patch 21Feb17 sync with GHub

Merge pull request #385 from akohlmey/collected-small-bugfixes
collected small bugfixes and updates
2017-02-21 16:07:26 -07:00 · 2017-02-21 15:59:06 -07:00 · 2017-02-21 15:57:23 -07:00 · 2017-02-21 15:57:03 -07:00 · 2017-02-21 15:52:10 -07:00 · 2017-02-21 15:51:35 -07:00
508 changed files with 36487 additions and 33589 deletions
--- 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/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="17 Jan 2017 version">
+<META NAME="docnumber" CONTENT="21 Feb 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
-17 Jan 2017 version :c,h4
+21 Feb 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,
@ -967,7 +969,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lubricateU/poly"_pair_lubricateU.html,
 "meam"_pair_meam.html,
 "mie/cut (o)"_pair_mie.html,
-"morse (got)"_pair_morse.html,
+"morse (gkot)"_pair_morse.html,
 "nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
 "nm/cut (o)"_pair_nm.html,
 "nm/cut/coul/cut (o)"_pair_nm.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,
@ -1069,7 +1076,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "none"_bond_none.html,
 "zero"_bond_zero.html,
 "hybrid"_bond_hybrid.html,
-"class2 (o)"_bond_class2.html,
+"class2 (ko)"_bond_class2.html,
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
 "harmonic (ko)"_bond_harmonic.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

@ -1101,7 +1109,7 @@ USER-OMP, t = OPT.
 "zero"_angle_zero.html,
 "hybrid"_angle_hybrid.html,
 "charmm (ko)"_angle_charmm.html,
-"class2 (o)"_angle_class2.html,
+"class2 (ko)"_angle_class2.html,
 "cosine (o)"_angle_cosine.html,
 "cosine/delta (o)"_angle_cosine_delta.html,
 "cosine/periodic (o)"_angle_cosine_periodic.html,
@ -1137,7 +1145,7 @@ USER-OMP, t = OPT.
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
 "charmm (ko)"_dihedral_charmm.html,
-"class2 (o)"_dihedral_class2.html,
+"class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
 "helix (o)"_dihedral_helix.html,
 "multi/harmonic (o)"_dihedral_multi_harmonic.html,
@ -1169,7 +1177,7 @@ USER-OMP, t = OPT.
 "none"_improper_none.html,
 "zero"_improper_zero.html,
 "hybrid"_improper_hybrid.html,
-"class2 (o)"_improper_class2.html,
+"class2 (ko)"_improper_class2.html,
 "cvff (io)"_improper_cvff.html,
 "harmonic (ko)"_improper_harmonic.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@ -22,7 +22,7 @@ either conceptually, or as printed out by the program.

 12.1 Common problems :link(err_1),h4

-If two LAMMPS runs do not produce the same answer on different
+If two LAMMPS runs do not produce the exact same answer on different
 machines or different numbers of processors, this is typically not a
 bug.  In theory you should get identical answers on any number of
 processors and on any machine.  In practice, numerical round-off can
@ -80,12 +80,24 @@ order.  If you mess this up, LAMMPS will often flag the error, but it
 may also simply read a bogus argument and assign a value that is
 valid, but not what you wanted.  E.g. trying to read the string "abc"
 as an integer value of 0.  Careful reading of the associated doc page
-for the command should allow you to fix these problems.  Note that
-some commands allow for variables to be specified in place of numeric
-constants so that the value can be evaluated and change over the
-course of a run.  This is typically done with the syntax {v_name} for
-a parameter, where name is the name of the variable.  This is only
-allowed if the command documentation says it is.
+for the command should allow you to fix these problems. In most cases,
+where LAMMPS expects to read a number, either integer or floating point,
+it performs a stringent test on whether the provided input actually
+is an integer or floating-point number, respectively, and reject the
+input with an error message (for instance, when an integer is required,
+but a floating-point number 1.0 is provided):
+
+ERROR: Expected integer parameter in input script or data file :pre
+
+Some commands allow for using variable references in place of numeric
+constants so that the value can be evaluated and may change over the
+course of a run.  This is typically done with the syntax {v_name} for a
+parameter, where name is the name of the variable. On the other hand,
+immediate variable expansion with the syntax ${name} is performed while
+reading the input and before parsing commands,
+
+NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
+the documentation of the corresponding command explicitly says it is.

 Generally, LAMMPS will print a message to the screen and logfile and
 exit gracefully when it encounters a fatal error.  Sometimes it will
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -2573,7 +2573,7 @@ well.
 6.26 Adiabatic core/shell model :link(howto_26),h4

 The adiabatic core-shell model by "Mitchell and
-Finchham"_#MitchellFinchham is a simple method for adding
+Fincham"_#MitchellFincham is a simple method for adding
 polarizability to a system.  In order to mimic the electron shell of
 an ion, a satellite particle is attached to it. This way the ions are
 split into a core and a shell where the latter is meant to react to
@ -2667,13 +2667,16 @@ bond_coeff      1 63.014 0.0
 bond_coeff      2 25.724 0.0 :pre

 When running dynamics with the adiabatic core/shell model, the
-following issues should be considered.  Since the relative motion of
-the core and shell particles corresponds to the polarization, typical
-thermostats can alter the polarization behaviour, meaning the shell
-will not react freely to its electrostatic environment.  This is
-critical during the equilibration of the system. Therefore
-it's typically desirable to decouple the relative motion of the
-core/shell pair, which is an imaginary degree of freedom, from the
+following issues should be considered.  The relative motion of
+the core and shell particles corresponds to the polarization, 
+hereby an instantaneous relaxation of the shells is approximated 
+and a fast core/shell spring frequency ensures a nearly constant
+internal kinetic energy during the simulation. 
+Thermostats can alter this polarization behaviour, by scaling the
+internal kinetic energy, meaning the shell will not react freely to 
+its electrostatic environment. 
+Therefore it is typically desirable to decouple the relative motion of 
+the core/shell pair, which is an imaginary degree of freedom, from the
 real physical system.  To do that, the "compute
 temp/cs"_compute_temp_cs.html command can be used, in conjunction with
 any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
@ -2704,6 +2707,22 @@ fix thermostatequ all nve                               # integrator as needed f
 fix_modify thermoberendsen temp CSequ
 thermo_modify temp CSequ                                # output of center-of-mass derived temperature :pre

+The pressure for the core/shell system is computed via the regular 
+LAMMPS convention by "treating the cores and shells as individual 
+particles"_#MitchellFincham2. For the thermo output of the pressure 
+as well as for the application of a barostat, it is necessary to 
+use an additional "pressure"_compute_pressure compute based on the 
+default "temperature"_compute_temp and specifying it as a second 
+argument in "fix modify"_fix_modify.html and 
+"thermo_modify"_thermo_modify.html resulting in:
+
+(...)
+compute CSequ all temp/cs cores shells
+compute thermo_press_lmp all pressure thermo_temp       # pressure for individual particles
+thermo_modify temp CSequ press thermo_press_lmp         # modify thermo to regular pressure
+fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
+fix_modify press_bar temp CSequ press thermo_press_lmp  # pressure modification for correct kinetic scalar :pre
+
 If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
 relative motion of the core and the shell should in theory be
 stable.  However numerical fluctuation can introduce a small
@ -2724,24 +2743,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
 velocity all create 1427 134 bias yes temp CSequ
 velocity all scale 1427 temp CSequ :pre

-It is important to note that the polarizability of the core/shell
-pairs is based on their relative motion. Therefore the choice of
-spring force and mass ratio need to ensure much faster relative motion
-of the 2 atoms within the core/shell pair than their center-of-mass
-velocity. This allow the shells to effectively react instantaneously
-to the electrostatic environment.  This fast movement also limits the
-timestep size that can be used.
+To maintain the correct polarizability of the core/shell pairs, the 
+kinetic energy of the internal motion shall remain nearly constant. 
+Therefore the choice of spring force and mass ratio need to ensure 
+much faster relative motion of the 2 atoms within the core/shell pair 
+than their center-of-mass velocity. This allows the shells to 
+effectively react instantaneously to the electrostatic environment and 
+limits energy transfer to or from the core/shell oscillators.
+This fast movement also dictates the timestep that can be used.

 The primary literature of the adiabatic core/shell model suggests that
 the fast relative motion of the core/shell pairs only allows negligible
-energy transfer to the environment. Therefore it is not intended to
-decouple the core/shell degree of freedom from the physical system
-during production runs. In other words, the "compute
-temp/cs"_compute_temp_cs.html command should not be used during
-production runs and is only required during equilibration. This way one
-is consistent with literature (based on the code packages DL_POLY or
-GULP for instance).
-
+energy transfer to the environment. 
 The mentioned energy transfer will typically lead to a small drift
 in total energy over time.  This internal energy can be monitored
 using the "compute chunk/atom"_compute_chunk_atom.html and "compute
@ -2761,14 +2774,20 @@ command, to use as input to the "compute
 chunk/atom"_compute_chunk_atom.html command to define the core/shell
 pairs as chunks.

-For example,
+For example if core/shell pairs are the only molecules:
+
+read_data NaCl_CS_x0.1_prop.data 
+compute prop all property/atom molecule
+compute cs_chunk all chunk/atom c_prop
+compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
+fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
+
+For example if core/shell pairs and other molecules are present:

 fix csinfo all property/atom i_CSID                       # property/atom command
 read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info  # atom property added in the data-file
 compute prop all property/atom i_CSID
-compute cs_chunk all chunk/atom c_prop
-compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
-fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
+(...) :pre

 The additional section in the date file would be formatted like this:

@ -2890,9 +2909,13 @@ Phys, 79, 926 (1983).
 :link(Shinoda)
 [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

-:link(MitchellFinchham)
-[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
+:link(MitchellFincham)
+[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter,
 5, 1031-1038 (1993).

+:link(MitchellFincham2)
+[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
+6, 393-404 (1994).
+
 :link(howto-Lamoureux)
 [(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
--- 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, -, -
@ -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
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -413,7 +413,7 @@ uses (for performing 1d FFTs) when running the particle-particle
 particle-mesh (PPPM) option for long-range Coulombics via the
 "kspace_style"_kspace_style.html command.

-LAMMPS supports various open-source or vendor-supplied FFT libraries
+LAMMPS supports common open-source or vendor-supplied FFT libraries
 for this purpose.  If you leave these 3 variables blank, LAMMPS will
 use the open-source "KISS FFT library"_http://kissfft.sf.net, which is
 included in the LAMMPS distribution.  This library is portable to all
@ -423,10 +423,9 @@ package in your build, you can also leave the 3 variables blank.

 Otherwise, select which kinds of FFTs to use as part of the FFT_INC
 setting by a switch of the form -DFFT_XXX.  Recommended values for XXX
-are: MKL, SCSL, FFTW2, and FFTW3.  Legacy options are: INTEL, SGI,
-ACML, and T3E.  For backward compatability, using -DFFT_FFTW will use
-the FFTW2 library.  Using -DFFT_NONE will use the KISS library
-described above.
+are: MKL or FFTW3.  FFTW2 and NONE are supported as legacy options.
+Selecting -DFFT_FFTW will use the FFTW3 library and -DFFT_NONE will
+use the KISS library described above.

 You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
 so the compiler and linker can find the needed FFT header and library
--- a/doc/src/angle_class2.txt
+++ b/doc/src/angle_class2.txt
@ -8,6 +8,7 @@

 angle_style class2 command :h3
 angle_style class2/omp command :h3
+angle_style class2/kk command :h3

 [Syntax:]

--- a/doc/src/bond_class2.txt
+++ b/doc/src/bond_class2.txt
@ -8,6 +8,7 @@

 bond_style class2 command :h3
 bond_style class2/omp command :h3
+bond_style class2/kk command :h3

 [Syntax:]

--- 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/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@ -12,19 +12,16 @@ compute coord/atom command :h3

 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
-one cstyle must be appended :ul
-
-cstyle = {cutoff} or {orientorder}
-
-{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) :pre
-
-{orientorder} args = orientorderID threshold
-  orientorderID = ID of a previously defined orientorder/atom compute
-  threshold = minimum value of the scalar product between two 'connected' atoms (see text for explanation) :pre
+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:]

@ -35,21 +32,21 @@ compute 1 all coord/atom orientorder 2 0.5 :pre

 [Description:]

-This compute performs generic calculations between neighboring atoms. So far,
-there are two cstyles implemented: {cutoff} and {orientorder}.
-The {cutoff} cstyle 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
@ -61,16 +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 {orientorder} cstyle calculates the number of 'connected' atoms j 
-around each atom i. The atom j is connected to i if the scalar product
-({Ybar_lm(i)},{Ybar_lm(j)}) is larger than {threshold}. Thus, this cstyle
-will work only if a "compute orientorder/atom"_compute_orientorder_atom.html
-has been previously defined. This cstyle allows one to apply the 
-ten Wolde's criterion to identify cristal-like atoms in a system 
-(see "ten Wolde et al."_#tenWolde).
+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 value of all coordination numbers will be 0.0 for atoms not in the
-specified compute group.
+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
@ -92,21 +100,23 @@ 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.

 The per-atom vector or array values will be a number >= 0.0, as
 explained above.

-[Restrictions:]
-The cstyle {orientorder} can only be used if a 
-"compute orientorder/atom"_compute_orientorder_atom.html command
-was previously defined. Otherwise, an error message will be issued.
+[Restrictions:] none

 [Related commands:]

@ -118,4 +128,5 @@ was previously defined. Otherwise, an error message will be issued.
 :line

 :link(tenWolde)
-[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
+J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_group_group.txt
+++ b/doc/src/compute_group_group.txt
@ -16,10 +16,11 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
 group/group = style name of this compute command :l
 group2-ID = group ID of second (or same) group :l
 zero or more keyword/value pairs may be appended :l
-keyword = {pair} or {kspace} or {boundary} :l
+keyword = {pair} or {kspace} or {boundary} or {molecule} :l
  {pair} value = {yes} or {no}
  {kspace} value = {yes} or {no}
-  {boundary} value = {yes} or {no} :pre
+  {boundary} value = {yes} or {no}
+  {molecule} value = {off} or {inter} or {intra} :pre
 :ule

 [Examples:]
@ -46,6 +47,13 @@ NOTE: The energies computed by the {pair} keyword do not include tail
 corrections, even if they are enabled via the
 "pair_modify"_pair_modify.html command.

+If the {molecule} keyword is set to {inter} or {intra} than an
+additional check is made based on the molecule IDs of the two atoms in
+each pair before including their pairwise interaction energy and
+force.  For the {inter} setting, the two atoms must be in different
+molecules.  For the {intra} setting, the two atoms must be in the same
+molecule.
+
 If the {kspace} keyword is set to {yes}, which is not the default, and
 if a "kspace_style"_kspace_style.html is defined, then the interaction
 energy will include a Kspace component which is the long-range
@ -66,6 +74,10 @@ affect the force calculation and will be zero if one or both of the
 groups are charge neutral.  This energy correction term is the same as
 that included in the regular Ewald and PPPM routines.

+NOTE: The {molecule} setting only affects the group/group
+contributions calculated by the {pair} keyword.  It does not affect
+the group/group contributions calculated by the {kspace} keyword.
+
 This compute does not calculate any bond or angle or dihedral or
 improper interactions between atoms in the two groups.

@ -78,6 +90,22 @@ work (FFTs, Ewald summation) as computing long-range forces for the
 entire system.  Thus it can be costly to invoke this compute too
 frequently.

+NOTE: If you have a bonded system, then the settings of
+"special_bonds"_special_bonds.html command can remove pairwise
+interactions between atoms in the same bond, angle, or dihedral.  This
+is the default setting for the "special_bonds"_special_bonds.html
+command, and means those pairwise interactions do not appear in the
+neighbor list.  Because this compute uses a neighbor list, it also
+means those pairs will not be included in the group/group interaction.
+This does not apply when using long-range coulomb interactions
+({coul/long}, {coul/msm}, {coul/wolf} or similar.  One way to get
+around this would be to set special_bond scaling factors to very tiny
+numbers that are not exactly zero (e.g. 1.0e-50). Another workaround
+is to write a dump file, and use the "rerun"_rerun.html command to
+compute the group/group interactions for snapshots in the dump file.
+The rerun script can use a "special_bonds"_special_bonds.html command
+that includes all pairs in the neighbor list.
+
 If you desire a breakdown of the interactions into a pairwise and
 Kspace component, simply invoke the compute twice with the appropriate
 yes/no settings for the {pair} and {kspace} keywords.  This is no more
@ -119,7 +147,8 @@ The {ewald} and {pppm} styles do.

 [Default:]

-The option defaults are pair = yes, kspace = no, and boundary = yes.
+The option defaults are pair = yes, kspace = no, boundary = yes,
+molecule = off.

 :line

--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@ -19,7 +19,7 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
  {cutoff} value = distance cutoff
  {nnn} value = number of nearest neighbors
  {degrees} values = nlvalues, l1, l2,...
-  {components} value = l  :pre
+  {components} value = ldegree  :pre

 :ule

@ -64,21 +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 {l}, which must be
+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
-(see "ten Wolde et al."_#tenWolde96).
+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
@ -104,14 +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.
+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
@ -122,19 +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(tenWolde96)
-[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
+:link(tenWolde)
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
+J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_rdf.txt
+++ b/doc/src/compute_rdf.txt
@ -10,21 +10,27 @@ compute rdf command :h3

 [Syntax:]

-compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... :pre
+compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... keyword/value ... :pre

-ID, group-ID are documented in "compute"_compute.html command
-rdf = style name of this compute command
-Nbin = number of RDF bins
-itypeN = central atom type for Nth RDF histogram (see asterisk form below)
-jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+rdf = style name of this compute command :l
+Nbin = number of RDF bins :l
+itypeN = central atom type for Nth RDF histogram (see asterisk form below) :l
+jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) :l
+
+zero or more keyword/value pairs may be appended :l
+keyword = {cutoff} :l
+  {cutoff} value = Rcut
+    Rcut = cutoff distance for RDF computation (distance units) :pre
+:ule

 [Examples:]

 compute 1 all rdf 100
 compute 1 all rdf 100 1 1
-compute 1 all rdf 100 * 3
+compute 1 all rdf 100 * 3 cutoff 5.0
 compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
-compute 1 fluid rdf 500 1*3 2 5 *10 :pre
+compute 1 fluid rdf 500 1*3 2 5 *10 cutoff 3.5 :pre

 [Description:]

@ -32,7 +38,8 @@ Define a computation that calculates the radial distribution function
 (RDF), also called g(r), and the coordination number for a group of
 particles.  Both are calculated in histogram form by binning pairwise
 distances into {Nbin} bins from 0.0 to the maximum force cutoff
-defined by the "pair_style"_pair_style.html command.  The bins are of
+defined by the "pair_style"_pair_style.html command or the cutoff
+distance {Rcut} specified via the {cutoff} keyword.  The bins are of
 uniform size in radial distance.  Thus a single bin encompasses a thin
 shell of distances in 3d and a thin ring of distances in 2d.

@ -41,17 +48,41 @@ NOTE: If you have a bonded system, then the settings of
 interactions between atoms in the same bond, angle, or dihedral.  This
 is the default setting for the "special_bonds"_special_bonds.html
 command, and means those pairwise interactions do not appear in the
-neighbor list.  Because this fix uses the neighbor list, it also means
+neighbor list.  Because this fix uses a neighbor list, it also means
 those pairs will not be included in the RDF. This does not apply when
-using long-range coulomb ({coul/long}, {coul/msm}, {coul/wolf} or
-similar.  One way to get around this would be to set special_bond
-scaling factors to very tiny numbers that are not exactly zero
-(e.g. 1.0e-50). Another workaround is to write a dump file, and use
-the "rerun"_rerun.html command to compute the RDF for snapshots in the
-dump file.  The rerun script can use a
+using long-range coulomb interactions ({coul/long}, {coul/msm},
+{coul/wolf} or similar.  One way to get around this would be to set
+special_bond scaling factors to very tiny numbers that are not exactly
+zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
+use the "rerun"_rerun.html command to compute the RDF for snapshots in
+the dump file.  The rerun script can use a
 "special_bonds"_special_bonds.html command that includes all pairs in
 the neighbor list.

+By default the RDF is computed out to the maximum force cutoff defined
+by the "pair_style"_pair_style.html command.  If the {cutoff} keyword
+is used, then the RDF is computed accurately out to the {Rcut} > 0.0
+distance specified.
+
+NOTE: Normally, you should only use the {cutoff} keyword if no pair
+style is defined, e.g. the "rerun"_rerun.html command is being used to
+post-process a dump file of snapshots.  Or if you really want the RDF
+for distances beyond the pair_style force cutoff and cannot easily
+post-process a dump file to calculate it.  This is because using the
+{cutoff} keyword incurs extra computation and possibly communication,
+which may slow down your simulation.  If you specify a {Rcut} <= force
+cutoff, you will force an additional neighbor list to be built at
+every timestep this command is invoked (or every reneighboring
+timestep, whichever is less frequent), which is inefficent.  LAMMPS
+will warn you if this is the case.  If you specify a {Rcut} > force
+cutoff, you must insure ghost atom information out to {Rcut} + {skin}
+is communicated, via the "comm_modify cutoff"_comm_modify.html
+command, else the RDF computation cannot be performed, and LAMMPS will
+give an error message.  The {skin} value is what is specified with the
+"neighbor"_neighbor.html command.  In this case, you are forcing a
+large neighbor list to be built just for the RDF computation, and
+extra communication to be performed every timestep.
+
 The {itypeN} and {jtypeN} arguments are optional.  These arguments
 must come in pairs.  If no pairs are listed, then a single histogram
 is computed for g(r) between all atom types.  If one or more pairs are
@ -153,4 +184,6 @@ change from zero to one at the location of the spike in g(r).

 "fix ave/time"_fix_ave_time.html

-[Default:] none
+[Default:]
+
+The keyword defaults are cutoff = 0.0 (use the pairwise force cutoff).
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@ -8,6 +8,7 @@

 dihedral_style class2 command :h3
 dihedral_style class2/omp command :h3
+dihedral_style class2/kk command :h3

 [Syntax:]

--- 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/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/improper_class2.txt
+++ b/doc/src/improper_class2.txt
@ -8,6 +8,7 @@

 improper_style class2 command :h3
 improper_style class2/omp command :h3
+improper_style class2/kk command :h3

 [Syntax:]

--- 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
@ -194,7 +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
@ -210,6 +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
@ -217,7 +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
@ -458,6 +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
@ -496,6 +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/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@ -13,6 +13,7 @@ pair_style morse/opt command :h3
 pair_style morse/smooth/linear command :h3
 pair_style morse/smooth/linear/omp command :h3
 pair_style morse/soft command :h3
+pair_style morse/kk command :h3

 [Syntax:]

--- 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/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/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/VISCOSITY/in.einstein.2d
+++ b/examples/VISCOSITY/in.einstein.2d
@ -54,7 +54,8 @@ reset_timestep  0
 variable         pxy equal pxy
 variable         pxx equal pxx-press

-fix              avstress all ave/time $s $p $d v_pxy v_pxx ave one file einstein.dat
+fix              avstress all ave/time $s $p $d v_pxy v_pxx ave one &
+                 file profile.einstein.2d

 # Diagonal components of SS are larger by factor 2-2/d,
 # which is 4/3 for d=3, but 1 for d=2.
--- a/examples/coreshell/in.coreshell
+++ b/examples/coreshell/in.coreshell
@ -40,7 +40,8 @@ thermo 50
 thermo_style custom step etotal pe ke temp press &
             epair evdwl ecoul elong ebond fnorm fmax vol

-compute CSequ all temp/cs cores shells 
+compute CStemp all temp/cs cores shells 
+compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar

 # output via chunk method

@ -49,16 +50,18 @@ compute CSequ all temp/cs cores shells
 #compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
 #fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector 

-thermo_modify temp CSequ
+thermo_modify temp CStemp press thermo_press_lmp

 # velocity bias option

-velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
-velocity all scale 1427 temp CSequ
+velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp
+velocity all scale 1427 temp CStemp
+
+# thermostating using the core/shell decoupling

 fix thermoberendsen all temp/berendsen 1427 1427 0.4
 fix nve all nve
-fix_modify thermoberendsen temp CSequ
+fix_modify thermoberendsen temp CStemp

 # 2 fmsec timestep

--- a/examples/coreshell/in.coreshell.thermostats
+++ b/examples/coreshell/in.coreshell.thermostats
@ -0,0 +1,86 @@
+# Testsystem for core-shell model compared to Mitchell and Fincham
+# Hendrik Heenen, June 2014
+
+# ------------------------ INITIALIZATION ----------------------------
+
+units 		metal
+dimension	3
+boundary	p	p	p
+atom_style	full
+
+# ----------------------- ATOM DEFINITION ----------------------------
+
+fix csinfo all property/atom i_CSID
+read_data data.coreshell fix csinfo NULL CS-Info
+
+group cores type 1 2
+group shells type 3 4
+
+neighbor 2.0 bin
+comm_modify vel yes
+
+# ------------------------ FORCE FIELDS ------------------------------
+
+kspace_style ewald 1.0e-6
+pair_style   born/coul/long/cs 20.0 20.0    # A, rho, sigma=0, C, D 
+pair_coeff   * *      0.0 1.000   0.00  0.00   0.00
+pair_coeff   3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+pair_coeff   3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+pair_coeff   4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+
+bond_style harmonic
+bond_coeff 1 63.014 0.0
+bond_coeff 2 25.724 0.0
+
+# ------------------------ Equilibration Run -------------------------------
+
+reset_timestep 0
+
+thermo 50
+thermo_style custom step etotal pe ke temp press &
+             epair evdwl ecoul elong ebond fnorm fmax vol
+
+compute CStemp all temp/cs cores shells 
+compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar
+
+# output via chunk method
+
+#compute prop all property/atom i_CSID
+#compute cs_chunk all chunk/atom c_prop
+#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
+#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector 
+
+thermo_modify temp CStemp press thermo_press_lmp
+
+# 2 fmsec timestep
+
+timestep 0.002
+
+# velocity bias option
+
+velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp
+velocity all scale 1427 temp CStemp
+
+# thermostating using the core/shell decoupling 
+
+fix thermoberendsen all temp/berendsen 1427 1427 0.4
+fix nve all nve
+fix_modify thermoberendsen temp CStemp
+
+run 500
+
+unfix thermoberendsen
+unfix nve
+
+fix npt_equ all npt temp 1427 1427 0.04 iso 0 0 0.4
+fix_modify npt_equ temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar
+
+run 500
+
+unfix npt_equ
+
+# ------------------------ Dynamic Run -------------------------------
+
+fix npt_dyn all npt temp 1427 1427 0.04 iso 0 0 0.4
+fix_modify npt_dyn temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar
+run 1000
--- a/examples/coreshell/log.9Nov16.coreshell.dsf.g++.1
+++ b/examples/coreshell/log.9Nov16.coreshell.dsf.g++.1
--- a/examples/coreshell/log.9Nov16.coreshell.dsf.g++.4
+++ b/examples/coreshell/log.9Nov16.coreshell.dsf.g++.4
@ -0,0 +1,189 @@
+LAMMPS (26 Jan 2017)
+# Testsystem for core-shell model compared to Mitchel and Finchham
+# Hendrik Heenen, June 2014
+
+# ------------------------ INITIALIZATION ----------------------------
+
+units 		metal
+dimension	3
+boundary	p	p	p
+atom_style	full
+
+# ----------------------- ATOM DEFINITION ----------------------------
+
+fix csinfo all property/atom i_CSID
+read_data data.coreshell fix csinfo NULL CS-Info
+  orthogonal box = (0 0 0) to (24.096 24.096 24.096)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  432 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  216 bonds
+  1 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+group cores type 1 2
+216 atoms in group cores
+group shells type 3 4
+216 atoms in group shells
+
+neighbor 2.0 bin
+comm_modify vel yes
+
+# ------------------------ FORCE FIELDS ------------------------------
+
+pair_style   born/coul/dsf/cs 0.1 20.0 20.0    # A, rho, sigma=0, C, D
+pair_coeff   * *      0.0 1.000   0.00  0.00   0.00
+pair_coeff   3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+pair_coeff   3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+pair_coeff   4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+
+bond_style harmonic
+bond_coeff 1 63.014 0.0
+bond_coeff 2 25.724 0.0
+
+# ------------------------ Equilibration Run -------------------------------
+
+reset_timestep 0
+
+thermo 50
+thermo_style custom step etotal pe ke temp press              epair evdwl ecoul elong ebond fnorm fmax vol
+
+compute CSequ all temp/cs cores shells
+
+# output via chunk method
+
+#compute prop all property/atom i_CSID
+#compute cs_chunk all chunk/atom c_prop
+#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
+#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
+
+thermo_modify temp CSequ
+
+# velocity bias option
+
+velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 22
+  ghost atom cutoff = 22
+  binsize = 11, bins = 3 3 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair born/coul/dsf/cs, half, perpetual
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+velocity all scale 1427 temp CSequ
+
+fix thermoberendsen all temp/berendsen 1427 1427 0.4
+fix nve all nve
+fix_modify thermoberendsen temp CSequ
+
+# 2 fmsec timestep
+
+timestep 0.002
+run 500
+Memory usage per processor = 6.8559 Mbytes
+Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 
+       0   -635.80596   -675.46362    39.657659         1427   -21302.622   -675.46362    1.6320365   -677.09565            0            0 1.5814015e-14 3.2317898e-15      13990.5 
+      50   -634.07021   -666.11867    32.048452    1153.1982    -4560.945   -668.28236    37.756542    -706.0389            0     2.163691    13.802484     3.022372      13990.5 
+     100   -631.97128   -662.02544    30.054164    1081.4378    -3497.564   -664.61825    39.275003   -703.89325            0    2.5928078    13.956833    2.5417699      13990.5 
+     150   -630.14953   -663.04215    32.892622    1183.5739    -88.43828   -665.63444    46.239965   -711.87441            0    2.5922927    14.667898    2.4964255      13990.5 
+     200   -628.52878    -663.9795     35.45072    1275.6219   -1755.9004   -666.73564    41.758052   -708.49369            0    2.7561421    14.230743    3.0924004      13990.5 
+     250   -627.27102     -662.025    34.753978    1250.5511   -1234.0918   -665.13519    43.170874   -708.30606            0    3.1101887    14.221086     1.941354      13990.5 
+     300    -626.5495   -663.74287    37.193368    1338.3275   -2049.3444   -666.45574    40.476148   -706.93188            0    2.7128711    13.330425    1.7756755      13990.5 
+     350   -625.87313   -665.21855    39.345421    1415.7647   -1543.1723   -667.90872    41.577366   -709.48609            0    2.6901682    13.541311     1.854662      13990.5 
+     400   -625.09344   -661.26404      36.1706    1301.5253   -729.96729   -664.10334    43.468765   -707.57211            0    2.8392963    13.663555    1.9067551      13990.5 
+     450   -624.46214   -660.01362    35.551477    1279.2474   -1617.7158   -663.06571    41.644856   -704.71057            0    3.0520921    14.527005    1.7280213      13990.5 
+     500   -623.49246    -659.2527     35.76024    1286.7593   -935.99238   -662.32953    43.038808   -705.36834            0    3.0768302    14.099593    1.9831106      13990.5 
+Loop time of 4.09864 on 4 procs for 500 steps with 432 atoms
+
+Performance: 21.080 ns/day, 1.139 hours/ns, 121.992 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.3804     | 3.568      | 3.8354     |   8.9 | 87.05
+Bond    | 0.00074339 | 0.00079519 | 0.00087976 |   0.0 |  0.02
+Neigh   | 0.045851   | 0.046084   | 0.046361   |   0.1 |  1.12
+Comm    | 0.20413    | 0.47123    | 0.65875    |  24.3 | 11.50
+Output  | 0.00044298 | 0.00046057 | 0.00051165 |   0.0 |  0.01
+Modify  | 0.0064909  | 0.0067219  | 0.0069766  |   0.2 |  0.16
+Other   |            | 0.005345   |            |       |  0.13
+
+Nlocal:    108 ave 114 max 105 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+Nghost:    6527 ave 6599 max 6472 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:    74388.2 ave 75855 max 73680 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 297553
+Ave neighs/atom = 688.78
+Ave special neighs/atom = 1
+Neighbor list builds = 20
+Dangerous builds = 0
+
+unfix thermoberendsen
+
+# ------------------------ Dynamic Run -------------------------------
+
+run 1000
+Memory usage per processor = 6.85787 Mbytes
+Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 
+     500   -623.49319    -659.2527    35.759511    1286.7331   -936.04802   -662.32953    43.038808   -705.36834            0    3.0768302    14.099593    1.9831106      13990.5 
+     550   -623.44059   -663.57938    40.138795    1444.3127   -935.73484    -666.2789    42.563337   -708.84224            0    2.6995167    13.918509    2.3189805      13990.5 
+     600    -623.4703   -660.01592    36.545618    1315.0196    1327.3492   -663.08845    47.985462   -711.07391            0    3.0725254    15.192713    2.4098428      13990.5 
+     650   -623.46796   -661.56776    38.099807    1370.9439    457.82439   -664.81976    45.495622   -710.31538            0    3.2519966    15.026057    1.8500226      13990.5 
+     700   -623.50158    -659.5131    36.011523    1295.8012   -460.03772    -663.1078    43.938203     -707.046            0    3.5946908    14.660979    2.4825518      13990.5 
+     750   -623.44787   -661.93353    38.485658    1384.8279    97.429626    -664.9551    45.083146   -710.03825            0    3.0215753     15.10043    2.3433897      13990.5 
+     800   -623.48215   -659.50655    36.024402    1296.2647    1097.3866   -662.61124    47.251998   -709.86324            0    3.1046914    14.556382    2.0543766      13990.5 
+     850   -623.45868   -661.13782    37.679134    1355.8068   -1802.1624   -664.41257     40.70845   -705.12102            0    3.2747525    14.691444    2.2054332      13990.5 
+     900   -623.43556   -663.59137    40.155815    1444.9251    534.99197   -666.71877    45.601619   -712.32039            0     3.127395    14.741411    2.5807895      13990.5 
+     950   -623.51318   -661.57916     38.06598    1369.7267   -678.12625   -664.37535    43.207862   -707.58322            0    2.7961988    14.430307    2.3936105      13990.5 
+    1000   -623.47287   -661.22274    37.749874    1358.3523     634.7979   -664.42973    46.373361   -710.80309            0    3.2069879    15.891192    2.4042765      13990.5 
+    1050   -623.48133   -661.52868    38.047347    1369.0562   -583.15228    -664.6098    43.618772   -708.22857            0     3.081116    14.806856    2.3447613      13990.5 
+    1100   -623.47867   -661.83761    38.358946    1380.2685    -868.9779    -664.8826     42.84846   -707.73106            0     3.044983     14.69567     2.399143      13990.5 
+    1150   -623.44713   -661.21299    37.765857    1358.9274    405.14554   -664.09567    45.578739    -709.6744            0    2.8826753    15.437367    3.1381305      13990.5 
+    1200   -623.46549   -660.91706    37.451568    1347.6183    699.78996    -664.0883     46.36297   -710.45127            0    3.1712473    15.109665    1.8891886      13990.5 
+    1250   -623.49296    -658.2218    34.728838    1249.6464    1061.0154   -661.29052    47.668699   -708.95922            0    3.0687228    14.901367    2.3964137      13990.5 
+    1300   -623.49837   -660.91022    37.411844    1346.1889    226.99512   -664.35989    45.352287   -709.71217            0    3.4496704    15.161542    2.2137993      13990.5 
+    1350   -623.46718   -658.80365    35.336469    1271.5108    1039.6469   -662.16908    47.565671   -709.73475            0    3.3654314    15.892516    2.7888426      13990.5 
+    1400   -623.47124   -661.45375    37.982513    1366.7233   -379.56023    -664.6321    43.788306   -708.42041            0    3.1783497    14.251126    1.7415409      13990.5 
+    1450   -623.46671   -660.17518    36.708464    1320.8792   -374.37056   -662.92706    44.083648   -707.01071            0    2.7518803    15.210167    1.9984277      13990.5 
+    1500   -623.50515   -659.06488    35.559725    1279.5442    260.37822   -662.39548    45.779764   -708.17524            0    3.3306005    14.682396    2.4201107      13990.5 
+Loop time of 8.26746 on 4 procs for 1000 steps with 432 atoms
+
+Performance: 20.901 ns/day, 1.148 hours/ns, 120.956 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.706      | 7.1568     | 7.6597     |  12.7 | 86.57
+Bond    | 0.0014617  | 0.0015531  | 0.0016506  |   0.2 |  0.02
+Neigh   | 0.10511    | 0.10522    | 0.10532    |   0.0 |  1.27
+Comm    | 0.48547    | 0.98841    | 1.4393     |  34.0 | 11.96
+Output  | 0.0012085  | 0.0012462  | 0.0013196  |   0.1 |  0.02
+Modify  | 0.0021446  | 0.0021989  | 0.0022545  |   0.1 |  0.03
+Other   |            | 0.01204    |            |       |  0.15
+
+Nlocal:    108 ave 114 max 94 min
+Histogram: 1 0 0 0 0 0 0 0 1 2
+Nghost:    6512.25 ave 6586 max 6456 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Neighs:    74248.2 ave 77441 max 65858 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+
+Total # of neighbors = 296993
+Ave neighs/atom = 687.484
+Ave special neighs/atom = 1
+Neighbor list builds = 46
+Dangerous builds = 0
+Total wall time: 0:00:12
--- a/examples/snap/He_He_JW2013.table
+++ b/examples/snap/He_He_JW2013.table
--- a/examples/snap/W.SNAP_HePair.pot
+++ b/examples/snap/W.SNAP_HePair.pot
@ -0,0 +1,17 @@
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+#
+# Definition of SNAP+ZBL+Tabulated potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 74
+
+# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
+pair_coeff 	1 1 zbl ${zblz} ${zblz}
+pair_coeff 	* * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
+pair_coeff      2 2 table 1 He_He_JW2013.table HeHe
+pair_coeff      1 2 table 2 W_He_JW2013.table WHe
+#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
+#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
+
--- a/examples/snap/W_2940_2017_2.pot.snap
+++ b/examples/snap/W_2940_2017_2.pot.snap
@ -0,0 +1,16 @@
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+#
+# Definition of SNAP+ZBL potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 74
+
+# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+
+pair_style hybrid/overlay &
+zbl ${zblcutinner} ${zblcutouter} &
+snap
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
+
+#Nomenclature on the snap files are Element_DakotaID_Year_Month
--- a/examples/snap/W_2940_2017_2.snapcoeff
+++ b/examples/snap/W_2940_2017_2.snapcoeff
@ -0,0 +1,62 @@
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# 
+# LAMMPS SNAP coefficients for W
+
+1 56
+W 0.5 1
+  0.781170857801
+ -0.001794941735
+ -0.016628679036
+ -0.066625537037
+ -0.073716343967
+ -0.062913923923
+  0.032552694672
+ -0.134901744419
+ -0.075076334103
+ -0.148558616547
+ -0.140808831101
+ -0.166749145704
+ -0.047487675984
+ -0.049892090603
+ -0.032483739965
+ -0.114766534860
+ -0.106759718242
+ -0.125894850485
+ -0.103409735225
+ -0.095247335447
+ -0.061998736346
+ -0.053895610976
+ -0.010799734206
+ -0.011644828900
+ -0.028316826924
+  0.011176085541
+  0.064619474684
+ -0.023886279996
+ -0.004099224312
+ -0.056084222496
+ -0.035551497650
+ -0.056678501024
+ -0.004905851656
+ -0.015701146162
+ -0.008462280779
+  0.016429018676
+  0.032432633993
+ -0.010805361272
+ -0.014841893457
+  0.019414134562
+ -0.008112452759
+ -0.002700775447
+  0.007032887063
+ -0.009706065042
+  0.008385967833
+  0.028606085876
+ -0.007003591067
+  0.006467260152
+ -0.006666986361
+  0.029243285316
+  0.002477673872
+ -0.000199497504
+  0.004068954075
+  0.006036129972
+ -0.013010633924
+ -0.008314173699
--- a/examples/snap/W_2940_2017_2.snapparam
+++ b/examples/snap/W_2940_2017_2.snapparam
@ -0,0 +1,12 @@
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+# 
+# required
+rcutfac 4.73442
+twojmax 8
+
+# optional
+
+gamma 1
+rfac0 0.99363
+rmin0 0
+diagonalstyle 3
--- a/examples/snap/W_He_JW2013.table
+++ b/examples/snap/W_He_JW2013.table
@ -0,0 +1,333 @@
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+# 
+#-> LAMMPS Potential File in tabular format.                    <-#
+# N. Juslin and B.D. Wirth, J. Nucl. Mater. 432: 61-66 (2013).    #
+# Implemented by K.D. Hammond (2013) karlh@utk.edu
+WHe
+N 325
+
+1       0.000001 193967.941432641     21165142.7035409
+2       0.02     88781.7058271842     5199760.86773195
+3       0.03     54461.7226844158     2255783.27652381
+4       0.04     37754.4525147374     1233285.07338825
+5       0.05     28027.0551422937     765154.791685769
+6       0.06     21746.7711436002     514318.047209743
+7       0.07     17407.2122555268     365457.111099578
+8       0.08      14260.380890756     270524.172812057
+9       0.09      11894.315375388     206649.630589727
+10        0.1     10064.3593879466     161847.200920021
+11       0.11     8616.61401638085     129358.142417815
+12       0.12      7449.7679909506     105145.917230655
+13       0.13     6494.61875555217     86685.1834957916
+14       0.14     5702.42313976808     72334.2424211515
+15       0.15     5037.94580316996     60990.8171175998
+16       0.16     4475.14199778904     51894.0939422829
+17       0.17     3994.38401078788      44506.229619365
+18       0.18     3580.62666819885     38438.9489608325
+19       0.19     3222.16279673461     33406.7013437966
+20        0.2     2909.75986785247      29195.976537891
+21       0.21     2636.04908399207     25644.7364933058
+22       0.22     2395.08534986163     22628.3414553063
+23       0.23     2182.02521022247      20049.740107058
+24       0.24     1992.88767473625     17832.5164484929
+25       0.25       1824.374223221     15915.8858113167
+26       0.26     1673.73168801722     14251.0430039002
+27       0.27     1538.64662154286     12798.4627755747
+28       0.28     1417.16307190682     11525.8804272463
+29       0.29     1307.61796220838     10406.7644777657
+30        0.3     1208.58985019291     9419.14958758174
+31       0.31      1118.8579596074     8544.73619272459
+32       0.32     1037.36917029033     7768.18965475981
+33       0.33     963.211228625566     7076.59012069084
+34       0.34     895.590859433663      6458.9972713357
+35       0.35     833.815769676712     5906.10340798657
+36       0.36      777.27976462076      5409.9550164674
+37       0.37     725.450370074705     4963.72782166695
+38       0.38     677.858485369477     4561.54392990095
+39       0.39     634.089691821654      4198.3223154716
+40        0.4     593.776918443069     3869.65589682796
+41       0.41     556.594226358163     3571.70994736531
+42       0.42     522.251519987548     3301.13772506169
+43       0.43     490.490029664824     3055.01007668961
+44       0.44      461.07843929567     2830.75644369566
+45       0.45     433.809555685745     2626.11521737135
+46       0.46     408.497434574275     2439.09179705296
+47       0.47     384.974893215623     2267.92302383156
+48       0.48     363.091351319355     2111.04691385653
+49       0.49     342.710951882019     1967.07681501168
+50        0.5     323.710921379843     1834.77927007332
+51       0.51     305.980135298364     1713.05499722693
+52       0.52     289.417860333203      1600.9225017701
+53       0.53     273.932649026687     1497.50391617084
+54       0.54      259.44136628296      1402.0127334168
+55       0.55      245.86833026895     1313.74315392891
+56       0.56     233.144552771494     1232.06081168718
+57       0.57     221.207066231741      1156.3946825672
+58       0.58     209.998326488761     1086.23000874818
+59       0.59     199.465681793803     1021.10209864685
+60        0.6     189.560899952328     960.590883129588
+61       0.61     180.239746551915     904.316126537919
+62       0.62     171.461608172096     851.933205957983
+63       0.63     163.189155273495     803.129384679904
+64       0.64     155.388040149985      757.62051633995
+65       0.65     148.026625916815     715.148125151611
+66       0.66     141.075743014823     675.476815185188
+67       0.67     134.508470148273     638.391968073426
+68       0.68     128.299936952045     603.697693987706
+69       0.69     122.427146011509     571.215005397664
+70        0.7     116.868812142757     540.780187122909
+71       0.71     111.605217088269     512.243339613345
+72       0.72     106.618077998551     485.467075341772
+73       0.73     101.890428258492      460.32535073159
+74       0.74     97.4065093817089     436.702418234594
+75       0.75     93.1516728402801     414.491885070093
+76       0.76     89.1122908237631     393.595866780115
+77       0.77     85.2756750325343      373.92422518237
+78       0.78     81.6300027083206     355.393881543952
+79       0.79     78.1642491910339     337.928196880203
+80        0.8     74.8681263671512     321.456412227117
+81       0.81     71.7320264421784     305.913142560798
+82       0.82     68.7469705293107     291.237918759986
+83       0.83     65.9045615992059     277.374772641144
+84       0.84     63.1969413826496     264.271860652001
+85       0.85     60.6167508595336     251.881122298665
+86       0.86     58.1570940046202     240.157969812335
+87       0.87     55.8115044935616     229.061005941579
+88       0.88     53.5739151020755     218.551767091662
+89       0.89     51.4386295574478     208.594489329042
+90        0.9      49.400296625012      199.15589503172
+91       0.91     47.4538862332645     190.204998198848
+92       0.92     45.5946674600827     181.712926639528
+93       0.93      43.818188219384     173.652759444123
+94       0.94     42.1202565026948     165.999378304597
+95       0.95     40.4969230436942     158.729331395598
+96       0.96      38.944465286023     151.820708657476
+97       0.97     37.4593725456438     145.253027437895
+98       0.98       36.03833226895      139.00712755184
+99       0.99     34.6782172967515     133.065074912029
+100          1     33.3760740523261     127.410072964226
+101       1.01     32.1291115790037     122.026381235854
+102       1.02     30.9346913593292     116.899240372539
+103       1.03     29.7903178538011     112.014803096661
+104       1.04     28.6936297025718     107.360070575369
+105       1.05     27.6423915383737     102.922833733498
+106       1.06     26.6344863633652       98.69161908997
+107       1.07     25.6679084466039     94.6556387351718
+108       1.08     24.7407567025028      90.804744101767
+109       1.09     23.8272933774771     87.0424919424945
+110        1.1     22.9746938084833      83.501083250349
+111       1.11     22.1568053467682     80.0995862713648
+112       1.12      21.372249301539     76.8339257499533
+113       1.13     20.6196874341871     73.7000865054019
+114       1.14     19.8978213575361     70.6941134318681
+115       1.15     19.2053919350916     67.8121114983956
+116       1.16     18.5411786802966     65.0502457488983
+117       1.17     17.9039991557794     62.4047413021631
+118       1.18     17.2927083726064     59.8718833518619
+119       1.19     16.7061981895337     57.4480171665332
+120        1.2     16.1433967122567     55.1295480895992
+121       1.21     15.6032676926612     52.9129415393513
+122       1.22     15.0848099280771     50.7947230089626
+123       1.23     14.5870566605305     48.7714780664787
+124       1.24     14.1090749759875     46.8398523548244
+125       1.25     13.6499652036138     44.9965515917961
+126       1.26     13.2088603150229     43.2383415700692
+127       1.27      12.784925323525     41.5620481571964
+128       1.28     12.3773566833817     39.9645572956038
+129       1.29     11.9853816890583     38.4428150025965
+130        1.3       11.60825787447     36.9938273703497
+131       1.31     11.2452724122346     35.6146605659201
+132       1.32     10.8957415129272     34.3024408312399
+133       1.33     10.5590098243284     33.0543544831148
+134       1.34      10.234449830679     31.8676479132323
+135       1.35     9.92146125192414      30.739627588146
+136       1.36     9.61947044297006     29.6676600492951
+137       1.37     9.32792979293674     28.6491719129885
+138       1.38     9.04631712440562     27.6816498704143
+139       1.39     8.77413509267092     26.7626406876384
+140        1.4     8.51091058499253     25.8897512055996
+141       1.41     8.25619411984519     25.0606483401084
+142       1.42     8.00955924617449     24.2730590818669
+143       1.43     7.77060194264106      23.524770496429
+144       1.44     7.53894001687615     22.8136297242495
+145       1.45     7.31421250473534     22.1375439806457
+146       1.46     7.09607906954318     21.4944805558102
+147       1.47     6.88421940134788     20.8824668148159
+148       1.48       6.678332616175     20.2995901976151
+149       1.49     6.47813665527576      19.743998219024
+150        1.5     6.28336768437487     19.2138984687485
+151       1.51     6.09377949293196     18.7075586113629
+152       1.52     5.90914289338127     18.2233063863173
+153       1.53     5.72924512039265      17.759529607943
+154       1.54     5.55388923011117     17.3146761654411
+155       1.55     5.38289349942409     16.8872540228954
+156       1.56     5.21609082520001     16.4758312192575
+157       1.57     5.05332812353902     16.0790358683639
+158       1.58     4.89446572903546     15.6955561589207
+159       1.59     4.73937679401809     15.3241403545121
+160        1.6     4.58794668780786     14.9635967935988
+161       1.61     4.44007239596442     14.6127938895147
+162       1.62     4.29566191954302     14.2706601304803
+163       1.63     4.15463367433779     13.9361840795741
+164       1.64     4.01691589014092     13.6084143747644
+165       1.65     3.88244600998598     13.2864597288958
+166       1.66     3.75117008941481     12.9694889296766
+167       1.67     3.62304219570535     12.6567308397093
+168       1.68     3.49802380713948     12.3474743964548
+169       1.69     3.37608321225264       12.04106861226
+170        1.7     3.25719490908079     11.7369225743464
+171       1.71     3.14133900441368     11.4345054448136
+172       1.72     3.02850061304264     11.1333464606264
+173       1.73     2.91866925702027     10.8330349336425
+174       1.74     2.81183826489826      10.533220250582
+175       1.75     2.70800417099883      10.233611873045
+176       1.76     2.60716611463897     9.93397933750975
+177       1.77     2.50932523941003     9.63415225533254
+178       1.78     2.41448409240832      9.3340203127359
+179       1.79      2.3226460234938     9.03353327083141
+180        1.8     2.23381458454253       8.732700965596
+181       1.81     2.14799292869986     8.43159330788831
+182       1.82     2.06518320961743     8.13034028344418
+183       1.83     1.98538598072548     7.82913195286937
+184       1.84     1.90859959447164     7.52821845164772
+185       1.85     1.83481960157053      7.2279099901466
+186       1.86      1.7640381502589     6.92857685359786
+187       1.87     1.69624338555161     6.63064940211416
+188       1.88     1.63141884849222     6.33461807069079
+189       1.89     1.56954287538349     6.04103336918388
+190        1.9     1.51058799706618     5.75050588234672
+191       1.91     1.45452033816503     5.46370626978796
+192       1.92     1.40129901631838     5.18136526601165
+193       1.93     1.35087554145878     4.90427368037354
+194       1.94     1.30319321504351     4.63328239712837
+195       1.95     1.25818652931969     4.36930237539354
+196       1.96     1.21578056655756     4.11330464916909
+197       1.97     1.17589039832831     3.86632032733041
+198       1.98     1.13842048472736     3.62944059362462
+199       1.99     1.10326407363948      3.4038167066833
+200          2     1.07030260000113     3.19065999999702
+201       2.01     1.03940508502285     2.99124188195356
+202       2.02     1.01042753546074     2.80689383580147
+203       2.03     0.98321234287971     2.63900741967382
+204       2.04    0.957587682867711     2.48903426657353
+205       2.05     0.93336691431989     2.35848608439528
+206       2.06    0.910347978676441     2.24893465587638
+207       2.07    0.888312799175878     2.16201183866769
+208       2.08    0.867026680100139     2.09940956527362
+209       2.09    0.846311972535292      2.0501194750481
+210        2.1    0.826052090711088     2.00205155230487
+211       2.11    0.806267097861257     1.95513674544071
+212       2.12    0.786945609506685     1.90934585391834
+213       2.13      0.7680765291529     1.86465047725327
+214       2.14    0.749649040410966     1.82102299086693
+215       2.15    0.731652599355765     1.77843652275056
+216       2.16    0.714076927113717     1.73686493090964
+217       2.17    0.696912002672274     1.69628278155967
+218       2.18    0.680148055903811     1.65666532804561
+219       2.19    0.663775560796824     1.61798849045792
+220        2.2    0.647785228887586      1.5802288359199
+221       2.21    0.632168002885678     1.54336355952145
+222       2.22    0.616915050487049     1.50737046587586
+223       2.23    0.602017758368489     1.47222795127685
+224       2.24    0.587467726357617     1.43791498643425
+225       2.25    0.573256761772716     1.40441109976729
+226       2.26    0.559376873926913     1.37169636123572
+227       2.27     0.54582026879146     1.33975136668933
+228       2.28    0.532579343812991     1.30855722271748
+229       2.29    0.519646682879861     1.27809553198093
+230        2.3    0.507015051432831     1.24834837900889
+231       2.31    0.494677391715517     1.21929831644497
+232       2.32    0.482626818160208     1.19092835172618
+233       2.33    0.470856612904789     1.16322193418007
+234       2.34    0.459360221436662      1.1361629425252
+235       2.35    0.448131248359705     1.10973567276124
+236       2.36    0.437163453280438     1.08392482643501
+237       2.37    0.426450746809703     1.05871549926971
+238       2.38    0.415987186676291      1.0340931701448
+239       2.39    0.405766973949056     1.01004369041464
+240        2.4    0.395784449364215    0.986553273554313
+241       2.41     0.38603408975458    0.963608485121541
+242       2.42    0.376510504577652    0.941196233024116
+243       2.43    0.367208432539548    0.919303758082476
+244       2.44    0.358122738311864    0.897918624877599
+245       2.45    0.349248409338683    0.877028712874665
+246       2.46    0.340580552730998     0.85662220781334
+247       2.47    0.332114392245936     0.83668759335581
+248       2.48    0.323845265348255      0.8172136429841
+249       2.49    0.315768620351645    0.798189412138432
+250        2.5    0.307880013637488    0.779604230588763
+251       2.51    0.300175106948751    0.761447695031842
+252       2.52    0.292649664756829    0.743709661906479
+253       2.53    0.285299551699157    0.726380240419923
+254       2.54    0.278120730085547     0.70944978577854
+255       2.55    0.271109257471214     0.69290889261619
+256       2.56    0.264149883217677    0.704309455966822
+257       2.57    0.257023670963235    0.720548414483017
+258       2.58    0.249746544950963     0.73449858053557
+259       2.59    0.242341191411443    0.746201328856265
+260        2.6    0.234829852474346    0.755704032488528
+261       2.61    0.227234268357011    0.763059628544665
+262       2.62    0.219575623890343    0.768326185205915
+263       2.63    0.211874499363033    0.771566471270733
+264       2.64    0.204150825652343    0.772847529495918
+265       2.65    0.196423843597567    0.772240254912945
+266       2.66    0.188712067560753    0.769818979238484
+267       2.67    0.181033253108439    0.765661062433794
+268       2.68     0.17340436873789    0.759846492402718
+269       2.69    0.165841571561793    0.752457493752577
+270        2.7    0.158360186856416    0.743578146476553
+271       2.71    0.150974691370005    0.733294015350452
+272       2.72     0.14369870028059    0.721691790771177
+273       2.73    0.136544957685405    0.708858941699004
+274       2.74    0.129525330497857     0.69488338130108
+275       2.75    0.122650805622294    0.679853145829612
+276       2.76    0.115931490271846    0.663856087205069
+277       2.77     0.10937661529017    0.646979579712699
+278       2.78    0.102994541334199    0.629310241159726
+279       2.79   0.0967927677717845    0.610933668781077
+280        2.8   0.0907779441455664    0.591934190123306
+281       2.81   0.0849558840523623    0.572394629079895
+282       2.82   0.0793315812859323    0.552396087196204
+283       2.83   0.0739092280900552    0.532017740309284
+284       2.84   0.0686922353684514     0.51133665053656
+285       2.85   0.0636832546982004    0.490427593578163
+286       2.86    0.058884201993894    0.469362901250494
+287       2.87   0.0542962826708072    0.448212319123508
+288       2.88   0.0499200181568738    0.427042879091302
+289       2.89     0.04575527360515    0.405918786664859
+290        2.9   0.0418012866607671    0.384901322737369
+291       2.91   0.0380566971390415    0.364048759536354
+292       2.92   0.0345195774744505    0.343416290443013
+293       2.93   0.0311874638035265    0.323055973327595
+294       2.94   0.0280573875483925    0.303016687020528
+295       2.95   0.0251259073715924    0.283344100512051
+296       2.96   0.0223891413770724    0.264080654448684
+297       2.97   0.0198427994365954    0.245265554472591
+298       2.98    0.017482215525515    0.226934775930029
+299       2.99   0.0153023799566589     0.20912107945741
+300          3   0.0132979714060716    0.191854036938167
+301       3.01   0.0114633886294948    0.175160067310366
+302       3.02    0.009792781773727    0.159062481694054
+303       3.03  0.00828008319235769    0.143581537298372
+304       3.04  0.00691903768080766    0.128734499561665
+305       3.05  0.00570323205109961    0.114535711972949
+306       3.06   0.0046261239723178    0.100996673020243
+307       3.07  0.00368107000826405    0.088126119710232
+308       3.08  0.00286135278937321   0.0759301171045549
+309       3.09  0.00216020726148435   0.0644121533205429
+310        3.1  0.00157084595956787   0.0535732394484653
+311       3.11  0.00108648325995938   0.0434120138431347
+312       3.12 0.000700358570037423   0.0339248502550448
+313       3.13 0.000405758419588332   0.0251059692749879
+314       3.14 0.000196037423311657   0.0169475525761798
+315       3.15 6.46380890244662E-05  0.00943985944932857
+316       3.16  5.1094511057313E-06  0.00257134513861945
+317       3.17                    0                    0
+318       3.18                    0                    0
+319       3.19                    0                    0
+320        3.2                    0                    0
+321       3.21                    0                    0
+322       3.22                    0                    0
+323       3.23                    0                    0
+324       3.24                    0                    0
+325       3.25                    0                    0
--- a/examples/snap/in.snap.Ta06A
+++ b/examples/snap/in.snap.Ta06A
--- a/examples/snap/in.snap.W.2940
+++ b/examples/snap/in.snap.W.2940
@ -0,0 +1,45 @@
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary	p p p
+
+lattice         bcc $a
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box	1 box
+create_atoms	1 box
+
+mass 1 183.84
+
+# choose potential
+
+include W_2940_2017_2.pot.snap
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+
--- a/examples/snap/in.snap.hybrid.WSNAP.HePair
+++ b/examples/snap/in.snap.hybrid.WSNAP.HePair
@ -0,0 +1,48 @@
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary	p p p
+
+lattice         bcc $a
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box	2 box
+create_atoms	1 box
+mass 1 183.84
+mass 2 4.0026
+
+set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+group	tungsten type 1
+group	helium	type 2
+# choose potential
+
+include W.SNAP_HePair.pot
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+
--- a/examples/snap/log.21Feb17.snap.W.2940.g++.1
+++ b/examples/snap/log.21Feb17.snap.W.2940.g++.1
@ -0,0 +1,144 @@
+LAMMPS (13 Feb 2017)
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary	p p p
+
+lattice         bcc $a
+lattice         bcc 3.1803
+Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 4 0 ${ny} 0 ${nz}
+region		box block 0 4 0 4 0 ${nz}
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 128 atoms
+
+mass 1 183.84
+
+# choose potential
+
+include W_2940_2017_2.pot.snap
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+#
+# Definition of SNAP+ZBL potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 74
+
+# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.8 snap
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 74 ${zblz}
+pair_coeff 1 1 zbl 74 74
+pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
+Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
+SNAP Element = W, Radius 0.5, Weight 1 
+Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
+SNAP keyword rcutfac 4.73442 
+SNAP keyword twojmax 8 
+SNAP keyword gamma 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword diagonalstyle 3 
+
+#Nomenclature on the snap files are Element_DakotaID_Year_Month
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Memory usage per processor = 5.14696 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -11.028325            0    -10.98985     3010.497 
+      10    293.40666   -11.027479            0   -10.989849    3246.0559 
+      20    274.27375   -11.025025            0   -10.989849    3927.9497 
+      30    244.50457   -11.021207            0   -10.989849    4983.5484 
+      40     207.0784   -11.016407            0   -10.989849    6299.9473 
+      50    165.74442   -11.011105            0   -10.989848    7736.5123 
+      60    124.62181   -11.005831            0   -10.989848    9140.8587 
+      70    87.744792   -11.001101            0   -10.989848    10366.489 
+      80    58.605244   -10.997364            0   -10.989848    11289.914 
+      90    39.754503   -10.994946            0   -10.989848    11824.945 
+     100    32.524085   -10.994019            0   -10.989848    11932.118 
+Loop time of 11.8271 on 1 procs for 100 steps with 128 atoms
+
+Performance: 0.365 ns/day, 65.706 hours/ns, 8.455 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.826     | 11.826     | 11.826     |   0.0 | 99.99
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00044084 | 0.00044084 | 0.00044084 |   0.0 |  0.00
+Output  | 0.00013232 | 0.00013232 | 0.00013232 |   0.0 |  0.00
+Modify  | 0.00021887 | 0.00021887 | 0.00021887 |   0.0 |  0.00
+Other   |            | 0.0002718  |            |       |  0.00
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    727 ave 727 max 727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3712 ave 3712 max 3712 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  7424 ave 7424 max 7424 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:11
--- a/examples/snap/log.21Feb17.snap.W.2940.g++.4
+++ b/examples/snap/log.21Feb17.snap.W.2940.g++.4
@ -0,0 +1,144 @@
+LAMMPS (13 Feb 2017)
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary	p p p
+
+lattice         bcc $a
+lattice         bcc 3.1803
+Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 4 0 ${ny} 0 ${nz}
+region		box block 0 4 0 4 0 ${nz}
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 128 atoms
+
+mass 1 183.84
+
+# choose potential
+
+include W_2940_2017_2.pot.snap
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+#
+# Definition of SNAP+ZBL potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 74
+
+# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.8 snap
+pair_coeff 1 1 zbl ${zblz} ${zblz}
+pair_coeff 1 1 zbl 74 ${zblz}
+pair_coeff 1 1 zbl 74 74
+pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
+Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
+SNAP Element = W, Radius 0.5, Weight 1 
+Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
+SNAP keyword rcutfac 4.73442 
+SNAP keyword twojmax 8 
+SNAP keyword gamma 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword diagonalstyle 3 
+
+#Nomenclature on the snap files are Element_DakotaID_Year_Month
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Memory usage per processor = 5.12833 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -11.028325            0    -10.98985     3010.497 
+      10    293.22504   -11.027456            0   -10.989849     3258.275 
+      20    273.60084   -11.024939            0   -10.989849    3973.9038 
+      30    243.15327   -11.021034            0   -10.989849    5077.9172 
+      40    205.01905   -11.016142            0   -10.989849    6448.4941 
+      50    163.10914   -11.010767            0   -10.989848    7935.6835 
+      60    121.67854   -11.005453            0   -10.989848    9378.9959 
+      70    84.846972   -11.000729            0   -10.989848    10626.301 
+      80    56.127265   -10.997046            0   -10.989848    11551.687 
+      90    38.025013   -10.994724            0   -10.989847    12069.936 
+     100    31.768127   -10.993922            0   -10.989847    12145.648 
+Loop time of 3.03545 on 4 procs for 100 steps with 128 atoms
+
+Performance: 1.423 ns/day, 16.864 hours/ns, 32.944 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.9594     | 2.9866     | 3.0319     |   1.6 | 98.39
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0024238  | 0.047825   | 0.075032   |  12.5 |  1.58
+Output  | 0.00021601 | 0.00024045 | 0.00027442 |   0.0 |  0.01
+Modify  | 9.6798e-05 | 0.00011188 | 0.00011802 |   0.0 |  0.00
+Other   |            | 0.000698   |            |       |  0.02
+
+Nlocal:    32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    431 ave 431 max 431 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    928 ave 928 max 928 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1856 ave 1856 max 1856 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:03
--- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1
+++ b/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1
@ -0,0 +1,179 @@
+LAMMPS (13 Feb 2017)
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary	p p p
+
+lattice         bcc $a
+lattice         bcc 3.1803
+Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 4 0 ${ny} 0 ${nz}
+region		box block 0 4 0 4 0 ${nz}
+region		box block 0 4 0 4 0 4
+create_box	2 box
+Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 128 atoms
+mass 1 183.84
+mass 2 4.0026
+
+set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+  5 settings made for type/fraction
+group	tungsten type 1
+123 atoms in group tungsten
+group	helium	type 2
+5 atoms in group helium
+# choose potential
+
+include W.SNAP_HePair.pot
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+#
+# Definition of SNAP+ZBL+Tabulated potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 74
+
+# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
+pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000
+pair_coeff 	1 1 zbl ${zblz} ${zblz}
+pair_coeff 	1 1 zbl 74 ${zblz}
+pair_coeff 	1 1 zbl 74 74
+pair_coeff 	* * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
+Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
+SNAP Element = W, Radius 0.5, Weight 1 
+Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
+SNAP keyword rcutfac 4.73442 
+SNAP keyword twojmax 8 
+SNAP keyword gamma 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword diagonalstyle 3 
+pair_coeff      2 2 table 1 He_He_JW2013.table HeHe
+Reading potential file He_He_JW2013.table with DATE: 2017-02-20
+WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:476)
+pair_coeff      1 2 table 2 W_He_JW2013.table WHe
+Reading potential file W_He_JW2013.table with DATE: 2017-02-20
+WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:476)
+#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
+#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
+
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton/skip
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual, skip from (6)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) pair table, perpetual, skip from (5)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) pair table, perpetual, skip from (5)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, half/full from (6)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (6) neighbor class addition, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Memory usage per processor = 7.6729 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -10.438105            0    -10.39963   -5445.2808 
+      10    290.48923   -10.436885            0   -10.399629   -5646.4813 
+      20    271.18868   -10.434409            0   -10.399629   -5654.4646 
+      30     246.2601   -10.431212            0   -10.399629   -5281.8873 
+      40    218.69918   -10.427677            0   -10.399629   -4343.3636 
+      50    189.12519   -10.423885            0   -10.399629   -2903.1138 
+      60    155.55701   -10.419579            0   -10.399629   -1402.2278 
+      70    118.83581   -10.414869            0   -10.399629   -146.36141 
+      80    85.903126   -10.410645            0   -10.399628    857.74986 
+      90    65.223651   -10.407993            0   -10.399628    1494.2746 
+     100    59.833542   -10.407302            0   -10.399628    1938.9164 
+Loop time of 11.0736 on 1 procs for 100 steps with 128 atoms
+
+Performance: 0.390 ns/day, 61.520 hours/ns, 9.030 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.072     | 11.072     | 11.072     |   0.0 | 99.99
+Neigh   | 0.00041604 | 0.00041604 | 0.00041604 |   0.0 |  0.00
+Comm    | 0.00046253 | 0.00046253 | 0.00046253 |   0.0 |  0.00
+Output  | 0.0001657  | 0.0001657  | 0.0001657  |   0.0 |  0.00
+Modify  | 0.0002265  | 0.0002265  | 0.0002265  |   0.0 |  0.00
+Other   |            | 0.0003119  |            |       |  0.00
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    727 ave 727 max 727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3425 ave 3425 max 3425 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  6850 ave 6850 max 6850 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 6850
+Ave neighs/atom = 53.5156
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:11
--- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4
+++ b/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4
@ -0,0 +1,179 @@
+LAMMPS (13 Feb 2017)
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.1803
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary	p p p
+
+lattice         bcc $a
+lattice         bcc 3.1803
+Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+region		box block 0 4 0 ${ny} 0 ${nz}
+region		box block 0 4 0 4 0 ${nz}
+region		box block 0 4 0 4 0 4
+create_box	2 box
+Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 128 atoms
+mass 1 183.84
+mass 2 4.0026
+
+set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He
+  5 settings made for type/fraction
+group	tungsten type 1
+123 atoms in group tungsten
+group	helium	type 2
+5 atoms in group helium
+# choose potential
+
+include W.SNAP_HePair.pot
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+#
+# Definition of SNAP+ZBL+Tabulated potential.
+variable zblcutinner equal 4
+variable zblcutouter equal 4.8
+variable zblz equal 74
+
+# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
+pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000
+pair_coeff 	1 1 zbl ${zblz} ${zblz}
+pair_coeff 	1 1 zbl 74 ${zblz}
+pair_coeff 	1 1 zbl 74 74
+pair_coeff 	* * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
+Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
+SNAP Element = W, Radius 0.5, Weight 1 
+Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
+SNAP keyword rcutfac 4.73442 
+SNAP keyword twojmax 8 
+SNAP keyword gamma 1 
+SNAP keyword rfac0 0.99363 
+SNAP keyword rmin0 0 
+SNAP keyword diagonalstyle 3 
+pair_coeff      2 2 table 1 He_He_JW2013.table HeHe
+Reading potential file He_He_JW2013.table with DATE: 2017-02-20
+WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:476)
+pair_coeff      1 2 table 2 W_He_JW2013.table WHe
+Reading potential file W_He_JW2013.table with DATE: 2017-02-20
+WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:476)
+#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
+#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
+
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.8
+  ghost atom cutoff = 5.8
+  binsize = 2.9, bins = 5 5 5
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair zbl, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton/skip
+      stencil: none
+      bin: none
+  (2) pair snap, perpetual, skip from (6)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) pair table, perpetual, skip from (5)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) pair table, perpetual, skip from (5)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, half/full from (6)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (6) neighbor class addition, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Memory usage per processor = 7.65426 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -10.438105            0    -10.39963   -5445.2808 
+      10    292.13979   -10.437097            0    -10.39963   -5516.3963 
+      20    272.55728   -10.434585            0   -10.399629   -5460.4268 
+      30    245.06559   -10.431059            0   -10.399629   -5016.6351 
+      40    212.79459    -10.42692            0   -10.399629   -3924.2175 
+      50    178.03903   -10.422462            0   -10.399629   -2354.5485 
+      60    141.62155   -10.417791            0   -10.399628   -595.41345 
+      70    107.24843   -10.413383            0   -10.399628    1138.4107 
+      80    79.985938   -10.409886            0   -10.399628    2392.1106 
+      90    62.568933   -10.407652            0   -10.399628    3141.7027 
+     100    56.697933   -10.406899            0   -10.399628    3583.9538 
+Loop time of 2.8757 on 4 procs for 100 steps with 128 atoms
+
+Performance: 1.502 ns/day, 15.976 hours/ns, 34.774 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.7363     | 2.8122     | 2.8636     |   2.9 | 97.79
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.011014   | 0.062439   | 0.13842    |  19.3 |  2.17
+Output  | 0.00023842 | 0.00025076 | 0.0002861  |   0.0 |  0.01
+Modify  | 9.2506e-05 | 9.9301e-05 | 0.00010395 |   0.0 |  0.00
+Other   |            | 0.0006654  |            |       |  0.02
+
+Nlocal:    32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    431 ave 431 max 431 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    856.25 ave 885 max 818 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+FullNghs:  1712.5 ave 1738 max 1658 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+
+Total # of neighbors = 6850
+Ave neighs/atom = 53.5156
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:02
--- a/examples/snap/log.5Oct16.snap.Ta06A.g++.1
+++ b/examples/snap/log.5Oct16.snap.Ta06A.g++.1
--- a/examples/snap/log.5Oct16.snap.Ta06A.g++.4
+++ b/examples/snap/log.5Oct16.snap.Ta06A.g++.4
--- a/lib/kokkos/CHANGELOG.md
+++ b/lib/kokkos/CHANGELOG.md
@ -1,5 +1,27 @@
 # Change Log

+## [2.02.15](https://github.com/kokkos/kokkos/tree/2.02.15) (2017-02-10)
+[Full Changelog](https://github.com/kokkos/kokkos/compare/2.02.07...2.02.15)
+
+**Implemented enhancements:**
+
+- Containers: Adding block partitioning to StaticCrsGraph [\#625](https://github.com/kokkos/kokkos/issues/625)
+- Kokkos Make System can induce Errors on Cray Volta System [\#610](https://github.com/kokkos/kokkos/issues/610)
+- OpenMP: error out if KOKKOS\_HAVE\_OPENMP is defined but not \_OPENMP [\#605](https://github.com/kokkos/kokkos/issues/605)
+- CMake: fix standalone build with tests [\#604](https://github.com/kokkos/kokkos/issues/604)
+- Change README \(that GitHub shows when opening Kokkos project page\) to tell users how to submit PRs [\#597](https://github.com/kokkos/kokkos/issues/597)
+- Add correctness testing for all operators of Atomic View [\#420](https://github.com/kokkos/kokkos/issues/420)
+- Allow assignment of Views with compatible memory spaces [\#290](https://github.com/kokkos/kokkos/issues/290)
+- Build only one version of Kokkos library for tests [\#213](https://github.com/kokkos/kokkos/issues/213)
+- Clean out old KOKKOS\_HAVE\_CXX11 macros clauses [\#156](https://github.com/kokkos/kokkos/issues/156)
+- Harmonize Macro names [\#150](https://github.com/kokkos/kokkos/issues/150)
+
+**Fixed bugs:**
+
+- Cray and PGI: Kokkos\_Parallel\_Reduce [\#634](https://github.com/kokkos/kokkos/issues/634)
+- Kokkos Make System can induce Errors on Cray Volta System [\#610](https://github.com/kokkos/kokkos/issues/610)
+- Normal\(\) function random number generator doesn't give the expected distribution [\#592](https://github.com/kokkos/kokkos/issues/592)
+
 ## [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)

--- a/lib/kokkos/CMakeLists.txt
+++ b/lib/kokkos/CMakeLists.txt
@ -1,4 +1,3 @@
-
 IF(COMMAND TRIBITS_PACKAGE_DECL)
  SET(KOKKOS_HAS_TRILINOS ON CACHE BOOL "")
 ELSE()
@ -8,6 +7,7 @@ ENDIF()
 IF(NOT KOKKOS_HAS_TRILINOS)
  CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11 FATAL_ERROR)
  INCLUDE(cmake/tribits.cmake)
+  SET(CMAKE_CXX_STANDARD 11)
 ENDIF()

 #
--- a/lib/kokkos/LICENSE
+++ b/lib/kokkos/LICENSE
@ -6,6 +6,8 @@
 // 
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
+//
+// Kokkos is licensed under 3-clause BSD terms of use:
 // 
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
--- a/lib/kokkos/Makefile.kokkos
+++ b/lib/kokkos/Makefile.kokkos
@ -7,7 +7,7 @@ CXXFLAGS=$(CCFLAGS)
 #Options: OpenMP,Serial,Pthreads,Cuda
 KOKKOS_DEVICES ?= "OpenMP"
 #KOKKOS_DEVICES ?= "Pthreads"
-#Options: KNC,SNB,HSW,Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal61,ARMv80,ARMv81,ARMv8-ThunderX,BGQ,Power7,Power8,KNL,BDW,SKX
+#Options: KNC,SNB,HSW,Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal61,ARMv80,ARMv81,ARMv8-ThunderX,BGQ,Power7,Power8,Power9,KNL,BDW,SKX
 KOKKOS_ARCH ?= ""
 #Options: yes,no
 KOKKOS_DEBUG ?= "no"
@ -192,7 +192,8 @@ KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX := $(strip $(shell echo $(KOKKOS_ARCH) |
 KOKKOS_INTERNAL_USE_ARCH_BGQ := $(strip $(shell echo $(KOKKOS_ARCH) | grep BGQ | wc -l))
 KOKKOS_INTERNAL_USE_ARCH_POWER7 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Power7 | wc -l))
 KOKKOS_INTERNAL_USE_ARCH_POWER8 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Power8 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_BGQ)+$(KOKKOS_INTERNAL_USE_ARCH_POWER7)+$(KOKKOS_INTERNAL_USE_ARCH_POWER8) | bc))
+KOKKOS_INTERNAL_USE_ARCH_POWER9 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Power9 | wc -l))
+KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_BGQ)+$(KOKKOS_INTERNAL_USE_ARCH_POWER7)+$(KOKKOS_INTERNAL_USE_ARCH_POWER8)+$(KOKKOS_INTERNAL_USE_ARCH_POWER9) | bc))

 #AMD based
 KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(strip $(shell echo $(KOKKOS_ARCH) | grep AMDAVX | wc -l))
@ -206,7 +207,7 @@ KOKKOS_INTERNAL_USE_ARCH_AVX512XEON := $(strip $(shell echo $(KOKKOS_INTERNAL_US
 # Decide what ISA level we are able to support
 KOKKOS_INTERNAL_USE_ISA_X86_64     := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_SNB)+$(KOKKOS_INTERNAL_USE_ARCH_HSW)+$(KOKKOS_INTERNAL_USE_ARCH_BDW)+$(KOKKOS_INTERNAL_USE_ARCH_KNL)+$(KOKKOS_INTERNAL_USE_ARCH_SKX) | bc ))
 KOKKOS_INTERNAL_USE_ISA_KNC        := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_KNC) | bc ))
-KOKKOS_INTERNAL_USE_ISA_POWERPCLE  := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_POWER8) | bc ))
+KOKKOS_INTERNAL_USE_ISA_POWERPCLE  := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_POWER8)+$(KOKKOS_INTERNAL_USE_ARCH_POWER9) | bc ))

 #Incompatible flags?
 KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_AMDAVX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)>1" | bc ))
@ -453,6 +454,17 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER8), 1)
 	endif
 endif

+ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER9), 1)
+    tmp := $(shell echo "\#define KOKKOS_ARCH_POWER9 1" >> KokkosCore_config.tmp )
+	ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) 
+
+	else
+		# Assume that this is a really a GNU compiler or it could be XL on P9
+		KOKKOS_CXXFLAGS += -mcpu=power9 -mtune=power9
+		KOKKOS_LDFLAGS  += -mcpu=power9 -mtune=power9
+	endif
+endif
+
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX2), 1)
    tmp := $(shell echo "\#define KOKKOS_ARCH_AVX2 1" >> KokkosCore_config.tmp )
 	ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
--- a/lib/kokkos/README
+++ b/lib/kokkos/README
@ -5,6 +5,9 @@ Kokkos is designed to target complex node architectures with N-level memory
 hierarchies and multiple types of execution resources. It currently can use
 OpenMP, Pthreads and CUDA as backend programming models.

+Kokkos is licensed under standard 3-clause BSD terms of use. For specifics
+see the LICENSE file contained in the repository or distribution.
+
 The core developers of Kokkos are Carter Edwards and Christian Trott
 at the Computer Science Research Institute of the Sandia National
 Laboratories.
@ -151,4 +154,12 @@ MPI rank of an application uses a single GPU [can be the same GPU for
 multiple MPI ranks]) you can set CUDA_MANAGED_FORCE_DEVICE_ALLOC=1.
 This will enforce proper UVM allocations, but can lead to errors if 
 more than a single GPU is used by a single process.
- 
+
+===========================================================================
+====Contributing===========================================================
+===========================================================================
+
+Contributions to Kokkos are welcome. In order to do so, please open an issue
+where a feature request or bug can be discussed. Then issue a pull request
+with your contribution. Pull requests must be issued against the develop branch. 
+
--- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp
+++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp
@ -1014,7 +1014,7 @@ namespace Kokkos {
    }
  };

-#if defined(KOKKOS_HAVE_CUDA) && defined(__CUDACC__)
+#if defined(KOKKOS_ENABLE_CUDA) && defined(__CUDACC__)

  template<>
  class Random_XorShift1024<Kokkos::Cuda> {
--- a/lib/kokkos/algorithms/unit_tests/TestCuda.cpp
+++ b/lib/kokkos/algorithms/unit_tests/TestCuda.cpp
@ -49,7 +49,7 @@

 #include <Kokkos_Core.hpp>

-#ifdef KOKKOS_HAVE_CUDA
+#ifdef KOKKOS_ENABLE_CUDA

 #include <TestRandom.hpp>
 #include <TestSort.hpp>
@ -106,5 +106,5 @@ CUDA_SORT_UNSIGNED(171)
 #undef CUDA_SORT_UNSIGNED
 }

-#endif  /* #ifdef KOKKOS_HAVE_CUDA */
+#endif  /* #ifdef KOKKOS_ENABLE_CUDA */

--- a/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp
+++ b/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp
@ -52,7 +52,7 @@

 namespace Test {

-#ifdef KOKKOS_HAVE_OPENMP
+#ifdef KOKKOS_ENABLE_OPENMP
 class openmp : public ::testing::Test {
 protected:
  static void SetUpTestCase()
--- a/lib/kokkos/algorithms/unit_tests/TestSerial.cpp
+++ b/lib/kokkos/algorithms/unit_tests/TestSerial.cpp
@ -55,7 +55,7 @@

 namespace Test {

-#ifdef KOKKOS_HAVE_SERIAL
+#ifdef KOKKOS_ENABLE_SERIAL
 class serial : public ::testing::Test {
 protected:
  static void SetUpTestCase()
@ -93,7 +93,7 @@ SERIAL_SORT_UNSIGNED(171)
 #undef SERIAL_RANDOM_XORSHIFT1024
 #undef SERIAL_SORT_UNSIGNED

-#endif // KOKKOS_HAVE_SERIAL
+#endif // KOKKOS_ENABLE_SERIAL
 } // namespace Test


--- a/lib/kokkos/algorithms/unit_tests/TestThreads.cpp
+++ b/lib/kokkos/algorithms/unit_tests/TestThreads.cpp
@ -55,7 +55,7 @@

 namespace Test {

-#ifdef KOKKOS_HAVE_PTHREAD
+#ifdef KOKKOS_ENABLE_PTHREAD
 class threads : public ::testing::Test {
 protected:
  static void SetUpTestCase()
--- a/lib/kokkos/cmake/tribits.cmake
+++ b/lib/kokkos/cmake/tribits.cmake
@ -4,13 +4,31 @@ INCLUDE(CTest)
 cmake_policy(SET CMP0054 NEW)

 IF(NOT DEFINED ${PROJECT_NAME})
-  project(Kokkos) 
+  project(KokkosCMake) 
 ENDIF()

-IF(NOT DEFINED ${${PROJECT_NAME}_ENABLE_DEBUG}})
+MESSAGE(WARNING "The project name is: ${PROJECT_NAME}")
+
+IF(NOT DEFINED ${PROJECT_NAME}_ENABLE_OpenMP)
+  SET(${PROJECT_NAME}_ENABLE_OpenMP OFF)
+ENDIF()
+
+IF(NOT DEFINED ${PROJECT_NAME}_ENABLE_DEBUG)
  SET(${PROJECT_NAME}_ENABLE_DEBUG OFF)
 ENDIF()

+IF(NOT DEFINED ${PROJECT_NAME}_ENABLE_CXX11)
+  SET(${PROJECT_NAME}_ENABLE_CXX11 ON)
+ENDIF()
+
+IF(NOT DEFINED ${PROJECT_NAME}_ENABLE_TESTS)
+  SET(${PROJECT_NAME}_ENABLE_TESTS OFF)
+ENDIF()
+
+IF(NOT DEFINED TPL_ENABLE_Pthread)
+  SET(TPL_ENABLE_Pthread OFF)
+ENDIF()
+
 FUNCTION(ASSERT_DEFINED VARS)
  FOREACH(VAR ${VARS})
    IF(NOT DEFINED ${VAR})
@ -70,9 +88,11 @@ ENDMACRO()


 MACRO(TRIBITS_ADD_TEST_DIRECTORIES)
-  FOREACH(TEST_DIR ${ARGN})
-    ADD_SUBDIRECTORY(${TEST_DIR})
-  ENDFOREACH()
+  IF(${${PROJECT_NAME}_ENABLE_TESTS})
+    FOREACH(TEST_DIR ${ARGN})
+      ADD_SUBDIRECTORY(${TEST_DIR})
+    ENDFOREACH()
+  ENDIF()
 ENDMACRO()

 MACRO(TRIBITS_ADD_EXAMPLE_DIRECTORIES)
@ -264,11 +284,11 @@ FUNCTION(TRIBITS_ADD_EXECUTABLE EXE_NAME)
    SET(EXE_BINARY_NAME ${PACKAGE_NAME}_${EXE_BINARY_NAME})
  ENDIF()

-  IF (PARSE_TESTONLY)
-    SET(EXCLUDE_FROM_ALL_KEYWORD "EXCLUDE_FROM_ALL")
-  ELSE()
-    SET(EXCLUDE_FROM_ALL_KEYWORD)
-  ENDIF()
+  # IF (PARSE_TESTONLY)
+  #   SET(EXCLUDE_FROM_ALL_KEYWORD "EXCLUDE_FROM_ALL")
+  # ELSE()
+  #   SET(EXCLUDE_FROM_ALL_KEYWORD)
+  # ENDIF()
  ADD_EXECUTABLE(${EXE_BINARY_NAME} ${EXCLUDE_FROM_ALL_KEYWORD} ${EXE_SOURCES})

  TARGET_LINK_AND_INCLUDE_LIBRARIES(${EXE_BINARY_NAME} ${LINK_LIBS})
@ -470,9 +490,8 @@ ENDMACRO(TRIBITS_SUBPACKAGE_POSTPROCESS)

 MACRO(TRIBITS_PACKAGE_DECL NAME)

-  PROJECT(${NAME})
-  STRING(TOUPPER ${PROJECT_NAME} PROJECT_NAME_UC)
-  SET(PACKAGE_NAME ${PROJECT_NAME})
+  SET(PACKAGE_NAME ${NAME})
+  SET(${PACKAGE_NAME}_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
  STRING(TOUPPER ${PACKAGE_NAME} PACKAGE_NAME_UC)

  SET(TRIBITS_DEPS_DIR "${CMAKE_SOURCE_DIR}/cmake/deps")
@ -489,7 +508,7 @@ MACRO(TRIBITS_PROCESS_SUBPACKAGES)
  FOREACH(SUBPACKAGE ${SUBPACKAGES})
    GET_FILENAME_COMPONENT(SUBPACKAGE_CMAKE ${SUBPACKAGE} DIRECTORY)
    GET_FILENAME_COMPONENT(SUBPACKAGE_DIR ${SUBPACKAGE_CMAKE} DIRECTORY)
-    ADD_SUBDIRECTORY(${SUBPACKAGE_DIR})
+    ADD_SUBDIRECTORY(${CMAKE_BINARY_DIR}/../${SUBPACKAGE_DIR})
  ENDFOREACH()
 ENDMACRO(TRIBITS_PROCESS_SUBPACKAGES)

--- a/lib/kokkos/config/master_history.txt
+++ b/lib/kokkos/config/master_history.txt
@ -4,3 +4,4 @@ tag:  2.01.10    date: 09:27:2016    master: e4119325    develop: e6cda11e
 tag:  2.02.00    date: 10:30:2016    master: 6c90a581    develop: ca3dd56e
 tag:  2.02.01    date: 11:01:2016    master: 9c698c86    develop: b0072304
 tag:  2.02.07    date: 12:16:2016    master: 4b4cc4ba    develop: 382c0966
+tag:  2.02.15    date: 02:10:2017    master: 8c64cd93    develop: 28dea8b6 
--- a/lib/kokkos/config/test_all_sandia
+++ b/lib/kokkos/config/test_all_sandia
@ -10,12 +10,18 @@ set -o pipefail

 MACHINE=""
 HOSTNAME=$(hostname)
+PROCESSOR=`uname -p`
+
 if [[ "$HOSTNAME" =~ (white|ride).* ]]; then
    MACHINE=white
 elif [[ "$HOSTNAME" =~ .*bowman.* ]]; then
    MACHINE=bowman
 elif [[ "$HOSTNAME" =~ node.* ]]; then # Warning: very generic name
-    MACHINE=shepard
+    if [[ "$PROCESSOR" = "aarch64" ]]; then
+        MACHINE=sullivan
+    else
+        MACHINE=shepard
+    fi
 elif [[ "$HOSTNAME" =~ apollo ]]; then
    MACHINE=apollo
 elif [ ! -z "$SEMS_MODULEFILES_ROOT" ]; then
@ -27,6 +33,7 @@ fi

 GCC_BUILD_LIST="OpenMP,Pthread,Serial,OpenMP_Serial,Pthread_Serial"
 IBM_BUILD_LIST="OpenMP,Serial,OpenMP_Serial"
+ARM_GCC_BUILD_LIST="OpenMP,Serial,OpenMP_Serial"
 INTEL_BUILD_LIST="OpenMP,Pthread,Serial,OpenMP_Serial,Pthread_Serial"
 CLANG_BUILD_LIST="Pthread,Serial,Pthread_Serial"
 CUDA_BUILD_LIST="Cuda_OpenMP,Cuda_Pthread,Cuda_Serial"
@ -200,6 +207,23 @@ elif [ "$MACHINE" = "bowman" ]; then
    if [ -z "$ARCH_FLAG" ]; then
      ARCH_FLAG="--arch=KNL"
    fi
+
+    NUM_JOBS_TO_RUN_IN_PARALLEL=2
+
+elif [ "$MACHINE" = "sullivan" ]; then
+    source /etc/profile.d/modules.sh
+    SKIP_HWLOC=True
+    export SLURM_TASKS_PER_NODE=96
+
+    BASE_MODULE_LIST="<COMPILER_NAME>/<COMPILER_VERSION>"
+
+    # Format: (compiler module-list build-list exe-name warning-flag)
+    COMPILERS=("gcc/5.3.0 $BASE_MODULE_LIST $ARM_GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS")
+
+    if [ -z "$ARCH_FLAG" ]; then
+      ARCH_FLAG="--arch=ARMv8-ThunderX"
+    fi
+
    NUM_JOBS_TO_RUN_IN_PARALLEL=2

 elif [ "$MACHINE" = "shepard" ]; then
@ -297,7 +321,8 @@ echo "    Defaults to root repo containing this script"
 echo "--debug: Run tests in debug. Defaults to False"
 echo "--test-script: Test this script, not Kokkos"
 echo "--skip-hwloc: Do not do hwloc tests"
-echo "--num=N: Number of jobs to run in parallel "
+echo "--num=N: Number of jobs to run in parallel"
+echo "--spot-check: Minimal test set to issue pull request"
 echo "--dry-run: Just print what would be executed"
 echo "--build-only: Just do builds, don't run anything"
 echo "--opt-flag=FLAG: Optimization flag (default: -O3)"
--- a/lib/kokkos/config/test_kokkos_master_develop_promotion.sh
+++ b/lib/kokkos/config/test_kokkos_master_develop_promotion.sh
@ -0,0 +1,66 @@
+#!/bin/bash 
+
+. /etc/profile.d/modules.sh
+
+echo "build-dir $1"
+echo "backend $2"
+echo "module $3"
+echo "compiler $4"
+echo "cxxflags $5"
+echo "architecrure $6"
+echo "debug $7"
+echo "kokkos-options $8"
+echo "kokkos-cuda-options $9"
+echo "hwloc $9"
+
+NOW=`date "+%Y%m%d%H%M%S"`
+BASEDIR="$1-$NOW"
+
+mkdir $BASEDIR
+cd $BASEDIR
+
+module load $2
+
+if [ $9 == "yes" ]; then
+if [ $7 == "debug" ]; then
+  ../generate_makefile.sh --with-devices=$2 \
+  	--compiler=$4 \
+	--cxxflags=$5 \
+        --arch=$6 \
+        --debug \
+	--with-options=$8 \
+        --with-cuda-options=$9
+        --with-hwloc=${HWLOC_ROOT}
+else
+    ../generate_makefile.sh --with-devices=$2 \
+        --compiler=$4 \
+        --cxxflags=$5 \
+        --arch=$6 \
+        --debug \
+        --with-options=$8 \
+        --with-cuda-options=$9 
+        --with-hwloc=${HWLOC_ROOT}
+fi
+else
+if [ $7 == "debug" ]; then
+  ../generate_makefile.sh --with-devices=$2 \
+        --compiler=$4 \
+        --cxxflags=$5 \
+        --arch=$6 \
+        --debug \
+        --with-options=$8 \
+        --with-cuda-options=$9
+else
+    ../generate_makefile.sh --with-devices=$2 \
+        --compiler=$4 \
+        --cxxflags=$5 \
+        --arch=$6 \
+        --debug \
+        --with-options=$8 \
+        --with-cuda-options=$9 
+fi
+fi
+
+
+make test
+return $?
--- a/lib/kokkos/config/trilinos-integration/prepare_trilinos_repos.sh
+++ b/lib/kokkos/config/trilinos-integration/prepare_trilinos_repos.sh
@ -27,13 +27,13 @@ cd ${TRILINOS_UPDATED_PATH}
 echo ""
 echo ""
 echo "Trilinos State:"
-git log --pretty=oneline --since=2.days
-SHA=`git log --pretty=oneline --since=2.days | head -n 2 | tail -n 1 | awk '{print $1}'`
+git log --pretty=oneline --since=7.days
+SHA=`git log --pretty=oneline --since=7.days | head -n 2 | tail -n 1 | awk '{print $1}'`
 cd ..

 cd ${TRILINOS_PRISTINE_PATH}
 git status
-git log --pretty=oneline --since=2.days
+git log --pretty=oneline --since=7.days
 echo "Checkout develop"
 git checkout develop
 echo "Pull"
@ -46,5 +46,5 @@ cd ${TRILINOS_PRISTINE_PATH}
 echo ""
 echo ""
 echo "Trilinos Pristine State:"
-git log --pretty=oneline --since=2.days
+git log --pretty=oneline --since=7.days
 cd ..
--- a/lib/kokkos/containers/performance_tests/TestCuda.cpp
+++ b/lib/kokkos/containers/performance_tests/TestCuda.cpp
@ -52,7 +52,7 @@

 #include <Kokkos_Core.hpp>

-#if defined( KOKKOS_HAVE_CUDA )
+#if defined( KOKKOS_ENABLE_CUDA )

 #include <TestDynRankView.hpp>

@ -106,4 +106,4 @@ TEST_F( cuda, unordered_map_performance_far)

 }

-#endif  /* #if defined( KOKKOS_HAVE_CUDA ) */
+#endif  /* #if defined( KOKKOS_ENABLE_CUDA ) */
--- a/lib/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp
+++ b/lib/kokkos/containers/performance_tests/TestUnorderedMapPerformance.hpp
@ -1,12 +1,12 @@
 //@HEADER
 // ************************************************************************
-// 
+//
 //                        Kokkos v. 2.0
 //              Copyright (2014) Sandia Corporation
-// 
+//
 // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
 // the U.S. Government retains certain rights in this software.
-// 
+//
 // Redistribution and use in source and binary forms, with or without
 // modification, are permitted provided that the following conditions are
 // met:
@ -35,7 +35,7 @@
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // Questions? Contact  H. Carter Edwards (hcedwar@sandia.gov)
-// 
+//
 // ************************************************************************
 //@HEADER

@ -164,12 +164,10 @@ struct UnorderedMapTest

 };

-//#define KOKKOS_COLLECT_UNORDERED_MAP_METRICS
-
 template <typename Device, bool Near>
 void run_performance_tests(std::string const & base_file_name)
 {
-#if defined(KOKKOS_COLLECT_UNORDERED_MAP_METRICS)
+#if 0
  std::string metrics_file_name = base_file_name + std::string("-metrics.csv");
  std::string length_file_name = base_file_name  + std::string("-length.csv");
  std::string distance_file_name = base_file_name + std::string("-distance.csv");
--- a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp
+++ b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp
@ -586,13 +586,13 @@ private:
 #if defined( KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK )

 // rank of the calling operator - included as first argument in ARG
-#define KOKKOS_VIEW_OPERATOR_VERIFY( ARG ) \
+#define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( ARG ) \
  DynRankView::template verify_space< Kokkos::Impl::ActiveExecutionMemorySpace >::check(); \
  Kokkos::Experimental::Impl::dyn_rank_view_verify_operator_bounds ARG ; 

 #else

-#define KOKKOS_VIEW_OPERATOR_VERIFY( ARG ) \
+#define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( ARG ) \
  DynRankView::template verify_space< Kokkos::Impl::ActiveExecutionMemorySpace >::check();

 #endif
@ -609,9 +609,9 @@ public:
  reference_type operator()() const
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (0 , this->rank() ,  NULL , m_map) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank() ,  NULL , m_map) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (0 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map) )
      #endif
      return implementation_map().reference();
      //return m_map.reference(0,0,0,0,0,0,0); 
@ -650,9 +650,9 @@ public:
  operator()(const iType & i0 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (1 , this->rank() , NULL , m_map , i0) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , NULL , m_map , i0) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (1 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0) )
      #endif
      return m_map.reference(i0); 
    }
@ -663,9 +663,9 @@ public:
  operator()(const iType & i0 ) const
    {
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (1 , this->rank() , NULL , m_map , i0) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , NULL , m_map , i0) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (1 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0) )
      #endif
      return m_map.reference(i0,0,0,0,0,0,0);
    }
@ -677,9 +677,9 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (2 , this->rank() , NULL , m_map , i0 , i1) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , NULL , m_map , i0 , i1) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (2 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1) )
      #endif
      return m_map.reference(i0,i1); 
    }
@ -690,9 +690,9 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (2 , this->rank() , NULL , m_map , i0 , i1) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , NULL , m_map , i0 , i1) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (2 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1) )
      #endif
      return m_map.reference(i0,i1,0,0,0,0,0); 
    }
@ -704,9 +704,9 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (3 , this->rank() , NULL , m_map , i0 , i1 , i2) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , NULL , m_map , i0 , i1 , i2) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (3 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2) )
      #endif
      return m_map.reference(i0,i1,i2); 
    }
@ -717,9 +717,9 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (3 , this->rank() , NULL , m_map , i0 , i1 , i2) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , NULL , m_map , i0 , i1 , i2) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (3 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2) )
      #endif
      return m_map.reference(i0,i1,i2,0,0,0,0); 
    }
@ -731,9 +731,9 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (4 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (4 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3) )
      #endif
      return m_map.reference(i0,i1,i2,i3); 
    }
@ -744,9 +744,9 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (4 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (4 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3) )
      #endif
      return m_map.reference(i0,i1,i2,i3,0,0,0); 
    }
@ -758,9 +758,9 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (5 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (5 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3,i4) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3,i4) )
      #endif
      return m_map.reference(i0,i1,i2,i3,i4); 
    }
@ -771,9 +771,9 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (5 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (5 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3,i4) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3,i4) )
      #endif
      return m_map.reference(i0,i1,i2,i3,i4,0,0); 
    }
@ -785,9 +785,9 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (6 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (6 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3,i4,i5) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3,i4,i5) )
      #endif
      return m_map.reference(i0,i1,i2,i3,i4,i5); 
    }
@ -798,9 +798,9 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (6 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (6 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3,i4,i5) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3,i4,i5) )
      #endif
      return m_map.reference(i0,i1,i2,i3,i4,i5,0); 
    }
@ -812,14 +812,14 @@ public:
  operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 , const iType6 & i6 ) const 
    { 
      #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
-        KOKKOS_VIEW_OPERATOR_VERIFY( (7 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5 , i6) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (7 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5 , i6) )
      #else
-        KOKKOS_VIEW_OPERATOR_VERIFY( (7 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3,i4,i5,i6) )
+        KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (7 , this->rank() , m_track.template get_label<typename traits::memory_space>().c_str(),m_map,i0,i1,i2,i3,i4,i5,i6) )
      #endif
      return m_map.reference(i0,i1,i2,i3,i4,i5,i6); 
    }

-#undef KOKKOS_VIEW_OPERATOR_VERIFY
+#undef KOKKOS_IMPL_VIEW_OPERATOR_VERIFY

  //----------------------------------------
  // Standard constructor, destructor, and assignment operators... 
@ -960,7 +960,7 @@ public:
      alloc_prop prop( arg_prop );

 //------------------------------------------------------------
-#if defined( KOKKOS_HAVE_CUDA )
+#if defined( KOKKOS_ENABLE_CUDA )
      // If allocating in CudaUVMSpace must fence before and after
      // the allocation to protect against possible concurrent access
      // on the CPU and the GPU.
@ -976,7 +976,7 @@ public:
        record = m_map.allocate_shared( prop , Impl::DynRankDimTraits<typename traits::specialize>::createLayout(arg_layout) );

 //------------------------------------------------------------
-#if defined( KOKKOS_HAVE_CUDA )
+#if defined( KOKKOS_ENABLE_CUDA )
      if ( std::is_same< Kokkos::CudaUVMSpace , typename traits::device_type::memory_space >::value ) {
        traits::device_type::memory_space::execution_space::fence();
      }
--- a/lib/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp
+++ b/lib/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp
@ -51,6 +51,80 @@

 namespace Kokkos {

+namespace Impl {
+  template<class RowOffsetsType, class RowBlockOffsetsType>
+  struct StaticCrsGraphBalancerFunctor {
+    typedef typename RowOffsetsType::non_const_value_type int_type;
+    RowOffsetsType row_offsets;
+    RowBlockOffsetsType row_block_offsets;
+
+    int_type cost_per_row, num_blocks;
+
+    StaticCrsGraphBalancerFunctor(RowOffsetsType row_offsets_,
+                                  RowBlockOffsetsType row_block_offsets_,
+                                  int_type cost_per_row_, int_type num_blocks_):
+                                    row_offsets(row_offsets_),
+                                    row_block_offsets(row_block_offsets_),
+                                    cost_per_row(cost_per_row_),
+                                    num_blocks(num_blocks_){}
+
+    KOKKOS_INLINE_FUNCTION
+    void operator() (const int_type& iRow) const {
+      const int_type num_rows = row_offsets.dimension_0()-1;
+      const int_type num_entries = row_offsets(num_rows);
+      const int_type total_cost = num_entries + num_rows*cost_per_row;
+
+      const double cost_per_workset = 1.0*total_cost/num_blocks;
+
+      const int_type row_cost = row_offsets(iRow+1)-row_offsets(iRow) + cost_per_row;
+
+      int_type count = row_offsets(iRow+1) + cost_per_row*iRow;
+
+      if(iRow == num_rows-1) row_block_offsets(num_blocks) = num_rows;
+
+      if(true) {
+        int_type current_block = (count-row_cost-cost_per_row)/cost_per_workset;
+        int_type end_block = count/cost_per_workset;
+
+        // Handle some corner cases for the last two blocks.
+        if(current_block >= num_blocks-2) {
+          if((current_block == num_blocks-2) && (count >= (current_block + 1) * cost_per_workset)) {
+            int_type row = iRow;
+            int_type cc = count-row_cost-cost_per_row;
+            int_type block = cc/cost_per_workset;
+            while((block>0) && (block==current_block)) {
+              cc = row_offsets(row)+row*cost_per_row;
+              block = cc/cost_per_workset;
+              row--;
+            }
+            if((count-cc-row_cost-cost_per_row) < num_entries-row_offsets(iRow+1)) {
+              row_block_offsets(current_block+1) = iRow+1;
+            } else {
+              row_block_offsets(current_block+1) = iRow;
+            }
+          }
+        } else {
+          if((count >= (current_block + 1) * cost_per_workset) ||
+             (iRow+2 == row_offsets.dimension_0())) {
+            if(end_block>current_block+1) {
+              int_type num_block = end_block-current_block;
+              row_block_offsets(current_block+1) = iRow;
+              for(int_type block = current_block+2; block <= end_block; block++)
+                if((block<current_block+2+(num_block-1)/2))
+                  row_block_offsets(block) = iRow;
+                else
+                  row_block_offsets(block) = iRow+1;
+            } else {
+              row_block_offsets(current_block+1) = iRow+1;
+            }
+          }
+        }
+
+      }
+    }
+  };
+}
+
 /// \class StaticCrsGraph
 /// \brief Compressed row storage array.
 ///
@ -100,19 +174,23 @@ public:
  typedef StaticCrsGraph< DataType , array_layout , typename traits::host_mirror_space , SizeType > HostMirror;
  typedef View< const size_type* , array_layout, device_type >  row_map_type;
  typedef View<       DataType*  , array_layout, device_type >  entries_type;
+  typedef View< const size_type* , array_layout, device_type >  row_block_type;

  entries_type entries;
  row_map_type row_map;
+  row_block_type row_block_offsets;

  //! Construct an empty view.
-  StaticCrsGraph () : entries(), row_map() {}
+  StaticCrsGraph () : entries(), row_map(), row_block_offsets() {}

  //! Copy constructor (shallow copy).
-  StaticCrsGraph (const StaticCrsGraph& rhs) : entries (rhs.entries), row_map (rhs.row_map)
+  StaticCrsGraph (const StaticCrsGraph& rhs) : entries (rhs.entries), row_map (rhs.row_map),
+                                               row_block_offsets(rhs.row_block_offsets)
  {}

  template<class EntriesType, class RowMapType>
-  StaticCrsGraph (const EntriesType& entries_,const RowMapType& row_map_) : entries (entries_), row_map (row_map_)
+  StaticCrsGraph (const EntriesType& entries_,const RowMapType& row_map_) : entries (entries_), row_map (row_map_),
+  row_block_offsets()
  {}

  /** \brief  Assign to a view of the rhs array.
@ -122,6 +200,7 @@ public:
  StaticCrsGraph& operator= (const StaticCrsGraph& rhs) {
    entries = rhs.entries;
    row_map = rhs.row_map;
+    row_block_offsets = rhs.row_block_offsets;
    return *this;
  }

@ -130,12 +209,30 @@ public:
   */
  ~StaticCrsGraph() {}

+  /**  \brief  Return number of rows in the graph
+   */
  KOKKOS_INLINE_FUNCTION
  size_type numRows() const {
    return (row_map.dimension_0 () != 0) ?
      row_map.dimension_0 () - static_cast<size_type> (1) :
      static_cast<size_type> (0);
  }
+
+  /**  \brief  Create a row partitioning into a given number of blocks
+   *           balancing non-zeros + a fixed cost per row.
+   */
+  void create_block_partitioning(size_type num_blocks, size_type fix_cost_per_row = 4) {
+    View< size_type* , array_layout, device_type >
+      block_offsets("StatisCrsGraph::load_balance_offsets",num_blocks+1);
+
+    Impl::StaticCrsGraphBalancerFunctor<row_map_type,View< size_type* , array_layout, device_type > >
+      partitioner(row_map,block_offsets,fix_cost_per_row,num_blocks);
+
+    Kokkos::parallel_for(Kokkos::RangePolicy<execution_space>(0,numRows()),partitioner);
+    Kokkos::fence();
+
+    row_block_offsets = block_offsets;
+  }
 };

 //----------------------------------------------------------------------------
--- a/lib/kokkos/containers/src/Kokkos_Vector.hpp
+++ b/lib/kokkos/containers/src/Kokkos_Vector.hpp
@ -72,7 +72,7 @@ private:


 public:
-#ifdef KOKKOS_CUDA_USE_UVM
+#ifdef KOKKOS_ENABLE_CUDA_UVM
  KOKKOS_INLINE_FUNCTION Scalar& operator() (int i) const {return DV::h_view(i);};
  KOKKOS_INLINE_FUNCTION Scalar& operator[] (int i) const {return DV::h_view(i);};
 #else
--- a/lib/kokkos/containers/src/impl/Kokkos_Functional_impl.hpp
+++ b/lib/kokkos/containers/src/impl/Kokkos_Functional_impl.hpp
@ -133,11 +133,11 @@ uint32_t MurmurHash3_x86_32 ( const void * key, int len, uint32_t seed )
    defined( __GNUG__ ) /* GNU C++ */ || \
    defined( __clang__ )

-#define KOKKOS_MAY_ALIAS __attribute__((__may_alias__))
+#define KOKKOS_IMPL_MAY_ALIAS __attribute__((__may_alias__))

 #else

-#define KOKKOS_MAY_ALIAS
+#define KOKKOS_IMPL_MAY_ALIAS

 #endif

@ -145,10 +145,10 @@ template <typename T>
 KOKKOS_FORCEINLINE_FUNCTION
 bool bitwise_equal(T const * const a_ptr, T const * const b_ptr)
 {
-  typedef uint64_t KOKKOS_MAY_ALIAS T64;
-  typedef uint32_t KOKKOS_MAY_ALIAS T32;
-  typedef uint16_t KOKKOS_MAY_ALIAS T16;
-  typedef uint8_t  KOKKOS_MAY_ALIAS T8;
+  typedef uint64_t KOKKOS_IMPL_MAY_ALIAS T64;
+  typedef uint32_t KOKKOS_IMPL_MAY_ALIAS T32;
+  typedef uint16_t KOKKOS_IMPL_MAY_ALIAS T16;
+  typedef uint8_t  KOKKOS_IMPL_MAY_ALIAS T8;

  enum {
    NUM_8  = sizeof(T),
@ -188,7 +188,7 @@ bool bitwise_equal(T const * const a_ptr, T const * const b_ptr)



-#undef KOKKOS_MAY_ALIAS
+#undef KOKKOS_IMPL_MAY_ALIAS

 }} // namespace Kokkos::Impl

--- a/lib/kokkos/containers/src/impl/Kokkos_StaticCrsGraph_factory.hpp
+++ b/lib/kokkos/containers/src/impl/Kokkos_StaticCrsGraph_factory.hpp
@ -69,15 +69,17 @@ create_mirror( const StaticCrsGraph<DataType,Arg1Type,Arg2Type,SizeType > & view

  typename staticcrsgraph_type::HostMirror               tmp ;
  typename staticcrsgraph_type::row_map_type::HostMirror tmp_row_map = create_mirror( view.row_map);
+  typename staticcrsgraph_type::row_block_type::HostMirror tmp_row_block_offsets = create_mirror( view.row_block_offsets);

  // Allocation to match:
  tmp.row_map = tmp_row_map ; // Assignment of 'const' from 'non-const'
  tmp.entries = create_mirror( view.entries );
-
+  tmp.row_block_offsets = tmp_row_block_offsets ; // Assignment of 'const' from 'non-const'

  // Deep copy:
  deep_copy( tmp_row_map , view.row_map );
  deep_copy( tmp.entries , view.entries );
+  deep_copy( tmp_row_block_offsets , view.row_block_offsets );

  return tmp ;
 }
--- a/lib/kokkos/containers/unit_tests/TestCuda.cpp
+++ b/lib/kokkos/containers/unit_tests/TestCuda.cpp
@ -69,7 +69,7 @@
 //----------------------------------------------------------------------------


-#ifdef KOKKOS_HAVE_CUDA
+#ifdef KOKKOS_ENABLE_CUDA

 namespace Test {

@ -96,6 +96,18 @@ TEST_F( cuda , staticcrsgraph )
 {
  TestStaticCrsGraph::run_test_graph< Kokkos::Cuda >();
  TestStaticCrsGraph::run_test_graph2< Kokkos::Cuda >();
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(1, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(1, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(1, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(1, 100000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(3, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(3, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(3, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(3, 100000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(75, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(75, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(75, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Cuda >(75, 100000);
 }


@ -225,5 +237,5 @@ TEST_F(cuda, ErrorReporter)

 }

-#endif  /* #ifdef KOKKOS_HAVE_CUDA */
+#endif  /* #ifdef KOKKOS_ENABLE_CUDA */

--- a/lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp
+++ b/lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp
@ -1298,7 +1298,7 @@ public:
    // For CUDA the constant random access View does not return
    // an lvalue reference due to retrieving through texture cache
    // therefore not allowed to query the underlying pointer.
-#if defined(KOKKOS_HAVE_CUDA)
+#if defined(KOKKOS_ENABLE_CUDA)
    if ( ! std::is_same< typename device::execution_space , Kokkos::Cuda >::value )
 #endif
    {
@ -1408,7 +1408,7 @@ public:
    ASSERT_EQ( ds5.dimension_4() , ds5plus.dimension_4() );
    ASSERT_EQ( ds5.dimension_5() , ds5plus.dimension_5() );

-#if ! defined( KOKKOS_HAVE_CUDA ) || defined ( KOKKOS_USE_CUDA_UVM )
+#if ! defined( KOKKOS_ENABLE_CUDA ) || defined ( KOKKOS_ENABLE_CUDA_UVM )
    ASSERT_EQ( & ds5(1,1,1,1,0) - & ds5plus(1,1,1,1,0) , 0 );
    ASSERT_EQ( & ds5(1,1,1,1,0,0) - & ds5plus(1,1,1,1,0,0) , 0 );  // passing argument to rank beyond the view's rank is allowed iff it is a 0. 
 #endif
--- a/lib/kokkos/containers/unit_tests/TestErrorReporter.hpp
+++ b/lib/kokkos/containers/unit_tests/TestErrorReporter.hpp
@ -200,7 +200,7 @@ struct ErrorReporterDriverUseLambda : public ErrorReporterDriverBase<DeviceType>
 #endif


-#ifdef KOKKOS_HAVE_OPENMP
+#ifdef KOKKOS_ENABLE_OPENMP
 struct ErrorReporterDriverNativeOpenMP : public ErrorReporterDriverBase<Kokkos::OpenMP>
 {
  typedef ErrorReporterDriverBase<Kokkos::OpenMP>  driver_base;
--- a/lib/kokkos/containers/unit_tests/TestOpenMP.cpp
+++ b/lib/kokkos/containers/unit_tests/TestOpenMP.cpp
@ -68,7 +68,7 @@

 namespace Test {

-#ifdef KOKKOS_HAVE_OPENMP
+#ifdef KOKKOS_ENABLE_OPENMP
 class openmp : public ::testing::Test {
 protected:
  static void SetUpTestCase()
@ -109,6 +109,18 @@ TEST_F( openmp , staticcrsgraph )
 {
  TestStaticCrsGraph::run_test_graph< Kokkos::OpenMP >();
  TestStaticCrsGraph::run_test_graph2< Kokkos::OpenMP >();
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(1, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(1, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(1, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(1, 100000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(3, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(3, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(3, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(3, 100000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(75, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(75, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(75, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::OpenMP >(75, 100000);
 }

 #define OPENMP_INSERT_TEST( name, num_nodes, num_inserts, num_duplicates, repeat, near )                                \
--- a/lib/kokkos/containers/unit_tests/TestSerial.cpp
+++ b/lib/kokkos/containers/unit_tests/TestSerial.cpp
@ -45,7 +45,7 @@

 #include <Kokkos_Core.hpp>

-#if ! defined(KOKKOS_HAVE_SERIAL)
+#if ! defined(KOKKOS_ENABLE_SERIAL)
 #  error "It doesn't make sense to build this file unless the Kokkos::Serial device is enabled.  If you see this message, it probably means that there is an error in Kokkos' CMake build infrastructure."
 #else

@ -91,6 +91,18 @@ TEST_F( serial , staticcrsgraph )
 {
  TestStaticCrsGraph::run_test_graph< Kokkos::Serial >();
  TestStaticCrsGraph::run_test_graph2< Kokkos::Serial >();
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(1, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(1, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(1, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(1, 100000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(3, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(3, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(3, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(3, 100000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(75, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(75, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(75, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Serial >(75, 100000);
 }

 TEST_F( serial, complex )
@ -178,6 +190,6 @@ TEST_F(serial, ErrorReporter)

 } // namespace Test

-#endif // KOKKOS_HAVE_SERIAL
+#endif // KOKKOS_ENABLE_SERIAL


--- a/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp
+++ b/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp
@ -144,6 +144,44 @@ void run_test_graph2()
  }
 }

+template< class Space >
+void run_test_graph3(size_t B, size_t N)
+{
+  srand(10310);
+
+  typedef Kokkos::StaticCrsGraph< int , Space > dView ;
+  typedef typename dView::HostMirror hView ;
+
+  const unsigned LENGTH = 2000 ;
+
+  std::vector< size_t > sizes( LENGTH );
+
+  size_t total_length = 0 ;
+
+  for ( size_t i = 0 ; i < LENGTH ; ++i ) {
+    sizes[i] = rand()%1000;
+  }
+
+  sizes[1] = N;
+  sizes[1998] = N;
+
+  for ( size_t i = 0 ; i < LENGTH ; ++i ) {
+    total_length += sizes[i];
+  }
+
+  int C = 0;
+  dView dx = Kokkos::create_staticcrsgraph<dView>( "test" , sizes );
+  dx.create_block_partitioning(B,C);
+  hView hx = Kokkos::create_mirror( dx );
+
+  for( size_t i = 0; i<B; i++) {
+    size_t ne = 0;
+    for(size_t j = hx.row_block_offsets(i); j<hx.row_block_offsets(i+1); j++)
+      ne += hx.row_map(j+1)-hx.row_map(j)+C;
+
+    ASSERT_FALSE((ne>2*((hx.row_map(hx.numRows())+C*hx.numRows())/B))&&(hx.row_block_offsets(i+1)>hx.row_block_offsets(i)+1));
+  }
+}
 } /* namespace TestStaticCrsGraph */


--- a/lib/kokkos/containers/unit_tests/TestThreads.cpp
+++ b/lib/kokkos/containers/unit_tests/TestThreads.cpp
@ -45,7 +45,7 @@

 #include <Kokkos_Core.hpp>

-#if defined( KOKKOS_HAVE_PTHREAD )
+#if defined( KOKKOS_ENABLE_PTHREAD )

 #include <Kokkos_Bitset.hpp>
 #include <Kokkos_UnorderedMap.hpp>
@ -106,6 +106,18 @@ TEST_F( threads , staticcrsgraph )
 {
  TestStaticCrsGraph::run_test_graph< Kokkos::Threads >();
  TestStaticCrsGraph::run_test_graph2< Kokkos::Threads >();
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(1, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(1, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(1, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(1, 100000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(3, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(3, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(3, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(3, 100000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(75, 0);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(75, 1000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(75, 10000);
+  TestStaticCrsGraph::run_test_graph3< Kokkos::Threads >(75, 100000);
 }

 /*TEST_F( threads, bitset )
@ -190,5 +202,5 @@ TEST_F(threads, ErrorReporter)
 } // namespace Test


-#endif /* #if defined( KOKKOS_HAVE_PTHREAD ) */
+#endif /* #if defined( KOKKOS_ENABLE_PTHREAD ) */

--- a/lib/kokkos/core/perf_test/PerfTestCuda.cpp
+++ b/lib/kokkos/core/perf_test/PerfTestCuda.cpp
@ -48,7 +48,7 @@

 #include <Kokkos_Core.hpp>

-#if defined( KOKKOS_HAVE_CUDA )
+#if defined( KOKKOS_ENABLE_CUDA )

 #include <impl/Kokkos_Timer.hpp>

@ -185,5 +185,5 @@ TEST_F( cuda, texture_double )

 } // namespace Test

-#endif /* #if defined( KOKKOS_HAVE_CUDA ) */
+#endif /* #if defined( KOKKOS_ENABLE_CUDA ) */

--- a/lib/kokkos/core/perf_test/PerfTestDriver.hpp
+++ b/lib/kokkos/core/perf_test/PerfTestDriver.hpp
@ -51,8 +51,8 @@
 // macro, so I'm commenting out the macro to avoid compiler complaints
 // about an unused macro.

-// #define KOKKOS_MACRO_IMPL_TO_STRING( X ) #X
-// #define KOKKOS_MACRO_TO_STRING( X )  KOKKOS_MACRO_IMPL_TO_STRING( X )
+// #define KOKKOS_IMPL_MACRO_TO_STRING( X ) #X
+// #define KOKKOS_MACRO_TO_STRING( X )  KOKKOS_IMPL_MACRO_TO_STRING( X )

 //------------------------------------------------------------------------

--- a/lib/kokkos/core/perf_test/PerfTestHost.cpp
+++ b/lib/kokkos/core/perf_test/PerfTestHost.cpp
@ -45,17 +45,17 @@

 #include <Kokkos_Core.hpp>

-#if defined( KOKKOS_HAVE_OPENMP )
+#if defined( KOKKOS_ENABLE_OPENMP )

 typedef Kokkos::OpenMP TestHostDevice ;
 const char TestHostDeviceName[] = "Kokkos::OpenMP" ;

-#elif defined( KOKKOS_HAVE_PTHREAD )
+#elif defined( KOKKOS_ENABLE_PTHREAD )

 typedef Kokkos::Threads TestHostDevice ;
 const char TestHostDeviceName[] = "Kokkos::Threads" ;

-#elif defined( KOKKOS_HAVE_SERIAL )
+#elif defined( KOKKOS_ENABLE_SERIAL )

 typedef Kokkos::Serial TestHostDevice ;
 const char TestHostDeviceName[] = "Kokkos::Serial" ;
--- a/lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp
@ -47,7 +47,7 @@
 #include <Kokkos_Macros.hpp>

 /* only compile this file if CUDA is enabled for Kokkos */
-#ifdef KOKKOS_HAVE_CUDA
+#ifdef KOKKOS_ENABLE_CUDA

 #include <string>
 #include <Kokkos_Parallel.hpp>
@ -112,7 +112,7 @@ CudaSpace::size_type * cuda_internal_scratch_unified( const CudaSpace::size_type
 #if defined( __CUDACC__ )

 /** \brief  Access to constant memory on the device */
-#ifdef KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
+#ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE

 __device__ __constant__
 extern unsigned long kokkos_impl_cuda_constant_memory_buffer[] ;
@ -135,7 +135,7 @@ namespace Impl {
 }
 }
 __device__ __constant__
-#ifdef KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
+#ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE
 extern
 #endif
 Kokkos::Impl::CudaLockArraysStruct kokkos_impl_cuda_lock_arrays ;
@ -245,7 +245,7 @@ struct CudaParallelLaunch< DriverType , true > {
      // Copy functor to constant memory on the device
      cudaMemcpyToSymbol( kokkos_impl_cuda_constant_memory_buffer , & driver , sizeof(DriverType) );

-      #ifndef KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
+      #ifndef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE
      Kokkos::Impl::CudaLockArraysStruct locks;
      locks.atomic = atomic_lock_array_cuda_space_ptr(false);
      locks.scratch = scratch_lock_array_cuda_space_ptr(false);
@ -287,7 +287,7 @@ struct CudaParallelLaunch< DriverType , false > {
      }
      #endif

-      #ifndef KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
+      #ifndef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE
      Kokkos::Impl::CudaLockArraysStruct locks;
      locks.atomic = atomic_lock_array_cuda_space_ptr(false);
      locks.scratch = scratch_lock_array_cuda_space_ptr(false);
@ -314,5 +314,5 @@ struct CudaParallelLaunch< DriverType , false > {
 //----------------------------------------------------------------------------

 #endif /* defined( __CUDACC__ ) */
-#endif /* defined( KOKKOS_HAVE_CUDA ) */
+#endif /* defined( KOKKOS_ENABLE_CUDA ) */
 #endif /* #ifndef KOKKOS_CUDAEXEC_HPP */
--- a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp
@ -50,7 +50,7 @@
 #include <Kokkos_Macros.hpp>

 /* only compile this file if CUDA is enabled for Kokkos */
-#ifdef KOKKOS_HAVE_CUDA
+#ifdef KOKKOS_ENABLE_CUDA

 #include <Kokkos_Core.hpp>
 #include <Kokkos_Cuda.hpp>
@ -910,5 +910,5 @@ void* cuda_resize_scratch_space(size_t bytes, bool force_shrink) {

 }
 }
-#endif // KOKKOS_HAVE_CUDA
+#endif // KOKKOS_ENABLE_CUDA

--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Alloc.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Alloc.hpp
@ -47,7 +47,7 @@
 #include <Kokkos_Macros.hpp>

 /* only compile this file if CUDA is enabled for Kokkos */
-#ifdef KOKKOS_HAVE_CUDA
+#ifdef KOKKOS_ENABLE_CUDA

 #include <impl/Kokkos_Traits.hpp>

@ -176,7 +176,7 @@ public:

 }} // namespace Kokkos::Impl

-#endif //KOKKOS_HAVE_CUDA
+#endif //KOKKOS_ENABLE_CUDA

 #endif // #ifndef KOKKOS_CUDA_ALLOCATION_TRACKING_HPP

--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp
@ -47,7 +47,7 @@
 #include <Kokkos_Macros.hpp>

 /* only compile this file if CUDA is enabled for Kokkos */
-#ifdef KOKKOS_HAVE_CUDA
+#ifdef KOKKOS_ENABLE_CUDA

 namespace Kokkos { namespace Impl {

@ -65,5 +65,5 @@ inline void cuda_internal_safe_call( cudaError e , const char * name, const char

 }} // namespace Kokkos::Impl

-#endif //KOKKOS_HAVE_CUDA
+#endif //KOKKOS_ENABLE_CUDA
 #endif //KOKKOS_CUDA_ERROR_HPP
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp
@ -47,7 +47,7 @@
 #include <Kokkos_Core.hpp>

 /* only compile this file if CUDA is enabled for Kokkos */
-#ifdef KOKKOS_HAVE_CUDA
+#ifdef KOKKOS_ENABLE_CUDA

 #include <Cuda/Kokkos_Cuda_Error.hpp>
 #include <Cuda/Kokkos_Cuda_Internal.hpp>
@ -64,7 +64,7 @@
 #include <sstream>
 #include <string>

-#ifdef KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
+#ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE

 __device__ __constant__
 unsigned long kokkos_impl_cuda_constant_memory_buffer[ Kokkos::Impl::CudaTraits::ConstantMemoryUsage / sizeof(unsigned long) ] ;
@ -299,8 +299,8 @@ void CudaInternal::print_configuration( std::ostream & s ) const
 {
  const CudaInternalDevices & dev_info = CudaInternalDevices::singleton();

-#if defined( KOKKOS_HAVE_CUDA )
-    s << "macro  KOKKOS_HAVE_CUDA      : defined" << std::endl ;
+#if defined( KOKKOS_ENABLE_CUDA )
+    s << "macro  KOKKOS_ENABLE_CUDA      : defined" << std::endl ;
 #endif
 #if defined( CUDA_VERSION )
    s << "macro  CUDA_VERSION          = " << CUDA_VERSION
@ -500,7 +500,7 @@ void CudaInternal::initialize( int cuda_device_id , int stream_count )
    Kokkos::Impl::throw_runtime_exception( msg.str() );
  }

-  #ifdef KOKKOS_CUDA_USE_UVM
+  #ifdef KOKKOS_ENABLE_CUDA_UVM
    if(!cuda_launch_blocking()) {
      std::cout << "Kokkos::Cuda::initialize WARNING: Cuda is allocating into UVMSpace by default" << std::endl;
      std::cout << "                                  without setting CUDA_LAUNCH_BLOCKING=1." << std::endl;
@ -531,7 +531,7 @@ void CudaInternal::initialize( int cuda_device_id , int stream_count )
  // Init the array for used for arbitrarily sized atomics
  Impl::init_lock_arrays_cuda_space();

-  #ifdef KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE
+  #ifdef KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE
  Kokkos::Impl::CudaLockArraysStruct locks;
  locks.atomic = atomic_lock_array_cuda_space_ptr(false);
  locks.scratch = scratch_lock_array_cuda_space_ptr(false);
@ -773,6 +773,6 @@ void Cuda::fence()

 } // namespace Kokkos

-#endif // KOKKOS_HAVE_CUDA
+#endif // KOKKOS_ENABLE_CUDA
 //----------------------------------------------------------------------------

--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp
@ -47,7 +47,7 @@
 #include <Kokkos_Macros.hpp>

 /* only compile this file if CUDA is enabled for Kokkos */
-#ifdef KOKKOS_HAVE_CUDA
+#ifdef KOKKOS_ENABLE_CUDA

 #include <Cuda/Kokkos_Cuda_Error.hpp>

@ -197,6 +197,6 @@ struct CudaGetOptBlockSize<DriverType,false> {

 }} // namespace Kokkos::Impl

-#endif // KOKKOS_HAVE_CUDA
+#endif // KOKKOS_ENABLE_CUDA
 #endif /* #ifndef KOKKOS_CUDA_INTERNAL_HPP */

--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp
@ -51,7 +51,7 @@
 #include <Kokkos_Macros.hpp>

 /* only compile this file if CUDA is enabled for Kokkos */
-#if defined( __CUDACC__ ) && defined( KOKKOS_HAVE_CUDA )
+#if defined( __CUDACC__ ) && defined( KOKKOS_ENABLE_CUDA )

 #include <utility>
 #include <Kokkos_Parallel.hpp>
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp
@ -47,7 +47,7 @@
 #include <Kokkos_Macros.hpp>

 /* only compile this file if CUDA is enabled for Kokkos */
-#if defined( __CUDACC__ ) && defined( KOKKOS_HAVE_CUDA )
+#if defined( __CUDACC__ ) && defined( KOKKOS_ENABLE_CUDA )

 #include <utility>

@ -312,7 +312,7 @@ void cuda_intra_block_reduce_scan( const FunctorType & functor ,
            ( rtid_intra & 16 ) ? 16 : 0 ))));

    if ( ! ( rtid_intra + n < blockDim.y ) ) n = 0 ;
-    #ifdef KOKKOS_CUDA_CLANG_WORKAROUND
+    #ifdef KOKKOS_IMPL_CUDA_CLANG_WORKAROUND
    BLOCK_SCAN_STEP(tdata_intra,n,4) __syncthreads();//__threadfence_block();
    BLOCK_SCAN_STEP(tdata_intra,n,3) __syncthreads();//__threadfence_block();
    BLOCK_SCAN_STEP(tdata_intra,n,2) __syncthreads();//__threadfence_block();
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.cpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.cpp
@ -43,7 +43,7 @@

 #include <Kokkos_Core.hpp>

-#if defined( KOKKOS_HAVE_CUDA ) && defined( KOKKOS_ENABLE_TASKDAG )
+#if defined( KOKKOS_ENABLE_CUDA ) && defined( KOKKOS_ENABLE_TASKDAG )

 #include <impl/Kokkos_TaskQueue_impl.hpp>

@ -174,6 +174,6 @@ printf("cuda_task_queue_execute after\n");

 //----------------------------------------------------------------------------

-#endif /* #if defined( KOKKOS_HAVE_CUDA ) && defined( KOKKOS_ENABLE_TASKDAG ) */
+#endif /* #if defined( KOKKOS_ENABLE_CUDA ) && defined( KOKKOS_ENABLE_TASKDAG ) */


--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Steve Plimpton	49e83b4348	patch 21Feb17 sync with GHub	2017-02-21 16:07:26 -07:00
sjplimp	6e89ccd522	Merge pull request #385 from akohlmey/collected-small-bugfixes collected small bugfixes and updates	2017-02-21 15:59:06 -07:00
sjplimp	53f3df5bfc	Merge pull request #384 from lammps/another_neigh_refactor more neighbor list changes, some new options	2017-02-21 15:57:23 -07:00
Steve Plimpton	3dbbea342a	remove a debug print line	2017-02-21 15:57:03 -07:00
sjplimp	b70c670aac	Merge pull request #383 from stanmoore1/rshan_class2_kk Kokkos version of class2 bond, angle, dihedral, and improper from Ray Shan	2017-02-21 15:52:10 -07:00
sjplimp	1d17cae407	Merge pull request #382 from timattox/master_kokkos_neigh_bugfix neighbor_kokkos.cpp: Don't call grow() on neighbor lists that are copies	2017-02-21 15:51:35 -07:00
sjplimp	429264a12b	Merge pull request #380 from hheenen/core_shell_documentation updated documentation and examples for coreshell	2017-02-21 15:50:53 -07:00
sjplimp	d001a09345	Merge pull request #379 from ndtrung81/pppm-gpu-compute-group-group Fixed bugs with pppm/gpu when used with compute group/group	2017-02-21 15:50:28 -07:00
sjplimp	cb9d42da08	Merge pull request #378 from timattox/USER-DPD_ssa_update USER-DPD: performance optimizations to ssa_update() in fix_shardlow	2017-02-21 15:50:07 -07:00
sjplimp	7185ec92b3	Merge pull request #377 from stanmoore1/kokkos_update Kokkos library update	2017-02-21 15:49:50 -07:00
Steve Plimpton	1cd4c48ccc	new SNAP potential for W	2017-02-21 15:49:21 -07:00
Axel Kohlmeyer	a88136c3f5	correct a logic bug in fix wall/gran/region	2017-02-17 17:58:24 -05:00
Axel Kohlmeyer	ce20c7ffe9	remove debug code	2017-02-17 12:42:07 -05:00
Steve Plimpton	4a80df3a99	more neighbor list changes, some new options	2017-02-15 16:45:33 -07:00
Stan Moore	5f93fad012	Add copymode protection to class2 styles	2017-02-15 13:56:16 -07:00
Stan Moore	ccaec315db	Updating docs for Kokkos class2	2017-02-15 13:00:33 -07:00
Stan Moore	c6c1852b3b	Fix a few issues with Kokkos class2 files	2017-02-15 12:44:54 -07:00
Stan Moore	69a8e19dc5	Add files from Ray Shan for Kokkos version of class2 angle, bond, etc.	2017-02-15 12:29:52 -07:00
Tim Mattox	928947dcea	neighbor_kokkos.cpp: Don't call grow() on neighbor lists that are copies. This corresponds to a bugfix from commit `9161bd98` on neighbor.cpp	2017-02-15 11:49:34 -05:00
Axel Kohlmeyer	48070011d9	update names in example, too	2017-02-14 07:42:36 -05:00
Axel Kohlmeyer	0fb8dacc00	one more Finchham to Fincham change	2017-02-14 07:41:05 -05:00
Hendrik Heenen	6b923476b9	updated documentation and examples for coreshell	2017-02-14 13:14:22 +01:00
Trung Nguyen	20806dd86a	Fixed bugs with pppm/gpu when used with compute group/group	2017-02-14 00:26:55 -06:00
Stan Moore	90e5ae965d	Add missing flags to Kokkos Makefile	2017-02-13 11:19:46 -07:00
Tim Mattox	15008c9d18	USER-DPD: performance optimizations to ssa_update() in fix_shardlow Overall improvements range from 2% to 18% on our benchmarks 1) Newton has to be turned on for SSA, so remove those conditionals 2) Rework the math in ssa_update() to eliminate many ops and temporaries 3) Split ssa_update() into two versions, based on DPD vs. DPDE 4) Reorder code in ssa_update_*() to reduce register pressure	2017-02-13 13:11:19 -05:00
Stan Moore	33af7ab248	Remove merge line	2017-02-13 10:59:22 -07:00
Stan Moore	8f9b2aca06	Removing unused files in Kokkos lib	2017-02-13 10:53:51 -07:00
Stan Moore	383da816c2	Updating Kokkos lib	2017-02-13 10:50:34 -07:00
Steve Plimpton	cb982f2f28	sync 13Feb17 patch back to GH	2017-02-13 09:05:03 -07:00
sjplimp	4843296d4e	Merge pull request #372 from akohlmey/fft-cleanup simplify FFT3d code by removing support for outdated FFT libraries	2017-02-13 08:53:13 -07:00
Steve Plimpton	2bdda8f6c0	patch 12Feb17 - change int to tagint for compute group/group	2017-02-13 08:40:54 -07:00
Steve Plimpton	0068ef5616	added molecule option to compute group/group command	2017-02-10 09:25:32 -07:00
sjplimp	02b0e6cc55	Merge pull request #375 from akohlmey/small-updates-and-fixes Small updates and fixes	2017-02-10 09:23:51 -07:00
sjplimp	fbb24c2406	Merge pull request #374 from agiliopadua/master Updated polarizer.py in USER-DRUDE to use coul/long/cs	2017-02-10 09:22:22 -07:00
Axel Kohlmeyer	a5f830c40c	fix typo (cherry picked from commit `6410797697`)	2017-02-08 14:33:45 -05:00
Axel Kohlmeyer	8c074a363a	Merge branch 'master' into small-updates-and-fixes	2017-02-08 14:32:44 -05:00
Agilio Padua	27aca14094	Updated polarizer.py to use coul/long/cs	2017-02-04 15:02:08 +01:00
Axel Kohlmeyer	191453e1c7	Merge branch 'master' into fft-cleanup	2017-02-03 16:53:10 -05:00
sjplimp	207adc3968	Merge pull request #373 from stanmoore1/kk_more_bugfixes Fixing Kokkos per-atom energy/virial issues	2017-02-03 14:45:31 -07:00
sjplimp	84c517159d	Merge pull request #368 from Pakketeretet2/kokkos_morse Kokkos morse	2017-02-03 14:45:07 -07:00
sjplimp	6ca377436f	Merge pull request #366 from rbberger/kokkos_lammps_bigbig_fix Fix data type of molecule array in npair_kokkos.h	2017-02-03 14:43:33 -07:00
sjplimp	dc34a32602	Merge pull request #362 from ibaned/warnings2 fix Kokkos+kspace warnings	2017-02-03 14:43:12 -07:00
Stan Moore	067119f6c6	Adding missing friend statement to pair_lj_class2_coul_cut_kokkos	2017-02-02 15:21:30 -07:00
Stan Moore	1834a5e46c	Fixing more Kokkos per-atom and fdotr issues	2017-02-02 15:21:21 -07:00
Stan Moore	6a4918b39a	Fixing typo in pair_buck_coul_cut_kokkos	2017-02-02 15:21:05 -07:00
Stan Moore	5da0d39392	Fixing fdotr in pair_buck_coul_cut_kokkos	2017-02-02 13:35:51 -07:00
Stan Moore	6f92429602	Fixing per-atom ev issue	2017-02-02 13:34:27 -07:00
Stan Moore	38e0e4bb69	Add missing typedef in Kokkos pair styles	2017-02-02 13:24:05 -07:00
Stan Moore	daf9f95381	Fixing Kokkos per-atom e/v issue	2017-02-02 13:09:52 -07:00
Axel Kohlmeyer	6595fde0a1	explain in more detail the handling of error checking for numerical inputs	2017-02-02 11:58:12 -05:00
Richard Berger	6bcec9c61d	Merge pull request #2 from stanmoore1/kk_tag_bugfixes Fixing tagint and imageint issues in Kokkos package	2017-02-02 08:57:21 -05:00
Axel Kohlmeyer	9d1991bf84	remove support for obsolete legacy FFT libraries and point -DFFT_FFTW to FFTW3	2017-02-02 08:10:23 -05:00
Stefan Paquay	0a87b7443a	Updated contributing authors and docs	2017-02-02 13:42:47 +01:00
Stan Moore	7ee45ec5f3	Fixing tagint and imageint issues in Kokkos package	2017-02-01 11:52:27 -07:00
Stefan Paquay	d4c9e2500b	Ported Morse to KOKKOS	2017-02-01 17:45:21 +01:00
Stefan Paquay	6232073d3b	Removed traces of pair morse/kk	2017-02-01 17:39:37 +01:00
Stefan Paquay	ed59193d13	Removed traces of pair morse/kk	2017-02-01 17:39:06 +01:00
Richard Berger	67bed8e853	Merge pull request #1 from akohlmey/tagint-issue Fix additional tagint issue in fix qeq/reax/kk	2017-01-31 18:34:35 -05:00
Axel Kohlmeyer	bcb1d94b9a	silence compiler warning about dead code	2017-01-31 18:28:04 -05:00
Axel Kohlmeyer	fbe30b5683	correct issue with compiling for -DLAMMPS_BIGBIG in fix qeq/reax/kk	2017-01-31 18:13:44 -05:00
Axel Kohlmeyer	9ef55fedf7	Merge branch 'kokkos_lammps_bigbig_fix' of https://github.com/rbberger/lammps into tagint-issue	2017-01-31 17:23:51 -05:00
sjplimp	997142a4c1	Merge pull request #364 from stanmoore1/kk_triclinic_neighlist Add triclinic neighbor list support to Kokkos	2017-01-30 07:27:02 -07:00
sjplimp	033b07fdb7	Merge pull request #363 from ibaned/obey-datamask Fix GPU sync bugs	2017-01-30 07:26:49 -07:00
Richard Berger	51a0b6b445	Fix data type of molecule array in npair_kokkos.h This showed up when trying to compile with -DLAMMPS_BIGBIG. Fixes issue #365	2017-01-28 07:49:08 -05:00
Stan Moore	59f4a77dd5	Whitespace change to npair_kokkos	2017-01-27 15:17:39 -07:00
Stan Moore	579cc6d7aa	More tweaks to npair_kokkos for triclinic	2017-01-27 15:13:37 -07:00
Stan Moore	5afd3e995b	Adding support to npair_kokkos for triclinic-newton-on neighborlists	2017-01-27 14:18:01 -07:00
Dan Ibanez	2a6f5e651c	more preference of datamask over custom sync see commit `09fc8b0` for details on why	2017-01-27 09:35:55 -07:00
Dan Ibanez	09fc8b0bd7	kspace & dihedral can't do their own sync/modify because the verlet_kokkos system has a "clever" optimization which will alter the datamasks before calling sync/modify, so the datamask framework must be strictly obeyed for GPU correctness. (the optimization is to concurrently compute forces on the host and GPU, and add them up at the end of an iteration. calling your own sync will overwrite the partial GPU forces with the partial host forces).	2017-01-27 08:39:55 -07:00
Dan Ibanez	e5d0bde783	pppm_kokkos: remove useless statement	2017-01-27 08:35:37 -07:00
Dan Ibanez	9daf7fb650	pppm_kokkos: don't shadow member variables	2017-01-27 08:35:37 -07:00
Dan Ibanez	b5d622c6a3	pppm_kokkos: remove unused variables	2017-01-27 08:35:37 -07:00
Dan Ibanez	2023fa28e0	consistent #ifdefs for fft3d variable (2) this variable is only used when FFTW3 is enabled, so its declaration and initialization should be protected under the same conditions to avoid compiler warnings	2017-01-27 08:35:37 -07:00
Dan Ibanez	5b29515849	fft3d: use C++ loop declarations the variable (offset) is only used in a subset of numerous scenarios with #ifdef, it seems better just to have each loop declare it as needed. (avoids compiler warnings)	2017-01-27 08:35:37 -07:00
Dan Ibanez	5b18421dd2	fft3d : remove unused variables	2017-01-27 08:35:37 -07:00
Dan Ibanez	cf95ea0709	fft3d: only declare variables when used avoids compiler warnings	2017-01-27 08:35:36 -07:00
Dan Ibanez	6a74a81da0	consistent #ifdefs for fft3d variable this variable is only used when FFTW3 is enabled, so its declaration and initialization should be protected under the same conditions to avoid compiler warnings	2017-01-27 08:35:36 -07:00
Dan Ibanez	f0a4ed615d	add missing KOKKOS_INLINE_FUNCTION for params	2017-01-27 08:35:36 -07:00
Dan Ibanez	cfe818a175	remove unused variables from fix_cmap	2017-01-27 08:35:36 -07:00
Steve Plimpton	f8506fee23	sync GHub with SVN	2017-01-26 14:06:43 -07:00
sjplimp	18e5584311	Merge pull request #354 from stanmoore1/kokkos_bugfixes Kokkos bugfixes	2017-01-26 13:51:47 -07:00
sjplimp	851f80464f	Merge pull request #361 from akohlmey/user-omp-fix-per-atom-data fix USER-OMP bug on per-atom data with hybrid styles	2017-01-26 13:50:13 -07:00
sjplimp	5971d4c994	Merge pull request #358 from ibaned/warnings warning fixes (Kokkos+CUDA)	2017-01-26 13:49:56 -07:00
sjplimp	868d95f0a5	Merge pull request #352 from akohlmey/fix-skip-with-ghost-issue Fix skip with ghost issue	2017-01-26 13:47:12 -07:00
sjplimp	a5ff35435a	Merge pull request #351 from timattox/USER-DPD_pair_exp6_bugfix USER-DPD: Possible uninitialized variable in pair_exp6_rx.cpp bugfix.	2017-01-26 13:45:45 -07:00
Axel Kohlmeyer	8b7bd9d88e	fix bug where per atom data for USER-OMP was reducing the wrong arrays with hybrid styles	2017-01-26 14:59:10 -05:00
Dan Ibanez	672bbbe494	add more missing KOKKOS_INLINE_FUNCTION attributes	2017-01-25 16:03:11 -07:00
Dan Ibanez	03c9c46533	add missing KOKKOS_INLINE_FUNCTION attributes	2017-01-25 15:49:05 -07:00
Dan Ibanez	e992bfe510	remove unused variable	2017-01-25 15:40:52 -07:00
Dan Ibanez	053ee54a27	remove unused variable	2017-01-25 15:38:41 -07:00
Dan Ibanez	1074c6734b	add missing return keywords	2017-01-25 15:37:27 -07:00
Dan Ibanez	60b48c9d66	add missing KOKKOS_INLINE_FUNCTION attributes this structure gets put inside a DualView, so these members need to be able to execute on the GPU	2017-01-25 15:36:24 -07:00
Dan Ibanez	3d40b51708	remove unused variable	2017-01-25 15:24:52 -07:00
Dan Ibanez	effbe18c46	fix domain boundary indexing the compiler pointed out that boundary[2][2] doesn't exist. If I understand this correctly, those checks should be against boundary[*][0].	2017-01-25 15:24:01 -07:00
Dan Ibanez	6328beb7d7	fix double-return warning this #ifdef adds a return statement for little endian machines, but leaves the old one, which the compiler comlains is unreachable. this commit combines the conditionals so we can use #else	2017-01-25 15:22:42 -07:00
Stan Moore	26c8d3d98f	Fixing GPU memory issue in fix_langevin_kokkos	2017-01-25 12:53:55 -07:00
Stan Moore	73177d650d	Fixing GPU memory issue in domain_kokkos	2017-01-25 11:18:03 -07:00
Axel Kohlmeyer	b5cb74bd33	skip list build is compatible with NP_GHOST	2017-01-23 19:21:48 -05:00
Axel Kohlmeyer	31976d1dee	skip list definition was missing NP_HALFFULL flag	2017-01-23 19:20:05 -05:00
Christopher Stone	c8260af37c	Possible uninitialized variable in USER-DPD/pair_exp6_rx.cpp bugfix. Added explicit initialization (to zero) for several variables inside the inner j-loop to avoid using them uninitialized or from prior iterations within rmOldij_12 == 0.	2017-01-23 13:34:51 -05:00
Steve Plimpton	caea8973a3	add neighbor list kind output to screen	2017-01-20 13:24:09 -07:00
sjplimp	aa0ad9b483	Merge pull request #349 from akohlmey/collected-small-fixes collected fixes and improvements	2017-01-20 13:19:43 -07:00
sjplimp	5d0e4e1ba9	Merge pull request #346 from stanmoore1/kokkos_fixes Kokkos fixes	2017-01-20 13:15:16 -07:00
sjplimp	f8d3c4c740	Merge pull request #345 from timattox/USER-DPD_another_zero_compute USER-DPD another zero compute optimization	2017-01-20 13:14:59 -07:00
Axel Kohlmeyer	e6996121d1	remove dead code	2017-01-20 14:30:46 -05:00
Axel Kohlmeyer	fbfb1df5eb	fix typo causing wrong neighbor list copy selections	2017-01-19 20:47:10 -05:00
Steve Plimpton	9a299875da	simplified neighbor list copying to avoid possible same-timestep re-build issues	2017-01-19 17:01:15 -07:00
Stan Moore	fc94f1bd18	Fixing GPU memory issues in Kokkos	2017-01-19 12:14:25 -07:00
Stan Moore	5ce8e2fbae	Fixing GPU memory issue in modify_kokkos, need to cherry pick back to Master	2017-01-19 12:13:48 -07:00
Tim Mattox	f6cd98636b	USER-DPD: Also apply "check if a0 is zero" optimization to pair_dpd_fdt This relates to commit `4eb08a5822` that was applied to pair_dpd_fdt_energy	2017-01-18 16:17:11 -05:00
Tim Mattox	05cafb716f	USER-DPD: cleanup initialization of splitFDT_flag in pair_dpd_fdt.cpp	2017-01-18 15:51:50 -05:00
sjplimp	3af4b3c28c	Merge pull request #337 from ohenrich/user-cgdna Added source code and documentation for USER-CGDNA	2017-01-18 11:31:35 -07:00
sjplimp	7fc0970587	Merge pull request #344 from timattox/USER-DPD_zero_compute USER-DPD: Skip a0*stuff computations, if a0 was set to zero in pair_coeff	2017-01-18 11:31:14 -07:00
sjplimp	93262b52b4	Merge pull request #343 from timattox/USER-DPD_bugfix_molecule USER-DPD: bugfix for a segfault when using MOLECULE and DPD together.	2017-01-18 11:30:58 -07:00
Tim Mattox	4eb08a5822	USER-DPD: Skip a0*stuff computations, if a0 was set to zero in pair_coeff. This saves around 10% of the runtime for many of our tests using SSA.	2017-01-17 15:55:39 -05:00
Tim Mattox	01609f55e2	USER-DPD: bugfix for a segfault when using MOLECULE and DPD together.	2017-01-17 12:47:59 -05:00
Axel Kohlmeyer	8360e70f4e	update USER-CGDNA examples to follow LAMMPS style	2017-01-13 18:56:45 -05:00
Axel Kohlmeyer	b988b29413	remove dead code	2017-01-13 18:43:35 -05:00
Axel Kohlmeyer	5d48bfdcab	USER-CGDNA whitespace cleanup: expand tabs and remove trailing whitespace	2017-01-13 18:40:34 -05:00
Axel Kohlmeyer	fe8caa8a56	apply some LAMMPS formatting style conventions for include files	2017-01-13 18:33:32 -05:00
Axel Kohlmeyer	afaacc6173	add USER-CGDNA package with dependencies into the build system	2017-01-13 18:32:32 -05:00
Axel Kohlmeyer	374abea0f0	some minor documentation integration tweaks for USER-CGDNA package	2017-01-13 18:09:45 -05:00
Oliver Henrich	96259ea2d2	Added source code and documentation for USER-CGDNA	2017-01-13 13:36:54 +00:00