patch 19May17

Merge pull request #493 from akohlmey/doc-and-example-fixes
Doc and example fixes
2017-05-19 07:35:36 -06:00 · 2017-05-18 16:40:46 -06:00 · 2017-05-18 18:34:27 -04:00 · 2017-05-18 18:34:03 -04:00 · 2017-05-18 13:44:34 -06:00 · 2017-05-18 13:14:47 -06:00
310 changed files with 19554 additions and 1339 deletions
--- a/doc/Makefile
+++ b/doc/Makefile
@ -158,7 +158,7 @@ $(VENV):
 	@( \
 		virtualenv -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install Sphinx; \
+		pip install Sphinx==1.5.6; \
 		pip install sphinxcontrib-images; \
 		deactivate;\
 	)
--- a/doc/src/Eqs/pair_meam_spline.jpg
+++ b/doc/src/Eqs/pair_meam_spline.jpg
--- a/doc/src/Eqs/pair_meam_spline.tex
+++ b/doc/src/Eqs/pair_meam_spline.tex
@ -1,13 +1,14 @@
 \documentclass[12pt]{article}
+\usepackage{amsmath}

 \begin{document}

 $$
-   E=\sum_{ij}\phi(r_{ij})+\sum_{i}U(\rho_{i}),
+   E=\sum_{i<j}\phi(r_{ij})+\sum_{i}U(n_{i}),
 $$

 $$
-   \rho_{i}=\sum_{j}\rho(r_{ij})+\sum_{jk}f(r_{ij})f(r_{ik})g[\cos(\theta_{jik})]
+   n_{i}=\sum_{j}\rho(r_{ij})+\sum_{\substack{j<k,\\j,k\neq i}}f(r_{ij})f(r_{ik})g[\cos(\theta_{jik})]
 $$

 \end{document}
--- a/doc/src/Eqs/pair_meam_spline_multicomponent.jpg
+++ b/doc/src/Eqs/pair_meam_spline_multicomponent.jpg
--- a/doc/src/Eqs/pair_meam_spline_multicomponent.tex
+++ b/doc/src/Eqs/pair_meam_spline_multicomponent.tex
@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+\usepackage{amsmath}
+
+\begin{document}
+
+$$
+   E=\sum_{i<j}\phi_{ij}(r_{ij})+\sum_{i}U_i(n_{i}),
+$$
+
+$$
+   n_{i}=\sum_{j\ne i}\rho_j(r_{ij})+\sum_{\substack{j<k,\\j,k\neq i}}f_{j}(r_{ij})f_{k}(r_{ik})g_{jk}[\cos(\theta_{jik})]
+$$
+
+\end{document}
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="4 May 2017 version">
+<META NAME="docnumber" CONTENT="19 May 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
-4 May 2017 version :c,h4
+19 May 2017 version :c,h4

 Version info: :h4

--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -527,9 +527,9 @@ These are additional commands in USER packages, which can be used if
 "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.

-"dump custom/vtk"_dump_custom_vtk.html,
-"dump nc"_dump_nc.html,
-"dump nc/mpiio"_dump_nc.html,
+"dump netcdf"_dump_netcdf.html,
+"dump netcdf/mpiio"_dump_netcdf.html,
+"dump vtk"_dump_vtk.html,
 "group2ndx"_group2ndx.html,
 "ndx2group"_group2ndx.html,
 "temper/grem"_temper_grem.html :tb(c=3,ea=c)
@ -618,6 +618,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "press/berendsen"_fix_press_berendsen.html,
 "print"_fix_print.html,
 "property/atom"_fix_property_atom.html,
+"python"_fix_python.html,
 "qeq/comb (o)"_fix_qeq_comb.html,
 "qeq/dynamic"_fix_qeq.html,
 "qeq/fire"_fix_qeq.html,
@ -931,6 +932,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "gran/hertz/history (o)"_pair_gran.html,
 "gran/hooke (o)"_pair_gran.html,
 "gran/hooke/history (o)"_pair_gran.html,
+"gw"_pair_gw.html,
+"gw/zbl"_pair_gw.html,
 "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
 "hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
 "kim"_pair_kim.html,
@ -982,6 +985,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "peri/pmb (o)"_pair_peri.html,
 "peri/ves"_pair_peri.html,
 "polymorphic"_pair_polymorphic.html,
+"python"_pair_python.html,
 "reax"_pair_reax.html,
 "rebo (o)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
@ -1016,6 +1020,7 @@ package"_Section_start.html#start_3.
 "dpd/fdt/energy"_pair_dpd_fdt.html,
 "eam/cd (o)"_pair_eam.html,
 "edip (o)"_pair_edip.html,
+"edip/multi"_pair_edip.html,
 "eff/cut"_pair_eff.html,
 "exp6/rx"_pair_exp6_rx.html,
 "gauss/cut"_pair_gauss.html,
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -123,7 +123,7 @@ Package, Description, Doc page, Example, Library
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
 "USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
-"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
+"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
 "USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
 "USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, WWW bench, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
@ -135,7 +135,7 @@ Package, Description, Doc page, Example, Library
 "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
 "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
 "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-VTK"_#USER-VTK, dump output via VTK, "compute custom/vtk"_dump_custom_vtk.html, -, ext
+"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext
 :tb(ea=c,ca1=l)

 :line
@ -529,7 +529,7 @@ what hardware and software is required on your system, and how to
 build and use this package.  Its styles can be invoked at run time via
 the "-sf kk" or "-suffix kk" "command-line
 switches"_Section_start.html#start_7.  Also see the "GPU"_#GPU,
-"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER_OMP
+"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
 packages, which have styles optimized for CPUs, KNLs, and GPUs.

 You must have a C++11 compatible compiler to use this package.
@ -856,15 +856,15 @@ src/MPIIO: filenames -> commands

 :line
 
-MSCG package :link(MSCG),h4
+MSCG package :link(mscg),h4

 [Contents:]

 A "fix mscg"_fix_mscg.html command which can parameterize a
 Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
-library"_mscg.
+library"_mscg_home.

-:link(mscg,https://github.com/uchicago-voth/MSCG-release)
+:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)

 To use this package you must have the MS-CG library available on your
 system.
@ -1323,11 +1323,11 @@ VORONOI package :link(VORONOI),h4
 [Contents:]

 A compute command which calculates the Voronoi tesselation of a
-collection of atoms by wrapping the "Voro++ library"_voronoi.  This
+collection of atoms by wrapping the "Voro++ library"_voro_home.  This
 can be used to calculate the local volume or each atoms or its near
 neighbors.

-:link(voronoi,http://math.lbl.gov/voro++)
+:link(voro_home,http://math.lbl.gov/voro++)

 To use this package you must have the Voro++ library available on your
 system.
@ -1488,7 +1488,6 @@ make machine :pre
 src/USER-AWPMD: filenames -> commands
 src/USER-AWPMD/README
 "pair awpmd/cut"_pair_awpmd.html
-"fix nve/awpmd"_fix_nve_awpmd.html
 examples/USER/awpmd :ul

 :line
@ -1520,7 +1519,7 @@ src/USER-CGDNA: filenames -> commands
 "pair_style oxdna/*"_pair_oxdna.html
 "pair_style oxdna2/*"_pair_oxdna2.html
 "bond_style oxdna/*"_bond_oxdna.html
-"bond_style oxdna2/*"_bond_oxdna2.html
+"bond_style oxdna2/*"_bond_oxdna.html
 "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul

 :line
@ -1748,8 +1747,8 @@ src/USER-EFF: filenames -> commands
 src/USER-EFF/README
 "atom_style electron"_atom_style.html
 "fix nve/eff"_fix_nve_eff.html
-"fix nvt/eff"_fix_nvt_eff.html
-"fix npt/eff"_fix_npt_eff.html
+"fix nvt/eff"_fix_nh_eff.html
+"fix npt/eff"_fix_nh_eff.html
 "fix langevin/eff"_fix_langevin_eff.html
 "compute temp/eff"_compute_temp_eff.html
 "pair eff/cut"_pair_eff.html
@ -2045,8 +2044,8 @@ src/USER-MANIFOLD: filenames -> commands
 src/USER-MANIFOLD/README
 "doc/manifolds"_manifolds.html
 "fix manifoldforce"_fix_manifoldforce.html
-"fix nve/manifold/rattle"_fix_nve_manifold/rattle.html
-"fix nvt/manifold/rattle"_fix_nvt_manifold/rattle.html
+"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
+"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
 examples/USER/manifold
 http://lammps.sandia.gov/movies.html#manifold :ul

@ -2057,11 +2056,13 @@ USER-MOLFILE package :link(USER-MOLFILE),h4
 [Contents:]

 A "dump molfile"_dump_molfile.html command which uses molfile plugins
-that are bundled with the "VMD"_http://www.ks.uiuc.edu/Research/vmd
+that are bundled with the "VMD"_vmd_home
 molecular visualization and analysis program, to enable LAMMPS to dump
 snapshots in formats compatible with various molecular simulation
 tools.

+:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)
+
 To use this package you must have the desired VMD plugins available on
 your system.

@ -2118,7 +2119,7 @@ Note that NetCDF files can be directly visualized with the following
 tools:

 "Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above)
-"VMD"_vmd
+"VMD"_vmd_home
 "AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul

 :link(ovito,http://www.ovito.org)
@ -2563,7 +2564,7 @@ USER-VTK package :link(USER-VTK),h4

 [Contents:]

-A "dump custom/vtk"_dump_custom_vtk.html command which outputs
+A "dump vtk"_dump_vtk.html command which outputs
 snapshot info in the "VTK format"_vtk, enabling visualization by
 "Paraview"_paraview or other visuzlization packages.

@ -2598,4 +2599,4 @@ make machine :pre
 src/USER-VTK: filenames -> commands
 src/USER-VTK/README
 lib/vtk/README
-"dump custom/vtk"_dump_custom_vtk.html :ul
+"dump vtk"_dump_vtk.html :ul
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@ -118,18 +118,21 @@ check which version of Python you have installed, by simply typing

 11.2 Overview of using Python from a LAMMPS script :link(py_2),h4

-NOTE: It is not currently possible to use the "python"_python.html
-command described in this section with Python 3, only with Python 2.
-The C API changed from Python 2 to 3 and the LAMMPS code is not
-compatible with both.
+LAMMPS has several commands which can be used to invoke Python
+code directly from an input script:

-LAMMPS has a "python"_python.html command which can be used in an
-input script to define and execute a Python function that you write
-the code for.  The Python function can also be assigned to a LAMMPS
-python-style variable via the "variable"_variable.html command.  Each
-time the variable is evaluated, either in the LAMMPS input script
-itself, or by another LAMMPS command that uses the variable, this will
-trigger the Python function to be invoked.
+"python"_python.html
+"variable python"_variable.html
+"fix python"_fix_python.html
+"pair_style python"_pair_python.html :ul
+
+The "python"_python.html command which can be used to define and
+execute a Python function that you write the code for.  The Python
+function can also be assigned to a LAMMPS python-style variable via
+the "variable"_variable.html command.  Each time the variable is
+evaluated, either in the LAMMPS input script itself, or by another
+LAMMPS command that uses the variable, this will trigger the Python
+function to be invoked.

 The Python code for the function can be included directly in the input
 script or in an auxiliary file.  The function can have arguments which
@ -162,8 +165,16 @@ doc page for its python-style variables for more info, including
 examples of Python code you can write for both pure Python operations
 and callbacks to LAMMPS.

-To run pure Python code from LAMMPS, you only need to build LAMMPS
-with the PYTHON package installed:
+The "fix python"_fix_python.html command can execute
+Python code at selected timesteps during a simulation run.
+
+The "pair_style python"_pair_python command allows you to define
+pairwise potentials as python code which encodes a single pairwise
+interaction.  This is useful for rapid-developement and debugging of a
+new potential.
+
+To use any of these commands, you only need to build LAMMPS with the
+PYTHON package installed:

 make yes-python
 make machine :pre
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -655,8 +655,7 @@ This section has the following sub-sections:

 2.3.1 "Package basics"_#start_3_1
 2.3.2 "Including/excluding packages"_#start_3_2
-2.3.3 "Packages that require extra libraries"_#start_3_3
-2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)
+2.3.3 "Packages that require extra libraries"_#start_3_3 :all(b)

 :line

@ -828,13 +827,13 @@ Packages in the tables "Section 4"_Section_packages.html with an "ext"
 in the last column link to exernal libraries whose source code is not
 included with LAMMPS.  You must first download and install the library
 before building LAMMPS with that package installed.  E.g. the voronoi
-package links to the freely available "Voro++ library"_voronoi.  You
+package links to the freely available "Voro++ library"_voro_home2.  You
 can often do the download/build in one step by typing "make lib-name
 args=..." from the src dir, with appropriate arguments.  You can leave
 off the args to see a help message.  See "Section
 4"_Section_packages.html for details for each package.

-:link(voronoi,http://math.lbl.gov/voro++)
+:link(voro_home2,http://math.lbl.gov/voro++)

 [Possible errors:]

--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -69,8 +69,9 @@ not {hardware thread}.
 For Intel Xeon CPUs:

 Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
-If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better
-performance. :l
+If using {kspace_style pppm} in the input script, add "neigh_modify binsize cutoff" and "kspace_modify diff ad" to the input script for better
+performance.  Cutoff should be roughly the neighbor list cutoff.  By
+default the binsize is half the neighbor list cutoff.  :l
 "-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
 :ule

--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@ -415,15 +415,15 @@ For binding threads with the KOKKOS OMP option, use thread affinity
 environment variables to force binding.  With OpenMP 3.1 (gcc 4.7 or
 later, intel 12 or later) setting the environment variable
 OMP_PROC_BIND=true should be sufficient.  For binding threads with the
-KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as
-discussed in "Section 2.3.4"_Sections_start.html#start_3_4 of the
-manual.
+KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
+(see "this section"_Section_packages.html#KOKKOS of the manual for
+details).

 [Running on GPUs:]

 Insure the -arch setting in the machine makefile you are using,
-e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
-(see "this section"_Section_start.html#start_3_4 of the manual for
+e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software.
+(see "this section"_Section_packages.html#KOKKOS of the manual for
 details).

 The -np setting of the mpirun command should set the number of MPI
--- a/doc/src/commands.txt
+++ b/doc/src/commands.txt
@ -32,12 +32,12 @@ Commands :h1
   dimension
   displace_atoms
   dump
-   dump_custom_vtk
   dump_h5md
   dump_image
   dump_modify
   dump_molfile
-   dump_nc
+   dump_netcdf
+   dump_vtk
   echo
   fix
   fix_modify
--- a/doc/src/dihedral_spherical.txt
+++ b/doc/src/dihedral_spherical.txt
@ -14,10 +14,10 @@ dihedral_style spherical :pre

 [Examples:]

-dihedral_coeff 1 1  286.1  1 124 1   1 90.0 0   1 90.0 0
-dihedral_coeff 1 3  286.1  1 114 1   1 90  0    1 90.0  0  &
-                    17.3   0 0.0 0   1 158 1    0 0.0   0  &
-                    15.1   0 0.0 0   0 0.0 0    1 167.3 1   :pre
+dihedral_coeff 1 1  286.1  1 124  1    1 90.0 0    1 90.0 0
+dihedral_coeff 1 3  69.3   1 93.9 1    1 90   0    1 90   0  &
+                    49.1   0 0.00 0    1 74.4 1    0 0.00 0  &
+                    25.2   0 0.00 0    0 0.00 0    1 48.1 1

 [Description:]

@ -35,13 +35,14 @@ the dihedral interaction even if it requires adding additional terms to
 the expansion (as was done in the second example).  A careful choice of
 parameters can prevent singularities that occur with traditional
 force-fields whenever theta1 or theta2 approach 0 or 180 degrees.
+
 The last example above corresponds to an interaction with a single energy
-minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains
+minima located near phi=93.9, theta1=74.4, theta2=48.1 degrees, and it remains
 numerically stable at all angles (phi, theta1, theta2). In this example,
-the coefficients 17.3, and 15.1 can be physically interpreted as the
+the coefficients 49.1, and 25.2 can be physically interpreted as the
 harmonic spring constants for theta1 and theta2 around their minima.
-The coefficient 286.1 is the harmonic spring constant for phi after
-division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2).
+The coefficient 69.3 is the harmonic spring constant for phi after
+division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2).

 The following coefficients must be defined for each dihedral type via the
 "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
--- a/doc/src/fix_box_relax.txt
+++ b/doc/src/fix_box_relax.txt
@ -245,8 +245,8 @@ appear the system is converging to your specified pressure.  The
 solution for this is to either (a) zero the velocities of all atoms
 before performing the minimization, or (b) make sure you are
 monitoring the pressure without its kinetic component.  The latter can
-be done by outputting the pressure from the fix this command creates
-(see below) or a pressure fix you define yourself.
+be done by outputting the pressure from the pressure compute this 
+command creates (see below) or a pressure compute you define yourself.

 NOTE: Because pressure is often a very sensitive function of volume,
 it can be difficult for the minimizer to equilibrate the system the
@ -308,7 +308,7 @@ thermo_modify command (or in two separate commands), then the order in
 which the keywords are specified is important.  Note that a "pressure
 compute"_compute_pressure.html defines its own temperature compute as
 an argument when it is specified.  The {temp} keyword will override
-this (for the pressure compute being used by fix npt), but only if the
+this (for the pressure compute being used by fix box/relax), but only if the
 {temp} keyword comes after the {press} keyword.  If the {temp} keyword
 comes before the {press} keyword, then the new pressure compute
 specified by the {press} keyword will be unaffected by the {temp}
@ -316,18 +316,16 @@ setting.

 This fix computes a global scalar which can be accessed by various
 "output commands"_Section_howto.html#howto_15. The scalar is the
-pressure-volume energy, plus the strain energy, if it exists.
-
-This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15. The scalar is given
-by the energy expression shown above. The energy values reported
-at the end of a minimization run under "Minimization stats" include
-this energy, and so differ from what LAMMPS normally reports as
-potential energy. This fix does not support the
-"fix_modify"_fix_modify.html {energy} option,
-because that would result in double-counting of the fix energy in the
-minimization energy. Instead, the fix energy can be explicitly
-added to the potential energy using one of these two variants:
+pressure-volume energy, plus the strain energy, if it exists,
+as described above.
+The energy values reported at the
+end of a minimization run under "Minimization stats" include this
+energy, and so differ from what LAMMPS normally reports as potential
+energy. This fix does not support the "fix_modify"_fix_modify.html
+{energy} option, because that would result in double-counting of the
+fix energy in the minimization energy. Instead, the fix energy can be
+explicitly added to the potential energy using one of these two
+variants:

 variable emin equal pe+f_1  :pre

--- a/doc/src/fix_python.txt
+++ b/doc/src/fix_python.txt
@ -0,0 +1,76 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix python command :h3
+
+[Syntax:]
+
+fix ID group-ID python N callback function_name :pre
+
+ID, group-ID are ignored by this fix :ulb,l
+python = style name of this fix command :l
+N = execute every N steps :l
+callback = {post_force} or {end_of_step} :l
+  {post_force} = callback after force computations on atoms every N time steps
+  {end_of_step} = callback after every N time steps :pre
+:ule
+
+[Examples:]
+
+python post_force_callback here """
+from lammps import lammps :pre
+
+def post_force_callback(lammps_ptr, vflag):
+    lmp = lammps(ptr=lammps_ptr)
+    # access LAMMPS state using Python interface
+""" :pre
+
+python end_of_step_callback here """
+def end_of_step_callback(lammps_ptr):
+    lmp = lammps(ptr=lammps_ptr)
+    # access LAMMPS state using Python interface
+""" :pre
+
+fix pf  all python 50 post_force post_force_callback
+fix eos all python 50 end_of_step end_of_step_callback :pre
+
+[Description:]
+
+This fix allows you to call a Python function during a simulation run.
+The callback is either executed after forces have been applied to atoms
+or at the end of every N time steps.
+
+Callback functions must be declared in the global scope of the
+active Python interpreter. This can either be done by defining it
+inline using the python command or by importing functions from other
+Python modules. If LAMMPS is driven using the library interface from
+Python, functions defined in the driving Python interpreter can also
+be executed.
+
+Each callback is given a pointer object as first argument. This can be
+used to initialize an instance of the lammps Python interface, which
+gives access to the LAMMPS state from Python.
+
+IMPORTANT NOTE: While you can access the state of LAMMPS via library functions
+from these callbacks, trying to execute input script commands will in the best
+case not work or in the worst case result in undefined behavior.
+
+[Restrictions:]
+
+This fix is part of the PYTHON package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+Building LAMMPS with the PYTHON package will link LAMMPS with the
+Python library on your system.  Settings to enable this are in the
+lib/python/Makefile.lammps file.  See the lib/python/README file for
+information on those settings.
+
+[Related commands:]
+
+"python command"_python.html
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@ -34,7 +34,24 @@ written to {filename} on timesteps that are multiples of {Nevery},
 including timestep 0.  For time-averaged chemical species analysis,
 please see the "fix reaxc/c/species"_fix_reaxc_species.html command.

-The format of the output file should be self-explanatory.
+The format of the output file should be reasonably self-explanatory.
+The meaning of the column header abbreviations is as follows:
+
+id = atom id
+type = atom type
+nb = number of bonds
+id_1 = atom id of first bond
+id_nb = atom id of Nth bond
+mol = molecule id
+bo_1 = bond order of first bond
+bo_nb = bond order of Nth bond
+abo = atom bond order (sum of all bonds)
+nlp = number of lone pairs
+q = atomic charge :ul
+
+If the filename ends with ".gz", the output file is written in gzipped
+format.  A gzipped dump file will be about 3x smaller than the text
+version, but will also take longer to write.

 :line

@ -85,6 +102,9 @@ USER-REAXC package.  It is only enabled if LAMMPS was built with that
 package.  See the "Making LAMMPS"_Section_start.html#start_3 section
 for more info.

+To write gzipped bond files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option.
+
 [Related commands:]

 "pair_style reax"_pair_reax.html, "pair_style
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@ -52,6 +52,10 @@ number of molecules of each species.  In this context, "species" means
 a unique molecule.  The chemical formula of each species is given in
 the first line.

+If the filename ends with ".gz", the output file is written in gzipped
+format.  A gzipped dump file will be about 3x smaller than the text version,
+but will also take longer to write.
+
 Optional keyword {cutoff} can be assigned to change the minimum
 bond-order values used in identifying chemical bonds between pairs of
 atoms.  Bond-order cutoffs should be carefully chosen, as bond-order
@ -164,6 +168,9 @@ USER-REAXC package.  It is only enabled if LAMMPS was built with that
 package.  See the "Making LAMMPS"_Section_start.html#start_3 section
 for more info.

+To write gzipped species files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option.
+
 It should be possible to extend it to other reactive pair_styles (such as
 "rebo"_pair_airebo.html, "airebo"_pair_airebo.html,
 "comb"_pair_comb.html, and "bop"_pair_bop.html), but this has not yet been done.
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@ -111,6 +111,7 @@ Fixes :h1
   fix_press_berendsen
   fix_print
   fix_property_atom
+   fix_python
   fix_qbmsst
   fix_qeq
   fix_qeq_comb
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -55,12 +55,12 @@ dihedral_style.html
 dimension.html
 displace_atoms.html
 dump.html
-dump_custom_vtk.html
 dump_h5md.html
 dump_image.html
 dump_modify.html
 dump_molfile.html
-dump_nc.html
+dump_netcdf.html
+dump_vtk.html
 echo.html
 fix.html
 fix_modify.html
@ -237,6 +237,7 @@ fix_pour.html
 fix_press_berendsen.html
 fix_print.html
 fix_property_atom.html
+fix_python.html
 fix_qbmsst.html
 fix_qeq.html
 fix_qeq_comb.html
@ -432,6 +433,7 @@ pair_gauss.html
 pair_gayberne.html
 pair_gran.html
 pair_gromacs.html
+pair_gw.html
 pair_hbond_dreiding.html
 pair_hybrid.html
 pair_kim.html
@ -467,6 +469,7 @@ pair_oxdna.html
 pair_oxdna2.html
 pair_peri.html
 pair_polymorphic.html
+pair_python.html
 pair_quip.html
 pair_reax.html
 pair_reaxc.html
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@ -7,11 +7,13 @@
 :line

 pair_style edip command :h3
+pair_style edip/multi command :h3

 [Syntax:]

-pair_style edip :pre
-pair_style edip/omp :pre
+pair_style style :pre
+
+style = {edip} or {edip/multi} :ul

 [Examples:]

@ -20,11 +22,14 @@ pair_coeff * * Si.edip Si

 [Description:]

-The {edip} style computes a 3-body "EDIP"_#EDIP potential which is
-popular for modeling silicon materials where it can have advantages
-over other models such as the "Stillinger-Weber"_pair_sw.html or
-"Tersoff"_pair_tersoff.html potentials.  In EDIP, the energy E of a
-system of atoms is
+The {edip} and {edip/multi} styles compute a 3-body "EDIP"_#EDIP
+potential which is popular for modeling silicon materials where
+it can have advantages over other models such as the
+"Stillinger-Weber"_pair_sw.html or "Tersoff"_pair_tersoff.html
+potentials. The {edip} style has been programmed for single element
+potentials, while {edip/multi} supports multi-element EDIP runs.
+
+In EDIP, the energy E of a system of atoms is

 :c,image(Eqs/pair_edip.jpg)

@ -142,7 +147,7 @@ This pair style can only be used via the {pair} keyword of the

 [Restrictions:]

-This angle style can only be used if LAMMPS was built with the
+This pair style can only be used if LAMMPS was built with the
 USER-MISC package.  See the "Making LAMMPS"_Section_start.html#start_3
 section for more info on packages.

@ -151,7 +156,7 @@ for pair interactions.

 The EDIP potential files provided with LAMMPS (see the potentials directory)
 are parameterized for metal "units"_units.html.
-You can use the SW potential with any LAMMPS units, but you would need
+You can use the EDIP potential with any LAMMPS units, but you would need
 to create your own EDIP potential file with coefficients listed in the
 appropriate units if your simulation doesn't use "metal" units.

@ -164,4 +169,4 @@ appropriate units if your simulation doesn't use "metal" units.
 :line

 :link(EDIP)
-[(EDIP)] J. F. Justo et al., Phys. Rev. B 58, 2539 (1998).
+[(EDIP)] J F Justo et al, Phys Rev B 58, 2539 (1998).
--- a/doc/src/pair_gauss.txt
+++ b/doc/src/pair_gauss.txt
@ -128,7 +128,7 @@ The B parameter is converted to a distance (sigma), before mixing
 afterwards (using B=sigma^2).
 Negative A values are converted to positive A values (using abs(A))
 before mixing, and converted back after mixing
-(by multiplying by sign(Ai)*sign(Aj)).
+(by multiplying by min(sign(Ai),sign(Aj))).
 This way, if either particle is repulsive (if Ai<0 or Aj<0),
 then the default interaction between both particles will be repulsive.

--- a/doc/src/pair_gw.txt
+++ b/doc/src/pair_gw.txt
@ -0,0 +1,120 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style gw command :h3
+pair_style gw/zbl command :h3
+
+[Syntax:]
+
+pair_style style :pre
+
+style = {gw} or {gw/zbl} :ul
+
+[Examples:]
+
+pair_style gw
+pair_coeff * * SiC.gw Si C C
+
+pair_style gw/zbl
+pair_coeff * * SiC.gw.zbl C Si :pre
+
+[Description:]
+
+The {gw} style computes a 3-body "Gao-Weber"_#Gao potential;
+similarly {gw/zbl} combines this potential with a modified
+repulsive ZBL core function in a similar fashion as implemented
+in the "tersoff/zbl"_pair_tersoff_zbl.html pair style.
+
+Unfortunately the author of this contributed code has not been
+able to submit a suitable documentation explaining the details
+of the potentials. The LAMMPS developers thus have finally decided
+to release the code anyway with only the technical explanations.
+For details of the model and the parameters, please refer to the
+linked publication.
+
+Only a single pair_coeff command is used with the {gw} and {gw/zbl}
+styles which specifies a Gao-Weber potential file with parameters
+for all needed elements.  These are mapped to LAMMPS atom types by
+specifying N additional arguments after the filename in the pair_coeff
+command, where N is the number of LAMMPS atom types:
+
+filename
+N element names = mapping of GW elements to atom types :ul
+
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the potential file.
+
+As an example, imagine a file SiC.gw has Gao-Weber values for Si and C.
+If your LAMMPS simulation has 4 atoms types and you want the first 3 to
+be Si, and the 4th to be C, you would use the following pair_coeff command:
+
+pair_coeff * * SiC.gw Si Si Si C :pre
+
+The first 2 arguments must be * * so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
+element in the GW file.  The final C argument maps LAMMPS atom type 4
+to the C element in the GW file.  If a mapping value is specified as
+NULL, the mapping is not performed.  This can be used when a {gw}
+potential is used as part of the {hybrid} pair style.  The NULL values
+are placeholders for atom types that will be used with other
+potentials.
+
+Gao-Weber files in the {potentials} directory of the LAMMPS
+distribution have a ".gw" suffix.  Gao-Weber with ZBL files
+have a ".gz.zbl" suffix. The structure of the potential files
+is similar to other many-body potentials supported by LAMMPS.
+You have to refer to the comments in the files and the literature
+to learn more details.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as
+described above from values in the potential file.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+This pair style is part of the USER-MISC package. It is only enabled
+if LAMMPS was built with that package.  See
+the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This pair style requires the "newton"_newton.html setting to be "on"
+for pair interactions.
+
+The Gao-Weber potential files provided with LAMMPS (see the
+potentials directory) are parameterized for metal "units"_units.html.
+You can use the GW potential with any LAMMPS units, but you would need
+to create your own GW potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+:link(Gao)
+[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@ -23,7 +23,8 @@ pair_coeff * * Ti.meam.spline Ti Ti Ti :pre

 The {meam/spline} style computes pairwise interactions for metals
 using a variant of modified embedded-atom method (MEAM) potentials
-"(Lenosky)"_#Lenosky1.  The total energy E is given by
+"(Lenosky)"_#Lenosky1.  For a single species ("old-style") MEAM,
+the total energy E is given by

 :c,image(Eqs/pair_meam_spline.jpg)

@ -31,6 +32,20 @@ where rho_i is the density at atom I, theta_jik is the angle between
 atoms J, I, and K centered on atom I. The five functions Phi, U, rho,
 f, and g are represented by cubic splines.

+The {meam/spline} style also supports a new style multicomponent
+modified embedded-atom method (MEAM) potential "(Zhang)"_#Zhang4, where
+the total energy E is given by
+
+:c,image(Eqs/pair_meam_spline_multicomponent.jpg)
+
+where the five functions Phi, U, rho, f, and g depend on the chemistry
+of the atoms in the interaction.  In particular, if there are N different
+chemistries, there are N different U, rho, and f functions, while there
+are N(N+1)/2 different Phi and g functions.  The new style multicomponent
+MEAM potential files are indicated by the second line in the file starts
+with "meam/spline" followed by the number of elements and the name of each
+element.
+
 The cutoffs and the coefficients for these spline functions are listed
 in a parameter file which is specified by the
 "pair_coeff"_pair_coeff.html command.  Parameter files for different
@ -59,7 +74,7 @@ N element names = mapping of spline-based MEAM elements to atom types :ul
 See the "pair_coeff"_pair_coeff.html doc page for alternate ways
 to specify the path for the potential file.

-As an example, imagine the Ti.meam.spline file has values for Ti.  If
+As an example, imagine the Ti.meam.spline file has values for Ti (old style).  If
 your LAMMPS simulation has 3 atoms types and they are all to be
 treated with this potentials, you would use the following pair_coeff
 command:
@ -72,10 +87,19 @@ in the potential file.  If a mapping value is specified as NULL, the
 mapping is not performed.  This can be used when a {meam/spline}
 potential is used as part of the {hybrid} pair style.  The NULL values
 are placeholders for atom types that will be used with other
-potentials.
+potentials. The old-style potential maps any non-NULL species named
+on the command line to that single type.

-NOTE: The {meam/spline} style currently supports only single-element
-MEAM potentials.  It may be extended for alloy systems in the future.
+An example with a two component spline (new style) is TiO.meam.spline, where
+the command
+
+pair_coeff * * TiO.meam.spline Ti O :pre
+
+will map the 1st atom type to Ti and the second atom type to O. Note
+in this case that the species names need to match exactly with the
+names of the elements in the TiO.meam.spline file; otherwise an
+error will be raised. This behavior is different than the old style
+MEAM files.

 :line

@ -104,9 +128,6 @@ more instructions on how to use the accelerated styles effectively.

 [Mixing, shift, table, tail correction, restart, rRESPA info]:

-The current version of this pair style does not support multiple
-element types or mixing.  It has been designed for pure elements only.
-
 This pair style does not support the "pair_modify"_pair_modify.html
 shift, table, and tail options.

@ -142,3 +163,6 @@ for more info.
 [(Lenosky)] Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter,
 Kress, Modelling Simulation Materials Science Engineering, 8, 825
 (2000).
+
+:link(Zhang4)
+[(Zhang)] Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016).
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@ -0,0 +1,216 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style python command :h3
+
+[Syntax:]
+
+pair_style python cutoff :pre
+
+cutoff = global cutoff for interactions in python potential classes
+
+[Examples:]
+
+pair_style python 2.5
+pair_coeff * * py_pot.LJCutMelt lj :pre
+
+pair_style hybrid/overlay coul/long 12.0 python 12.0
+pair_coeff * * coul/long
+pair_coeff * * python py_pot.LJCutSPCE OW NULL :pre
+
+[Description:]
+
+The {python} pair style provides a way to define pairwise additive
+potential functions as python script code that is loaded into LAMMPS
+from a python file which must contain specific python class definitions.
+This allows to rapidly evaluate different potential functions without
+having to modify and recompile LAMMPS. Due to python being an
+interpreted language, however, the performance of this pair style is
+going to be significantly slower (often between 20x and 100x) than
+corresponding compiled code. This penalty can be significantly reduced
+through generating tabulations from the python code through the
+"pair_write"_pair_write.html command, which is supported by this style.
+
+Only a single pair_coeff command is used with the {python} pair style
+which specifies a python class inside a python module or file that
+LAMMPS will look up in the current directory, the folder pointed to by
+the LAMMPS_POTENTIALS environment variable or somewhere in your python
+path.  A single python module can hold multiple python pair class
+definitions. The class definitions itself have to follow specific
+rules that are explained below.
+
+Atom types in the python class are specified through symbolic
+constants, typically strings. These are mapped to LAMMPS atom types by
+specifying N additional arguments after the class name in the
+pair_coeff command, where N must be the number of currently defined
+atom types:
+
+As an example, imagine a file {py_pot.py} has a python potential class
+names {LJCutMelt} with parameters and potential functions for a two
+Lennard-Jones atom types labeled as 'LJ1' and 'LJ2'. In your LAMMPS
+input and you would have defined 3 atom types, out of which the first
+two are supposed to be using the 'LJ1' parameters and the third the
+'LJ2' parameters, then you would use the following pair_coeff command:
+
+pair_coeff * * py_pot.LJCutMelt LJ1 LJ1 LJ2 :pre
+
+The first two arguments [must] be * * so as to span all LAMMPS atom
+types.  The first two LJ1 arguments map LAMMPS atom types 1 and 2 to
+the LJ1 atom type in the LJCutMelt class of the py_pot.py file.  The
+final LJ2 argument maps LAMMPS atom type 3 to the LJ2 atom type the
+python file.  If a mapping value is specified as NULL, the mapping is
+not performed, any pair interaction with this atom type will be
+skipped. This can be used when a {python} potential is used as part of
+the {hybrid} or {hybrid/overlay} pair style. The NULL values are then
+placeholders for atom types that will be used with other potentials.
+
+:line
+
+The python potential file has to start with the following code:
+
+from __future__ import print_function
+
+class LAMMPSPairPotential(object):
+    def __init__(self):
+        self.pmap=dict()
+        self.units='lj'
+    def map_coeff(self,name,ltype):
+        self.pmap\[ltype\]=name
+    def check_units(self,units):
+        if (units != self.units):
+           raise Exception("Conflicting units: %s vs. %s" % (self.units,units))
+:pre
+
+Any classes with definitions of specific potentials have to be derived
+from this class and should be initialize in a similar fashion to the
+example given below.
+
+NOTE: The class constructor has to set up a data structure containing
+the potential parameters supported by this class.  It should also
+define a variable {self.units} containing a string matching one of the
+options of LAMMPS' "units"_units.html command, which is used to
+verify, that the potential definition in the python class and in the
+LAMMPS input match.
+
+Here is an example for a single type Lennard-Jones potential class
+{LJCutMelt} in reducted units, which defines an atom type {lj} for
+which the parameters epsilon and sigma are both 1.0:
+
+class LJCutMelt(LAMMPSPairPotential):
+    def __init__(self):
+        super(LJCutMelt,self).__init__()
+        # set coeffs: 48*eps*sig**12, 24*eps*sig**6,
+        #              4*eps*sig**12,  4*eps*sig**6
+        self.units = 'lj'
+        self.coeff = \{'lj'  : \{'lj'  : (48.0,24.0,4.0,4.0)\}\}
+:pre
+
+The class also has to provide two methods for the computation of the
+potential energy and forces, which have be named {compute_force},
+and {compute_energy}, which both take 3 numerical arguments:
+
+  rsq   = the square of the distance between a pair of atoms (float) :l
+  itype = the (numerical) type of the first atom :l
+  jtype = the (numerical) type of the second atom :ul
+
+This functions need to compute the force and the energy, respectively,
+and use the result as return value. The functions need to use the
+{pmap} dictionary to convert the LAMMPS atom type number to the symbolic
+value of the internal potential parameter data structure. Following
+the {LJCutMelt} example, here are the two functions:
+
+   def compute_force(self,rsq,itype,jtype):
+        coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\]
+        r2inv  = 1.0/rsq
+        r6inv  = r2inv*r2inv*r2inv
+        lj1 = coeff\[0\]
+        lj2 = coeff\[1\]
+        return (r6inv * (lj1*r6inv - lj2))*r2inv :pre
+
+    def compute_energy(self,rsq,itype,jtype):
+        coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\]
+        r2inv  = 1.0/rsq
+        r6inv  = r2inv*r2inv*r2inv
+        lj3 = coeff\[2\]
+        lj4 = coeff\[3\]
+        return (r6inv * (lj3*r6inv - lj4)) :pre
+
+NOTE: for consistency with the C++ pair styles in LAMMPS, the
+{compute_force} function follows the conventions of the Pair::single()
+methods and does not return the full force, but the force scaled by
+the distance between the two atoms, so this value only needs to be
+multiplied by delta x, delta y, and delta z to conveniently obtain the
+three components of the force vector between these two atoms.
+
+:line
+
+NOTE: The evaluation of scripted python code will slow down the
+computation pair-wise interactions quite significantly. However, this
+can be largely worked around through using the python pair style not
+for the actual simulation, but to generate tabulated potentials on the
+fly using the "pair_write"_pair_write.html command. Please see below
+for an example LAMMPS input of how to build a table file:
+
+pair_style python 2.5
+pair_coeff * * py_pot.LJCutMelt lj
+shell rm -f melt.table
+pair_write  1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj :pre
+
+Note that it is strongly recommended to try to [delete] the potential
+table file before generating it. Since the {pair_write} command will
+always append to a table file, which pair style table will use the
+first match. Thus when changing the potential function in the python
+class, the table pair style will still read the old variant.
+
+After switching the pair style to {table}, the potential tables need
+to be assigned to the LAMMPS atom types like this:
+
+pair_style      table linear 2000
+pair_coeff      1  1  melt.table lj :pre
+
+This can also be done for more complex systems.  Please see the
+{examples/python} folders for a few more examples.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+Mixing of potential parameters has to be handled inside the provided
+python module. The python pair style simply assumes that force and
+energy computation can be correctly performed for all pairs of atom
+types as they are mapped to the atom type labels inside the python
+potential class.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+This pair style is part of the PYTHON package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html, "pair_write"_pair_write.html,
+"pair style table"_pair_table.html
+
+[Default:] none
+
+
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@ -18,7 +18,7 @@ pair_style tersoff/table/omp command :h3

 pair_style style :pre

-style = {tersoff} or {tersoff/table} or {tersoff/gpu} or {tersoff/omp} or {tersoff/table/omp}
+style = {tersoff} or {tersoff/table} or {tersoff/gpu} or {tersoff/omp} or {tersoff/table/omp} :ul

 [Examples:]

--- a/doc/src/pair_yukawa_colloid.txt
+++ b/doc/src/pair_yukawa_colloid.txt
@ -35,7 +35,7 @@ cutoff.
 In contrast to "pair_style yukawa"_pair_yukawa.html, this functional
 form arises from the Coulombic interaction between two colloid
 particles, screened due to the presence of an electrolyte, see the
-book by "Safran"_#Safran for a derivation in the context of DVLO
+book by "Safran"_#Safran for a derivation in the context of DLVO
 theory.  "Pair_style yukawa"_pair_yukawa.html is a screened Coulombic
 potential between two point-charges and uses no such approximation.

--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@ -36,6 +36,7 @@ Pair Styles :h1
   pair_gayberne
   pair_gran
   pair_gromacs
+   pair_gw
   pair_hbond_dreiding
   pair_hybrid
   pair_kim
@ -71,6 +72,7 @@ Pair Styles :h1
   pair_oxdna2
   pair_peri
   pair_polymorphic
+   pair_python
   pair_quip
   pair_reax
   pair_reaxc
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@ -14,7 +14,7 @@ python func keyword args ... :pre

 func = name of Python function :ulb,l
 one or more keyword/args pairs must be appended :l
-keyword = {invoke} or {input} or {return} or {format} or {length} or {file} or {here} or {exists}
+keyword = {invoke} or {input} or {return} or {format} or {length} or {file} or {here} or {exists} or {source}
  {invoke} arg = none = invoke the previously defined Python function
  {input} args = N i1 i2 ... iN
    N = # of inputs to function
@ -36,7 +36,12 @@ keyword = {invoke} or {input} or {return} or {format} or {length} or {file} or {
  {here} arg = inline
    inline = one or more lines of Python code which defines func
             must be a single argument, typically enclosed between triple quotes
-  {exists} arg = none = Python code has been loaded by previous python command :pre
+  {exists} arg = none = Python code has been loaded by previous python command
+  {source} arg = {filename} or {inline}
+    filename = file of Python code which will be executed immediately
+    inline = one or more lines of Python code which will be executed immediately
+             must be a single argument, typically enclosed between triple quotes
+:pre
 :ule

 [Examples:]
@ -50,7 +55,7 @@ def factorial(n):
  return n * factorial(n-1)
 """ :pre

-python loop input 1 SELF return v_value format -f here """
+python loop input 1 SELF return v_value format pf here """
 def loop(lmpptr,N,cut0):
  from lammps import lammps
  lmp = lammps(ptr=lmpptr) :pre
@ -59,7 +64,7 @@ def loop(lmpptr,N,cut0):

  for i in range(N):
    cut = cut0 + i*0.1
-    lmp.set_variable("cut",cut)               # set a variable in LAMMPS
+    lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
    lmp.command("pair_style lj/cut $\{cut\}")   # LAMMPS commands
    lmp.command("pair_coeff * * 1.0 1.0")
    lmp.command("run 100")
@ -67,12 +72,8 @@ def loop(lmpptr,N,cut0):

 [Description:]

-NOTE: It is not currently possible to use the "python"_python.html
-command described in this section with Python 3, only with Python 2.
-The C API changed from Python 2 to 3 and the LAMMPS code is not
-compatible with both.
-
-Define a Python function or execute a previously defined function.
+Define a Python function or execute a previously defined function or
+execute some arbitrary python code.
 Arguments, including LAMMPS variables, can be passed to the function
 from the LAMMPS input script and a value returned by the Python
 function to a LAMMPS variable.  The Python code for the function can
@ -107,7 +108,8 @@ command.

 The {func} setting specifies the name of the Python function.  The
 code for the function is defined using the {file} or {here} keywords
-as explained below.
+as explained below. In case of the {source} keyword, the name of
+the function is ignored.

 If the {invoke} keyword is used, no other keywords can be used, and a
 previous python command must have defined the Python function
@ -116,6 +118,13 @@ previously defined arguments and return value processed as explained
 below.  You can invoke the function as many times as you wish in your
 input script.

+If the {source} keyword is used, no other keywords can be used.
+The argument can be a filename or a string with python commands,
+either on a single line enclosed in quotes, or as multiple lines
+enclosed in triple quotes. These python commands will be passed
+to the python interpreter and executed immediately without registering
+a python function for future execution.
+
 The {input} keyword defines how many arguments {N} the Python function
 expects.  If it takes no arguments, then the {input} keyword should
 not be used.  Each argument can be specified directly as a value,
@ -396,6 +405,9 @@ or other variables may have hidden side effects as well.  In these
 cases, LAMMPS has no simple way to check that something illogical is
 being attempted.

+The same applies to Python functions called during a simulation run at
+each time step using "fix python"_fix_python.html.
+
 :line

 If you run Python code directly on your workstation, either
@ -477,19 +489,10 @@ python"_Section_python.html.  Note that it is important that the
 stand-alone LAMMPS executable and the LAMMPS shared library be
 consistent (built from the same source code files) in order for this
 to work.  If the two have been built at different times using
-different source files, problems may occur.
-
-As described above, you can use the python command to invoke a Python
-function which calls back to LAMMPS through its Python-wrapped library
-interface.  However you cannot do the opposite.  I.e. you cannot call
-LAMMPS from Python and invoke the python command to "callback" to
-Python and execute a Python function.  LAMMPS will generate an error
-if you try to do that.  Note that we think there actually should be a
-way to do that, but haven't yet been able to figure out how to do it
-successfully.
+different source files, problems may occur. 

 [Related commands:]

-"shell"_shell.html, "variable"_variable.html
+"shell"_shell.html, "variable"_variable.html, "fix python"_fix_python.html

 [Default:] none
--- a/doc/src/rerun.txt
+++ b/doc/src/rerun.txt
@ -15,7 +15,7 @@ rerun file1 file2 ... keyword args ... :pre
 file1,file2,... = dump file(s) to read :ulb,l
 one or more keywords may be appended, keyword {dump} must appear and be last :l
 keyword = {first} or {last} or {every} or {skip} or {start} or {stop} or {dump}
- {first} args = Nfirts
+ {first} args = Nfirst
   Nfirst = dump timestep to start on
 {last} args = Nlast
   Nlast = dumptimestep to stop on
--- a/doc/src/tutorial_pylammps.txt
+++ b/doc/src/tutorial_pylammps.txt
@ -55,7 +55,7 @@ using the generated {auto} Makefile.
 cd $LAMMPS_DIR/src :pre

 # generate custom Makefile
-python2 Make.py -jpg -png -s ffmpeg exceptions -m mpi -a file :pre
+python Make.py -jpg -png -s ffmpeg exceptions -m mpi -a file :pre

 # add packages if necessary
 make yes-MOLECULE :pre
--- a/doc/src/velocity.txt
+++ b/doc/src/velocity.txt
@ -61,7 +61,7 @@ keyword/value parameters.  Not all options are used by each style.
 Each option has a default as listed below.

 The {create} style generates an ensemble of velocities using a random
-number generator with the specified seed as the specified temperature.
+number generator with the specified seed at the specified temperature.

 The {set} style sets the velocities of all atoms in the group to the
 specified values.  If any component is specified as NULL, then it is
--- a/examples/ASPHERE/poly/in.poly
+++ b/examples/ASPHERE/poly/in.poly
@ -62,6 +62,7 @@ pair_coeff	3 3 1.0 1.5
 pair_coeff	1 4 0.0 1.0 0.5
 pair_coeff	2 4 0.0 1.0 1.0
 pair_coeff	3 4 0.0 1.0 0.75
+pair_coeff	4 4 0.0 1.0 0.0

 delete_atoms	overlap 1.0 small big

--- a/examples/ASPHERE/poly/in.poly.mp
+++ b/examples/ASPHERE/poly/in.poly.mp
@ -62,6 +62,7 @@ pair_coeff	3 3 1.0 1.5
 pair_coeff	1 4 0.0 1.0 0.5
 pair_coeff	2 4 0.0 1.0 1.0
 pair_coeff	3 4 0.0 1.0 0.75
+pair_coeff	4 4 0.0 1.0 0.0

 delete_atoms	overlap 1.0 small big

--- a/examples/USER/misc/edip/Si.edip
+++ b/examples/USER/misc/edip/Si.edip
@ -0,0 +1,26 @@
+# DATE: 2011-09-15 CONTRIBUTOR: Unknown CITATION: Justo, Bazant, Kaxiras, Bulatov and Yip, Phys Rev B, 58, 2539 (1998)
+
+# EDIP parameters for various elements and mixtures
+# multiple entries can be added to this file, LAMMPS reads the ones it needs
+# these entries are in LAMMPS "metal" units
+
+# format of a single entry (one or more lines)
+#
+#   element 1, element 2, element 3, 
+#     A   B   cutoffA   cutoffC   alpha   beta   eta 
+#     gamma   lambda    mu   rho   sigma   Q0 
+#     u1   u2   u3   u4
+#
+# units for each parameters:
+#     A , lambda are in eV  
+#     B, cutoffA, cutoffC, gamma, sigma are in Angstrom
+#     alpha, beta, eta, mu, rho, Q0, u1-u4 are pure numbers 
+
+# Here are the original parameters in metal units, for Silicon from:
+# J. F. Justo, M. Z. Bazant, E. Kaxiras, V. V. Bulatov, S. Yip
+#       Phys. Rev. B 58, 2539 (1998)
+#
+
+Si Si Si 7.9821730 1.5075463 3.1213820 2.5609104 3.1083847 0.0070975 0.2523244
+         1.1247945 1.4533108 0.6966326 1.2085196 0.5774108 312.1341346
+         -0.165799 32.557 0.286198 0.66
--- a/examples/USER/misc/edip/SiC.edip
+++ b/examples/USER/misc/edip/SiC.edip
@ -0,0 +1,38 @@
+# DATE: 2017-05-16 CONTRIBUTOR: Laurent Pizzagalli CITATION: G. Lucas, M. Bertolus, and L. Pizzagalli, J. Phys. : Condens. Matter 22, 035802 (2010)
+#   element 1, element 2, element 3, 
+#     A   B   cutoffA   cutoffC   alpha   beta   eta 
+#     gamma   lambda    mu   rho   sigma   Q0 
+#     u1   u2   u3   u4
+#
+Si Si Si 5.488043 1.446435 2.941586 2.540193 3.066580 0.008593 0.589390
+         1.135256 2.417497 0.629131 1.343679 0.298443 208.924548
+         -0.165799 32.557 0.286198 0.66
+
+C C C    10.222599 0.959814 2.212263 1.741598 1.962090 0.025661 0.275605
+         1.084183 3.633621 0.594236 2.827634 0.536561 289.305617
+         -0.165799 32.557 0.286198 0.66
+
+C Si Si  7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.432497
+         1.191567 3.025559 0.611684 2.061835 0.423863 249.115082
+         -0.165799 32.557000 0.286198 0.660000
+
+Si C C   7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.432497
+         1.191567 3.025559 0.611684 2.061835 0.423863 249.115082
+         -0.165799 32.557000 0.286198 0.660000
+
+Si Si C  5.488043 1.446435 2.941586 2.540193 3.066580 0.008593 0.510944
+         1.135256 2.721528 0.620407 1.343679 0.298443 229.019815
+         -0.165799 32.557000 0.286198 0.660000
+
+Si C Si  7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.510944
+         1.191567 2.721528 0.620407 2.061835 0.423863 229.019815
+         -0.165799 32.557000 0.286198 0.660000
+
+C C Si   10.222599 0.959814 2.212263 1.741598 1.962090 0.025661 0.354051
+         1.084183 3.329590 0.602960 2.827634 0.536561 269.210350
+         -0.165799 32.557000 0.286198 0.660000
+
+C Si C   7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.354051
+         1.191567 3.329590 0.602960 2.061835 0.423863 269.210350
+         -0.165799 32.557000 0.286198 0.660000
+
--- a/examples/USER/misc/edip/data.SiC
+++ b/examples/USER/misc/edip/data.SiC
@ -0,0 +1,138 @@
+Position data for Silicon-Carbon system
+
+	128 	atoms
+	2 	atom types
+  -6.00 	5.97232152 	xlo xhi
+  -6.00		5.97232152 	ylo yhi
+  -6.00 	5.97232152 	zlo zhi
+
+ Atoms
+
+1	2       -2.9378454      -4.4592615      -4.8109196
+2	2        5.6222143      -2.7335026      -1.7157569
+3	2       -2.6614623      -5.5431059       1.6353686
+4	2       -5.4326838      -4.6174577       5.9452279
+5	2        5.8679239      -0.1120535      -3.5839373
+6	2       -3.7174621      -0.6623311      -0.3714789
+7	2       -5.0724728      -2.5671623       4.4103461
+8	2       -3.3951436       0.9341126       4.9310702
+9	2       -5.4347593       1.9523767      -5.6180938
+10	2       -4.5884719       2.2904528      -1.0597739
+11	2       -5.9058662       0.6212406       2.0127574
+12	2       -4.7680660       0.1965740       4.3267764
+13	2       -5.4228882       5.2569673      -4.5162920
+14	2       -5.2683965      -5.9193658      -2.8648668
+15	2       -2.8610884       1.0484664       2.0299077
+16	2       -4.0711084       5.3133026       3.8009514
+17	2       -0.1947147      -4.1677696      -5.6950931
+18	2       -2.9892710      -3.1647368      -1.6173910
+19	2       -0.9129311      -4.3819066      -0.1601859
+20	2       -2.4513693      -5.2466501       4.8882912
+21	2       -2.8879952      -0.1633446      -3.3401150
+22	1       -4.6738762      -1.3807254      -2.2946777
+23	2       -0.6973948      -1.4885343       0.6005156
+24	1       -2.7392164      -2.4774843       0.2387186
+25	2       -2.6551254      -2.7229952       2.6350264
+26	1       -3.4644263      -4.6028144       3.3817786
+27	2        0.7227614      -2.0709446       2.9214737
+28	1       -2.1000577      -3.2131296       5.7273437
+29	2       -3.1057649       2.3204819      -2.2725622
+30	1       -2.2298751       0.7168389      -1.3107201
+31	2       -1.8698261       1.4006751       0.7265108
+32	1       -4.1103409      -0.7093340       1.9341753
+33	2       -0.3505581       3.2707182      -0.2880656
+34	1       -3.4045407      -1.4383961       4.3903527
+35	2       -3.0940529       1.4132478      -5.3635505
+36	1       -4.4560663       1.2072875      -3.7310176
+37	2       -2.6061002       4.6373499      -4.6903941
+38	1       -3.3477444       4.6768137      -2.6284678
+39	2        0.8121697       4.8602418      -4.6710946
+40	1       -2.5756922       3.3740738      -0.2136350
+41	2       -0.3867976       5.8745611      -2.1119905
+42	1       -1.6766249       1.3374292       3.8741477
+43	2       -0.8770613       3.3735941       4.3846975
+44	1       -1.8609254       3.3158245      -5.9786556
+45	1       -5.2732321      -4.6073253      -0.9581754
+46	1       -2.7888697      -5.6910152      -0.7922023
+47	1       -2.4717165       4.5801880       2.5083210
+48	1       -3.8819950       5.8456589      -5.7563384
+49	2        2.2314782      -2.7729214      -5.2356862
+50	2        0.2981976      -3.1385279      -3.1608167
+51	2        2.8810785      -3.4658695      -0.5823196
+52	2        0.2509625      -5.7595229       2.7389761
+53	2       -0.2934120      -0.8029431      -3.3698507
+54	1       -1.0075690      -2.0481922      -1.9419298
+55	2        2.0729069       1.4922441      -2.3898096
+56	1        1.1110944      -3.2004208       0.9491078
+57	2        1.6774298      -0.7901860       2.5158773
+58	1       -0.8342297      -4.3342518       2.0971458
+59	2        3.2747406      -1.3107897       4.7884706
+60	1        1.7126246      -3.3691471       4.5581012
+61	2        0.4770605       1.7769008      -5.3339915
+62	1        0.2944391       0.5892781      -2.2030106
+63	2        2.2039275       3.1557557      -2.0276796
+64	1       -0.0404494       0.4767818       1.0396418
+65	2        1.1395867       2.3763443       2.3481007
+66	1       -0.9738374      -1.6325161       3.7538567
+67	2       -0.3291998       0.2996990       5.2770809
+68	1       -1.6185604      -0.3964274      -5.1771220
+69	2        2.5999949      -5.1977715       5.8230717
+70	1       -1.6270675       2.3210900      -3.6299941
+71	2        3.6532700       4.9282597      -5.4319276
+72	1        0.0788934       4.0241037      -2.5011530
+73	2        2.8556507       2.6168653       2.1125546
+74	1        0.9738989       2.6255364       4.3412121
+75	2        3.7452938       3.4521356       4.5946426
+76	1        2.0805182       4.7039015       5.3280260
+77	1       -1.0324174      -5.8155041      -4.3265820
+78	1        0.7622442      -4.3631629      -1.3156572
+79	1        0.3263684       3.9937357       1.6172321
+80	1       -0.4350105      -5.7997058       4.5959134
+81	2        3.9161132      -4.6052788      -3.3191717
+82	2        1.9240657       5.7345079      -1.9754251
+83	2       -5.9794488      -4.2369359       1.8646522
+84	2        4.3339975      -4.4845227       5.3737440
+85	2        2.2755456      -0.6327737      -5.7931837
+86	1        1.8728190      -1.5504906      -3.4560010
+87	2        3.4558100      -1.1054068      -1.8333071
+88	1        4.3788172      -1.9466494      -0.3284637
+89	2        2.5999235      -3.7548996       2.5740569
+90	1        3.9983910      -4.4856603       1.1968663
+91	2       -5.7295580      -2.1475672      -5.9963645
+92	1        4.2664051      -2.6988975      -5.8005478
+93	2        4.5254685       2.2906832      -3.4765798
+94	1        2.3603088       1.3416442      -4.4173836
+95	2        4.7767057       1.4061217      -0.7524620
+96	1        1.8072666      -0.7835973      -0.4581995
+97	2        4.4745018       0.3736224       2.1068274
+98	1        3.6081170      -1.7315713       2.4019053
+99	2        4.6281423      -0.2865409       4.4756524
+100	1        1.7975239       0.2893530       4.2330830
+101	2        5.8341452       4.4986472      -5.9664541
+102	1        3.2401308       4.1655227      -3.5070029
+103	2        4.8720339       4.8709982      -2.3364366
+104	1        3.5526476       1.2262752       0.6926826
+105	2       -5.8173342       4.5420479       1.5578881
+106	1        3.9683224       1.5441137       3.8284375
+107	2       -5.5349308       1.9067049       3.7504113
+108	1        4.4728615       2.6415574      -5.5952809
+109	1        1.7000950      -4.8115440      -4.1953920
+110	1        1.7221527       4.1878404      -0.3712681
+111	1        3.9218156       4.5935583       1.3263407
+112	1        3.1310195      -5.8922481       3.6001155
+113	1        4.7558719      -2.2877771      -3.4742052
+114	1       -5.5050300      -2.7027381       0.8748867
+115	1        5.8418594      -4.6064370       3.8714113
+116	1       -4.7516868      -3.1691984      -4.4099768
+117	1        3.9404971       0.7188702      -2.2898786
+118	1       -5.6869740       0.2042380      -0.1916738
+119	1        5.8949589      -1.2422560       3.1201292
+120	1        5.9675804      -0.0712572       5.8964022
+121	1       -5.6208517       3.3600036      -2.9493510
+122	1        5.2065263       3.4517912      -0.3800894
+123	1       -4.6994522       2.5489583       1.8297431
+124	1       -4.0758407       3.0726196       5.0647973
+125	1        4.1587591      -5.0896820      -1.1443498
+126	1       -4.6963753      -5.7429833       1.1357818
+127	1        5.5994192       4.6887008       3.5948264
+128	1        5.0988369      -5.3774409      -4.9051267
--- a/examples/USER/misc/edip/in.edip-Si
+++ b/examples/USER/misc/edip/in.edip-Si
@ -0,0 +1,72 @@
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+atom_modify	sort 0 0.0
+
+# temperature
+
+variable t equal 1800.0
+
+# coordination number cutoff
+
+variable r equal 2.835
+
+# minimization parameters
+
+variable etol equal 1.0e-5
+variable ftol equal 1.0e-5
+variable maxiter equal 100
+variable maxeval equal 100
+variable dmax equal 1.0e-1
+
+# diamond unit cell
+
+variable a equal 5.431
+lattice         custom $a               &
+                a1 1.0 0.0 0.0          &
+                a2 0.0 1.0 0.0          &
+                a3 0.0 0.0 1.0          &
+                basis 0.0 0.0 0.0       &
+                basis 0.0 0.5 0.5       &
+                basis 0.5 0.0 0.5       &
+                basis 0.5 0.5 0.0       &
+                basis 0.25 0.25 0.25    &
+                basis 0.25 0.75 0.75    &
+                basis 0.75 0.25 0.75    &
+                basis 0.75 0.75 0.25
+
+region          myreg block     0 4 &
+                                0 4 &
+                                0 4
+create_box      1 myreg
+create_atoms    1 region myreg
+
+mass            1       28.06
+
+group Si type 1
+
+velocity all create $t 5287287 mom yes rot yes dist gaussian
+
+# make a vacancy
+
+group del id 300
+delete_atoms group del
+
+pair_style      edip
+pair_coeff * * Si.edip Si
+
+thermo          10
+
+fix             1 all nvt temp $t $t 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             500
+
--- a/examples/USER/misc/edip/in.edip-Si-multi
+++ b/examples/USER/misc/edip/in.edip-Si-multi
@ -0,0 +1,72 @@
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+atom_modify	sort 0 0.0
+
+# temperature
+
+variable t equal 1800.0
+
+# coordination number cutoff
+
+variable r equal 2.835
+
+# minimization parameters
+
+variable etol equal 1.0e-5
+variable ftol equal 1.0e-5
+variable maxiter equal 100
+variable maxeval equal 100
+variable dmax equal 1.0e-1
+
+# diamond unit cell
+
+variable a equal 5.431
+lattice         custom $a               &
+                a1 1.0 0.0 0.0          &
+                a2 0.0 1.0 0.0          &
+                a3 0.0 0.0 1.0          &
+                basis 0.0 0.0 0.0       &
+                basis 0.0 0.5 0.5       &
+                basis 0.5 0.0 0.5       &
+                basis 0.5 0.5 0.0       &
+                basis 0.25 0.25 0.25    &
+                basis 0.25 0.75 0.75    &
+                basis 0.75 0.25 0.75    &
+                basis 0.75 0.75 0.25
+
+region          myreg block     0 4 &
+                                0 4 &
+                                0 4
+create_box      1 myreg
+create_atoms    1 region myreg
+
+mass            1       28.06
+
+group Si type 1
+
+velocity all create $t 5287287 mom yes rot yes dist gaussian
+
+# make a vacancy
+
+group del id 300
+delete_atoms group del
+
+pair_style      edip/multi
+pair_coeff * * Si.edip Si
+
+thermo          10
+
+fix             1 all nvt temp $t $t 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             500
+
--- a/examples/USER/misc/edip/in.edip-SiC
+++ b/examples/USER/misc/edip/in.edip-SiC
@ -0,0 +1,33 @@
+# Test of MEAM potential for SiC system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data.SiC
+
+pair_style	edip/multi
+pair_coeff	* * SiC.edip Si C
+
+mass 1 28.085
+mass 2 12.001
+
+neighbor	1.0 bin
+neigh_modify	delay 1
+
+fix		1 all nve
+thermo		10
+timestep	0.001
+
+#dump		1 all atom 50 dump.meam
+
+#dump		2 all image 10 image.*.jpg element element &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3 element Si C
+
+#dump		3 all movie 10 movie.mpg element element &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3 element Si C
+
+run		100
--- a/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1
+++ b/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1
@ -0,0 +1,167 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+atom_modify	sort 0 0.0
+
+# temperature
+
+variable t equal 1800.0
+
+# coordination number cutoff
+
+variable r equal 2.835
+
+# minimization parameters
+
+variable etol equal 1.0e-5
+variable ftol equal 1.0e-5
+variable maxiter equal 100
+variable maxeval equal 100
+variable dmax equal 1.0e-1
+
+# diamond unit cell
+
+variable a equal 5.431
+lattice         custom $a                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+lattice         custom 5.431                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+
+region          myreg block     0 4                                 0 4                                 0 4
+create_box      1 myreg
+Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 region myreg
+Created 512 atoms
+
+mass            1       28.06
+
+group Si type 1
+512 atoms in group Si
+
+velocity all create $t 5287287 mom yes rot yes dist gaussian
+velocity all create 1800 5287287 mom yes rot yes dist gaussian
+
+# make a vacancy
+
+group del id 300
+1 atoms in group del
+delete_atoms group del
+Deleted 1 atoms, new total = 511
+
+pair_style      edip/multi
+pair_coeff * * Si.edip Si
+Reading potential file Si.edip with DATE: 2011-09-15
+
+thermo          10
+
+fix             1 all nvt temp $t $t 0.1
+fix             1 all nvt temp 1800 $t 0.1
+fix             1 all nvt temp 1800 1800 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             500
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.12138
+  ghost atom cutoff = 4.12138
+  binsize = 2.06069, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair edip/multi, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    1802.5039   -2372.6618            0   -2253.8359    12261.807 
+      10    952.62744    -2316.428            0   -2253.6283    723.08194 
+      20    549.13801    -2289.442            0   -2253.2413   -2444.5204 
+      30    1047.0106   -2321.1523            0   -2252.1305     9013.201 
+      40    663.46141   -2294.2083            0   -2250.4711    2942.5348 
+      50    504.74535    -2282.849            0   -2249.5748   -461.44909 
+      60    1019.2173   -2315.5639            0   -2248.3744    7706.4286 
+      70    844.51195   -2302.5251            0   -2246.8526    3116.8302 
+      80    814.90407   -2299.3372            0   -2245.6166    794.77455 
+      90    1269.5636   -2327.4775            0   -2243.7845    7729.3968 
+     100    977.61563   -2306.1118            0   -2241.6647    2969.9939 
+     110    843.08539   -2295.6547            0   -2240.0763    1393.4039 
+     120    1161.6968   -2314.6587            0   -2238.0766    7398.3492 
+     130    918.19451   -2296.4321            0   -2235.9022    2537.3997 
+     140    881.42548   -2292.2768            0   -2234.1709    1550.3339 
+     150    1231.1005   -2313.1054            0   -2231.9479    8112.7566 
+     160    967.01862    -2293.332            0   -2229.5836    3422.9627 
+     170    833.51248   -2282.7489            0   -2227.8015    43.991459 
+     180    1240.8488   -2307.3633            0   -2225.5632    6557.8651 
+     190    1126.4621   -2297.1922            0   -2222.9328    4289.0067 
+     200    947.59571     -2283.29            0    -2220.822     586.2811 
+     210     1228.153   -2299.4702            0   -2218.5071    5315.0425 
+     220    1215.4104   -2295.9408            0   -2215.8176    4870.3417 
+     230     1112.436   -2286.7552            0   -2213.4204    2527.1879 
+     240     1300.081   -2296.6013            0   -2210.8965    5738.3708 
+     250    1192.5738   -2286.8463            0   -2208.2286      4076.49 
+     260    1004.7055   -2272.1753            0   -2205.9424    359.37589 
+     270    1241.2018   -2285.3632            0   -2203.5399    4160.5763 
+     280    1360.1974    -2290.325            0   -2200.6572    5802.3902 
+     290    1151.9365   -2273.9467            0    -2198.008    1418.8887 
+     300    1174.3518   -2273.0089            0   -2195.5925     1998.229 
+     310    1329.2727   -2280.5049            0   -2192.8757    4721.7297 
+     320    1284.4414   -2274.7519            0   -2190.0781    2985.4674 
+     330    1328.3761   -2274.9545            0   -2187.3844    4543.2109 
+     340    1446.3847   -2279.8693            0   -2184.5198    6254.4059 
+     350    1366.2165   -2271.7475            0   -2181.6828    3637.8335 
+     360    1358.9609   -2268.5982            0   -2179.0118    3049.5798 
+     370     1552.208   -2278.4802            0   -2176.1545    6334.0058 
+     380    1562.5295   -2276.1793            0   -2173.1732    5787.5547 
+     390    1415.5498   -2263.7824            0   -2170.4655    3438.5766 
+     400    1323.1568   -2255.1641            0    -2167.938    2427.2294 
+     410    1260.7186   -2248.5373            0   -2165.4273    1208.6299 
+     420    1282.1118   -2247.3718            0   -2162.8516    462.65374 
+     430     1451.944   -2255.7551            0   -2160.0391    2037.8025 
+     440    1568.9415    -2260.417            0   -2156.9882    3531.1602 
+     450    1565.8262   -2257.2396            0   -2154.0162    2586.7886 
+     460    1677.7143   -2261.7214            0    -2151.122    4112.9756 
+     470    1762.9071   -2264.4244            0   -2148.2089    5053.2139 
+     480    1704.5898   -2257.8678            0   -2145.4967    4077.4626 
+     490    1731.2619   -2257.1048            0   -2142.9753    4710.5263 
+     500    1723.9777    -2254.161            0   -2140.5118    4760.7295 
+Loop time of 0.679564 on 1 procs for 500 steps with 511 atoms
+
+Performance: 63.570 ns/day, 0.378 hours/ns, 735.765 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.65181    | 0.65181    | 0.65181    |   0.0 | 95.92
+Neigh   | 0.013857   | 0.013857   | 0.013857   |   0.0 |  2.04
+Comm    | 0.0033884  | 0.0033884  | 0.0033884  |   0.0 |  0.50
+Output  | 0.00070739 | 0.00070739 | 0.00070739 |   0.0 |  0.10
+Modify  | 0.0083694  | 0.0083694  | 0.0083694  |   0.0 |  1.23
+Other   |            | 0.001432   |            |       |  0.21
+
+Nlocal:    511 ave 511 max 511 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    845 ave 845 max 845 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  7902 ave 7902 max 7902 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7902
+Ave neighs/atom = 15.4638
+Neighbor list builds = 19
+Dangerous builds = 0
+
+Total wall time: 0:00:00
--- a/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4
+++ b/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4
@ -0,0 +1,167 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+atom_modify	sort 0 0.0
+
+# temperature
+
+variable t equal 1800.0
+
+# coordination number cutoff
+
+variable r equal 2.835
+
+# minimization parameters
+
+variable etol equal 1.0e-5
+variable ftol equal 1.0e-5
+variable maxiter equal 100
+variable maxeval equal 100
+variable dmax equal 1.0e-1
+
+# diamond unit cell
+
+variable a equal 5.431
+lattice         custom $a                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+lattice         custom 5.431                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+
+region          myreg block     0 4                                 0 4                                 0 4
+create_box      1 myreg
+Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 region myreg
+Created 512 atoms
+
+mass            1       28.06
+
+group Si type 1
+512 atoms in group Si
+
+velocity all create $t 5287287 mom yes rot yes dist gaussian
+velocity all create 1800 5287287 mom yes rot yes dist gaussian
+
+# make a vacancy
+
+group del id 300
+1 atoms in group del
+delete_atoms group del
+Deleted 1 atoms, new total = 511
+
+pair_style      edip/multi
+pair_coeff * * Si.edip Si
+Reading potential file Si.edip with DATE: 2011-09-15
+
+thermo          10
+
+fix             1 all nvt temp $t $t 0.1
+fix             1 all nvt temp 1800 $t 0.1
+fix             1 all nvt temp 1800 1800 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             500
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.12138
+  ghost atom cutoff = 4.12138
+  binsize = 2.06069, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair edip/multi, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    1802.3816   -2372.6618            0    -2253.844    12260.967 
+      10    938.75954   -2315.5185            0   -2253.6329    558.21646 
+      20    534.27233   -2288.4721            0   -2253.2514    -2710.768 
+      30    1043.7796   -2320.9485            0   -2252.1398    8679.4381 
+      40     658.0916   -2293.8597            0   -2250.4765    2165.3742 
+      50    517.93009   -2283.7238            0   -2249.5805   -1124.9373 
+      60    1063.3594   -2318.4409            0   -2248.3414    7277.8526 
+      70    868.14006   -2304.0134            0   -2246.7832    2050.2848 
+      80    826.37805   -2300.0187            0   -2245.5416    91.099408 
+      90    1289.6772   -2328.7151            0   -2243.6961    8180.7423 
+     100    976.36208   -2305.9371            0   -2241.5727    3614.0499 
+     110    810.81713   -2293.4705            0   -2240.0193     1359.368 
+     120     1165.707   -2314.9026            0    -2238.056      7336.45 
+     130    929.81245    -2297.139            0   -2235.8432    2793.8451 
+     140    804.47874   -2287.2074            0    -2234.174    704.92455 
+     150    1182.4141   -2310.0266            0   -2232.0787    7822.2337 
+     160    979.92391   -2294.2969            0   -2229.6977    3206.7458 
+     170    830.14748   -2282.6079            0   -2227.8824   -296.87377 
+     180    1271.1133   -2309.4274            0   -2225.6322     7199.614 
+     190    1209.6006   -2302.6407            0   -2222.9006    5528.3784 
+     200    954.67693   -2283.6621            0   -2220.7273     47.02795 
+     210     1260.814   -2301.5582            0    -2218.442     4829.788 
+     220    1274.9954   -2299.7285            0   -2215.6774    5518.0597 
+     230    1048.0074    -2282.398            0   -2213.3106    1754.4144 
+     240    1261.7072   -2294.1108            0   -2210.9356    5233.2712 
+     250    1272.6178   -2292.0793            0   -2208.1849    4795.9325 
+     260    989.14205   -2271.0278            0   -2205.8209    -820.1828 
+     270    1212.0445   -2283.4212            0     -2203.52    3395.8634 
+     280    1391.9572   -2292.3809            0   -2200.6194    6666.2451 
+     290    1093.1204   -2270.0421            0   -2197.9807    206.94523 
+     300    1159.4831    -2272.102            0   -2195.6657    778.53806 
+     310    1407.3528   -2285.6228            0   -2192.8463     5223.048 
+     320    1236.7163   -2271.5389            0   -2190.0113    1865.3943 
+     330    1258.8275   -2270.4611            0   -2187.4758    2333.3209 
+     340    1507.9519   -2283.9906            0   -2184.5824    6775.5456 
+     350    1366.5116   -2271.7287            0   -2181.6446     3432.115 
+     360    1305.2829   -2265.1092            0   -2179.0614    1498.4073 
+     370    1581.4335   -2280.4645            0   -2176.2122    6518.5597 
+     380    1589.5319   -2277.9428            0   -2173.1567    6334.6506 
+     390    1402.6781   -2262.9323            0    -2170.464    3278.3038 
+     400    1374.9587   -2258.5717            0   -2167.9307    3608.7284 
+     410    1295.7416   -2250.7752            0   -2165.3565    1877.5222 
+     420    1278.6727   -2247.1099            0   -2162.8164    1599.4181 
+     430    1508.1328   -2259.4245            0   -2160.0044    4300.2224 
+     440    1624.2957   -2263.9806            0   -2156.9026     4432.625 
+     450    1597.3356    -2259.263            0   -2153.9624    3370.3816 
+     460    1772.0922   -2267.9106            0   -2151.0895    5788.3214 
+     470    1806.4047    -2267.304            0    -2148.221    5950.1166 
+     480    1593.0406   -2250.7469            0   -2145.7294    2518.0576 
+     490    1660.9767    -2252.894            0    -2143.398    4282.1643 
+     500     1714.283   -2253.9295            0   -2140.9194    5740.0247 
+Loop time of 0.205398 on 4 procs for 500 steps with 511 atoms
+
+Performance: 210.324 ns/day, 0.114 hours/ns, 2434.304 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.16285    | 0.1688     | 0.17446    |   1.1 | 82.18
+Neigh   | 0.0035172  | 0.0036234  | 0.0038214  |   0.2 |  1.76
+Comm    | 0.018727   | 0.024851   | 0.030996   |   2.9 | 12.10
+Output  | 0.0013061  | 0.0014012  | 0.0015635  |   0.3 |  0.68
+Modify  | 0.0046582  | 0.0048603  | 0.0050988  |   0.2 |  2.37
+Other   |            | 0.001861   |            |       |  0.91
+
+Nlocal:    127.75 ave 131 max 124 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost:    433.75 ave 441 max 426 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1979.5 ave 2040 max 1895 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 7918
+Ave neighs/atom = 15.4951
+Neighbor list builds = 19
+Dangerous builds = 0
+
+Total wall time: 0:00:00
--- a/examples/USER/misc/edip/log.4May2017.g++.edip-Si.1
+++ b/examples/USER/misc/edip/log.4May2017.g++.edip-Si.1
@ -0,0 +1,167 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+atom_modify	sort 0 0.0
+
+# temperature
+
+variable t equal 1800.0
+
+# coordination number cutoff
+
+variable r equal 2.835
+
+# minimization parameters
+
+variable etol equal 1.0e-5
+variable ftol equal 1.0e-5
+variable maxiter equal 100
+variable maxeval equal 100
+variable dmax equal 1.0e-1
+
+# diamond unit cell
+
+variable a equal 5.431
+lattice         custom $a                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+lattice         custom 5.431                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+
+region          myreg block     0 4                                 0 4                                 0 4
+create_box      1 myreg
+Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 region myreg
+Created 512 atoms
+
+mass            1       28.06
+
+group Si type 1
+512 atoms in group Si
+
+velocity all create $t 5287287 mom yes rot yes dist gaussian
+velocity all create 1800 5287287 mom yes rot yes dist gaussian
+
+# make a vacancy
+
+group del id 300
+1 atoms in group del
+delete_atoms group del
+Deleted 1 atoms, new total = 511
+
+pair_style      edip
+pair_coeff * * Si.edip Si
+Reading potential file Si.edip with DATE: 2011-09-15
+
+thermo          10
+
+fix             1 all nvt temp $t $t 0.1
+fix             1 all nvt temp 1800 $t 0.1
+fix             1 all nvt temp 1800 1800 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             500
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.12138
+  ghost atom cutoff = 4.12138
+  binsize = 2.06069, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair edip, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    1802.5039   -2372.6618            0   -2253.8359    12261.807 
+      10    952.62744    -2316.428            0   -2253.6283    723.08283 
+      20      549.138    -2289.442            0   -2253.2413   -2444.5194 
+      30    1047.0106   -2321.1522            0   -2252.1305    9013.2015 
+      40    663.46143   -2294.2083            0   -2250.4711    2942.5358 
+      50    504.74533    -2282.849            0   -2249.5748   -461.44817 
+      60    1019.2173   -2315.5639            0   -2248.3744     7706.429 
+      70    844.51197   -2302.5251            0   -2246.8526    3116.8313 
+      80    814.90406   -2299.3372            0   -2245.6165    794.77536 
+      90    1269.5635   -2327.4775            0   -2243.7845    7729.3971 
+     100    977.61566   -2306.1118            0   -2241.6647    2969.9952 
+     110    843.08538   -2295.6547            0   -2240.0763    1393.4046 
+     120    1161.6968   -2314.6587            0   -2238.0766    7398.3495 
+     130    918.19453   -2296.4321            0   -2235.9022    2537.4011 
+     140    881.42546   -2292.2768            0   -2234.1709    1550.3345 
+     150    1231.1005   -2313.1054            0   -2231.9479    8112.7568 
+     160    967.01865    -2293.332            0   -2229.5836     3422.964 
+     170    833.51246   -2282.7489            0   -2227.8015     43.99251 
+     180    1240.8487   -2307.3633            0   -2225.5632    6557.8652 
+     190    1126.4621   -2297.1922            0   -2222.9328    4289.0083 
+     200     947.5957     -2283.29            0   -2220.8219    586.28203 
+     210     1228.153   -2299.4702            0   -2218.5071    5315.0427 
+     220    1215.4104   -2295.9407            0   -2215.8176     4870.343 
+     230     1112.436   -2286.7552            0   -2213.4204    2527.1887 
+     240     1300.081   -2296.6013            0   -2210.8965    5738.3711 
+     250    1192.5739   -2286.8463            0   -2208.2286    4076.4913 
+     260    1004.7055   -2272.1753            0   -2205.9424     359.3769 
+     270    1241.2018   -2285.3632            0   -2203.5399    4160.5764 
+     280    1360.1974    -2290.325            0   -2200.6572    5802.3912 
+     290    1151.9366   -2273.9467            0    -2198.008    1418.8905 
+     300    1174.3518   -2273.0089            0   -2195.5925    1998.2297 
+     310    1329.2726   -2280.5049            0   -2192.8757    4721.7304 
+     320    1284.4414   -2274.7519            0   -2190.0781    2985.4687 
+     330    1328.3761   -2274.9545            0   -2187.3844    4543.2115 
+     340    1446.3847   -2279.8693            0   -2184.5198    6254.4071 
+     350    1366.2165   -2271.7475            0   -2181.6828    3637.8351 
+     360    1358.9609   -2268.5982            0   -2179.0118    3049.5811 
+     370    1552.2079   -2278.4802            0   -2176.1545    6334.0061 
+     380    1562.5295   -2276.1793            0   -2173.1731    5787.5565 
+     390    1415.5498   -2263.7823            0   -2170.4655    3438.5782 
+     400    1323.1568   -2255.1641            0    -2167.938    2427.2311 
+     410    1260.7186   -2248.5373            0   -2165.4273    1208.6316 
+     420    1282.1118   -2247.3718            0   -2162.8516    462.65508 
+     430    1451.9439   -2255.7551            0   -2160.0391    2037.8027 
+     440    1568.9415    -2260.417            0   -2156.9882    3531.1613 
+     450    1565.8261   -2257.2396            0   -2154.0161    2586.7896 
+     460    1677.7143   -2261.7214            0    -2151.122     4112.976 
+     470    1762.9071   -2264.4244            0   -2148.2089    5053.2148 
+     480    1704.5898   -2257.8678            0   -2145.4966    4077.4649 
+     490    1731.2619   -2257.1048            0   -2142.9753    4710.5276 
+     500    1723.9777    -2254.161            0   -2140.5118    4760.7316 
+Loop time of 0.312472 on 1 procs for 500 steps with 511 atoms
+
+Performance: 138.252 ns/day, 0.174 hours/ns, 1600.143 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.28525    | 0.28525    | 0.28525    |   0.0 | 91.29
+Neigh   | 0.013753   | 0.013753   | 0.013753   |   0.0 |  4.40
+Comm    | 0.0033333  | 0.0033333  | 0.0033333  |   0.0 |  1.07
+Output  | 0.00071096 | 0.00071096 | 0.00071096 |   0.0 |  0.23
+Modify  | 0.008044   | 0.008044   | 0.008044   |   0.0 |  2.57
+Other   |            | 0.001385   |            |       |  0.44
+
+Nlocal:    511 ave 511 max 511 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    845 ave 845 max 845 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  7902 ave 7902 max 7902 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7902
+Ave neighs/atom = 15.4638
+Neighbor list builds = 19
+Dangerous builds = 0
+
+Total wall time: 0:00:00
--- a/examples/USER/misc/edip/log.4May2017.g++.edip-Si.4
+++ b/examples/USER/misc/edip/log.4May2017.g++.edip-Si.4
@ -0,0 +1,167 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+
+units           metal
+
+atom_style      atomic
+atom_modify     map array
+boundary        p p p
+atom_modify	sort 0 0.0
+
+# temperature
+
+variable t equal 1800.0
+
+# coordination number cutoff
+
+variable r equal 2.835
+
+# minimization parameters
+
+variable etol equal 1.0e-5
+variable ftol equal 1.0e-5
+variable maxiter equal 100
+variable maxeval equal 100
+variable dmax equal 1.0e-1
+
+# diamond unit cell
+
+variable a equal 5.431
+lattice         custom $a                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+lattice         custom 5.431                               a1 1.0 0.0 0.0                          a2 0.0 1.0 0.0                          a3 0.0 0.0 1.0                          basis 0.0 0.0 0.0                       basis 0.0 0.5 0.5                       basis 0.5 0.0 0.5                       basis 0.5 0.5 0.0                       basis 0.25 0.25 0.25                    basis 0.25 0.75 0.75                    basis 0.75 0.25 0.75                    basis 0.75 0.75 0.25
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+
+region          myreg block     0 4                                 0 4                                 0 4
+create_box      1 myreg
+Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 region myreg
+Created 512 atoms
+
+mass            1       28.06
+
+group Si type 1
+512 atoms in group Si
+
+velocity all create $t 5287287 mom yes rot yes dist gaussian
+velocity all create 1800 5287287 mom yes rot yes dist gaussian
+
+# make a vacancy
+
+group del id 300
+1 atoms in group del
+delete_atoms group del
+Deleted 1 atoms, new total = 511
+
+pair_style      edip
+pair_coeff * * Si.edip Si
+Reading potential file Si.edip with DATE: 2011-09-15
+
+thermo          10
+
+fix             1 all nvt temp $t $t 0.1
+fix             1 all nvt temp 1800 $t 0.1
+fix             1 all nvt temp 1800 1800 0.1
+
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+
+# equilibrate
+
+run             500
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.12138
+  ghost atom cutoff = 4.12138
+  binsize = 2.06069, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair edip, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    1802.3816   -2372.6618            0   -2253.8439    12260.967 
+      10    938.75954   -2315.5185            0   -2253.6329    558.21736 
+      20    534.27232   -2288.4721            0   -2253.2514    -2710.767 
+      30    1043.7796   -2320.9485            0   -2252.1398    8679.4385 
+      40    658.09162   -2293.8597            0   -2250.4765    2165.3752 
+      50    517.93008   -2283.7238            0   -2249.5805   -1124.9362 
+      60    1063.3594   -2318.4409            0   -2248.3414     7277.853 
+      70    868.14007   -2304.0133            0   -2246.7832    2050.2859 
+      80    826.37803   -2300.0187            0   -2245.5416    91.100098 
+      90    1289.6772   -2328.7151            0   -2243.6961    8180.7427 
+     100    976.36211   -2305.9371            0   -2241.5727    3614.0511 
+     110    810.81711   -2293.4705            0   -2240.0193    1359.3687 
+     120     1165.707   -2314.9026            0    -2238.056    7336.4505 
+     130    929.81248    -2297.139            0   -2235.8432    2793.8463 
+     140    804.47872   -2287.2074            0    -2234.174    704.92524 
+     150     1182.414   -2310.0266            0   -2232.0787    7822.2339 
+     160    979.92395   -2294.2969            0   -2229.6977    3206.7474 
+     170    830.14746   -2282.6079            0   -2227.8824   -296.87288 
+     180    1271.1133   -2309.4274            0   -2225.6322     7199.614 
+     190    1209.6006   -2302.6407            0   -2222.9006    5528.3799 
+     200    954.67692   -2283.6621            0   -2220.7272     47.02925 
+     210     1260.814   -2301.5582            0    -2218.442    4829.7879 
+     220    1274.9954   -2299.7285            0   -2215.6774    5518.0611 
+     230    1048.0074    -2282.398            0   -2213.3106    1754.4157 
+     240    1261.7071   -2294.1107            0   -2210.9356    5233.2714 
+     250    1272.6179   -2292.0793            0   -2208.1849     4795.934 
+     260    989.14207   -2271.0278            0   -2205.8209   -820.18098 
+     270    1212.0444   -2283.4212            0     -2203.52    3395.8631 
+     280    1391.9572   -2292.3809            0   -2200.6194    6666.2464 
+     290    1093.1205   -2270.0421            0   -2197.9807    206.94752 
+     300     1159.483    -2272.102            0   -2195.6657    778.53823 
+     310    1407.3528   -2285.6227            0   -2192.8463    5223.0487 
+     320    1236.7164   -2271.5389            0   -2190.0112    1865.3963 
+     330    1258.8275   -2270.4611            0   -2187.4758     2333.321 
+     340    1507.9519   -2283.9906            0   -2184.5824     6775.546 
+     350    1366.5116   -2271.7287            0   -2181.6446    3432.1175 
+     360    1305.2828   -2265.1091            0   -2179.0614    1498.4079 
+     370    1581.4334   -2280.4645            0   -2176.2122    6518.5598 
+     380    1589.5319   -2277.9428            0   -2173.1566    6334.6527 
+     390    1402.6782   -2262.9323            0    -2170.464    3278.3048 
+     400    1374.9587   -2258.5717            0   -2167.9307    3608.7293 
+     410    1295.7416   -2250.7752            0   -2165.3565    1877.5245 
+     420    1278.6727   -2247.1099            0   -2162.8164    1599.4189 
+     430    1508.1328   -2259.4245            0   -2160.0044    4300.2235 
+     440    1624.2957   -2263.9806            0   -2156.9026    4432.6267 
+     450    1597.3356    -2259.263            0   -2153.9623    3370.3829 
+     460    1772.0921   -2267.9105            0   -2151.0895    5788.3219 
+     470    1806.4047    -2267.304            0    -2148.221    5950.1188 
+     480    1593.0406   -2250.7469            0   -2145.7294    2518.0601 
+     490    1660.9766    -2252.894            0    -2143.398    4282.1654 
+     500    1714.2831   -2253.9295            0   -2140.9194    5740.0268 
+Loop time of 0.109584 on 4 procs for 500 steps with 511 atoms
+
+Performance: 394.220 ns/day, 0.061 hours/ns, 4562.726 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.074678   | 0.077817   | 0.084705   |   1.4 | 71.01
+Neigh   | 0.0036662  | 0.0037943  | 0.0039661  |   0.2 |  3.46
+Comm    | 0.013665   | 0.020312   | 0.023178   |   2.7 | 18.54
+Output  | 0.0010247  | 0.0010931  | 0.0012922  |   0.3 |  1.00
+Modify  | 0.0043213  | 0.0047521  | 0.0051889  |   0.6 |  4.34
+Other   |            | 0.001814   |            |       |  1.66
+
+Nlocal:    127.75 ave 131 max 124 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost:    433.75 ave 441 max 426 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1979.5 ave 2040 max 1895 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+
+Total # of neighbors = 7918
+Ave neighs/atom = 15.4951
+Neighbor list builds = 19
+Dangerous builds = 0
+
+Total wall time: 0:00:00
--- a/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1
+++ b/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1
@ -0,0 +1,92 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Test of MEAM potential for SiC system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data.SiC
+  orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  128 atoms
+
+pair_style	edip/multi
+pair_coeff	* * SiC.edip Si C
+Reading potential file SiC.edip with DATE: 2017-05-16
+
+mass 1 28.085
+mass 2 12.001
+
+neighbor	1.0 bin
+neigh_modify	delay 1
+
+fix		1 all nve
+thermo		10
+timestep	0.001
+
+#dump		1 all atom 50 dump.meam
+
+#dump		2 all image 10 image.*.jpg element element #		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3 element Si C
+
+#dump		3 all movie 10 movie.mpg element element #		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3 element Si C
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.94159
+  ghost atom cutoff = 3.94159
+  binsize = 1.97079, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair edip/multi, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.692 | 2.692 | 2.692 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -563.61621            0   -563.61621   -726147.34 
+      10    4224.3601   -633.24829            0   -563.90103   -312355.55 
+      20    4528.5661   -638.15183            0   -563.81071   -20091.291 
+      30    4817.3654   -642.92111            0   -563.83905     106625.5 
+      40    4619.4324    -639.6884            0   -563.85562    107180.42 
+      50    4783.0025   -642.26961            0   -563.75166    75134.335 
+      60     4525.145   -638.06177            0   -563.77681    71591.713 
+      70    4685.2578   -640.72377            0    -563.8104    63956.042 
+      80    4621.8393   -639.75912            0   -563.88682    18177.383 
+      90    4834.7702   -643.34582            0   -563.97805    15282.823 
+     100    4424.0589   -636.60208            0   -563.97656    47963.501 
+Loop time of 0.0552888 on 1 procs for 100 steps with 128 atoms
+
+Performance: 156.270 ns/day, 0.154 hours/ns, 1808.685 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.051872   | 0.051872   | 0.051872   |   0.0 | 93.82
+Neigh   | 0.0023525  | 0.0023525  | 0.0023525  |   0.0 |  4.25
+Comm    | 0.0004518  | 0.0004518  | 0.0004518  |   0.0 |  0.82
+Output  | 0.00014806 | 0.00014806 | 0.00014806 |   0.0 |  0.27
+Modify  | 0.00024796 | 0.00024796 | 0.00024796 |   0.0 |  0.45
+Other   |            | 0.0002165  |            |       |  0.39
+
+Nlocal:    128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    473 ave 473 max 473 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  2376 ave 2376 max 2376 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2376
+Ave neighs/atom = 18.5625
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:00
--- a/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4
+++ b/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4
@ -0,0 +1,92 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Test of MEAM potential for SiC system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data.SiC
+  orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  128 atoms
+
+pair_style	edip/multi
+pair_coeff	* * SiC.edip Si C
+Reading potential file SiC.edip with DATE: 2017-05-16
+
+mass 1 28.085
+mass 2 12.001
+
+neighbor	1.0 bin
+neigh_modify	delay 1
+
+fix		1 all nve
+thermo		10
+timestep	0.001
+
+#dump		1 all atom 50 dump.meam
+
+#dump		2 all image 10 image.*.jpg element element #		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3 element Si C
+
+#dump		3 all movie 10 movie.mpg element element #		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3 element Si C
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 1 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.94159
+  ghost atom cutoff = 3.94159
+  binsize = 1.97079, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair edip/multi, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.686 | 2.686 | 2.686 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -563.61621            0   -563.61621   -726147.34 
+      10    4224.3601   -633.24829            0   -563.90103   -312355.55 
+      20    4528.5661   -638.15183            0   -563.81071   -20091.291 
+      30    4817.3654   -642.92111            0   -563.83905     106625.5 
+      40    4619.4324    -639.6884            0   -563.85562    107180.42 
+      50    4783.0025   -642.26961            0   -563.75166    75134.335 
+      60     4525.145   -638.06177            0   -563.77681    71591.713 
+      70    4685.2578   -640.72377            0    -563.8104    63956.042 
+      80    4621.8393   -639.75912            0   -563.88682    18177.383 
+      90    4834.7702   -643.34582            0   -563.97805    15282.823 
+     100    4424.0589   -636.60208            0   -563.97656    47963.501 
+Loop time of 0.020755 on 4 procs for 100 steps with 128 atoms
+
+Performance: 416.285 ns/day, 0.058 hours/ns, 4818.118 timesteps/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.011816   | 0.013825   | 0.016871   |   1.6 | 66.61
+Neigh   | 0.00061321 | 0.00066817 | 0.00074816 |   0.0 |  3.22
+Comm    | 0.0023363  | 0.0054012  | 0.0075014  |   2.7 | 26.02
+Output  | 0.00020909 | 0.00022268 | 0.00025558 |   0.0 |  1.07
+Modify  | 8.3208e-05 | 9.346e-05  | 0.00010395 |   0.0 |  0.45
+Other   |            | 0.0005446  |            |       |  2.62
+
+Nlocal:    32 ave 36 max 25 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Nghost:    262.75 ave 273 max 255 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  594 ave 687 max 453 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 2376
+Ave neighs/atom = 18.5625
+Neighbor list builds = 11
+Dangerous builds = 0
+Total wall time: 0:00:00
--- a/examples/USER/misc/filter_corotate/data.bpti
+++ b/examples/USER/misc/filter_corotate/data.bpti
--- a/examples/USER/misc/filter_corotate/data.peptide
+++ b/examples/USER/misc/filter_corotate/data.peptide
--- a/examples/USER/misc/filter_corotate/in.bpti
+++ b/examples/USER/misc/filter_corotate/in.bpti
--- a/examples/USER/misc/filter_corotate/in.peptide
+++ b/examples/USER/misc/filter_corotate/in.peptide
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1
+++ b/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4
+++ b/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1
+++ b/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4
+++ b/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4
--- a/examples/USER/misc/gauss_diel/data.gauss-diel
+++ b/examples/USER/misc/gauss_diel/data.gauss-diel
--- a/examples/USER/misc/gauss_diel/in.gauss-diel
+++ b/examples/USER/misc/gauss_diel/in.gauss-diel
--- a/examples/USER/misc/gauss_diel/in.gauss-diel-cg
+++ b/examples/USER/misc/gauss_diel/in.gauss-diel-cg
--- a/examples/USER/misc/gauss_diel/in.gauss-diel-split
+++ b/examples/USER/misc/gauss_diel/in.gauss-diel-split
--- a/examples/USER/misc/gauss_diel/log.gauss-diel
+++ b/examples/USER/misc/gauss_diel/log.gauss-diel
--- a/examples/USER/misc/gauss_diel/log.gauss-diel-cg
+++ b/examples/USER/misc/gauss_diel/log.gauss-diel-cg
--- a/examples/USER/misc/gauss_diel/log.gauss-diel-split
+++ b/examples/USER/misc/gauss_diel/log.gauss-diel-split
--- a/examples/USER/misc/i-pi/C.opt.tersoff
+++ b/examples/USER/misc/i-pi/C.opt.tersoff
--- a/examples/USER/misc/i-pi/README
+++ b/examples/USER/misc/i-pi/README
--- a/examples/USER/misc/i-pi/data.graphene
+++ b/examples/USER/misc/i-pi/data.graphene
--- a/examples/USER/misc/i-pi/i-pi_input.xml
+++ b/examples/USER/misc/i-pi/i-pi_input.xml
--- a/examples/USER/misc/i-pi/i-pi_positions.xyz
+++ b/examples/USER/misc/i-pi/i-pi_positions.xyz
--- a/examples/USER/misc/i-pi/in.graphene
+++ b/examples/USER/misc/i-pi/in.graphene
--- a/examples/USER/misc/kolmogorov_crespi/data.bilayer-graphene
+++ b/examples/USER/misc/kolmogorov_crespi/data.bilayer-graphene
--- a/examples/USER/misc/kolmogorov_crespi/data.graphene-adsorbant
+++ b/examples/USER/misc/kolmogorov_crespi/data.graphene-adsorbant
--- a/examples/USER/misc/kolmogorov_crespi/in.atom-diffusion
+++ b/examples/USER/misc/kolmogorov_crespi/in.atom-diffusion
--- a/examples/USER/misc/kolmogorov_crespi/in.bilayer-graphene
+++ b/examples/USER/misc/kolmogorov_crespi/in.bilayer-graphene
--- a/examples/USER/misc/kolmogorov_crespi/log.atom-diffusion
+++ b/examples/USER/misc/kolmogorov_crespi/log.atom-diffusion
--- a/examples/USER/misc/kolmogorov_crespi/log.bilayer-graphene
+++ b/examples/USER/misc/kolmogorov_crespi/log.bilayer-graphene
--- a/examples/USER/misc/meam_spline/Si_1.meam.spline
+++ b/examples/USER/misc/meam_spline/Si_1.meam.spline
@ -0,0 +1,63 @@
+DATE: 2012-02-01 CONTRIBUTOR: Alexander Stukowski, stukowski@mm.tu-darmstadt.de CITATION: Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter and Kress, Modell Simul Mater Sci Eng, 8, 825 (2000) COMMENT: Spline-based MEAM potential for Si. Reference: T. J. Lenosky, B. Sadigh, E. Alonso, V. V. Bulatov, T. D. de la Rubia, J. Kim, A. F. Voter, and J. D. Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000)
+10
+-4.266966781858503300e+01 0.000000000000000000e+00
+1 0 1 0
+1.500000000000000000e+00 6.929943430771341000e+00 1.653321602557917600e+02
+1.833333333333333300e+00 -4.399503747408950400e-01 3.941543472528634600e+01
+2.166666666666666500e+00 -1.701233725061446700e+00 6.871065423413908100e+00
+2.500000000000000000e+00 -1.624732919215791800e+00 5.340648014033163800e+00
+2.833333333333333000e+00 -9.969641728342462100e-01 1.534811309391571000e+00
+3.166666666666667000e+00 -2.739141845072665100e-01 -6.334706186546093900e+00
+3.500000000000000000e+00 -2.499156963774082700e-02 -1.798864729909626500e+00
+3.833333333333333500e+00 -1.784331481529976400e-02 4.743496636420091500e-01
+4.166666666666666100e+00 -9.612303290166881000e-03 -4.006506271304824400e-02
+4.500000000000000000e+00 0.000000000000000000e+00 -2.394996574779807200e-01
+11
+-1.000000000000000000e+00 0.000000000000000000e+00
+1 0 0 0
+1.500000000000000000e+00 1.374674212682983900e-01 -3.227795813279568500e+00
+1.700000000000000000e+00 -1.483141815327918000e-01 -6.411648793604404900e+00
+1.899999999999999900e+00 -5.597204896096039700e-01 1.003068519633888300e+01
+2.100000000000000100e+00 -7.310964379372824100e-01 2.293461970618954700e+00
+2.299999999999999800e+00 -7.628287071954063000e-01 1.742018781618444500e+00
+2.500000000000000000e+00 -7.291769685066557000e-01 5.460640949384478700e-01
+2.700000000000000200e+00 -6.662022220044453400e-01 4.721760106467195500e-01
+2.899999999999999900e+00 -5.732830582550895200e-01 2.056894449546524200e+00
+3.100000000000000100e+00 -4.069014309729406300e-01 2.319615721086100800e+00
+3.299999999999999800e+00 -1.666155295956388300e-01 -2.497162196179187900e-01
+3.500000000000000000e+00 0.000000000000000000e+00 -1.237130660986393100e+01
+8
+7.351364478015182100e-01 6.165217237728655200e-01
+1 1 1 1
+-1.770934559908718700e+00 -1.074925682941420000e+00 -1.482768170233858500e-01
+-3.881557649503457600e-01 -2.004503493658201000e-01 -1.492100354067345500e-01
+9.946230300080272100e-01 4.142241371345077300e-01 -7.012475119623896900e-02
+2.377401824966400000e+00 8.793892953828742500e-01 -3.944355024164965900e-02
+3.760180619924772900e+00 1.266888024536562100e+00 -1.581431192239436000e-02
+5.142959414883146800e+00 1.629979548834614900e+00 2.611224310900800400e-02
+6.525738209841518900e+00 1.977379549636293600e+00 -1.378738550324104500e-01
+7.908517004799891800e+00 2.396177220616657200e+00 7.494253977092666400e-01
+10
+-3.618936018538757300e+00 0.000000000000000000e+00
+1 0 1 0
+1.500000000000000000e+00 1.250311510312851300e+00 2.790400588857243500e+01
+1.722222222222222300e+00 8.682060369372680600e-01 -4.522554291731776900e+00
+1.944444444444444400e+00 6.084604017544847900e-01 5.052931618779816800e+00
+2.166666666666666500e+00 4.875624808097850400e-01 1.180825096539679600e+00
+2.388888888888888800e+00 4.416345603457190700e-01 -6.673769465415171400e-01
+2.611111111111111200e+00 3.760976313325982700e-01 -8.938118490837722000e-01
+2.833333333333333000e+00 2.714524157414608400e-01 -5.090324763524399800e-01
+3.055555555555555400e+00 1.481440300150710900e-01 6.623665830603995300e-01
+3.277777777777777700e+00 4.854596610856590900e-02 7.403702452268122700e-01
+3.500000000000000000e+00 0.000000000000000000e+00 2.578982318481970500e+00
+8
+-1.395041572145673000e+01 1.134616739799360700e+00
+1 1 1 1
+-1.000000000000000900e+00 5.254163992149617700e+00 1.582685381253900500e+01
+-7.428367052748285900e-01 2.359149452448745100e+00 3.117611233789983400e+01
+-4.856734105496561800e-01 1.195946960915646100e+00 1.658962813584905800e+01
+-2.285101158244838800e-01 1.229952028074150000e+00 1.108360928564026400e+01
+2.865317890068852500e-02 2.035650777568434500e+00 9.088861456447702400e+00
+2.858164736258610400e-01 3.424741418405580000e+00 5.489943377538379500e+00
+5.429797683510331200e-01 4.948585892304984100e+00 -1.882291580187675700e+01
+8.001430630762056400e-01 5.617988713941801200e+00 -7.718625571850646200e+00
--- a/examples/USER/misc/meam_spline/TiO.meam.spline
+++ b/examples/USER/misc/meam_spline/TiO.meam.spline
@ -0,0 +1,130 @@
+# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle
+meam/spline 2 Ti O
+spline3eq
+13
+-20 0
+1.742692837 3.744277175966 99.4865081627958
+2.05580176725 0.910839730906 10.8702523265355
+2.3689106975 0.388045896634 -1.55322418749562
+2.68201962775 -0.018840906533 2.43630041329215
+2.995128558 -0.248098929639 2.67912713976835
+3.30823748825 -0.264489550297 -0.125056384603077
+3.6213464185 -0.227196189283 1.10662555360438
+3.93445534875 -0.129293090176 -0.592053676745914
+4.247564279 -0.059685366933 -0.470123414607672
+4.56067320925 -0.031100025561 -0.0380739973059663
+4.8737821395 -0.013847363202 -0.0711547960695406
+5.18689106975 -0.003203412728 -0.081768292420175
+5.5 0 -0.0571422964883619
+spline3eq
+5
+0.155001355787331 0
+1.9 0.533321679606674 0
+2.8 0.456402081843862 -1.60311717015859
+3.7 -0.324281383502201 1.19940299483249
+4.6 -0.474029826906675 1.47909794595154
+5.5 0 -2.49521499855605
+spline3eq
+13
+0 0
+1.742692837 0 0
+2.05580176725 0 0
+2.3689106975 0 0
+2.68201962775 0 0
+2.995128558 0 0
+3.30823748825 0 0
+3.6213464185 0 0
+3.93445534875 0 0
+4.247564279 0 0
+4.56067320925 0 0
+4.8737821395 0 0
+5.18689106975 0 0
+5.5 0 0
+spline3eq
+11
+-1 0
+2.055801767 1.7475279661 -525.869786904802
+2.2912215903 -5.8677963945 252.796316927755
+2.5266414136 -8.3376288737 71.7318388721015
+2.7620612369 -5.8398712842 -1.93587742753693
+2.9974810602 -3.1140648231 -39.2999192667503
+3.2329008835 -1.7257245065 14.3424136002004
+3.4683207068 -0.4428977017 -29.4925534559498
+3.7037405301 -0.1466643003 -3.18010534572236
+3.9391603534 -0.2095507945 3.33490838803603
+4.1745801767 -0.1442384563 3.71918691359508
+4.41 0 -9.66717019857564
+spline3eq
+5
+-61.9827585211652 0
+1.9 11.2293641315584 0
+2.8 -27.9976343076148 122.648031332411
+3.7 -8.32979773113248 -54.3340881766381
+4.6 -1.00863195297399 3.23150064581724
+5.5 0 -5.3514242228123
+spline3eq
+4
+0.00776934946045395 0.105197706160344
+-55.14233165 -0.29745568008 0.00152870603877451
+-44.7409899033333 -0.15449458722 0.00038933722543571
+-34.3396481566667 0.05098657168 0.00038124926922248
+-23.93830641 0.57342694704 0.0156639264890892
+spline3eq
+5
+-0.00676745157022662 -0.0159520381982146
+-23.9928 0.297607384684645 0
+-15.9241175 0.216691597077105 -0.0024248755353942
+-7.855435 0.0637598673719069 0.00306245895013358
+0.213247499999998 -0.00183450621970427 -0.00177588407633909
+8.28193 -0.111277018874367 0
+spline3eq
+10
+2.77327511656661 0
+2.055801767 -0.1485215264 72.2010867146919
+2.31737934844444 1.6845304918 -47.2744689053404
+2.57895692988889 2.0113365977 -15.1859578405326
+2.84053451133333 1.1444092747 3.33978204841873
+3.10211209277778 0.2861606803 2.587867603808
+3.36368967422222 -0.3459281126 6.14070694084556
+3.62526725566667 -0.6257480601 3.7397696717154
+3.88684483711111 -0.6119510826 4.64749084871402
+4.14842241855556 -0.3112059651 2.83275746415936
+4.41 0 -15.0612086827734
+spline3eq
+5
+12.3315547862781 0
+1.9 2.62105440156724 0
+2.8 10.2850803058354 -25.439802988016
+3.7 3.23933763743897 -7.20203673434025
+4.6 -5.79049355858613 39.5509978688682
+5.5 0 -41.221771373642
+spline3eq
+8
+8.33642274810572 -60.4024574736564
+-1 0.07651409193 -110.652321293778
+-0.724509054371429 0.14155824541 44.8853405500508
+-0.449018108742857 0.75788697341 -25.3065115342002
+-0.173527163114286 0.63011570378 -2.48510144915082
+0.101963782514286 0.09049597305 2.68769386908235
+0.377454728142857 -0.35741586657 -1.01558570129633
+0.652945673771428 -0.65293217647 13.4224786001212
+0.9284366194 -6.00912190653 -452.752542694929
+spline3eq
+5
+0.137191606537625 -1.55094230968985
+-1 0.0513843442016519 0
+-0.5 0.0179024412245673 -2.44986494990154
+0 -0.260650876879273 3.91774583656401
+0.5 -0.190163791764901 -4.84414871911743
+1 -0.763795416646599 0
+spline3eq
+8
+0 0
+-1 0 0
+-0.724509054371429 0 0
+-0.449018108742857 0 0
+-0.173527163114286 0 0
+0.101963782514286 0 0
+0.377454728142857 0 0
+0.652945673771428 0 0
+0.9284366194 0 0
--- a/examples/USER/misc/meam_spline/in.meam-spline.Si
+++ b/examples/USER/misc/meam_spline/in.meam-spline.Si
@ -0,0 +1,22 @@
+# Si fcc phase
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+lattice		fcc 3.98
+region		box block 0 5 0 5 0 5
+create_box		1 box
+create_atoms	1 box
+
+pair_style      meam/spline
+pair_coeff      * * Si_1.meam.spline Si
+mass            * 28.085
+
+velocity        all create 500.0 44226611
+
+fix             1 all nvt temp 500.0 500.0 1.0
+
+thermo          50
+run             500
+
--- a/examples/USER/misc/meam_spline/in.meam-spline.TiO2
+++ b/examples/USER/misc/meam_spline/in.meam-spline.TiO2
@ -0,0 +1,92 @@
+# 
+
+variable T_depart equal 300
+
+variable dt equal 0.0002
+
+variable a equal 4.5937
+variable c equal 2.9587
+variable ca equal ${c}/${a}
+
+variable nx equal 6
+variable ny equal 6
+variable nz equal 11
+
+variable bx equal ${a}*${nx}
+variable by equal ${a}*${ny}
+variable bz equal ${c}*${nz}
+# =======================================================================
+
+units		metal
+atom_style	atomic
+dimension       3
+boundary        p p p
+
+
+lattice		sc 1.0
+region          box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
+create_box      2 box_vide
+
+#lattice         sc 1.0
+#region          box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
+
+# titanium atoms
+lattice 	custom ${a} origin 0.0 0.0 0.0 &
+                            orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 &
+                            a1 1.0  0.0  0.0  &
+                            a2 0.0  1.0  0.0  &
+                            a3 0.0  0.0 ${ca} &
+                            basis 0.0    0.0     0.0 &
+ 			    basis 0.5    0.5     0.5
+
+create_atoms 	2 region box_vide
+
+# Oxygen atoms
+lattice         custom ${a} origin 0.0 0.0 0.0 &
+                            orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 &
+                            a1 1.0  0.0  0.0  &
+                            a2 0.0  1.0  0.0  &
+                            a3 0.0  0.0 ${ca} &
+                            basis 0.30478    0.30478     0.0 &
+                            basis 0.69522    0.69522     0.0 &
+			    basis 0.19522    0.80478     0.5 &
+			    basis 0.80478    0.19522     0.5 
+
+create_atoms	1 region box_vide
+ 
+
+mass            1 16.00
+group           Oxy type 1
+
+mass		2 47.867
+group    	Ti type 2
+
+velocity	all create ${T_depart} 277387
+
+pair_style	meam/spline
+pair_coeff	* * TiO.meam.spline O Ti
+
+neighbor	0.5 bin
+neigh_modify	every 2 delay 0 check yes
+
+timestep        ${dt}
+
+thermo_style    custom step temp press pe ke etotal lx ly lz vol 
+thermo		10
+
+
+#dump            5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z  
+
+fix		3 all nve
+run		100
+
+unfix		3
+fix             1 all box/relax tri 0.0 vmax 0.001
+minimize        1.0e-3 1.0e-5 1000 10000
+
+unfix		1
+reset_timestep  0
+thermo          50
+fix             3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0
+run             500
+
--- a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.1
+++ b/examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.1
@ -0,0 +1,88 @@
+LAMMPS (13 Apr 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Si fcc phase
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+lattice		fcc 3.98
+Lattice spacing in x,y,z = 3.98 3.98 3.98
+region		box block 0 5 0 5 0 5
+create_box		1 box
+Created orthogonal box = (0 0 0) to (19.9 19.9 19.9)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+
+pair_style      meam/spline
+pair_coeff      * * Si_1.meam.spline Si
+Reading potential file Si_1.meam.spline with DATE: 2012-02-01
+mass            * 28.085
+
+velocity        all create 500.0 44226611
+
+fix             1 all nvt temp 500.0 500.0 1.0
+
+thermo          50
+run             500
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.5
+  ghost atom cutoff = 6.5
+  binsize = 3.25, bins = 7 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/spline, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/spline, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.892 | 3.892 | 3.892 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          500    -1847.729            0   -1815.4786    1813162.7 
+      50    1934.0932   -1940.8016            0    -1816.051   -48657.676 
+     100    2570.1286   -1984.8725            0   -1819.0971    8002.4248 
+     150    2566.7917   -1990.2724            0   -1824.7123    16819.447 
+     200    2555.1319   -1995.2233            0   -1830.4152    5891.5313 
+     250    2487.2881   -1995.8302            0   -1835.3981   -4339.7172 
+     300    2381.4836   -1994.2492            0   -1840.6415     16508.04 
+     350    2330.8663   -1996.6588            0   -1846.3161    24194.447 
+     400    2212.6035   -1994.9278            0   -1852.2131   -9856.3709 
+     450    2257.7531   -2003.8187            0   -1858.1918   -8029.6019 
+     500    2211.4385   -2006.9846            0    -1864.345    4152.4867 
+Loop time of 5.13837 on 1 procs for 500 steps with 500 atoms
+
+Performance: 8.407 ns/day, 2.855 hours/ns, 97.307 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.0952     | 5.0952     | 5.0952     |   0.0 | 99.16
+Neigh   | 0.026447   | 0.026447   | 0.026447   |   0.0 |  0.51
+Comm    | 0.0063307  | 0.0063307  | 0.0063307  |   0.0 |  0.12
+Output  | 0.0001905  | 0.0001905  | 0.0001905  |   0.0 |  0.00
+Modify  | 0.0082877  | 0.0082877  | 0.0082877  |   0.0 |  0.16
+Other   |            | 0.00187    |            |       |  0.04
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1767 ave 1767 max 1767 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    18059 ave 18059 max 18059 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  36118 ave 36118 max 36118 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 36118
+Ave neighs/atom = 72.236
+Neighbor list builds = 14
+Dangerous builds = 0
+
+Total wall time: 0:00:05
--- a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.4
+++ b/examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.4
@ -0,0 +1,88 @@
+LAMMPS (13 Apr 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Si fcc phase
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+lattice		fcc 3.98
+Lattice spacing in x,y,z = 3.98 3.98 3.98
+region		box block 0 5 0 5 0 5
+create_box		1 box
+Created orthogonal box = (0 0 0) to (19.9 19.9 19.9)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 500 atoms
+
+pair_style      meam/spline
+pair_coeff      * * Si_1.meam.spline Si
+Reading potential file Si_1.meam.spline with DATE: 2012-02-01
+mass            * 28.085
+
+velocity        all create 500.0 44226611
+
+fix             1 all nvt temp 500.0 500.0 1.0
+
+thermo          50
+run             500
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.5
+  ghost atom cutoff = 6.5
+  binsize = 3.25, bins = 7 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/spline, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/spline, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.861 | 3.861 | 3.861 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          500    -1847.729            0   -1815.4786    1813162.7 
+      50    1923.4262   -1940.0936            0   -1816.0311   -38700.835 
+     100    2535.2542   -1982.6249            0   -1819.0989    10216.821 
+     150    2592.8247   -1992.1569            0   -1824.9176    4839.3385 
+     200    2484.7391   -1990.8452            0   -1830.5775    14040.141 
+     250    2597.4401   -2003.1619            0    -1835.625    1261.5199 
+     300    2513.0793    -2002.942            0   -1840.8463    6690.9815 
+     350     2390.933   -2001.0761            0    -1846.859   -4880.1146 
+     400    2269.0782   -1999.3441            0   -1852.9867   -4921.4391 
+     450    2287.5096   -2006.8236            0   -1859.2774   -7313.6151 
+     500    2303.0918   -2014.0693            0    -1865.518   -9995.1789 
+Loop time of 1.46588 on 4 procs for 500 steps with 500 atoms
+
+Performance: 29.470 ns/day, 0.814 hours/ns, 341.093 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.4273     | 1.4292     | 1.432      |   0.1 | 97.50
+Neigh   | 0.0068567  | 0.0070301  | 0.0073655  |   0.2 |  0.48
+Comm    | 0.019111   | 0.022127   | 0.024148   |   1.2 |  1.51
+Output  | 0.00023174 | 0.00024784 | 0.00029206 |   0.0 |  0.02
+Modify  | 0.005043   | 0.0052016  | 0.0054417  |   0.2 |  0.35
+Other   |            | 0.002066   |            |       |  0.14
+
+Nlocal:    125 ave 131 max 118 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Nghost:    979.25 ave 986 max 975 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+Neighs:    4541.75 ave 4712 max 4362 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+FullNghs:  9083.5 ave 9485 max 8601 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 36334
+Ave neighs/atom = 72.668
+Neighbor list builds = 14
+Dangerous builds = 0
+
+Total wall time: 0:00:01
--- a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.1
+++ b/examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.1
@ -0,0 +1,248 @@
+LAMMPS (13 Apr 2017)
+  using 1 OpenMP thread(s) per MPI task
+#
+
+variable T_depart equal 300
+
+variable dt equal 0.0002
+
+variable a equal 4.5937
+variable c equal 2.9587
+variable ca equal ${c}/${a}
+variable ca equal 2.9587/${a}
+variable ca equal 2.9587/4.5937
+
+variable nx equal 6
+variable ny equal 6
+variable nz equal 11
+
+variable bx equal ${a}*${nx}
+variable bx equal 4.5937*${nx}
+variable bx equal 4.5937*6
+variable by equal ${a}*${ny}
+variable by equal 4.5937*${ny}
+variable by equal 4.5937*6
+variable bz equal ${c}*${nz}
+variable bz equal 2.9587*${nz}
+variable bz equal 2.9587*11
+# =======================================================================
+
+units		metal
+atom_style	atomic
+dimension       3
+boundary        p p p
+
+
+lattice		sc 1.0
+Lattice spacing in x,y,z = 1 1 1
+region          box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
+region          box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0
+region          box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0
+region          box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0
+create_box      2 box_vide
+Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0)
+  1 by 1 by 1 MPI processor grid
+
+#lattice         sc 1.0
+#region          box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
+
+# titanium atoms
+lattice 	custom ${a} origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 ${ca}                             basis 0.0    0.0     0.0  			    basis 0.5    0.5     0.5
+lattice 	custom 4.5937 origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 ${ca}                             basis 0.0    0.0     0.0  			    basis 0.5    0.5     0.5
+lattice 	custom 4.5937 origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 0.644077758669482                             basis 0.0    0.0     0.0  			    basis 0.5    0.5     0.5
+Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
+
+create_atoms 	2 region box_vide
+Created 792 atoms
+
+# Oxygen atoms
+lattice         custom ${a} origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 ${ca}                             basis 0.30478    0.30478     0.0                             basis 0.69522    0.69522     0.0 			    basis 0.19522    0.80478     0.5 			    basis 0.80478    0.19522     0.5
+lattice         custom 4.5937 origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 ${ca}                             basis 0.30478    0.30478     0.0                             basis 0.69522    0.69522     0.0 			    basis 0.19522    0.80478     0.5 			    basis 0.80478    0.19522     0.5
+lattice         custom 4.5937 origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 0.644077758669482                             basis 0.30478    0.30478     0.0                             basis 0.69522    0.69522     0.0 			    basis 0.19522    0.80478     0.5 			    basis 0.80478    0.19522     0.5
+Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
+
+create_atoms	1 region box_vide
+Created 1584 atoms
+
+
+mass            1 16.00
+group           Oxy type 1
+1584 atoms in group Oxy
+
+mass		2 47.867
+group    	Ti type 2
+792 atoms in group Ti
+
+velocity	all create ${T_depart} 277387
+velocity	all create 300 277387
+
+pair_style	meam/spline
+pair_coeff	* * TiO.meam.spline O Ti
+Reading potential file TiO.meam.spline with DATE: 2016-06-05
+
+neighbor	0.5 bin
+neigh_modify	every 2 delay 0 check yes
+
+timestep        ${dt}
+timestep        0.0002
+
+thermo_style    custom step temp press pe ke etotal lx ly lz vol
+thermo		10
+
+
+#dump            5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
+
+fix		3 all nve
+run		100
+Neighbor list info ...
+  update every 2 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6
+  ghost atom cutoff = 6
+  binsize = 3, bins = 10 10 11
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/spline, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/spline, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 5.146 | 5.146 | 5.146 Mbytes
+Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume 
+       0          300    22403.656   -14374.073    92.097853   -14281.975      27.5622      27.5622      32.5457     24724.15 
+      10    301.41345    23612.297   -14374.507    92.531772   -14281.975      27.5622      27.5622      32.5457     24724.15 
+      20    305.11674    25127.832   -14375.643    93.668657   -14281.974      27.5622      27.5622      32.5457     24724.15 
+      30    313.28903     26655.89   -14378.151     96.17749   -14281.974      27.5622      27.5622      32.5457     24724.15 
+      40    328.94567    26999.049   -14382.957    100.98397   -14281.974      27.5622      27.5622      32.5457     24724.15 
+      50    354.05827    23023.294   -14390.667    108.69336   -14281.974      27.5622      27.5622      32.5457     24724.15 
+      60    390.48404    13594.655   -14401.849    119.87581   -14281.973      27.5622      27.5622      32.5457     24724.15 
+      70    442.69928    151.15709   -14417.877    135.90551   -14281.972      27.5622      27.5622      32.5457     24724.15 
+      80    516.89551   -14984.124   -14440.654    158.68322   -14281.971      27.5622      27.5622      32.5457     24724.15 
+      90    618.22135   -29948.066    -14471.76    189.78953   -14281.971      27.5622      27.5622      32.5457     24724.15 
+     100     747.6193   -41964.291   -14511.487    229.51378   -14281.973      27.5622      27.5622      32.5457     24724.15 
+Loop time of 38.7948 on 1 procs for 100 steps with 2376 atoms
+
+Performance: 0.045 ns/day, 538.817 hours/ns, 2.578 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 38.774     | 38.774     | 38.774     |   0.0 | 99.95
+Neigh   | 0.010751   | 0.010751   | 0.010751   |   0.0 |  0.03
+Comm    | 0.0039313  | 0.0039313  | 0.0039313  |   0.0 |  0.01
+Output  | 0.00048804 | 0.00048804 | 0.00048804 |   0.0 |  0.00
+Modify  | 0.0039241  | 0.0039241  | 0.0039241  |   0.0 |  0.01
+Other   |            | 0.001809   |            |       |  0.00
+
+Nlocal:    2376 ave 2376 max 2376 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    4479 ave 4479 max 4479 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    106396 ave 106396 max 106396 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  212792 ave 212792 max 212792 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 212792
+Ave neighs/atom = 89.5589
+Neighbor list builds = 1
+Dangerous builds = 0
+
+unfix		3
+fix             1 all box/relax tri 0.0 vmax 0.001
+minimize        1.0e-3 1.0e-5 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 6.271 | 6.271 | 6.271 Mbytes
+Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume 
+     100     747.6193   -41964.291   -14511.487    229.51378   -14281.973      27.5622      27.5622      32.5457     24724.15 
+     101     747.6193    -39284.65   -14517.424    229.51378    -14287.91    27.569615    27.569695    32.513154    24712.789 
+Loop time of 0.814693 on 1 procs for 1 steps with 2376 atoms
+
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+        -14511.4866189     -14511.4866189     -14517.4235162
+  Force two-norm initial, final = 5602.25 5486.97
+  Force max component initial, final = 5232.05 5109.43
+  Final line search alpha, max atom move = 1.9113e-07 0.000976563
+  Iterations, force evaluations = 1 1
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.81429    | 0.81429    | 0.81429    |   0.0 | 99.95
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 6.485e-05  | 6.485e-05  | 6.485e-05  |   0.0 |  0.01
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.0003347  |            |       |  0.04
+
+Nlocal:    2376 ave 2376 max 2376 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    4449 ave 4449 max 4449 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    105639 ave 105639 max 105639 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  211278 ave 211278 max 211278 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 211278
+Ave neighs/atom = 88.9217
+Neighbor list builds = 0
+Dangerous builds = 0
+
+unfix		1
+reset_timestep  0
+thermo          50
+fix             3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0
+run             500
+Per MPI rank memory allocation (min/avg/max) = 5.162 | 5.162 | 5.162 Mbytes
+Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume 
+       0     747.6193    -39284.65   -14517.424    229.51378    -14287.91    27.569615    27.569695    32.513154    24712.789 
+      50    1155.2849    30650.319   -14678.807     354.6642   -14324.143    27.608688     27.60914    32.375311     24678.15 
+     100    790.03926    99869.991   -14678.858     242.5364   -14436.322    27.777994     27.77799    32.017001    24704.857 
+     150    938.86463   -21488.442   -14803.782    288.22472   -14515.557    27.996584    27.995139     31.67008    24822.003 
+     200    420.11331   -790.80799   -14671.687    128.97178   -14542.715    28.126911    28.125909    31.431033     24864.93 
+     250    352.18149   -3244.2491   -14665.007     108.1172   -14556.889    28.222686    28.223673    31.238649    24883.078 
+     300    622.91245    3657.7097   -14758.201    191.22967   -14566.972    28.301771     28.30503     31.07216    24891.363 
+     350    888.25374    26274.358   -14852.568    272.68754   -14579.881    28.370312    28.375107    30.937051    24904.656 
+     400    735.44163    63109.066   -14823.872    225.77532   -14598.097    28.446905     28.45227    30.838015    24959.642 
+     450    804.81905    6221.0364   -14861.113    247.07369   -14614.039    28.543942    28.548719    30.775793    25078.977 
+     500    628.19106   -33912.026   -14814.726    192.85016   -14621.876    28.611997    28.615169     30.74081    25168.642 
+Loop time of 176.167 on 1 procs for 500 steps with 2376 atoms
+
+Performance: 0.049 ns/day, 489.353 hours/ns, 2.838 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 175.9      | 175.9      | 175.9      |   0.0 | 99.85
+Neigh   | 0.17043    | 0.17043    | 0.17043    |   0.0 |  0.10
+Comm    | 0.018243   | 0.018243   | 0.018243   |   0.0 |  0.01
+Output  | 0.00040984 | 0.00040984 | 0.00040984 |   0.0 |  0.00
+Modify  | 0.067142   | 0.067142   | 0.067142   |   0.0 |  0.04
+Other   |            | 0.00828    |            |       |  0.00
+
+Nlocal:    2376 ave 2376 max 2376 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    4358 ave 4358 max 4358 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    102634 ave 102634 max 102634 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  205268 ave 205268 max 205268 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 205268
+Ave neighs/atom = 86.3923
+Neighbor list builds = 16
+Dangerous builds = 0
+
+Total wall time: 0:03:37
--- a/examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.4
+++ b/examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.4
@ -0,0 +1,248 @@
+LAMMPS (13 Apr 2017)
+  using 1 OpenMP thread(s) per MPI task
+#
+
+variable T_depart equal 300
+
+variable dt equal 0.0002
+
+variable a equal 4.5937
+variable c equal 2.9587
+variable ca equal ${c}/${a}
+variable ca equal 2.9587/${a}
+variable ca equal 2.9587/4.5937
+
+variable nx equal 6
+variable ny equal 6
+variable nz equal 11
+
+variable bx equal ${a}*${nx}
+variable bx equal 4.5937*${nx}
+variable bx equal 4.5937*6
+variable by equal ${a}*${ny}
+variable by equal 4.5937*${ny}
+variable by equal 4.5937*6
+variable bz equal ${c}*${nz}
+variable bz equal 2.9587*${nz}
+variable bz equal 2.9587*11
+# =======================================================================
+
+units		metal
+atom_style	atomic
+dimension       3
+boundary        p p p
+
+
+lattice		sc 1.0
+Lattice spacing in x,y,z = 1 1 1
+region          box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
+region          box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0
+region          box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0
+region          box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0
+create_box      2 box_vide
+Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0)
+  1 by 2 by 2 MPI processor grid
+
+#lattice         sc 1.0
+#region          box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
+
+# titanium atoms
+lattice 	custom ${a} origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 ${ca}                             basis 0.0    0.0     0.0  			    basis 0.5    0.5     0.5
+lattice 	custom 4.5937 origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 ${ca}                             basis 0.0    0.0     0.0  			    basis 0.5    0.5     0.5
+lattice 	custom 4.5937 origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 0.644077758669482                             basis 0.0    0.0     0.0  			    basis 0.5    0.5     0.5
+Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
+
+create_atoms 	2 region box_vide
+Created 792 atoms
+
+# Oxygen atoms
+lattice         custom ${a} origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 ${ca}                             basis 0.30478    0.30478     0.0                             basis 0.69522    0.69522     0.0 			    basis 0.19522    0.80478     0.5 			    basis 0.80478    0.19522     0.5
+lattice         custom 4.5937 origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 ${ca}                             basis 0.30478    0.30478     0.0                             basis 0.69522    0.69522     0.0 			    basis 0.19522    0.80478     0.5 			    basis 0.80478    0.19522     0.5
+lattice         custom 4.5937 origin 0.0 0.0 0.0                             orient x 1 0 0 orient y 0 1 0 orient z 0 0 1                             a1 1.0  0.0  0.0                              a2 0.0  1.0  0.0                              a3 0.0  0.0 0.644077758669482                             basis 0.30478    0.30478     0.0                             basis 0.69522    0.69522     0.0 			    basis 0.19522    0.80478     0.5 			    basis 0.80478    0.19522     0.5
+Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
+
+create_atoms	1 region box_vide
+Created 1584 atoms
+
+
+mass            1 16.00
+group           Oxy type 1
+1584 atoms in group Oxy
+
+mass		2 47.867
+group    	Ti type 2
+792 atoms in group Ti
+
+velocity	all create ${T_depart} 277387
+velocity	all create 300 277387
+
+pair_style	meam/spline
+pair_coeff	* * TiO.meam.spline O Ti
+Reading potential file TiO.meam.spline with DATE: 2016-06-05
+
+neighbor	0.5 bin
+neigh_modify	every 2 delay 0 check yes
+
+timestep        ${dt}
+timestep        0.0002
+
+thermo_style    custom step temp press pe ke etotal lx ly lz vol
+thermo		10
+
+
+#dump            5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
+
+fix		3 all nve
+run		100
+Neighbor list info ...
+  update every 2 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6
+  ghost atom cutoff = 6
+  binsize = 3, bins = 10 10 11
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/spline, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/spline, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.922 | 3.922 | 3.922 Mbytes
+Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume 
+       0          300    22403.656   -14374.073    92.097853   -14281.975      27.5622      27.5622      32.5457     24724.15 
+      10    301.16725    23582.084   -14374.431    92.456192   -14281.975      27.5622      27.5622      32.5457     24724.15 
+      20    304.58237    25059.749   -14375.479    93.504609   -14281.974      27.5622      27.5622      32.5457     24724.15 
+      30    312.41477    26504.358   -14377.883      95.9091   -14281.974      27.5622      27.5622      32.5457     24724.15 
+      40    327.67099    26687.057   -14382.566    100.59265   -14281.974      27.5622      27.5622      32.5457     24724.15 
+      50    352.32125    22677.292   -14390.134     108.1601   -14281.974      27.5622      27.5622      32.5457     24724.15 
+      60    388.40592    12472.705   -14401.211    119.23784   -14281.973      27.5622      27.5622      32.5457     24724.15 
+      70    439.97199   -1520.4694    -14417.04    135.06825   -14281.972      27.5622      27.5622      32.5457     24724.15 
+      80    513.34361   -16733.316   -14439.564    157.59282   -14281.971      27.5622      27.5622      32.5457     24724.15 
+      90     613.3542   -31099.591   -14470.267    188.29535   -14281.971      27.5622      27.5622      32.5457     24724.15 
+     100    741.02836   -42358.226   -14509.464     227.4904   -14281.973      27.5622      27.5622      32.5457     24724.15 
+Loop time of 8.92317 on 4 procs for 100 steps with 2376 atoms
+
+Performance: 0.194 ns/day, 123.933 hours/ns, 11.207 timesteps/s
+99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.8912     | 8.9        | 8.9064     |   0.2 | 99.74
+Neigh   | 0.0027034  | 0.0028808  | 0.0032032  |   0.4 |  0.03
+Comm    | 0.010964   | 0.017648   | 0.026568   |   5.0 |  0.20
+Output  | 0.00037575 | 0.00047809 | 0.00053835 |   0.0 |  0.01
+Modify  | 0.00099134 | 0.001001   | 0.0010085  |   0.0 |  0.01
+Other   |            | 0.001162   |            |       |  0.01
+
+Nlocal:    594 ave 599 max 589 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:    2290.25 ave 2296 max 2282 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:    26671.5 ave 26934 max 26495 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+FullNghs:  53343 ave 53828 max 52922 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 213372
+Ave neighs/atom = 89.803
+Neighbor list builds = 1
+Dangerous builds = 0
+
+unfix		3
+fix             1 all box/relax tri 0.0 vmax 0.001
+minimize        1.0e-3 1.0e-5 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes
+Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume 
+     100    741.02836   -42358.226   -14509.464     227.4904   -14281.973      27.5622      27.5622      32.5457     24724.15 
+     101    741.02836   -39686.588   -14515.398     227.4904   -14287.907    27.569587    27.569656    32.513154    24712.729 
+Loop time of 0.193516 on 4 procs for 1 steps with 2376 atoms
+
+99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+          -14509.46351       -14509.46351     -14515.3978891
+  Force two-norm initial, final = 5602.69 5487.77
+  Force max component initial, final = 5235.27 5113.06
+  Final line search alpha, max atom move = 1.91012e-07 0.000976657
+  Iterations, force evaluations = 1 1
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.19287    | 0.19299    | 0.19318    |   0.0 | 99.73
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00014043 | 0.00033247 | 0.00045896 |   0.0 |  0.17
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.0001886  |            |       |  0.10
+
+Nlocal:    594 ave 601 max 586 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Nghost:    2263.25 ave 2271 max 2251 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Neighs:    26425.8 ave 26807 max 26121 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+FullNghs:  52851.5 ave 53580 max 52175 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 211406
+Ave neighs/atom = 88.9756
+Neighbor list builds = 0
+Dangerous builds = 0
+
+unfix		1
+reset_timestep  0
+thermo          50
+fix             3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0
+run             500
+Per MPI rank memory allocation (min/avg/max) = 3.937 | 3.937 | 3.937 Mbytes
+Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume 
+       0    741.02836   -39686.588   -14515.398     227.4904   -14287.907    27.569587    27.569656    32.513154    24712.729 
+      50     1157.347    29332.549   -14679.321    355.29725   -14324.024     27.60903    27.609325    32.375509    24678.772 
+     100    777.55858    101883.12   -14674.854    238.70492   -14436.149    27.778518    27.777373    32.017262    24704.976 
+     150    945.49014   -18305.383   -14806.687    290.25871   -14516.428    27.998313     27.99535    31.670225    24823.838 
+     200    427.46608   -4045.0095   -14674.887    131.22903   -14543.658    28.130283    28.127147    31.431578    24869.438 
+     250    362.82166   -7283.1332    -14669.07    111.38365   -14557.687    28.225232    28.222707    31.238451    24884.314 
+     300     626.2858    7228.0309   -14760.128    192.26526   -14567.862    28.302384    28.299949    31.070038    24885.734 
+     350    859.84293    30084.735   -14845.064    263.96563   -14581.099    28.372349    28.369334    30.934424    24899.261 
+     400    755.26136    54745.408   -14830.701    231.85983   -14598.842    28.450301    28.448361    30.836159    24957.691 
+     450    802.52344    5690.2863   -14860.193    246.36895   -14613.824    28.542311    28.541672    30.773339    25069.354 
+     500    631.84734   -31473.795   -14816.101    193.97261   -14622.128    28.605857    28.605891    30.737955    25152.746 
+Loop time of 39.7881 on 4 procs for 500 steps with 2376 atoms
+
+Performance: 0.217 ns/day, 110.522 hours/ns, 12.567 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 39.617     | 39.633     | 39.653     |   0.2 | 99.61
+Neigh   | 0.043624   | 0.046792   | 0.051708   |   1.4 |  0.12
+Comm    | 0.05215    | 0.072616   | 0.092142   |   5.6 |  0.18
+Output  | 0.00042915 | 0.00045079 | 0.00051546 |   0.0 |  0.00
+Modify  | 0.029836   | 0.030341   | 0.03094    |   0.2 |  0.08
+Other   |            | 0.004489   |            |       |  0.01
+
+Nlocal:    594 ave 606 max 582 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost:    2226 ave 2238 max 2214 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:    25652.8 ave 26129 max 25153 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+FullNghs:  51305.5 ave 52398 max 50251 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 205222
+Ave neighs/atom = 86.3729
+Neighbor list builds = 16
+Dangerous builds = 0
+
+Total wall time: 0:00:49
--- a/examples/USER/vtk/.gitignore
+++ b/examples/USER/vtk/.gitignore
@ -0,0 +1 @@
+dump
--- a/examples/USER/vtk/in.vtk
+++ b/examples/USER/vtk/in.vtk
@ -0,0 +1,35 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+shell mkdir dump
+
+dump dmpvtk all vtk 50 dump/dump*.vtk id type vx vy vz fx fy fz
+
+#dump		2 all image 25 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3
+
+#dump		3 all movie 25 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3
+
+thermo		50
+run		250
--- a/examples/USER/vtk/in.vtp
+++ b/examples/USER/vtk/in.vtp
@ -0,0 +1,35 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+shell mkdir dump
+
+dump dmpvtk all vtk 50 dump/dump*.vtp id type vx vy vz fx fy fz
+
+#dump		2 all image 25 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3
+
+#dump		3 all movie 25 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3
+
+thermo		50
+run		250
--- a/examples/python/README.pair_python
+++ b/examples/python/README.pair_python
@ -0,0 +1,41 @@
+This folder contains several LAMMPS input scripts and a python module
+file py_pot.py to demonstrate the use of the pair style python.
+
+in.pair_python_melt:
+This is a version of the melt example using the python pair style.  The first
+part of the output should have identical energies, temperature and pressure
+than the melt example.  The following two sections then demonstrate how to
+restart with pair style python from a restart file and a data file.
+
+in.pair_python_hybrid:
+This versions shows how to mix regular pair styles with a python pair style.
+However, in this case both potentials are the same, so the energies and
+pressure in the output should be identical to that of the previous example.
+
+in.pair_python_spce:
+This input shows a simulation of small bulk water system with the SPC/E
+water potential. Since the python pair style does not support computing
+coulomb contributions, pair style hybrid/overload is used to combine
+the python style containing the Lennard-Jones part with the long-range coulomb.
+Same as for the previous example, it also showcases restarting.
+
+in.pair_python_table:
+This input demonstrates the use of using the python pair style to build
+a table file for use with pair style table. This will run much faster
+than the python pair style. This example tabulates the melt example from
+above. Note that tabulation is approximative, so the output will only
+agree with the melt result to some degree. 
+
+in.pair_python_coulomb:
+This is another tabulation example, this time for the SPC/E water example
+with cutoff coulomb interactions.
+Please note, that tabulating long-range coulomb has a systematic error in
+forces and energies for all systems with bonds, angle and dihedrals.
+In this case, this will only affect the energies, since the water molecules
+are held rigid with fix shake. To enable long-range coulomb the coul/cut
+style needs to be replaced with coul/long, a suitable kspace style added
+and the pppm keyword added to the table pair style definition.
+
+in.pair_python_long:
+The final example shows how to combine long-range coulomb with tabulation
+for only the short range interactions via pair style hybrid/overlay.
--- a/examples/python/data.spce
+++ b/examples/python/data.spce
--- a/examples/python/funcs.py
+++ b/examples/python/funcs.py
@ -1,9 +1,10 @@
 # Python function that implements a loop of short runs
 # calls back to LAMMPS via "lmp" instance
 # lammps() must be called with ptr=lmpptr for this to work
+from __future__ import print_function

 def loop(N,cut0,thresh,lmpptr):
-  print "LOOP ARGS",N,cut0,thresh,lmpptr
+  print("LOOP ARGS",N,cut0,thresh,lmpptr)
  from lammps import lammps
  lmp = lammps(ptr=lmpptr)
  natoms = lmp.get_natoms()
@ -12,11 +13,12 @@ def loop(N,cut0,thresh,lmpptr):
    cut = cut0 + i*0.1

    lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
+
    lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
    #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option

    lmp.command("pair_coeff * * 1.0 1.0")       # ditto
    lmp.command("run 10")                       # ditto
    pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS
-    print "PE",pe/natoms,thresh
+    print("PE",pe/natoms,thresh)
    if pe/natoms < thresh: return
--- a/examples/python/in.fix_python
+++ b/examples/python/in.fix_python
@ -0,0 +1,50 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+python         end_of_step_callback here """
+from __future__ import print_function
+from lammps import lammps
+
+def end_of_step_callback(lmp):
+  L = lammps(ptr=lmp)
+  t = L.extract_global("ntimestep", 0)
+  print("### END OF STEP ###", t)
+
+def post_force_callback(lmp, v):
+  L = lammps(ptr=lmp)
+  t = L.extract_global("ntimestep", 0)
+  print("### POST_FORCE ###", t)
+"""
+
+fix		1 all nve
+fix     2 all python 50 end_of_step end_of_step_callback
+fix     3 all python 50 post_force post_force_callback
+
+#dump		id all atom 50 dump.melt
+
+#dump		2 all image 25 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3
+
+#dump		3 all movie 25 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3
+
+thermo		50
+run		250
--- a/examples/python/in.pair_python_coulomb
+++ b/examples/python/in.pair_python_coulomb
@ -0,0 +1,42 @@
+units		real	
+atom_style	full
+
+read_data	data.spce
+
+pair_style	hybrid/overlay coul/cut 12.0 python 12.0
+
+pair_coeff	* * coul/cut
+pair_coeff	* * python py_pot.LJCutSPCE OW NULL
+
+bond_style	harmonic
+angle_style	harmonic
+dihedral_style	none
+improper_style	none
+
+bond_coeff	1 1000.00 1.000
+angle_coeff	1 100.0 109.47
+
+special_bonds   lj/coul 0.0 0.0 1.0
+
+neighbor        2.0 bin
+
+fix		1 all shake 0.0001 20 0 b 1 a 1
+fix		2 all nvt temp 300.0 300.0 100.0
+
+# create combined lj/coul table for all atom types
+# generate tabulated potential from python variant
+pair_write      1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
+pair_write      1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472  0.4236
+pair_write      2 2 2000 rsq 0.1 12 spce.table HW-HW  0.4236  0.4236
+
+# switch to tabulated potential
+pair_style      table linear 2000 pppm
+pair_coeff      1 1 spce.table OW-OW
+pair_coeff      1 2 spce.table OW-HW
+pair_coeff      2 2 spce.table HW-HW
+
+thermo 10
+run 100
+
+shell rm spce.table
+
--- a/examples/python/in.pair_python_hybrid
+++ b/examples/python/in.pair_python_hybrid
@ -0,0 +1,63 @@
+# 3d Lennard-Jones hybrid
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	2 box
+create_atoms	1 box
+mass		* 1.0
+region          half block -0.1 4.9 0 10 0 10
+set region half type 2
+
+velocity	all create 3.0 87287
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python py_pot.LJCutMelt lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+write_data      hybrid.data
+write_restart   hybrid.restart
+
+clear
+
+read_restart    hybrid.restart
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python py_pot.LJCutMelt lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+clear
+
+units		lj
+atom_style	atomic
+
+read_data       hybrid.data
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python py_pot.LJCutMelt lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+shell rm hybrid.data hybrid.restart
--- a/examples/python/in.pair_python_long
+++ b/examples/python/in.pair_python_long
@ -0,0 +1,38 @@
+units		real	
+atom_style	full
+
+read_data	data.spce
+
+pair_style	python 12.0
+pair_coeff	* * py_pot.LJCutSPCE OW HW
+
+bond_style	harmonic
+angle_style	harmonic
+dihedral_style	none
+improper_style	none
+
+bond_coeff	1 1000.00 1.000
+angle_coeff	1 100.0 109.47
+
+special_bonds   lj/coul 0.0 0.0 1.0
+
+neighbor        2.0 bin
+
+fix		1 all shake 0.0001 20 0 b 1 a 1
+fix		2 all nvt temp 300.0 300.0 100.0
+
+# create only lj/cut table for the oxygen atoms from python
+shell rm -f spce.table
+pair_write      1 1 2000 rsq 0.1 12 spce.table OW-OW
+
+# switch to tabulated potential with long-range coulomb as overlay
+pair_style      hybrid/overlay coul/long 12.0 table linear 2000
+kspace_style	pppm 1.0e-6
+pair_coeff      * * coul/long
+pair_coeff      1 1 table spce.table OW-OW
+
+thermo 10
+run 100
+
+shell rm spce.table
+
--- a/examples/python/in.pair_python_melt
+++ b/examples/python/in.pair_python_melt
@ -0,0 +1,58 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	1 box
+create_atoms	1 box
+mass		* 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	python 2.5
+pair_coeff	* * py_pot.LJCutMelt lj
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+write_data      melt.data
+write_restart   melt.restart
+
+clear
+
+read_restart    melt.restart
+
+pair_style	python 2.5
+pair_coeff	* * py_pot.LJCutMelt lj
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+clear
+
+units		lj
+atom_style	atomic
+
+read_data       melt.data
+
+pair_style	python 2.5
+pair_coeff	* * py_pot.LJCutMelt lj
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+shell rm melt.data melt.restart
--- a/examples/python/in.pair_python_spce
+++ b/examples/python/in.pair_python_spce
@ -0,0 +1,28 @@
+units		real	
+atom_style	full
+
+read_data	data.spce
+
+pair_style	hybrid/overlay coul/long 12.0 python 12.0
+kspace_style	pppm 1.0e-6
+
+pair_coeff	* * coul/long
+pair_coeff	* * python py_pot.LJCutSPCE OW NULL
+
+bond_style	harmonic
+angle_style	harmonic
+dihedral_style	none
+improper_style	none
+
+bond_coeff	1 1000.00 1.000
+angle_coeff	1 100.0 109.47
+
+special_bonds   lj/coul 0.0 0.0 1.0
+
+neighbor        2.0 bin
+
+fix		1 all shake 0.0001 20 0 b 1 a 1
+fix		2 all nvt temp 300.0 300.0 100.0
+
+thermo 10
+run 100
--- a/examples/python/in.pair_python_table
+++ b/examples/python/in.pair_python_table
@ -0,0 +1,32 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	1 box
+create_atoms	1 box
+mass		* 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	python 2.5
+pair_coeff	* * py_pot.LJCutMelt lj
+
+# generate tabulated potential from python variant
+pair_write      1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
+
+pair_style      table linear 2000
+pair_coeff      1 1 lj_1_1.table LJ
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+
+shell rm lj_1_1.table
+
--- a/examples/python/in.python
+++ b/examples/python/in.python
@ -25,13 +25,14 @@ run		10
 # example of catching a syntax error

 python          simple here """
+from __future__ import print_function
+
 def simple():
-  import exceptions
-  print "Inside simple function"
+  print("Inside simple function")
  try:
    foo += 1
-  except Exception, e:
-    print "FOO error:",e
+  except Exception as e:
+    print("FOO error:", e)
 """

 python          simple invoke
--- a/examples/python/log.4May17.pair_python_coulomb.1
+++ b/examples/python/log.4May17.pair_python_coulomb.1
@ -0,0 +1,178 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+units		real
+atom_style	full
+
+read_data	data.spce
+  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  3000 bonds
+  reading angles ...
+  1500 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+
+pair_style	hybrid/overlay python 12.0 coul/long 12.0
+kspace_style	pppm 1.0e-6
+
+pair_coeff	* * coul/long
+pair_coeff	* * python potentials.LJCutSPCE OW NULL
+
+pair_modify     table 0
+
+bond_style	harmonic
+angle_style	harmonic
+dihedral_style	none
+improper_style	none
+
+bond_coeff	1 1000.00 1.000
+angle_coeff	1 100.0 109.47
+
+special_bonds   lj/coul 0.0 0.0 1.0
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  2 = max # of special neighbors
+
+neighbor        2.0 bin
+
+fix		1 all shake 0.0001 20 0 b 1 a 1
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  1500 = # of frozen angles
+fix		2 all nvt temp 300.0 300.0 100.0
+
+# create combined lj/coul table for all atom types
+# generate tabulated potential from python variant
+pair_write      1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
+PPPM initialization ...
+WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.279652
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.000394206
+  estimated relative force accuracy = 1.18714e-06
+  using double precision FFTs
+  3d grid and FFT values/proc = 103823 64000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair python, perpetual, skip from (2)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+pair_write      1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472  0.4236
+PPPM initialization ...
+WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.279652
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.000394206
+  estimated relative force accuracy = 1.18714e-06
+  using double precision FFTs
+  3d grid and FFT values/proc = 103823 64000
+pair_write      2 2 2000 rsq 0.1 12 spce.table HW-HW  0.4236  0.4236
+PPPM initialization ...
+WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.279652
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.000394206
+  estimated relative force accuracy = 1.18714e-06
+  using double precision FFTs
+  3d grid and FFT values/proc = 103823 64000
+
+# switch to tabulated potential
+pair_style      table linear 2000 pppm
+pair_coeff      1 1 spce.table OW-OW
+pair_coeff      1 2 spce.table OW-HW
+pair_coeff      2 2 spce.table HW-HW
+
+thermo 10
+run 100
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.279652
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.000394674
+  estimated relative force accuracy = 1.18855e-06
+  using double precision FFTs
+  3d grid and FFT values/proc = 103823 64000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 35.26 | 35.26 | 35.26 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -100272.97            0   -100272.97   -1282.0708 
+      10    120.61568   -101350.63            0   -100272.39   -4077.5051 
+      20    136.11379   -101465.43            0   -100248.65   -5136.5677 
+      30    137.01602    -101455.3            0   -100230.46   -5347.8311 
+      40      153.424   -101582.46            0   -100210.93   -5223.1676 
+      50    167.73654   -101686.24            0   -100186.77   -4468.6687 
+      60    163.11642   -101618.16            0   -100159.99   -3291.7815 
+      70    169.64512   -101647.89            0   -100131.35    -2611.638 
+      80     182.9979   -101737.01            0   -100101.11   -2390.6293 
+      90    191.33873   -101778.71            0   -100068.24    -2239.386 
+     100     194.7458   -101775.84            0   -100034.92   -1951.9128 
+Loop time of 7.60221 on 1 procs for 100 steps with 4500 atoms
+
+Performance: 1.137 ns/day, 21.117 hours/ns, 13.154 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.7401     | 5.7401     | 5.7401     |   0.0 | 75.51
+Bond    | 0.00017881 | 0.00017881 | 0.00017881 |   0.0 |  0.00
+Kspace  | 1.5387     | 1.5387     | 1.5387     |   0.0 | 20.24
+Neigh   | 0.2299     | 0.2299     | 0.2299     |   0.0 |  3.02
+Comm    | 0.024311   | 0.024311   | 0.024311   |   0.0 |  0.32
+Output  | 0.00057936 | 0.00057936 | 0.00057936 |   0.0 |  0.01
+Modify  | 0.063158   | 0.063158   | 0.063158   |   0.0 |  0.83
+Other   |            | 0.005243   |            |       |  0.07
+
+Nlocal:    4500 ave 4500 max 4500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    21216 ave 21216 max 21216 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2601766
+Ave neighs/atom = 578.17
+Ave special neighs/atom = 2
+Neighbor list builds = 3
+Dangerous builds = 0
+
+shell rm spce.table
+
+Total wall time: 0:00:07
--- a/examples/python/log.4May17.pair_python_coulomb.g++.1
+++ b/examples/python/log.4May17.pair_python_coulomb.g++.1
@ -0,0 +1,138 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+units		real
+atom_style	full
+
+read_data	data.spce
+  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  3000 bonds
+  reading angles ...
+  1500 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+
+pair_style	hybrid/overlay coul/cut 12.0 python 12.0
+
+pair_coeff	* * coul/cut
+pair_coeff	* * python py_pot.LJCutSPCE OW NULL
+
+bond_style	harmonic
+angle_style	harmonic
+dihedral_style	none
+improper_style	none
+
+bond_coeff	1 1000.00 1.000
+angle_coeff	1 100.0 109.47
+
+special_bonds   lj/coul 0.0 0.0 1.0
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  2 = max # of special neighbors
+
+neighbor        2.0 bin
+
+fix		1 all shake 0.0001 20 0 b 1 a 1
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  1500 = # of frozen angles
+fix		2 all nvt temp 300.0 300.0 100.0
+
+# create combined lj/coul table for all atom types
+# generate tabulated potential from python variant
+pair_write      1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair coul/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair python, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+pair_write      1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472  0.4236
+pair_write      2 2 2000 rsq 0.1 12 spce.table HW-HW  0.4236  0.4236
+
+# switch to tabulated potential
+pair_style      table linear 2000 pppm
+pair_coeff      1 1 spce.table OW-OW
+pair_coeff      1 2 spce.table OW-HW
+pair_coeff      2 2 spce.table HW-HW
+
+thermo 10
+run 100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 25.08 | 25.08 | 25.08 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -18284.922            0   -18284.922   -2080.7739 
+      10    146.83806   -19552.072            0   -18239.421     -4865.31 
+      20    183.15761   -18706.872            0   -17069.543   -4865.6695 
+      30    205.96203   -18901.541            0   -17060.354   -4454.8634 
+      40    241.62768   -18323.117            0   -16163.099   -3269.1475 
+      50    265.98384   -19883.562            0   -17505.813   -2788.5194 
+      60    274.01897   -21320.575            0   -18870.996   -2387.0708 
+      70     288.7601   -19849.269            0   -17267.913    -1235.818 
+      80    300.64724   -20958.602            0   -18270.981   -1714.7988 
+      90    304.19113     -21580.4            0   -18861.099   -2144.1614 
+     100    304.22027   -21239.014            0   -18519.452   -2092.6759 
+Loop time of 6.01861 on 1 procs for 100 steps with 4500 atoms
+
+Performance: 1.436 ns/day, 16.718 hours/ns, 16.615 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.698      | 5.698      | 5.698      |   0.0 | 94.67
+Bond    | 0.0001626  | 0.0001626  | 0.0001626  |   0.0 |  0.00
+Neigh   | 0.23235    | 0.23235    | 0.23235    |   0.0 |  3.86
+Comm    | 0.018961   | 0.018961   | 0.018961   |   0.0 |  0.32
+Output  | 0.00058126 | 0.00058126 | 0.00058126 |   0.0 |  0.01
+Modify  | 0.063452   | 0.063452   | 0.063452   |   0.0 |  1.05
+Other   |            | 0.005146   |            |       |  0.09
+
+Nlocal:    4500 ave 4500 max 4500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    21285 ave 21285 max 21285 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    2.59766e+06 ave 2.59766e+06 max 2.59766e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2597662
+Ave neighs/atom = 577.258
+Ave special neighs/atom = 2
+Neighbor list builds = 3
+Dangerous builds = 0
+
+shell rm spce.table
+
+Total wall time: 0:00:06
--- a/examples/python/log.4May17.pair_python_coulomb.g++.4
+++ b/examples/python/log.4May17.pair_python_coulomb.g++.4
@ -0,0 +1,138 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+units		real
+atom_style	full
+
+read_data	data.spce
+  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  4500 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  3000 bonds
+  reading angles ...
+  1500 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+
+pair_style	hybrid/overlay coul/cut 12.0 python 12.0
+
+pair_coeff	* * coul/cut
+pair_coeff	* * python py_pot.LJCutSPCE OW NULL
+
+bond_style	harmonic
+angle_style	harmonic
+dihedral_style	none
+improper_style	none
+
+bond_coeff	1 1000.00 1.000
+angle_coeff	1 100.0 109.47
+
+special_bonds   lj/coul 0.0 0.0 1.0
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  2 = max # of special neighbors
+
+neighbor        2.0 bin
+
+fix		1 all shake 0.0001 20 0 b 1 a 1
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  1500 = # of frozen angles
+fix		2 all nvt temp 300.0 300.0 100.0
+
+# create combined lj/coul table for all atom types
+# generate tabulated potential from python variant
+pair_write      1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair coul/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair python, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+pair_write      1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472  0.4236
+pair_write      2 2 2000 rsq 0.1 12 spce.table HW-HW  0.4236  0.4236
+
+# switch to tabulated potential
+pair_style      table linear 2000 pppm
+pair_coeff      1 1 spce.table OW-OW
+pair_coeff      1 2 spce.table OW-HW
+pair_coeff      2 2 spce.table HW-HW
+
+thermo 10
+run 100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 9.962 | 9.963 | 9.963 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -18284.922            0   -18284.922   -2080.7739 
+      10    146.83806   -19552.072            0   -18239.421     -4865.31 
+      20    183.15761   -18706.872            0   -17069.543   -4865.6695 
+      30    205.96203   -18901.541            0   -17060.354   -4454.8634 
+      40    241.62768   -18323.117            0   -16163.099   -3269.1475 
+      50    265.98384   -19883.562            0   -17505.813   -2788.5194 
+      60    274.01897   -21320.575            0   -18870.996   -2387.0708 
+      70     288.7601   -19849.269            0   -17267.913    -1235.818 
+      80    300.64724   -20958.602            0   -18270.981   -1714.7988 
+      90    304.19113     -21580.4            0   -18861.099   -2144.1614 
+     100    304.22027   -21239.014            0   -18519.452   -2092.6759 
+Loop time of 1.7361 on 4 procs for 100 steps with 4500 atoms
+
+Performance: 4.977 ns/day, 4.823 hours/ns, 57.600 timesteps/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.4424     | 1.5149     | 1.6066     |   5.3 | 87.26
+Bond    | 8.9407e-05 | 0.00010258 | 0.00012374 |   0.0 |  0.01
+Neigh   | 0.064205   | 0.064241   | 0.064295   |   0.0 |  3.70
+Comm    | 0.023643   | 0.1155     | 0.18821    |  19.2 |  6.65
+Output  | 0.00038004 | 0.00042355 | 0.00054145 |   0.0 |  0.02
+Modify  | 0.037507   | 0.037787   | 0.038042   |   0.1 |  2.18
+Other   |            | 0.003148   |            |       |  0.18
+
+Nlocal:    1125 ave 1162 max 1098 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost:    12267.8 ave 12302 max 12238 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:    649416 ave 681458 max 630541 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+
+Total # of neighbors = 2597662
+Ave neighs/atom = 577.258
+Ave special neighs/atom = 2
+Neighbor list builds = 3
+Dangerous builds = 0
+
+shell rm spce.table
+
+Total wall time: 0:00:01
--- a/examples/python/log.4May17.pair_python_hybrid.g++.1
+++ b/examples/python/log.4May17.pair_python_hybrid.g++.1
@ -0,0 +1,250 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+# 3d Lennard-Jones hybrid
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 10 0 10 0 10
+create_box	2 box
+Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 4000 atoms
+mass		* 1.0
+region          half block -0.1 4.9 0 10 0 10
+set region half type 2
+  2000 settings made for type
+
+velocity	all create 3.0 87287
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python py_pot.LJCutMelt lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 12 12 12
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair lj/cut, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair python, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            3   -6.7733681            0   -2.2744931   -3.7033504 
+      50    1.6758903   -4.7955425            0   -2.2823355     5.670064 
+     100    1.6458363   -4.7492704            0   -2.2811332    5.8691042 
+     150    1.6324555   -4.7286791            0    -2.280608    5.9589514 
+     200    1.6630725   -4.7750988            0   -2.2811136    5.7364886 
+     250    1.6275257   -4.7224992            0    -2.281821    5.9567365 
+Loop time of 10.0384 on 1 procs for 250 steps with 4000 atoms
+
+Performance: 10758.705 tau/day, 24.904 timesteps/s
+98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.913      | 9.913      | 9.913      |   0.0 | 98.75
+Neigh   | 0.095569   | 0.095569   | 0.095569   |   0.0 |  0.95
+Comm    | 0.012686   | 0.012686   | 0.012686   |   0.0 |  0.13
+Output  | 0.00027537 | 0.00027537 | 0.00027537 |   0.0 |  0.00
+Modify  | 0.01386    | 0.01386    | 0.01386    |   0.0 |  0.14
+Other   |            | 0.003027   |            |       |  0.03
+
+Nlocal:    4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5499 ave 5499 max 5499 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    85978 ave 85978 max 85978 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 85978
+Ave neighs/atom = 21.4945
+Neighbor list builds = 12
+Dangerous builds not checked
+
+write_data      hybrid.data
+write_restart   hybrid.restart
+
+clear
+  using 1 OpenMP thread(s) per MPI task
+
+read_restart    hybrid.restart
+  orthogonal box = (0 0 0) to (16.796 16.796 16.796)
+  1 by 1 by 1 MPI processor grid
+  4000 atoms
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python py_pot.LJCutMelt lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+fix		1 all nve
+
+thermo		50
+run		250
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 12 12 12
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair lj/cut, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair python, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.245 | 4.245 | 4.245 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     250    1.6275257   -4.7224992            0    -2.281821    5.9567365 
+     300     1.645592   -4.7496711            0   -2.2819002    5.8734193 
+     350    1.6514972   -4.7580756            0   -2.2814491     5.810167 
+     400    1.6540555   -4.7622999            0    -2.281837    5.8200413 
+     450    1.6264734   -4.7200865            0   -2.2809863    5.9546991 
+     500    1.6366891   -4.7350979            0   -2.2806781    5.9369284 
+Loop time of 10.0803 on 1 procs for 250 steps with 4000 atoms
+
+Performance: 10713.932 tau/day, 24.801 timesteps/s
+98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.8479     | 9.8479     | 9.8479     |   0.0 | 97.69
+Neigh   | 0.20002    | 0.20002    | 0.20002    |   0.0 |  1.98
+Comm    | 0.01437    | 0.01437    | 0.01437    |   0.0 |  0.14
+Output  | 0.00024033 | 0.00024033 | 0.00024033 |   0.0 |  0.00
+Modify  | 0.013422   | 0.013422   | 0.013422   |   0.0 |  0.13
+Other   |            | 0.004348   |            |       |  0.04
+
+Nlocal:    4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5472 ave 5472 max 5472 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    86930 ave 86930 max 86930 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 86930
+Ave neighs/atom = 21.7325
+Neighbor list builds = 25
+Dangerous builds = 25
+
+clear
+  using 1 OpenMP thread(s) per MPI task
+
+units		lj
+atom_style	atomic
+
+read_data       hybrid.data
+  orthogonal box = (0 0 0) to (16.796 16.796 16.796)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4000 atoms
+  reading velocities ...
+  4000 velocities
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python py_pot.LJCutMelt lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 12 12 12
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair lj/cut, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair python, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.745 | 3.745 | 3.745 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    1.6275257   -4.7224992            0    -2.281821    5.9567365 
+      50    1.6454666   -4.7497515            0   -2.2821686    5.8729175 
+     100    1.6512008   -4.7582693            0   -2.2820874    5.8090548 
+     150    1.6537193   -4.7627023            0   -2.2827434    5.8177704 
+     200    1.6258731   -4.7205017            0   -2.2823017     5.952511 
+     250    1.6370862   -4.7373176            0   -2.2823022     5.925807 
+Loop time of 9.93686 on 1 procs for 250 steps with 4000 atoms
+
+Performance: 10868.626 tau/day, 25.159 timesteps/s
+98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.8119     | 9.8119     | 9.8119     |   0.0 | 98.74
+Neigh   | 0.096041   | 0.096041   | 0.096041   |   0.0 |  0.97
+Comm    | 0.01243    | 0.01243    | 0.01243    |   0.0 |  0.13
+Output  | 0.00028133 | 0.00028133 | 0.00028133 |   0.0 |  0.00
+Modify  | 0.013261   | 0.013261   | 0.013261   |   0.0 |  0.13
+Other   |            | 0.002994   |            |       |  0.03
+
+Nlocal:    4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    5487 ave 5487 max 5487 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    86831 ave 86831 max 86831 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 86831
+Ave neighs/atom = 21.7078
+Neighbor list builds = 12
+Dangerous builds not checked
+
+shell rm hybrid.data hybrid.restart
+Total wall time: 0:00:30
--- a/examples/python/log.4May17.pair_python_hybrid.g++.4
+++ b/examples/python/log.4May17.pair_python_hybrid.g++.4
@ -0,0 +1,250 @@
+LAMMPS (4 May 2017)
+  using 1 OpenMP thread(s) per MPI task
+# 3d Lennard-Jones hybrid
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 10 0 10 0 10
+create_box	2 box
+Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 4000 atoms
+mass		* 1.0
+region          half block -0.1 4.9 0 10 0 10
+set region half type 2
+  2000 settings made for type
+
+velocity	all create 3.0 87287
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python py_pot.LJCutMelt lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 12 12 12
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair lj/cut, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair python, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.953 | 3.953 | 3.953 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            3   -6.7733681            0   -2.2744931   -3.7033504 
+      50    1.6754119   -4.7947589            0   -2.2822693    5.6615925 
+     100    1.6503357    -4.756014            0   -2.2811293    5.8050524 
+     150    1.6596605   -4.7699432            0   -2.2810749    5.7830138 
+     200    1.6371874   -4.7365462            0   -2.2813789    5.9246674 
+     250    1.6323462   -4.7292021            0   -2.2812949    5.9762238 
+Loop time of 2.71748 on 4 procs for 250 steps with 4000 atoms
+
+Performance: 39742.745 tau/day, 91.997 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.4777     | 2.5639     | 2.6253     |   3.9 | 94.35
+Neigh   | 0.024626   | 0.025331   | 0.02598    |   0.3 |  0.93
+Comm    | 0.061933   | 0.12297    | 0.20987    |  18.0 |  4.53
+Output  | 0.00026131 | 0.00027591 | 0.00031352 |   0.0 |  0.01
+Modify  | 0.0036087  | 0.0036573  | 0.0037553  |   0.1 |  0.13
+Other   |            | 0.001337   |            |       |  0.05
+
+Nlocal:    1000 ave 1010 max 982 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+Nghost:    2703.75 ave 2713 max 2689 min
+Histogram: 1 0 0 0 0 0 0 2 0 1
+Neighs:    21469.8 ave 22167 max 20546 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+
+Total # of neighbors = 85879
+Ave neighs/atom = 21.4698
+Neighbor list builds = 12
+Dangerous builds not checked
+
+write_data      hybrid.data
+write_restart   hybrid.restart
+
+clear
+  using 1 OpenMP thread(s) per MPI task
+
+read_restart    hybrid.restart
+  orthogonal box = (0 0 0) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+  4000 atoms
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python py_pot.LJCutMelt lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+fix		1 all nve
+
+thermo		50
+run		250
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 12 12 12
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair lj/cut, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair python, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.612 | 3.612 | 3.612 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     250    1.6323462   -4.7292062            0   -2.2812991    5.9762168 
+     300    1.6451788   -4.7488091            0   -2.2816578    5.8375485 
+     350    1.6171909   -4.7064928            0   -2.2813129    6.0094235 
+     400    1.6388136   -4.7387093            0   -2.2811035    5.9331084 
+     450    1.6431295   -4.7452215            0   -2.2811435    5.8929898 
+     500     1.643316   -4.7454222            0   -2.2810644    5.8454817 
+Loop time of 2.75827 on 4 procs for 250 steps with 4000 atoms
+
+Performance: 39155.038 tau/day, 90.637 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.3631     | 2.5412     | 2.6672     |   7.2 | 92.13
+Neigh   | 0.050358   | 0.052316   | 0.053312   |   0.5 |  1.90
+Comm    | 0.032793   | 0.15893    | 0.33904    |  29.1 |  5.76
+Output  | 0.00018525 | 0.00020212 | 0.00024509 |   0.0 |  0.01
+Modify  | 0.0034482  | 0.0035321  | 0.0036578  |   0.1 |  0.13
+Other   |            | 0.002039   |            |       |  0.07
+
+Nlocal:    1000 ave 1012 max 983 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Nghost:    2699 ave 2706 max 2693 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Neighs:    21802 ave 22700 max 21236 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 87208
+Ave neighs/atom = 21.802
+Neighbor list builds = 25
+Dangerous builds = 25
+
+clear
+  using 1 OpenMP thread(s) per MPI task
+
+units		lj
+atom_style	atomic
+
+read_data       hybrid.data
+  orthogonal box = (0 0 0) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  4000 atoms
+  reading velocities ...
+  4000 velocities
+
+pair_style	hybrid lj/cut 2.5 python 2.5
+pair_coeff	* * python py_pot.LJCutMelt lj NULL
+pair_coeff      * 2 lj/cut 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	every 20 delay 0 check no
+
+fix		1 all nve
+
+thermo		50
+run		250
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 12 12 12
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair lj/cut, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair python, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    1.6323462   -4.7292062            0   -2.2812991    5.9762168 
+      50    1.6450626   -4.7488948            0   -2.2819177    5.8370409 
+     100    1.6169004   -4.7066969            0   -2.2819526    6.0082546 
+     150    1.6384234   -4.7389689            0   -2.2819482    5.9315273 
+     200    1.6428814   -4.7460743            0   -2.2823683    5.8888228 
+     250    1.6432631   -4.7466603            0   -2.2823818    5.8398819 
+Loop time of 2.71936 on 4 procs for 250 steps with 4000 atoms
+
+Performance: 39715.257 tau/day, 91.933 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.3769     | 2.5432     | 2.6447     |   6.6 | 93.52
+Neigh   | 0.024088   | 0.025093   | 0.025748   |   0.4 |  0.92
+Comm    | 0.044614   | 0.14598    | 0.31339    |  27.5 |  5.37
+Output  | 0.00026488 | 0.00028872 | 0.00034189 |   0.0 |  0.01
+Modify  | 0.0034099  | 0.0035709  | 0.0036535  |   0.2 |  0.13
+Other   |            | 0.001215   |            |       |  0.04
+
+Nlocal:    1000 ave 1013 max 989 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:    2695.5 ave 2706 max 2682 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs:    21792 ave 22490 max 21457 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 87168
+Ave neighs/atom = 21.792
+Neighbor list builds = 12
+Dangerous builds not checked
+
+shell rm hybrid.data hybrid.restart
+Total wall time: 0:00:08
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Steve Plimpton	2225fce94e	patch 19May17	2017-05-19 07:35:36 -06:00
sjplimp	941b737319	Merge pull request #493 from akohlmey/doc-and-example-fixes Doc and example fixes	2017-05-18 16:40:46 -06:00
Axel Kohlmeyer	654e09e999	correct input examples affected by the Pair::settings() bugfix	2017-05-18 18:34:27 -04:00
Axel Kohlmeyer	8751850eca	a few formatting fixes for pair style python	2017-05-18 18:34:03 -04:00
sjplimp	0f88348917	Merge pull request #492 from lammps/pre-patch update docs before patch release	2017-05-18 13:44:34 -06:00
Steve Plimpton	b28ecd44c2	update docs before patch release	2017-05-18 13:14:47 -06:00
sjplimp	9db9fc9de3	Merge pull request #491 from akohlmey/fix-bigint-thermo-in-variables-bug convert bigint values for bonds/angles/dihedrals/impropers to doubles	2017-05-18 13:08:42 -06:00
sjplimp	6ac9b7a1b0	Merge pull request #482 from akohlmey/add-pair-python Add python pair style for implementing simple pairwise additive potentials in python	2017-05-18 11:15:58 -06:00
Axel Kohlmeyer	34dbf6b225	do not compute properties twice	2017-05-18 12:45:43 -04:00
Axel Kohlmeyer	26d71b66e4	convert bigint values for bonds/angles/dihedrals/impropers to doubles when evaluating those keywords in variable expressions	2017-05-18 12:41:48 -04:00
Richard Berger	65eacb6b90	Fix compilation warnings in fix_python	2017-05-18 12:20:39 -04:00
sjplimp	cb3344a337	Merge pull request #489 from akohlmey/thread-safe-biasing port thread-safe temperature biasing from LAMMPS-ICMS	2017-05-18 09:15:07 -06:00
sjplimp	5d38cbbce9	Merge pull request #487 from akohlmey/pair_edip_multi_element Import multi-element compatible pair style edip as edip/multi	2017-05-18 09:13:30 -06:00
sjplimp	30babd8157	Merge pull request #485 from akohlmey/pair_settings_cut_bugfix Bugfix for correct resetting of previously set cutoffs to various Pair::settings() functions	2017-05-18 09:12:47 -06:00
sjplimp	aa09f45b7e	Merge pull request #484 from akohlmey/add-gao-weber-styles Add Gao-Weber manybody styles	2017-05-18 09:10:03 -06:00
sjplimp	4b61cf6f52	Merge pull request #483 from akohlmey/airebo-spline-bugfix-refactor AIREBO spline code out-of-bounds and bondorder derivative bugfix and refactor	2017-05-18 09:01:33 -06:00
sjplimp	683f3d9d2a	Merge pull request #481 from akohlmey/collected-small-changes Collected small updates and bugfixes	2017-05-18 09:01:04 -06:00
sjplimp	ce18524251	Merge pull request #480 from akohlmey/pair_morse_smooth_linear_bugfix corrections to pair style morse/smooth/linear	2017-05-18 08:57:24 -06:00
sjplimp	95dae9737b	Merge pull request #488 from lammps/neigh_occasional_bugfix bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species update from Stan	2017-05-18 08:53:54 -06:00
Axel Kohlmeyer	4b1914aa1f	update citations for multi-element edip potential	2017-05-18 01:07:52 -04:00
Axel Kohlmeyer	bd11479a16	lock the sphinx command to version 1.5.6, since version 1.6.x seems to break one of the extensions we use	2017-05-18 00:50:35 -04:00
Axel Kohlmeyer	0208fe9996	update example outputs	2017-05-18 00:46:49 -04:00
Axel Kohlmeyer	24654ad28f	small formatting corrections to pair python style	2017-05-18 00:38:36 -04:00
Axel Kohlmeyer	8d46aa6056	add readme file to discuss various python pair style usage examples	2017-05-18 00:31:54 -04:00
Axel Kohlmeyer	09f3b687f7	new long-rance example with using hybrid/overlay and table only for lj part	2017-05-18 00:31:15 -04:00
Axel Kohlmeyer	436d3fd761	make hybrid example use half the atoms with python, half with lj/cut	2017-05-18 00:30:41 -04:00
Axel Kohlmeyer	9833f38499	change coulomb example to use cutoff coulomb	2017-05-18 00:30:19 -04:00
Axel Kohlmeyer	9725708b90	update pair style python docs	2017-05-18 00:29:02 -04:00
Axel Kohlmeyer	67962b15fc	a bunch refactoring changes in the python pair style and the examples - make all python potential classes derived from LAMMPSPairPotential which contains shared functionality. We currently don't check for supported atom types. may want to add that again later. - keep track of skipped atom types in the C++ code. - add test against units setting. must set self.units='...' in constructor - make compute_force method consistent with Pair::single() in LAMMPS and return force/r instead of force. - rename potentials.py to py_pot.py - update test runs. some small tweaks.	2017-05-17 20:55:48 -04:00
Axel Kohlmeyer	1d48f287f0	add partial documentation for pair style python	2017-05-17 19:05:18 -04:00
Axel Kohlmeyer	43efe9e417	adding Pair::single() support to python pair style and examples with the single function, python pair styles can be massively sped up and made compatible to accelerators, as one can translate the analytic force and energy functions through LAMMPS into suitable tables and then simply use the on-the-fly tables for production runs	2017-05-17 17:20:56 -04:00
Axel Kohlmeyer	278b9f7fba	move pair gw and gw/zbl to USER-MISC package	2017-05-17 14:59:46 -04:00
Axel Kohlmeyer	085f3afdfb	fix typo in docs	2017-05-17 09:59:30 -04:00
Axel Kohlmeyer	45becfb235	correct author attributions	2017-05-17 09:59:01 -04:00
Axel Kohlmeyer	a34c935e20	update log files in python pair style example	2017-05-17 08:00:21 -04:00
Axel Kohlmeyer	13e16dc3f1	update log files for pair style python examples	2017-05-17 07:52:13 -04:00
Axel Kohlmeyer	96f0a82aa5	simplify class names in pair style python examples. add SPC/E water example	2017-05-17 07:48:15 -04:00
Richard Berger	7caf6cf459	Change how a Python pair style is loaded Implements a class loader which takes a fully qualified Python class name, loads the module and creates an object instance. To add flexibility, the current working directory and the directory specified by the LAMMPS_POTENTIALS environment variable are added to the module search path.	2017-05-16 23:29:48 -04:00
Axel Kohlmeyer	8936b99e9f	add contributed SiC.edip potential file	2017-05-16 18:15:53 -04:00
Axel Kohlmeyer	d2810f9f83	port thread-safe temperature biasing from LAMMPS-ICMS	2017-05-16 18:15:13 -04:00
Axel Kohlmeyer	597f95fb1b	fix duplicate reference	2017-05-16 17:53:12 -04:00
Steve Plimpton	7f9a331c73	bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue	2017-05-16 15:51:41 -06:00
Axel Kohlmeyer	35e92733e9	import multi-element compatible pair style edip as edip/multi	2017-05-16 17:40:59 -04:00
Axel Kohlmeyer	c11e87618b	implement second bugfix suggestion from @CF17 on issue #59	2017-05-16 14:18:56 -04:00
Axel Kohlmeyer	ca87e57129	improved version of AIREBO splines based on a suggestion by markus hoehnerbach	2017-05-16 11:58:34 -04:00
Axel Kohlmeyer	66084ad1f4	fix typo in rerun docs. closes #486	2017-05-16 04:27:15 -04:00
Axel Kohlmeyer	d807ba1974	whitespace cleanup	2017-05-16 00:26:39 -04:00
Axel Kohlmeyer	51fc386e72	correct the inner loop range for resetting cutoffs when redefining a pair style this was reported by frank uhlig on lammps-users for lj/cut, but it applies to many more pair styles	2017-05-16 00:26:18 -04:00
Richard Berger	a6f0d700f1	Merge branch 'add-pair-python' of github.com:akohlmey/lammps into add-pair-python	2017-05-15 18:44:52 -04:00
Richard Berger	14f3deed6b	Minor coefficient lookup improvement	2017-05-15 18:43:46 -04:00
Axel Kohlmeyer	d66a696a84	avoid preprocessor warnings, by placing Python.h include file on the top, as suggested by python docs	2017-05-15 18:02:02 -04:00
Richard Berger	69ccbd1562	Extract common wrappers to Python compatibility header	2017-05-15 17:46:57 -04:00
Axel Kohlmeyer	d9d4ef17c8	add gao-weber potentials (regular and with ZBL core) with SiC potential files NOTE: documentation is missing	2017-05-15 17:44:25 -04:00
Richard Berger	93cc6f4a5d	Use in syntax for key lookup for Python 3 compatibility	2017-05-15 17:34:48 -04:00
Axel Kohlmeyer	0a40a7af7b	whitespace cleanup	2017-05-15 17:00:41 -04:00
Axel Kohlmeyer	eb6f6a77e5	dead code removal	2017-05-15 16:16:12 -04:00
Axel Kohlmeyer	fb7164a811	replace pow(x,-0.5) with 1.0/sqrt(x)	2017-05-15 16:16:01 -04:00
Axel Kohlmeyer	64cf52d3b5	address spline out-of-bounds bug reported in issue #59 and refactor high-level spline code for consistency and efficiency	2017-05-15 15:55:15 -04:00
Axel Kohlmeyer	6a1f7e61f2	provide reference output for python pair style inputs	2017-05-15 00:25:11 -04:00
Axel Kohlmeyer	d662f5d429	whitspace cleanup and gitignore update	2017-05-15 00:22:22 -04:00
Axel Kohlmeyer	df55a90ef6	some example input file tweaks	2017-05-15 00:22:03 -04:00
Axel Kohlmeyer	6e113c1eaf	basic feature complete version of lj melt example with python interaction function	2017-05-15 00:15:41 -04:00
Axel Kohlmeyer	f484ab6dfb	completed lj parameter set and compute functions for melt example	2017-05-15 00:14:36 -04:00
Axel Kohlmeyer	86283c6309	make melt input consistent with melt example again	2017-05-15 00:13:32 -04:00
Axel Kohlmeyer	34cc3946b8	first few pieces of pair style python	2017-05-14 18:29:06 -04:00
Axel Kohlmeyer	6aa0250bc5	corrections to pair style morse/smooth/linear contributed by David R. Heine	2017-05-12 23:40:24 -04:00
Axel Kohlmeyer	c5db3ff401	two small doc corrections from Andrew Jewett for pair style gauss and dihedral style spherical	2017-05-12 23:27:58 -04:00
sjplimp	06c151421c	Merge pull request #478 from akohlmey/add-python-source-cmd Add python support features	2017-05-12 13:28:20 -06:00
sjplimp	0008b6fc2d	Merge pull request #477 from lammps/renamings rename some USER/misc dirs	2017-05-12 08:54:12 -06:00
Richard Berger	b6a70ec6fd	fixup docs after last change	2017-05-12 00:34:47 -04:00
Richard Berger	c4d0f07093	Allow fix python to only execute every N steps	2017-05-12 00:29:58 -04:00
Richard Berger	93f6033061	Add documentation about fix python	2017-05-11 23:50:40 -04:00
Richard Berger	110bb79b14	Implement fix python mentioned in issue #454 Allows to call a python function at defined points in the integration loop	2017-05-11 23:50:30 -04:00
Axel Kohlmeyer	d84f8898b7	implement functions to execute arbitrary python code from strings or files and recast the python source keyword through using them.	2017-05-11 22:39:08 -04:00
Axel Kohlmeyer	27a6371f9b	implement a `python source` command as suggested in issue #454	2017-05-11 19:18:09 -04:00
Steve Plimpton	7c3b8e014c	rename some USER/misc dirs	2017-05-11 10:15:28 -06:00
sjplimp	a069d21621	Merge pull request #476 from akohlmey/dump_custom_bugfix dump custom memory allocation bugfix	2017-05-11 09:27:08 -06:00
sjplimp	d7f54464c6	Merge pull request #474 from rbberger/dump_vtk_fixes Various dump vtk fixes	2017-05-11 09:25:42 -06:00
sjplimp	998eb44e83	Merge pull request #473 from akohlmey/compress-for-reaxc-fixes compressed output via gzip for some ReaxFF fixes	2017-05-11 09:25:18 -06:00
sjplimp	96d1de8575	Merge pull request #471 from akohlmey/fix-4may2017-issues Fix a bunch of remaining issues in the 4 may 2017 release	2017-05-11 09:24:35 -06:00
sjplimp	deff6ffaac	Merge pull request #466 from DallasTrinkle/meam-spline-multicomponent Meam spline multicomponent	2017-05-11 09:22:25 -06:00
Axel Kohlmeyer	328ef873d8	fix mixed memory alloc bug in dump custom. this closes #475	2017-05-10 22:41:41 -04:00
Richard Berger	4ecf876a64	Added two examples of using the VTK dump style	2017-05-10 19:52:00 -04:00
Richard Berger	c4ac5773cb	Fix segmentation fault in dump vtk	2017-05-10 19:51:14 -04:00
Richard Berger	cac1bf83ef	Work around VTK 7 API change	2017-05-10 19:41:48 -04:00
Axel Kohlmeyer	abeb1e096a	add support for gzip compressed output to fix reax/bonds, reax/c/bonds and reax/c/species	2017-05-10 11:19:18 -04:00
Axel Kohlmeyer	9f7ce39f9f	correct some more omitted updates	2017-05-09 18:14:34 -04:00
Axel Kohlmeyer	29ae8d4ca3	correct broken links and references in documentation	2017-05-09 17:15:07 -04:00
Axel Kohlmeyer	3f4aee1046	implement overlooked changes from 4may2017 patch	2017-05-09 15:57:35 -04:00
Axel Kohlmeyer	d0da0639f0	add a couple of simple example single/multi-elment inputs for meam/spline pair styles	2017-05-09 15:51:59 -04:00
Axel Kohlmeyer	390ceb1475	whitespace cleanup	2017-05-09 15:49:37 -04:00
Axel Kohlmeyer	6c5edf6c70	performance improvement through avoiding function call and dereference overhead - make i_to_potl() and ij_to_potl() functions inline and const - don't dereference inside the functions, but cache, if possible in external variables => up to 15% speedup.	2017-05-09 15:38:10 -04:00
Axel Kohlmeyer	9cd994f57c	fix issues with potential file parser - use Force::open_potential() - replace ftell()/fseek() with rewind()/fgets() which is safer on windows and other platforms with automatic CR/LF to LF conversion on text files - make parser use properly NULL terminated strings through using strtok()	2017-05-09 15:35:48 -04:00
sjplimp	a6e2d5b5f7	Merge pull request #470 from lammps/integration neighbor list bugfix to prevent cycle in copy lists	2017-05-09 10:32:25 -06:00
Steve Plimpton	08ec55743e	neighbor list bugfix to prevent cycle in copy lists	2017-05-09 08:55:18 -06:00
sjplimp	c4f90b3841	Merge pull request #449 from rbberger/python_refactoring Add Python 3 compatibility and expand Python interface availability	2017-05-08 08:29:24 -06:00
Richard Berger	f8af7edf92	Merge remote-tracking branch 'upstream/master' into python_refactoring	2017-05-06 16:00:22 -04:00
Steve Plimpton	a73402ad93	update src/Purge.list with renamed reaxc src files	2017-05-04 14:53:08 -06:00
Steve Plimpton	d7dbff0f54	jive Kokkos/reaxc file names with new user-reaxc file names	2017-05-04 14:46:59 -06:00
DallasTrinkle	42531389df	Cleanup of style (removing all tabs, shortened long lines).	2017-05-04 15:28:11 -05:00
DallasTrinkle	f7230006fe	OpenMP version added.	2017-05-04 15:08:04 -05:00
DallasTrinkle	754b40cb31	Removed unused functions.	2017-05-04 13:16:46 -05:00
DallasTrinkle	ffdc8b556d	Cleanup.	2017-05-04 13:03:09 -05:00
DallasTrinkle	5accce976a	Cleanup.	2017-05-04 13:02:09 -05:00
DallasTrinkle	349c1443a1	Cleanup.	2017-05-04 13:01:45 -05:00
DallasTrinkle	2f71245d82	Removed extra "helper" functions.	2017-05-04 13:00:06 -05:00
DallasTrinkle	480727815a	Starting to refactor in preparation to contruct OMP version.	2017-05-04 11:27:55 -05:00
DallasTrinkle	45187a0fc7	Fix system header #include style.	2017-05-04 11:05:50 -05:00
DallasTrinkle	7409c6d781	Cleaned up atom->x and atom->f deferences.	2017-05-03 16:56:07 -05:00
DallasTrinkle	11cb0212b7	Cleanup: two space indent + no trailing spaces on lines.	2017-05-03 16:49:43 -05:00
DallasTrinkle	50c7234f26	Fix to communication for mpi. Tested, and now working correctly with MPI.	2017-05-02 09:43:57 -05:00
DallasTrinkle	f58fc9488f	Fixed neighbor list building that caused error in parallel runs with pair_meam_spline.	2017-05-01 21:56:19 -05:00
DallasTrinkle	408cc19885	Fix for seg fault.	2017-05-01 20:36:09 -05:00
DallasTrinkle	c76d27373e	Another fix for seg fault in parallel allocation.	2017-05-01 20:33:07 -05:00
DallasTrinkle	fb08dc09f3	Small error in elements allocation causing seg. fault for parallel runs; fixed.	2017-05-01 13:38:37 -05:00
DallasTrinkle	8bddf105bf	Updated version of equations, documentation.	2017-04-28 20:22:22 -05:00
DallasTrinkle	31446e35b9	Cleanup on equations; JPG to be constructed.	2017-04-28 15:31:49 -05:00
DallasTrinkle	9bdc43bb66	Updates to pair/meam/spline documentation.	2017-04-28 15:15:21 -05:00
DallasTrinkle	a0b61d17b5	Updates to documentation: equation.	2017-04-28 15:08:59 -05:00
DallasTrinkle	8cc8441367	Cleanup on pair_meam_spline.cpp	2017-04-28 14:53:25 -05:00
DallasTrinkle	7d9670bc6c	Addition of potential, code modifications to incorporate multicomponent spline MEAM in pair_meam_spline. Backwards compatible with previous version of pair_meam_spline.	2017-04-28 14:48:34 -05:00
Axel Kohlmeyer	2e1f8b4aef	make Python::init() method public and remove the now redundant Python::request() method	2017-04-25 10:21:02 -04:00
Giacomo Fiorin	958f05a6f3	Allow requesting Python interpreter without having to define a function just for that	2017-04-25 01:09:05 -04:00
Axel Kohlmeyer	c9bc141335	remove doc text explaining restrictions that are lifted with the changes in this branch	2017-04-14 12:57:35 -04:00
Axel Kohlmeyer	3cbf4f3b58	correct logic bug in else branch of the conditional	2017-04-14 11:57:53 -04:00
Axel Kohlmeyer	6c2dd7ebb1	pass the name of the python interpreter compatible with the python package to 'make install-python'	2017-04-14 11:44:36 -04:00
Axel Kohlmeyer	d3187b22c4	restore lost change to PYTHON/Install.sh	2017-04-13 18:11:57 -04:00
Richard Berger	e6f30ebc9c	Merge remote-tracking branch 'origin/master' into python_refactoring	2017-04-12 20:26:57 -04:00
Richard Berger	3fa9f0a27b	Delete python_wrapper.h	2017-04-11 21:51:21 -04:00
Richard Berger	05d7bc556f	Initialize Python interpreter in PythonImpl constructor	2017-04-11 21:46:33 -04:00
Richard Berger	2d8bce78a6	Refactor PYTHON package and wrapper classes	2017-04-11 21:22:30 -04:00
Richard Berger	9a027a01da	Add Python 3 compatibility to PYTHON package	2017-04-11 20:24:42 -04:00