git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@16053 f3b2605a-c512-4ea7-a41b-209d697bcdaa

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@16052 f3b2605a-c512-4ea7-a41b-209d697bcdaa
sync with latest GHub bug fixes
2017-01-26 21:05:57 +00:00 · 2017-01-26 21:05:55 +00:00 · 2017-01-26 20:54:58 +00:00 · 2017-01-26 02:07:37 +00:00 · 2017-01-23 23:04:40 +00:00 · 2017-01-23 22:40:21 +00:00
812 changed files with 34916 additions and 29491 deletions
--- a/.gitignore
+++ b/.gitignore
@ -1,34 +0,0 @@
-*~
-*.o
-*.so
-*.cu_o
-*.ptx
-*_ptx.h
-*.a
-*.d
-*.x
-*.exe
-*.dll
-*.pyc
-__pycache__
-
-Obj_*
-log.lammps
-log.cite
-*.bz2
-*.gz
-*.tar
-.*.swp
-*.orig
-*.rej
-.vagrant
-\#*#
-.#*
-
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
--- a/doc/.gitignore
+++ b/doc/.gitignore
@ -1,5 +0,0 @@
-/html
-/LAMMPS.epub
-/LAMMPS.mobi
-/Manual.pdf
-/Developer.pdf
--- a/doc/src/Eqs/bond_oxdna_fene.jpg
+++ b/doc/src/Eqs/bond_oxdna_fene.jpg
--- a/doc/src/Eqs/bond_oxdna_fene.tex
+++ b/doc/src/Eqs/bond_oxdna_fene.tex
@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+$$ 
+  E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
+$$
+
+\end{document}
--- a/doc/src/JPG/tutorial_merged.png
+++ b/doc/src/JPG/tutorial_merged.png
--- a/doc/src/JPG/tutorial_reverse_pull_request7.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request7.png
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="9 Jan 2017 version">
+<META NAME="docnumber" CONTENT="26 Jan 2017 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>

 LAMMPS Documentation :c,h3
-9 Jan 2017 version :c,h4
+26 Jan 2017 version :c,h4

 Version info: :h4

--- a/doc/src/PDF/USER-CGDNA-overview.pdf
+++ b/doc/src/PDF/USER-CGDNA-overview.pdf
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -702,6 +702,8 @@ package"_Section_start.html#start_3.
 "meso"_fix_meso.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
+"nve/dot"_fix_nve_dot.html,
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
 "nvk"_fix_nvk.html,
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
@ -1035,6 +1037,11 @@ package"_Section_start.html#start_3.
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx"_pair_multi_lucy_rx.html,
+"oxdna/coaxstk"_pair_oxdna.html,
+"oxdna/excv"_pair_oxdna.html,
+"oxdna/hbond"_pair_oxdna.html,
+"oxdna/stk"_pair_oxdna.html,
+"oxdna/xstk"_pair_oxdna.html,
 "quip"_pair_quip.html,
 "reax/c (k)"_pair_reax_c.html,
 "smd/hertz"_pair_smd_hertz.html,
@ -1083,7 +1090,8 @@ if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.

 "harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
+"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)

 :line

--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@ -55,12 +55,13 @@ LAMMPS errors are detected at setup time; others like a bond
 stretching too far may not occur until the middle of a run.

 LAMMPS tries to flag errors and print informative error messages so
-you can fix the problem.  Of course, LAMMPS cannot figure out your
-physics or numerical mistakes, like choosing too big a timestep,
-specifying erroneous force field coefficients, or putting 2 atoms on
-top of each other!  If you run into errors that LAMMPS doesn't catch
-that you think it should flag, please send an email to the
-"developers"_http://lammps.sandia.gov/authors.html.
+you can fix the problem.  For most errors it will also print the last
+input script command that it was processing.  Of course, LAMMPS cannot
+figure out your physics or numerical mistakes, like choosing too big a
+timestep, specifying erroneous force field coefficients, or putting 2
+atoms on top of each other!  If you run into errors that LAMMPS
+doesn't catch that you think it should flag, please send an email to
+the "developers"_http://lammps.sandia.gov/authors.html.

 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -84,7 +84,7 @@ Package, Description, Author(s), Doc page, Example, Library
 "PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
 "POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
 "PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
-"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax
+"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
 "REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
 "RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
 "SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
@ -1140,6 +1140,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
 "USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
 "USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
+"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Edinburgh), src/USER-CGDNA/README, USER/cgdna, -, -
 "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
 "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
 "USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
@ -1153,7 +1154,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
-"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
 "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@ -1284,6 +1285,31 @@ him directly if you have questions.

 :line

+USER-CGDNA package :link(USER-CGDNA),h5
+
+Contents: The CGDNA package implements coarse-grained force fields for
+single- and double-stranded DNA. This is at the moment mainly the
+oxDNA model, developed by Doye, Louis and Ouldridge at the University
+of Oxford.  The package also contains Langevin-type rigid-body
+integrators with improved stability.
+
+See these doc pages to get started:
+
+"bond_style oxdna_fene"_bond_oxdna_fene.html
+"pair_style oxdna_excv"_pair_oxdna_excv.html
+"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
+
+Supporting info: /src/USER-CGDNA/README, "bond_style
+oxdna_fene"_bond_oxdna_fene.html, "pair_style
+oxdna_excv"_pair_oxdna_excv.html, "fix
+nve/dotc/langevin"_fix_nve_dotc_langevin.html
+
+Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
+at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk).  Contact him directly if
+you have any questions.
+
+:line
+
 USER-COLVARS package :link(USER-COLVARS),h5

 Contents: COLVARS stands for collective variables which can be used to
@ -1610,11 +1636,12 @@ and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
 in this format.  See src/USER-NC-DUMP/README for more details.

 NetCDF files can be directly visualized with the following tools:
+
 Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
-  and all of the above extensions. :ulb,l
+and all of the above extensions. :ulb,l
 VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
 AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
-  a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule

 The person who created these files is Lars Pastewka at
 Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -1727,7 +1727,7 @@ thermodynamic state and a total run time for the simulation.  It then
 appends statistics about the CPU time and storage requirements for the
 simulation.  An example set of statistics is shown here:

-Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre

 Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
 97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
@ -1757,14 +1757,14 @@ Ave special neighs/atom = 2.34032
 Neighbor list builds = 26
 Dangerous builds = 0 :pre

-The first section provides a global loop timing summary. The loop time
+The first section provides a global loop timing summary. The {loop time}
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
-continuations required and for comparing performance with other
-similar MD codes.  The CPU use line provides the CPU utilzation per
+continuations required and for comparing performance with other,
+similar MD codes.  The {CPU use} line provides the CPU utilzation per
 MPI task; it should be close to 100% times the number of OpenMP
-threads (or 1). Lower numbers correspond to delays due to file I/O or
-insufficient thread utilization.
+threads (or 1 of no OpenMP). Lower numbers correspond to delays due
+to file I/O or insufficient thread utilization.

 The MPI task section gives the breakdown of the CPU run time (in
 seconds) into major categories:
@ -1791,7 +1791,7 @@ is present that also prints the CPU utilization in percent. In
 addition, when using {timer full} and the "package omp"_package.html
 command are active, a similar timing summary of time spent in threaded
 regions to monitor thread utilization and load balance is provided. A
-new entry is the {Reduce} section, which lists the time spend in
+new entry is the {Reduce} section, which lists the time spent in
 reducing the per-thread data elements to the storage for non-threaded
 computation. These thread timings are taking from the first MPI rank
 only and and thus, as the breakdown for MPI tasks can change from MPI
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@ -110,14 +110,14 @@ mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis :p
 [Required hardware/software:]

 Kokkos support within LAMMPS must be built with a C++11 compatible
-compiler.  If using gcc, version 4.8.1 or later is required.
+compiler.  If using gcc, version 4.7.2 or later is required.

 To build with Kokkos support for CPUs, your compiler must support the
 OpenMP interface.  You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.

 To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
-version 6.5 or later must be installed on your system.  See the
+version 7.5 or later must be installed on your system.  See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.

--- a/doc/src/bond_oxdna_fene.txt
+++ b/doc/src/bond_oxdna_fene.txt
@ -0,0 +1,70 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+bond_style oxdna_fene command :h3
+
+[Syntax:]
+
+bond_style oxdna_fene :pre
+
+[Examples:]
+
+bond_style oxdna_fene
+bond_coeff * 2.0 0.25 0.7525 :pre
+
+[Description:]
+
+The {oxdna_fene} bond style uses the potential
+
+:c,image(Eqs/bond_oxdna_fene.jpg)
+
+to define a modified finite extensible nonlinear elastic (FENE) potential
+"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
+in the oxDNA force field for coarse-grained modelling of DNA. 
+
+The following coefficients must be defined for the bond type via the
+"bond_coeff"_bond_coeff.html command as given in the above example, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+epsilon (energy)
+Delta (distance)
+r0 (distance) :ul
+
+NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
+for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
+and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of 
+"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients 
+in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
+
+Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
+A simple python setup tool which creates single straight or helical DNA strands,
+DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
+A technical report with more information on the model, the structure of the input file,
+the setup tool and the performance of the LAMMPS-implementation of oxDNA
+can be found "here"_PDF/USER-CGDNA-overview.pdf.
+
+:line
+
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+
+[Related commands:]
+
+"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
+
+[Default:] none
+
+:line
+
+:link(oxdna_fene)
+[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
--- a/doc/src/bonds.txt
+++ b/doc/src/bonds.txt
@ -15,6 +15,7 @@ Bond Styles :h1
   bond_morse
   bond_none
   bond_nonlinear
+   bond_oxdna_fene
   bond_quartic
   bond_table
   bond_zero
--- a/doc/src/commands.txt
+++ b/doc/src/commands.txt
@ -91,6 +91,7 @@ Commands :h1
   suffix
   tad
   temper
+   temper_grem
   thermo
   thermo_modify
   thermo_style
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@ -10,34 +10,43 @@ compute coord/atom command :h3

 [Syntax:]

-compute ID group-ID coord/atom cutoff type1 type2 ... :pre
+compute ID group-ID coord/atom cstyle args ... :pre

-ID, group-ID are documented in "compute"_compute.html command
-coord/atom = style name of this compute command
-cutoff = distance within which to count coordination neighbors (distance units)
-typeN = atom type for Nth coordination count (see asterisk form below) :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+coord/atom = style name of this compute command :l
+cstyle = {cutoff} or {orientorder} :l
+  {cutoff} args = cutoff typeN
+    cutoff = distance within which to count coordination neighbors (distance units)
+    typeN = atom type for Nth coordination count (see asterisk form below)
+  {orientorder} args = orientorderID threshold
+    orientorderID = ID of an orientorder/atom compute
+    threshold = minimum value of the product of two "connected" atoms :pre
+:ule

 [Examples:]

-compute 1 all coord/atom 2.0
-compute 1 all coord/atom 6.0 1 2
-compute 1 all coord/atom 6.0 2*4 5*8 * :pre
+compute 1 all coord/atom cutoff 2.0
+compute 1 all coord/atom cutoff 6.0 1 2
+compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
+compute 1 all coord/atom orientorder 2 0.5 :pre

 [Description:]

-Define a computation that calculates one or more coordination numbers
-for each atom in a group.
+This compute performs calculations between neighboring atoms to
+determine a coordination value.  The specific calculation and the
+meaning of the resulting value depend on the {cstyle} keyword used.

-A coordination number is defined as the number of neighbor atoms with
-specified atom type(s) that are within the specified cutoff distance
-from the central atom.  Atoms not in the group are included in a
-coordination number of atoms in the group.
+The {cutoff} cstyle calculates one or more traditional coordination
+numbers for each atom.  A coordination number is defined as the number
+of neighbor atoms with specified atom type(s) that are within the
+specified cutoff distance from the central atom.  Atoms not in the
+specified group are included in the coordination number tally.

-The {typeN} keywords allow you to specify which atom types contribute
-to each coordination number.  One coordination number is computed for
-each of the {typeN} keywords listed.  If no {typeN} keywords are
-listed, a single coordination number is calculated, which includes
-atoms of all types (same as the "*" format, see below).
+The {typeN} keywords allow specification of which atom types
+contribute to each coordination number.  One coordination number is
+computed for each of the {typeN} keywords listed.  If no {typeN}
+keywords are listed, a single coordination number is calculated, which
+includes atoms of all types (same as the "*" format, see below).

 The {typeN} keywords can be specified in one of two ways.  An explicit
 numeric value can be used, as in the 2nd example above.  Or a
@ -49,8 +58,27 @@ from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).

-The value of all coordination numbers will be 0.0 for atoms not in the
-specified compute group.
+The {orientorder} cstyle calculates the number of "connected" neighbor
+atoms J around each central atom I.  For this {cstyle}, connected is
+defined by the orientational order parameter calculated by the
+"compute orientorder/atom"_compute_orientorder_atom.html command.
+This {cstyle} thus allows one to apply the ten Wolde's criterion to
+identify crystal-like atoms in a system, as discussed in "ten
+Wolde"_#tenWolde.
+
+The ID of the previously specified "compute
+orientorder/atom"_compute_orientorder/atom command is specified as
+{orientorderID}.  The compute must invoke its {components} option to
+calculate components of the {Ybar_lm} vector for each atoms, as
+described in its documenation.  Note that orientorder/atom compute
+defines its own criteria for identifying neighboring atoms.  If the
+scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
+orientorder/atom compute is larger than the specified {threshold},
+then I and J are connected, and the coordination value of I is
+incremented by one.
+
+For all {cstyle} settings, all coordination values will be 0.0 for
+atoms not in the specified compute group.

 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@ -72,11 +100,16 @@ the neighbor list.

 [Output info:]

-If single {type1} keyword is specified (or if none are specified),
-this compute calculates a per-atom vector.  If multiple {typeN}
-keywords are specified, this compute calculates a per-atom array, with
-N columns.  These values can be accessed by any command that uses
-per-atom values from a compute as input.  See "Section
+For {cstyle} cutoff, this compute can calculate a per-atom vector or
+array.  If single {type1} keyword is specified (or if none are
+specified), this compute calculates a per-atom vector.  If multiple
+{typeN} keywords are specified, this compute calculates a per-atom
+array, with N columns.
+
+For {cstyle} orientorder, this compute calculates a per-atom vector.
+
+These values can be accessed by any command that uses per-atom values
+from a compute as input.  See "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
 options.

@ -88,5 +121,12 @@ explained above.
 [Related commands:]

 "compute cluster/atom"_compute_cluster_atom.html
+"compute orientorder/atom"_compute_orientorder_atom.html

 [Default:] none
+
+:line
+
+:link(tenWolde)
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
+J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@ -15,17 +15,19 @@ compute ID group-ID orientorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 orientorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {cutoff} or {nnn} or {degrees}
+keyword = {cutoff} or {nnn} or {degrees} or {components}
  {cutoff} value = distance cutoff
  {nnn} value = number of nearest neighbors
-  {degrees} values = nlvalues, l1, l2,...  :pre
+  {degrees} values = nlvalues, l1, l2,...
+  {components} value = ldegree  :pre

 :ule

 [Examples:]

 compute 1 all orientorder/atom
-compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 :pre
+compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
+compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre

 [Description:]

@ -62,14 +64,21 @@ specified distance cutoff are used.
 The optional keyword {degrees} defines the list of order parameters to
 be computed.  The first argument {nlvalues} is the number of order
 parameters. This is followed by that number of integers giving the
-degree of each order parameter. Because {Q}2 and all odd-degree
-order parameters are zero for atoms in cubic crystals
-(see "Steinhardt"_#Steinhardt), the default order parameters
-are {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. For the
-FCC crystal with {nnn}=12, {Q}4 = sqrt(7/3)/8 = 0.19094....
-The numerical values of all order parameters up to {Q}12
-for a range of commonly encountered high-symmetry structures are given
-in Table I of "Mickel et al."_#Mickel.
+degree of each order parameter. Because {Q}2 and all odd-degree order
+parameters are zero for atoms in cubic crystals (see
+"Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
+{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn}=12, {Q}4
+= sqrt(7/3)/8 = 0.19094....  The numerical values of all order
+parameters up to {Q}12 for a range of commonly encountered
+high-symmetry structures are given in Table I of "Mickel et
+al."_#Mickel.
+
+The optional keyword {components} will output the components of the
+normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
+explicitly included in the keyword {degrees}. This option can be used
+in conjunction with "compute coord_atom"_compute_coord_atom.html to
+calculate the ten Wolde's criterion to identify crystal-like
+particles, as discussed in "ten Wolde"_#tenWolde.

 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
@ -95,8 +104,16 @@ the neighbor list.

 [Output info:]

-This compute calculates a per-atom array with {nlvalues} columns, giving the
-{Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.
+This compute calculates a per-atom array with {nlvalues} columns,
+giving the {Ql} values for each atom, which are real numbers on the
+range 0 <= {Ql} <= 1.
+
+If the keyword {components} is set, then the real and imaginary parts
+of each component of (normalized) {Ybar_lm} will be added to the
+output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
+Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}).  This
+way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1)
+columns.

 These values can be accessed by any command that uses
 per-atom values from a compute as input.  See "Section
@ -107,15 +124,25 @@ options.

 [Related commands:]

-"compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html, "compute hexorder/atom"_compute_hexorder_atom.html
+"compute coord/atom"_compute_coord_atom.html, "compute
+centro/atom"_compute_centro_atom.html, "compute
+hexorder/atom"_compute_hexorder_atom.html

 [Default:]

-The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+The option defaults are {cutoff} = pair style cutoff, {nnn} = 12,
+{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.

 :line

 :link(Steinhardt)
-[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
+[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti,
+Phys. Rev. B 28, 784 (1983).
+
 :link(Mickel)
-[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
+[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke,
+J. Chem. Phys. 138, 044501 (2013).
+
+:link(tenWolde)
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
+J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
--- a/doc/src/compute_temp_sphere.txt
+++ b/doc/src/compute_temp_sphere.txt
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@ -35,6 +35,7 @@ Computes :h1
   compute_erotate_sphere_atom
   compute_event_displace
   compute_fep
+   compute_global_atom
   compute_group_group
   compute_gyration
   compute_gyration_chunk
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
--- a/doc/src/fix_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@ -151,7 +151,7 @@ The option default for the {energy} keyword is energy = no.
 :line

 :link(Strong)
-[(Strong)] Strong and Eaves, J. Phys. Chem. Lett. 7, 1907 (2016).
+[(Strong)] Strong and Eaves, J. Phys. Chem. B 121, 189 (2017).

 :link(Evans)
 [(Evans)] Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@ -29,7 +29,7 @@ fix             fxgREM all grem 502 -0.15 -80000 fxnvt :pre
 [Description:]

 This fix implements the molecular dynamics version of the generalized
-replica exchange method (gREM) originally developed by "(Kim)"_#Kim,
+replica exchange method (gREM) originally developed by "(Kim)"_#Kim2010,
 which uses non-Boltzmann ensembles to sample over first order phase
 transitions. The is done by defining replicas with an enthalpy
 dependent effective temperature
@ -103,7 +103,7 @@ npt"_fix_nh.html, "thermo_modify"_thermo_modify.html

 :line

-:link(Kim)
+:link(Kim2010)
 [(Kim)] Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).

 :link(Malolepsza)
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@ -0,0 +1,61 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix nve/dot command :h3
+
+[Syntax:]
+
+fix ID group-ID nve/dot :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+nve/dot = style name of this fix command :l
+:ule
+
+[Examples:]
+
+fix 1 all nve/dot :pre
+
+[Description:]
+
+Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack
+to a group of atoms, but without Langevin dynamics. 
+This command performs Molecular dynamics (MD)
+via a velocity-Verlet algorithm and an evolution operator that rotates 
+the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller. 
+
+This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
+without damping and noise and can be used to determine the stability range 
+in a NVE ensemble prior to using the Langevin-type DOTC-integrator
+(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
+The command is equivalent to the "fix nve"_fix_nve.html.
+The particles are always considered to have a finite size.
+
+An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
+A technical report with more information on this integrator can be found
+"here"_PDF/USER-CGDNA-overview.pdf.
+
+:line
+
+[Restrictions:]
+
+These pair styles can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+[Related commands:]
+
+"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "fix nve"_fix_nve.html
+
+[Default:] none
+
+:line
+
+:link(Davidchack)
+[(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
+:link(Miller)
+[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@ -0,0 +1,134 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix nve/dotc/langevin command :h3
+
+[Syntax:]
+
+fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+nve/dotc/langevin = style name of this fix command :l
+Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
+damp = damping parameter (time units) :l
+seed = random number seed to use for white noise (positive integer) :l
+keyword = {angmom} :l
+  {angmom} value = factor
+    factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below :pre
+:ule
+
+[Examples:]
+
+fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
+
+[Description:]
+
+Apply a rigid-body Langevin-type integrator of the kind "Langevin C" 
+as described in "(Davidchack)"_#Davidchack
+to a group of atoms, which models an interaction with an implicit background
+solvent.  This command performs Brownian dynamics (BD)
+via a technique that splits the integration into a deterministic Hamiltonian 
+part and the Ornstein-Uhlenbeck process for noise and damping. 
+The quaternion degrees of freedom are updated though an evolution
+operator which performs a rotation in quaternion space, preserves
+the quaternion norm and is akin to "(Miller)"_#Miller.
+
+In terms of syntax this command has been closely modelled on the 
+"fix langevin"_fix_langevin.html and its {angmom} option. But it combines 
+the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in 
+one single command. The main feature is improved stability 
+over the standard integrator, permitting slightly larger timestep sizes.
+
+NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
+also time integration of the translational and quaternion degrees of freedom.
+
+The total force on each atom will have the form:
+
+F = Fc + Ff + Fr
+Ff = - (m / damp) v
+Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
+
+Fc is the conservative force computed via the usual inter-particle
+interactions ("pair_style"_pair_style.html,
+"bond_style"_bond_style.html, etc).
+
+The Ff and Fr terms are implicitly taken into account by this fix 
+on a per-particle basis.
+
+Ff is a frictional drag or viscous damping term proportional to the
+particle's velocity.  The proportionality constant for each atom is
+computed as m/damp, where m is the mass of the particle and damp is
+the damping factor specified by the user.
+
+Fr is a force due to solvent atoms at a temperature T randomly bumping
+into the particle.  As derived from the fluctuation/dissipation
+theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
+dt damp), where Kb is the Boltzmann constant, T is the desired
+temperature, m is the mass of the particle, dt is the timestep size,
+and damp is the damping factor.  Random numbers are used to randomize
+the direction and magnitude of this force as described in
+"(Dunweg)"_#Dunweg, where a uniform random number is used (instead of
+a Gaussian random number) for speed.
+
+:line
+
+{Tstart} and {Tstop} have to be constant values, i.e. they cannot 
+be variables.
+
+The {damp} parameter is specified in time units and determines how
+rapidly the temperature is relaxed.  For example, a value of 0.03
+means to relax the temperature in a timespan of (roughly) 0.03 time
+units tau (see the "units"_units.html command).
+The damp factor can be thought of as inversely related to the
+viscosity of the solvent, i.e. a small relaxation time implies a
+hi-viscosity solvent and vice versa.  See the discussion about gamma
+and viscosity in the documentation for the "fix
+viscous"_fix_viscous.html command for more details.
+
+The random # {seed} must be a positive integer. A Marsaglia random
+number generator is used.  Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+
+The keyword/value option has to be used in the following way:
+
+This fix has to be used together with the {angmom} keyword. The 
+particles are always considered to have a finite size. 
+The keyword {angmom} enables thermostatting of the rotational degrees of 
+freedom in addition to the usual translational degrees of freedom. 
+
+The scale factor after the {angmom} keyword gives the ratio of the rotational to 
+the translational friction coefficient.
+
+An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
+A technical report with more information on this integrator can be found 
+"here"_PDF/USER-CGDNA-overview.pdf.
+
+:line
+
+[Restrictions:]
+
+These pair styles can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+[Related commands:]
+
+"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,  
+
+[Default:] none
+
+:line
+
+:link(Davidchack)
+[(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
+:link(Miller)
+[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
+:link(Dunweg)
+[(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
--- a/doc/src/fix_spring.txt
+++ b/doc/src/fix_spring.txt
@ -89,11 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
 group can straddle a periodic boundary.  See the "dump"_dump.html doc
 page for a discussion of unwrapped coordinates.  It also means that a
 spring connecting two groups or a group and the tether point can cross
-a periodic boundary and its length be calculated correctly.  One
-exception is for rigid bodies, which should not be used with the fix
-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 "fix rigid"_fix_rigid.html doc page.
+a periodic boundary and its length be calculated correctly.  

 [Restart, fix_modify, output, run start/stop, minimize info:]

--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@ -84,6 +84,8 @@ Fixes :h1
   fix_nve_asphere
   fix_nve_asphere_noforce
   fix_nve_body
+   fix_nve_dot
+   fix_nve_dotc_langevin
   fix_nve_eff
   fix_nve_limit
   fix_nve_line
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@ -229,11 +229,16 @@ dramatically in z.  For example, for a triclinic system with all three
 tilt factors set to the maximum limit, the PPPM grid should be
 increased roughly by a factor of 1.5 in the y direction and 2.0 in the
 z direction as compared to the same system using a cubic orthogonal
-simulation cell. One way to ensure the accuracy requirement is being
-met is to run a short simulation at the maximum expected tilt or
-length, note the required grid size, and then use the
+simulation cell.  One way to handle this issue if you have a long
+simulation where the box size changes dramatically, is to break it
+into shorter simulations (multiple "run"_run.html commands).  This
+works because the grid size is re-computed at the beginning of each
+run.  Another way to ensure the descired accuracy requirement is met
+is to run a short simulation at the maximum expected tilt or length,
+note the required grid size, and then use the
 "kspace_modify"_kspace_modify.html {mesh} command to manually set the
-PPPM grid size to this value.
+PPPM grid size to this value for the long run.  The simulation then
+will be "too accurate" for some portion of the run.

 RMS force errors in real space for {ewald} and {pppm} are estimated
 using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as
@ -285,6 +290,8 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 See "Section 5"_Section_accelerate.html of the manual for
 more instructions on how to use the accelerated styles effectively.

+:line
+
 [Restrictions:]

 Note that the long-range electrostatic solvers in LAMMPS assume conducting
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -23,6 +23,7 @@ Section_history.html

 tutorial_drude.html
 tutorial_github.html
+tutorial_pylammps.html

 body.html
 manifolds.html
@ -113,6 +114,7 @@ special_bonds.html
 suffix.html
 tad.html
 temper.html
+temper_grem.html
 thermo.html
 thermo_modify.html
 thermo_style.html
@ -192,7 +194,6 @@ fix_meso.html
 fix_meso_stationary.html
 fix_momentum.html
 fix_move.html
-fix_mscg.html
 fix_msst.html
 fix_neb.html
 fix_nh.html
@ -208,6 +209,8 @@ fix_nve.html
 fix_nve_asphere.html
 fix_nve_asphere_noforce.html
 fix_nve_body.html
+fix_nve_dot.html
+fix_nve_dotc_langevin.html
 fix_nve_eff.html
 fix_nve_limit.html
 fix_nve_line.html
@ -215,7 +218,6 @@ fix_nve_manifold_rattle.html
 fix_nve_noforce.html
 fix_nve_sphere.html
 fix_nve_tri.html
-fix_nvk.html
 fix_nvt_asphere.html
 fix_nvt_body.html
 fix_nvt_manifold_rattle.html
@ -456,6 +458,7 @@ pair_multi_lucy_rx.html
 pair_nb3b_harmonic.html
 pair_nm.html
 pair_none.html
+pair_oxdna_excv.html
 pair_peri.html
 pair_polymorphic.html
 pair_quip.html
@ -494,6 +497,7 @@ pair_zero.html
 bond_class2.html
 bond_fene.html
 bond_fene_expand.html
+bond_oxdna_fene.html
 bond_harmonic.html
 bond_harmonic_shift.html
 bond_harmonic_shift_cut.html
--- a/doc/src/min_style.txt
+++ b/doc/src/min_style.txt
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
--- a/doc/src/pair_oxdna_excv.txt
+++ b/doc/src/pair_oxdna_excv.txt
@ -0,0 +1,80 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style oxdna_excv command :h3
+pair_style oxdna_stk command :h3
+pair_style oxdna_hbond command :h3
+pair_style oxdna_xstk command :h3
+pair_style oxdna_coaxstk command :h3
+
+[Syntax:]
+
+pair_style style :pre
+
+style = {hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk} :ul
+
+[Examples:]
+
+pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
+pair_coeff * * oxdna_excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna_stk     1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna_hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna_hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna_hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna_xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
+
+[Description:]
+
+The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field 
+for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the 
+excluded volume interaction {oxdna_excv}, the stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
+and coaxial stacking interaction {oxdna_coaxstk} as well
+as the hydrogen-bonding interaction {oxdna_hbond} between complementary pairs of nucleotides on
+opposite strands.
+
+The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients 
+in the above example. The individual potentials consist of products of modulation factors, 
+which themselves are constructed from a number of more basic potentials 
+(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. 
+We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil and "(Ouldridge)"_#Ouldridge
+for a detailed description of the oxDNA force field.
+
+NOTE: These pair styles have to be used together with the related oxDNA bond style
+{oxdna_fene} for the connectivity of the phosphate backbone (see also documentation of
+"bond_style oxdna_fene"_bond_oxdna_fene.html). The coefficients
+in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
+
+Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
+A simple python setup tool which creates single straight or helical DNA strands, 
+DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
+A technical report with more information on the model, the structure of the input file,
+the setup tool and the performance of the LAMMPS-implementation of oxDNA 
+can be found "here"_PDF/USER-CGDNA-overview.pdf.
+
+:line
+
+[Restrictions:]
+
+These pair styles can only be used if LAMMPS was built with the
+USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+[Related commands:]
+
+"bond_style oxdna_fene"_bond_oxdna_fene.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html 
+
+[Default:] none
+
+:line
+
+:link(Ouldridge-DPhil)
+[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
+:link(Ouldridge)
+[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@ -65,6 +65,7 @@ Pair Styles :h1
   pair_nb3b_harmonic
   pair_nm
   pair_none
+   pair_oxdna_excv
   pair_peri
   pair_polymorphic
   pair_quip
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@ -32,7 +32,7 @@ Run a parallel tempering or replica exchange simulation in LAMMPS
 partition mode using multiple generalized replicas (ensembles) of a
 system defined by "fix grem"_fix_grem.html, which stands for the
 generalized replica exchange method (gREM) originally developed by
-"(Kim)"_#Kim.  It uses non-Boltzmann ensembles to sample over first
+"(Kim)"_#KimStraub.  It uses non-Boltzmann ensembles to sample over first
 order phase transitions. The is done by defining replicas with an
 enthalpy dependent effective temperature

@ -105,5 +105,5 @@ This command must be used with "fix grem"_fix_grem.html.

 [Default:] none

-:link(Kim)
+:link(KimStraub)
 [(Kim)] Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010).
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@ -33,14 +33,14 @@ timer loop :pre
 Select the level of detail at which LAMMPS performs its CPU timings.
 Multiple keywords can be specified with the {timer} command.  For
 keywords that are mutually exclusive, the last one specified takes
-effect.
+precedence.

 During a simulation run LAMMPS collects information about how much
 time is spent in different sections of the code and thus can provide
 information for determining performance and load imbalance problems.
 This can be done at different levels of detail and accuracy.  For more
 information about the timing output, see this "discussion of screen
-output"_Section_start.html#start_8.
+output in Section 2.8"_Section_start.html#start_8.

 The {off} setting will turn all time measurements off. The {loop}
 setting will only measure the total time for a run and not collect any
@ -52,20 +52,22 @@ procsessors.  The {full} setting adds information about CPU
 utilization and thread utilization, when multi-threading is enabled.

 With the {sync} setting, all MPI tasks are synchronized at each timer
-call which meaures load imbalance more accuractly, though it can also
-slow down the simulation.  Using the {nosync} setting (which is the
-default) turns off this synchronization.
+call which measures load imbalance for each section more accuractly,
+though it can also slow down the simulation by prohibiting overlapping
+independent computations on different MPI ranks  Using the {nosync}
+setting (which is the default) turns this synchronization off.

-With the {timeout} keyword a walltime limit can be imposed that
+With the {timeout} keyword a walltime limit can be imposed, that
 affects the "run"_run.html and "minimize"_minimize.html commands.
-This can be convenient when runs have to confirm to time limits,
-e.g. when running under a batch system and you want to maximize
-the utilization of the batch time slot, especially when the time
-per timestep varies and is thus difficult to predict how many
-steps a simulation can perform, or for difficult to converge
-minimizations. The timeout {elapse} value should be somewhat smaller
-than the time requested from the batch system, as there is usually
-some overhead to launch jobs, and it may be advisable to write
+This can be convenient when calculations have to comply with execution
+time limits, e.g. when running under a batch system when you want to
+maximize the utilization of the batch time slot, especially for runs
+where the time per timestep varies much and thus it becomes difficult
+to predict how many steps a simulation can perform for a given walltime
+limit. This also applies for difficult to converge minimizations.
+The timeout {elapse} value should be somewhat smaller than the maximum
+wall time requested from the batch system, as there is usually
+some overhead to launch jobs, and it is advisable to write
 out a restart after terminating a run due to a timeout.

 The timeout timer starts when the command is issued. When the time
--- a/doc/src/tutorial_github.txt
+++ b/doc/src/tutorial_github.txt
@ -336,12 +336,15 @@ commit and push again:
 $ git commit -m "Merged Axel's suggestions and updated text"
 $ git push git@github.com:Pakketeretet2/lammps :pre

+This merge also shows up on the lammps Github page:
+
+:c,image(JPG/tutorial_reverse_pull_request7.png)

 :line

 [After a merge]

-When everything is fine, the feature branch is merged into the master branch.
+When everything is fine, the feature branch is merged into the master branch:

 :c,image(JPG/tutorial_merged.png)

--- a/doc/utils/converters/.gitignore
+++ b/doc/utils/converters/.gitignore
@ -1 +1,2 @@
+__pycache__
 *.egg-info
--- a/examples/COUPLE/fortran2/.gitignore
+++ b/examples/COUPLE/fortran2/.gitignore
@ -1 +0,0 @@
-*.mod
--- a/examples/USER/cgdna/README
+++ b/examples/USER/cgdna/README
@ -0,0 +1,28 @@
+This directory contains example data and input files 
+and utility scripts for the oxDNA coarse-grained model 
+for DNA.
+
+/examples/duplex1:
+Input, data and log files for a DNA duplex (double-stranded DNA) 
+consisiting of 5 base pairs. The duplex contains two strands with 
+complementary base pairs. The topology is
+
+A - A - A - A - A
+|   |   |   |   |
+T - T - T - T - T     
+
+/examples/duplex2:
+Input, data and log files for a nicked DNA duplex (double-stranded DNA) 
+consisiting of 8 base pairs. The duplex contains strands with 
+complementary base pairs, but the backbone on one side is not continuous: 
+two individual strands on one side form a duplex with a longer single 
+strand on the other side. The topology is
+
+A - A - A - A - A - A - A - A
+|   |   |   |   |   |   |   |
+T - T - T   T - T - T - T - T
+
+/util:
+This directory contains a simple python setup tool which creates 
+single straight or helical DNA strands, DNA duplexes or arrays of DNA 
+duplexes.
--- a/examples/USER/cgdna/examples/duplex1/data.duplex1
+++ b/examples/USER/cgdna/examples/duplex1/data.duplex1
@ -0,0 +1,74 @@
+# LAMMPS data file
+10 atoms
+10 ellipsoids
+8 bonds
+
+4 atom types
+1 bond types
+
+# System size
+-20.000000 20.000000 xlo xhi
+-20.000000 20.000000 ylo yhi
+-20.000000 20.000000 zlo zhi
+
+# Atom masses for each atom type
+Masses
+
+1 3.1575
+2 3.1575
+3 3.1575
+4 3.1575
+
+# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
+Atoms
+
+1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1 1 1
+2 1 1.3274493266864451e-01 -4.2912827978022683e-01 3.7506163469402809e-01 1 1 1
+3 1 4.8460810659772807e-01 -7.0834970533509178e-01 7.5012326938805618e-01 1 1 1
+4 1 9.3267359196674593e-01 -7.4012419946742802e-01 1.1251849040820843e+00 1 1 1
+5 1 1.3204192238113461e+00 -5.1335201721887447e-01 1.5002465387761124e+00 1 1 1
+6 4 1.9958077618865377e-01 5.1335201721887447e-01 1.5002465387761124e+00 1 1 1
+7 4 5.8732640803325409e-01 7.4012419946742802e-01 1.1251849040820843e+00 1 1 1
+8 4 1.0353918934022719e+00 7.0834970533509178e-01 7.5012326938805618e-01 1 1 1
+9 4 1.3872550673313555e+00 4.2912827978022683e-01 3.7506163469402809e-01 1 1 1
+10 4 1.5200000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1 1 1
+
+# Atom-ID, translational, rotational velocity
+Velocities
+
+1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+2 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 9.5533648912560598e-01 0.0000000000000000e+00 0.0000000000000000e+00 2.9552020666133955e-01
+3 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 8.2533561490967822e-01 0.0000000000000000e+00 0.0000000000000000e+00 5.6464247339503526e-01
+4 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 6.2160996827066439e-01 0.0000000000000000e+00 0.0000000000000000e+00 7.8332690962748319e-01
+5 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 3.6235775447667351e-01 0.0000000000000000e+00 0.0000000000000000e+00 9.3203908596722607e-01
+6 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 9.3203908596722607e-01 -3.6235775447667351e-01 0.0000000000000000e+00
+7 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 7.8332690962748319e-01 -6.2160996827066439e-01 0.0000000000000000e+00
+8 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 5.6464247339503526e-01 -8.2533561490967822e-01 0.0000000000000000e+00
+9 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 2.9552020666133955e-01 -9.5533648912560598e-01 0.0000000000000000e+00
+10 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00
+
+# Bond topology
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 6 7
+6 1 7 8
+7 1 8 9
+8 1 9 10
--- a/examples/USER/cgdna/examples/duplex1/input.duplex1
+++ b/examples/USER/cgdna/examples/duplex1/input.duplex1
@ -0,0 +1,75 @@
+variable number	equal 1
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+
+set atom * mass 3.1575
+
+group all type 1 4
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna_fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
+pair_coeff * * oxdna_excv   2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna_stk    1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna_hbond  0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna_xstk   47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+#fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+fix 1 all   nve/dot
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+dump_modify quat sort id
+dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+dump_modify out sort id
+dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 1000000
+
+#write_restart config.${number}.*
--- a/examples/USER/cgdna/examples/duplex1/log.9Jan17.duplex1.g++.1
+++ b/examples/USER/cgdna/examples/duplex1/log.9Jan17.duplex1.g++.1
--- a/examples/USER/cgdna/examples/duplex1/log.9Jan17.duplex1.g++.4
+++ b/examples/USER/cgdna/examples/duplex1/log.9Jan17.duplex1.g++.4
--- a/examples/USER/cgdna/examples/duplex2/data.duplex2
+++ b/examples/USER/cgdna/examples/duplex2/data.duplex2
@ -0,0 +1,97 @@
+# LAMMPS data file
+16 atoms
+16 ellipsoids
+13 bonds
+
+4 atom types
+1 bond types
+
+# System size
+-20.0 20.0 xlo xhi
+-20.0 20.0 ylo yhi
+-20.0 20.0 zlo zhi
+
+# Atom masses for each atom type
+Masses
+
+1 3.1575
+2 3.1575
+3 3.1575
+4 3.1575
+
+# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
+Atoms
+
+1  1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  1 1 1
+2  1  1.327449326686445e-01 -4.291282797802268e-01  3.750616346940281e-01  1 1 1
+3  1  4.846081065977281e-01 -7.083497053350921e-01  7.501232693880562e-01  1 1 1
+4  1  9.326735919667459e-01 -7.401241994674285e-01  1.125184904082084e+00  1 1 1
+5  1  1.320419223811347e+00 -5.133520172188747e-01  1.500246538776112e+00  1 1 1
+6  1  1.512394297416339e+00 -1.072512061254991e-01  1.875308173470140e+00  1 1 1
+7  1  1.441536396413952e+00  3.363155369040876e-01  2.250369808164169e+00  1 1 1
+8  1  1.132598224218932e+00  6.623975870343269e-01  2.625431442858197e+00  1 1 1
+9  4  5.873264080332541e-01  7.401241994674285e-01  1.125184904082084e+00  1 1 1
+10 4  1.035391893402272e+00  7.083497053350921e-01  7.501232693880562e-01  1 1 1
+11 4  1.387255067331356e+00  4.291282797802267e-01  3.750616346940281e-01  1 1 1
+12 4  1.520000000000000e+00  1.260981291332700e-33  0.000000000000000e+00  1 1 1
+13 4  3.874017757810680e-01 -6.623975870343268e-01  2.625431442858197e+00  1 1 1
+14 4  7.846360358604798e-02 -3.363155369040874e-01  2.250369808164169e+00  1 1 1
+15 4  7.605702583661333e-03  1.072512061254995e-01  1.875308173470140e+00  1 1 1
+16 4  1.995807761886533e-01  5.133520172188748e-01  1.500246538776112e+00  1 1 1
+
+# Atom-ID, translational, rotational velocity
+Velocities
+
+1  0.0  0.0  0.0  0.0  0.0  0.0 
+2  0.0  0.0  0.0  0.0  0.0  0.0 
+3  0.0  0.0  0.0  0.0  0.0  0.0 
+4  0.0  0.0  0.0  0.0  0.0  0.0 
+5  0.0  0.0  0.0  0.0  0.0  0.0 
+6  0.0  0.0  0.0  0.0  0.0  0.0 
+7  0.0  0.0  0.0  0.0  0.0  0.0 
+8  0.0  0.0  0.0  0.0  0.0  0.0 
+9  0.0  0.0  0.0  0.0  0.0  0.0 
+10 0.0  0.0  0.0  0.0  0.0  0.0 
+11 0.0  0.0  0.0  0.0  0.0  0.0 
+12 0.0  0.0  0.0  0.0  0.0  0.0 
+13 0.0  0.0  0.0  0.0  0.0  0.0 
+14 0.0  0.0  0.0  0.0  0.0  0.0 
+15 0.0  0.0  0.0  0.0  0.0  0.0 
+16 0.0  0.0  0.0  0.0  0.0  0.0 
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1   1.1739845031423408 1.1739845031423408 1.1739845031423408  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2   1.1739845031423408 1.1739845031423408 1.1739845031423408  9.553364891256060e-01  0.000000000000000e+00  0.000000000000000e+00  2.955202066613395e-01 
+3   1.1739845031423408 1.1739845031423408 1.1739845031423408  8.253356149096783e-01  0.000000000000000e+00  0.000000000000000e+00  5.646424733950354e-01 
+4   1.1739845031423408 1.1739845031423408 1.1739845031423408  6.216099682706646e-01  0.000000000000000e+00  0.000000000000000e+00  7.833269096274833e-01 
+5   1.1739845031423408 1.1739845031423408 1.1739845031423408  3.623577544766736e-01  0.000000000000000e+00  0.000000000000000e+00  9.320390859672263e-01 
+6   1.1739845031423408 1.1739845031423408 1.1739845031423408  7.073720166770291e-02  0.000000000000000e+00  0.000000000000000e+00  9.974949866040544e-01 
+7   1.1739845031423408 1.1739845031423408 1.1739845031423408 -2.272020946930869e-01 -0.000000000000000e+00  0.000000000000000e+00  9.738476308781953e-01 
+8   1.1739845031423408 1.1739845031423408 1.1739845031423408 -5.048461045998575e-01 -0.000000000000000e+00  0.000000000000000e+00  8.632093666488738e-01 
+9   1.1739845031423408 1.1739845031423408 1.1739845031423408  4.796493962806427e-17  7.833269096274833e-01 -6.216099682706646e-01  3.806263289803786e-17 
+10  1.1739845031423408 1.1739845031423408 1.1739845031423408  5.707093416549944e-17  5.646424733950354e-01 -8.253356149096784e-01  2.218801320830406e-17 
+11  1.1739845031423408 1.1739845031423408 1.1739845031423408  6.107895212550935e-17  2.955202066613394e-01 -9.553364891256061e-01  4.331404380149668e-18 
+12  1.1739845031423408 1.1739845031423408 1.1739845031423408  5.963096920061075e-17  0.000000000000000e+00 -1.000000000000000e+00 -1.391211590127312e-17 
+13  1.1739845031423408 1.1739845031423408 1.1739845031423408  5.285632939302787e-17  8.632093666488739e-01  5.048461045998572e-01 -3.091290830301125e-17 
+14  1.1739845031423408 1.1739845031423408 1.1739845031423408  4.136019110019290e-17  9.738476308781953e-01  2.272020946930868e-01 -4.515234267244800e-17 
+15  1.1739845031423408 1.1739845031423408 1.1739845031423408  2.616947011741696e-17  9.974949866040544e-01 -7.073720166770313e-02 -5.535845274597425e-17 
+16  1.1739845031423408 1.1739845031423408 1.1739845031423408  8.641108308308281e-18  9.320390859672264e-01 -3.623577544766736e-01 -6.061955710708163e-17 
+
+# Bond-ID, type, atom pairs
+Bonds
+
+1	1	1	2
+2	1	2	3
+3	1	3	4
+4	1	4	5
+5	1	5	6
+6	1	6	7
+7	1	7	8
+8	1	13	14
+9	1	14	15
+10	1	15	16
+11	1	9	10
+12	1	10	11
+13	1	11	12
--- a/examples/USER/cgdna/examples/duplex2/input.duplex2
+++ b/examples/USER/cgdna/examples/duplex2/input.duplex2
@ -0,0 +1,75 @@
+variable number	equal 2
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+
+set atom * mass 3.1575
+
+group all type 1 4
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna_fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
+pair_coeff * * oxdna_excv   2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna_stk    1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
+pair_coeff * * oxdna_hbond  0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna_xstk   47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
+pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all   nve/dot
+
+timestep 1e-5 
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+dump pos all xyz ${ofreq} traj.${number}.xyz
+
+compute quat all property/atom quatw quati quatj quatk
+dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+dump_modify quat sort id
+dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+dump_modify out sort id
+dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 1000000
+
+#write_restart config.${number}.*
--- a/examples/USER/cgdna/examples/duplex2/log.9Jan17.duplex2.g++.1
+++ b/examples/USER/cgdna/examples/duplex2/log.9Jan17.duplex2.g++.1
--- a/examples/USER/cgdna/examples/duplex2/log.9Jan17.duplex2.g++.4
+++ b/examples/USER/cgdna/examples/duplex2/log.9Jan17.duplex2.g++.4
--- a/examples/USER/cgdna/util/generate_input.py
+++ b/examples/USER/cgdna/util/generate_input.py
@ -0,0 +1,388 @@
+# Setup tool for oxDNA input in LAMMPS format.
+
+import math,numpy as np,sys,os
+
+# system size
+lxmin = -115.0
+lxmax = +115.0
+lymin = -115.0
+lymax = +115.0
+lzmin = -115.0
+lzmax = +115.0
+
+# rise in z-direction
+r0 = 0.7
+
+# definition of single untwisted strand
+def single():
+
+  strand = inp[1].split(':')
+
+  com_start=strand[0].split(',')
+
+  posx=float(com_start[0])
+  posy=float(com_start[1])
+  posz=float(com_start[2])
+  risex=0
+  risey=0
+  risez=r0
+
+  strandstart=len(nucleotide)+1
+
+  for letter in strand[2]:
+    temp=[]
+
+    temp.append(nt2num[letter])
+    temp.append([posx,posy,posz])
+    vel=[0,0,0,0,0,0]
+    temp.append(vel)
+    temp.append(shape)
+
+    quat=[1,0,0,0]
+    temp.append(quat)
+
+    posx=posx+risex
+    posy=posy+risey
+    posz=posz+risez
+
+    if (len(nucleotide)+1 > strandstart):
+      topology.append([1,len(nucleotide),len(nucleotide)+1])
+
+    nucleotide.append(temp)
+
+  return
+
+# definition of single twisted strand
+def single_helix():
+
+  strand = inp[1].split(':')
+
+  com_start=strand[0].split(',')
+  twist=float(strand[1])
+
+  posx = float(com_start[0])
+  posy = float(com_start[1])
+  posz = float(com_start[2])
+  risex=0
+  risey=0
+  risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2) 
+
+  dcomh=0.76
+  axisx=dcomh + posx
+  axisy=posy
+
+  strandstart=len(nucleotide)+1
+  quat=[1,0,0,0]
+
+  qrot0=math.cos(0.5*twist)
+  qrot1=0
+  qrot2=0
+  qrot3=math.sin(0.5*twist)
+
+  for letter in strand[2]:
+    temp=[]
+
+    temp.append(nt2num[letter])
+    temp.append([posx,posy,posz])
+    vel=[0,0,0,0,0,0]
+    temp.append(vel)
+    temp.append(shape)
+
+    temp.append(quat)
+
+    quat0 = quat[0]*qrot0 - quat[1]*qrot1 - quat[2]*qrot2 - quat[3]*qrot3 
+    quat1 = quat[0]*qrot1 + quat[1]*qrot0 + quat[2]*qrot3 - quat[3]*qrot2 
+    quat2 = quat[0]*qrot2 + quat[2]*qrot0 + quat[3]*qrot1 - quat[1]*qrot3 
+    quat3 = quat[0]*qrot3 + quat[3]*qrot0 + quat[1]*qrot2 + quat[2]*qrot1 
+
+    quat = [quat0,quat1,quat2,quat3]
+
+    posx=axisx - dcomh*(quat[0]**2+quat[1]**2-quat[2]**2-quat[3]**2)
+    posy=axisy - dcomh*(2*(quat[1]*quat[2]+quat[0]*quat[3]))
+    posz=posz+risez
+
+    if (len(nucleotide)+1 > strandstart):
+      topology.append([1,len(nucleotide),len(nucleotide)+1])
+
+    nucleotide.append(temp)
+
+  return
+
+# definition of twisted duplex  
+def duplex():
+
+  strand = inp[1].split(':')
+
+  com_start=strand[0].split(',')
+  twist=float(strand[1])
+
+  compstrand=[]
+  comptopo=[]
+
+  posx1 = float(com_start[0])
+  posy1 = float(com_start[1])
+  posz1 = float(com_start[2])
+
+  risex=0
+  risey=0
+  risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2) 
+
+  dcomh=0.76
+  axisx=dcomh + posx1
+  axisy=posy1
+
+  posx2 = axisx + dcomh  
+  posy2 = posy1
+  posz2 = posz1
+
+  strandstart=len(nucleotide)+1
+
+  quat1=[1,0,0,0]
+  quat2=[0,0,-1,0]
+
+  qrot0=math.cos(0.5*twist)
+  qrot1=0
+  qrot2=0
+  qrot3=math.sin(0.5*twist)
+
+  for letter in strand[2]:
+    temp1=[]
+    temp2=[]
+
+    temp1.append(nt2num[letter])
+    temp2.append(compnt2num[letter])
+
+    temp1.append([posx1,posy1,posz1])
+    temp2.append([posx2,posy2,posz2])
+
+    vel=[0,0,0,0,0,0]
+    temp1.append(vel)
+    temp2.append(vel)
+
+    temp1.append(shape)
+    temp2.append(shape)
+
+    temp1.append(quat1)
+    temp2.append(quat2)
+
+    quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3 
+    quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2 
+    quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3 
+    quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1 
+
+    quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
+
+    posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
+    posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
+    posz1=posz1+risez
+
+    quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3 
+    quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2 
+    quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3 
+    quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1 
+
+    quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
+
+    posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
+    posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
+    posz2=posz1
+
+    if (len(nucleotide)+1 > strandstart):
+      topology.append([1,len(nucleotide),len(nucleotide)+1])
+      comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
+
+    nucleotide.append(temp1)
+    compstrand.append(temp2)
+
+  for ib in range(len(compstrand)):
+    nucleotide.append(compstrand[len(compstrand)-1-ib])
+
+  for ib in range(len(comptopo)):
+    topology.append(comptopo[ib])
+
+  return
+
+# definition of array of duplexes  
+def duplex_array():
+
+  strand = inp[1].split(':')
+  number=strand[0].split(',')
+  posz1_0 = float(strand[1])
+  twist=float(strand[2])
+
+  nx = int(number[0])
+  ny = int(number[1])
+
+  dx = (lxmax-lxmin)/nx
+  dy = (lymax-lymin)/ny
+
+  risex=0
+  risey=0
+  risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2) 
+  dcomh=0.76
+
+  for ix in range(nx):
+
+    axisx=lxmin + dx/2 + ix * dx
+
+    for iy in range(ny):
+
+      axisy=lymin + dy/2 + iy * dy
+
+      compstrand=[]
+      comptopo=[]
+
+      posx1 = axisx - dcomh
+      posy1 = axisy
+      posz1 = posz1_0
+
+      posx2 = axisx + dcomh  
+      posy2 = posy1
+      posz2 = posz1
+
+      strandstart=len(nucleotide)+1
+      quat1=[1,0,0,0]
+      quat2=[0,0,-1,0]
+
+      qrot0=math.cos(0.5*twist)
+      qrot1=0
+      qrot2=0
+      qrot3=math.sin(0.5*twist)
+
+      for letter in strand[3]:
+	temp1=[]
+	temp2=[]
+
+	temp1.append(nt2num[letter])
+	temp2.append(compnt2num[letter])
+
+	temp1.append([posx1,posy1,posz1])
+	temp2.append([posx2,posy2,posz2])
+
+	vel=[0,0,0,0,0,0]
+	temp1.append(vel)
+	temp2.append(vel)
+
+	temp1.append(shape)
+	temp2.append(shape)
+
+	temp1.append(quat1)
+	temp2.append(quat2)
+
+	quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3 
+	quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2 
+	quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3 
+	quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1 
+
+	quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
+
+	posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
+	posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
+	posz1=posz1+risez
+
+	quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3 
+	quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2 
+	quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3 
+	quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1 
+
+	quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
+
+	posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
+	posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
+	posz2=posz1
+
+	if (len(nucleotide)+1 > strandstart):
+	  topology.append([1,len(nucleotide),len(nucleotide)+1])
+	  comptopo.append([1,len(nucleotide)+len(strand[3]),len(nucleotide)+len(strand[3])+1])
+
+	nucleotide.append(temp1)
+	compstrand.append(temp2)
+
+      for ib in range(len(compstrand)):
+	nucleotide.append(compstrand[len(compstrand)-1-ib])
+
+      for ib in range(len(comptopo)):
+	topology.append(comptopo[ib])
+
+  return
+
+# main part
+nt2num = {'A':1, 'C':2, 'G':3, 'T':4}
+compnt2num = {'T':1, 'G':2, 'C':3, 'A':4}
+shape = [1.1739845031423408,1.1739845031423408,1.1739845031423408]
+
+nucleotide=[]
+topology=[]
+
+seqfile = open(sys.argv[1],'r')
+
+# process sequence file line by line
+for line in seqfile:
+
+  inp = line.split()
+  if inp[0] == 'single':
+    single()
+  if inp[0] == 'single_helix':
+    single_helix()
+  if inp[0] == 'duplex':
+    duplex()
+  if inp[0] == 'duplex_array':
+    duplex_array()
+
+# output atom data in LAMMPS format
+out = open(sys.argv[2],'w')
+
+out.write('# LAMMPS data file\n')
+out.write('%d atoms\n' % len(nucleotide))
+out.write('%d ellipsoids\n' % len(nucleotide))
+out.write('%d bonds\n' % len(topology))
+out.write('\n')
+out.write('4 atom types\n')
+out.write('1 bond types\n')
+out.write('\n')
+out.write('# System size\n')
+out.write('%f %f xlo xhi\n' % (lxmin,lxmax))
+out.write('%f %f ylo yhi\n' % (lymin,lymax))
+out.write('%f %f zlo zhi\n' % (lzmin,lzmax))
+out.write('\n')
+out.write('Masses\n')
+out.write('\n')
+out.write('1 3.1575\n')
+out.write('2 3.1575\n')
+out.write('3 3.1575\n')
+out.write('4 3.1575\n')
+
+out.write('\n')
+out.write('# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n')
+out.write('Atoms\n')
+out.write('\n')
+for ib in range(len(nucleotide)):
+  out.write("%d %d %22.16le %22.16le %22.16le 1 1 1\n" % (ib+1,nucleotide[ib][0],nucleotide[ib][1][0],nucleotide[ib][1][1],nucleotide[ib][1][2]))
+
+out.write('\n')
+out.write('# Atom-ID, translational, rotational velocity\n')
+out.write('Velocities\n')
+out.write('\n')
+for ib in range(len(nucleotide)):
+  out.write("%d %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le\n" % (ib+1,nucleotide[ib][2][0],nucleotide[ib][2][1],nucleotide[ib][2][2],nucleotide[ib][2][3],nucleotide[ib][2][4],nucleotide[ib][2][5]))
+
+out.write('\n')
+out.write('# Atom-ID, shape, quaternion\n')
+out.write('Ellipsoids\n')
+out.write('\n')
+for ib in range(len(nucleotide)):
+  out.write("%d %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le\n" % (ib+1,nucleotide[ib][3][0],nucleotide[ib][3][1],nucleotide[ib][3][2],nucleotide[ib][4][0],nucleotide[ib][4][1],nucleotide[ib][4][2],nucleotide[ib][4][3]))
+
+out.write('\n')
+out.write('# Bond topology\n')
+out.write('Bonds\n')
+out.write('\n')
+for ib in range(len(topology)):
+  out.write("%d %d %d %d\n" % (ib+1,topology[ib][0],topology[ib][1],topology[ib][2]))
+
+out.close() 
+
+seqfile.close()
+sys.exit(0)
+
+
--- a/examples/USER/cgdna/util/input.ref
+++ b/examples/USER/cgdna/util/input.ref
@ -0,0 +1,77 @@
+variable number	equal 8
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+processors 1 1 1
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+
+set atom * mass 3.1575
+
+group all type 1 4
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna_fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
+pair_coeff * * oxdna_excv   2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna_stk    1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
+pair_coeff * * oxdna_hbond  0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna_xstk   47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
+pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+#fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+fix 1 all   nve/dot
+
+timestep 1e-5 
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+dump_modify out sort id
+dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 1000000
+
+#write_restart config.${number}.*
--- a/examples/USER/cgdna/util/sequence.txt
+++ b/examples/USER/cgdna/util/sequence.txt
@ -0,0 +1,4 @@
+single 0,0,0:0.6:AAAAA
+single_helix 0,0,0:0.6:AAAAA
+duplex 0,0,0:0.6:AAAAA
+duplex_array 10,10:-112.0:0.6:AAAAA
--- a/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow
+++ b/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow
@ -18,7 +18,7 @@ neigh_modify    every 1 delay 0 check no once no
 timestep        0.001

 compute         dpdU all dpd
-variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[1]+press*vol
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]+press*vol

 thermo          1
 thermo_style    custom step temp press vol pe ke v_totEnergy cella cellb cellc
--- a/examples/USER/dpd/dpdh-shardlow/log.dpdh-shardlow.reference
+++ b/examples/USER/dpd/dpdh-shardlow/log.dpdh-shardlow.reference
@ -22,7 +22,7 @@ neigh_modify    every 1 delay 0 check no once no
 timestep        0.001

 compute         dpdU all dpd
-variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[1]+press*vol
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]+press*vol

 thermo          1
 thermo_style    custom step temp press vol pe ke v_totEnergy cella cellb cellc
@ -34,129 +34,137 @@ fix             2 all eos/cv 0.0005

 run             100
 Neighbor list info ...
-  1 neighbor list requests
  update every 1 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
-  binsize = 6 -> bins = 22 22 22
-Memory usage per processor = 6.48143 Mbytes
+  binsize = 6, bins = 22 22 22
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair dpd/fdt/energy, perpetual
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix shardlow, perpetual, ssa
+      pair build: half/bin/newton/ssa
+      stencil: half/bin/3d/newton/ssa
+      bin: ssa
+Memory usage per processor = 8.55503 Mbytes
 Step Temp Press Volume PotEng KinEng v_totEnergy Cella Cellb Cellc 
-       0  239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740  313.3218455755 6048176597.3066043854  129.0000000000  129.0000000000  129.0000000000 
-       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.9450111389  129.0000000012  129.0000000012  129.0000000012 
-       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391577.0431985855  129.0000000047  129.0000000047  129.0000000047 
-       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.5712032318  129.0000000105  129.0000000105  129.0000000105 
-       4  239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043  313.4653942786 6048377030.7404460907  129.0000000186  129.0000000186  129.0000000186 
-       5  239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340  313.6147686202 6048548267.9007377625  129.0000000291  129.0000000291  129.0000000291 
-       6  239.5617886781 2817.5624195435 2146689.0020948485 2639.8617493725  313.4976735610 6048434730.8592004776  129.0000000420  129.0000000420  129.0000000420 
-       7  239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407  313.4467287471 6048390900.5748577118  129.0000000571  129.0000000571  129.0000000571 
-       8  239.6066877934 2817.6008649264 2146689.0037241788 2639.8710757645  313.5564298772 6048517265.7987136841  129.0000000746  129.0000000746  129.0000000746 
-       9  239.5719861485 2817.5823530300 2146689.0047134170 2639.8752557893  313.5110182737 6048477529.2603597641  129.0000000944  129.0000000944  129.0000000944 
-      10  239.5800176776 2817.5915671176 2146689.0058190385 2639.8793778438  313.5215285712 6048497312.1706552505  129.0000001166  129.0000001166  129.0000001166 
-      11  239.6299830954 2817.6281223139 2146689.0070410441 2639.8829762049  313.5869148014 6048575788.3208351135  129.0000001410  129.0000001410  129.0000001410 
-      12  239.6011995911 2817.6132377273 2146689.0083794324 2639.8860704236  313.5492478526 6048543839.4788360596  129.0000001678  129.0000001678  129.0000001678 
-      13  239.6407681166 2817.6427924824 2146689.0098342048 2639.8889816934  313.6010284005 6048607288.5005025864  129.0000001970  129.0000001970  129.0000001970 
-      14  239.6981172055 2817.6844100046 2146689.0114053637 2639.8913405110  313.6760771219 6048696632.8825626373  129.0000002285  129.0000002285  129.0000002285 
-      15  239.8563971968 2817.7922519039 2146689.0130929090 2639.8934358481  313.8832070208 6048928140.8671455383  129.0000002623  129.0000002623  129.0000002623 
-      16  239.8561894618 2817.7971208197 2146689.0148968464 2639.8950496967  313.8829351726 6048938597.9994916916  129.0000002984  129.0000002984  129.0000002984 
-      17  239.8816520361 2817.8185621543 2146689.0168171758 2639.8961257823  313.9162562538 6048984631.3226108551  129.0000003369  129.0000003369  129.0000003369 
-      18  239.9099966096 2817.8417368960 2146689.0188538977 2639.8965743204  313.9533488047 6049034386.0627622604  129.0000003777  129.0000003777  129.0000003777 
-      19  240.0514024347 2817.9389205774 2146689.0210070144 2639.8966103811  314.1383966683 6049243015.4568052292  129.0000004208  129.0000004208  129.0000004208 
-      20  239.8802541140 2817.8327386176 2146689.0232765260 2639.8962085210  313.9144268914 6049015081.9802341461  129.0000004662  129.0000004662  129.0000004662 
-      21  239.8462621903 2817.8160306167 2146689.0256624296 2639.8953174755  313.8699440502 6048979221.7758703232  129.0000005140  129.0000005140  129.0000005140 
-      22  240.0487944678 2817.9533849157 2146689.0281647225 2639.8938590354  314.1349838054 6049274086.0571212769  129.0000005642  129.0000005642  129.0000005642 
-      23  240.0966314441 2817.9897873787 2146689.0307834130 2639.8918104774  314.1975846937 6049352238.2649183273  129.0000006166  129.0000006166  129.0000006166 
-      24  240.1765312516 2818.0463843765 2146689.0335185044 2639.8891292321  314.3021439554 6049473742.2287187576  129.0000006714  129.0000006714  129.0000006714 
-      25  240.1500705973 2818.0336048048 2146689.0363699966 2639.8858785483  314.2675167572 6049446316.4600162506  129.0000007285  129.0000007285  129.0000007285 
-      26  240.2681423500 2818.1151708195 2146689.0393378921 2639.8825176506  314.4220289603 6049621421.8445177078  129.0000007880  129.0000007880  129.0000007880 
-      27  240.4728815247 2818.2527327079 2146689.0424221945 2639.8784158747  314.6899567267 6049916733.3989181519  129.0000008498  129.0000008498  129.0000008498 
-      28  240.4793027032 2818.2613348477 2146689.0456229053 2639.8736089473  314.6983596717 6049935208.5421981812  129.0000009139  129.0000009139  129.0000009139 
-      29  240.5020619198 2818.2805472685 2146689.0489400285 2639.8681043704  314.7281430587 6049976461.0082206726  129.0000009803  129.0000009803  129.0000009803 
-      30  240.5513721776 2818.3167157263 2146689.0523735629 2639.8623484053  314.7926719270 6050054113.1760177612  129.0000010491  129.0000010491  129.0000010491 
-      31  240.7340393104 2818.4391703712 2146689.0559235099 2639.8563442170  315.0317155636 6050316995.4599781036  129.0000011202  129.0000011202  129.0000011202 
-      32  240.8254719483 2818.5014640740 2146689.0595898777 2639.8498122053  315.1513670299 6050450731.1168394089  129.0000011936  129.0000011936  129.0000011936 
-      33  240.9681573541 2818.5965480750 2146689.0633726656 2639.8425779528  315.3380893908 6050654857.7432861328  129.0000012694  129.0000012694  129.0000012694 
-      34  241.0039494187 2818.6217008564 2146689.0672718794 2639.8347174393  315.3849279499 6050708863.9733209610  129.0000013475  129.0000013475  129.0000013475 
-      35  241.0314566197 2818.6411150538 2146689.0712875174 2639.8262983643  315.4209246902 6050750551.5649127960  129.0000014279  129.0000014279  129.0000014279 
-      36  241.0829173424 2818.6763455617 2146689.0754195810 2639.8174397481  315.4882677207 6050826192.2165899277  129.0000015107  129.0000015107  129.0000015107 
-      37  241.2845682012 2818.8087982181 2146689.0796680767 2639.8080129872  315.7521540252 6051110539.1171846390  129.0000015958  129.0000015958  129.0000015958 
-      38  241.3214712920 2818.8336260248 2146689.0840330068 2639.7981963574  315.8004465062 6051163849.0412235260  129.0000016833  129.0000016833  129.0000016833 
-      39  241.3392127125 2818.8456991528 2146689.0885143690 2639.7879618658  315.8236634561 6051189778.9386901855  129.0000017730  129.0000017730  129.0000017730 
-      40  241.5383770555 2818.9753950055 2146689.0931121684 2639.7769824244  316.0842958321 6051468208.8210506439  129.0000018651  129.0000018651  129.0000018651 
-      41  241.5059730674 2818.9543817992 2146689.0978264087 2639.7656512498  316.0418910106 6051423113.2358427048  129.0000019595  129.0000019595  129.0000019595 
-      42  241.3907605672 2818.8793800508 2146689.1026570834 2639.7541331920  315.8911205101 6051262121.2551422119  129.0000020563  129.0000020563  129.0000020563 
-      43  241.5095917610 2818.9559595711 2146689.1076041958 2639.7424355740  316.0466265406 6051426527.7663059235  129.0000021554  129.0000021554  129.0000021554 
-      44  241.6271631762 2819.0312325531 2146689.1126677482 2639.7297705654  316.2004839873 6051588129.8722610474  129.0000022568  129.0000022568  129.0000022568 
-      45  241.5702411838 2818.9923790176 2146689.1178477411 2639.7163554760  316.1259941770 6051504737.9250564575  129.0000023606  129.0000023606  129.0000023606 
-      46  241.7029985068 2819.0771124986 2146689.1231441777 2639.7024246704  316.2997243538 6051686649.4576120377  129.0000024667  129.0000024667  129.0000024667 
-      47  241.7966144965 2819.1357830868 2146689.1285570571 2639.6882106593  316.4222330191 6051812612.3391046524  129.0000025751  129.0000025751  129.0000025751 
-      48  241.8573480255 2819.1726205120 2146689.1340863821 2639.6735287925  316.5017107195 6051891706.4921989441  129.0000026859  129.0000026859  129.0000026859 
-      49  241.9611147338 2819.2374095379 2146689.1397321564 2639.6583357477  316.6375029166 6052030804.4275226593  129.0000027990  129.0000027990  129.0000027990 
-      50  242.1023518806 2819.3259059811 2146689.1454943856 2639.6424863169  316.8223300428 6052220795.1955394745  129.0000029144  129.0000029144  129.0000029144 
-      51  242.1174105473 2819.3319633044 2146689.1513730693 2639.6264141131  316.8420362613 6052233814.9634265900  129.0000030321  129.0000030321  129.0000030321 
-      52  242.2534914901 2819.4164594322 2146689.1573682069 2639.6098392670  317.0201158259 6052415218.9485445023  129.0000031522  129.0000031522  129.0000031522 
-      53  242.3504633236 2819.4754119996 2146689.1634798055 2639.5930076506  317.1470160479 6052541789.1274013519  129.0000032746  129.0000032746  129.0000032746 
-      54  242.2982323323 2819.4368568264 2146689.1697078613 2639.5756353782  317.0786650211 6052459040.6286897659  129.0000033994  129.0000033994  129.0000033994 
-      55  242.3452896272 2819.4623310219 2146689.1760523771 2639.5575918586  317.1402455951 6052513743.7400159836  129.0000035265  129.0000035265  129.0000035265 
-      56  242.4181903333 2819.5048897011 2146689.1825133534 2639.5390347547  317.2356456249 6052605122.2894439697  129.0000036559  129.0000036559  129.0000036559 
-      57  242.5317091656 2819.5739975787 2146689.1890907930 2639.5199828249  317.3841997413 6052753494.0979280472  129.0000037876  129.0000037876  129.0000037876 
-      58  242.5478978740 2819.5796954935 2146689.1957846982 2639.5006137388  317.4053847660 6052765744.6257629395  129.0000039217  129.0000039217  129.0000039217 
-      59  242.6655316466 2819.6519225743 2146689.2025950695 2639.4808234811  317.5593238156 6052920813.0568208694  129.0000040582  129.0000040582  129.0000040582 
-      60  242.8126131177 2819.7431588157 2146689.2095219092 2639.4607996998  317.7517989980 6053116688.6155729294  129.0000041969  129.0000041969  129.0000041969 
-      61  242.7957124913 2819.7275989047 2146689.2165652174 2639.4406312730  317.7296823362 6053083306.1403274536  129.0000043380  129.0000043380  129.0000043380 
-      62  242.9276177041 2819.8088790098 2146689.2237249981 2639.4201279058  317.9022974164 6053257809.6067762375  129.0000044814  129.0000044814  129.0000044814 
-      63  243.0465445938 2819.8814758895 2146689.2310012528 2639.3991657500  318.0579286774 6053413673.1989650726  129.0000046272  129.0000046272  129.0000046272 
-      64  242.9890585501 2819.8387587817 2146689.2383939880 2639.3781767844  317.9827007328 6053321993.5937871933  129.0000047752  129.0000047752  129.0000047752 
-      65  242.9653746583 2819.8180104181 2146689.2459031967 2639.3568184374  317.9517072884 6053277474.4272727966  129.0000049256  129.0000049256  129.0000049256 
-      66  243.0259297024 2819.8514334947 2146689.2535288804 2639.3352568621  318.0309514181 6053349244.9473772049  129.0000050784  129.0000050784  129.0000050784 
-      67  242.9638979697 2819.8046112742 2146689.2612710390 2639.3134547096  317.9497748498 6053248753.9180717468  129.0000052335  129.0000052335  129.0000052335 
-      68  243.0283540775 2819.8395632725 2146689.2691296688 2639.2912303374  318.0341240273 6053323807.2197017670  129.0000053909  129.0000053909  129.0000053909 
-      69  243.2256418664 2819.9609646019 2146689.2771047787 2639.2684509205  318.2923006889 6053584440.8757400513  129.0000055506  129.0000055506  129.0000055506 
-      70  243.2507495334 2819.9706145524 2146689.2851963686 2639.2450126010  318.3251573278 6053605179.1483964920  129.0000057127  129.0000057127  129.0000057127 
-      71  243.4287155518 2820.0794853386 2146689.2934044413 2639.2213699915  318.5580489464 6053838914.2552747726  129.0000058771  129.0000058771  129.0000058771 
-      72  243.5097518574 2820.1249498194 2146689.3017290002 2639.1971212009  318.6640954635 6053936535.9274711609  129.0000060439  129.0000060439  129.0000060439 
-      73  243.5356790969 2820.1337977544 2146689.3101700447 2639.1723394661  318.6980246193 6053955553.5090074539  129.0000062130  129.0000062130  129.0000062130 
-      74  243.5479180498 2820.1331964183 2146689.3187275808 2639.1473868749  318.7140408766 6053954286.7515821457  129.0000063844  129.0000063844  129.0000063844 
-      75  243.7115573025 2820.2314361523 2146689.3274016059 2639.1220411207  318.9281840641 6054165201.5909118652  129.0000065581  129.0000065581  129.0000065581 
-      76  243.7457279618 2820.2454531429 2146689.3361921217 2639.0963868224  318.9729008040 6054195316.5254154205  129.0000067342  129.0000067342  129.0000067342 
-      77  243.8345031069 2820.2948644965 2146689.3450991292 2639.0700900389  319.0890745962 6054301412.5615310669  129.0000069126  129.0000069126  129.0000069126 
-      78  244.0193931195 2820.4067881628 2146689.3541226317 2639.0435094409  319.3310271594 6054541703.5689058304  129.0000070934  129.0000070934  129.0000070934 
-      79  243.9919100078 2820.3799166166 2146689.3632626338 2639.0164249037  319.2950619430 6054484044.4218587875  129.0000072765  129.0000072765  129.0000072765 
-      80  244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882  319.4320116291 6054610332.4174261093  129.0000074619  129.0000074619  129.0000074619 
-      81  244.1334315951 2820.4535208568 2146689.3818921377 2638.9608330195  319.4802612965 6054642102.5347270966  129.0000076496  129.0000076496  129.0000076496 
-      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858575.1664342880  129.0000078397  129.0000078397  129.0000078397 
-      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895140.1710596085  129.0000080321  129.0000080321  129.0000080321 
-      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768957.6739044189  129.0000082269  129.0000082269  129.0000082269 
-      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091776.5361995697  129.0000084240  129.0000084240  129.0000084240 
-      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136595.0767974854  129.0000086234  129.0000086234  129.0000086234 
-      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072877.2416200638  129.0000088251  129.0000088251  129.0000088251 
-      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271926.6536149979  129.0000090292  129.0000090292  129.0000090292 
-      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507852.1186332703  129.0000092356  129.0000092356  129.0000092356 
-      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482985.2258749008  129.0000094444  129.0000094444  129.0000094444 
-      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561333.3803453445  129.0000096555  129.0000096555  129.0000096555 
-      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590051.6433181763  129.0000098689  129.0000098689  129.0000098689 
-      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758210.2774200439  129.0000100846  129.0000100846  129.0000100846 
-      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948551.7882709503  129.0000103027  129.0000103027  129.0000103027 
-      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000363.5151576996  129.0000105232  129.0000105232  129.0000105232 
-      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176929.0169925690  129.0000107459  129.0000107459  129.0000107459 
-      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028008.1910057068  129.0000109710  129.0000109710  129.0000109710 
-      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991214.3494396210  129.0000111984  129.0000111984  129.0000111984 
-      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018909.4480972290  129.0000114282  129.0000114282  129.0000114282 
-     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403111.1006488800  129.0000116603  129.0000116603  129.0000116603 
-Loop time of 4.05006 on 1 procs for 100 steps with 10125 atoms
+       0  239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740  313.3218455755 6048176597.3066034317  129.0000000000  129.0000000000  129.0000000000 
+       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.8720483780  129.0000000012  129.0000000012  129.0000000012 
+       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391576.8485937119  129.0000000047  129.0000000047  129.0000000047 
+       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.2404479980  129.0000000105  129.0000000105  129.0000000105 
+       4  239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043  313.4653942786 6048377030.5689325333  129.0000000186  129.0000000186  129.0000000186 
+       5  239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340  313.6147686202 6048548267.5742130280  129.0000000291  129.0000000291  129.0000000291 
+       6  239.5617886781 2817.5624195435 2146689.0020948485 2639.8617493725  313.4976735610 6048434730.6441593170  129.0000000420  129.0000000420  129.0000000420 
+       7  239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407  313.4467287471 6048390900.4058599472  129.0000000571  129.0000000571  129.0000000571 
+       8  239.6066877934 2817.6008649264 2146689.0037241788 2639.8710757645  313.5564298772 6048517265.5155982971  129.0000000746  129.0000000746  129.0000000746 
+       9  239.5719861485 2817.5823530300 2146689.0047134170 2639.8752557893  313.5110182737 6048477529.0184717178  129.0000000944  129.0000000944  129.0000000944 
+      10  239.5800176776 2817.5915671176 2146689.0058190385 2639.8793778438  313.5215285712 6048497311.9141387939  129.0000001166  129.0000001166  129.0000001166 
+      11  239.6299830954 2817.6281223139 2146689.0070410441 2639.8829762049  313.5869148014 6048575787.9953098297  129.0000001410  129.0000001410  129.0000001410 
+      12  239.6011995911 2817.6132377273 2146689.0083794324 2639.8860704236  313.5492478526 6048543839.1878814697  129.0000001678  129.0000001678  129.0000001678 
+      13  239.6407681166 2817.6427924824 2146689.0098342048 2639.8889816934  313.6010284005 6048607288.1548709869  129.0000001970  129.0000001970  129.0000001970 
+      14  239.6981172055 2817.6844100046 2146689.0114053637 2639.8913405110  313.6760771219 6048696632.4595127106  129.0000002285  129.0000002285  129.0000002285 
+      15  239.8563971968 2817.7922519039 2146689.0130929090 2639.8934358481  313.8832070208 6048928140.2348766327  129.0000002623  129.0000002623  129.0000002623 
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+      17  239.8816520361 2817.8185621543 2146689.0168171758 2639.8961257823  313.9162562538 6048984630.6545839310  129.0000003369  129.0000003369  129.0000003369 
+      18  239.9099966096 2817.8417368960 2146689.0188538977 2639.8965743204  313.9533488047 6049034385.3571958542  129.0000003777  129.0000003777  129.0000003777 
+      19  240.0514024347 2817.9389205774 2146689.0210070144 2639.8966103811  314.1383966683 6049243014.5661621094  129.0000004208  129.0000004208  129.0000004208 
+      20  239.8802541140 2817.8327386176 2146689.0232765260 2639.8962085210  313.9144268914 6049015081.3139505386  129.0000004662  129.0000004662  129.0000004662 
+      21  239.8462621903 2817.8160306167 2146689.0256624296 2639.8953174755  313.8699440502 6048979221.1549577713  129.0000005140  129.0000005140  129.0000005140 
+      22  240.0487944678 2817.9533849157 2146689.0281647225 2639.8938590354  314.1349838054 6049274085.1726217270  129.0000005642  129.0000005642  129.0000005642 
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+      32  240.8254719483 2818.5014640740 2146689.0595898777 2639.8498122053  315.1513670299 6050450729.2599506378  129.0000011936  129.0000011936  129.0000011936 
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+      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028001.7295455933  129.0000109710  129.0000109710  129.0000109710 
+      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991207.9293851852  129.0000111984  129.0000111984  129.0000111984 
+      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018903.0102539062  129.0000114282  129.0000114282  129.0000114282 
+     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403104.3106222153  129.0000116603  129.0000116603  129.0000116603 
+Loop time of 5.22601 on 1 procs for 100 steps with 10125 atoms

-Performance: 2.133 ns/day, 11.250 hours/ns, 24.691 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.653 ns/day, 14.517 hours/ns, 19.135 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads

 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.46587    | 0.46587    | 0.46587    |   0.0 | 11.50
-Neigh   | 1.4713     | 1.4713     | 1.4713     |   0.0 | 36.33
-Comm    | 0.05567    | 0.05567    | 0.05567    |   0.0 |  1.37
-Output  | 0.011364   | 0.011364   | 0.011364   |   0.0 |  0.28
-Modify  | 2.0158     | 2.0158     | 2.0158     |   0.0 | 49.77
-Other   |            | 0.03004    |            |       |  0.74
+Pair    | 0.44045    | 0.44045    | 0.44045    |   0.0 |  8.43
+Neigh   | 2.669      | 2.669      | 2.669      |   0.0 | 51.07
+Comm    | 0.056143   | 0.056143   | 0.056143   |   0.0 |  1.07
+Output  | 0.012469   | 0.012469   | 0.012469   |   0.0 |  0.24
+Modify  | 2.0163     | 2.0163     | 2.0163     |   0.0 | 38.58
+Other   |            | 0.03168    |            |       |  0.61

 Nlocal:    10125 ave 10125 max 10125 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -172,4 +180,4 @@ Dangerous builds not checked

 Please see the log.cite file for references relevant to this simulation

-Total wall time: 0:00:04
+Total wall time: 0:00:05
--- a/examples/USER/misc/basal/in.basal
+++ b/examples/USER/misc/basal/in.basal
@ -1,163 +1,163 @@
-############################################################################
-# Input file for investigating twinning nucleation under uniaxial loading with basal plane vector analysis
-# Christopher Barrett, March 2013
-# This script requires a Mg pair potential file to be in the same directory.
-
-# fname is the file name.  It is necessary for loops to work correctly. (See jump command)
-variable fname index in.basal
-
-######################################
-# POTENTIAL VARIABLES
-# lattice parameters and the minimum energy per atom which should be obtained with the current pair potential and homogeneous lattice
-variable lx equal 3.181269601 
-variable b equal sqrt(3)
-variable c equal sqrt(8/3)
-variable ly equal ${b}*${lx}
-variable lz equal ${c}*${lx}
-variable pairlocation index almg.liu
-variable pairstyle index eam/alloy/opt
-
-######################################
-# EQUILIBRATION/DEFORMATION VARIABLES
-# eqpress = 10 bar = 1 MPa
-# tstep (the timestep) is set to a default value of 0.001 (1 fs) 
-# seed randomizes the velocity
-# srate is the rate of strain in 1/s
-# Ndump is the number of timesteps in between each dump of the atom coordinates
-variable tstep equal 0.001
-variable seed equal 95812384
-variable srate equal 1e9
-
-######################################
-# INITIALIZATION
-units 		metal
-dimension		3
-boundary		s	s	s
-atom_style		atomic
-
-######################################
-# ATOM BUILD
-atom_modify map array
-
-# lattice custom scale a1 "coordinates of a1" a2 "coordinates of a2" a3 "coordinates of a3" basis "atom1 coordinates" basis "atom2 coordinates" basis "atom3 coordinates" basis "atom4 coordinates" orient x "crystallagraphic orientation of x axis" orient y "crystallagraphic orientation of y axis" z "crystallagraphic orientation of z axis"
-lattice custom 3.181269601 a1 1 0 0 a2 0 1.732050808 0 a3 0 0 1.632993162 basis 0.0 0.0 0.0 basis 0.5 0.5 0 basis 0 0.3333333 0.5 basis 0.5 0.833333 0.5 orient x 0 1 1 orient y 1 0 0 orient z 0 1 -1
-variable multiple equal 20
-variable mx equal "v_lx*v_multiple"
-variable my equal "v_ly*v_multiple"
-variable mz equal "v_lz*v_multiple"
-
-# the simulation region should be from 0 to a multiple of the periodic boundary in x, y and z.
-region		whole block 0 ${mz} 0 ${mx} 0 ${my} units box 
-create_box		2 whole
-create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 
-
-region fixed1 block INF INF INF INF INF 10 units box
-region fixed2 block INF INF INF INF  100 INF units box
-group lower region fixed1
-group upper region fixed2
-group boundary union upper lower
-group mobile subtract all boundary
-
-variable natoms equal "count(all)"
-print "# of atoms are: ${natoms}"
-
-######################################
-# INTERATOMIC POTENTIAL
-pair_style	${pairstyle}
-pair_coeff	* * ${pairlocation} Mg Mg
-
-######################################
-# COMPUTES REQUIRED
-compute csym all centro/atom 12
-compute eng all pe/atom
-compute eatoms all reduce sum c_eng
-compute basal all basal/atom
-
-######################################
-# MINIMIZATION
-# Primarily adjusts the c/a ratio to value predicted by EAM potential
-reset_timestep	0
-thermo 1
-thermo_style custom step pe c_eatoms
-min_style cg
-minimize	1e-15 1e-15 1000 2000
-variable eminimum equal "c_eatoms / count(all)"
-print "%%e(it,1)=${eminimum}"
-
-######################################
-# EQUILIBRATION
-reset_timestep	0
-timestep ${tstep}
-# atoms are given a random velocity based on a temperature of 100K.
-velocity all create 100 ${seed} mom yes rot no
-
-# temperature and pressure are set to 100 and 0
-fix 1 all nve
-
-# Set thermo output
-thermo 100
-thermo_style custom step lx ly lz press pxx pyy pzz pe temp
-
-# Run for at least 2 picosecond (assuming 1 fs timestep)
-run 2000
-
-# Loop to run until pressure is below the variable eqpress (defined at beginning of file)
-label loopeq 
-variable eq loop 100 
-run 250
-variable converge equal press
-if "${converge} <= 0" then "variable converge equal -press" else "variable converge equal press" 
-if "${converge} <= 50" then "jump ${fname} breakeq" 
-next eq 
-jump ${fname} loopeq 
-label breakeq 
-
-# Store length for strain rate calculations
-variable tmp equal "lx"
-variable L0 equal ${tmp}
-print "Initial Length, L0: ${L0}"
-unfix 1
-
-######################################
-# DEFORMATION
-reset_timestep	0
-timestep ${tstep}
-
-# Impose constant strain rate 
-variable srate1 equal "v_srate / 1.0e10"
-velocity	upper set 0.0 NULL 0.0 units box
-velocity        lower set 0.0 NULL 0.0 units box
-
-fix 2 upper setforce 0.0 NULL 0.0
-fix 3 lower setforce 0.0 NULL 0.0
-fix 1 all nve
-
-# Output strain and stress info to file
-# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
-# p2 is in GPa
-variable strain equal "(lx - v_L0)/v_L0"
-variable p1 equal "v_strain"
-variable p2 equal "-pxz/10000"
-variable p3 equal "lx"
-variable p4 equal "temp"
-variable p5 equal "pe"
-variable p6 equal "ke"
-fix def1 all print 100 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6}" file output.def1.txt screen no
-# Dump coordinates to file (for void size calculations)
-dump 		1 all custom 1000 output.dump.* id x y z c_basal[1] c_basal[2] c_basal[3]
-
-# Display thermo
-thermo_style	custom step v_strain pxz lx temp pe ke
-restart 50000 output.restart
-
-# run deformation for 100000 timesteps (10% strain assuming 1 fs timestep and 1e9/s strainrate)
-variable runtime equal 0
-label loop
-displace_atoms	all ramp x 0.0 ${srate1} z 10 100 units box
-run		100
-variable runtime equal ${runtime}+100
-if "${runtime} < 100000" then "jump ${fname} loop"
-
-######################################
-# SIMULATION DONE
-print "All done"
+############################################################################
+# Input file for investigating twinning nucleation under uniaxial loading with basal plane vector analysis
+# Christopher Barrett, March 2013
+# This script requires a Mg pair potential file to be in the same directory.
+
+# fname is the file name.  It is necessary for loops to work correctly. (See jump command)
+variable fname index in.basal
+
+######################################
+# POTENTIAL VARIABLES
+# lattice parameters and the minimum energy per atom which should be obtained with the current pair potential and homogeneous lattice
+variable lx equal 3.181269601 
+variable b equal sqrt(3)
+variable c equal sqrt(8/3)
+variable ly equal ${b}*${lx}
+variable lz equal ${c}*${lx}
+variable pairlocation index almg.liu
+variable pairstyle index eam/alloy/opt
+
+######################################
+# EQUILIBRATION/DEFORMATION VARIABLES
+# eqpress = 10 bar = 1 MPa
+# tstep (the timestep) is set to a default value of 0.001 (1 fs) 
+# seed randomizes the velocity
+# srate is the rate of strain in 1/s
+# Ndump is the number of timesteps in between each dump of the atom coordinates
+variable tstep equal 0.001
+variable seed equal 95812384
+variable srate equal 1e9
+
+######################################
+# INITIALIZATION
+units 		metal
+dimension		3
+boundary		s	s	s
+atom_style		atomic
+
+######################################
+# ATOM BUILD
+atom_modify map array
+
+# lattice custom scale a1 "coordinates of a1" a2 "coordinates of a2" a3 "coordinates of a3" basis "atom1 coordinates" basis "atom2 coordinates" basis "atom3 coordinates" basis "atom4 coordinates" orient x "crystallagraphic orientation of x axis" orient y "crystallagraphic orientation of y axis" z "crystallagraphic orientation of z axis"
+lattice custom 3.181269601 a1 1 0 0 a2 0 1.732050808 0 a3 0 0 1.632993162 basis 0.0 0.0 0.0 basis 0.5 0.5 0 basis 0 0.3333333 0.5 basis 0.5 0.833333 0.5 orient x 0 1 1 orient y 1 0 0 orient z 0 1 -1
+variable multiple equal 20
+variable mx equal "v_lx*v_multiple"
+variable my equal "v_ly*v_multiple"
+variable mz equal "v_lz*v_multiple"
+
+# the simulation region should be from 0 to a multiple of the periodic boundary in x, y and z.
+region		whole block 0 ${mz} 0 ${mx} 0 ${my} units box 
+create_box		2 whole
+create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 
+
+region fixed1 block INF INF INF INF INF 10 units box
+region fixed2 block INF INF INF INF  100 INF units box
+group lower region fixed1
+group upper region fixed2
+group boundary union upper lower
+group mobile subtract all boundary
+
+variable natoms equal "count(all)"
+print "# of atoms are: ${natoms}"
+
+######################################
+# INTERATOMIC POTENTIAL
+pair_style	${pairstyle}
+pair_coeff	* * ${pairlocation} Mg Mg
+
+######################################
+# COMPUTES REQUIRED
+compute csym all centro/atom 12
+compute eng all pe/atom
+compute eatoms all reduce sum c_eng
+compute basal all basal/atom
+
+######################################
+# MINIMIZATION
+# Primarily adjusts the c/a ratio to value predicted by EAM potential
+reset_timestep	0
+thermo 1
+thermo_style custom step pe c_eatoms
+min_style cg
+minimize	1e-15 1e-15 1000 2000
+variable eminimum equal "c_eatoms / count(all)"
+print "%%e(it,1)=${eminimum}"
+
+######################################
+# EQUILIBRATION
+reset_timestep	0
+timestep ${tstep}
+# atoms are given a random velocity based on a temperature of 100K.
+velocity all create 100 ${seed} mom yes rot no
+
+# temperature and pressure are set to 100 and 0
+fix 1 all nve
+
+# Set thermo output
+thermo 100
+thermo_style custom step lx ly lz press pxx pyy pzz pe temp
+
+# Run for at least 2 picosecond (assuming 1 fs timestep)
+run 2000
+
+# Loop to run until pressure is below the variable eqpress (defined at beginning of file)
+label loopeq 
+variable eq loop 100 
+run 250
+variable converge equal press
+if "${converge} <= 0" then "variable converge equal -press" else "variable converge equal press" 
+if "${converge} <= 50" then "jump ${fname} breakeq" 
+next eq 
+jump ${fname} loopeq 
+label breakeq 
+
+# Store length for strain rate calculations
+variable tmp equal "lx"
+variable L0 equal ${tmp}
+print "Initial Length, L0: ${L0}"
+unfix 1
+
+######################################
+# DEFORMATION
+reset_timestep	0
+timestep ${tstep}
+
+# Impose constant strain rate 
+variable srate1 equal "v_srate / 1.0e10"
+velocity	upper set 0.0 NULL 0.0 units box
+velocity        lower set 0.0 NULL 0.0 units box
+
+fix 2 upper setforce 0.0 NULL 0.0
+fix 3 lower setforce 0.0 NULL 0.0
+fix 1 all nve
+
+# Output strain and stress info to file
+# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
+# p2 is in GPa
+variable strain equal "(lx - v_L0)/v_L0"
+variable p1 equal "v_strain"
+variable p2 equal "-pxz/10000"
+variable p3 equal "lx"
+variable p4 equal "temp"
+variable p5 equal "pe"
+variable p6 equal "ke"
+fix def1 all print 100 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6}" file output.def1.txt screen no
+# Dump coordinates to file (for void size calculations)
+dump 		1 all custom 1000 output.dump.* id x y z c_basal[1] c_basal[2] c_basal[3]
+
+# Display thermo
+thermo_style	custom step v_strain pxz lx temp pe ke
+restart 50000 output.restart
+
+# run deformation for 100000 timesteps (10% strain assuming 1 fs timestep and 1e9/s strainrate)
+variable runtime equal 0
+label loop
+displace_atoms	all ramp x 0.0 ${srate1} z 10 100 units box
+run		100
+variable runtime equal ${runtime}+100
+if "${runtime} < 100000" then "jump ${fname} loop"
+
+######################################
+# SIMULATION DONE
+print "All done"
--- a/examples/USER/misc/srp/in.srp
+++ b/examples/USER/misc/srp/in.srp
@ -15,6 +15,7 @@ bond_style      harmonic
 bond_coeff      * 225.0 0.85

 comm_modify vel yes
+comm_modify cutoff 3.6

 # must use pair hybrid, since srp bond particles
 # do not interact with other atoms types
--- a/examples/USER/misc/ti/in.ti_spring
+++ b/examples/USER/misc/ti/in.ti_spring
--- a/examples/mscg/output_9Jan17/log.lammps
+++ b/examples/mscg/output_9Jan17/log.lammps
@ -0,0 +1,140 @@
+LAMMPS (4 Nov 2016)
+units real
+atom_style full
+pair_style zero 10.0
+
+read_data data.meoh
+  orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1000 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+pair_coeff * *
+
+thermo 1
+thermo_style custom step
+
+# Test 1a: range finder functionality
+fix 1 all mscg 1 range on
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6 -> bins = 7 7 7
+Memory usage per processor = 5.44227 Mbytes
+Step 
+       0 
+     250 
+     500 
+     750 
+    1000 
+    1250 
+    1500 
+    1750 
+    2000 
+    2250 
+    2500 
+    2750 
+    3000 
+    3250 
+    3500 
+    3750 
+    4000 
+    4250 
+    4500 
+Loop time of 0.695789 on 1 procs for 19 steps with 1000 atoms
+
+Performance: 2.359 ns/day, 10.172 hours/ns, 27.307 timesteps/s
+92.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Bond    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.6958     |            |       |100.00
+
+Nlocal:    1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2934 ave 2934 max 2934 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    50654 ave 50654 max 50654 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 50654
+Ave neighs/atom = 50.654
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_1a mscg range finder"
+TEST_1a mscg range finder
+unfix 1
+
+# Test 1b: force matching functionality
+fix 1 all mscg 1
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+Memory usage per processor = 5.44227 Mbytes
+Step 
+       0 
+     250 
+     500 
+     750 
+    1000 
+    1250 
+    1500 
+    1750 
+    2000 
+    2250 
+    2500 
+    2750 
+    3000 
+    3250 
+    3500 
+    3750 
+    4000 
+    4250 
+    4500 
+Loop time of 1.48638 on 1 procs for 19 steps with 1000 atoms
+
+Performance: 1.104 ns/day, 21.731 hours/ns, 12.783 timesteps/s
+88.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Bond    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 1.486      |            |       |100.00
+
+Nlocal:    1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2934 ave 2934 max 2934 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    50654 ave 50654 max 50654 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 50654
+Ave neighs/atom = 50.654
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_1b mscg force matching"
+TEST_1b mscg force matching
+
+print TEST_DONE
+TEST_DONE
+Total wall time: 0:00:02
--- a/examples/prd/in.prd
+++ b/examples/prd/in.prd
@ -78,7 +78,7 @@ run             100

 # only output atoms near vacancy

-compute coord all coord/atom $r
+compute coord all coord/atom cutoff $r

 #dump events all custom 1 dump.prd id type x y z
 #dump_modify events thresh c_coord != 4
--- a/examples/tad/in.tad
+++ b/examples/tad/in.tad
@ -80,7 +80,7 @@ velocity all zero linear

 # only output atoms near vacancy

-compute coord all coord/atom $r
+compute coord all coord/atom cutoff $r

 #dump events all custom 1 dump.prd id type x y z
 #dump_modify events thresh c_coord != 4
--- a/examples/vashishta/InP.vashishta
+++ b/examples/vashishta/InP.vashishta
--- a/examples/vashishta/SiO.1990.vashishta
+++ b/examples/vashishta/SiO.1990.vashishta
--- a/lib/.gitignore
+++ b/lib/.gitignore
@ -1 +0,0 @@
-Makefile.lammps
--- a/lib/gpu/cudpp_mini/cudpp.h
+++ b/lib/gpu/cudpp_mini/cudpp.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // CUDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_globals.h
+++ b/lib/gpu/cudpp_mini/cudpp_globals.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_maximal_launch.h
+++ b/lib/gpu/cudpp_mini/cudpp_maximal_launch.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_plan.h
+++ b/lib/gpu/cudpp_mini/cudpp_plan.h
@ -2,7 +2,7 @@
 // CUDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
 // $Revision: 3572$
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Date$
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_plan_manager.h
+++ b/lib/gpu/cudpp_mini/cudpp_plan_manager.h
@ -2,7 +2,7 @@
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
 // $Revision: 3572$
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Date$
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_radixsort.h
+++ b/lib/gpu/cudpp_mini/cudpp_radixsort.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_scan.h
+++ b/lib/gpu/cudpp_mini/cudpp_scan.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_util.h
+++ b/lib/gpu/cudpp_mini/cudpp_util.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/sharedmem.h
+++ b/lib/gpu/cudpp_mini/sharedmem.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision: 5289 $
-// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
+// $Revision$
+// $Date$
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/kokkos/CHANGELOG.md
+++ b/lib/kokkos/CHANGELOG.md
@ -0,0 +1,284 @@
+# Change Log
+
+## [2.02.07](https://github.com/kokkos/kokkos/tree/2.02.07) (2016-12-16)
+[Full Changelog](https://github.com/kokkos/kokkos/compare/2.02.01...2.02.07)
+
+**Implemented enhancements:**
+
+- Add CMake option to enable Cuda Lambda support [\#589](https://github.com/kokkos/kokkos/issues/589)
+- Add CMake option to enable Cuda RDC support [\#588](https://github.com/kokkos/kokkos/issues/588)
+- Add Initial Intel Sky Lake Xeon-HPC Compiler Support to Kokkos Make System [\#584](https://github.com/kokkos/kokkos/issues/584)
+- Building Tutorial Examples  [\#582](https://github.com/kokkos/kokkos/issues/582)
+- Internal way for using ThreadVectorRange without TeamHandle  [\#574](https://github.com/kokkos/kokkos/issues/574)
+- Testing: Add testing for uvm and rdc [\#571](https://github.com/kokkos/kokkos/issues/571)
+- Profiling: Add Memory Tracing and Region Markers [\#557](https://github.com/kokkos/kokkos/issues/557)
+- nvcc\_wrapper not installed with Kokkos built with CUDA through CMake [\#543](https://github.com/kokkos/kokkos/issues/543)
+- Improve DynRankView debug check [\#541](https://github.com/kokkos/kokkos/issues/541)
+- Benchmarks: Add Gather benchmark [\#536](https://github.com/kokkos/kokkos/issues/536)
+- Testing: add spot\_check option to test\_all\_sandia [\#535](https://github.com/kokkos/kokkos/issues/535)
+- Deprecate Kokkos::Impl::VerifyExecutionCanAccessMemorySpace [\#527](https://github.com/kokkos/kokkos/issues/527)
+- Add AtomicAdd support for 64bit float for Pascal [\#522](https://github.com/kokkos/kokkos/issues/522)
+- Add Restrict and Aligned memory trait [\#517](https://github.com/kokkos/kokkos/issues/517)
+- Kokkos Tests are Not Run using Compiler Optimization [\#501](https://github.com/kokkos/kokkos/issues/501)
+- Add support for clang 3.7 w/ openmp backend [\#393](https://github.com/kokkos/kokkos/issues/393)
+- Provide an error throw class [\#79](https://github.com/kokkos/kokkos/issues/79)
+
+**Fixed bugs:**
+
+- Cuda UVM Allocation test broken with UVM as default space [\#586](https://github.com/kokkos/kokkos/issues/586)
+- Bug \(develop branch only\): multiple tests are now failing when forcing uvm usage. [\#570](https://github.com/kokkos/kokkos/issues/570)
+- Error in generate\_makefile.sh for Kokkos when Compiler is Empty String/Fails [\#568](https://github.com/kokkos/kokkos/issues/568)
+- XL 13.1.4 incorrect C++11 flag [\#553](https://github.com/kokkos/kokkos/issues/553)
+- Improve DynRankView debug check [\#541](https://github.com/kokkos/kokkos/issues/541)
+- Installing Library on MAC broken due to cp -u [\#539](https://github.com/kokkos/kokkos/issues/539)
+- Intel Nightly Testing with Debug enabled fails [\#534](https://github.com/kokkos/kokkos/issues/534)
+
+## [2.02.01](https://github.com/kokkos/kokkos/tree/2.02.01) (2016-11-01)
+[Full Changelog](https://github.com/kokkos/kokkos/compare/2.02.00...2.02.01)
+
+**Implemented enhancements:**
+
+- Add Changelog generation to our process. [\#506](https://github.com/kokkos/kokkos/issues/506)
+
+**Fixed bugs:**
+
+- Test scratch\_request fails in Serial with Debug enabled [\#520](https://github.com/kokkos/kokkos/issues/520)
+- Bug In BoundsCheck for DynRankView [\#516](https://github.com/kokkos/kokkos/issues/516)
+
+## [2.02.00](https://github.com/kokkos/kokkos/tree/2.02.00) (2016-10-30)
+[Full Changelog](https://github.com/kokkos/kokkos/compare/2.01.10...2.02.00)
+
+**Implemented enhancements:**
+
+- Add PowerPC assembly for grabbing clock register in memory pool [\#511](https://github.com/kokkos/kokkos/issues/511)
+- Add GCC 6.x support [\#508](https://github.com/kokkos/kokkos/issues/508)
+- Test install and build against installed library [\#498](https://github.com/kokkos/kokkos/issues/498)
+- Makefile.kokkos adds expt-extended-lambda to cuda build with clang [\#490](https://github.com/kokkos/kokkos/issues/490)
+- Add top-level makefile option to just test kokkos-core unit-test [\#485](https://github.com/kokkos/kokkos/issues/485)
+- Split and harmonize Object Files of Core UnitTests to increase build parallelism [\#484](https://github.com/kokkos/kokkos/issues/484)
+- LayoutLeft to LayoutLeft subview for 3D and 4D views [\#473](https://github.com/kokkos/kokkos/issues/473)
+- Add official Cuda 8.0 support [\#468](https://github.com/kokkos/kokkos/issues/468)
+- Allow C++1Z Flag for Class Lambda capture [\#465](https://github.com/kokkos/kokkos/issues/465)
+- Add Clang 4.0+ compilation of Cuda code [\#455](https://github.com/kokkos/kokkos/issues/455)
+- Possible Issue with Intel 17.0.098 and GCC 6.1.0 in Develop Branch [\#445](https://github.com/kokkos/kokkos/issues/445)
+- Add name of view to "View bounds error" [\#432](https://github.com/kokkos/kokkos/issues/432)
+- Move Sort Binning Operators into Kokkos namespace [\#421](https://github.com/kokkos/kokkos/issues/421)
+- TaskPolicy - generate error when attempt to use uninitialized  [\#396](https://github.com/kokkos/kokkos/issues/396)
+- Import WithoutInitializing and AllowPadding into Kokkos namespace [\#325](https://github.com/kokkos/kokkos/issues/325)
+- TeamThreadRange requires begin, end to be the same type [\#305](https://github.com/kokkos/kokkos/issues/305)
+- CudaUVMSpace should track \# allocations, due to CUDA limit on \# UVM allocations [\#300](https://github.com/kokkos/kokkos/issues/300)
+- Remove old View and its infrastructure [\#259](https://github.com/kokkos/kokkos/issues/259)
+
+**Fixed bugs:**
+
+- Bug in TestCuda\_Other.cpp: most likely assembly inserted into Device code [\#515](https://github.com/kokkos/kokkos/issues/515)
+- Cuda Compute Capability check of GPU is outdated [\#509](https://github.com/kokkos/kokkos/issues/509)
+- multi\_scratch test with hwloc and pthreads seg-faults.  [\#504](https://github.com/kokkos/kokkos/issues/504)
+- generate\_makefile.bash: "make install" is broken [\#503](https://github.com/kokkos/kokkos/issues/503)
+- make clean in Out of Source Build/Tests Does Not Work Correctly [\#502](https://github.com/kokkos/kokkos/issues/502)
+- Makefiles for test and examples have issues in Cuda when CXX is not explicitly specified [\#497](https://github.com/kokkos/kokkos/issues/497)
+- Dispatch lambda test directly inside GTEST macro doesn't work with nvcc [\#491](https://github.com/kokkos/kokkos/issues/491)
+- UnitTests with HWLOC enabled fail if run with mpirun bound to a single core [\#489](https://github.com/kokkos/kokkos/issues/489)
+- Failing Reducer Test on Mac with Pthreads [\#479](https://github.com/kokkos/kokkos/issues/479)
+- make test Dumps Error with Clang Not Found [\#471](https://github.com/kokkos/kokkos/issues/471)
+- OpenMP TeamPolicy member broadcast not using correct volatile shared variable [\#424](https://github.com/kokkos/kokkos/issues/424)
+- TaskPolicy - generate error when attempt to use uninitialized  [\#396](https://github.com/kokkos/kokkos/issues/396)
+- New task policy implementation is pulling in old experimental code. [\#372](https://github.com/kokkos/kokkos/issues/372)
+- MemoryPool unit test hangs on Power8 with GCC 6.1.0 [\#298](https://github.com/kokkos/kokkos/issues/298)
+
+## [2.01.10](https://github.com/kokkos/kokkos/tree/2.01.10) (2016-09-27)
+[Full Changelog](https://github.com/kokkos/kokkos/compare/2.01.06...2.01.10)
+
+**Implemented enhancements:**
+
+- Enable Profiling by default in Tribits build [\#438](https://github.com/kokkos/kokkos/issues/438)
+- parallel\_reduce\(0\), parallel\_scan\(0\) unit tests [\#436](https://github.com/kokkos/kokkos/issues/436)
+- data\(\)==NULL after realloc with LayoutStride [\#351](https://github.com/kokkos/kokkos/issues/351)
+- Fix tutorials to track new Kokkos::View [\#323](https://github.com/kokkos/kokkos/issues/323)
+- Rename team policy set\_scratch\_size. [\#195](https://github.com/kokkos/kokkos/issues/195)
+
+**Fixed bugs:**
+
+- Possible Issue with Intel 17.0.098 and GCC 6.1.0 in Develop Branch [\#445](https://github.com/kokkos/kokkos/issues/445)
+- Makefile spits syntax error [\#435](https://github.com/kokkos/kokkos/issues/435)
+- Kokkos::sort fails for view with all the same values [\#422](https://github.com/kokkos/kokkos/issues/422)
+- Generic Reducers: can't accept inline constructed reducer [\#404](https://github.com/kokkos/kokkos/issues/404)
+- data\\(\\)==NULL after realloc with LayoutStride [\#351](https://github.com/kokkos/kokkos/issues/351)
+- const subview of const view with compile time dimensions on Cuda backend [\#310](https://github.com/kokkos/kokkos/issues/310)
+- Kokkos \(in Trilinos\) Causes Internal Compiler Error on CUDA 8.0.21-EA on POWER8 [\#307](https://github.com/kokkos/kokkos/issues/307)
+- Core Oversubscription Detection Broken? [\#159](https://github.com/kokkos/kokkos/issues/159)
+
+
+## [2.01.06](https://github.com/kokkos/kokkos/tree/2.01.06) (2016-09-02)
+[Full Changelog](https://github.com/kokkos/kokkos/compare/2.01.00...2.01.06)
+
+**Implemented enhancements:**
+
+- Add "standard" reducers for lambda-supportable customized reduce [\#411](https://github.com/kokkos/kokkos/issues/411)
+- TaskPolicy - single thread back-end execution [\#390](https://github.com/kokkos/kokkos/issues/390)
+- Kokkos master clone tag [\#387](https://github.com/kokkos/kokkos/issues/387)
+- Query memory requirements from task policy [\#378](https://github.com/kokkos/kokkos/issues/378)
+- Output order of test\_atomic.cpp is confusing [\#373](https://github.com/kokkos/kokkos/issues/373)
+- Missing testing for atomics [\#341](https://github.com/kokkos/kokkos/issues/341)
+- Feature request for Kokkos to provide Kokkos::atomic\_fetch\_max and atomic\_fetch\_min [\#336](https://github.com/kokkos/kokkos/issues/336)
+- TaskPolicy\<Cuda\> performance requires teams mapped to warps [\#218](https://github.com/kokkos/kokkos/issues/218)
+
+**Fixed bugs:**
+
+- Reduce with Teams broken for custom initialize [\#407](https://github.com/kokkos/kokkos/issues/407)
+- Failing Kokkos build on Debian [\#402](https://github.com/kokkos/kokkos/issues/402)
+- Failing Tests on NVIDIA Pascal GPUs [\#398](https://github.com/kokkos/kokkos/issues/398)
+- Algorithms: fill\_random assumes dimensions fit in unsigned int [\#389](https://github.com/kokkos/kokkos/issues/389)
+- Kokkos::subview with RandomAccess Memory Trait [\#385](https://github.com/kokkos/kokkos/issues/385)
+- Build warning \(signed / unsigned comparison\) in Cuda implementation [\#365](https://github.com/kokkos/kokkos/issues/365)
+- wrong results for a parallel\_reduce with CUDA8 / Maxwell50 [\#352](https://github.com/kokkos/kokkos/issues/352)
+- Hierarchical parallelism - 3 level unit test [\#344](https://github.com/kokkos/kokkos/issues/344)
+- Can I allocate a View w/ both WithoutInitializing & AllowPadding? [\#324](https://github.com/kokkos/kokkos/issues/324)
+- subview View layout determination [\#309](https://github.com/kokkos/kokkos/issues/309)
+- Unit tests with Cuda - Maxwell [\#196](https://github.com/kokkos/kokkos/issues/196)
+
+## [2.01.00](https://github.com/kokkos/kokkos/tree/2.01.00) (2016-07-21)
+[Full Changelog](https://github.com/kokkos/kokkos/compare/End_C++98...2.01.00)
+
+**Implemented enhancements:**
+
+- Edit ViewMapping so assigning Views with the same custom layout compiles when const casting [\#327](https://github.com/kokkos/kokkos/issues/327)
+- DynRankView: Performance improvement for operator\(\) [\#321](https://github.com/kokkos/kokkos/issues/321)
+- Interoperability between static and dynamic rank views [\#295](https://github.com/kokkos/kokkos/issues/295)
+- subview member function ? [\#280](https://github.com/kokkos/kokkos/issues/280)
+- Inter-operatibility between View and DynRankView. [\#245](https://github.com/kokkos/kokkos/issues/245)
+- \(Trilinos\) build warning in atomic\_assign, with Kokkos::complex [\#177](https://github.com/kokkos/kokkos/issues/177)
+- View\<\>::shmem\_size should runtime check for number of arguments equal to rank [\#176](https://github.com/kokkos/kokkos/issues/176)
+- Custom reduction join via lambda argument [\#99](https://github.com/kokkos/kokkos/issues/99)
+- DynRankView with 0 dimensions passed in at construction [\#293](https://github.com/kokkos/kokkos/issues/293)
+- Inject view\_alloc and friends into Kokkos namespace [\#292](https://github.com/kokkos/kokkos/issues/292)
+- Less restrictive TeamPolicy reduction on Cuda [\#286](https://github.com/kokkos/kokkos/issues/286)
+- deep\_copy using remap with source execution space [\#267](https://github.com/kokkos/kokkos/issues/267)
+- Suggestion:  Enable opt-in L1 caching via nvcc-wrapper [\#261](https://github.com/kokkos/kokkos/issues/261)
+- More flexible create\_mirror functions [\#260](https://github.com/kokkos/kokkos/issues/260)
+- Rename View::memory\_span to View::required\_allocation\_size [\#256](https://github.com/kokkos/kokkos/issues/256)
+- Use of subviews and views with compile-time dimensions [\#237](https://github.com/kokkos/kokkos/issues/237)
+- Use of subviews and views with compile-time dimensions [\#237](https://github.com/kokkos/kokkos/issues/237)
+- Kokkos::Timer [\#234](https://github.com/kokkos/kokkos/issues/234)
+- Fence CudaUVMSpace allocations [\#230](https://github.com/kokkos/kokkos/issues/230)
+- View::operator\(\) accept std::is\_integral and std::is\_enum [\#227](https://github.com/kokkos/kokkos/issues/227)
+- Allocating zero size View [\#216](https://github.com/kokkos/kokkos/issues/216)
+- Thread scalable memory pool [\#212](https://github.com/kokkos/kokkos/issues/212)
+- Add a way to disable memory leak output [\#194](https://github.com/kokkos/kokkos/issues/194)
+- Kokkos exec space init should init Kokkos profiling [\#192](https://github.com/kokkos/kokkos/issues/192)
+- Runtime rank wrapper for View [\#189](https://github.com/kokkos/kokkos/issues/189)
+- Profiling Interface [\#158](https://github.com/kokkos/kokkos/issues/158)
+- Fix View assignment \(of managed to unmanaged\) [\#153](https://github.com/kokkos/kokkos/issues/153)
+- Add unit test for assignment of managed View to unmanaged View [\#152](https://github.com/kokkos/kokkos/issues/152)
+- Check for oversubscription of threads with MPI in Kokkos::initialize [\#149](https://github.com/kokkos/kokkos/issues/149)
+- Dynamic resizeable 1dimensional view [\#143](https://github.com/kokkos/kokkos/issues/143)
+- Develop TaskPolicy for CUDA [\#142](https://github.com/kokkos/kokkos/issues/142)
+- New View : Test Compilation Downstream [\#138](https://github.com/kokkos/kokkos/issues/138)
+- New View Implementation [\#135](https://github.com/kokkos/kokkos/issues/135)
+- Add variant of subview that lets users add traits [\#134](https://github.com/kokkos/kokkos/issues/134)
+- NVCC-WRAPPER: Add --host-only flag [\#121](https://github.com/kokkos/kokkos/issues/121)
+- Address gtest issue with TriBITS Kokkos build outside of Trilinos [\#117](https://github.com/kokkos/kokkos/issues/117)
+- Make tests pass with -expt-extended-lambda on CUDA [\#108](https://github.com/kokkos/kokkos/issues/108)
+- Dynamic scheduling for parallel\_for and parallel\_reduce [\#106](https://github.com/kokkos/kokkos/issues/106)
+- Runtime or compile time error when reduce functor's join is not properly specified as const member function or with volatile arguments [\#105](https://github.com/kokkos/kokkos/issues/105)
+- Error out when the number of threads is modified after kokkos is initialized [\#104](https://github.com/kokkos/kokkos/issues/104)
+- Porting to POWER and remove assumption of X86 default [\#103](https://github.com/kokkos/kokkos/issues/103)
+- Dynamic scheduling option for RangePolicy [\#100](https://github.com/kokkos/kokkos/issues/100)
+- SharedMemory Support for Lambdas [\#81](https://github.com/kokkos/kokkos/issues/81)
+- Recommended TeamSize for Lambdas [\#80](https://github.com/kokkos/kokkos/issues/80)
+- Add Aggressive Vectorization Compilation mode [\#72](https://github.com/kokkos/kokkos/issues/72)
+- Dynamic scheduling team execution policy [\#53](https://github.com/kokkos/kokkos/issues/53)
+- UVM allocations in multi-GPU systems [\#50](https://github.com/kokkos/kokkos/issues/50)
+- Synchronic in Kokkos::Impl [\#44](https://github.com/kokkos/kokkos/issues/44)
+- index and dimension types in for loops [\#28](https://github.com/kokkos/kokkos/issues/28)
+- Subview assign of 1D Strided with stride 1 to LayoutLeft/Right [\#1](https://github.com/kokkos/kokkos/issues/1)
+
+**Fixed bugs:**
+
+- misspelled variable name in Kokkos\_Atomic\_Fetch + missing unit tests [\#340](https://github.com/kokkos/kokkos/issues/340)
+- seg fault Kokkos::Impl::CudaInternal::print\_configuration [\#338](https://github.com/kokkos/kokkos/issues/338)
+- Clang compiler error with named parallel\_reduce, tags, and TeamPolicy. [\#335](https://github.com/kokkos/kokkos/issues/335)
+- Shared Memory Allocation Error at parallel\_reduce [\#311](https://github.com/kokkos/kokkos/issues/311)
+- DynRankView: Fix resize and realloc [\#303](https://github.com/kokkos/kokkos/issues/303)
+- Scratch memory and dynamic scheduling [\#279](https://github.com/kokkos/kokkos/issues/279)
+- MemoryPool infinite loop when out of memory [\#312](https://github.com/kokkos/kokkos/issues/312)
+- Kokkos DynRankView changes break Sacado and Panzer [\#299](https://github.com/kokkos/kokkos/issues/299)
+- MemoryPool fails to compile on non-cuda non-x86 [\#297](https://github.com/kokkos/kokkos/issues/297)
+- Random Number Generator Fix [\#296](https://github.com/kokkos/kokkos/issues/296)
+- View template parameter ordering Bug [\#282](https://github.com/kokkos/kokkos/issues/282)
+- Serial task policy broken. [\#281](https://github.com/kokkos/kokkos/issues/281)
+- deep\_copy with LayoutStride should not memcpy [\#262](https://github.com/kokkos/kokkos/issues/262)
+- DualView::need\_sync should be a const method [\#248](https://github.com/kokkos/kokkos/issues/248)
+- Arbitrary-sized atomics on GPUs broken; loop forever [\#238](https://github.com/kokkos/kokkos/issues/238)
+- boolean reduction value\_type changes answer [\#225](https://github.com/kokkos/kokkos/issues/225)
+- Custom init\(\) function for parallel\_reduce with array value\_type [\#210](https://github.com/kokkos/kokkos/issues/210)
+- unit\_test Makefile is Broken - Recursively Calls itself until Machine Apocalypse. [\#202](https://github.com/kokkos/kokkos/issues/202)
+- nvcc\_wrapper Does Not Support  -Xcompiler \<compiler option\> [\#198](https://github.com/kokkos/kokkos/issues/198)
+- Kokkos exec space init should init Kokkos profiling [\#192](https://github.com/kokkos/kokkos/issues/192)
+- Kokkos Threads Backend impl\_shared\_alloc Broken on Intel 16.1 \(Shepard Haswell\) [\#186](https://github.com/kokkos/kokkos/issues/186)
+- pthread back end hangs if used uninitialized [\#182](https://github.com/kokkos/kokkos/issues/182)
+- parallel\_reduce of size 0, not calling init/join [\#175](https://github.com/kokkos/kokkos/issues/175)
+- Bug in Threads with OpenMP enabled [\#173](https://github.com/kokkos/kokkos/issues/173)
+- KokkosExp\_SharedAlloc, m\_team\_work\_index inaccessible [\#166](https://github.com/kokkos/kokkos/issues/166)
+- 128-bit CAS without Assembly Broken? [\#161](https://github.com/kokkos/kokkos/issues/161)
+- fatal error: Cuda/Kokkos\_Cuda\_abort.hpp: No such file or directory [\#157](https://github.com/kokkos/kokkos/issues/157)
+- Power8: Fix OpenMP backend [\#139](https://github.com/kokkos/kokkos/issues/139)
+- Data race in Kokkos OpenMP initialization [\#131](https://github.com/kokkos/kokkos/issues/131)
+- parallel\_launch\_local\_memory and cuda 7.5 [\#125](https://github.com/kokkos/kokkos/issues/125)
+- Resize can fail with Cuda due to asynchronous dispatch [\#119](https://github.com/kokkos/kokkos/issues/119)
+- Qthread taskpolicy initialization bug. [\#92](https://github.com/kokkos/kokkos/issues/92)
+- Windows: sys/mman.h [\#89](https://github.com/kokkos/kokkos/issues/89)
+- Windows: atomic\_fetch\_sub\(\) [\#88](https://github.com/kokkos/kokkos/issues/88)
+- Windows: snprintf [\#87](https://github.com/kokkos/kokkos/issues/87)
+- Parallel\_Reduce with TeamPolicy and league size of 0 returns garbage [\#85](https://github.com/kokkos/kokkos/issues/85)
+- Throw with Cuda when using \(2D\) team\_policy parallel\_reduce with less than a warp size [\#76](https://github.com/kokkos/kokkos/issues/76)
+- Scalar views don't work with Kokkos::Atomic memory trait [\#69](https://github.com/kokkos/kokkos/issues/69)
+- Reduce the number of threads per team for Cuda [\#63](https://github.com/kokkos/kokkos/issues/63)
+- Named Kernels fail for reductions with CUDA [\#60](https://github.com/kokkos/kokkos/issues/60)
+- Kokkos View dimension\_\(\) for long returning unsigned int [\#20](https://github.com/kokkos/kokkos/issues/20)
+- atomic test hangs with LLVM [\#6](https://github.com/kokkos/kokkos/issues/6)
+- OpenMP Test should set omp\_set\_num\_threads to 1 [\#4](https://github.com/kokkos/kokkos/issues/4)
+
+**Closed issues:**
+
+- develop branch broken with CUDA 8 and --expt-extended-lambda  [\#354](https://github.com/kokkos/kokkos/issues/354)
+- --arch=KNL with Intel 2016 build failure [\#349](https://github.com/kokkos/kokkos/issues/349)
+- Error building with Cuda when passing -DKOKKOS\_CUDA\_USE\_LAMBDA to generate\_makefile.bash [\#343](https://github.com/kokkos/kokkos/issues/343)
+- Can I safely use int indices in a 2-D View with capacity \> 2B? [\#318](https://github.com/kokkos/kokkos/issues/318)
+- Kokkos::ViewAllocateWithoutInitializing is not working [\#317](https://github.com/kokkos/kokkos/issues/317)
+- Intel build on Mac OS X [\#277](https://github.com/kokkos/kokkos/issues/277)
+- deleted [\#271](https://github.com/kokkos/kokkos/issues/271)
+- Broken Mira build [\#268](https://github.com/kokkos/kokkos/issues/268)
+- 32-bit build [\#246](https://github.com/kokkos/kokkos/issues/246)
+- parallel\_reduce with RDC crashes linker [\#232](https://github.com/kokkos/kokkos/issues/232)
+- build of Kokkos\_Sparse\_MV\_impl\_spmv\_Serial.cpp.o fails if you use nvcc and have cuda disabled [\#209](https://github.com/kokkos/kokkos/issues/209)
+- Kokkos Serial execution space is not tested with TeamPolicy. [\#207](https://github.com/kokkos/kokkos/issues/207)
+- Unit test failure on Hansen  KokkosCore\_UnitTest\_Cuda\_MPI\_1 [\#200](https://github.com/kokkos/kokkos/issues/200)
+- nvcc compiler warning: calling a \_\_host\_\_ function from a \_\_host\_\_ \_\_device\_\_ function is not allowed [\#180](https://github.com/kokkos/kokkos/issues/180)
+- Intel 15 build error with defaulted "move" operators [\#171](https://github.com/kokkos/kokkos/issues/171)
+- missing libkokkos.a during Trilinos 12.4.2 build, yet other libkokkos\*.a libs are there [\#165](https://github.com/kokkos/kokkos/issues/165)
+- Tie atomic updates to execution space or even to thread team? \(speculation\) [\#144](https://github.com/kokkos/kokkos/issues/144)
+- New View: Compiletime/size Test [\#137](https://github.com/kokkos/kokkos/issues/137)
+- New View : Performance Test [\#136](https://github.com/kokkos/kokkos/issues/136)
+- Signed/unsigned  comparison warning in CUDA parallel [\#130](https://github.com/kokkos/kokkos/issues/130)
+- Kokkos::complex: Need op\* w/ std::complex & real [\#126](https://github.com/kokkos/kokkos/issues/126)
+- Use uintptr\_t for casting pointers [\#110](https://github.com/kokkos/kokkos/issues/110)
+- Default thread mapping behavior between P and Q threads. [\#91](https://github.com/kokkos/kokkos/issues/91)
+- Windows: Atomic\_Fetch\_Exchange\(\) return type [\#90](https://github.com/kokkos/kokkos/issues/90)
+- Synchronic unit test is way too long [\#84](https://github.com/kokkos/kokkos/issues/84)
+- nvcc\_wrapper -\> $\(NVCC\_WRAPPER\) [\#42](https://github.com/kokkos/kokkos/issues/42)
+- Check compiler version and print helpful message [\#39](https://github.com/kokkos/kokkos/issues/39)
+- Kokkos shared memory on Cuda uses a lot of registers [\#31](https://github.com/kokkos/kokkos/issues/31)
+- Can not pass unit test `cuda.space` without a GT 720 [\#25](https://github.com/kokkos/kokkos/issues/25)
+- Makefile.kokkos lacks bounds checking option that CMake has [\#24](https://github.com/kokkos/kokkos/issues/24)
+- Kokkos can not complete unit tests with CUDA UVM enabled [\#23](https://github.com/kokkos/kokkos/issues/23)
+- Simplify teams + shared memory histogram example to remove vectorization [\#21](https://github.com/kokkos/kokkos/issues/21)
+- Kokkos needs to rever to ${PROJECT\_NAME}\_ENABLE\_CXX11 not Trilinos\_ENABLE\_CXX11 [\#17](https://github.com/kokkos/kokkos/issues/17)
+- Kokkos Base Makefile adds AVX to KNC Build [\#16](https://github.com/kokkos/kokkos/issues/16)
+- MS Visual Studio 2013 Build Errors [\#9](https://github.com/kokkos/kokkos/issues/9)
+- subview\(X, ALL\(\), j\) for 2-D LayoutRight View X: should it view a column? [\#5](https://github.com/kokkos/kokkos/issues/5)
+
+## [End_C++98](https://github.com/kokkos/kokkos/tree/End_C++98) (2015-04-15)
+
+
+\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*
--- a/lib/kokkos/CMakeLists.txt
+++ b/lib/kokkos/CMakeLists.txt
@ -34,8 +34,8 @@ TRIBITS_PACKAGE_DECL(Kokkos) # ENABLE_SHADOWING_WARNINGS)
 # for compatibility with Kokkos' Makefile build system.

 TRIBITS_ADD_OPTION_AND_DEFINE(
-  ${PACKAGE_NAME}_ENABLE_DEBUG
-  ${PACKAGE_NAME_UC}_HAVE_DEBUG
+  Kokkos_ENABLE_DEBUG
+  KOKKOS_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}
 )
@ -57,7 +57,21 @@ TRIBITS_ADD_OPTION_AND_DEFINE(
 TRIBITS_ADD_OPTION_AND_DEFINE(
  Kokkos_ENABLE_Cuda_UVM
  KOKKOS_USE_CUDA_UVM
-  "Enable CUDA Unified Virtual Memory support in Kokkos."
+  "Enable CUDA Unified Virtual Memory as the default in Kokkos."
+  OFF
+  )
+
+TRIBITS_ADD_OPTION_AND_DEFINE(
+  Kokkos_ENABLE_Cuda_RDC
+  KOKKOS_HAVE_CUDA_RDC
+  "Enable CUDA Relocatable Device Code support in Kokkos."
+  OFF
+  )
+
+TRIBITS_ADD_OPTION_AND_DEFINE(
+  Kokkos_ENABLE_Cuda_Lambda
+  KOKKOS_HAVE_CUDA_LAMBDA
+  "Enable CUDA LAMBDA support in Kokkos."
  OFF
  )

@ -72,6 +86,9 @@ ASSERT_DEFINED(TPL_ENABLE_Pthread)
 IF (Kokkos_ENABLE_Pthread AND NOT TPL_ENABLE_Pthread)
  MESSAGE(FATAL_ERROR "You set Kokkos_ENABLE_Pthread=ON, but Trilinos' support for Pthread(s) is not enabled (TPL_ENABLE_Pthread=OFF).  This is not allowed.  Please enable Pthreads in Trilinos before attempting to enable Kokkos' support for Pthreads.")
 ENDIF ()
+IF (NOT TPL_ENABLE_Pthread)
+  ADD_DEFINITIONS(-DGTEST_HAS_PTHREAD=0)
+ENDIF()

 TRIBITS_ADD_OPTION_AND_DEFINE(
  Kokkos_ENABLE_OpenMP
@ -162,13 +179,28 @@ TRIBITS_ADD_OPTION_AND_DEFINE(

 #------------------------------------------------------------------------------
 #
-# C) Process the subpackages for Kokkos
+# C) Install Kokkos' executable scripts
+#
+
+
+# nvcc_wrapper is Kokkos' wrapper for NVIDIA's NVCC CUDA compiler.
+# Kokkos needs nvcc_wrapper in order to build.  Other libraries and
+# executables also need nvcc_wrapper.  Thus, we need to install it.
+# If the argument of DESTINATION is a relative path, CMake computes it
+# as relative to ${CMAKE_INSTALL_PATH}.
+
+INSTALL(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/bin/nvcc_wrapper DESTINATION bin)
+
+
+#------------------------------------------------------------------------------
+#
+# D) Process the subpackages for Kokkos
 #

 TRIBITS_PROCESS_SUBPACKAGES()

 #
-# D) If Kokkos itself is enabled, process the Kokkos package
+# E) If Kokkos itself is enabled, process the Kokkos package
 #

 TRIBITS_PACKAGE_DEF()
--- a/Show More
+++ b/Show More