_vector )
-{
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(0) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(1) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(2) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(3) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(4) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(5) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(6) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(7) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(8) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(9) ) );
-  ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(10) ) );
-}
-*/
-}
-
-//----------------------------------------------------------------------------
-/*
-#if defined( KOKKOS_ENABLE_CUDA_TASK_POLICY )
-
-TEST_F( cuda , task_policy )
-{
-  TestTaskPolicy::test_task_dep< Kokkos::Cuda >( 10 );
-
-  for ( long i = 0 ; i < 15 ; ++i ) {
-      // printf("TestTaskPolicy::test_fib< Kokkos::Cuda >(%d);\n",i);
-    TestTaskPolicy::test_fib< Kokkos::Cuda >(i,4096);
-  }
-  for ( long i = 0 ; i < 35 ; ++i ) {
-      // printf("TestTaskPolicy::test_fib2< Kokkos::Cuda >(%d);\n",i);
-    TestTaskPolicy::test_fib2< Kokkos::Cuda >(i,4096);
-  }
-}
-
-TEST_F( cuda , task_team )
-{
-  TestTaskPolicy::test_task_team< Kokkos::Cuda >(1000);
-}
-
-TEST_F( cuda , task_latch )
-{
-  TestTaskPolicy::test_latch< Kokkos::Cuda >(10);
-  TestTaskPolicy::test_latch< Kokkos::Cuda >(1000);
-}
-
-#endif /* #if defined( KOKKOS_ENABLE_CUDA_TASK_POLICY ) */
-
diff --git a/lib/kokkos/core/unit_test/TestCuda_c.cpp b/lib/kokkos/core/unit_test/TestCuda_c.cpp
index 24635959c5..70584cead1 100644
--- a/lib/kokkos/core/unit_test/TestCuda_c.cpp
+++ b/lib/kokkos/core/unit_test/TestCuda_c.cpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -60,6 +60,7 @@
 
 #include <TestViewImpl.hpp>
 #include <TestAtomic.hpp>
+#include <TestAtomicOperations.hpp>
 
 #include <TestViewAPI.hpp>
 #include <TestViewSubview.hpp>
@@ -85,358 +86,14 @@
 
 class cuda : public ::testing::Test {
 protected:
-  static void SetUpTestCase()
-  {
-    Kokkos::Cuda::print_configuration( std::cout );
-    Kokkos::HostSpace::execution_space::initialize();
-    Kokkos::Cuda::initialize( Kokkos::Cuda::SelectDevice(0) );
-  }
-  static void TearDownTestCase()
-  {
-    Kokkos::Cuda::finalize();
-    Kokkos::HostSpace::execution_space::finalize();
-  }
+  static void SetUpTestCase();
+  static void TearDownTestCase();
 };
 
 //----------------------------------------------------------------------------
 
 namespace Test {
-/*
-__global__
-void test_abort()
-{
-  Kokkos::Impl::VerifyExecutionCanAccessMemorySpace<
-    Kokkos::CudaSpace ,
-    Kokkos::HostSpace >::verify();
-}
-
-__global__
-void test_cuda_spaces_int_value( int * ptr )
-{
-  if ( *ptr == 42 ) { *ptr = 2 * 42 ; }
-}
-
-
-TEST_F( cuda , compiler_macros )
-{
-  ASSERT_TRUE( ( TestCompilerMacros::Test< Kokkos::Cuda >() ) );
-}
-
-TEST_F( cuda , memory_space )
-{
-  TestMemorySpace< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, uvm )
-{
-  if ( Kokkos::CudaUVMSpace::available() ) {
-
-    int * uvm_ptr = (int*) Kokkos::kokkos_malloc< Kokkos::CudaUVMSpace >("uvm_ptr",sizeof(int));
-
-    *uvm_ptr = 42 ;
-
-    Kokkos::Cuda::fence();
-    test_cuda_spaces_int_value<<<1,1>>>(uvm_ptr);
-    Kokkos::Cuda::fence();
-
-    EXPECT_EQ( *uvm_ptr, int(2*42) );
-
-    Kokkos::kokkos_free< Kokkos::CudaUVMSpace >(uvm_ptr );
-  }
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda , impl_shared_alloc )
-{
-  test_shared_alloc< Kokkos::CudaSpace , Kokkos::HostSpace::execution_space >();
-  test_shared_alloc< Kokkos::CudaUVMSpace , Kokkos::HostSpace::execution_space >();
-  test_shared_alloc< Kokkos::CudaHostPinnedSpace , Kokkos::HostSpace::execution_space >();
-}
-
-TEST_F( cuda, policy_construction) {
-  TestRangePolicyConstruction< Kokkos::Cuda >();
-  TestTeamPolicyConstruction< Kokkos::Cuda >();
-}
-
-TEST_F( cuda , impl_view_mapping )
-{
-  test_view_mapping< Kokkos::Cuda >();
-  test_view_mapping< Kokkos::CudaUVMSpace >();
-  test_view_mapping_subview< Kokkos::Cuda >();
-  test_view_mapping_subview< Kokkos::CudaUVMSpace >();
-  test_view_mapping_operator< Kokkos::Cuda >();
-  test_view_mapping_operator< Kokkos::CudaUVMSpace >();
-  TestViewMappingAtomic< Kokkos::Cuda >::run();
-}
-
-TEST_F( cuda , view_of_class )
-{
-  TestViewMappingClassValue< Kokkos::CudaSpace >::run();
-  TestViewMappingClassValue< Kokkos::CudaUVMSpace >::run();
-}
-
-template< class MemSpace >
-struct TestViewCudaTexture {
 
-  enum { N = 1000 };
-
-  using V = Kokkos::Experimental::View<double*,MemSpace> ;
-  using T = Kokkos::Experimental::View<const double*, MemSpace, Kokkos::MemoryRandomAccess > ;
-
-  V m_base ;
-  T m_tex ;
-
-  struct TagInit {};
-  struct TagTest {};
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagInit & , const int i ) const { m_base[i] = i + 1 ; }
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagTest & , const int i , long & error_count ) const
-    { if ( m_tex[i] != i + 1 ) ++error_count ; }
-
-  TestViewCudaTexture()
-    : m_base("base",N)
-    , m_tex( m_base )
-    {}
-
-  static void run()
-    {
-      EXPECT_TRUE( ( std::is_same< typename V::reference_type
-                                 , double &
-                                 >::value ) );
-
-      EXPECT_TRUE( ( std::is_same< typename T::reference_type
-                                 , const double
-                                 >::value ) );
-
-      EXPECT_TRUE(  V::reference_type_is_lvalue_reference ); // An ordinary view
-      EXPECT_FALSE( T::reference_type_is_lvalue_reference ); // Texture fetch returns by value
-
-      TestViewCudaTexture self ;
-      Kokkos::parallel_for( Kokkos::RangePolicy< Kokkos::Cuda , TagInit >(0,N) , self );
-      long error_count = -1 ;
-      Kokkos::parallel_reduce( Kokkos::RangePolicy< Kokkos::Cuda , TagTest >(0,N) , self , error_count );
-      EXPECT_EQ( error_count , 0 );
-    }
-};
-
-
-TEST_F( cuda , impl_view_texture )
-{
-  TestViewCudaTexture< Kokkos::CudaSpace >::run();
-  TestViewCudaTexture< Kokkos::CudaUVMSpace >::run();
-}
-
-template< class MemSpace , class ExecSpace >
-struct TestViewCudaAccessible {
-
-  enum { N = 1000 };
-
-  using V = Kokkos::Experimental::View<double*,MemSpace> ;
-
-  V m_base ;
-
-  struct TagInit {};
-  struct TagTest {};
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagInit & , const int i ) const { m_base[i] = i + 1 ; }
-
-  KOKKOS_INLINE_FUNCTION
-  void operator()( const TagTest & , const int i , long & error_count ) const
-    { if ( m_base[i] != i + 1 ) ++error_count ; }
-
-  TestViewCudaAccessible()
-    : m_base("base",N)
-    {}
-
-  static void run()
-    {
-      TestViewCudaAccessible self ;
-      Kokkos::parallel_for( Kokkos::RangePolicy< typename MemSpace::execution_space , TagInit >(0,N) , self );
-      MemSpace::execution_space::fence();
-      // Next access is a different execution space, must complete prior kernel.
-      long error_count = -1 ;
-      Kokkos::parallel_reduce( Kokkos::RangePolicy< ExecSpace , TagTest >(0,N) , self , error_count );
-      EXPECT_EQ( error_count , 0 );
-    }
-};
-
-
-TEST_F( cuda , impl_view_accessible )
-{
-  TestViewCudaAccessible< Kokkos::CudaSpace , Kokkos::Cuda >::run();
-
-  TestViewCudaAccessible< Kokkos::CudaUVMSpace , Kokkos::Cuda >::run();
-  TestViewCudaAccessible< Kokkos::CudaUVMSpace , Kokkos::HostSpace::execution_space >::run();
-
-  TestViewCudaAccessible< Kokkos::CudaHostPinnedSpace , Kokkos::Cuda >::run();
-  TestViewCudaAccessible< Kokkos::CudaHostPinnedSpace , Kokkos::HostSpace::execution_space >::run();
-}
-
-//----------------------------------------------------------------------------
-
-TEST_F( cuda, view_impl )
-{
-  // test_abort<<<32,32>>>(); // Aborts the kernel with CUDA version 4.1 or greater
-
-  test_view_impl< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_api )
-{
-  typedef Kokkos::View< const int * , Kokkos::Cuda , Kokkos::MemoryTraits< Kokkos::RandomAccess > > view_texture_managed ;
-  typedef Kokkos::View< const int * , Kokkos::Cuda , Kokkos::MemoryTraits< Kokkos::RandomAccess | Kokkos::Unmanaged > > view_texture_unmanaged ;
-
-  TestViewAPI< double , Kokkos::Cuda >();
-  TestViewAPI< double , Kokkos::CudaUVMSpace >();
-
-#if 0
-  Kokkos::View<double, Kokkos::Cuda > x("x");
-  Kokkos::View<double[1], Kokkos::Cuda > y("y");
-  // *x = 10 ;
-  // x() = 10 ;
-  // y[0] = 10 ;
-  // y(0) = 10 ;
-#endif
-}
-
-
-TEST_F( cuda , view_nested_view )
-{
-  ::Test::view_nested_view< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_auto_1d_left ) {
-  TestViewSubview::test_auto_1d< Kokkos::LayoutLeft,Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_auto_1d_right ) {
-  TestViewSubview::test_auto_1d< Kokkos::LayoutRight,Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_auto_1d_stride ) {
-  TestViewSubview::test_auto_1d< Kokkos::LayoutStride,Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_assign_strided ) {
-  TestViewSubview::test_1d_strided_assignment< Kokkos::Cuda >();
-}
-
-TEST_F( cuda, view_subview_left_0 ) {
-  TestViewSubview::test_left_0< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_left_1 ) {
-  TestViewSubview::test_left_1< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_left_2 ) {
-  TestViewSubview::test_left_2< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_left_3 ) {
-  TestViewSubview::test_left_3< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_right_0 ) {
-  TestViewSubview::test_right_0< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_right_1 ) {
-  TestViewSubview::test_right_1< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_right_3 ) {
-  TestViewSubview::test_right_3< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_1d_assign ) {
-  TestViewSubview::test_1d_assign< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_2d_from_3d ) {
-  TestViewSubview::test_2d_subview_3d< Kokkos::CudaUVMSpace >();
-}
-
-TEST_F( cuda, view_subview_2d_from_5d ) {
-  TestViewSubview::test_2d_subview_5d< Kokkos::CudaUVMSpace >();
-}
-
-
-TEST_F( cuda, range_tag )
-{
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_scan(1000);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(1001);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(1001);
-  TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_scan(1001);
-  //TestRange< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_dynamic_policy(1000);
-}
-
-TEST_F( cuda, team_tag )
-{
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(1000);
-  TestTeamPolicy< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(1000);
-}
-
-TEST_F( cuda, reduce )
-{
-  TestReduce< long ,   Kokkos::Cuda >( 10000000 );
-  TestReduce< double , Kokkos::Cuda >( 1000000 );
-  TestReduce< int , Kokkos::Cuda >( 0 );
-}
-
-TEST_F( cuda, reduce_team )
-{
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 3 );
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 3 );
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 100000 );
-  TestReduceTeam< long ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 100000 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 3 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 3 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >( 100000 );
-  TestReduceTeam< double ,   Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >( 100000 );
-}
-
-TEST_F( cuda, shared_team )
-{
-  TestSharedTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static> >();
-  TestSharedTeam< Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic> >();
-}
-
-
-#if defined (KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA)
-TEST_F( cuda, lambda_shared_team )
-{
-  TestLambdaSharedTeam< Kokkos::CudaSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Static> >();
-  TestLambdaSharedTeam< Kokkos::CudaUVMSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Static> >();
-  TestLambdaSharedTeam< Kokkos::CudaHostPinnedSpace, Kokkos::Cuda , Kokkos::Schedule<Kokkos::Static>  >();
-  TestLambdaSharedTeam< Kokkos::CudaSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Dynamic> >();
-  TestLambdaSharedTeam< Kokkos::CudaUVMSpace, Kokkos::Cuda, Kokkos::Schedule<Kokkos::Dynamic> >();
-  TestLambdaSharedTeam< Kokkos::CudaHostPinnedSpace, Kokkos::Cuda , Kokkos::Schedule<Kokkos::Dynamic>  >();
-}
-#endif
-
-
-TEST_F( cuda, reduce_dynamic )
-{
-  TestReduceDynamic< long ,   Kokkos::Cuda >( 10000000 );
-  TestReduceDynamic< double , Kokkos::Cuda >( 1000000 );
-}
-
-TEST_F( cuda, reduce_dynamic_view )
-{
-  TestReduceDynamicView< long ,   Kokkos::Cuda >( 10000000 );
-  TestReduceDynamicView< double , Kokkos::Cuda >( 1000000 );
-}
-*/
 TEST_F( cuda, atomic )
 {
   const int loop_count = 1e3 ;
@@ -479,6 +136,75 @@ TEST_F( cuda, atomic )
 
 }
 
+TEST_F( cuda , atomic_operations )
+{
+  const int start = 1; //Avoid zero for division
+  const int end = 11;
+  for (int i = start; i < end; ++i)
+  {
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Cuda>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Cuda>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Cuda>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Cuda>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Cuda>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Cuda>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Cuda>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Cuda>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Cuda>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Cuda>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Cuda>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Cuda>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Cuda>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Cuda>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Cuda>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Cuda>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Cuda>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Cuda>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Cuda>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Cuda>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Cuda>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Cuda>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Cuda>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Cuda>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Cuda>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Cuda>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Cuda>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Cuda>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Cuda>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Cuda>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Cuda>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Cuda>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Cuda>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Cuda>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Cuda>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Cuda>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Cuda>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Cuda>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Cuda>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Cuda>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Cuda>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Cuda>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Cuda>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Cuda>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Cuda>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Cuda>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Cuda>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Cuda>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Cuda>(start, end-i, 4 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Cuda>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Cuda>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Cuda>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Cuda>(start, end-i, 4 ) ) );
+  }
+
+}
+
 //----------------------------------------------------------------------------
 
 TEST_F( cuda, tile_layout)
@@ -512,7 +238,6 @@ TEST_F( cuda , view_aggregate )
   TestViewAggregateReduction< Kokkos::Cuda >();
 }
 
-
 TEST_F( cuda , scan )
 {
   TestScan< Kokkos::Cuda >::test_range( 1 , 1000 );
@@ -535,12 +260,19 @@ TEST_F( cuda , team_scan )
 
 TEST_F( cuda , memory_pool )
 {
-  bool val_uvm = TestMemoryPool::test_mempool< Kokkos::Cuda, Kokkos::CudaUVMSpace >( 128, 128000 );
-  ASSERT_TRUE( val_uvm );
+//  typedef Kokkos::CudaUVMSpace  device_type;
+  typedef Kokkos::Cuda          device_type;
+
+  bool val = TestMemoryPool::test_mempool< device_type >( 128, 128000000 );
+  ASSERT_TRUE( val );
 
   Kokkos::Cuda::fence();
 
-  TestMemoryPool::test_mempool2< Kokkos::Cuda, Kokkos::CudaUVMSpace >( 128, 2560000 );
+  TestMemoryPool::test_mempool2< device_type >( 64, 4, 100000, 200000 );
+
+  Kokkos::Cuda::fence();
+
+  TestMemoryPool::test_memory_exhaustion< Kokkos::Cuda >();
 
   Kokkos::Cuda::fence();
 }
@@ -578,13 +310,43 @@ TEST_F( cuda , team_vector )
   ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Cuda >(10) ) );
 }
 
+TEST_F( cuda, triple_nested_parallelism )
+{
+  TestTripleNestedReduce< double, Kokkos::Cuda >( 8192, 2048 , 32 , 32 );
+  TestTripleNestedReduce< double, Kokkos::Cuda >( 8192, 2048 , 32 , 16 );
+  TestTripleNestedReduce< double, Kokkos::Cuda >( 8192, 2048 , 16 , 16 );
+}
+
 }
 
 //----------------------------------------------------------------------------
 
-#if defined( KOKKOS_ENABLE_CUDA_TASK_POLICY )
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
 
-TEST_F( cuda , task_policy )
+TEST_F( cuda , task_fib )
+{
+  for ( int i = 0 ; i < 25 ; ++i ) {
+    TestTaskPolicy::TestFib< Kokkos::Cuda >::run(i, (i+1)*1000000 );
+  }
+}
+
+TEST_F( cuda , task_depend )
+{
+  for ( int i = 0 ; i < 25 ; ++i ) {
+    TestTaskPolicy::TestTaskDependence< Kokkos::Cuda >::run(i);
+  }
+}
+
+TEST_F( cuda , task_team )
+{
+  //TestTaskPolicy::TestTaskTeam< Kokkos::Cuda >::run(1000);
+  TestTaskPolicy::TestTaskTeam< Kokkos::Cuda >::run(104);
+  TestTaskPolicy::TestTaskTeamValue< Kokkos::Cuda >::run(1000);
+}
+
+//----------------------------------------------------------------------------
+
+TEST_F( cuda , old_task_policy )
 {
   TestTaskPolicy::test_task_dep< Kokkos::Cuda >( 10 );
 
@@ -598,16 +360,16 @@ TEST_F( cuda , task_policy )
   }
 }
 
-TEST_F( cuda , task_team )
+TEST_F( cuda , old_task_team )
 {
   TestTaskPolicy::test_task_team< Kokkos::Cuda >(1000);
 }
 
-TEST_F( cuda , task_latch )
+TEST_F( cuda , old_task_latch )
 {
   TestTaskPolicy::test_latch< Kokkos::Cuda >(10);
   TestTaskPolicy::test_latch< Kokkos::Cuda >(1000);
 }
 
-#endif /* #if defined( KOKKOS_ENABLE_CUDA_TASK_POLICY ) */
+#endif // #if defined( KOKKOS_ENABLE_TASKPOLICY )
 
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp
similarity index 93%
rename from lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.cpp
rename to lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp
index a1e3f8fb0a..a17ed97a9f 100644
--- a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.cpp
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp
@@ -257,11 +257,13 @@ protected:
   }
 };
 
-
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_01
 TEST_F( defaultdevicetypeinit, no_args) {
   Impl::test_no_arguments();
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_02
 TEST_F( defaultdevicetypeinit, commandline_args_empty) {
   Kokkos::InitArguments argstruct;
   int nargs = 0;
@@ -271,7 +273,9 @@ TEST_F( defaultdevicetypeinit, commandline_args_empty) {
     delete [] args[i];
   delete [] args;
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_03
 TEST_F( defaultdevicetypeinit, commandline_args_other) {
   Kokkos::InitArguments argstruct;
   int nargs = 0;
@@ -281,7 +285,9 @@ TEST_F( defaultdevicetypeinit, commandline_args_other) {
     delete [] args[i];
   delete [] args;
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_04
 TEST_F( defaultdevicetypeinit, commandline_args_nthreads) {
   Kokkos::InitArguments argstruct;
   int nargs = 0;
@@ -291,7 +297,9 @@ TEST_F( defaultdevicetypeinit, commandline_args_nthreads) {
     delete [] args[i];
   delete [] args;
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_05
 TEST_F( defaultdevicetypeinit, commandline_args_nthreads_numa) {
   Kokkos::InitArguments argstruct;
   int nargs = 0;
@@ -301,7 +309,9 @@ TEST_F( defaultdevicetypeinit, commandline_args_nthreads_numa) {
     delete [] args[i];
   delete [] args;
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_06
 TEST_F( defaultdevicetypeinit, commandline_args_nthreads_numa_device) {
   Kokkos::InitArguments argstruct;
   int nargs = 0;
@@ -311,7 +321,9 @@ TEST_F( defaultdevicetypeinit, commandline_args_nthreads_numa_device) {
     delete [] args[i];
   delete [] args;
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_07
 TEST_F( defaultdevicetypeinit, commandline_args_nthreads_device) {
   Kokkos::InitArguments argstruct;
   int nargs = 0;
@@ -321,7 +333,9 @@ TEST_F( defaultdevicetypeinit, commandline_args_nthreads_device) {
     delete [] args[i];
   delete [] args;
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_08
 TEST_F( defaultdevicetypeinit, commandline_args_numa_device) {
   Kokkos::InitArguments argstruct;
   int nargs = 0;
@@ -331,7 +345,9 @@ TEST_F( defaultdevicetypeinit, commandline_args_numa_device) {
     delete [] args[i];
   delete [] args;
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_09
 TEST_F( defaultdevicetypeinit, commandline_args_device) {
   Kokkos::InitArguments argstruct;
   int nargs = 0;
@@ -341,7 +357,9 @@ TEST_F( defaultdevicetypeinit, commandline_args_device) {
     delete [] args[i];
   delete [] args;
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_10
 TEST_F( defaultdevicetypeinit, commandline_args_nthreads_numa_device_other) {
   Kokkos::InitArguments argstruct;
   int nargs = 0;
@@ -351,38 +369,49 @@ TEST_F( defaultdevicetypeinit, commandline_args_nthreads_numa_device_other) {
     delete [] args[i];
   delete [] args;
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_11
 TEST_F( defaultdevicetypeinit, initstruct_default) {
   Kokkos::InitArguments args;
   Impl::test_initstruct_args(args);
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_12
 TEST_F( defaultdevicetypeinit, initstruct_nthreads) {
   Kokkos::InitArguments args = Impl::init_initstruct(true,false,false);
   Impl::test_initstruct_args(args);
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_13
 TEST_F( defaultdevicetypeinit, initstruct_nthreads_numa) {
   Kokkos::InitArguments args = Impl::init_initstruct(true,true,false);
   Impl::test_initstruct_args(args);
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_14
 TEST_F( defaultdevicetypeinit, initstruct_device) {
   Kokkos::InitArguments args = Impl::init_initstruct(false,false,true);
   Impl::test_initstruct_args(args);
 }
+#endif
 
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_15
 TEST_F( defaultdevicetypeinit, initstruct_nthreads_device) {
   Kokkos::InitArguments args = Impl::init_initstruct(true,false,true);
   Impl::test_initstruct_args(args);
 }
+#endif
 
-
+#ifdef KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_16
 TEST_F( defaultdevicetypeinit, initstruct_nthreads_numa_device) {
   Kokkos::InitArguments args = Impl::init_initstruct(true,true,true);
   Impl::test_initstruct_args(args);
 }
-
+#endif
 
 
 } // namespace test
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_1.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_1.cpp
new file mode 100644
index 0000000000..40a773b3b8
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_1.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_01
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_10.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_10.cpp
new file mode 100644
index 0000000000..f12c4f62b2
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_10.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_10
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_11.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_11.cpp
new file mode 100644
index 0000000000..c7ffd7b94e
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_11.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_11
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_12.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_12.cpp
new file mode 100644
index 0000000000..24e2b15201
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_12.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_12
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_13.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_13.cpp
new file mode 100644
index 0000000000..7968c13b66
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_13.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_13
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_14.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_14.cpp
new file mode 100644
index 0000000000..ab0563c6dc
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_14.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_14
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_15.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_15.cpp
new file mode 100644
index 0000000000..70a8ca1727
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_15.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_15
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_16.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_16.cpp
new file mode 100644
index 0000000000..727c7a95eb
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_16.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_16
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_2.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_2.cpp
new file mode 100644
index 0000000000..88fba34c50
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_2.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_02
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_3.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_3.cpp
new file mode 100644
index 0000000000..b3562cc53d
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_3.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_03
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_4.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_4.cpp
new file mode 100644
index 0000000000..0d4983319c
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_4.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_04
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_5.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_5.cpp
new file mode 100644
index 0000000000..026fb01f88
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_5.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_05
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_6.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_6.cpp
new file mode 100644
index 0000000000..937a13160e
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_6.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_06
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_7.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_7.cpp
new file mode 100644
index 0000000000..992c854c1a
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_7.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_07
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_8.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_8.cpp
new file mode 100644
index 0000000000..07a8b1cb7c
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_8.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_08
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_9.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_9.cpp
new file mode 100644
index 0000000000..4d8c05be2d
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit_9.cpp
@@ -0,0 +1,2 @@
+#define KOKKOS_DEFAULTDEVICETYPE_INIT_TEST_09
+#include<TestDefaultDeviceTypeInit.hpp>
diff --git a/lib/kokkos/core/src/impl/Kokkos_MemoryPool.cpp b/lib/kokkos/core/unit_test/TestDefaultDeviceType_a.cpp
similarity index 77%
rename from lib/kokkos/core/src/impl/Kokkos_MemoryPool.cpp
rename to lib/kokkos/core/unit_test/TestDefaultDeviceType_a.cpp
index 70f0545b2c..c15f812233 100644
--- a/lib/kokkos/core/src/impl/Kokkos_MemoryPool.cpp
+++ b/lib/kokkos/core/unit_test/TestDefaultDeviceType_a.cpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-//
+// 
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-//
+// 
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-//
+// 
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,9 +36,41 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-//
+// 
 // ************************************************************************
 //@HEADER
 */
 
-#include<impl/Kokkos_MemoryPool_Inline.hpp>
+#include <gtest/gtest.h>
+
+#include <Kokkos_Core.hpp>
+
+#if !defined(KOKKOS_HAVE_CUDA) || defined(__CUDACC__)
+//----------------------------------------------------------------------------
+
+#include <TestReduce.hpp>
+
+
+namespace Test {
+
+class defaultdevicetype : public ::testing::Test {
+protected:
+  static void SetUpTestCase()
+  {
+    Kokkos::initialize();
+  }
+
+  static void TearDownTestCase()
+  {
+    Kokkos::finalize();
+  }
+};
+
+
+TEST_F( defaultdevicetype, reduce_instantiation) {
+  TestReduceCombinatoricalInstantiation<>::execute();
+}
+
+} // namespace test
+
+#endif
diff --git a/lib/kokkos/core/unit_test/TestMDRange.hpp b/lib/kokkos/core/unit_test/TestMDRange.hpp
new file mode 100644
index 0000000000..9894d1ce69
--- /dev/null
+++ b/lib/kokkos/core/unit_test/TestMDRange.hpp
@@ -0,0 +1,555 @@
+/*
+//@HEADER
+// ************************************************************************
+//
+//                        Kokkos v. 2.0
+//              Copyright (2014) Sandia Corporation
+//
+// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
+// the U.S. Government retains certain rights in this software.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the Corporation nor the names of the
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
+// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
+// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
+//
+// ************************************************************************
+//@HEADER
+*/
+
+#include <stdio.h>
+
+#include <gtest/gtest.h>
+
+#include <Kokkos_Core.hpp>
+
+/*--------------------------------------------------------------------------*/
+
+namespace Test {
+namespace {
+
+template <typename ExecSpace >
+struct TestMDRange_2D {
+
+  using DataType     = int ;
+  using ViewType     = typename Kokkos::View< DataType** ,  ExecSpace > ;
+  using HostViewType = typename ViewType::HostMirror ;
+
+  ViewType input_view ;
+
+  TestMDRange_2D( const DataType N0, const DataType N1 ) : input_view("input_view", N0, N1) {}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()( const int i , const int j ) const
+  {
+    input_view(i,j) = 1;
+  }
+
+
+  static void test_for2( const int64_t N0, const int64_t N1 )
+  {
+
+    using namespace Kokkos::Experimental;
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<2>, Kokkos::IndexType<int> >;
+      range_type range( {0,0}, {N0,N1} );
+      TestMDRange_2D functor(N0,N1);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          if ( h_view(i,j) != 1 ) {
+            ++counter;
+          }
+        }}
+      if ( counter != 0 )
+        printf(" Errors in test_for2; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<2, Iterate::Default, Iterate::Default >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0}, {N0,N1} );
+      TestMDRange_2D functor(N0,N1);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          if ( h_view(i,j) != 1 ) {
+            ++counter;
+          }
+        }}
+      if ( counter != 0 )
+        printf(" Errors in test_for2; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<2, Iterate::Default, Iterate::Flat >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0}, {N0,N1} );
+      TestMDRange_2D functor(N0,N1);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          if ( h_view(i,j) != 1 ) {
+            ++counter;
+          }
+        }}
+      if ( counter != 0 )
+        printf(" Errors in test_for2; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<2, Iterate::Right, Iterate::Flat >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0}, {N0,N1} );
+      TestMDRange_2D functor(N0,N1);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          if ( h_view(i,j) != 1 ) {
+            ++counter;
+          }
+        }}
+      if ( counter != 0 )
+        printf(" Errors in test_for2; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<2, Iterate::Left, Iterate::Flat >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0}, {N0,N1} );
+      TestMDRange_2D functor(N0,N1);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          if ( h_view(i,j) != 1 ) {
+            ++counter;
+          }
+        }}
+      if ( counter != 0 )
+        printf(" Errors in test_for2; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<2, Iterate::Left , Iterate::Left >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0}, {N0,N1}, {3,3} );
+      TestMDRange_2D functor(N0,N1);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          if ( h_view(i,j) != 1 ) {
+            ++counter;
+          }
+        }}
+      if ( counter != 0 )
+        printf(" Errors in test_for2; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<2, Iterate::Left , Iterate::Right >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0}, {N0,N1}, {7,7} );
+      TestMDRange_2D functor(N0,N1);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          if ( h_view(i,j) != 1 ) {
+            ++counter;
+          }
+        }}
+      if ( counter != 0 )
+        printf(" Errors in test_for2; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<2, Iterate::Right, Iterate::Left >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0}, {N0,N1}, {16,16} );
+      TestMDRange_2D functor(N0,N1);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          if ( h_view(i,j) != 1 ) {
+            ++counter;
+          }
+        }}
+      if ( counter != 0 )
+        printf(" Errors in test_for2; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<2, Iterate::Right, Iterate::Right >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0}, {N0,N1}, {5,16} );
+      TestMDRange_2D functor(N0,N1);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          if ( h_view(i,j) != 1 ) {
+            ++counter;
+          }
+        }}
+      if ( counter != 0 )
+        printf(" Errors in test_for2; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+  } //end test_for2
+}; //MDRange_2D
+
+template <typename ExecSpace >
+struct TestMDRange_3D {
+
+  using DataType = int ;
+  using ViewType     = typename Kokkos::View< DataType*** ,  ExecSpace > ;
+  using HostViewType = typename ViewType::HostMirror ;
+
+  ViewType input_view ;
+
+  TestMDRange_3D( const DataType N0, const DataType N1, const DataType N2 ) : input_view("input_view", N0, N1, N2) {}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()( const int i , const int j , const int k ) const
+  {
+    input_view(i,j,k) = 1;
+  }
+
+  static void test_for3( const int64_t N0, const int64_t N1, const int64_t N2 )
+  {
+    using namespace Kokkos::Experimental;
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<3>, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0,0}, {N0,N1,N2} );
+      TestMDRange_3D functor(N0,N1,N2);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          for ( int k=0; k<N2; ++k ) {
+          if ( h_view(i,j,k) != 1 ) {
+            ++counter;
+          }
+        }}}
+      if ( counter != 0 )
+        printf(" Errors in test_for3; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<3, Iterate::Default, Iterate::Default >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0,0}, {N0,N1,N2} );
+      TestMDRange_3D functor(N0,N1,N2);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          for ( int k=0; k<N2; ++k ) {
+          if ( h_view(i,j,k) != 1 ) {
+            ++counter;
+          }
+        }}}
+      if ( counter != 0 )
+        printf(" Errors in test_for3; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<3, Iterate::Flat, Iterate::Default>, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0,0}, {N0,N1,N2} );
+      TestMDRange_3D functor(N0,N1,N2);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          for ( int k=0; k<N2; ++k ) {
+          if ( h_view(i,j,k) != 1 ) {
+            ++counter;
+          }
+        }}}
+      if ( counter != 0 )
+        printf(" Errors in test_for3; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<3, Iterate::Flat, Iterate::Flat >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0,0}, {N0,N1,N2} );
+      TestMDRange_3D functor(N0,N1,N2);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          for ( int k=0; k<N2; ++k ) {
+          if ( h_view(i,j,k) != 1 ) {
+            ++counter;
+          }
+        }}}
+      if ( counter != 0 )
+        printf(" Errors in test_for3; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<3, Iterate::Left, Iterate::Flat >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0,0}, {N0,N1,N2} );
+      TestMDRange_3D functor(N0,N1,N2);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          for ( int k=0; k<N2; ++k ) {
+          if ( h_view(i,j,k) != 1 ) {
+            ++counter;
+          }
+        }}}
+      if ( counter != 0 )
+        printf(" Errors in test_for3; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<3, Iterate::Right, Iterate::Flat >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0,0}, {N0,N1,N2} );
+      TestMDRange_3D functor(N0,N1,N2);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          for ( int k=0; k<N2; ++k ) {
+          if ( h_view(i,j,k) != 1 ) {
+            ++counter;
+          }
+        }}}
+      if ( counter != 0 )
+        printf(" Errors in test_for3; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<3, Iterate::Left, Iterate::Left >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0,0}, {N0,N1,N2}, {2,4,2} );
+      TestMDRange_3D functor(N0,N1,N2);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          for ( int k=0; k<N2; ++k ) {
+          if ( h_view(i,j,k) != 1 ) {
+            ++counter;
+          }
+        }}}
+      if ( counter != 0 )
+        printf(" Errors in test_for3; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<3, Iterate::Left, Iterate::Right >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0,0}, {N0,N1,N2}, {3,5,7} );
+      TestMDRange_3D functor(N0,N1,N2);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          for ( int k=0; k<N2; ++k ) {
+          if ( h_view(i,j,k) != 1 ) {
+            ++counter;
+          }
+        }}}
+      if ( counter != 0 )
+        printf(" Errors in test_for3; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<3, Iterate::Right, Iterate::Left >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0,0}, {N0,N1,N2}, {8,8,8} );
+      TestMDRange_3D functor(N0,N1,N2);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          for ( int k=0; k<N2; ++k ) {
+          if ( h_view(i,j,k) != 1 ) {
+            ++counter;
+          }
+        }}}
+      if ( counter != 0 )
+        printf(" Errors in test_for3; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+    {
+      using range_type = MDRangePolicy< ExecSpace, Rank<3, Iterate::Right, Iterate::Right >, Kokkos::IndexType<int> >;
+
+      range_type range( {0,0,0}, {N0,N1,N2}, {2,4,2} );
+      TestMDRange_3D functor(N0,N1,N2);
+
+      md_parallel_for( range, functor );
+
+      HostViewType h_view = Kokkos::create_mirror_view( functor.input_view );
+      Kokkos::deep_copy( h_view , functor.input_view );
+
+      int counter = 0;
+      for ( int i=0; i<N0; ++i ) {
+        for ( int j=0; j<N1; ++j ) {
+          for ( int k=0; k<N2; ++k ) {
+          if ( h_view(i,j,k) != 1 ) {
+            ++counter;
+          }
+        }}}
+      if ( counter != 0 )
+        printf(" Errors in test_for3; mismatches = %d\n\n",counter);
+      ASSERT_EQ( counter , 0 );
+    }
+
+  } //end test_for3
+};
+
+} /* namespace */
+} /* namespace Test */
+
+/*--------------------------------------------------------------------------*/
+
diff --git a/lib/kokkos/core/unit_test/TestMemoryPool.hpp b/lib/kokkos/core/unit_test/TestMemoryPool.hpp
index b49d91e6a8..cf650b0bc8 100644
--- a/lib/kokkos/core/unit_test/TestMemoryPool.hpp
+++ b/lib/kokkos/core/unit_test/TestMemoryPool.hpp
@@ -48,37 +48,45 @@
 #include <stdio.h>
 #include <iostream>
 #include <cmath>
+#include <algorithm>
 
 #include <impl/Kokkos_Timer.hpp>
 
 //#define TESTMEMORYPOOL_PRINT
 //#define TESTMEMORYPOOL_PRINT_STATUS
 
+#ifdef KOKKOS_HAVE_CUDA
+#define STRIDE 32
+#else
+#define STRIDE 1
+#endif
+
 namespace TestMemoryPool {
 
 struct pointer_obj {
-  uint64_t * ptr;
+  uint64_t *  ptr;
+};
+
+struct pointer_obj2 {
+  void *  ptr;
+  size_t  size;
 };
 
-template < typename PointerView, typename MemorySpace >
+template < typename PointerView, typename Allocator >
 struct allocate_memory {
   typedef typename PointerView::execution_space  execution_space;
   typedef typename execution_space::size_type    size_type;
 
-  enum { STRIDE = 32 };
+  PointerView  m_pointers;
+  size_t       m_chunk_size;
+  Allocator    m_mempool;
 
-  PointerView m_pointers;
-  size_t m_num_ptrs;
-  size_t m_chunk_size;
-  MemorySpace m_space;
-
-  allocate_memory( PointerView & ptrs, size_t nptrs,
-                   size_t cs, MemorySpace & sp )
-    : m_pointers( ptrs ), m_num_ptrs( nptrs ),
-      m_chunk_size( cs ), m_space( sp )
+  allocate_memory( PointerView & ptrs, size_t num_ptrs,
+                   size_t cs, Allocator & m )
+    : m_pointers( ptrs ), m_chunk_size( cs ), m_mempool( m )
   {
     // Initialize the view with the out degree of each vertex.
-    Kokkos::parallel_for( m_num_ptrs * STRIDE , *this );
+    Kokkos::parallel_for( num_ptrs * STRIDE, *this );
   }
 
   KOKKOS_INLINE_FUNCTION
@@ -86,26 +94,55 @@ struct allocate_memory {
   {
     if ( i % STRIDE == 0 ) {
       m_pointers[i / STRIDE].ptr =
-        static_cast< uint64_t * >( m_space.allocate( m_chunk_size ) );
+        static_cast< uint64_t * >( m_mempool.allocate( m_chunk_size ) );
     }
   }
 };
 
 template < typename PointerView >
-struct fill_memory {
+struct count_invalid_memory {
   typedef typename PointerView::execution_space  execution_space;
   typedef typename execution_space::size_type    size_type;
+  typedef uint64_t                               value_type;
+
+  PointerView  m_pointers;
+  uint64_t &   m_result;
+
+  count_invalid_memory( PointerView & ptrs, size_t num_ptrs, uint64_t & res )
+    : m_pointers( ptrs ), m_result( res )
+  {
+    // Initialize the view with the out degree of each vertex.
+    Kokkos::parallel_reduce( num_ptrs * STRIDE, *this, m_result );
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type & v ) const
+  { v = 0; }
+
+  KOKKOS_INLINE_FUNCTION
+  void join( volatile value_type & dst, volatile value_type const & src ) const
+  { dst += src; }
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()( size_type i, value_type & r ) const
+  {
+    if ( i % STRIDE == 0 ) {
+      r += ( m_pointers[i / STRIDE].ptr == 0 );
+    }
+  }
+};
 
-  enum { STRIDE = 32 };
+template < typename PointerView >
+struct fill_memory {
+  typedef typename PointerView::execution_space  execution_space;
+  typedef typename execution_space::size_type    size_type;
 
   PointerView m_pointers;
-  size_t m_num_ptrs;
 
-  fill_memory( PointerView & ptrs, size_t nptrs )
-    : m_pointers( ptrs ), m_num_ptrs( nptrs )
+  fill_memory( PointerView & ptrs, size_t num_ptrs ) : m_pointers( ptrs )
   {
     // Initialize the view with the out degree of each vertex.
-    Kokkos::parallel_for( m_num_ptrs * STRIDE , *this );
+    Kokkos::parallel_for( num_ptrs * STRIDE, *this );
   }
 
   KOKKOS_INLINE_FUNCTION
@@ -123,17 +160,14 @@ struct sum_memory {
   typedef typename execution_space::size_type    size_type;
   typedef uint64_t                               value_type;
 
-  enum { STRIDE = 32 };
+  PointerView  m_pointers;
+  uint64_t &   m_result;
 
-  PointerView m_pointers;
-  size_t m_num_ptrs;
-  uint64_t & result;
-
-  sum_memory( PointerView & ptrs, size_t nptrs, uint64_t & res )
-    : m_pointers( ptrs ), m_num_ptrs( nptrs ), result( res )
+  sum_memory( PointerView & ptrs, size_t num_ptrs, uint64_t & res )
+    : m_pointers( ptrs ), m_result( res )
   {
     // Initialize the view with the out degree of each vertex.
-    Kokkos::parallel_reduce( m_num_ptrs * STRIDE , *this, result );
+    Kokkos::parallel_reduce( num_ptrs * STRIDE, *this, m_result );
   }
 
   KOKKOS_INLINE_FUNCTION
@@ -153,65 +187,70 @@ struct sum_memory {
   }
 };
 
-template < typename PointerView, typename MemorySpace >
+template < typename PointerView, typename Allocator >
 struct deallocate_memory {
   typedef typename PointerView::execution_space  execution_space;
   typedef typename execution_space::size_type    size_type;
 
-  enum { STRIDE = 32 };
+  PointerView  m_pointers;
+  size_t       m_chunk_size;
+  Allocator    m_mempool;
 
-  PointerView m_pointers;
-  size_t m_num_ptrs;
-  size_t m_chunk_size;
-  MemorySpace m_space;
-
-  deallocate_memory( PointerView & ptrs, size_t nptrs,
-                     size_t cs, MemorySpace & sp )
-    : m_pointers( ptrs ), m_num_ptrs( nptrs ), m_chunk_size( cs ), m_space( sp )
+  deallocate_memory( PointerView & ptrs, size_t num_ptrs,
+                     size_t cs, Allocator & m )
+    : m_pointers( ptrs ), m_chunk_size( cs ), m_mempool( m )
   {
     // Initialize the view with the out degree of each vertex.
-    Kokkos::parallel_for( m_num_ptrs * STRIDE , *this );
+    Kokkos::parallel_for( num_ptrs * STRIDE, *this );
   }
 
   KOKKOS_INLINE_FUNCTION
   void operator()( size_type i ) const
   {
     if ( i % STRIDE == 0 ) {
-      m_space.deallocate( m_pointers[i / STRIDE].ptr, m_chunk_size );
+      m_mempool.deallocate( m_pointers[i / STRIDE].ptr, m_chunk_size );
     }
   }
 };
 
-template < typename ExecutionSpace, typename MemorySpace >
+template < typename WorkView, typename PointerView, typename ScalarView,
+           typename Allocator >
 struct allocate_deallocate_memory {
-  typedef ExecutionSpace                       execution_space;
+  typedef typename WorkView::execution_space   execution_space;
   typedef typename execution_space::size_type  size_type;
 
-  enum { STRIDE = 32 };
-
-  size_t m_num_max_chunks;
-  size_t m_max_chunk_size;
-  size_t m_min_chunk_size;
-  size_t m_chunk_spacing;
-  MemorySpace m_space;
+  WorkView     m_work;
+  PointerView  m_pointers;
+  ScalarView   m_ptrs_front;
+  ScalarView   m_ptrs_back;
+  Allocator    m_mempool;
 
-  allocate_deallocate_memory( size_t nmc, size_t max_cs,
-                              size_t min_cs, size_t cs, MemorySpace & sp )
-    : m_num_max_chunks( nmc ), m_max_chunk_size( max_cs ),
-      m_min_chunk_size( min_cs ), m_chunk_spacing( cs ), m_space( sp )
+  allocate_deallocate_memory( WorkView & w, size_t work_size, PointerView & p,
+                              ScalarView pf, ScalarView pb, Allocator & m )
+    : m_work( w ), m_pointers( p ), m_ptrs_front( pf ), m_ptrs_back( pb ),
+      m_mempool( m )
   {
-    Kokkos::parallel_for( m_num_max_chunks * STRIDE, *this );
+    // Initialize the view with the out degree of each vertex.
+    Kokkos::parallel_for( work_size * STRIDE, *this );
   }
 
   KOKKOS_INLINE_FUNCTION
   void operator()( size_type i ) const
   {
     if ( i % STRIDE == 0 ) {
-      for ( size_t j = m_max_chunk_size; j >= m_min_chunk_size; j /= m_chunk_spacing ) {
-        for ( size_t k = 0; k < 10; ++k ) {
-          void * mem = m_space.allocate( j );
-          m_space.deallocate( mem, j );
-        }
+      unsigned my_work = m_work[i / STRIDE];
+
+      if ( ( my_work & 1 ) == 0 ) {
+        // Allocation.
+        size_t pos = Kokkos::atomic_fetch_add( &m_ptrs_back(), 1 );
+        size_t alloc_size = my_work >> 1;
+        m_pointers[pos].ptr = m_mempool.allocate( alloc_size );
+        m_pointers[pos].size = alloc_size;
+      }
+      else {
+        // Deallocation.
+        size_t pos = Kokkos::atomic_fetch_add( &m_ptrs_front(), 1 );
+        m_mempool.deallocate( m_pointers[pos].ptr, m_pointers[pos].size );
       }
     }
   }
@@ -255,12 +294,14 @@ void print_results( const std::string & text, unsigned long long width,
 // pool and breaking large chunks into smaller chunks to fulfill allocation
 // requests.  It verifies that MemoryPool(), allocate(), and deallocate() work
 // correctly.
-template < class ExecSpace, class MemorySpace = typename ExecSpace::memory_space >
+template < class Device >
 bool test_mempool( size_t chunk_size, size_t total_size )
 {
-  typedef Kokkos::View< pointer_obj *, ExecSpace >       pointer_view;
-  typedef Kokkos::Experimental::MemoryPool< MemorySpace , ExecSpace >
-   pool_memory_space;
+  typedef typename Device::execution_space                 execution_space;
+  typedef typename Device::memory_space                    memory_space;
+  typedef Device                                           device_type;
+  typedef Kokkos::View< pointer_obj *, device_type >       pointer_view;
+  typedef Kokkos::Experimental::MemoryPool< device_type >  pool_memory_space;
 
   uint64_t result;
   size_t num_chunks = total_size / chunk_size;
@@ -269,7 +310,8 @@ bool test_mempool( size_t chunk_size, size_t total_size )
   pointer_view pointers( "pointers", num_chunks );
 
 #ifdef TESTMEMORYPOOL_PRINT
-  std::cout << std::setw( SHIFTW ) << "chunk_size: " << std::setw( 12 )
+  std::cout << "*** test_mempool() ***" << std::endl
+            << std::setw( SHIFTW ) << "chunk_size: " << std::setw( 12 )
             << chunk_size << std::endl
             << std::setw( SHIFTW ) << "total_size: " << std::setw( 12 )
             << total_size << std::endl
@@ -277,46 +319,53 @@ bool test_mempool( size_t chunk_size, size_t total_size )
             << num_chunks << std::endl;
 
   double elapsed_time = 0;
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
 #endif
 
-  pool_memory_space m_space( MemorySpace(), chunk_size, total_size );
+  pool_memory_space mempool( memory_space(), total_size * 1.2, 20 );
 
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
+  execution_space::fence();
   elapsed_time = timer.seconds();
   print_results( "initialize mempool: ", elapsed_time );
 #ifdef TESTMEMORYPOOL_PRINT_STATUS
-  m_space.print_status();
+  mempool.print_status();
 #endif
   timer.reset();
 #endif
 
-  // Tests:
-  //   test for correct behvior when out of memory
-  //   test for correct behvior when interleaving allocate() and deallocate()
-
   {
     allocate_memory< pointer_view, pool_memory_space >
-      am( pointers, num_chunks, chunk_size, m_space );
+      am( pointers, num_chunks, chunk_size, mempool );
   }
 
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
+  execution_space::fence();
   elapsed_time = timer.seconds();
   print_results( "allocate chunks: ", elapsed_time );
 #ifdef TESTMEMORYPOOL_PRINT_STATUS
-  m_space.print_status();
+  mempool.print_status();
 #endif
   timer.reset();
 #endif
 
+  {
+    count_invalid_memory< pointer_view > sm( pointers, num_chunks, result );
+  }
+
+#ifdef TESTMEMORYPOOL_PRINT
+  execution_space::fence();
+  elapsed_time = timer.seconds();
+  print_results( "invalid chunks: ", 16, elapsed_time, result );
+  timer.reset();
+#endif
+
   {
     fill_memory< pointer_view > fm( pointers, num_chunks );
   }
 
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
+  execution_space::fence();
   elapsed_time = timer.seconds();
   print_results( "fill chunks: ", elapsed_time );
   timer.reset();
@@ -326,10 +375,11 @@ bool test_mempool( size_t chunk_size, size_t total_size )
     sum_memory< pointer_view > sm( pointers, num_chunks, result );
   }
 
+  execution_space::fence();
+
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
   elapsed_time = timer.seconds();
-  print_results( "sum chunks: ", 10, elapsed_time, result );
+  print_results( "sum chunks: ", 16, elapsed_time, result );
 #endif
 
   if ( result != ( num_chunks * ( num_chunks - 1 ) ) / 2 ) {
@@ -343,40 +393,51 @@ bool test_mempool( size_t chunk_size, size_t total_size )
 
   {
     deallocate_memory< pointer_view, pool_memory_space >
-      dm( pointers, num_chunks, chunk_size, m_space );
+      dm( pointers, num_chunks, chunk_size, mempool );
   }
 
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
+  execution_space::fence();
   elapsed_time = timer.seconds();
   print_results( "deallocate chunks: ", elapsed_time );
 #ifdef TESTMEMORYPOOL_PRINT_STATUS
-  m_space.print_status();
+  mempool.print_status();
 #endif
   timer.reset();
 #endif
 
   {
     allocate_memory< pointer_view, pool_memory_space >
-      am( pointers, num_chunks, chunk_size, m_space );
+      am( pointers, num_chunks, chunk_size, mempool );
   }
 
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
+  execution_space::fence();
   elapsed_time = timer.seconds();
   print_results( "allocate chunks: ", elapsed_time );
 #ifdef TESTMEMORYPOOL_PRINT_STATUS
-  m_space.print_status();
+  mempool.print_status();
 #endif
   timer.reset();
 #endif
 
+  {
+    count_invalid_memory< pointer_view > sm( pointers, num_chunks, result );
+  }
+
+#ifdef TESTMEMORYPOOL_PRINT
+  execution_space::fence();
+  elapsed_time = timer.seconds();
+  print_results( "invalid chunks: ", 16, elapsed_time, result );
+  timer.reset();
+#endif
+
   {
     fill_memory< pointer_view > fm( pointers, num_chunks );
   }
 
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
+  execution_space::fence();
   elapsed_time = timer.seconds();
   print_results( "fill chunks: ", elapsed_time );
   timer.reset();
@@ -386,10 +447,11 @@ bool test_mempool( size_t chunk_size, size_t total_size )
     sum_memory< pointer_view > sm( pointers, num_chunks, result );
   }
 
+  execution_space::fence();
+
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
   elapsed_time = timer.seconds();
-  print_results( "sum chunks: ", 10, elapsed_time, result );
+  print_results( "sum chunks: ", 16, elapsed_time, result );
 #endif
 
   if ( result != ( num_chunks * ( num_chunks - 1 ) ) / 2 ) {
@@ -403,78 +465,340 @@ bool test_mempool( size_t chunk_size, size_t total_size )
 
   {
     deallocate_memory< pointer_view, pool_memory_space >
-      dm( pointers, num_chunks, chunk_size, m_space );
+      dm( pointers, num_chunks, chunk_size, mempool );
   }
 
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
+  execution_space::fence();
   elapsed_time = timer.seconds();
   print_results( "deallocate chunks: ", elapsed_time );
 #ifdef TESTMEMORYPOOL_PRINT_STATUS
-  m_space.print_status();
+  mempool.print_status();
 #endif
 #endif
 
   return return_val;
 }
 
+template < typename T >
+T smallest_power2_ge( T val )
+{
+  // Find the most significant nonzero bit.
+  int first_nonzero_bit = Kokkos::Impl::bit_scan_reverse( val );
+
+  // If val is an integral power of 2, ceil( log2(val) ) is equal to the
+  // most significant nonzero bit.  Otherwise, you need to add 1.
+  int lg2_size = first_nonzero_bit +
+                 !Kokkos::Impl::is_integral_power_of_two( val );
+
+  return T(1) << T(lg2_size);
+}
+
 // This test makes allocation requests for multiple sizes and interleaves
 // allocation and deallocation.
-template < class ExecSpace, class MemorySpace = typename ExecSpace::memory_space >
-void test_mempool2( size_t chunk_size, size_t total_size )
+//
+// There are 3 phases.  The first phase does only allocations to build up a
+// working state for the allocator.  The second phase interleaves allocations
+// and deletions.  The third phase does only deallocations to undo all the
+// allocations from the first phase.  By building first to a working state,
+// allocations and deallocations can happen in any order for the second phase.
+// Each phase performs on multiple chunk sizes.
+template < class Device >
+void test_mempool2( unsigned base_chunk_size, size_t num_chunk_sizes,
+                    size_t phase1_size, size_t phase2_size )
 {
-  typedef Kokkos::Experimental::MemoryPool< MemorySpace , ExecSpace >
-    pool_memory_space;
+#ifdef TESTMEMORYPOOL_PRINT
+  typedef typename Device::execution_space                 execution_space;
+#endif
+  typedef typename Device::memory_space                    memory_space;
+  typedef Device                                           device_type;
+  typedef Kokkos::View< unsigned *, device_type >          work_view;
+  typedef Kokkos::View< size_t, device_type >              scalar_view;
+  typedef Kokkos::View< pointer_obj2 *, device_type >      pointer_view;
+  typedef Kokkos::Experimental::MemoryPool< device_type >  pool_memory_space;
+
+  enum {
+    MIN_CHUNK_SIZE      = 64,
+    MIN_BASE_CHUNK_SIZE = MIN_CHUNK_SIZE / 2 + 1
+  };
+
+  // Make sure the base chunk size is at least MIN_BASE_CHUNK_SIZE bytes, so
+  // all the different chunk sizes translate to different block sizes for the
+  // allocator.
+  if ( base_chunk_size < MIN_BASE_CHUNK_SIZE ) {
+    base_chunk_size = MIN_BASE_CHUNK_SIZE;
+  }
+
+  // Get the smallest power of 2 >= the base chunk size.  The size must be
+  // >= MIN_CHUNK_SIZE, though.
+  unsigned ceil_base_chunk_size = smallest_power2_ge( base_chunk_size );
+  if ( ceil_base_chunk_size < MIN_CHUNK_SIZE ) {
+    ceil_base_chunk_size = MIN_CHUNK_SIZE;
+  }
+
+  // Make sure the phase 1 size is multiples of num_chunk_sizes.
+  phase1_size = ( ( phase1_size + num_chunk_sizes - 1 ) / num_chunk_sizes ) *
+                num_chunk_sizes;
+
+  // Make sure the phase 2 size is multiples of (2 * num_chunk_sizes).
+  phase2_size =
+    ( ( phase2_size + 2 * num_chunk_sizes - 1 ) / ( 2 * num_chunk_sizes ) ) *
+    2 * num_chunk_sizes;
+
+  // The phase2 size must be <= twice the phase1 size so that deallocations
+  // can't happen before allocations.
+  if ( phase2_size > 2 * phase1_size ) phase2_size = 2 * phase1_size;
+
+  size_t phase3_size = phase1_size;
+  size_t half_phase2_size = phase2_size / 2;
+
+  // Each entry in the work views has the following format.  The least
+  // significant bit indicates allocation (0) vs. deallocation (1).  For
+  // allocation, the other bits indicate the desired allocation size.
+
+  // Initialize the phase 1 work view with an equal number of allocations for
+  // each chunk size.
+  work_view phase1_work( "Phase 1 Work", phase1_size );
+  typename work_view::HostMirror host_phase1_work =
+    create_mirror_view(phase1_work);
+
+  size_t inner_size = phase1_size / num_chunk_sizes;
+  unsigned chunk_size = base_chunk_size;
+
+  for ( size_t i = 0; i < num_chunk_sizes; ++i ) {
+    for ( size_t j = 0; j < inner_size; ++j ) {
+      host_phase1_work[i * inner_size + j] = chunk_size << 1;
+    }
+
+    chunk_size *= 2;
+  }
+
+  std::random_shuffle( host_phase1_work.ptr_on_device(),
+                       host_phase1_work.ptr_on_device() + phase1_size );
+
+  deep_copy( phase1_work, host_phase1_work );
+
+  // Initialize the phase 2 work view with half allocations and half
+  // deallocations with an equal number of allocations for each chunk size.
+  work_view phase2_work( "Phase 2 Work", phase2_size );
+  typename work_view::HostMirror host_phase2_work =
+    create_mirror_view(phase2_work);
 
-  size_t num_chunk_sizes = 4;
-  size_t chunk_spacing = 4;
+  inner_size = half_phase2_size / num_chunk_sizes;
+  chunk_size = base_chunk_size;
+
+  for ( size_t i = 0; i < num_chunk_sizes; ++i ) {
+    for ( size_t j = 0; j < inner_size; ++j ) {
+      host_phase2_work[i * inner_size + j] = chunk_size << 1;
+    }
+
+    chunk_size *= 2;
+  }
+
+  for ( size_t i = half_phase2_size; i < phase2_size; ++i ) {
+    host_phase2_work[i] = 1;
+  }
+
+  std::random_shuffle( host_phase2_work.ptr_on_device(),
+                       host_phase2_work.ptr_on_device() + phase2_size );
+
+  deep_copy( phase2_work, host_phase2_work );
+
+  // Initialize the phase 3 work view with all deallocations.
+  work_view phase3_work( "Phase 3 Work", phase3_size );
+  typename work_view::HostMirror host_phase3_work =
+    create_mirror_view(phase3_work);
+
+  inner_size = phase3_size / num_chunk_sizes;
+
+  for ( size_t i = 0; i < phase3_size; ++i ) host_phase3_work[i] = 1;
+
+  deep_copy( phase3_work, host_phase3_work );
+
+  // Calculate the amount of memory needed for the allocator.  We need to know
+  // the number of superblocks required for each chunk size and use that to
+  // calculate the amount of memory for each chunk size.
+  size_t lg_sb_size = 18;
+  size_t sb_size = 1 << lg_sb_size;
+  size_t total_size = 0;
+  size_t allocs_per_size = phase1_size / num_chunk_sizes +
+                           half_phase2_size / num_chunk_sizes;
+
+  chunk_size = ceil_base_chunk_size;
+  for ( size_t i = 0; i < num_chunk_sizes; ++i ) {
+    size_t my_size = allocs_per_size * chunk_size;
+    total_size += ( my_size + sb_size - 1 ) / sb_size * sb_size;
+    chunk_size *= 2;
+  }
+
+  // Declare the queue to hold the records for allocated memory.  An allocation
+  // adds a record to the back of the queue, and a deallocation removes a
+  // record from the front of the queue.
+  size_t num_allocations = phase1_size + half_phase2_size;
+  scalar_view ptrs_front( "Pointers front" );
+  scalar_view ptrs_back( "Pointers back" );
+
+  pointer_view pointers( "pointers", num_allocations );
 
 #ifdef TESTMEMORYPOOL_PRINT
+  printf( "\n*** test_mempool2() ***\n" );
+  printf( "       num_chunk_sizes: %12zu\n", num_chunk_sizes );
+  printf( "       base_chunk_size: %12u\n", base_chunk_size );
+  printf( "  ceil_base_chunk_size: %12u\n", ceil_base_chunk_size );
+  printf( "           phase1_size: %12zu\n", phase1_size );
+  printf( "           phase2_size: %12zu\n", phase2_size );
+  printf( "           phase3_size: %12zu\n", phase3_size );
+  printf( "       allocs_per_size: %12zu\n", allocs_per_size );
+  printf( "       num_allocations: %12zu\n", num_allocations );
+  printf( "            total_size: %12zu\n", total_size );
+  fflush( stdout );
+
   double elapsed_time = 0;
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
 #endif
 
-  pool_memory_space m_space( MemorySpace(), chunk_size, total_size,
-                             num_chunk_sizes, chunk_spacing );
+  pool_memory_space mempool( memory_space(), total_size * 1.2, lg_sb_size );
 
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
+  execution_space::fence();
   elapsed_time = timer.seconds();
   print_results( "initialize mempool: ", elapsed_time );
+
+#ifdef TESTMEMORYPOOL_PRINT_STATUS
+  mempool.print_status();
+#endif
+
+  timer.reset();
+#endif
+
+  {
+    allocate_deallocate_memory< work_view, pointer_view, scalar_view,
+                                pool_memory_space >
+      adm( phase1_work, phase1_size, pointers, ptrs_front, ptrs_back, mempool );
+  }
+
+#ifdef TESTMEMORYPOOL_PRINT
+  execution_space::fence();
+  elapsed_time = timer.seconds();
+  print_results( "phase1: ", elapsed_time );
+
+#ifdef TESTMEMORYPOOL_PRINT_STATUS
+  mempool.print_status();
+#endif
+
+  timer.reset();
+#endif
+
+  {
+    allocate_deallocate_memory< work_view, pointer_view, scalar_view,
+                                pool_memory_space >
+      adm( phase2_work, phase2_size, pointers, ptrs_front, ptrs_back, mempool );
+  }
+
+#ifdef TESTMEMORYPOOL_PRINT
+  execution_space::fence();
+  elapsed_time = timer.seconds();
+  print_results( "phase2: ", elapsed_time );
+
+#ifdef TESTMEMORYPOOL_PRINT_STATUS
+  mempool.print_status();
 #endif
 
-  chunk_size = m_space.get_min_chunk_size();
-  total_size = m_space.get_mem_size();
+  timer.reset();
+#endif
 
-  // Get the chunk size for the largest possible chunk.
-  //   max_chunk_size =
-  //     chunk_size * (MEMPOOL_CHUNK_SPACING ^ (MEMPOOL_NUM_CHUNK_SIZES - 1))
-  size_t max_chunk_size = chunk_size;
-  for (size_t i = 1; i < num_chunk_sizes; ++i) {
-    max_chunk_size *= chunk_spacing;
+  {
+    allocate_deallocate_memory< work_view, pointer_view, scalar_view,
+                                pool_memory_space >
+      adm( phase3_work, phase3_size, pointers, ptrs_front, ptrs_back, mempool );
   }
 
-  size_t num_max_chunks = total_size / ( max_chunk_size * num_chunk_sizes );
+#ifdef TESTMEMORYPOOL_PRINT
+  execution_space::fence();
+  elapsed_time = timer.seconds();
+  print_results( "phase3: ", elapsed_time );
+#ifdef TESTMEMORYPOOL_PRINT_STATUS
+  mempool.print_status();
+#endif
+#endif
+}
+
+// Tests for correct behavior when the allocator is out of memory.
+template < class Device >
+void test_memory_exhaustion()
+{
+#ifdef TESTMEMORYPOOL_PRINT
+  typedef typename Device::execution_space                 execution_space;
+#endif
+  typedef typename Device::memory_space                    memory_space;
+  typedef Device                                           device_type;
+  typedef Kokkos::View< pointer_obj *, device_type >       pointer_view;
+  typedef Kokkos::Experimental::MemoryPool< device_type >  pool_memory_space;
+
+  // The allocator will have a single superblock, and allocations will all be
+  // of the same chunk size.  The allocation loop will attempt to allocate
+  // twice the number of chunks as are available in the allocator.  The
+  // deallocation loop will only free the successfully allocated chunks.
+
+  size_t chunk_size = 128;
+  size_t num_chunks = 128;
+  size_t half_num_chunks = num_chunks / 2;
+  size_t superblock_size = chunk_size * half_num_chunks;
+  size_t lg_superblock_size =
+    Kokkos::Impl::integral_power_of_two( superblock_size );
 
+  pointer_view pointers( "pointers", num_chunks );
+
+#ifdef TESTMEMORYPOOL_PRINT
+  std::cout << "\n*** test_memory_exhaustion() ***" << std::endl;
+
+  double elapsed_time = 0;
+  Kokkos::Timer timer;
+#endif
+
+  pool_memory_space mempool( memory_space(), superblock_size,
+                             lg_superblock_size );
+
+#ifdef TESTMEMORYPOOL_PRINT
+  execution_space::fence();
+  elapsed_time = timer.seconds();
+  print_results( "initialize mempool: ", elapsed_time );
 #ifdef TESTMEMORYPOOL_PRINT_STATUS
-  m_space.print_status();
+  mempool.print_status();
+#endif
+  timer.reset();
 #endif
 
+  {
+    allocate_memory< pointer_view, pool_memory_space >
+      am( pointers, num_chunks, chunk_size, mempool );
+  }
+
 #ifdef TESTMEMORYPOOL_PRINT
+  execution_space::fence();
+  elapsed_time = timer.seconds();
+  print_results( "allocate chunks: ", elapsed_time );
+#ifdef TESTMEMORYPOOL_PRINT_STATUS
+  mempool.print_status();
+#endif
   timer.reset();
 #endif
 
   {
-    allocate_deallocate_memory< ExecSpace, pool_memory_space >
-      am( num_max_chunks, max_chunk_size, chunk_size, chunk_spacing, m_space );
+    // In parallel, the allocations that succeeded were not put contiguously
+    // into the pointers View.  The whole View can still be looped over and
+    // have deallocate called because deallocate will just do nothing for NULL
+    // pointers.
+    deallocate_memory< pointer_view, pool_memory_space >
+      dm( pointers, num_chunks, chunk_size, mempool );
   }
 
 #ifdef TESTMEMORYPOOL_PRINT
-  ExecSpace::fence();
+  execution_space::fence();
   elapsed_time = timer.seconds();
-  print_results( "allocate / deallocate: ", elapsed_time );
+  print_results( "deallocate chunks: ", elapsed_time );
 #ifdef TESTMEMORYPOOL_PRINT_STATUS
-  m_space.print_status();
+  mempool.print_status();
 #endif
 #endif
 }
@@ -489,4 +813,8 @@ void test_mempool2( size_t chunk_size, size_t total_size )
 #undef TESTMEMORYPOOL_PRINT_STATUS
 #endif
 
+#ifdef STRIDE
+#undef STRIDE
+#endif
+
 #endif
diff --git a/lib/kokkos/core/unit_test/TestOpenMP.cpp b/lib/kokkos/core/unit_test/TestOpenMP.cpp
index 35bc7c9869..6e8fc45179 100644
--- a/lib/kokkos/core/unit_test/TestOpenMP.cpp
+++ b/lib/kokkos/core/unit_test/TestOpenMP.cpp
@@ -55,6 +55,7 @@
 
 #include <TestViewImpl.hpp>
 #include <TestAtomic.hpp>
+#include <TestAtomicOperations.hpp>
 
 #include <TestViewAPI.hpp>
 #include <TestViewSubview.hpp>
@@ -81,6 +82,7 @@
 
 #include <TestPolicyConstruction.hpp>
 
+#include <TestMDRange.hpp>
 
 namespace Test {
 
@@ -97,6 +99,7 @@ protected:
 
     Kokkos::OpenMP::initialize( threads_count );
     Kokkos::OpenMP::print_configuration( std::cout , true );
+    srand(10231);
   }
 
   static void TearDownTestCase()
@@ -110,6 +113,12 @@ protected:
 };
 
 
+TEST_F( openmp , md_range ) {
+  TestMDRange_2D< Kokkos::OpenMP >::test_for2(100,100);
+
+  TestMDRange_3D< Kokkos::OpenMP >::test_for3(100,100,100);
+}
+
 TEST_F( openmp , impl_shared_alloc ) {
   test_shared_alloc< Kokkos::HostSpace , Kokkos::OpenMP >();
 }
@@ -180,5 +189,74 @@ TEST_F( openmp , atomics )
   ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::OpenMP>(100,3) ) );
 }
 
+TEST_F( openmp , atomic_operations )
+{
+  const int start = 1; //Avoid zero for division
+  const int end = 11;
+  for (int i = start; i < end; ++i)
+  {
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::OpenMP>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::OpenMP>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::OpenMP>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::OpenMP>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::OpenMP>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::OpenMP>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::OpenMP>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::OpenMP>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::OpenMP>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::OpenMP>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::OpenMP>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::OpenMP>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::OpenMP>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::OpenMP>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::OpenMP>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::OpenMP>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::OpenMP>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::OpenMP>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::OpenMP>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::OpenMP>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::OpenMP>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::OpenMP>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::OpenMP>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::OpenMP>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::OpenMP>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::OpenMP>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::OpenMP>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::OpenMP>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::OpenMP>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::OpenMP>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::OpenMP>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::OpenMP>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::OpenMP>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::OpenMP>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::OpenMP>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::OpenMP>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::OpenMP>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::OpenMP>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::OpenMP>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::OpenMP>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::OpenMP>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::OpenMP>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::OpenMP>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::OpenMP>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::OpenMP>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::OpenMP>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::OpenMP>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::OpenMP>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::OpenMP>(start, end-i, 4 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::OpenMP>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::OpenMP>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::OpenMP>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::OpenMP>(start, end-i, 4 ) ) );
+  }
+
+}
+
 } // namespace test
 
diff --git a/lib/kokkos/core/unit_test/TestOpenMP_a.cpp b/lib/kokkos/core/unit_test/TestOpenMP_a.cpp
index 919eea7c80..64eac66804 100644
--- a/lib/kokkos/core/unit_test/TestOpenMP_a.cpp
+++ b/lib/kokkos/core/unit_test/TestOpenMP_a.cpp
@@ -86,27 +86,8 @@ namespace Test {
 
 class openmp : public ::testing::Test {
 protected:
-  static void SetUpTestCase()
-  {
-    const unsigned numa_count       = Kokkos::hwloc::get_available_numa_count();
-    const unsigned cores_per_numa   = Kokkos::hwloc::get_available_cores_per_numa();
-    const unsigned threads_per_core = Kokkos::hwloc::get_available_threads_per_core();
-
-    const unsigned threads_count = std::max( 1u , numa_count ) *
-                                   std::max( 2u , ( cores_per_numa * threads_per_core ) / 2 );
-
-    Kokkos::OpenMP::initialize( threads_count );
-    Kokkos::OpenMP::print_configuration( std::cout , true );
-  }
-
-  static void TearDownTestCase()
-  {
-    Kokkos::OpenMP::finalize();
-
-    omp_set_num_threads(1);
-
-    ASSERT_EQ( 1 , omp_get_max_threads() );
-  }
+  static void SetUpTestCase();
+  static void TearDownTestCase();
 };
 
 TEST_F( openmp, view_subview_auto_1d_left ) {
diff --git a/lib/kokkos/core/unit_test/TestOpenMP_b.cpp b/lib/kokkos/core/unit_test/TestOpenMP_b.cpp
index f024e22422..6cc2476014 100644
--- a/lib/kokkos/core/unit_test/TestOpenMP_b.cpp
+++ b/lib/kokkos/core/unit_test/TestOpenMP_b.cpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -86,27 +86,8 @@ namespace Test {
 
 class openmp : public ::testing::Test {
 protected:
-  static void SetUpTestCase()
-  {
-    const unsigned numa_count       = Kokkos::hwloc::get_available_numa_count();
-    const unsigned cores_per_numa   = Kokkos::hwloc::get_available_cores_per_numa();
-    const unsigned threads_per_core = Kokkos::hwloc::get_available_threads_per_core();
-
-    const unsigned threads_count = std::max( 1u , numa_count ) *
-                                   std::max( 2u , ( cores_per_numa * threads_per_core ) / 2 );
-
-    Kokkos::OpenMP::initialize( threads_count );
-    Kokkos::OpenMP::print_configuration( std::cout , true );
-  }
-
-  static void TearDownTestCase()
-  {
-    Kokkos::OpenMP::finalize();
-
-    omp_set_num_threads(1);
-
-    ASSERT_EQ( 1 , omp_get_max_threads() );
-  }
+  static void SetUpTestCase();
+  static void TearDownTestCase();
 };
 
 TEST_F( openmp , range_tag )
@@ -122,6 +103,10 @@ TEST_F( openmp , range_tag )
 
 TEST_F( openmp , team_tag )
 {
+  TestTeamPolicy< Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Static> >::test_for(2);
+  TestTeamPolicy< Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Static> >::test_reduce(2);
+  TestTeamPolicy< Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(2);
+  TestTeamPolicy< Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(2);
   TestTeamPolicy< Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
   TestTeamPolicy< Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
   TestTeamPolicy< Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(1000);
@@ -148,6 +133,14 @@ TEST_F( openmp, long_reduce_dynamic_view ) {
   TestReduceDynamicView< long ,   Kokkos::OpenMP >( 1000000 );
 }
 
+TEST_F( openmp , reducers )
+{
+  TestReducers<int, Kokkos::OpenMP>::execute_integer();
+  TestReducers<size_t, Kokkos::OpenMP>::execute_integer();
+  TestReducers<double, Kokkos::OpenMP>::execute_float();
+  TestReducers<Kokkos::complex<double>, Kokkos::OpenMP>::execute_basic();
+}
+
 TEST_F( openmp, team_long_reduce) {
   TestReduceTeam< long ,   Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Static> >( 3 );
   TestReduceTeam< long ,   Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Dynamic> >( 3 );
@@ -172,12 +165,21 @@ TEST_F( openmp, team_scratch_request) {
   TestScratchTeam< Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Dynamic> >();
 }
 
-#if defined(KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA) 
+#if defined(KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA)
 TEST_F( openmp, team_lambda_shared_request) {
   TestLambdaSharedTeam< Kokkos::HostSpace, Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Static> >();
   TestLambdaSharedTeam< Kokkos::HostSpace, Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Dynamic> >();
 }
 #endif
 
+TEST_F( openmp, shmem_size) {
+  TestShmemSize< Kokkos::OpenMP >();
+}
+
+TEST_F( openmp, multi_level_scratch) {
+  TestMultiLevelScratchTeam< Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Static> >();
+  TestMultiLevelScratchTeam< Kokkos::OpenMP , Kokkos::Schedule<Kokkos::Dynamic> >();
+}
+
 } // namespace test
 
diff --git a/lib/kokkos/core/unit_test/TestOpenMP_c.cpp b/lib/kokkos/core/unit_test/TestOpenMP_c.cpp
index d9ed87878a..f0cdabe913 100644
--- a/lib/kokkos/core/unit_test/TestOpenMP_c.cpp
+++ b/lib/kokkos/core/unit_test/TestOpenMP_c.cpp
@@ -71,6 +71,7 @@
 #include <TestAggregateReduction.hpp>
 #include <TestCompilerMacros.hpp>
 #include <TestMemoryPool.hpp>
+#include <TestTaskPolicy.hpp>
 
 
 #include <TestCXX11.hpp>
@@ -86,27 +87,8 @@ namespace Test {
 
 class openmp : public ::testing::Test {
 protected:
-  static void SetUpTestCase()
-  {
-    const unsigned numa_count       = Kokkos::hwloc::get_available_numa_count();
-    const unsigned cores_per_numa   = Kokkos::hwloc::get_available_cores_per_numa();
-    const unsigned threads_per_core = Kokkos::hwloc::get_available_threads_per_core();
-
-    const unsigned threads_count = std::max( 1u , numa_count ) *
-                                   std::max( 2u , ( cores_per_numa * threads_per_core ) / 2 );
-
-    Kokkos::OpenMP::initialize( threads_count );
-    Kokkos::OpenMP::print_configuration( std::cout , true );
-  }
-
-  static void TearDownTestCase()
-  {
-    Kokkos::OpenMP::finalize();
-
-    omp_set_num_threads(1);
-
-    ASSERT_EQ( 1 , omp_get_max_threads() );
-  }
+  static void SetUpTestCase();
+  static void TearDownTestCase();
 };
 
 TEST_F( openmp , view_remap )
@@ -197,7 +179,9 @@ TEST_F( openmp , memory_pool )
   bool val = TestMemoryPool::test_mempool< Kokkos::OpenMP >( 128, 128000000 );
   ASSERT_TRUE( val );
 
-  TestMemoryPool::test_mempool2< Kokkos::OpenMP >( 128, 128000000 );
+  TestMemoryPool::test_mempool2< Kokkos::OpenMP >( 64, 4, 1000000, 2000000 );
+
+  TestMemoryPool::test_memory_exhaustion< Kokkos::OpenMP >();
 }
 
 //----------------------------------------------------------------------------
@@ -240,5 +224,39 @@ TEST_F( openmp , team_vector )
   ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::OpenMP >(9) ) );
   ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::OpenMP >(10) ) );
 }
+
+//----------------------------------------------------------------------------
+
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
+TEST_F( openmp , task_fib )
+{
+  for ( int i = 0 ; i < 25 ; ++i ) {
+    TestTaskPolicy::TestFib< Kokkos::OpenMP >::run(i, (i+1)*1000000 );
+  }
+}
+
+TEST_F( openmp , task_depend )
+{
+  for ( int i = 0 ; i < 25 ; ++i ) {
+    TestTaskPolicy::TestTaskDependence< Kokkos::OpenMP >::run(i);
+  }
+}
+
+TEST_F( openmp , task_team )
+{
+  TestTaskPolicy::TestTaskTeam< Kokkos::OpenMP >::run(1000);
+  //TestTaskPolicy::TestTaskTeamValue< Kokkos::OpenMP >::run(1000); //TODO put back after testing
+}
+
+
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
+
+
 } // namespace test
 
+
+
+
+
+
diff --git a/lib/kokkos/core/unit_test/TestPolicyConstruction.hpp b/lib/kokkos/core/unit_test/TestPolicyConstruction.hpp
index 5aac8332fc..049138eb07 100644
--- a/lib/kokkos/core/unit_test/TestPolicyConstruction.hpp
+++ b/lib/kokkos/core/unit_test/TestPolicyConstruction.hpp
@@ -421,68 +421,68 @@ private:
     ASSERT_EQ  (p1.league_size() , league_size);
     ASSERT_EQ  (p1.team_size()   , team_size);
     ASSERT_TRUE(p1.chunk_size()  > 0);
-    ASSERT_EQ  (p1.scratch_size(), 0);
+    ASSERT_EQ  (p1.scratch_size(0), 0);
 
     policy_t p2 = p1.set_chunk_size(chunk_size);
     ASSERT_EQ  (p1.league_size() , league_size);
     ASSERT_EQ  (p1.team_size()   , team_size);
     ASSERT_TRUE(p1.chunk_size()  > 0);
-    ASSERT_EQ  (p1.scratch_size(), 0);
+    ASSERT_EQ  (p1.scratch_size(0), 0);
 
     ASSERT_EQ  (p2.league_size() , league_size);
     ASSERT_EQ  (p2.team_size()   , team_size);
     ASSERT_EQ  (p2.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p2.scratch_size(), 0);
+    ASSERT_EQ  (p2.scratch_size(0), 0);
 
     policy_t p3 = p2.set_scratch_size(0,Kokkos::PerTeam(per_team_scratch));
     ASSERT_EQ  (p2.league_size() , league_size);
     ASSERT_EQ  (p2.team_size()   , team_size);
     ASSERT_EQ  (p2.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p2.scratch_size(), 0);
+    ASSERT_EQ  (p2.scratch_size(0), 0);
     ASSERT_EQ  (p3.league_size() , league_size);
     ASSERT_EQ  (p3.team_size()   , team_size);
     ASSERT_EQ  (p3.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p3.scratch_size(), per_team_scratch);
+    ASSERT_EQ  (p3.scratch_size(0), per_team_scratch);
 
     policy_t p4 = p2.set_scratch_size(0,Kokkos::PerThread(per_thread_scratch));
     ASSERT_EQ  (p2.league_size() , league_size);
     ASSERT_EQ  (p2.team_size()   , team_size);
     ASSERT_EQ  (p2.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p2.scratch_size(), 0);
+    ASSERT_EQ  (p2.scratch_size(0), 0);
     ASSERT_EQ  (p4.league_size() , league_size);
     ASSERT_EQ  (p4.team_size()   , team_size);
     ASSERT_EQ  (p4.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p4.scratch_size(), per_thread_scratch*team_size);
+    ASSERT_EQ  (p4.scratch_size(0), per_thread_scratch*team_size);
 
     policy_t p5 = p2.set_scratch_size(0,Kokkos::PerThread(per_thread_scratch),Kokkos::PerTeam(per_team_scratch));
     ASSERT_EQ  (p2.league_size() , league_size);
     ASSERT_EQ  (p2.team_size()   , team_size);
     ASSERT_EQ  (p2.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p2.scratch_size(), 0);
+    ASSERT_EQ  (p2.scratch_size(0), 0);
     ASSERT_EQ  (p5.league_size() , league_size);
     ASSERT_EQ  (p5.team_size()   , team_size);
     ASSERT_EQ  (p5.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p5.scratch_size(), scratch_size);
+    ASSERT_EQ  (p5.scratch_size(0), scratch_size);
 
     policy_t p6 = p2.set_scratch_size(0,Kokkos::PerTeam(per_team_scratch),Kokkos::PerThread(per_thread_scratch));
     ASSERT_EQ  (p2.league_size() , league_size);
     ASSERT_EQ  (p2.team_size()   , team_size);
     ASSERT_EQ  (p2.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p2.scratch_size(), 0);
+    ASSERT_EQ  (p2.scratch_size(0), 0);
     ASSERT_EQ  (p6.league_size() , league_size);
     ASSERT_EQ  (p6.team_size()   , team_size);
     ASSERT_EQ  (p6.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p6.scratch_size(), scratch_size);
+    ASSERT_EQ  (p6.scratch_size(0), scratch_size);
 
     policy_t p7 = p3.set_scratch_size(0,Kokkos::PerTeam(per_team_scratch),Kokkos::PerThread(per_thread_scratch));
     ASSERT_EQ  (p3.league_size() , league_size);
     ASSERT_EQ  (p3.team_size()   , team_size);
     ASSERT_EQ  (p3.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p3.scratch_size(), per_team_scratch);
+    ASSERT_EQ  (p3.scratch_size(0), per_team_scratch);
     ASSERT_EQ  (p7.league_size() , league_size);
     ASSERT_EQ  (p7.team_size()   , team_size);
     ASSERT_EQ  (p7.chunk_size()  , chunk_size);
-    ASSERT_EQ  (p7.scratch_size(), scratch_size);
+    ASSERT_EQ  (p7.scratch_size(0), scratch_size);
 }
   void test_run_time_parameters() {
     test_run_time_parameters_type<Kokkos::TeamPolicy<ExecutionSpace> >();
diff --git a/lib/kokkos/core/unit_test/TestQthread.cpp b/lib/kokkos/core/unit_test/TestQthread.cpp
index a8f2acea1d..431b844c9f 100644
--- a/lib/kokkos/core/unit_test/TestQthread.cpp
+++ b/lib/kokkos/core/unit_test/TestQthread.cpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -249,6 +249,10 @@ TEST_F( qthread, team_shared ) {
   TestSharedTeam< Kokkos::Qthread , Kokkos::Schedule<Kokkos::Static> >();
 }
 
+TEST_F( qthread, shmem_size) {
+  TestShmemSize< Kokkos::Qthread >();
+}
+
 TEST_F( qthread , team_scan )
 {
   TestScanTeam< Kokkos::Qthread , Kokkos::Schedule<Kokkos::Static> >( 10 );
diff --git a/lib/kokkos/core/unit_test/TestRange.hpp b/lib/kokkos/core/unit_test/TestRange.hpp
index c7fb7e9004..be8b4f90a3 100644
--- a/lib/kokkos/core/unit_test/TestRange.hpp
+++ b/lib/kokkos/core/unit_test/TestRange.hpp
@@ -185,7 +185,7 @@ struct TestRange {
       },error);
       ASSERT_EQ(error,0);
 
-      if(ExecSpace::concurrency()>1) {
+      if( ( ExecSpace::concurrency()>(int)1) && (N>static_cast<const size_t>(4*ExecSpace::concurrency())) ) {
         size_t min = N;
         size_t max = 0;
         for(int t=0; t<ExecSpace::concurrency(); t++) {
@@ -196,6 +196,7 @@ struct TestRange {
         //if(ExecSpace::concurrency()>2)
         //  ASSERT_TRUE(2*min<max);
       }
+      
     }
 
     {
@@ -218,7 +219,7 @@ struct TestRange {
       },error);
       ASSERT_EQ(error,0);
 
-      if(ExecSpace::concurrency()>1) {
+      if( ( ExecSpace::concurrency()>(int)1) && (N>static_cast<const size_t>(4*ExecSpace::concurrency())) ) {
         size_t min = N;
         size_t max = 0;
         for(int t=0; t<ExecSpace::concurrency(); t++) {
diff --git a/lib/kokkos/core/unit_test/TestReduce.hpp b/lib/kokkos/core/unit_test/TestReduce.hpp
index f5ce0e4dd2..53fc393bcc 100644
--- a/lib/kokkos/core/unit_test/TestReduce.hpp
+++ b/lib/kokkos/core/unit_test/TestReduce.hpp
@@ -457,7 +457,1415 @@ public:
     }
   }
 };
+}
+
+// Computes y^T*A*x
+// (modified from kokkos-tutorials/GTC2016/Exercises/ThreeLevelPar )
+
+#if ( ! defined( KOKKOS_HAVE_CUDA ) ) || defined( KOKKOS_CUDA_USE_LAMBDA )
+
+template< typename ScalarType , class DeviceType >
+class TestTripleNestedReduce
+{
+public:
+  typedef DeviceType execution_space ;
+  typedef typename execution_space::size_type size_type ;
+
+  //------------------------------------
+
+  TestTripleNestedReduce( const size_type & nrows , const size_type & ncols 
+                        , const size_type & team_size , const size_type & vector_length )
+  {
+    run_test( nrows , ncols , team_size, vector_length );
+  }
+
+  void run_test( const size_type & nrows , const size_type & ncols 
+               , const size_type & team_size, const size_type & vector_length )
+  {
+    //typedef Kokkos::LayoutLeft Layout;
+    typedef Kokkos::LayoutRight Layout;
+
+    typedef Kokkos::View<ScalarType* , DeviceType>            ViewVector;
+    typedef Kokkos::View<ScalarType** , Layout , DeviceType>   ViewMatrix;
+    ViewVector y( "y" , nrows );
+    ViewVector x( "x" , ncols );
+    ViewMatrix A( "A" , nrows , ncols );
+
+    typedef Kokkos::RangePolicy<DeviceType> range_policy;
+
+    // Initialize y vector
+    Kokkos::parallel_for( range_policy( 0 , nrows ) , KOKKOS_LAMBDA( const int i ) { y( i ) = 1; } );
+
+    // Initialize x vector
+    Kokkos::parallel_for( range_policy( 0 , ncols ) , KOKKOS_LAMBDA( const int i ) { x( i ) = 1; } );
+
+    typedef Kokkos::TeamPolicy<DeviceType>                        team_policy;
+    typedef typename Kokkos::TeamPolicy<DeviceType>::member_type  member_type;
+
+    // Initialize A matrix, note 2D indexing computation
+    Kokkos::parallel_for( team_policy( nrows , Kokkos::AUTO ) , KOKKOS_LAMBDA( const member_type& teamMember ) {
+      const int j = teamMember.league_rank();
+      Kokkos::parallel_for( Kokkos::TeamThreadRange( teamMember , ncols ) , [&] ( const int i ) {
+        A( j , i ) = 1;
+      } );
+    } );
+
+    // Three level parallelism kernel to force caching of vector x 
+    ScalarType result = 0.0;
+    int chunk_size = 128;
+    Kokkos::parallel_reduce( team_policy( nrows/chunk_size , team_size , vector_length ) , KOKKOS_LAMBDA ( const member_type& teamMember , double &update ) {
+      const int row_start = teamMember.league_rank() * chunk_size;
+      const int row_end   = row_start + chunk_size;
+      Kokkos::parallel_for( Kokkos::TeamThreadRange( teamMember , row_start , row_end ) , [&] ( const int i ) {
+        ScalarType sum_i = 0.0;
+        Kokkos::parallel_reduce( Kokkos::ThreadVectorRange( teamMember , ncols ) , [&] ( const int j , ScalarType &innerUpdate ) {
+          innerUpdate += A( i , j ) * x( j );
+        } , sum_i );
+        Kokkos::single( Kokkos::PerThread( teamMember ) , [&] () {
+          update += y( i ) * sum_i;
+        } );
+      } );
+    } , result );
+
+    const ScalarType solution= ( ScalarType ) nrows * ( ScalarType ) ncols;
+    ASSERT_EQ( solution , result );
+  }
+};
+
+#else /* #if ( ! defined( KOKKOS_HAVE_CUDA ) ) || defined( KOKKOS_CUDA_USE_LAMBDA ) */
+
+template< typename ScalarType , class DeviceType >
+class TestTripleNestedReduce
+{
+public:
+  typedef DeviceType execution_space ;
+  typedef typename execution_space::size_type size_type ;
+
+  TestTripleNestedReduce( const size_type & , const size_type  
+                        , const size_type & , const size_type )
+  { }
+};
+
+#endif
+
+//--------------------------------------------------------------------------
+
+namespace Test {
+namespace ReduceCombinatorical {
+
+template<class Scalar,class Space = Kokkos::HostSpace>
+struct AddPlus {
+public:
+  //Required
+  typedef AddPlus reducer_type;
+  typedef Scalar value_type;
+
+  typedef Kokkos::View<value_type, Space, Kokkos::MemoryTraits<Kokkos::Unmanaged> > result_view_type;
+
+private:
+  result_view_type result;
+
+public:
+
+  AddPlus(value_type& result_):result(&result_) {}
+
+  //Required
+  KOKKOS_INLINE_FUNCTION
+  void join(value_type& dest, const value_type& src)  const {
+    dest += src + 1;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile value_type& dest, const volatile value_type& src) const {
+    dest += src + 1;
+  }
+
+  //Optional
+  KOKKOS_INLINE_FUNCTION
+  void init( value_type& val)  const {
+    val = value_type();
+  }
+
+  result_view_type result_view() const {
+    return result;
+  }
+};
+
+template<int ISTEAM>
+struct FunctorScalar;
+
+template<>
+struct FunctorScalar<0>{
+  FunctorScalar(Kokkos::View<double> r):result(r) {}
+  Kokkos::View<double> result;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const int& i,double& update) const {
+    update+=i;
+  }
+};
+
+template<>
+struct FunctorScalar<1>{
+  FunctorScalar(Kokkos::View<double> r):result(r) {}
+  Kokkos::View<double> result;
+
+  typedef Kokkos::TeamPolicy<>::member_type team_type;
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const team_type& team,double& update) const {
+    update+=1.0/team.team_size()*team.league_rank();
+  }
+};
+
+template<int ISTEAM>
+struct FunctorScalarInit;
+
+template<>
+struct FunctorScalarInit<0> {
+  FunctorScalarInit(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const int& i, double& update)  const {
+    update += i;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void init(double& update) const {
+    update = 0.0;
+  }
+};
+
+template<>
+struct FunctorScalarInit<1> {
+  FunctorScalarInit(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+
+  typedef Kokkos::TeamPolicy<>::member_type team_type;
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const team_type& team,double& update) const {
+    update+=1.0/team.team_size()*team.league_rank();
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void init(double& update) const {
+    update = 0.0;
+  }
+};
+
+template<int ISTEAM>
+struct FunctorScalarFinal;
+
+
+template<>
+struct FunctorScalarFinal<0> {
+  FunctorScalarFinal(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const int& i, double& update)  const {
+    update += i;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void final(double& update) const {
+    result() = update;
+  }
+};
+
+template<>
+struct FunctorScalarFinal<1> {
+  FunctorScalarFinal(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+
+  typedef Kokkos::TeamPolicy<>::member_type team_type;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const team_type& team, double& update) const {
+    update+=1.0/team.team_size()*team.league_rank();
+  }
+  KOKKOS_INLINE_FUNCTION
+  void final(double& update) const {
+    result() = update;
+  }
+};
+
+template<int ISTEAM>
+struct FunctorScalarJoin;
+
+template<>
+struct FunctorScalarJoin<0> {
+  FunctorScalarJoin(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const int& i, double& update)  const {
+    update += i;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile double& dst, const volatile double& update) const {
+    dst += update;
+  }
+};
+
+template<>
+struct FunctorScalarJoin<1> {
+  FunctorScalarJoin(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+
+  typedef Kokkos::TeamPolicy<>::member_type team_type;
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const team_type& team,double& update) const {
+    update+=1.0/team.team_size()*team.league_rank();
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile double& dst, const volatile double& update) const {
+    dst += update;
+  }
+};
+
+template<int ISTEAM>
+struct FunctorScalarJoinFinal;
+
+template<>
+struct FunctorScalarJoinFinal<0> {
+  FunctorScalarJoinFinal(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const int& i, double& update)  const {
+    update += i;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile double& dst, const volatile double& update) const {
+    dst += update;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void final(double& update) const {
+    result() = update;
+  }
+};
+
+template<>
+struct FunctorScalarJoinFinal<1> {
+  FunctorScalarJoinFinal(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+
+  typedef Kokkos::TeamPolicy<>::member_type team_type;
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const team_type& team,double& update) const {
+    update+=1.0/team.team_size()*team.league_rank();
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile double& dst, const volatile double& update) const {
+    dst += update;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void final(double& update) const {
+    result() = update;
+  }
+};
+
+template<int ISTEAM>
+struct FunctorScalarJoinInit;
+
+template<>
+struct FunctorScalarJoinInit<0> {
+  FunctorScalarJoinInit(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const int& i, double& update)  const {
+    update += i;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile double& dst, const volatile double& update) const {
+    dst += update;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void init(double& update) const {
+    update = 0.0;
+  }
+};
+
+template<>
+struct FunctorScalarJoinInit<1> {
+  FunctorScalarJoinInit(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+
+  typedef Kokkos::TeamPolicy<>::member_type team_type;
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const team_type& team,double& update) const {
+    update+=1.0/team.team_size()*team.league_rank();
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile double& dst, const volatile double& update) const {
+    dst += update;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void init(double& update) const {
+    update = 0.0;
+  }
+};
+
+template<int ISTEAM>
+struct FunctorScalarJoinFinalInit;
+
+template<>
+struct FunctorScalarJoinFinalInit<0> {
+  FunctorScalarJoinFinalInit(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const int& i, double& update)  const {
+    update += i;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile double& dst, const volatile double& update) const {
+    dst += update;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void final(double& update) const {
+    result() = update;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void init(double& update) const {
+    update = 0.0;
+  }
+};
+
+template<>
+struct FunctorScalarJoinFinalInit<1> {
+  FunctorScalarJoinFinalInit(Kokkos::View<double> r):result(r) {}
+
+  Kokkos::View<double> result;
+
+  typedef Kokkos::TeamPolicy<>::member_type team_type;
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const team_type& team,double& update) const {
+    update+=1.0/team.team_size()*team.league_rank();
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join(volatile double& dst, const volatile double& update) const {
+    dst += update;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void final(double& update) const {
+    result() = update;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void init(double& update) const {
+    update = 0.0;
+  }
+};
+struct Functor1 {
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const int& i,double& update) const {
+    update+=i;
+  }
+};
+
+struct Functor2 {
+  typedef double value_type[];
+  const unsigned value_count;
+
+  Functor2(unsigned n):value_count(n){}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const unsigned& i,double update[]) const {
+    for(unsigned j=0;j<value_count;j++)
+      update[j]+=i;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void init( double dst[] ) const
+  {
+    for ( unsigned i = 0 ; i < value_count ; ++i ) dst[i] = 0 ;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void join( volatile double dst[] ,
+             const volatile double src[] ) const
+  {
+    for ( unsigned i = 0 ; i < value_count ; ++i ) dst[i] += src[i] ;
+  }
+};
+
+}
+}
+
+namespace Test {
+
+template<class ExecSpace = Kokkos::DefaultExecutionSpace>
+struct TestReduceCombinatoricalInstantiation {
+  template<class ... Args>
+  static void CallParallelReduce(Args... args) {
+    Kokkos::parallel_reduce(args...);
+  }
+
+  template<class ... Args>
+  static void AddReturnArgument(Args... args) {
+    Kokkos::View<double,Kokkos::HostSpace> result_view("ResultView");
+    double expected_result = 1000.0*999.0/2.0;
+
+    double value = 0;
+    Kokkos::parallel_reduce(args...,value);
+    ASSERT_EQ(expected_result,value);
+
+    result_view() = 0;
+    CallParallelReduce(args...,result_view);
+    ASSERT_EQ(expected_result,result_view());
+
+    value = 0;
+    CallParallelReduce(args...,Kokkos::View<double,Kokkos::HostSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>(&value));
+    ASSERT_EQ(expected_result,value);
+
+    result_view() = 0;
+    const Kokkos::View<double,Kokkos::HostSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> result_view_const_um = result_view;
+    CallParallelReduce(args...,result_view_const_um);
+    ASSERT_EQ(expected_result,result_view_const_um());
+
+    value = 0;
+    CallParallelReduce(args...,Test::ReduceCombinatorical::AddPlus<double>(value));
+    if((Kokkos::DefaultExecutionSpace::concurrency() > 1) && (ExecSpace::concurrency()>1))
+      ASSERT_TRUE(expected_result<value);
+    else if((Kokkos::DefaultExecutionSpace::concurrency() > 1) || (ExecSpace::concurrency()>1))
+      ASSERT_TRUE(expected_result<=value);
+    else
+      ASSERT_EQ(expected_result,value);
+
+    value = 0;
+    Test::ReduceCombinatorical::AddPlus<double> add(value);
+    CallParallelReduce(args...,add);
+    if((Kokkos::DefaultExecutionSpace::concurrency() > 1) && (ExecSpace::concurrency()>1))
+      ASSERT_TRUE(expected_result<value);
+    else if((Kokkos::DefaultExecutionSpace::concurrency() > 1) || (ExecSpace::concurrency()>1))
+      ASSERT_TRUE(expected_result<=value);
+    else
+      ASSERT_EQ(expected_result,value);
+  }
+
+
+  template<class ... Args>
+  static void AddLambdaRange(void*,Args... args) {
+    AddReturnArgument(args...,  KOKKOS_LAMBDA (const int&i , double& lsum) {
+      lsum += i;
+    });
+  }
+
+  template<class ... Args>
+  static void AddLambdaTeam(void*,Args... args) {
+    AddReturnArgument(args..., KOKKOS_LAMBDA (const Kokkos::TeamPolicy<>::member_type& team, double& update) {
+      update+=1.0/team.team_size()*team.league_rank();
+    });
+  }
+
+  template<class ... Args>
+  static void AddLambdaRange(Kokkos::InvalidType,Args... args) {
+  }
+
+  template<class ... Args>
+  static void AddLambdaTeam(Kokkos::InvalidType,Args... args) {
+  }
+
+  template<int ISTEAM, class ... Args>
+  static void AddFunctor(Args... args) {
+    Kokkos::View<double> result_view("FunctorView");
+    auto h_r = Kokkos::create_mirror_view(result_view);
+    Test::ReduceCombinatorical::FunctorScalar<ISTEAM> functor(result_view);
+    double expected_result = 1000.0*999.0/2.0;
+
+    AddReturnArgument(args..., functor);
+    AddReturnArgument(args..., Test::ReduceCombinatorical::FunctorScalar<ISTEAM>(result_view));
+    AddReturnArgument(args..., Test::ReduceCombinatorical::FunctorScalarInit<ISTEAM>(result_view));
+    AddReturnArgument(args..., Test::ReduceCombinatorical::FunctorScalarJoin<ISTEAM>(result_view));
+    AddReturnArgument(args..., Test::ReduceCombinatorical::FunctorScalarJoinInit<ISTEAM>(result_view));
+
+    h_r() = 0;
+    Kokkos::deep_copy(result_view,h_r);
+    CallParallelReduce(args..., Test::ReduceCombinatorical::FunctorScalarFinal<ISTEAM>(result_view));
+    Kokkos::deep_copy(h_r,result_view);
+    ASSERT_EQ(expected_result,h_r());
+
+    h_r() = 0;
+    Kokkos::deep_copy(result_view,h_r);
+    CallParallelReduce(args..., Test::ReduceCombinatorical::FunctorScalarJoinFinal<ISTEAM>(result_view));
+    Kokkos::deep_copy(h_r,result_view);
+    ASSERT_EQ(expected_result,h_r());
+
+    h_r() = 0;
+    Kokkos::deep_copy(result_view,h_r);
+    CallParallelReduce(args..., Test::ReduceCombinatorical::FunctorScalarJoinFinalInit<ISTEAM>(result_view));
+    Kokkos::deep_copy(h_r,result_view);
+    ASSERT_EQ(expected_result,h_r());
+  }
+
+  template<class ... Args>
+  static void AddFunctorLambdaRange(Args... args) {
+    AddFunctor<0,Args...>(args...);
+    #ifdef  KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA
+    AddLambdaRange(typename std::conditional<std::is_same<ExecSpace,Kokkos::DefaultExecutionSpace>::value,void*,Kokkos::InvalidType>::type(), args...);
+    #endif
+  }
+
+  template<class ... Args>
+  static void AddFunctorLambdaTeam(Args... args) {
+    AddFunctor<1,Args...>(args...);
+    #ifdef  KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA
+    AddLambdaTeam(typename std::conditional<std::is_same<ExecSpace,Kokkos::DefaultExecutionSpace>::value,void*,Kokkos::InvalidType>::type(), args...);
+    #endif
+  }
+
+  template<class ... Args>
+  static void AddPolicy(Args... args) {
+    int N = 1000;
+    Kokkos::RangePolicy<ExecSpace> policy(0,N);
+
+    AddFunctorLambdaRange(args...,1000);
+    AddFunctorLambdaRange(args...,N);
+    AddFunctorLambdaRange(args...,policy);
+    AddFunctorLambdaRange(args...,Kokkos::RangePolicy<ExecSpace>(0,N));
+    AddFunctorLambdaRange(args...,Kokkos::RangePolicy<ExecSpace,Kokkos::Schedule<Kokkos::Dynamic> >(0,N));
+    AddFunctorLambdaRange(args...,Kokkos::RangePolicy<ExecSpace,Kokkos::Schedule<Kokkos::Static> >(0,N).set_chunk_size(10));
+    AddFunctorLambdaRange(args...,Kokkos::RangePolicy<ExecSpace,Kokkos::Schedule<Kokkos::Dynamic> >(0,N).set_chunk_size(10));
+
+    AddFunctorLambdaTeam(args...,Kokkos::TeamPolicy<ExecSpace>(N,Kokkos::AUTO));
+    AddFunctorLambdaTeam(args...,Kokkos::TeamPolicy<ExecSpace,Kokkos::Schedule<Kokkos::Dynamic> >(N,Kokkos::AUTO));
+    AddFunctorLambdaTeam(args...,Kokkos::TeamPolicy<ExecSpace,Kokkos::Schedule<Kokkos::Static> >(N,Kokkos::AUTO).set_chunk_size(10));
+    AddFunctorLambdaTeam(args...,Kokkos::TeamPolicy<ExecSpace,Kokkos::Schedule<Kokkos::Dynamic> >(N,Kokkos::AUTO).set_chunk_size(10));
+  }
+
+
+  static void AddLabel() {
+    std::string s("Std::String");
+    AddPolicy();
+    AddPolicy("Char Constant");
+    AddPolicy(s.c_str());
+    AddPolicy(s);
+  }
+
+  static void execute() {
+    AddLabel();
+  }
+};
+
+template<class Scalar, class ExecSpace = Kokkos::DefaultExecutionSpace>
+struct TestReducers {
+
+  struct SumFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i, Scalar& value) const {
+      value += values(i);
+    }
+  };
+
+  struct ProdFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i, Scalar& value) const {
+      value *= values(i);
+    }
+  };
+
+  struct MinFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i, Scalar& value) const {
+      if(values(i) < value)
+        value = values(i);
+    }
+  };
+
+  struct MaxFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i, Scalar& value) const {
+      if(values(i) > value)
+        value = values(i);
+    }
+  };
+
+  struct MinLocFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i,
+        typename Kokkos::Experimental::MinLoc<Scalar,int>::value_type& value) const {
+      if(values(i) < value.val) {
+        value.val = values(i);
+        value.loc = i;
+      }
+    }
+  };
+
+  struct MaxLocFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i,
+        typename Kokkos::Experimental::MaxLoc<Scalar,int>::value_type& value) const {
+      if(values(i) > value.val) {
+        value.val = values(i);
+        value.loc = i;
+      }
+    }
+  };
+
+  struct MinMaxLocFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i,
+        typename Kokkos::Experimental::MinMaxLoc<Scalar,int>::value_type& value) const {
+      if(values(i) > value.max_val) {
+        value.max_val = values(i);
+        value.max_loc = i;
+      }
+      if(values(i) < value.min_val) {
+        value.min_val = values(i);
+        value.min_loc = i;
+      }
+    }
+  };
+
+  struct BAndFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i, Scalar& value) const {
+      value = value & values(i);
+    }
+  };
+
+  struct BOrFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i, Scalar& value) const {
+      value = value | values(i);
+    }
+  };
+
+  struct BXorFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i, Scalar& value) const {
+      value = value ^ values(i);
+    }
+  };
+
+  struct LAndFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i, Scalar& value) const {
+      value = value && values(i);
+    }
+  };
+
+  struct LOrFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i, Scalar& value) const {
+      value = value || values(i);
+    }
+  };
+
+  struct LXorFunctor {
+    Kokkos::View<const Scalar*,ExecSpace> values;
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int& i, Scalar& value) const {
+      value = value ? (!values(i)) : values(i);
+    }
+  };
+
+  static void test_sum(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_sum = 0;
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)(rand()%100);
+      reference_sum += h_values(i);
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    SumFunctor f;
+    f.values = values;
+    Scalar init = 0;
+
+    {
+      Scalar sum_scalar = init;
+      Kokkos::Experimental::Sum<Scalar> reducer_scalar(sum_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(sum_scalar,reference_sum);
+      Scalar sum_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(sum_scalar_view,reference_sum);
+    }
+    {
+      Scalar sum_scalar_init = init;
+      Kokkos::Experimental::Sum<Scalar> reducer_scalar_init(sum_scalar_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar_init);
+      ASSERT_EQ(sum_scalar_init,reference_sum);
+      Scalar sum_scalar_init_view = reducer_scalar_init.result_view()();
+      ASSERT_EQ(sum_scalar_init_view,reference_sum);
+    }
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> sum_view("View");
+      sum_view() = init;
+      Kokkos::Experimental::Sum<Scalar> reducer_view(sum_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      Scalar sum_view_scalar = sum_view();
+      ASSERT_EQ(sum_view_scalar,reference_sum);
+      Scalar sum_view_view = reducer_view.result_view()();
+      ASSERT_EQ(sum_view_view,reference_sum);
+    }
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> sum_view_init("View");
+      sum_view_init() = init;
+      Kokkos::Experimental::Sum<Scalar> reducer_view_init(sum_view_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view_init);
+      Scalar sum_view_init_scalar = sum_view_init();
+      ASSERT_EQ(sum_view_init_scalar,reference_sum);
+      Scalar sum_view_init_view = reducer_view_init.result_view()();
+      ASSERT_EQ(sum_view_init_view,reference_sum);
+    }
+  }
+
+  static void test_prod(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_prod = 1;
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)(rand()%4+1);
+      reference_prod *= h_values(i);
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    ProdFunctor f;
+    f.values = values;
+    Scalar init = 1;
+
+    if(std::is_arithmetic<Scalar>::value)
+    {
+      Scalar prod_scalar = init;
+      Kokkos::Experimental::Prod<Scalar> reducer_scalar(prod_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(prod_scalar,reference_prod);
+      Scalar prod_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(prod_scalar_view,reference_prod);
+    }
+    {
+      Scalar prod_scalar_init = init;
+      Kokkos::Experimental::Prod<Scalar> reducer_scalar_init(prod_scalar_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar_init);
+      ASSERT_EQ(prod_scalar_init,reference_prod);
+      Scalar prod_scalar_init_view = reducer_scalar_init.result_view()();
+      ASSERT_EQ(prod_scalar_init_view,reference_prod);
+    }
+
+    if(std::is_arithmetic<Scalar>::value)
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> prod_view("View");
+      prod_view() = init;
+      Kokkos::Experimental::Prod<Scalar> reducer_view(prod_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      Scalar prod_view_scalar = prod_view();
+      ASSERT_EQ(prod_view_scalar,reference_prod);
+      Scalar prod_view_view = reducer_view.result_view()();
+      ASSERT_EQ(prod_view_view,reference_prod);
+    }
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> prod_view_init("View");
+      prod_view_init() = init;
+      Kokkos::Experimental::Prod<Scalar> reducer_view_init(prod_view_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view_init);
+      Scalar prod_view_init_scalar = prod_view_init();
+      ASSERT_EQ(prod_view_init_scalar,reference_prod);
+      Scalar prod_view_init_view = reducer_view_init.result_view()();
+      ASSERT_EQ(prod_view_init_view,reference_prod);
+    }
+  }
+
+  static void test_min(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_min = std::numeric_limits<Scalar>::max();
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)(rand()%100000);
+      if(h_values(i)<reference_min)
+        reference_min = h_values(i);
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    MinFunctor f;
+    f.values = values;
+    Scalar init = std::numeric_limits<Scalar>::max();
+
+    {
+      Scalar min_scalar = init;
+      Kokkos::Experimental::Min<Scalar> reducer_scalar(min_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(min_scalar,reference_min);
+      Scalar min_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(min_scalar_view,reference_min);
+    }
+    {
+      Scalar min_scalar_init = init;
+      Kokkos::Experimental::Min<Scalar> reducer_scalar_init(min_scalar_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar_init);
+      ASSERT_EQ(min_scalar_init,reference_min);
+      Scalar min_scalar_init_view = reducer_scalar_init.result_view()();
+      ASSERT_EQ(min_scalar_init_view,reference_min);
+    }
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> min_view("View");
+      min_view() = init;
+      Kokkos::Experimental::Min<Scalar> reducer_view(min_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      Scalar min_view_scalar = min_view();
+      ASSERT_EQ(min_view_scalar,reference_min);
+      Scalar min_view_view = reducer_view.result_view()();
+      ASSERT_EQ(min_view_view,reference_min);
+    }
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> min_view_init("View");
+      min_view_init() = init;
+      Kokkos::Experimental::Min<Scalar> reducer_view_init(min_view_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view_init);
+      Scalar min_view_init_scalar = min_view_init();
+      ASSERT_EQ(min_view_init_scalar,reference_min);
+      Scalar min_view_init_view = reducer_view_init.result_view()();
+      ASSERT_EQ(min_view_init_view,reference_min);
+    }
+  }
+
+  static void test_max(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_max = std::numeric_limits<Scalar>::min();
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)(rand()%100000+1);
+      if(h_values(i)>reference_max)
+        reference_max = h_values(i);
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    MaxFunctor f;
+    f.values = values;
+    Scalar init = std::numeric_limits<Scalar>::min();
+
+    {
+      Scalar max_scalar = init;
+      Kokkos::Experimental::Max<Scalar> reducer_scalar(max_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(max_scalar,reference_max);
+      Scalar max_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(max_scalar_view,reference_max);
+    }
+    {
+      Scalar max_scalar_init = init;
+      Kokkos::Experimental::Max<Scalar> reducer_scalar_init(max_scalar_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar_init);
+      ASSERT_EQ(max_scalar_init,reference_max);
+      Scalar max_scalar_init_view = reducer_scalar_init.result_view()();
+      ASSERT_EQ(max_scalar_init_view,reference_max);
+    }
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> max_view("View");
+      max_view() = init;
+      Kokkos::Experimental::Max<Scalar> reducer_view(max_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      Scalar max_view_scalar = max_view();
+      ASSERT_EQ(max_view_scalar,reference_max);
+      Scalar max_view_view = reducer_view.result_view()();
+      ASSERT_EQ(max_view_view,reference_max);
+    }
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> max_view_init("View");
+      max_view_init() = init;
+      Kokkos::Experimental::Max<Scalar> reducer_view_init(max_view_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view_init);
+      Scalar max_view_init_scalar = max_view_init();
+      ASSERT_EQ(max_view_init_scalar,reference_max);
+      Scalar max_view_init_view = reducer_view_init.result_view()();
+      ASSERT_EQ(max_view_init_view,reference_max);
+    }
+  }
+
+  static void test_minloc(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_min = std::numeric_limits<Scalar>::max();
+    int reference_loc = -1;
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)(rand()%100000);
+      if(h_values(i)<reference_min) {
+        reference_min = h_values(i);
+        reference_loc = i;
+      }
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    MinLocFunctor f;
+    typedef typename Kokkos::Experimental::MinLoc<Scalar,int>::value_type value_type;
+    f.values = values;
+    Scalar init = std::numeric_limits<Scalar>::max();
+
+
+    {
+      value_type min_scalar;
+      Kokkos::Experimental::MinLoc<Scalar,int> reducer_scalar(min_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(min_scalar.val,reference_min);
+      ASSERT_EQ(min_scalar.loc,reference_loc);
+      value_type min_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(min_scalar_view.val,reference_min);
+      ASSERT_EQ(min_scalar_view.loc,reference_loc);
+    }
+    {
+      value_type min_scalar_init;
+      Kokkos::Experimental::MinLoc<Scalar,int> reducer_scalar_init(min_scalar_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar_init);
+      ASSERT_EQ(min_scalar_init.val,reference_min);
+      ASSERT_EQ(min_scalar_init.loc,reference_loc);
+      value_type min_scalar_init_view = reducer_scalar_init.result_view()();
+      ASSERT_EQ(min_scalar_init_view.val,reference_min);
+      ASSERT_EQ(min_scalar_init_view.loc,reference_loc);
+    }
+    {
+      Kokkos::View<value_type,Kokkos::HostSpace> min_view("View");
+      Kokkos::Experimental::MinLoc<Scalar,int> reducer_view(min_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      value_type min_view_scalar = min_view();
+      ASSERT_EQ(min_view_scalar.val,reference_min);
+      ASSERT_EQ(min_view_scalar.loc,reference_loc);
+      value_type min_view_view = reducer_view.result_view()();
+      ASSERT_EQ(min_view_view.val,reference_min);
+      ASSERT_EQ(min_view_view.loc,reference_loc);
+    }
+    {
+      Kokkos::View<value_type,Kokkos::HostSpace> min_view_init("View");
+      Kokkos::Experimental::MinLoc<Scalar,int> reducer_view_init(min_view_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view_init);
+      value_type min_view_init_scalar = min_view_init();
+      ASSERT_EQ(min_view_init_scalar.val,reference_min);
+      ASSERT_EQ(min_view_init_scalar.loc,reference_loc);
+      value_type min_view_init_view = reducer_view_init.result_view()();
+      ASSERT_EQ(min_view_init_view.val,reference_min);
+      ASSERT_EQ(min_view_init_view.loc,reference_loc);
+    }
+  }
+
+  static void test_maxloc(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_max = std::numeric_limits<Scalar>::min();
+    int reference_loc = -1;
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)(rand()%100000);
+      if(h_values(i)>reference_max) {
+        reference_max = h_values(i);
+        reference_loc = i;
+      }
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    MaxLocFunctor f;
+    typedef typename Kokkos::Experimental::MaxLoc<Scalar,int>::value_type value_type;
+    f.values = values;
+    Scalar init = std::numeric_limits<Scalar>::min();
+
+
+    {
+      value_type max_scalar;
+      Kokkos::Experimental::MaxLoc<Scalar,int> reducer_scalar(max_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(max_scalar.val,reference_max);
+      ASSERT_EQ(max_scalar.loc,reference_loc);
+      value_type max_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(max_scalar_view.val,reference_max);
+      ASSERT_EQ(max_scalar_view.loc,reference_loc);
+    }
+    {
+      value_type max_scalar_init;
+      Kokkos::Experimental::MaxLoc<Scalar,int> reducer_scalar_init(max_scalar_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar_init);
+      ASSERT_EQ(max_scalar_init.val,reference_max);
+      ASSERT_EQ(max_scalar_init.loc,reference_loc);
+      value_type max_scalar_init_view = reducer_scalar_init.result_view()();
+      ASSERT_EQ(max_scalar_init_view.val,reference_max);
+      ASSERT_EQ(max_scalar_init_view.loc,reference_loc);
+    }
+    {
+      Kokkos::View<value_type,Kokkos::HostSpace> max_view("View");
+      Kokkos::Experimental::MaxLoc<Scalar,int> reducer_view(max_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      value_type max_view_scalar = max_view();
+      ASSERT_EQ(max_view_scalar.val,reference_max);
+      ASSERT_EQ(max_view_scalar.loc,reference_loc);
+      value_type max_view_view = reducer_view.result_view()();
+      ASSERT_EQ(max_view_view.val,reference_max);
+      ASSERT_EQ(max_view_view.loc,reference_loc);
+    }
+    {
+      Kokkos::View<value_type,Kokkos::HostSpace> max_view_init("View");
+      Kokkos::Experimental::MaxLoc<Scalar,int> reducer_view_init(max_view_init,init);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view_init);
+      value_type max_view_init_scalar = max_view_init();
+      ASSERT_EQ(max_view_init_scalar.val,reference_max);
+      ASSERT_EQ(max_view_init_scalar.loc,reference_loc);
+      value_type max_view_init_view = reducer_view_init.result_view()();
+      ASSERT_EQ(max_view_init_view.val,reference_max);
+      ASSERT_EQ(max_view_init_view.loc,reference_loc);
+    }
+  }
+
+  static void test_minmaxloc(int N) {
+     Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+     auto h_values = Kokkos::create_mirror_view(values);
+     Scalar reference_max = std::numeric_limits<Scalar>::min();
+     Scalar reference_min = std::numeric_limits<Scalar>::max();
+     int reference_minloc = -1;
+     int reference_maxloc = -1;
+     for(int i=0; i<N; i++) {
+       h_values(i) = (Scalar)(rand()%100000);
+       if(h_values(i)>reference_max) {
+         reference_max = h_values(i);
+         reference_maxloc = i;
+       }
+       if(h_values(i)<reference_min) {
+         reference_min = h_values(i);
+         reference_minloc = i;
+       }
+     }
+     Kokkos::deep_copy(values,h_values);
+
+     MinMaxLocFunctor f;
+     typedef typename Kokkos::Experimental::MinMaxLoc<Scalar,int>::value_type value_type;
+     f.values = values;
+     Scalar init_min = std::numeric_limits<Scalar>::max();
+     Scalar init_max = std::numeric_limits<Scalar>::min();
+
+
+     {
+       value_type minmax_scalar;
+       Kokkos::Experimental::MinMaxLoc<Scalar,int> reducer_scalar(minmax_scalar);
+       Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+       ASSERT_EQ(minmax_scalar.min_val,reference_min);
+       ASSERT_EQ(minmax_scalar.min_loc,reference_minloc);
+       ASSERT_EQ(minmax_scalar.max_val,reference_max);
+       ASSERT_EQ(minmax_scalar.max_loc,reference_maxloc);
+       value_type minmax_scalar_view = reducer_scalar.result_view()();
+       ASSERT_EQ(minmax_scalar_view.min_val,reference_min);
+       ASSERT_EQ(minmax_scalar_view.min_loc,reference_minloc);
+       ASSERT_EQ(minmax_scalar_view.max_val,reference_max);
+       ASSERT_EQ(minmax_scalar_view.max_loc,reference_maxloc);
+     }
+     {
+       value_type minmax_scalar_init;
+       Kokkos::Experimental::MinMaxLoc<Scalar,int> reducer_scalar_init(minmax_scalar_init,init_min,init_max);
+       Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar_init);
+       ASSERT_EQ(minmax_scalar_init.min_val,reference_min);
+       ASSERT_EQ(minmax_scalar_init.min_loc,reference_minloc);
+       ASSERT_EQ(minmax_scalar_init.max_val,reference_max);
+       ASSERT_EQ(minmax_scalar_init.max_loc,reference_maxloc);
+       value_type minmax_scalar_init_view = reducer_scalar_init.result_view()();
+       ASSERT_EQ(minmax_scalar_init_view.min_val,reference_min);
+       ASSERT_EQ(minmax_scalar_init_view.min_loc,reference_minloc);
+       ASSERT_EQ(minmax_scalar_init_view.max_val,reference_max);
+       ASSERT_EQ(minmax_scalar_init_view.max_loc,reference_maxloc);
+     }
+     {
+       Kokkos::View<value_type,Kokkos::HostSpace> minmax_view("View");
+       Kokkos::Experimental::MinMaxLoc<Scalar,int> reducer_view(minmax_view);
+       Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+       value_type minmax_view_scalar = minmax_view();
+       ASSERT_EQ(minmax_view_scalar.min_val,reference_min);
+       ASSERT_EQ(minmax_view_scalar.min_loc,reference_minloc);
+       ASSERT_EQ(minmax_view_scalar.max_val,reference_max);
+       ASSERT_EQ(minmax_view_scalar.max_loc,reference_maxloc);
+       value_type minmax_view_view = reducer_view.result_view()();
+       ASSERT_EQ(minmax_view_view.min_val,reference_min);
+       ASSERT_EQ(minmax_view_view.min_loc,reference_minloc);
+       ASSERT_EQ(minmax_view_view.max_val,reference_max);
+       ASSERT_EQ(minmax_view_view.max_loc,reference_maxloc);
+     }
+     {
+       Kokkos::View<value_type,Kokkos::HostSpace> minmax_view_init("View");
+       Kokkos::Experimental::MinMaxLoc<Scalar,int> reducer_view_init(minmax_view_init,init_min,init_max);
+       Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view_init);
+       value_type minmax_view_init_scalar = minmax_view_init();
+       ASSERT_EQ(minmax_view_init_scalar.min_val,reference_min);
+       ASSERT_EQ(minmax_view_init_scalar.min_loc,reference_minloc);
+       ASSERT_EQ(minmax_view_init_scalar.max_val,reference_max);
+       ASSERT_EQ(minmax_view_init_scalar.max_loc,reference_maxloc);
+       value_type minmax_view_init_view = reducer_view_init.result_view()();
+       ASSERT_EQ(minmax_view_init_view.min_val,reference_min);
+       ASSERT_EQ(minmax_view_init_view.min_loc,reference_minloc);
+       ASSERT_EQ(minmax_view_init_view.max_val,reference_max);
+       ASSERT_EQ(minmax_view_init_view.max_loc,reference_maxloc);
+     }
+   }
+
+  static void test_BAnd(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_band = Scalar() | (~Scalar());
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)(rand()%100000+1);
+      reference_band = reference_band & h_values(i);
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    BAndFunctor f;
+    f.values = values;
+    Scalar init = Scalar() | (~Scalar());
+
+    {
+      Scalar band_scalar = init;
+      Kokkos::Experimental::BAnd<Scalar> reducer_scalar(band_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(band_scalar,reference_band);
+      Scalar band_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(band_scalar_view,reference_band);
+    }
+
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> band_view("View");
+      band_view() = init;
+      Kokkos::Experimental::BAnd<Scalar> reducer_view(band_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      Scalar band_view_scalar = band_view();
+      ASSERT_EQ(band_view_scalar,reference_band);
+      Scalar band_view_view = reducer_view.result_view()();
+      ASSERT_EQ(band_view_view,reference_band);
+    }
+  }
+
+  static void test_BOr(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_bor = Scalar() & (~Scalar());
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)((rand()%100000+1)*2);
+      reference_bor = reference_bor | h_values(i);
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    BOrFunctor f;
+    f.values = values;
+    Scalar init = Scalar() & (~Scalar());
+
+    {
+      Scalar bor_scalar = init;
+      Kokkos::Experimental::BOr<Scalar> reducer_scalar(bor_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(bor_scalar,reference_bor);
+      Scalar bor_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(bor_scalar_view,reference_bor);
+    }
+
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> bor_view("View");
+      bor_view() = init;
+      Kokkos::Experimental::BOr<Scalar> reducer_view(bor_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      Scalar bor_view_scalar = bor_view();
+      ASSERT_EQ(bor_view_scalar,reference_bor);
+      Scalar bor_view_view = reducer_view.result_view()();
+      ASSERT_EQ(bor_view_view,reference_bor);
+    }
+  }
+
+  static void test_BXor(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_bxor = Scalar() & (~Scalar());
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)((rand()%100000+1)*2);
+      reference_bxor = reference_bxor ^ h_values(i);
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    BXorFunctor f;
+    f.values = values;
+    Scalar init = Scalar() & (~Scalar());
+
+    {
+      Scalar bxor_scalar = init;
+      Kokkos::Experimental::BXor<Scalar> reducer_scalar(bxor_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(bxor_scalar,reference_bxor);
+      Scalar bxor_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(bxor_scalar_view,reference_bxor);
+    }
+
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> bxor_view("View");
+      bxor_view() = init;
+      Kokkos::Experimental::BXor<Scalar> reducer_view(bxor_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      Scalar bxor_view_scalar = bxor_view();
+      ASSERT_EQ(bxor_view_scalar,reference_bxor);
+      Scalar bxor_view_view = reducer_view.result_view()();
+      ASSERT_EQ(bxor_view_view,reference_bxor);
+    }
+  }
 
+  static void test_LAnd(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_land = 1;
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)(rand()%2);
+      reference_land = reference_land && h_values(i);
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    LAndFunctor f;
+    f.values = values;
+    Scalar init = 1;
+
+    {
+      Scalar land_scalar = init;
+      Kokkos::Experimental::LAnd<Scalar> reducer_scalar(land_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(land_scalar,reference_land);
+      Scalar land_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(land_scalar_view,reference_land);
+    }
+
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> land_view("View");
+      land_view() = init;
+      Kokkos::Experimental::LAnd<Scalar> reducer_view(land_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      Scalar land_view_scalar = land_view();
+      ASSERT_EQ(land_view_scalar,reference_land);
+      Scalar land_view_view = reducer_view.result_view()();
+      ASSERT_EQ(land_view_view,reference_land);
+    }
+  }
+
+  static void test_LOr(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_lor = 0;
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)(rand()%2);
+      reference_lor = reference_lor || h_values(i);
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    LOrFunctor f;
+    f.values = values;
+    Scalar init = 0;
+
+    {
+      Scalar lor_scalar = init;
+      Kokkos::Experimental::LOr<Scalar> reducer_scalar(lor_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(lor_scalar,reference_lor);
+      Scalar lor_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(lor_scalar_view,reference_lor);
+    }
+
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> lor_view("View");
+      lor_view() = init;
+      Kokkos::Experimental::LOr<Scalar> reducer_view(lor_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      Scalar lor_view_scalar = lor_view();
+      ASSERT_EQ(lor_view_scalar,reference_lor);
+      Scalar lor_view_view = reducer_view.result_view()();
+      ASSERT_EQ(lor_view_view,reference_lor);
+    }
+  }
+
+  static void test_LXor(int N) {
+    Kokkos::View<Scalar*,ExecSpace> values("Values",N);
+    auto h_values = Kokkos::create_mirror_view(values);
+    Scalar reference_lxor = 0;
+    for(int i=0; i<N; i++) {
+      h_values(i) = (Scalar)(rand()%2);
+      reference_lxor = reference_lxor ? (!h_values(i)) : h_values(i);
+    }
+    Kokkos::deep_copy(values,h_values);
+
+    LXorFunctor f;
+    f.values = values;
+    Scalar init = 0;
+
+    {
+      Scalar lxor_scalar = init;
+      Kokkos::Experimental::LXor<Scalar> reducer_scalar(lxor_scalar);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_scalar);
+      ASSERT_EQ(lxor_scalar,reference_lxor);
+      Scalar lxor_scalar_view = reducer_scalar.result_view()();
+      ASSERT_EQ(lxor_scalar_view,reference_lxor);
+    }
+
+    {
+      Kokkos::View<Scalar,Kokkos::HostSpace> lxor_view("View");
+      lxor_view() = init;
+      Kokkos::Experimental::LXor<Scalar> reducer_view(lxor_view);
+      Kokkos::parallel_reduce(Kokkos::RangePolicy<ExecSpace>(0,N),f,reducer_view);
+      Scalar lxor_view_scalar = lxor_view();
+      ASSERT_EQ(lxor_view_scalar,reference_lxor);
+      Scalar lxor_view_view = reducer_view.result_view()();
+      ASSERT_EQ(lxor_view_view,reference_lxor);
+    }
+  }
+
+  static void execute_float() {
+    test_sum(10001);
+    test_prod(35);
+    test_min(10003);
+    test_minloc(10003);
+    test_max(10007);
+    test_maxloc(10007);
+    test_minmaxloc(10007);
+  }
+
+  static void execute_integer() {
+    test_sum(10001);
+    test_prod(35);
+    test_min(10003);
+    test_minloc(10003);
+    test_max(10007);
+    test_maxloc(10007);
+    test_minmaxloc(10007);
+    test_BAnd(35);
+    test_BOr(35);
+    test_BXor(35);
+    test_LAnd(35);
+    test_LOr(35);
+    test_LXor(35);
+  }
+
+  static void execute_basic() {
+    test_sum(10001);
+    test_prod(35);
+  }
+};
 }
 
 /*--------------------------------------------------------------------------*/
diff --git a/lib/kokkos/core/unit_test/TestSerial.cpp b/lib/kokkos/core/unit_test/TestSerial.cpp
index 7ddb54241c..d85614e66e 100644
--- a/lib/kokkos/core/unit_test/TestSerial.cpp
+++ b/lib/kokkos/core/unit_test/TestSerial.cpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -66,6 +66,7 @@
 #include <TestViewOfClass.hpp>
 #include <TestViewSubview.hpp>
 #include <TestAtomic.hpp>
+#include <TestAtomicOperations.hpp>
 #include <TestRange.hpp>
 #include <TestTeam.hpp>
 #include <TestReduce.hpp>
@@ -85,6 +86,8 @@
 
 #include <TestPolicyConstruction.hpp>
 
+#include <TestMDRange.hpp>
+
 namespace Test {
 
 class serial : public ::testing::Test {
@@ -99,6 +102,12 @@ protected:
     }
 };
 
+TEST_F( serial , md_range ) {
+  TestMDRange_2D< Kokkos::Serial >::test_for2(100,100);
+
+  TestMDRange_3D< Kokkos::Serial >::test_for3(100,100,100);
+}
+
 TEST_F( serial , impl_shared_alloc ) {
   test_shared_alloc< Kokkos::HostSpace , Kokkos::Serial >();
 }
@@ -199,6 +208,14 @@ TEST_F( serial, double_reduce) {
   TestReduce< double ,   Kokkos::Serial >( 1000000 );
 }
 
+TEST_F( serial , reducers )
+{
+  TestReducers<int, Kokkos::Serial>::execute_integer();
+  TestReducers<size_t, Kokkos::Serial>::execute_integer();
+  TestReducers<double, Kokkos::Serial>::execute_float();
+  TestReducers<Kokkos::complex<double>, Kokkos::Serial>::execute_basic();
+}
+
 TEST_F( serial, long_reduce_dynamic ) {
   TestReduceDynamic< long ,   Kokkos::Serial >( 1000000 );
 }
@@ -237,13 +254,17 @@ TEST_F( serial , team_shared_request) {
   TestSharedTeam< Kokkos::Serial , Kokkos::Schedule<Kokkos::Dynamic> >();
 }
 
-#if defined(KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA) 
+#if defined(KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA)
 TEST_F( serial , team_lambda_shared_request) {
   TestLambdaSharedTeam< Kokkos::HostSpace, Kokkos::Serial , Kokkos::Schedule<Kokkos::Static> >();
   TestLambdaSharedTeam< Kokkos::HostSpace, Kokkos::Serial , Kokkos::Schedule<Kokkos::Dynamic> >();
 }
 #endif
 
+TEST_F( serial, shmem_size) {
+  TestShmemSize< Kokkos::Serial >();
+}
+
 TEST_F( serial  , team_scan )
 {
   TestScanTeam< Kokkos::Serial , Kokkos::Schedule<Kokkos::Static> >( 10 );
@@ -345,6 +366,74 @@ TEST_F( serial , atomics )
   ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<4> ,Kokkos::Serial>(100,3) ) );
 }
 
+TEST_F( serial , atomic_operations )
+{
+  const int start = 1; //Avoid zero for division
+  const int end = 11;
+  for (int i = start; i < end; ++i)
+  {
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Serial>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Serial>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Serial>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Serial>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Serial>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Serial>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Serial>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Serial>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Serial>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Serial>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Serial>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Serial>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Serial>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Serial>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Serial>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Serial>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Serial>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Serial>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Serial>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Serial>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Serial>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Serial>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Serial>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Serial>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Serial>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Serial>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Serial>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Serial>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Serial>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Serial>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Serial>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Serial>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Serial>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Serial>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Serial>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Serial>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Serial>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Serial>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Serial>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Serial>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Serial>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Serial>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Serial>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Serial>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Serial>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Serial>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Serial>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Serial>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Serial>(start, end-i, 4 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Serial>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Serial>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Serial>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Serial>(start, end-i, 4 ) ) );
+  }
+
+}
 //----------------------------------------------------------------------------
 
 TEST_F( serial, tile_layout )
@@ -391,12 +480,36 @@ TEST_F( serial , memory_pool )
   bool val = TestMemoryPool::test_mempool< Kokkos::Serial >( 128, 128000000 );
   ASSERT_TRUE( val );
 
-  TestMemoryPool::test_mempool2< Kokkos::Serial >( 128, 128000000 );
+  TestMemoryPool::test_mempool2< Kokkos::Serial >( 64, 4, 1000000, 2000000 );
+
+  TestMemoryPool::test_memory_exhaustion< Kokkos::Serial >();
 }
 
 //----------------------------------------------------------------------------
 
-TEST_F( serial , task_policy )
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
+TEST_F( serial , task_fib )
+{
+  for ( int i = 0 ; i < 25 ; ++i ) {
+    TestTaskPolicy::TestFib< Kokkos::Serial >::run(i);
+  }
+}
+
+TEST_F( serial , task_depend )
+{
+  for ( int i = 0 ; i < 25 ; ++i ) {
+    TestTaskPolicy::TestTaskDependence< Kokkos::Serial >::run(i);
+  }
+}
+
+TEST_F( serial , task_team )
+{
+  TestTaskPolicy::TestTaskTeam< Kokkos::Serial >::run(1000);
+  //TestTaskPolicy::TestTaskTeamValue< Kokkos::Serial >::run(1000); //put back after testing
+}
+
+TEST_F( serial , old_task_policy )
 {
   TestTaskPolicy::test_task_dep< Kokkos::Serial >( 10 );
   // TestTaskPolicy::test_norm2< Kokkos::Serial >( 1000 );
@@ -406,11 +519,13 @@ TEST_F( serial , task_policy )
   for ( long i = 0 ; i < 25 ; ++i ) TestTaskPolicy::test_fib2< Kokkos::Serial >(i);
 }
 
-TEST_F( serial , task_team )
+TEST_F( serial , old_task_team )
 {
   TestTaskPolicy::test_task_team< Kokkos::Serial >(1000);
 }
 
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
+
 //----------------------------------------------------------------------------
 
 TEST_F( serial , template_meta_functions )
diff --git a/lib/kokkos/core/unit_test/TestTaskPolicy.hpp b/lib/kokkos/core/unit_test/TestTaskPolicy.hpp
index e5c461af01..71790f6def 100644
--- a/lib/kokkos/core/unit_test/TestTaskPolicy.hpp
+++ b/lib/kokkos/core/unit_test/TestTaskPolicy.hpp
@@ -50,10 +50,489 @@
 #include <cmath>
 #include <Kokkos_TaskPolicy.hpp>
 
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace TestTaskPolicy {
+
+namespace {
+
+long eval_fib( long n )
+{
+  constexpr long mask = 0x03 ;
+
+  long fib[4] = { 0 , 1 , 1 , 2 };
+
+  for ( long i = 2 ; i <= n ; ++i ) {
+    fib[ i & mask ] = fib[ ( i - 1 ) & mask ] + fib[ ( i - 2 ) & mask ];
+  }
+  
+  return fib[ n & mask ];
+}
+
+}
+
+template< typename Space >
+struct TestFib
+{
+  typedef Kokkos::TaskPolicy<Space>  policy_type ;
+  typedef Kokkos::Future<long,Space> future_type ;
+  typedef long value_type ;
+
+  policy_type policy ;
+  future_type fib_m1 ;
+  future_type fib_m2 ;
+  const value_type n ;
+
+  KOKKOS_INLINE_FUNCTION
+  TestFib( const policy_type & arg_policy , const value_type arg_n )
+    : policy(arg_policy)
+    , fib_m1() , fib_m2()
+    , n( arg_n )
+    {}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()( typename policy_type::member_type & , value_type & result )
+    {
+#if 0
+      printf( "\nTestFib(%ld) %d %d\n"
+             , n
+             , int( ! fib_m1.is_null() )
+             , int( ! fib_m2.is_null() )
+             );
+#endif
+
+      if ( n < 2 ) {
+        result = n ;
+      }
+      else if ( ! fib_m2.is_null() && ! fib_m1.is_null() ) {
+        result = fib_m1.get() + fib_m2.get();
+      }
+      else {
+
+        // Spawn new children and respawn myself to sum their results:
+        // Spawn lower value at higher priority as it has a shorter
+        // path to completion.
+
+        fib_m2 = policy.task_spawn( TestFib(policy,n-2)
+                                  , Kokkos::TaskSingle
+                                  , Kokkos::TaskHighPriority );
+
+        fib_m1 = policy.task_spawn( TestFib(policy,n-1)
+                                  , Kokkos::TaskSingle );
+
+        Kokkos::Future<Space> dep[] = { fib_m1 , fib_m2 };
+
+        Kokkos::Future<Space> fib_all = policy.when_all( 2 , dep );
+
+        if ( ! fib_m2.is_null() && ! fib_m1.is_null() && ! fib_all.is_null() ) {
+          // High priority to retire this branch
+          policy.respawn( this , Kokkos::TaskHighPriority , fib_all );
+        }
+        else {
+#if 0
+      printf( "TestFib(%ld) insufficient memory alloc_capacity(%d) task_max(%d) task_accum(%ld)\n"
+             , n
+             , policy.allocation_capacity()
+             , policy.allocated_task_count_max()
+             , policy.allocated_task_count_accum()
+             );
+#endif
+          Kokkos::abort("TestFib insufficient memory");
+
+        }
+      }
+    }
+
+  static void run( int i , size_t MemoryCapacity = 16000 )
+    {
+      typedef typename policy_type::memory_space memory_space ;
+
+      enum { Log2_SuperBlockSize = 12 };
+
+      policy_type root_policy( memory_space() , MemoryCapacity , Log2_SuperBlockSize );
+
+      future_type f = root_policy.host_spawn( TestFib(root_policy,i) , Kokkos::TaskSingle );
+      Kokkos::wait( root_policy );
+      ASSERT_EQ( eval_fib(i) , f.get() );
+
+#if 0
+      fprintf( stdout , "\nTestFib::run(%d) spawn_size(%d) when_all_size(%d) alloc_capacity(%d) task_max(%d) task_accum(%ld)\n"
+             , i
+             , int(root_policy.template spawn_allocation_size<TestFib>())
+             , int(root_policy.when_all_allocation_size(2))
+             , root_policy.allocation_capacity()
+             , root_policy.allocated_task_count_max()
+             , root_policy.allocated_task_count_accum()
+             );
+      fflush( stdout );
+#endif
+    }
+
+};
+
+} // namespace TestTaskPolicy
+
+//----------------------------------------------------------------------------
+
 namespace TestTaskPolicy {
 
+template< class Space >
+struct TestTaskDependence {
+
+  typedef Kokkos::TaskPolicy<Space>  policy_type ;
+  typedef Kokkos::Future<Space>      future_type ;
+  typedef Kokkos::View<long,Space>   accum_type ;
+  typedef void value_type ;
+
+  policy_type  m_policy ;
+  accum_type   m_accum ;
+  long         m_count ;
+
+  KOKKOS_INLINE_FUNCTION
+  TestTaskDependence( long n
+                    , const policy_type & arg_policy
+                    , const accum_type  & arg_accum )
+    : m_policy( arg_policy )
+    , m_accum( arg_accum )
+    , m_count( n )
+    {}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()( typename policy_type::member_type & )
+    {
+       enum { CHUNK = 8 };
+       const int n = CHUNK < m_count ? CHUNK : m_count ;
+
+       if ( 1 < m_count ) {
+         future_type f[ CHUNK ] ;
+
+         const int inc = ( m_count + n - 1 ) / n ;
+
+         for ( int i = 0 ; i < n ; ++i ) {
+           long begin = i * inc ;
+           long count = begin + inc < m_count ? inc : m_count - begin ;
+           f[i] = m_policy.task_spawn( TestTaskDependence(count,m_policy,m_accum) , Kokkos::TaskSingle );
+         }
+
+         m_count = 0 ;
+
+         m_policy.respawn( this , m_policy.when_all( n , f ) );
+       }
+       else if ( 1 == m_count ) {
+         Kokkos::atomic_increment( & m_accum() );
+       }
+    }
+
+  static void run( int n )
+    {
+      typedef typename policy_type::memory_space memory_space ;
+
+      // enum { MemoryCapacity = 4000 }; // Triggers infinite loop in memory pool
+      enum { MemoryCapacity = 16000 };
+      enum { Log2_SuperBlockSize = 12 };
+      policy_type policy( memory_space() , MemoryCapacity , Log2_SuperBlockSize );
+
+      accum_type accum("accum");
+
+      typename accum_type::HostMirror host_accum =
+        Kokkos::create_mirror_view( accum );
+
+      policy.host_spawn( TestTaskDependence(n,policy,accum) , Kokkos::TaskSingle );
+
+      Kokkos::wait( policy );
+
+      Kokkos::deep_copy( host_accum , accum );
+
+      ASSERT_EQ( host_accum() , n );
+    }
+};
+
+} // namespace TestTaskPolicy
+
 //----------------------------------------------------------------------------
 
+namespace TestTaskPolicy {
+
+template< class ExecSpace >
+struct TestTaskTeam {
+
+  //enum { SPAN = 8 };
+  enum { SPAN = 33 };
+  //enum { SPAN = 1 };
+
+  typedef void value_type ;
+  typedef Kokkos::TaskPolicy<ExecSpace>  policy_type ;
+  typedef Kokkos::Future<ExecSpace>      future_type ;
+  typedef Kokkos::View<long*,ExecSpace>  view_type ;
+
+  policy_type  policy ;
+  future_type  future ;
+
+  view_type  parfor_result ;
+  view_type  parreduce_check ;
+  view_type  parscan_result ;
+  view_type  parscan_check ;
+  const long nvalue ;
+
+  KOKKOS_INLINE_FUNCTION
+  TestTaskTeam( const policy_type & arg_policy
+              , const view_type   & arg_parfor_result
+              , const view_type   & arg_parreduce_check
+              , const view_type   & arg_parscan_result
+              , const view_type   & arg_parscan_check
+              , const long          arg_nvalue )
+    : policy(arg_policy)
+    , future()
+    , parfor_result( arg_parfor_result )
+    , parreduce_check( arg_parreduce_check )
+    , parscan_result( arg_parscan_result )
+    , parscan_check( arg_parscan_check )
+    , nvalue( arg_nvalue )
+    {}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()( typename policy_type::member_type & member )
+    {
+      const long end   = nvalue + 1 ;
+      const long begin = 0 < end - SPAN ? end - SPAN : 0 ;
+
+      if ( 0 < begin && future.is_null() ) {
+        if ( member.team_rank() == 0 ) {
+          future = policy.task_spawn
+            ( TestTaskTeam( policy ,
+                            parfor_result ,
+                            parreduce_check,
+                            parscan_result,
+                            parscan_check,
+                            begin - 1 )
+            , Kokkos::TaskTeam );
+
+          assert( ! future.is_null() );
+
+          policy.respawn( this , future );
+        }
+        return ;
+      }
+
+      Kokkos::parallel_for( Kokkos::TeamThreadRange(member,begin,end)
+                          , [&]( int i ) { parfor_result[i] = i ; }
+                          );
+
+      // test parallel_reduce without join
+    
+      long tot = 0;
+      long expected = (begin+end-1)*(end-begin)*0.5;
+      
+      Kokkos::parallel_reduce( Kokkos::TeamThreadRange(member,begin,end)
+                          , [&]( int i, long &res) { res += parfor_result[i]; }
+                          , tot);
+      Kokkos::parallel_for( Kokkos::TeamThreadRange(member,begin,end)
+                          , [&]( int i ) { parreduce_check[i] = expected-tot ; }
+                          );
+
+      // test parallel_reduce with join
+
+      tot = 0;
+      Kokkos::parallel_reduce( Kokkos::TeamThreadRange(member,begin,end)
+                          , [&]( int i, long &res) { res += parfor_result[i]; }
+                          , [&]( long& val1, const long& val2) { val1 += val2; }
+                          , tot);
+      Kokkos::parallel_for( Kokkos::TeamThreadRange(member,begin,end)
+                          , [&]( int i ) { parreduce_check[i] += expected-tot ; }
+                          );
+
+#if 0
+      // test parallel_scan
+
+      // Exclusive scan
+      Kokkos::parallel_scan<long>( Kokkos::TeamThreadRange(member,begin,end)
+                          , [&]( int i, long &val , const bool final ) {
+                              if ( final ) { parscan_result[i] = val; }
+                              val += i;
+                            }
+                          );
+
+      if ( member.team_rank() == 0 ) {
+        for ( long i = begin ; i < end ; ++i ) {
+          parscan_check[i] = (i*(i-1)-begin*(begin-1))*0.5-parscan_result[i];
+        }
+      }
+
+      // Inclusive scan
+      Kokkos::parallel_scan<long>( Kokkos::TeamThreadRange(member,begin,end)
+                          , [&]( int i, long &val , const bool final ) {
+                              val += i;
+                              if ( final ) { parscan_result[i] = val; }
+                            }
+                          );
+
+      if ( member.team_rank() == 0 ) {
+        for ( long i = begin ; i < end ; ++i ) {
+          parscan_check[i] += (i*(i+1)-begin*(begin-1))*0.5-parscan_result[i];
+        }
+      }
+#endif
+
+    }
+
+  static void run( long n )
+    {
+      // const unsigned memory_capacity = 10000 ; // causes memory pool infinite loop
+      // const unsigned memory_capacity = 100000 ; // fails with SPAN=1 for serial and OMP
+      const unsigned memory_capacity = 400000 ;
+
+      policy_type root_policy( typename policy_type::memory_space()
+                        , memory_capacity );
+
+      view_type   root_parfor_result("parfor_result",n+1);
+      view_type   root_parreduce_check("parreduce_check",n+1);
+      view_type   root_parscan_result("parscan_result",n+1);
+      view_type   root_parscan_check("parscan_check",n+1);
+
+      typename view_type::HostMirror
+        host_parfor_result = Kokkos::create_mirror_view( root_parfor_result );
+      typename view_type::HostMirror
+        host_parreduce_check = Kokkos::create_mirror_view( root_parreduce_check );
+      typename view_type::HostMirror
+        host_parscan_result = Kokkos::create_mirror_view( root_parscan_result );
+      typename view_type::HostMirror
+        host_parscan_check = Kokkos::create_mirror_view( root_parscan_check );
+
+      future_type f = root_policy.host_spawn(
+                        TestTaskTeam( root_policy ,
+                                      root_parfor_result ,
+                                      root_parreduce_check ,
+                                      root_parscan_result,
+                                      root_parscan_check,
+                                      n ) ,
+                        Kokkos::TaskTeam );
+
+      Kokkos::wait( root_policy );
+
+      Kokkos::deep_copy( host_parfor_result , root_parfor_result );
+      Kokkos::deep_copy( host_parreduce_check , root_parreduce_check );
+      Kokkos::deep_copy( host_parscan_result , root_parscan_result );
+      Kokkos::deep_copy( host_parscan_check , root_parscan_check );
+
+      for ( long i = 0 ; i <= n ; ++i ) {
+        const long answer = i ;
+        if ( host_parfor_result(i) != answer ) {
+          std::cerr << "TestTaskTeam::run ERROR parallel_for result(" << i << ") = "
+                    << host_parfor_result(i) << " != " << answer << std::endl ;
+        }
+        if ( host_parreduce_check(i) != 0 ) {
+          std::cerr << "TestTaskTeam::run ERROR parallel_reduce check(" << i << ") = "
+                    << host_parreduce_check(i) << " != 0" << std::endl ;
+        } //TODO
+        if ( host_parscan_check(i) != 0 ) {
+          std::cerr << "TestTaskTeam::run ERROR parallel_scan check(" << i << ") = "
+                    << host_parscan_check(i) << " != 0" << std::endl ;
+        }
+      }
+    }
+};
+
+template< class ExecSpace >
+struct TestTaskTeamValue {
+
+  enum { SPAN = 8 };
+
+  typedef long value_type ;
+  typedef Kokkos::TaskPolicy<ExecSpace>         policy_type ;
+  typedef Kokkos::Future<value_type,ExecSpace>  future_type ;
+  typedef Kokkos::View<long*,ExecSpace>         view_type ;
+
+  policy_type  policy ;
+  future_type  future ;
+
+  view_type  result ;
+  const long nvalue ;
+
+  KOKKOS_INLINE_FUNCTION
+  TestTaskTeamValue( const policy_type & arg_policy
+                   , const view_type   & arg_result
+                   , const long          arg_nvalue )
+    : policy(arg_policy)
+    , future()
+    , result( arg_result )
+    , nvalue( arg_nvalue )
+    {}
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()( typename policy_type::member_type const & member
+                 , value_type & final )
+    {
+      const long end   = nvalue + 1 ;
+      const long begin = 0 < end - SPAN ? end - SPAN : 0 ;
+
+      if ( 0 < begin && future.is_null() ) {
+        if ( member.team_rank() == 0 ) {
+
+          future = policy.task_spawn
+            ( TestTaskTeamValue( policy , result , begin - 1 )
+            , Kokkos::TaskTeam );
+
+          assert( ! future.is_null() );
+
+          policy.respawn( this , future );
+        }
+        return ;
+      }
+
+      Kokkos::parallel_for( Kokkos::TeamThreadRange(member,begin,end)
+                          , [&]( int i ) { result[i] = i + 1 ; }
+                          );
+
+      if ( member.team_rank() == 0 ) {
+        final = result[nvalue] ;
+      }
+
+      Kokkos::memory_fence();
+    }
+
+  static void run( long n )
+    {
+      // const unsigned memory_capacity = 10000 ; // causes memory pool infinite loop
+      const unsigned memory_capacity = 100000 ;
+
+      policy_type root_policy( typename policy_type::memory_space()
+                             , memory_capacity );
+
+      view_type   root_result("result",n+1);
+
+      typename view_type::HostMirror
+        host_result = Kokkos::create_mirror_view( root_result );
+
+      future_type fv = root_policy.host_spawn
+        ( TestTaskTeamValue( root_policy, root_result, n ) , Kokkos::TaskTeam );
+
+      Kokkos::wait( root_policy );
+
+      Kokkos::deep_copy( host_result , root_result );
+
+      if ( fv.get() != n + 1 ) {
+        std::cerr << "TestTaskTeamValue ERROR future = "
+                  << fv.get() << " != " << n + 1 << std::endl ;
+      }
+      for ( long i = 0 ; i <= n ; ++i ) {
+        const long answer = i + 1 ;
+        if ( host_result(i) != answer ) {
+          std::cerr << "TestTaskTeamValue ERROR result(" << i << ") = "
+                    << host_result(i) << " != " << answer << std::endl ;
+        }
+      }
+    }
+};
+} // namespace TestTaskPolicy
+
+//----------------------------------------------------------------------------
+//----------------------------------------------------------------------------
+
+namespace TestTaskPolicy {
+
 template< class ExecSpace >
 struct FibChild {
 
@@ -207,28 +686,8 @@ struct FibChild2 {
     }
 };
 
-namespace {
-
-long eval_fib( long n )
-{
-  if ( 2 <= n ) {
-    std::vector<long> fib(n+1);
-
-    fib[0] = 0 ;
-    fib[1] = 1 ;
-
-    for ( long i = 2 ; i <= n ; ++i ) { fib[i] = fib[i-2] + fib[i-1]; }
-
-    n = fib[n] ;
-  }
-
-  return n ;
-}
-
-}
-
 template< class ExecSpace >
-void test_fib( long n , const unsigned task_max_count = 1024 )
+void test_fib( long n , const unsigned task_max_count = 4096 )
 {
   const unsigned task_max_size   = 256 ;
   const unsigned task_dependence = 4 ;
@@ -654,9 +1113,15 @@ void test_latch( int n )
   typedef TaskLatchRun< ExecSpace >        task_type ;
   typedef typename task_type::policy_type  policy_type ;
 
-  // Primary + latch + n*LatchAdd
-  const unsigned task_max_count  = n + 2 ;
-  const unsigned task_max_size   = sizeof(task_type);
+  // Primary + latch + n * LatchAdd
+  //
+  // This test uses several two different block sizes for allocation from the
+  // memory pool, so the memory size requested must be big enough to cause two
+  // or more superblocks to be used.  Currently, the superblock size in the
+  // task policy is 2^16, so make the minimum requested memory size greater
+  // than this.
+  const unsigned task_max_count  = n + 2 < 256 ? 256 : n + 2;
+  const unsigned task_max_size   = 256;
   const unsigned task_dependence = 4 ;
 
   policy_type
@@ -664,16 +1129,17 @@ void test_latch( int n )
           , task_max_size
           , task_dependence );
 
-
   policy.spawn( policy.proc_create( TaskLatchRun<ExecSpace>(policy,n) ) );
 
   wait( policy );
 }
 
+//----------------------------------------------------------------------------
 //----------------------------------------------------------------------------
 
 } // namespace TestTaskPolicy
 
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
 #endif /* #ifndef KOKKOS_UNITTEST_TASKPOLICY_HPP */
 
 
diff --git a/lib/kokkos/core/unit_test/TestTeam.hpp b/lib/kokkos/core/unit_test/TestTeam.hpp
index 810e74abdc..db6b0cff7e 100644
--- a/lib/kokkos/core/unit_test/TestTeam.hpp
+++ b/lib/kokkos/core/unit_test/TestTeam.hpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -89,6 +89,34 @@ struct TestTeamPolicy {
       }
     }
 
+  // included for test_small_league_size
+  TestTeamPolicy()
+    : m_flags()
+  {}
+
+  // included for test_small_league_size
+  struct NoOpTag {} ;
+  KOKKOS_INLINE_FUNCTION
+  void operator()( const NoOpTag & , const team_member & member ) const
+    {}
+
+
+  static void test_small_league_size() {
+
+    int bs = 8; // batch size (number of elements per batch)
+    int ns = 16; // total number of "problems" to process
+
+    // calculate total scratch memory space size
+    const int level = 0;
+    int mem_size = 960;
+    const int num_teams = ns/bs;
+    const Kokkos::TeamPolicy< ExecSpace, NoOpTag > policy(num_teams, Kokkos::AUTO());
+
+    Kokkos::parallel_for ( policy.set_scratch_size(level, Kokkos::PerTeam(mem_size), Kokkos::PerThread(0))
+                         , TestTeamPolicy()
+                         );
+  }
+
   static void test_for( const size_t league_size )
     {
       TestTeamPolicy functor( league_size );
@@ -97,6 +125,8 @@ struct TestTeamPolicy {
 
       Kokkos::parallel_for( Kokkos::TeamPolicy< ScheduleType,  ExecSpace >( league_size , team_size ) , functor );
       Kokkos::parallel_for( Kokkos::TeamPolicy< ScheduleType,  ExecSpace , VerifyInitTag >( league_size , team_size ) , functor );
+
+      test_small_league_size();
     }
 
   struct ReduceTag {};
@@ -617,7 +647,7 @@ struct TestScratchTeam {
     int team_scratch_size   = Functor::shared_int_array_type::shmem_size(Functor::SHARED_TEAM_COUNT) +
                               Functor::shared_int_array_type::shmem_size(2*team_size);
     int thread_scratch_size = Functor::shared_int_array_type::shmem_size(Functor::SHARED_THREAD_COUNT);
-    Kokkos::parallel_reduce( team_exec.set_scratch_size(1,Kokkos::PerTeam(team_scratch_size),
+    Kokkos::parallel_reduce( team_exec.set_scratch_size(0,Kokkos::PerTeam(team_scratch_size),
                                                           Kokkos::PerThread(thread_scratch_size)) ,
                              Functor() , result_type( & error_count ) );
 
@@ -626,4 +656,255 @@ struct TestScratchTeam {
 };
 }
 
+namespace Test {
+template< class ExecSpace>
+KOKKOS_INLINE_FUNCTION
+int test_team_mulit_level_scratch_loop_body(const typename Kokkos::TeamPolicy<ExecSpace>::member_type& team) {
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> a_team1(team.team_scratch(0),128);
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> a_thread1(team.thread_scratch(0),16);
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> a_team2(team.team_scratch(0),128);
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> a_thread2(team.thread_scratch(0),16);
+
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> b_team1(team.team_scratch(1),128000);
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> b_thread1(team.thread_scratch(1),16000);
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> b_team2(team.team_scratch(1),128000);
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> b_thread2(team.thread_scratch(1),16000);
+
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> a_team3(team.team_scratch(0),128);
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> a_thread3(team.thread_scratch(0),16);
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> b_team3(team.team_scratch(1),128000);
+      Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>> b_thread3(team.thread_scratch(1),16000);
+
+
+      Kokkos::parallel_for(Kokkos::TeamThreadRange(team,0,128), [&] (const int& i) {
+        a_team1(i) = 1000000 + i;
+        a_team2(i) = 2000000 + i;
+        a_team3(i) = 3000000 + i;
+      });
+      team.team_barrier();
+      Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,16), [&] (const int& i){
+        a_thread1(i) = 1000000 + 100000*team.team_rank() + 16-i;
+        a_thread2(i) = 2000000 + 100000*team.team_rank() + 16-i;
+        a_thread3(i) = 3000000 + 100000*team.team_rank() + 16-i;
+      });
+
+      Kokkos::parallel_for(Kokkos::TeamThreadRange(team,0,128000), [&] (const int& i) {
+        b_team1(i) = 1000000 + i;
+        b_team2(i) = 2000000 + i;
+        b_team3(i) = 3000000 + i;
+      });
+      team.team_barrier();
+      Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,16000), [&] (const int& i){
+        b_thread1(i) = 1000000 + 100000*team.team_rank() + 16-i;
+        b_thread2(i) = 2000000 + 100000*team.team_rank() + 16-i;
+        b_thread3(i) = 3000000 + 100000*team.team_rank() + 16-i;
+      });
+
+      team.team_barrier();
+      int error = 0;
+      Kokkos::parallel_for(Kokkos::TeamThreadRange(team,0,128), [&] (const int& i) {
+        if(a_team1(i) != 1000000 + i) error++;
+        if(a_team2(i) != 2000000 + i) error++;
+        if(a_team3(i) != 3000000 + i) error++;
+      });
+      team.team_barrier();
+      Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,16), [&] (const int& i){
+        if(a_thread1(i) != 1000000 + 100000*team.team_rank() + 16-i) error++;
+        if(a_thread2(i) != 2000000 + 100000*team.team_rank() + 16-i) error++;
+        if(a_thread3(i) != 3000000 + 100000*team.team_rank() + 16-i) error++;
+      });
+
+      Kokkos::parallel_for(Kokkos::TeamThreadRange(team,0,128000), [&] (const int& i) {
+        if(b_team1(i) != 1000000 + i) error++;
+        if(b_team2(i) != 2000000 + i) error++;
+        if(b_team3(i) != 3000000 + i) error++;
+      });
+      team.team_barrier();
+      Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,16000), [&] (const int& i){
+        if(b_thread1(i) != 1000000 + 100000*team.team_rank() + 16-i) error++;
+        if(b_thread2(i) != 2000000 + 100000*team.team_rank() + 16-i) error++;
+        if( b_thread3(i) != 3000000 + 100000*team.team_rank() + 16-i) error++;
+      });
+
+  return error;
+}
+
+
+struct TagReduce {};
+struct TagFor {};
+
+template< class ExecSpace, class ScheduleType >
+struct ClassNoShmemSizeFunction {
+  Kokkos::View<int,ExecSpace,Kokkos::MemoryTraits<Kokkos::Atomic> > errors;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const TagFor&, const typename Kokkos::TeamPolicy<ExecSpace,ScheduleType>::member_type& team) const {
+    int error = test_team_mulit_level_scratch_loop_body<ExecSpace>(team);
+    errors() += error;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const TagReduce&, const typename Kokkos::TeamPolicy<ExecSpace,ScheduleType>::member_type& team, int& error) const {
+    error += test_team_mulit_level_scratch_loop_body<ExecSpace>(team);
+  }
+
+  void run() {
+    Kokkos::View<int,ExecSpace> d_errors = Kokkos::View<int,ExecSpace>("Errors");
+    errors = d_errors;
+
+    const int per_team0 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(128);
+    const int per_thread0 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(16);
+
+    const int per_team1 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(128000);
+    const int per_thread1 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(16000);
+    {
+    Kokkos::TeamPolicy<TagFor,ExecSpace,ScheduleType> policy(10,8,16);
+    Kokkos::parallel_for(policy.set_scratch_size(0,Kokkos::PerTeam(per_team0),Kokkos::PerThread(per_thread0)).set_scratch_size(1,Kokkos::PerTeam(per_team1),Kokkos::PerThread(per_thread1)),
+      *this);
+    Kokkos::fence();
+    typename Kokkos::View<int,ExecSpace>::HostMirror h_errors = Kokkos::create_mirror_view(d_errors);
+    Kokkos::deep_copy(h_errors,d_errors);
+    ASSERT_EQ(h_errors(),0);
+    }
+
+    {
+    int error = 0;
+    Kokkos::TeamPolicy<TagReduce,ExecSpace,ScheduleType> policy(10,8,16);
+    Kokkos::parallel_reduce(policy.set_scratch_size(0,Kokkos::PerTeam(per_team0),Kokkos::PerThread(per_thread0)).set_scratch_size(1,Kokkos::PerTeam(per_team1),Kokkos::PerThread(per_thread1)),
+      *this,error);
+    Kokkos::fence();
+    ASSERT_EQ(error,0);
+    }
+  };
+};
+
+template< class ExecSpace, class ScheduleType >
+struct ClassWithShmemSizeFunction {
+  Kokkos::View<int,ExecSpace,Kokkos::MemoryTraits<Kokkos::Atomic> > errors;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const TagFor&, const typename Kokkos::TeamPolicy<ExecSpace,ScheduleType>::member_type& team) const {
+    int error = test_team_mulit_level_scratch_loop_body<ExecSpace>(team);
+    errors() += error;
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const TagReduce&, const typename Kokkos::TeamPolicy<ExecSpace,ScheduleType>::member_type& team, int& error) const {
+    error += test_team_mulit_level_scratch_loop_body<ExecSpace>(team);
+  }
+
+  void run() {
+    Kokkos::View<int,ExecSpace> d_errors = Kokkos::View<int,ExecSpace>("Errors");
+    errors = d_errors;
+
+    const int per_team1 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(128000);
+    const int per_thread1 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(16000);
+    {
+    Kokkos::TeamPolicy<TagFor,ExecSpace,ScheduleType> policy(10,8,16);
+    Kokkos::parallel_for(policy.set_scratch_size(1,Kokkos::PerTeam(per_team1),Kokkos::PerThread(per_thread1)),
+      *this);
+    Kokkos::fence();
+    typename Kokkos::View<int,ExecSpace>::HostMirror h_errors= Kokkos::create_mirror_view(d_errors);
+    Kokkos::deep_copy(h_errors,d_errors);
+    ASSERT_EQ(h_errors(),0);
+    }
+
+    {
+    int error = 0;
+    Kokkos::TeamPolicy<TagReduce,ExecSpace,ScheduleType> policy(10,8,16);
+    Kokkos::parallel_reduce(policy.set_scratch_size(1,Kokkos::PerTeam(per_team1),Kokkos::PerThread(per_thread1)),
+      *this,error);
+    Kokkos::fence();
+    ASSERT_EQ(error,0);
+    }
+  };
+
+  unsigned team_shmem_size(int team_size) const {
+    const int per_team0 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(128);
+    const int per_thread0 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(16);
+    return per_team0 + team_size * per_thread0;
+  }
+};
+
+template< class ExecSpace, class ScheduleType >
+void test_team_mulit_level_scratch_test_lambda() {
+#ifdef KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA
+  Kokkos::View<int,ExecSpace,Kokkos::MemoryTraits<Kokkos::Atomic> > errors;
+  Kokkos::View<int,ExecSpace> d_errors("Errors");
+  errors = d_errors;
+
+  const int per_team0 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(128);
+  const int per_thread0 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(16);
+
+  const int per_team1 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(128000);
+  const int per_thread1 = 3*Kokkos::View<double*,ExecSpace,Kokkos::MemoryTraits<Kokkos::Unmanaged>>::shmem_size(16000);
+
+  Kokkos::TeamPolicy<ExecSpace,ScheduleType> policy(10,8,16);
+  Kokkos::parallel_for(policy.set_scratch_size(0,Kokkos::PerTeam(per_team0),Kokkos::PerThread(per_thread0)).set_scratch_size(1,Kokkos::PerTeam(per_team1),Kokkos::PerThread(per_thread1)),
+    KOKKOS_LAMBDA(const typename Kokkos::TeamPolicy<ExecSpace>::member_type& team) {
+    int error = test_team_mulit_level_scratch_loop_body<ExecSpace>(team);
+    errors() += error;
+  });
+  Kokkos::fence();
+  typename Kokkos::View<int,ExecSpace>::HostMirror h_errors= Kokkos::create_mirror_view(errors);
+  Kokkos::deep_copy(h_errors,d_errors);
+  ASSERT_EQ(h_errors(),0);
+
+  int error = 0;
+  Kokkos::parallel_reduce(policy.set_scratch_size(0,Kokkos::PerTeam(per_team0),Kokkos::PerThread(per_thread0)).set_scratch_size(1,Kokkos::PerTeam(per_team1),Kokkos::PerThread(per_thread1)),
+    KOKKOS_LAMBDA(const typename Kokkos::TeamPolicy<ExecSpace>::member_type& team, int& count) {
+      count += test_team_mulit_level_scratch_loop_body<ExecSpace>(team);
+  },error);
+  ASSERT_EQ(error,0);
+  Kokkos::fence();
+#endif
+}
+
+
+}
+
+namespace {
+template< class ExecSpace, class ScheduleType >
+struct TestMultiLevelScratchTeam {
+
+  TestMultiLevelScratchTeam()
+  { run(); }
+
+  void run()
+  {
+#ifdef KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA
+    Test::test_team_mulit_level_scratch_test_lambda<ExecSpace, ScheduleType>();
+#endif
+    Test::ClassNoShmemSizeFunction<ExecSpace, ScheduleType> c1;
+    c1.run();
+
+    Test::ClassWithShmemSizeFunction<ExecSpace, ScheduleType> c2;
+    c2.run();
+
+  }
+};
+}
+
+namespace Test {
+
+template< class ExecSpace >
+struct TestShmemSize {
+
+  TestShmemSize() { run(); }
+
+  void run()
+  {
+    typedef Kokkos::View< long***, ExecSpace > view_type;
+
+    size_t d1 = 5;
+    size_t d2 = 6;
+    size_t d3 = 7;
+
+    size_t size = view_type::shmem_size( d1, d2, d3 );
+
+    ASSERT_EQ( size, d1 * d2 * d3 * sizeof(long) );
+  }
+};
+}
+
 /*--------------------------------------------------------------------------*/
diff --git a/lib/kokkos/core/unit_test/TestThreads.cpp b/lib/kokkos/core/unit_test/TestThreads.cpp
index 03c7c44958..93049b95dd 100644
--- a/lib/kokkos/core/unit_test/TestThreads.cpp
+++ b/lib/kokkos/core/unit_test/TestThreads.cpp
@@ -1,13 +1,13 @@
 /*
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@@ -36,7 +36,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER
 */
@@ -66,6 +66,7 @@
 #include <TestViewSubview.hpp>
 #include <TestViewOfClass.hpp>
 #include <TestAtomic.hpp>
+#include <TestAtomicOperations.hpp>
 
 #include <TestReduce.hpp>
 #include <TestScan.hpp>
@@ -87,6 +88,8 @@
 
 #include <TestPolicyConstruction.hpp>
 
+#include <TestMDRange.hpp>
+
 namespace Test {
 
 class threads : public ::testing::Test {
@@ -112,7 +115,6 @@ protected:
     Kokkos::Threads::initialize( threads_count );
     Kokkos::Threads::finalize();
 
-    
     threads_count = std::max( 1u , numa_count * 2 )
                   * std::max( 2u , ( cores_per_numa * threads_per_core ) / 2 );
 
@@ -143,6 +145,12 @@ TEST_F( threads , init ) {
   ;
 }
 
+TEST_F( threads , md_range ) {
+  TestMDRange_2D< Kokkos::Threads >::test_for2(100,100);
+
+  TestMDRange_3D< Kokkos::Threads >::test_for3(100,100,100);
+}
+
 TEST_F( threads , dispatch )
 {
   const int repeat = 100 ;
@@ -235,6 +243,13 @@ TEST_F( threads, view_aggregate ) {
 
 TEST_F( threads , range_tag )
 {
+  TestRange< Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >::test_for(2);
+  TestRange< Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >::test_reduce(2);
+  TestRange< Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >::test_scan(2);
+  TestRange< Kokkos::Threads , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(3);
+  TestRange< Kokkos::Threads , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(3);
+  TestRange< Kokkos::Threads , Kokkos::Schedule<Kokkos::Dynamic> >::test_scan(3);
+  TestRange< Kokkos::Threads , Kokkos::Schedule<Kokkos::Dynamic> >::test_dynamic_policy(2);
   TestRange< Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
   TestRange< Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
   TestRange< Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >::test_scan(1000);
@@ -246,6 +261,10 @@ TEST_F( threads , range_tag )
 
 TEST_F( threads , team_tag )
 {
+  TestTeamPolicy< Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >::test_for(2);
+  TestTeamPolicy< Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >::test_reduce(2);
+  TestTeamPolicy< Kokkos::Threads , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(2);
+  TestTeamPolicy< Kokkos::Threads , Kokkos::Schedule<Kokkos::Dynamic> >::test_reduce(2);
   TestTeamPolicy< Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >::test_for(1000);
   TestTeamPolicy< Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >::test_reduce(1000);
   TestTeamPolicy< Kokkos::Threads , Kokkos::Schedule<Kokkos::Dynamic> >::test_for(1000);
@@ -260,6 +279,14 @@ TEST_F( threads, double_reduce) {
   TestReduce< double ,   Kokkos::Threads >( 1000000 );
 }
 
+TEST_F( threads , reducers )
+{
+  TestReducers<int, Kokkos::Threads>::execute_integer();
+  TestReducers<size_t, Kokkos::Threads>::execute_integer();
+  TestReducers<double, Kokkos::Threads>::execute_float();
+  TestReducers<Kokkos::complex<double>, Kokkos::Threads>::execute_basic();
+}
+
 TEST_F( threads, team_long_reduce) {
   TestReduceTeam< long ,   Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >( 3 );
   TestReduceTeam< long ,   Kokkos::Threads , Kokkos::Schedule<Kokkos::Dynamic> >( 3 );
@@ -291,13 +318,17 @@ TEST_F( threads, team_shared_request) {
   TestSharedTeam< Kokkos::Threads , Kokkos::Schedule<Kokkos::Dynamic> >();
 }
 
-#if defined(KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA) 
+#if defined(KOKKOS_HAVE_CXX11_DISPATCH_LAMBDA)
 TEST_F( threads, team_lambda_shared_request) {
   TestLambdaSharedTeam< Kokkos::HostSpace, Kokkos::Threads , Kokkos::Schedule<Kokkos::Static> >();
   TestLambdaSharedTeam< Kokkos::HostSpace, Kokkos::Threads , Kokkos::Schedule<Kokkos::Dynamic> >();
 }
 #endif
 
+TEST_F( threads, shmem_size) {
+  TestShmemSize< Kokkos::Threads >();
+}
+
 TEST_F( threads , view_remap )
 {
   enum { N0 = 3 , N1 = 2 , N2 = 8 , N3 = 9 };
@@ -382,6 +413,75 @@ TEST_F( threads , atomics )
   ASSERT_TRUE( ( TestAtomic::Loop<TestAtomic::SuperScalar<3>, Kokkos::Threads>(loop_count,3) ) );
 }
 
+TEST_F( threads , atomic_operations )
+{
+  const int start = 1; //Avoid zero for division
+  const int end = 11;
+  for (int i = start; i < end; ++i)
+  {
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Threads>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Threads>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Threads>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Threads>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Threads>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Threads>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Threads>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Threads>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<int,Kokkos::Threads>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Threads>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Threads>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Threads>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Threads>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Threads>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Threads>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Threads>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Threads>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned int,Kokkos::Threads>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Threads>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Threads>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Threads>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Threads>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Threads>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Threads>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Threads>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Threads>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long int,Kokkos::Threads>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Threads>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Threads>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Threads>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Threads>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Threads>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Threads>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Threads>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Threads>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<unsigned long int,Kokkos::Threads>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Threads>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Threads>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Threads>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Threads>(start, end-i, 4 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Threads>(start, end-i, 5 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Threads>(start, end-i, 6 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Threads>(start, end-i, 7 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Threads>(start, end-i, 8 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestIntegralType<long long int,Kokkos::Threads>(start, end-i, 9 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Threads>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Threads>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Threads>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<double,Kokkos::Threads>(start, end-i, 4 ) ) );
+
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Threads>(start, end-i, 1 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Threads>(start, end-i, 2 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Threads>(start, end-i, 3 ) ) );
+    ASSERT_TRUE( ( TestAtomicOperations::AtomicOperationsTestNonIntegralType<float,Kokkos::Threads>(start, end-i, 4 ) ) );
+  }
+
+}
+
 //----------------------------------------------------------------------------
 
 #if 0
@@ -434,7 +534,9 @@ TEST_F( threads , memory_pool )
   bool val = TestMemoryPool::test_mempool< Kokkos::Threads >( 128, 128000000 );
   ASSERT_TRUE( val );
 
-  TestMemoryPool::test_mempool2< Kokkos::Threads >( 128, 128000000 );
+  TestMemoryPool::test_mempool2< Kokkos::Threads >( 64, 4, 1000000, 2000000 );
+
+  TestMemoryPool::test_memory_exhaustion< Kokkos::Threads >();
 }
 
 //----------------------------------------------------------------------------
@@ -478,6 +580,8 @@ TEST_F( threads , team_vector )
   ASSERT_TRUE( ( TestTeamVector::Test< Kokkos::Threads >(10) ) );
 }
 
+#if defined( KOKKOS_ENABLE_TASKPOLICY )
+
 TEST_F( threads , task_policy )
 {
   TestTaskPolicy::test_task_dep< Kokkos::Threads >( 10 );
@@ -503,6 +607,8 @@ TEST_F( threads , task_latch )
   TestTaskPolicy::test_latch< Kokkos::Threads >(1000);
 }
 
+#endif /* #if defined( KOKKOS_ENABLE_TASKPOLICY ) */
+
 } // namespace Test
 
 #endif /* #if defined( KOKKOS_HAVE_PTHREAD ) */
diff --git a/lib/kokkos/core/unit_test/TestViewAPI.hpp b/lib/kokkos/core/unit_test/TestViewAPI.hpp
index 60c87472df..ae4c6d2185 100644
--- a/lib/kokkos/core/unit_test/TestViewAPI.hpp
+++ b/lib/kokkos/core/unit_test/TestViewAPI.hpp
@@ -63,7 +63,9 @@ size_t allocation_count( const Kokkos::View<T,P...> & view )
   const size_t card  = view.size();
   const size_t alloc = view.span();
 
-  return card <= alloc ? alloc : 0 ;
+  const int memory_span = Kokkos::View<int*>::required_allocation_size(100);
+
+  return (card <= alloc && memory_span == 400) ? alloc : 0 ;
 }
 
 #else
diff --git a/lib/kokkos/example/fenl/CGSolve.hpp b/lib/kokkos/example/fenl/CGSolve.hpp
index 370dee15ac..06a0030e09 100644
--- a/lib/kokkos/example/fenl/CGSolve.hpp
+++ b/lib/kokkos/example/fenl/CGSolve.hpp
@@ -245,8 +245,8 @@ void cgsolve( const ImportType & import
   norm_res  = sqrt( old_rdot );
   iteration = 0 ;
 
-  Kokkos::Impl::Timer wall_clock ;
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer wall_clock ;
+  Kokkos::Timer timer;
 
   while ( tolerance < norm_res && iteration < maximum_iteration ) {
 
diff --git a/lib/kokkos/example/fenl/fenl_functors.hpp b/lib/kokkos/example/fenl/fenl_functors.hpp
index 30f5274a51..3020c99a2f 100644
--- a/lib/kokkos/example/fenl/fenl_functors.hpp
+++ b/lib/kokkos/example/fenl/fenl_functors.hpp
@@ -138,7 +138,7 @@ public:
       //--------------------------------
       // Guess at capacity required for the map:
 
-      Kokkos::Impl::Timer wall_clock ;
+      Kokkos::Timer wall_clock ;
 
       wall_clock.reset();
       phase = FILL_NODE_SET ;
diff --git a/lib/kokkos/example/fenl/fenl_impl.hpp b/lib/kokkos/example/fenl/fenl_impl.hpp
index 9c57da2989..64070ce55f 100644
--- a/lib/kokkos/example/fenl/fenl_impl.hpp
+++ b/lib/kokkos/example/fenl/fenl_impl.hpp
@@ -312,7 +312,7 @@ Perf fenl(
 
   //------------------------------------
 
-  Kokkos::Impl::Timer wall_clock ;
+  Kokkos::Timer wall_clock ;
 
   Perf perf_stats = Perf() ;
 
diff --git a/lib/kokkos/example/global_2_local_ids/G2L.hpp b/lib/kokkos/example/global_2_local_ids/G2L.hpp
index d4198c61ac..9023ae0426 100644
--- a/lib/kokkos/example/global_2_local_ids/G2L.hpp
+++ b/lib/kokkos/example/global_2_local_ids/G2L.hpp
@@ -186,7 +186,7 @@ size_t test_global_to_local_ids(unsigned num_ids, unsigned capacity, unsigned nu
   typedef Kokkos::UnorderedMap<uint32_t,size_type,execution_space> global_id_view;
 
   double elasped_time = 0;
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
 
   local_id_view local_2_global("local_ids", num_ids);
   global_id_view global_2_local(capacity);
diff --git a/lib/kokkos/example/ichol/example/example_chol_performance_device.hpp b/lib/kokkos/example/ichol/example/example_chol_performance_device.hpp
index 837c74038c..ca819e4f97 100644
--- a/lib/kokkos/example/ichol/example/example_chol_performance_device.hpp
+++ b/lib/kokkos/example/ichol/example/example_chol_performance_device.hpp
@@ -76,7 +76,7 @@ namespace Tacho {
 
     int r_val = 0;
 
-    Kokkos::Impl::Timer timer;
+    Kokkos::Timer timer;
     double
       t_import = 0.0,
       t_reorder = 0.0,
diff --git a/lib/kokkos/example/md_skeleton/main.cpp b/lib/kokkos/example/md_skeleton/main.cpp
index 06287bc609..58cf76cab0 100644
--- a/lib/kokkos/example/md_skeleton/main.cpp
+++ b/lib/kokkos/example/md_skeleton/main.cpp
@@ -76,7 +76,7 @@ int main(int argc, char** argv) {
   int iter = 100;
 
   /* Default value for system size (4*nx*ny*nz atoms)
-   * nx, ny and nz are set to system_size if not specififed on commandline */
+   * nx, ny and nz are set to system_size if not specified on commandline */
 
   int system_size = 20;
   int nx = -1;
@@ -191,7 +191,7 @@ int main(int argc, char** argv) {
 
   printf("-> Running %i force calculations\n",iter);
 
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
 
   for(int i=0;i<iter;i++) {
     force(system,0);
diff --git a/lib/kokkos/example/multi_fem/Explicit.hpp b/lib/kokkos/example/multi_fem/Explicit.hpp
index ddeb53ae61..cef1a37a1a 100644
--- a/lib/kokkos/example/multi_fem/Explicit.hpp
+++ b/lib/kokkos/example/multi_fem/Explicit.hpp
@@ -127,7 +127,7 @@ PerformanceData run( const typename FixtureType::FEMeshType & mesh ,
 
   PerformanceData perf_data ;
 
-  Kokkos::Impl::Timer wall_clock ;
+  Kokkos::Timer wall_clock ;
 
   //------------------------------------
   // Generate fields
diff --git a/lib/kokkos/example/multi_fem/Implicit.hpp b/lib/kokkos/example/multi_fem/Implicit.hpp
index 0017cb8e88..53f602f11a 100644
--- a/lib/kokkos/example/multi_fem/Implicit.hpp
+++ b/lib/kokkos/example/multi_fem/Implicit.hpp
@@ -154,7 +154,7 @@ PerformanceData run( const typename FixtureType::FEMeshType & mesh ,
 
   typename graph_factory::element_map_type element_map ;
 
-  Kokkos::Impl::Timer wall_clock ;
+  Kokkos::Timer wall_clock ;
 
   //------------------------------------
   // Generate sparse matrix graph and element->graph map.
diff --git a/lib/kokkos/example/multi_fem/Nonlinear.hpp b/lib/kokkos/example/multi_fem/Nonlinear.hpp
index 96a05b97a9..1d243395c2 100644
--- a/lib/kokkos/example/multi_fem/Nonlinear.hpp
+++ b/lib/kokkos/example/multi_fem/Nonlinear.hpp
@@ -243,7 +243,7 @@ PerformanceData run( const typename FixtureType::FEMeshType & mesh ,
   //------------------------------------
   // Generate mesh and corresponding sparse matrix graph
 
-  Kokkos::Impl::Timer wall_clock ;
+  Kokkos::Timer wall_clock ;
 
   //------------------------------------
   // Generate sparse matrix graph and element->graph map.
diff --git a/lib/kokkos/example/multi_fem/SparseLinearSystem.hpp b/lib/kokkos/example/multi_fem/SparseLinearSystem.hpp
index 6ab42da50c..8d140b6d25 100644
--- a/lib/kokkos/example/multi_fem/SparseLinearSystem.hpp
+++ b/lib/kokkos/example/multi_fem/SparseLinearSystem.hpp
@@ -243,7 +243,7 @@ void cgsolve(
   normr     = sqrt( old_rdot );
   iteration = 0 ;
 
-  Kokkos::Impl::Timer wall_clock ;
+  Kokkos::Timer wall_clock ;
 
   while ( tolerance < normr && iteration < maximum_iteration ) {
 
diff --git a/lib/kokkos/example/sort_array/CMakeLists.txt b/lib/kokkos/example/sort_array/CMakeLists.txt
index 3e58198d7b..0c7da74f4a 100644
--- a/lib/kokkos/example/sort_array/CMakeLists.txt
+++ b/lib/kokkos/example/sort_array/CMakeLists.txt
@@ -1,4 +1,3 @@
-INCLUDE(TribitsAddExecutableAndTest)   
 
 INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
 INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
diff --git a/lib/kokkos/example/sort_array/sort_array.hpp b/lib/kokkos/example/sort_array/sort_array.hpp
index 018b1ee8e8..d21f998958 100644
--- a/lib/kokkos/example/sort_array/sort_array.hpp
+++ b/lib/kokkos/example/sort_array/sort_array.hpp
@@ -116,7 +116,7 @@ void sort_array( const size_t array_length /* length of spans of array to sort *
 
 #endif
 
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
 
   const device_array_type  work_array("work_array" , array_length );
   const host_array_type    host_array("host_array" , total_length );
diff --git a/lib/kokkos/example/tutorial/01_hello_world/Makefile b/lib/kokkos/example/tutorial/01_hello_world/Makefile
index 38fb1b8f86..78a9fed0cc 100644
--- a/lib/kokkos/example/tutorial/01_hello_world/Makefile
+++ b/lib/kokkos/example/tutorial/01_hello_world/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/01_hello_world_lambda/Makefile b/lib/kokkos/example/tutorial/01_hello_world_lambda/Makefile
index bd2371382a..95ee2c47fe 100644
--- a/lib/kokkos/example/tutorial/01_hello_world_lambda/Makefile
+++ b/lib/kokkos/example/tutorial/01_hello_world_lambda/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/02_simple_reduce/Makefile b/lib/kokkos/example/tutorial/02_simple_reduce/Makefile
index 38fb1b8f86..78a9fed0cc 100644
--- a/lib/kokkos/example/tutorial/02_simple_reduce/Makefile
+++ b/lib/kokkos/example/tutorial/02_simple_reduce/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/02_simple_reduce_lambda/Makefile b/lib/kokkos/example/tutorial/02_simple_reduce_lambda/Makefile
index bd2371382a..95ee2c47fe 100644
--- a/lib/kokkos/example/tutorial/02_simple_reduce_lambda/Makefile
+++ b/lib/kokkos/example/tutorial/02_simple_reduce_lambda/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/03_simple_view/Makefile b/lib/kokkos/example/tutorial/03_simple_view/Makefile
index 38fb1b8f86..78a9fed0cc 100644
--- a/lib/kokkos/example/tutorial/03_simple_view/Makefile
+++ b/lib/kokkos/example/tutorial/03_simple_view/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/03_simple_view_lambda/Makefile b/lib/kokkos/example/tutorial/03_simple_view_lambda/Makefile
index bd2371382a..95ee2c47fe 100644
--- a/lib/kokkos/example/tutorial/03_simple_view_lambda/Makefile
+++ b/lib/kokkos/example/tutorial/03_simple_view_lambda/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/04_simple_memoryspaces/Makefile b/lib/kokkos/example/tutorial/04_simple_memoryspaces/Makefile
index 38fb1b8f86..78a9fed0cc 100644
--- a/lib/kokkos/example/tutorial/04_simple_memoryspaces/Makefile
+++ b/lib/kokkos/example/tutorial/04_simple_memoryspaces/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/05_simple_atomics/Makefile b/lib/kokkos/example/tutorial/05_simple_atomics/Makefile
index 38fb1b8f86..78a9fed0cc 100644
--- a/lib/kokkos/example/tutorial/05_simple_atomics/Makefile
+++ b/lib/kokkos/example/tutorial/05_simple_atomics/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/01_data_layouts/Makefile b/lib/kokkos/example/tutorial/Advanced_Views/01_data_layouts/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/01_data_layouts/Makefile
+++ b/lib/kokkos/example/tutorial/Advanced_Views/01_data_layouts/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/01_data_layouts/data_layouts.cpp b/lib/kokkos/example/tutorial/Advanced_Views/01_data_layouts/data_layouts.cpp
index e61e8af59b..8406c504c9 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/01_data_layouts/data_layouts.cpp
+++ b/lib/kokkos/example/tutorial/Advanced_Views/01_data_layouts/data_layouts.cpp
@@ -142,7 +142,7 @@ int main (int narg, char* arg[]) {
   // Measure time to execute the contraction kernel when giving it a
   // LayoutLeft view for v1 and a LayoutRight view for v2. This should be
   // fast on GPUs and slow on CPUs
-  Kokkos::Impl::Timer time1;
+  Kokkos::Timer time1;
   Kokkos::parallel_for(size,contraction<left_type,right_type>(a,l,r));
   Kokkos::fence();
   double sec1 = time1.seconds();
@@ -154,7 +154,7 @@ int main (int narg, char* arg[]) {
   // Measure time to execute the contraction kernel when giving it a
   // LayoutRight view for v1 and a LayoutLeft view for v2. This should be
   // fast on CPUs and slow on GPUs
-  Kokkos::Impl::Timer time2;
+  Kokkos::Timer time2;
   Kokkos::parallel_for(size,contraction<right_type,left_type>(a,r,l));
   Kokkos::fence();
   double sec2 = time2.seconds();
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/02_memory_traits/Makefile b/lib/kokkos/example/tutorial/Advanced_Views/02_memory_traits/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/02_memory_traits/Makefile
+++ b/lib/kokkos/example/tutorial/Advanced_Views/02_memory_traits/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/02_memory_traits/memory_traits.cpp b/lib/kokkos/example/tutorial/Advanced_Views/02_memory_traits/memory_traits.cpp
index 8317c78bc9..ddd28a97c3 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/02_memory_traits/memory_traits.cpp
+++ b/lib/kokkos/example/tutorial/Advanced_Views/02_memory_traits/memory_traits.cpp
@@ -124,12 +124,12 @@ int main(int narg, char* arg[]) {
   // Run the localsum functor using the RandomAccess trait. On CPUs there should
   // not be any different in performance to not using the RandomAccess trait.
   // On GPUs where can be a dramatic difference
-  Kokkos::Impl::Timer time1;
+  Kokkos::Timer time1;
   Kokkos::parallel_for(size,localsum<view_type,view_type_rnd>(idx,dest,src));
   Kokkos::fence();
   double sec1 = time1.seconds();
 
-  Kokkos::Impl::Timer time2;
+  Kokkos::Timer time2;
   Kokkos::parallel_for(size,localsum<view_type,view_type>(idx,dest,src));
   Kokkos::fence();
   double sec2 = time2.seconds();
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/03_subviews/Makefile b/lib/kokkos/example/tutorial/Advanced_Views/03_subviews/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/03_subviews/Makefile
+++ b/lib/kokkos/example/tutorial/Advanced_Views/03_subviews/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/04_dualviews/Makefile b/lib/kokkos/example/tutorial/Advanced_Views/04_dualviews/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/04_dualviews/Makefile
+++ b/lib/kokkos/example/tutorial/Advanced_Views/04_dualviews/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/04_dualviews/dual_view.cpp b/lib/kokkos/example/tutorial/Advanced_Views/04_dualviews/dual_view.cpp
index 62ddb9c18a..4905e4bf88 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/04_dualviews/dual_view.cpp
+++ b/lib/kokkos/example/tutorial/Advanced_Views/04_dualviews/dual_view.cpp
@@ -87,9 +87,9 @@ struct localsum {
   // For example, the const_data_type version of double** is const
   // double**.
   Kokkos::View<idx_type::const_data_type, idx_type::array_layout, memory_space> idx;
-  // "array_intrinsic_type" is a typedef in ViewTraits (and DualView) which is the
+  // "scalar_array_type" is a typedef in ViewTraits (and DualView) which is the
   // array version of the value(s) stored in the View.
-  Kokkos::View<view_type::array_intrinsic_type, view_type::array_layout, memory_space> dest;
+  Kokkos::View<view_type::scalar_array_type, view_type::array_layout, memory_space> dest;
   Kokkos::View<view_type::const_data_type, view_type::array_layout,
                memory_space, Kokkos::MemoryRandomAccess> src;
 
@@ -150,6 +150,9 @@ protected:
 int main (int narg, char* arg[]) {
   Kokkos::initialize (narg, arg);
 
+// If View is non-trivial constructible type then add braces so it is out of scope
+// before Kokkos::finalize() call
+{
   ParticleTypes test("Test");
   Kokkos::fence();
   test.h_view(0) = ParticleType(-1e4,1);
@@ -182,7 +185,7 @@ int main (int narg, char* arg[]) {
 
   // Run on the device.  This will cause a sync of idx to the device,
   // since it was marked as modified on the host.
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
   Kokkos::parallel_for(size,localsum<view_type::execution_space>(idx,dest,src));
   Kokkos::fence();
   double sec1_dev = timer.seconds();
@@ -208,6 +211,7 @@ int main (int narg, char* arg[]) {
 
   printf("Device Time with Sync: %f without Sync: %f \n",sec1_dev,sec2_dev);
   printf("Host   Time with Sync: %f without Sync: %f \n",sec1_host,sec2_host);
+}
 
   Kokkos::finalize();
 }
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/05_NVIDIA_UVM/Makefile b/lib/kokkos/example/tutorial/Advanced_Views/05_NVIDIA_UVM/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/05_NVIDIA_UVM/Makefile
+++ b/lib/kokkos/example/tutorial/Advanced_Views/05_NVIDIA_UVM/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/05_NVIDIA_UVM/uvm_example.cpp b/lib/kokkos/example/tutorial/Advanced_Views/05_NVIDIA_UVM/uvm_example.cpp
index a7d460a1cc..cf5326b687 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/05_NVIDIA_UVM/uvm_example.cpp
+++ b/lib/kokkos/example/tutorial/Advanced_Views/05_NVIDIA_UVM/uvm_example.cpp
@@ -97,7 +97,7 @@ int main(int narg, char* arg[]) {
   Kokkos::fence();
   // Run on the device
   // This will cause a sync of idx to the device since it was modified on the host
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
   Kokkos::parallel_for(size,localsum<view_type::execution_space>(idx,dest,src));
   Kokkos::fence();
   double sec1_dev = timer.seconds();
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/06_AtomicViews/Makefile b/lib/kokkos/example/tutorial/Advanced_Views/06_AtomicViews/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/06_AtomicViews/Makefile
+++ b/lib/kokkos/example/tutorial/Advanced_Views/06_AtomicViews/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/07_Overlapping_DeepCopy/Makefile b/lib/kokkos/example/tutorial/Advanced_Views/07_Overlapping_DeepCopy/Makefile
index 06955b3641..60a514f4d5 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/07_Overlapping_DeepCopy/Makefile
+++ b/lib/kokkos/example/tutorial/Advanced_Views/07_Overlapping_DeepCopy/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3 --default-stream per-thread 
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Advanced_Views/07_Overlapping_DeepCopy/overlapping_deepcopy.cpp b/lib/kokkos/example/tutorial/Advanced_Views/07_Overlapping_DeepCopy/overlapping_deepcopy.cpp
index 8c7e26c850..5da3bf76c9 100644
--- a/lib/kokkos/example/tutorial/Advanced_Views/07_Overlapping_DeepCopy/overlapping_deepcopy.cpp
+++ b/lib/kokkos/example/tutorial/Advanced_Views/07_Overlapping_DeepCopy/overlapping_deepcopy.cpp
@@ -116,7 +116,7 @@ int main(int argc, char * argv[]) {
   Kokkos::parallel_for(Kokkos::RangePolicy<Kokkos::Cuda>(0,size),FillDevice(0.0,d_a));
   Kokkos::parallel_for(Kokkos::RangePolicy<Kokkos::Cuda>(0,size),FillDevice(1.3513,d_b));
   Kokkos::fence();
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
   Kokkos::parallel_for(Kokkos::RangePolicy<Kokkos::Cuda>(0,size),ComputeADevice(20,d_a,d_b));
 
   if(synch==1)
diff --git a/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/Makefile b/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/Makefile
+++ b/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/random_numbers.cpp b/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/random_numbers.cpp
index 52816333c2..3e6175a756 100644
--- a/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/random_numbers.cpp
+++ b/lib/kokkos/example/tutorial/Algorithms/01_random_numbers/random_numbers.cpp
@@ -122,7 +122,7 @@ int main(int argc, char* args[]) {
   Kokkos::DualView<uint64_t*> vals("Vals",size*samples);
 
   // Run some performance comparisons
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
   Kokkos::parallel_for(size,generate_random<Kokkos::Random_XorShift64_Pool<> >(vals.d_view,rand_pool64,samples));
   Kokkos::fence();
 
diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/Makefile b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/Makefile
+++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/Makefile b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/Makefile
index 3d056537c3..965b72b4e9 100644
--- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/Makefile
+++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/Makefile
@@ -5,13 +5,14 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
 EXE = $(SRC:.cpp=.cuda)
 KOKKOS_DEVICES = "Cuda,OpenMP"
 KOKKOS_ARCH = "SNB,Kepler35"
+KOKKOS_CUDA_OPTIONS = "enable_lambda"
 else
 CXX = g++
 CXXFLAGS = -O3
diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/thread_teams_lambda.cpp b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/thread_teams_lambda.cpp
index 5d081bf62b..565dd22e82 100644
--- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/thread_teams_lambda.cpp
+++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/thread_teams_lambda.cpp
@@ -62,7 +62,8 @@ int main (int narg, char* args[]) {
 
   // Set up a policy that launches 12 teams, with the maximum number
   // of threads per team.
-  const team_policy policy (12, team_policy::team_size_max ( [=]{} ));
+
+  const team_policy policy (12, Kokkos::AUTO);
 
   // This is a reduction with a team policy.  The team policy changes
   // the first argument of the lambda.  Rather than an integer index
diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/Makefile b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/Makefile
+++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/03_vectorization/Makefile b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/03_vectorization/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/03_vectorization/Makefile
+++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/03_vectorization/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/03_vectorization/vectorization.cpp b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/03_vectorization/vectorization.cpp
index 0eac4309a9..99d5958edf 100644
--- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/03_vectorization/vectorization.cpp
+++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/03_vectorization/vectorization.cpp
@@ -141,11 +141,11 @@ int main(int narg, char* args[]) {
 
   // Each team handles a slice of the data
   // Set up TeamPolicy with 512 teams with maximum number of threads per team and 16 vector lanes.
-  // The team_size_max function will determine the maximum number of threads taking into account
-  // shared memory requirements of the Functor.
+  // Kokkos::AUTO will determine the number of threads
   // The maximum vector length is hardware dependent but can always be smaller than the hardware allows.
   // The vector length must be a power of 2.
-  const Kokkos::TeamPolicy<> policy( 512 , Kokkos::TeamPolicy<>::team_size_max(SomeCorrelation(data,gsum)) , 16);
+
+  const Kokkos::TeamPolicy<> policy( 512 , Kokkos::AUTO , 16);
 
   Kokkos::parallel_for( policy , SomeCorrelation(data,gsum) );
 
diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/04_team_scan/Makefile b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/04_team_scan/Makefile
index 3d056537c3..12ad36b31e 100644
--- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/04_team_scan/Makefile
+++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/04_team_scan/Makefile
@@ -5,7 +5,7 @@ default: build
 	echo "Start Build"
 
 ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
-CXX = nvcc_wrapper
+CXX = ../../../../config/nvcc_wrapper
 CXXFLAGS = -O3
 LINK = ${CXX}
 LINKFLAGS = 
diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/04_team_scan/team_scan.cpp b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/04_team_scan/team_scan.cpp
index a9b20da1ae..c12b11d04d 100644
--- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/04_team_scan/team_scan.cpp
+++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/04_team_scan/team_scan.cpp
@@ -117,7 +117,7 @@ int main(int narg, char* args[]) {
   Kokkos::DualView<int**> histogram("histogram",TEAM_SIZE,TEAM_SIZE);
 
 
-  Kokkos::Impl::Timer timer;
+  Kokkos::Timer timer;
   // threads/team is automatically limited to maximum supported by the device.
   Kokkos::parallel_for( team_policy( nchunks , TEAM_SIZE )
                       , find_2_tuples(chunk_size,data,histogram) );
diff --git a/lib/kokkos/generate_makefile.bash b/lib/kokkos/generate_makefile.bash
index 016e5dfe35..86f136da96 100755
--- a/lib/kokkos/generate_makefile.bash
+++ b/lib/kokkos/generate_makefile.bash
@@ -107,7 +107,7 @@ case $key in
     exit 0
     ;;
     *)
-            # unknown option
+    echo "warning: ignoring unknown option $key"
     ;;
 esac
 shift
diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp
index aa030540f4..19f6017907 100755
--- a/src/MANYBODY/pair_vashishta.cpp
+++ b/src/MANYBODY/pair_vashishta.cpp
@@ -541,7 +541,7 @@ void PairVashishta::setup_params()
 /* ---------------------------------------------------------------------- */
 
 void PairVashishta::twobody(Param *param, double rsq, double &fforce,
-                     int eflag, double &eng)
+                            int eflag, double &eng)
 {
   double r,rinvsq,r4inv,r6inv,reta,lam1r,lam4r,vc2,vc3;
 
diff --git a/src/MANYBODY/pair_vashishta.h b/src/MANYBODY/pair_vashishta.h
index cdd2da3471..87077011e6 100755
--- a/src/MANYBODY/pair_vashishta.h
+++ b/src/MANYBODY/pair_vashishta.h
@@ -17,8 +17,8 @@ PairStyle(vashishta,PairVashishta)
 
 #else
 
-#ifndef LMP_PAIR_Vashishta_H
-#define LMP_PAIR_Vashishta_H
+#ifndef LMP_PAIR_VASHISHITA_H
+#define LMP_PAIR_VASHISHITA_H
 
 #include "pair.h"
 
@@ -29,10 +29,10 @@ class PairVashishta : public Pair {
   PairVashishta(class LAMMPS *);
   virtual ~PairVashishta();
   virtual void compute(int, int);
-  void settings(int, char **);
+  virtual void settings(int, char **);
   void coeff(int, char **);
-  virtual double init_one(int, int);
-  virtual void init_style();
+  double init_one(int, int);
+  void init_style();
 
  protected:
   struct Param {
@@ -55,9 +55,9 @@ class PairVashishta : public Pair {
   int maxparam;                 // max # of parameter sets
   Param *params;                // parameter set for an I-J-K interaction
 
-  virtual void allocate();
+  void allocate();
   void read_file(char *);
-  void setup_params();
+  virtual void setup_params();
   void twobody(Param *, double, double &, int, double &);
   void threebody(Param *, Param *, Param *, double, double, double *, double *,
                  double *, double *, int, double &);
diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp
index 9f7b4a9eaa..42cca31f6b 100644
--- a/src/fix_nve_sphere.cpp
+++ b/src/fix_nve_sphere.cpp
@@ -133,12 +133,13 @@ void FixNVESphere::initial_integrate(int vflag)
   
   // update mu for dipoles
   
-
   if (extra == DIPOLE) {
     double **mu = atom->mu;
     if (dlm == NODLM) {
+
       // d_mu/dt = omega cross mu
       // renormalize mu to dipole length
+
       for (int i = 0; i < nlocal; i++)
         if (mask[i] & groupbit)
           if (mu[i][3] > 0.0) {
@@ -152,7 +153,9 @@ void FixNVESphere::initial_integrate(int vflag)
             mu[i][2] = g[2]*scale;
           }
     } else {
-      // Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme
+
+      // integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme
+
       for (int i = 0; i < nlocal; i++) {
         if (mask[i] & groupbit && mu[i][3] > 0.0) {
           
@@ -160,8 +163,9 @@ void FixNVESphere::initial_integrate(int vflag)
           // Q is the rotation matrix from space frame to body frame
           // i.e. v_b = Q.v_s
           
-          // Define mu to lie along the z axis in the body frame
-          // We take the unit dipole to avoid getting a scaling matrix
+          // define mu to lie along the z axis in the body frame
+          // take the unit dipole to avoid getting a scaling matrix
+
           inv_len_mu = 1.0/mu[i][3];
           a[0] = mu[i][0]*inv_len_mu;
           a[1] = mu[i][1]*inv_len_mu;
@@ -180,9 +184,15 @@ void FixNVESphere::initial_integrate(int vflag)
           if (s2 != 0.0){ // i.e. the vectors are not parallel
             scale = (1.0 - a[2])/s2;
             
-            Q[0][0] = 1.0 - scale*a[0]*a[0]; Q[0][1] = -scale*a[0]*a[1];      Q[0][2] = -a[0];
-            Q[1][0] = -scale*a[0]*a[1];      Q[1][1] = 1.0 - scale*a[1]*a[1]; Q[1][2] = -a[1];
-            Q[2][0] = a[0];                  Q[2][1] = a[1];                  Q[2][2] = 1.0 - scale*(a[0]*a[0] + a[1]*a[1]);
+            Q[0][0] = 1.0 - scale*a[0]*a[0]; 
+            Q[0][1] = -scale*a[0]*a[1];
+            Q[0][2] = -a[0];
+            Q[1][0] = -scale*a[0]*a[1];
+            Q[1][1] = 1.0 - scale*a[1]*a[1];
+            Q[1][2] = -a[1];
+            Q[2][0] = a[0];
+            Q[2][1] = a[1];
+            Q[2][2] = 1.0 - scale*(a[0]*a[0] + a[1]*a[1]);
           } else { // if parallel then we just have I or -I
             Q[0][0] = 1.0/a[2];  Q[0][1] = 0.0;       Q[0][2] = 0.0;
             Q[1][0] = 0.0;       Q[1][1] = 1.0/a[2];  Q[1][2] = 0.0;
@@ -242,7 +252,9 @@ void FixNVESphere::initial_integrate(int vflag)
           
           // Transform w back into space frame w_temp = Q^T.w
           transpose_matvec(Q_temp,w,w_temp);
-          omega[i][0] = w_temp[0]; omega[i][1] = w_temp[1]; omega[i][2] = w_temp[2];
+          omega[i][0] = w_temp[0]; 
+          omega[i][1] = w_temp[1];
+          omega[i][2] = w_temp[2];
           
           // Set dipole according to updated Q: mu = Q^T.[0 0 1] * |mu|
           mu[i][0] = Q_temp[2][0] * mu[i][3];
@@ -289,7 +301,8 @@ void FixNVESphere::final_integrate()
       omega[i][0] += dtirotate * torque[i][0];
       omega[i][1] += dtirotate * torque[i][1];
       omega[i][2] += dtirotate * torque[i][2];
-      rke += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] + omega[i][2]*omega[i][2])*radius[i]*radius[i]*rmass[i];
+      rke += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] + 
+              omega[i][2]*omega[i][2])*radius[i]*radius[i]*rmass[i];
     }
   
 }
diff --git a/src/group.cpp b/src/group.cpp
index da0e94fc11..973fcbdcce 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -1665,46 +1665,93 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3], int iregion)
 
 /* ----------------------------------------------------------------------
    compute angular velocity omega from L and I
-   really not a group/region operation, but L,I were computed for a group/region
-   diagonalize I instead of inverting it, to allow for a singular matrix
 ------------------------------------------------------------------------- */
 
 void Group::omega(double *angmom, double inertia[3][3], double *w)
 {
   double idiag[3],ex[3],ey[3],ez[3],cross[3];
-  double evectors[3][3];
-  
-  int ierror = MathExtra::jacobi(inertia,idiag,evectors);
-  if (ierror) error->all(FLERR,
-                         "Insufficient Jacobi rotations for group::omega");
-
-  ex[0] = evectors[0][0];
-  ex[1] = evectors[1][0];
-  ex[2] = evectors[2][0];
-  ey[0] = evectors[0][1];
-  ey[1] = evectors[1][1];
-  ey[2] = evectors[2][1];
-  ez[0] = evectors[0][2];
-  ez[1] = evectors[1][2];
-  ez[2] = evectors[2][2];
-  
-  // enforce 3 evectors as a right-handed coordinate system
-  // flip 3rd vector if needed
-  
-  MathExtra::cross3(ex,ey,cross);
-  if (MathExtra::dot3(cross,ez) < 0.0) MathExtra::negate3(ez);
-  
-  // if any principal moment < scaled EPSILON, set to 0.0
+  double evectors[3][3],inverse[3][3];
+
+  // determinant = triple product of rows of inertia matrix
+
+  double determinant = inertia[0][0]*inertia[1][1]*inertia[2][2] +
+    inertia[0][1]*inertia[1][2]*inertia[2][0] +
+    inertia[0][2]*inertia[1][0]*inertia[2][1] -
+    inertia[0][0]*inertia[1][2]*inertia[2][1] -
+    inertia[0][1]*inertia[1][0]*inertia[2][2] -
+    inertia[2][0]*inertia[1][1]*inertia[0][2];
+
+  // non-singular I matrix
+  // use L = Iw, inverting I to solve for w
+  // this should give exact zeroing of angular momentum by velocity command
+
+  if (determinant > EPSILON) {
+
+    inverse[0][0] = inertia[1][1]*inertia[2][2] - inertia[1][2]*inertia[2][1];
+    inverse[0][1] = -(inertia[0][1]*inertia[2][2] - 
+                      inertia[0][2]*inertia[2][1]);
+    inverse[0][2] = inertia[0][1]*inertia[1][2] - inertia[0][2]*inertia[1][1];
+
+    inverse[1][0] = -(inertia[1][0]*inertia[2][2] - 
+                      inertia[1][2]*inertia[2][0]);
+    inverse[1][1] = inertia[0][0]*inertia[2][2] - inertia[0][2]*inertia[2][0];
+    inverse[1][2] = -(inertia[0][0]*inertia[1][2] - 
+                      inertia[0][2]*inertia[1][0]);
+
+    inverse[2][0] = inertia[1][0]*inertia[2][1] - inertia[1][1]*inertia[2][0];
+    inverse[2][1] = -(inertia[0][0]*inertia[2][1] - 
+                      inertia[0][1]*inertia[2][0]);
+    inverse[2][2] = inertia[0][0]*inertia[1][1] - inertia[0][1]*inertia[1][0];
+
+    for (int i = 0; i < 3; i++)
+      for (int j = 0; j < 3; j++)
+        inverse[i][j] /= determinant;
+
+    w[0] = inverse[0][0]*angmom[0] + inverse[0][1]*angmom[1] +
+      inverse[0][2]*angmom[2];
+    w[1] = inverse[1][0]*angmom[0] + inverse[1][1]*angmom[1] +
+      inverse[1][2]*angmom[2];
+    w[2] = inverse[2][0]*angmom[0] + inverse[2][1]*angmom[1] +
+      inverse[2][2]*angmom[2];
+
+  // handle (nearly) singular I matrix
+  // typically due to 2-atom group or linear molecule
+  // use jacobi() and angmom_to_omega() to calculate valid omega
+  // less exact answer than matrix inversion, due to iterative Jacobi method
+
+  } else {
+    int ierror = MathExtra::jacobi(inertia,idiag,evectors);
+    if (ierror) error->all(FLERR,
+                           "Insufficient Jacobi rotations for group::omega");
+
+    ex[0] = evectors[0][0];
+    ex[1] = evectors[1][0];
+    ex[2] = evectors[2][0];
+    ey[0] = evectors[0][1];
+    ey[1] = evectors[1][1];
+    ey[2] = evectors[2][1];
+    ez[0] = evectors[0][2];
+    ez[1] = evectors[1][2];
+    ez[2] = evectors[2][2];
   
-  double max;
-  max = MAX(idiag[0],idiag[1]);
-  max = MAX(max,idiag[2]);
+    // enforce 3 evectors as a right-handed coordinate system
+    // flip 3rd vector if needed
   
-  if (idiag[0] < EPSILON*max) idiag[0] = 0.0;
-  if (idiag[1] < EPSILON*max) idiag[1] = 0.0;
-  if (idiag[2] < EPSILON*max) idiag[2] = 0.0;
+    MathExtra::cross3(ex,ey,cross);
+    if (MathExtra::dot3(cross,ez) < 0.0) MathExtra::negate3(ez);
   
-  // calculate omega using diagonalized inertia matrix
+    // if any principal moment < scaled EPSILON, set to 0.0
   
-  MathExtra::angmom_to_omega(angmom,ex,ey,ez,idiag,w);
+    double max;
+    max = MAX(idiag[0],idiag[1]);
+    max = MAX(max,idiag[2]);
+    
+    if (idiag[0] < EPSILON*max) idiag[0] = 0.0;
+    if (idiag[1] < EPSILON*max) idiag[1] = 0.0;
+    if (idiag[2] < EPSILON*max) idiag[2] = 0.0;
+    
+    // calculate omega using diagonalized inertia matrix
+    
+    MathExtra::angmom_to_omega(angmom,ex,ey,ez,idiag,w);
+  }
 }
-- 
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