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
706 changed files with 23887 additions and 33524 deletions
--- a/.gitignore
+++ b/.gitignore
@ -0,0 +1,34 @@
+*~
+*.o
+*.so
+*.cu_o
+*.ptx
+*_ptx.h
+*.a
+*.d
+*.x
+*.exe
+*.dll
+*.pyc
+__pycache__
+
+Obj_*
+log.lammps
+log.cite
+*.bz2
+*.gz
+*.tar
+.*.swp
+*.orig
+*.rej
+.vagrant
+\#*#
+.#*
+
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
--- a/doc/.gitignore
+++ b/doc/.gitignore
@ -0,0 +1,5 @@
+/html
+/LAMMPS.epub
+/LAMMPS.mobi
+/Manual.pdf
+/Developer.pdf
--- 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="26 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
-26 Jan 2017 version :c,h4
+21 Feb 2017 version :c,h4

 Version info: :h4

--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -969,7 +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,
@ -1076,7 +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,
@ -1109,7 +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,
@ -1145,7 +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,
@ -1177,7 +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_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/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_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/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
--- a/doc/src/compute_temp_sphere.txt
+++ b/doc/src/compute_temp_sphere.txt
--- a/doc/src/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_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
--- 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/min_style.txt
+++ b/doc/src/min_style.txt
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
--- a/doc/src/pair_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_resquared.txt
+++ b/doc/src/pair_resquared.txt
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
--- a/doc/utils/converters/.gitignore
+++ b/doc/utils/converters/.gitignore
@ -1,2 +1 @@
-__pycache__
 *.egg-info
--- a/examples/COUPLE/fortran2/.gitignore
+++ b/examples/COUPLE/fortran2/.gitignore
@ -0,0 +1 @@
+*.mod
--- a/examples/USER/misc/ti/in.ti_spring
+++ b/examples/USER/misc/ti/in.ti_spring
--- 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/mscg/output_9Jan17/log.lammps
+++ b/examples/mscg/output_9Jan17/log.lammps
@ -1,140 +0,0 @@
-LAMMPS (4 Nov 2016)
-units real
-atom_style full
-pair_style zero 10.0
-
-read_data data.meoh
-  orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1000 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-pair_coeff * *
-
-thermo 1
-thermo_style custom step
-
-# Test 1a: range finder functionality
-fix 1 all mscg 1 range on
-rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6 -> bins = 7 7 7
-Memory usage per processor = 5.44227 Mbytes
-Step 
-       0 
-     250 
-     500 
-     750 
-    1000 
-    1250 
-    1500 
-    1750 
-    2000 
-    2250 
-    2500 
-    2750 
-    3000 
-    3250 
-    3500 
-    3750 
-    4000 
-    4250 
-    4500 
-Loop time of 0.695789 on 1 procs for 19 steps with 1000 atoms
-
-Performance: 2.359 ns/day, 10.172 hours/ns, 27.307 timesteps/s
-92.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Bond    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.6958     |            |       |100.00
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2934 ave 2934 max 2934 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    50654 ave 50654 max 50654 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 50654
-Ave neighs/atom = 50.654
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-print "TEST_1a mscg range finder"
-TEST_1a mscg range finder
-unfix 1
-
-# Test 1b: force matching functionality
-fix 1 all mscg 1
-rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
-Memory usage per processor = 5.44227 Mbytes
-Step 
-       0 
-     250 
-     500 
-     750 
-    1000 
-    1250 
-    1500 
-    1750 
-    2000 
-    2250 
-    2500 
-    2750 
-    3000 
-    3250 
-    3500 
-    3750 
-    4000 
-    4250 
-    4500 
-Loop time of 1.48638 on 1 procs for 19 steps with 1000 atoms
-
-Performance: 1.104 ns/day, 21.731 hours/ns, 12.783 timesteps/s
-88.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Bond    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 1.486      |            |       |100.00
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2934 ave 2934 max 2934 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    50654 ave 50654 max 50654 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 50654
-Ave neighs/atom = 50.654
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-print "TEST_1b mscg force matching"
-TEST_1b mscg force matching
-
-print TEST_DONE
-TEST_DONE
-Total wall time: 0:00:02
--- a/examples/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/examples/vashishta/InP.vashishta
+++ b/examples/vashishta/InP.vashishta
--- a/examples/vashishta/SiO.1990.vashishta
+++ b/examples/vashishta/SiO.1990.vashishta
--- a/lib/.gitignore
+++ b/lib/.gitignore
@ -0,0 +1 @@
+Makefile.lammps
--- a/lib/gpu/cudpp_mini/cudpp.h
+++ b/lib/gpu/cudpp_mini/cudpp.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // CUDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_globals.h
+++ b/lib/gpu/cudpp_mini/cudpp_globals.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_maximal_launch.h
+++ b/lib/gpu/cudpp_mini/cudpp_maximal_launch.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_plan.h
+++ b/lib/gpu/cudpp_mini/cudpp_plan.h
@ -2,7 +2,7 @@
 // CUDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
 // $Revision: 3572$
-// $Date$
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_plan_manager.h
+++ b/lib/gpu/cudpp_mini/cudpp_plan_manager.h
@ -2,7 +2,7 @@
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
 // $Revision: 3572$
-// $Date$
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_radixsort.h
+++ b/lib/gpu/cudpp_mini/cudpp_radixsort.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_scan.h
+++ b/lib/gpu/cudpp_mini/cudpp_scan.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_util.h
+++ b/lib/gpu/cudpp_mini/cudpp_util.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/sharedmem.h
+++ b/lib/gpu/cudpp_mini/sharedmem.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/kokkos/.gitignore
+++ b/lib/kokkos/.gitignore
@ -1,8 +0,0 @@
-# Standard ignores
-*~
-*.pyc
-\#*#
-.#*
-.*.swp
-.cproject
-.project
--- 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/configure_compton_cpu.sh
+++ b/lib/kokkos/config/configure_compton_cpu.sh
--- a/lib/kokkos/config/configure_compton_mic.sh
+++ b/lib/kokkos/config/configure_compton_mic.sh
--- a/lib/kokkos/config/configure_kokkos.sh
+++ b/lib/kokkos/config/configure_kokkos.sh
--- a/lib/kokkos/config/configure_kokkos_nvidia.sh
+++ b/lib/kokkos/config/configure_kokkos_nvidia.sh
--- a/lib/kokkos/config/configure_shannon.sh
+++ b/lib/kokkos/config/configure_shannon.sh
--- 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/Show More
+++ b/Show More