patch 17Jan18

Small character corrections to the file Developer.dox.lammps

cmake/CMakeLists.txt

@@ -198,14 +198,13 @@ if(ENABLE_PYTHON)
   add_definitions(-DLMP_PYTHON)
   include_directories(${PYTHON_INCLUDE_DIR})
   list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
-  if(NOT PYTHON_INSTDIR)
-    execute_process(COMMAND ${PYTHON_EXECUTABLE}
-	  -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
-      OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
-  endif()
-  install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
-  if(NOT BUILD_SHARED_LIBS)
-    message(FATAL_ERROR "Python package need lammps to be build shared, use -DBUILD_SHARED_LIBS=ON")
+  if(BUILD_SHARED_LIBS)
+    if(NOT PYTHON_INSTDIR)
+      execute_process(COMMAND ${PYTHON_EXECUTABLE}
+        -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
+        OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
+    endif()
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
   endif()
 endif()
 
@@ -401,6 +400,10 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
       target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
     elseif(PKG_LIB STREQUAL h5md)
       target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
+    elseif(PKG_LIB STREQUAL colvars)
+      target_compile_options(colvars PRIVATE -DLEPTON)
+      target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)
+      target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
     else()
       target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
     endif()
@@ -480,6 +483,8 @@ if(ENABLE_KOKKOS)
                          ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
   set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
@@ -487,6 +492,17 @@ if(ENABLE_KOKKOS)
   # detects styles which have KOKKOS version
   RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
 
+  # register kokkos-only styles
+  RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
+
+  if(ENABLE_USER-DPD)
+    get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
+    RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
+    set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+  endif()
+
   get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
 
   list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})

cmake/Modules/StyleHeaderUtils.cmake

@@ -11,6 +11,12 @@ function(FindStyleHeaders path style_class file_pattern headers)
     set_property(GLOBAL PROPERTY ${headers} "${hlist}")
 endfunction(FindStyleHeaders)
 
+function(AddStyleHeader path headers)
+    get_property(hlist GLOBAL PROPERTY ${headers})
+    list(APPEND hlist ${path})
+    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
+endfunction(AddStyleHeader)
+
 function(FindStyleHeadersExt path style_class extension headers sources)
     get_property(hlist GLOBAL PROPERTY ${headers})
     get_property(slist GLOBAL PROPERTY ${sources})
@@ -62,6 +68,22 @@ function(GenerateStyleHeader path property style)
     CreateStyleHeader("${path}" "style_${style}.h" ${files})
 endfunction(GenerateStyleHeader)
 
+function(RegisterNBinStyles search_path)
+    FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
+endfunction(RegisterNBinStyles)
+
+function(RegisterNPairStyles search_path)
+    FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor
+endfunction(RegisterNPairStyles)
+
+function(RegisterNBinStyle path)
+    AddStyleHeader(${path} NBIN)
+endfunction(RegisterNBinStyle)
+
+function(RegisterNPairStyle path)
+    AddStyleHeader(${path} NPAIR)
+endfunction(RegisterNPairStyle)
+
 function(RegisterStyles search_path)
     FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
     FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid

doc/Makefile

@@ -20,6 +20,7 @@ ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
 HAS_VIRTUALENV = YES
 endif
 
+SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
@@ -55,7 +56,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
-		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		echo "############################################" ;\
 		doc_anchor_check src/*.txt ;\
 		echo "############################################" ;\
@@ -91,7 +92,7 @@ epub: $(OBJECTS)
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
-		sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		deactivate ;\
 	)
 	@mv  epub/LAMMPS.epub .
@@ -159,7 +160,7 @@ $(VENV):
 	@( \
 		virtualenv -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install Sphinx==1.5.6; \
+		pip install Sphinx; \
 		pip install sphinxcontrib-images; \
 		deactivate;\
 	)

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="23 Oct 2017 version">
+<META NAME="docnumber" CONTENT="17 Jan 2018 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
-23 Oct 2017 version :c,h4
+17 Jan 2018 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -619,8 +619,9 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "pour"_fix_pour.html,
 "press/berendsen"_fix_press_berendsen.html,
 "print"_fix_print.html,
-"property/atom"_fix_property_atom.html,
-"python"_fix_python.html,
+"property/atom (k)"_fix_property_atom.html,
+"python/invoke"_fix_python_invoke.html,
+"python/move"_fix_python_move.html,
 "qeq/comb (o)"_fix_qeq_comb.html,
 "qeq/dynamic"_fix_qeq.html,
 "qeq/fire"_fix_qeq.html,
@@ -637,10 +638,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph (o)"_fix_rigid.html,
-"rigid/small/npt (o)"_fix_rigid.html,
-"rigid/small/nve (o)"_fix_rigid.html,
-"rigid/small/nvt (o)"_fix_rigid.html,
+"rigid/small/nph"_fix_rigid.html,
+"rigid/small/npt"_fix_rigid.html,
+"rigid/small/nve"_fix_rigid.html,
+"rigid/small/nvt"_fix_rigid.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "spring"_fix_spring.html,
@@ -668,7 +669,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,
 "wall/lj126"_fix_wall.html,
-"wall/lj93"_fix_wall.html,
+"wall/lj93 (k)"_fix_wall.html,
 "wall/piston"_fix_wall_piston.html,
 "wall/reflect (k)"_fix_wall_reflect.html,
 "wall/region"_fix_wall_region.html,
@@ -683,14 +684,14 @@ package"_Section_start.html#start_3.
 "atc"_fix_atc.html,
 "ave/correlate/long"_fix_ave_correlate_long.html,
 "colvars"_fix_colvars.html,
-"dpd/energy"_fix_dpd_energy.html,
+"dpd/energy (k)"_fix_dpd_energy.html,
 "drude"_fix_drude.html,
 "drude/transform/direct"_fix_drude_transform.html,
 "drude/transform/reverse"_fix_drude_transform.html,
 "edpd/source"_fix_dpd_source.html,
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
-"eos/table/rx"_fix_eos_table_rx.html,
+"eos/table/rx (k)"_fix_eos_table_rx.html,
 "filter/corotate"_fix_filter_corotate.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
@@ -728,12 +729,12 @@ package"_Section_start.html#start_3.
 "qeq/reax (ko)"_fix_qeq_reax.html,
 "qmmm"_fix_qmmm.html,
 "qtb"_fix_qtb.html,
-"reax/c/bonds"_fix_reax_bonds.html,
-"reax/c/species"_fix_reaxc_species.html,
+"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/species (k)"_fix_reaxc_species.html,
 "rhok"_fix_rhok.html,
-"rx"_fix_rx.html,
+"rx (k)"_fix_rx.html,
 "saed/vtk"_fix_saed_vtk.html,
-"shardlow"_fix_shardlow.html,
+"shardlow (k)"_fix_shardlow.html,
 "smd"_fix_smd.html,
 "smd/adjust/dt"_fix_smd_adjust_dt.html,
 "smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
@@ -906,7 +907,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "none"_pair_none.html,
 "zero"_pair_zero.html,
 "hybrid"_pair_hybrid.html,
-"hybrid/overlay"_pair_hybrid.html,
+"hybrid/overlay (k)"_pair_hybrid.html,
 "adp (o)"_pair_adp.html,
 "airebo (oi)"_pair_airebo.html,
 "airebo/morse (oi)"_pair_airebo.html,
@@ -1023,9 +1024,9 @@ KOKKOS, o = USER-OMP, t = OPT.
 "tri/lj"_pair_tri_lj.html,
 "vashishta (ko)"_pair_vashishta.html,
 "vashishta/table (o)"_pair_vashishta.html,
-"yukawa (go)"_pair_yukawa.html,
+"yukawa (gok)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (go)"_pair_zbl.html :tb(c=4,ea=c)
+"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
 
 These are additional pair styles in USER packages, which can be used
 if "LAMMPS is built with the appropriate
@@ -1038,13 +1039,14 @@ package"_Section_start.html#start_3.
 "coul/diel (o)"_pair_coul_diel.html,
 "coul/long/soft (o)"_pair_lj_soft.html,
 "dpd/fdt"_pair_dpd_fdt.html,
-"dpd/fdt/energy"_pair_dpd_fdt.html,
+"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
 "eam/cd (o)"_pair_eam.html,
 "edip (o)"_pair_edip.html,
 "edip/multi"_pair_edip.html,
 "edpd"_pair_meso.html,
 "eff/cut"_pair_eff.html,
-"exp6/rx"_pair_exp6_rx.html,
+"exp6/rx (k)"_pair_exp6_rx.html,
+"extep"_pair_extep.html,
 "gauss/cut"_pair_gauss.html,
 "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "lennard/mdf"_pair_mdf.html,
@@ -1070,7 +1072,7 @@ package"_Section_start.html#start_3.
 "morse/smooth/linear"_pair_morse.html,
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
-"multi/lucy/rx"_pair_multi_lucy_rx.html,
+"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
 "oxdna/coaxstk"_pair_oxdna.html,
 "oxdna/excv"_pair_oxdna.html,
 "oxdna/hbond"_pair_oxdna.html,
@@ -1087,6 +1089,7 @@ package"_Section_start.html#start_3.
 "smd/triangulated/surface"_pair_smd_triangulated_surface.html,
 "smd/ulsph"_pair_smd_ulsph.html,
 "smtbq"_pair_smtbq.html,
+"snap (k)"_pair_snap.html,
 "sph/heatconduction"_pair_sph_heatconduction.html,
 "sph/idealgas"_pair_sph_idealgas.html,
 "sph/lj"_pair_sph_lj.html,
@@ -1094,7 +1097,7 @@ package"_Section_start.html#start_3.
 "sph/taitwater"_pair_sph_taitwater.html,
 "sph/taitwater/morris"_pair_sph_taitwater_morris.html,
 "srp"_pair_srp.html,
-"table/rx"_pair_table_rx.html,
+"table/rx (k)"_pair_table_rx.html,
 "tdpd"_pair_meso.html,
 "tersoff/table (o)"_pair_tersoff.html,
 "thole"_pair_thole.html,
@@ -1249,7 +1252,7 @@ USER-OMP, t = OPT.
 "ewald/disp"_kspace_style.html,
 "msm (o)"_kspace_style.html,
 "msm/cg (o)"_kspace_style.html,
-"pppm (go)"_kspace_style.html,
+"pppm (gok)"_kspace_style.html,
 "pppm/cg (o)"_kspace_style.html,
 "pppm/disp (i)"_kspace_style.html,
 "pppm/disp/tip4p"_kspace_style.html,

doc/src/Section_howto.txt

@@ -454,7 +454,7 @@ NOTE: By default, for 2d systems, granular particles are still modeled
 as 3d spheres, not 2d discs (circles), meaning their moment of inertia
 will be the same as in 3d.  If you wish to model granular particles in
 2d as 2d discs, see the note on this topic in "Section
-6.2"_Section_howto.html#howto_2, where 2d simulations are disussed.
+6.2"_Section_howto.html#howto_2, where 2d simulations are discussed.
 
 :line
 

doc/src/Section_packages.txt

@@ -243,7 +243,7 @@ COLLOID package :link(COLLOID),h4
 
 [Contents:]
 
-Coarse-grained finite-size colloidal particles.  Pair stayle and fix
+Coarse-grained finite-size colloidal particles.  Pair styles and fix
 wall styles for colloidal interactions.  Includes the Fast Lubrication
 Dynamics (FLD) method for hydrodynamic interactions, which is a
 simplified approximation to Stokesian dynamics.
@@ -732,9 +732,9 @@ make lib-latte args="-b -m gfortran"    # download and build in lib/latte and
 :pre
 
 Note that 3 symbolic (soft) links, "includelink" and "liblink" and
-"filelink", are created in lib/latte to point into the LATTE home dir.
+"filelink.o", are created in lib/latte to point into the LATTE home dir.
 When LAMMPS builds in src it will use these links.  You should 
-also check that the Makefile.lammps file you create is apporpriate
+also check that the Makefile.lammps file you create is appropriate
 for the compiler you use on your system to build LATTE.
 
 You can then install/un-install the package and build LAMMPS in the
@@ -984,7 +984,7 @@ 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
+Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
 library"_mscg_home.
 
 :link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
@@ -1781,7 +1781,7 @@ coarse-grained DPD-based models for energetic, reactive molecular
 crystalline materials.  It includes many pair styles specific to these
 systems, including for reactive DPD, where each particle has internal
 state for multiple species and a coupled set of chemical reaction ODEs
-are integrated each timestep.  Highly accurate time intergrators for
+are integrated each timestep.  Highly accurate time integrators for
 isothermal, isoenergetic, isobaric and isenthalpic conditions are
 included.  These enable long timesteps via the Shardlow splitting
 algorithm.
@@ -2231,7 +2231,7 @@ Several extensions of the the dissipative particle dynamics (DPD)
 method.  Specifically, energy-conserving DPD (eDPD) that can model
 non-isothermal processes, many-body DPD (mDPD) for simulating
 vapor-liquid coexistence, and transport DPD (tDPD) for modeling
-advection-diffuion-reaction systems. The equations of motion of these
+advection-diffusion-reaction systems. The equations of motion of these
 DPD extensions are integrated through a modified velocity-Verlet (MVV)
 algorithm.
 
@@ -2495,7 +2495,7 @@ make machine :pre
 
 NOTE: The LAMMPS executable these steps produce is not yet functional
 for a QM/MM simulation.  You must also build Quantum ESPRESSO and
-create a new executable which links LAMMPS and Quanutm ESPRESSO
+create a new executable which links LAMMPS and Quantum ESPRESSO
 together.  These are steps 3 and 4 described in the lib/qmmm/README
 file.
 
@@ -2554,7 +2554,7 @@ developed by the Cambridge University group.
 
 :link(quip,https://github.com/libAtoms/QUIP)
 
-To use this package you must have the QUIP libAatoms library available
+To use this package you must have the QUIP libAtoms library available
 on your system.
 
 [Author:] Albert Bartok (Cambridge University)
@@ -2809,7 +2809,7 @@ USER-VTK package :link(USER-VTK),h4
 
 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.
+other visualization packages.
 
 :link(vtk,http://www.vtk.org)
 :link(paraview,http://www.paraview.org)

doc/src/Section_python.txt

@@ -123,7 +123,7 @@ code directly from an input script:
 
 "python"_python.html
 "variable python"_variable.html
-"fix python"_fix_python.html
+"fix python/invoke"_fix_python_invoke.html
 "pair_style python"_pair_python.html :ul
 
 The "python"_python.html command which can be used to define and
@@ -165,7 +165,7 @@ 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.
 
-The "fix python"_fix_python.html command can execute
+The "fix python/invoke"_fix_python_invoke.html command can execute
 Python code at selected timesteps during a simulation run.
 
 The "pair_style python"_pair_python command allows you to define

doc/src/Section_start.txt

@@ -79,7 +79,7 @@ This section has the following sub-sections:
 
 Read this first :h5,link(start_2_1)
 
-If you want to avoid building LAMMPS yourself, read the preceeding
+If you want to avoid building LAMMPS yourself, read the preceding
 section about options available for downloading and installing
 executables.  Details are discussed on the "download"_download page.
 
@@ -252,7 +252,7 @@ re-compile, after typing "make clean" (which will describe different
 clean options).
 
 The LMP_INC variable is used to include options that turn on ifdefs
-within the LAMMPS code.  The options that are currently recogized are:
+within the LAMMPS code.  The options that are currently recognized are:
 
 -DLAMMPS_GZIP
 -DLAMMPS_JPEG
@@ -363,7 +363,7 @@ installed on your platform.  If MPI is installed on your system in the
 usual place (under /usr/local), you also may not need to specify these
 3 variables, assuming /usr/local is in your path.  On some large
 parallel machines which use "modules" for their compile/link
-environements, you may simply need to include the correct module in
+environments, you may simply need to include the correct module in
 your build environment, before building LAMMPS.  Or the parallel
 machine may have a vendor-provided MPI which the compiler has no
 trouble finding.
@@ -431,7 +431,7 @@ use the KISS library described above.
 You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
 so the compiler and linker can find the needed FFT header and library
 files.  Note that on some large parallel machines which use "modules"
-for their compile/link environements, you may simply need to include
+for their compile/link environments, you may simply need to include
 the correct module in your build environment.  Or the parallel machine
 may have a vendor-provided FFT library which the compiler has no
 trouble finding.  See the src/MAKE/OPTIONS/Makefile.fftw file for an
@@ -470,7 +470,7 @@ precision.
 
 The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
 use single-precision FFTs with PPPM, which can speed-up long-range
-calulations, particularly in parallel or on GPUs.  Fourier transform
+calculations, particularly in parallel or on GPUs.  Fourier transform
 and related PPPM operations are somewhat insensitive to floating point
 truncation errors and thus do not always need to be performed in
 double precision.  Using the -DFFT_SINGLE setting trades off a little
@@ -483,7 +483,7 @@ with support for single-precision, as explained above.  For FFTW3 you
 also need to include -lfftw3f with the FFT_LIB setting, in addition to
 -lfftw3.  For FFTW2, you also need to specify -DFFT_SIZE with the
 FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of
--lfftw).  Similarly, if FFTW2 has been preinstalled with an explicit
+-lfftw).  Similarly, if FFTW2 has been pre-installed with an explicit
 double-precision library (libdfftw.a and not the default libfftw.a),
 then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify
 -ldfftw to use double-precision FFTs.
@@ -714,7 +714,7 @@ list various make commands that can be used to manage packages.
 If you use a command in a LAMMPS input script that is part of a
 package, you must have built LAMMPS with that package, else you will
 get an error that the style is invalid or the command is unknown.
-Every command's doc page specfies if it is part of a package.  You can
+Every command's doc page specifies if it is part of a package.  You can
 type
 
 lmp_machine -h :pre
@@ -859,7 +859,7 @@ details for each package.
 [External libraries:]
 
 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
+in the last column link to external 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"_voro_home2.  You
@@ -963,7 +963,7 @@ src/MAKE/Makefile.foo and perform the build in the directory
 Obj_shared_foo.  This is so that each file can be compiled with the
 -fPIC flag which is required for inclusion in a shared library.  The
 build will create the file liblammps_foo.so which another application
-can link to dyamically.  It will also create a soft link liblammps.so,
+can link to dynamically.  It will also create a soft link liblammps.so,
 which will point to the most recently built shared library.  This is
 the file the Python wrapper loads by default.
 
@@ -1329,8 +1329,8 @@ LAMMPS is compiled with CUDA=yes.
 numa Nm :pre
 
 This option is only relevant when using pthreads with hwloc support.
-In this case Nm defines the number of NUMA regions (typicaly sockets)
-on a node which will be utilizied by a single MPI rank.  By default Nm
+In this case Nm defines the number of NUMA regions (typically sockets)
+on a node which will be utilized by a single MPI rank.  By default Nm
 = 1.  If this option is used the total number of worker-threads per
 MPI rank is threads*numa.  Currently it is always almost better to
 assign at least one MPI rank per NUMA region, and leave numa set to
@@ -1394,7 +1394,7 @@ replica runs on on one or a few processors.  Note that with MPI
 installed on a machine (e.g. your desktop), you can run on more
 (virtual) processors than you have physical processors.
 
-To run multiple independent simulatoins from one input script, using
+To run multiple independent simulations from one input script, using
 multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
 of the manual.  World- and universe-style "variables"_variable.html
 are useful in this context.
@@ -1673,7 +1673,7 @@ The first section provides a global loop timing summary. The {loop time}
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
 continuations required and for comparing performance with other,
-similar MD codes.  The {CPU use} line provides the CPU utilzation per
+similar MD codes.  The {CPU use} line provides the CPU utilization per
 MPI task; it should be close to 100% times the number of OpenMP
 threads (or 1 of no OpenMP). Lower numbers correspond to delays due
 to file I/O or insufficient thread utilization.

doc/src/Section_tools.txt

@@ -48,6 +48,7 @@ own sub-directories with their own Makefiles and/or README files.
 "chain"_#chain
 "colvars"_#colvars
 "createatoms"_#createatoms
+"doxygen"_#doxygen
 "drude"_#drude
 "eam database"_#eamdb
 "eam generate"_#eamgn
@@ -172,6 +173,18 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
 
 :line
 
+doxygen tool :h4,link(doxygen)
+
+The tools/doxygen directory contains a shell script called
+doxygen.sh which can generate a call graph and API lists using
+the Doxygen_http://doxygen.org software.
+
+See the included README file for details.
+
+The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
+
+:line
+
 drude tool :h4,link(drude)
 
 The tools/drude directory contains a Python script called

doc/src/accelerate_intel.txt

@@ -78,7 +78,7 @@ order of operations compared to LAMMPS without acceleration:
 Neighbor lists can be created in a different order :ulb,l
 Bins used for sorting atoms can be oriented differently :l
 The default stencil order for PPPM is 7. By default, LAMMPS will
-calculate other PPPM parameters to fit the desired acuracy with
+calculate other PPPM parameters to fit the desired accuracy with
 this order :l
 The {newton} setting applies to all atoms, not just atoms shared
 between MPI tasks :l

doc/src/accelerate_kokkos.txt

@@ -11,336 +11,346 @@
 
 5.3.3 KOKKOS package :h5
 
-The KOKKOS package was developed primarily by Christian Trott (Sandia)
-with contributions of various styles by others, including Sikandar
-Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia).  The
-underlying Kokkos library was written primarily by Carter Edwards,
+Kokkos is a templated C++ library that provides abstractions to allow
+a single implementation of an application kernel (e.g. a pair style) to run efficiently on
+different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core
+CPUs. Kokkos maps the C++ kernel onto different backend languages such as CUDA, OpenMP, or Pthreads.
+The Kokkos library also provides data abstractions to adjust (at
+compile time) the memory layout of data structures like 2d and
+3d arrays to optimize performance on different hardware. For more information on Kokkos, see
+"Github"_https://github.com/kokkos/kokkos. Kokkos is part of
+"Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards,
 Christian Trott, and Dan Sunderland (all Sandia).
 
-The KOKKOS package contains versions of pair, fix, and atom styles
+The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles
 that use data structures and macros provided by the Kokkos library,
-which is included with LAMMPS in lib/kokkos.
-
-The Kokkos library is part of
-"Trilinos"_http://trilinos.sandia.gov/packages/kokkos and can also be
-downloaded from "Github"_https://github.com/kokkos/kokkos. Kokkos is a
-templated C++ library that provides two key abstractions for an
-application like LAMMPS.  First, it allows a single implementation of
-an application kernel (e.g. a pair style) to run efficiently on
-different kinds of hardware, such as a GPU, Intel Phi, or many-core
-CPU.
-
-The Kokkos library also provides data abstractions to adjust (at
-compile time) the memory layout of basic data structures like 2d and
-3d arrays and allow the transparent utilization of special hardware
-load and store operations.  Such data structures are used in LAMMPS to
-store atom coordinates or forces or neighbor lists.  The layout is
-chosen to optimize performance on different platforms.  Again this
-functionality is hidden from the developer, and does not affect how
-the kernel is coded.
-
-These abstractions are set at build time, when LAMMPS is compiled with
-the KOKKOS package installed.  All Kokkos operations occur within the
-context of an individual MPI task running on a single node of the
-machine.  The total number of MPI tasks used by LAMMPS (one or
-multiple per compute node) is set in the usual manner via the mpirun
-or mpiexec commands, and is independent of Kokkos.
+which is included with LAMMPS in /lib/kokkos. The KOKKOS package was developed primarily by Christian Trott (Sandia)
+and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar
+Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions
+see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf.
 
 Kokkos currently provides support for 3 modes of execution (per MPI
-task).  These are OpenMP (for many-core CPUs), Cuda (for NVIDIA GPUs),
-and OpenMP (for Intel Phi).  Note that the KOKKOS package supports
-running on the Phi in native mode, not offload mode like the
-USER-INTEL package supports.  You choose the mode at build time to
+task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP (threading
+for many-core CPUs and Intel Phi), and CUDA (for NVIDIA GPUs). You choose the mode at build time to
 produce an executable compatible with specific hardware.
 
-Here is a quick overview of how to use the KOKKOS package
-for CPU acceleration, assuming one or more 16-core nodes.
-More details follow.
-
-use a C++11 compatible compiler
-make yes-kokkos
-make mpi KOKKOS_DEVICES=OpenMP                 # build with the KOKKOS package
-make kokkos_omp                                # or Makefile.kokkos_omp already has variable set :pre
-
-mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
-mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
-mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj           # 1 node, 2 MPI tasks/node, 8 threads/task
-mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj   # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
-
-specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
-include the KOKKOS package and build LAMMPS
-enable the KOKKOS package and its hardware options via the "-k on" command-line switch use KOKKOS styles in your input script :ul
-
-Here is a quick overview of how to use the KOKKOS package for GPUs,
-assuming one or more nodes, each with 16 cores and a GPU.  More
-details follow.
-
-discuss use of NVCC, which Makefiles to examine
-
-use a C++11 compatible compiler
-KOKKOS_DEVICES = Cuda, OpenMP
-KOKKOS_ARCH = Kepler35
-make yes-kokkos
-make machine :pre
-
-mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj          # one MPI task, 6 threads on CPU
-mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj   # ditto on 4 nodes :pre
-
-mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj           # two MPI tasks, 8 threads per CPU
-mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj   # ditto on 16 nodes :pre
-
-Here is a quick overview of how to use the KOKKOS package
-for the Intel Phi:
-
-use a C++11 compatible compiler
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNC
-make yes-kokkos
-make machine :pre
-
-host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
-mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj           # 1 MPI task on 1 Phi, 1*240 = 240
-mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj            # 30 MPI tasks on 1 Phi, 30*8 = 240
-mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj           # 12 MPI tasks on 1 Phi, 12*20 = 240
-mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis :pre
-
-[Required hardware/software:]
-
-Kokkos support within LAMMPS must be built with a C++11 compatible
-compiler.  If using gcc, version 4.7.2 or later is required.
-
-To build with Kokkos support for CPUs, your compiler must support the
-OpenMP interface.  You should have one or more multi-core CPUs so that
-multiple threads can be launched by each MPI task running on a CPU.
-
-To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
-version 7.5 or later must be installed on your system.  See the
-discussion for the "GPU"_accelerate_gpu.html package for details of
-how to check and do this.
-
-NOTE: For good performance of the KOKKOS package on GPUs, you must
-have Kepler generation GPUs (or later).  The Kokkos library exploits
-texture cache options not supported by Telsa generation GPUs (or
-older).
-
-To build with Kokkos support for Intel Xeon Phi coprocessors, your
-sysmte must be configured to use them in "native" mode, not "offload"
-mode like the USER-INTEL package supports.
-
 [Building LAMMPS with the KOKKOS package:]
 
-You must choose at build time whether to build for CPUs (OpenMP),
-GPUs, or Phi.
+NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible
+compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
+Clang 3.5.2 or later is required.
 
-You can do any of these in one line, using the suitable make command
-line flags as described in "Section 4"_Section_packages.html of the
-manual. If run from the src directory, these
-commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda_mpi, and
-lmp_kokkos_phi.  Note that the OMP and PHI options use
-src/MAKE/Makefile.mpi as the starting Makefile.machine.  The CUDA
-option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi.
+The recommended method of building the KOKKOS package is to start with the provided Kokkos
+Makefiles in /src/MAKE/OPTIONS/. You may need to modify the KOKKOS_ARCH variable in the Makefile
+to match your specific hardware. For example:
 
-The latter two steps can be done using the "-k on", "-pk kokkos" and
-"-sf kk" "command-line switches"_Section_start.html#start_6
-respectively.  Or the effect of the "-pk" or "-sf" switches can be
-duplicated by adding the "package kokkos"_package.html or "suffix
-kk"_suffix.html commands respectively to your input script.
+for Sandy Bridge CPUs, set KOKKOS_ARCH=SNB
+for Broadwell CPUs, set KOKKOS_ARCH=BWD
+for K80 GPUs, set KOKKOS_ARCH=Kepler37
+for P100 GPUs and Power8 CPUs, set KOKKOS_ARCH=Pascal60,Power8 :ul
 
+See the [Advanced Kokkos Options] section below for a listing of all KOKKOS_ARCH options.
 
-Or you can follow these steps:
+[Compile for CPU-only (MPI only, no threading):]
 
-CPU-only (run all-MPI or with OpenMP threading):
-
-cd lammps/src
-make yes-kokkos
-make kokkos_omp :pre
-
-CPU-only (only MPI, no threading):
+use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+/src/MAKE/OPTIONS/Makefile.kokkos_mpi_only as described above. Then do the
+following:
 
 cd lammps/src
 make yes-kokkos
 make kokkos_mpi_only :pre
 
-Intel Xeon Phi (Intel Compiler, Intel MPI):
+[Compile for CPU-only (MPI plus OpenMP threading):]
+
+NOTE: To build with Kokkos support for OpenMP threading, your compiler must support the
+OpenMP interface. You should have one or more multi-core CPUs so that
+multiple threads can be launched by each MPI task running on a CPU.
+
+use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+/src/MAKE/OPTIONS/Makefile.kokkos_omp as described above.  Then do the
+following:
+
+cd lammps/src
+make yes-kokkos
+make kokkos_omp :pre
+
+[Compile for Intel KNL Xeon Phi (Intel Compiler, OpenMPI):]
+
+use a C++11 compatible compiler and do the following:
 
 cd lammps/src
 make yes-kokkos
 make kokkos_phi :pre
 
-CPUs and GPUs (with MPICH or OpenMPI):
+[Compile for CPUs and GPUs (with OpenMPI or MPICH):]
+
+NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
+version 7.5 or later must be installed on your system. See the
+discussion for the "GPU"_accelerate_gpu.html package for details of
+how to check and do this.
+
+use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described
+above.  Then do the following:
 
 cd lammps/src
 make yes-kokkos
 make kokkos_cuda_mpi :pre
 
-These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
-make command line which requires a GNU-compatible make command.  Try
+[Alternative Methods of Compiling:]
+
+Alternatively, the KOKKOS package can be built by specifying Kokkos variables
+on the make command line. For example:
+
+make mpi KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=SNB     # set the KOKKOS_DEVICES and KOKKOS_ARCH variable explicitly
+make kokkos_cuda_mpi KOKKOS_ARCH=Pascal60,Power8   # set the KOKKOS_ARCH variable explicitly :pre
+
+Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the
+make command line requires a GNU-compatible make command. Try
 "gmake" if your system's standard make complains.
 
 NOTE: If you build using make line variables and re-build LAMMPS twice
-with different KOKKOS options and the *same* target, e.g. g++ in the
-first two examples above, then you *must* perform a "make clean-all"
-or "make clean-machine" before each build.  This is to force all the
+with different KOKKOS options and the *same* target, then you *must* perform a "make clean-all"
+or "make clean-machine" before each build. This is to force all the
 KOKKOS-dependent files to be re-compiled with the new options.
 
-NOTE: Currently, there are no precision options with the KOKKOS
-package.  All compilation and computation is performed in double
-precision.
+[Running LAMMPS with the KOKKOS package:]
 
-There are other allowed options when building with the KOKKOS package.
-As above, they can be set either as variables on the make command line
-or in Makefile.machine.  This is the full list of options, including
-those discussed above, Each takes a value shown below.  The
-default value is listed, which is set in the
-lib/kokkos/Makefile.kokkos file.
+All Kokkos operations occur within the
+context of an individual MPI task running on a single node of the
+machine. The total number of MPI tasks used by LAMMPS (one or
+multiple per compute node) is set in the usual manner via the mpirun
+or mpiexec commands, and is independent of Kokkos. E.g. the mpirun
+command in OpenMPI does this via its
+-np and -npernode switches. Ditto for MPICH via -np and -ppn.
 
-#Default settings specific options
-#Options: force_uvm,use_ldg,rdc
+[Running on a multi-core CPU:]
 
-KOKKOS_DEVICES, values = {OpenMP}, {Serial}, {Pthreads}, {Cuda}, default = {OpenMP}
-KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {ARMv8}, {BGQ}, {Power7}, {Power8}, default = {none}
-KOKKOS_DEBUG, values = {yes}, {no}, default = {no}
-KOKKOS_USE_TPLS, values = {hwloc}, {librt}, default = {none}
-KOKKOS_CUDA_OPTIONS, values = {force_uvm}, {use_ldg}, {rdc} :ul
+Here is a quick overview of how to use the KOKKOS package
+for CPU acceleration, assuming one or more 16-core nodes.
 
-KOKKOS_DEVICE sets the parallelization method used for Kokkos code
-(within LAMMPS).  KOKKOS_DEVICES=OpenMP means that OpenMP will be
-used.  KOKKOS_DEVICES=Pthreads means that pthreads will be used.
-KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.
-
-If KOKKOS_DEVICES=Cuda, then the lo-level Makefile in the src/MAKE
-directory must use "nvcc" as its compiler, via its CC setting.  For
-best performance its CCFLAGS setting should use -O3 and have a
-KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
-hardware and software installation, e.g. KOKKOS_ARCH=Kepler30.  Note
-the minimal required compute capability is 2.0, but this will give
-significantly reduced performance compared to Kepler generation GPUs
-with compute capability 3.x.  For the LINK setting, "nvcc" should not
-be used; instead use g++ or another compiler suitable for linking C++
-applications.  Often you will want to use your MPI compiler wrapper
-for this setting (i.e. mpicxx).  Finally, the lo-level Makefile must
-also have a "Compilation rule" for creating *.o files from *.cu files.
-See src/Makefile.cuda for an example of a lo-level Makefile with all
-of these settings.
-
-KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
-migrate during a simulation.  KOKKOS_USE_TPLS=hwloc should always be
-used if running with KOKKOS_DEVICES=Pthreads for pthreads.  It is not
-necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
-provides alternative methods via environment variables for binding
-threads to hardware cores.  More info on binding threads to cores is
-given in "Section 5.3"_Section_accelerate.html#acc_3.
-
-KOKKOS_ARCH=KNC enables compiler switches needed when compiling for an
-Intel Phi processor.
-
-KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
-on most Unix platforms.  This library is not available on all
-platforms.
-
-KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
-within LAMMPS.  KOKKOS_DEBUG=yes enables printing of run-time
-debugging information that can be useful.  It also enables runtime
-bounds checking on Kokkos data structures.
-
-KOKKOS_CUDA_OPTIONS are additional options for CUDA.
-
-For more information on Kokkos see the Kokkos programmers' guide here:
-/lib/kokkos/doc/Kokkos_PG.pdf.
-
-[Run with the KOKKOS package from the command line:]
-
-The mpirun or mpiexec command sets the total number of MPI tasks used
-by LAMMPS (one or multiple per compute node) and the number of MPI
-tasks used per node.  E.g. the mpirun command in MPICH does this via
-its -np and -ppn switches.  Ditto for OpenMPI via -np and -npernode.
-
-When using KOKKOS built with host=OMP, you need to choose how many
-OpenMP threads per MPI task will be used (via the "-k" command-line
-switch discussed below).  Note that the product of MPI tasks * OpenMP
-threads/task should not exceed the physical number of cores (on a
-node), otherwise performance will suffer.
-
-When using the KOKKOS package built with device=CUDA, you must use
-exactly one MPI task per physical GPU.
-
-When using the KOKKOS package built with host=MIC for Intel Xeon Phi
-coprocessor support you need to insure there are one or more MPI tasks
-per coprocessor, and choose the number of coprocessor threads to use
-per MPI task (via the "-k" command-line switch discussed below).  The
-product of MPI tasks * coprocessor threads/task should not exceed the
-maximum number of threads the coprocessor is designed to run,
-otherwise performance will suffer.  This value is 240 for current
-generation Xeon Phi(TM) chips, which is 60 physical cores * 4
-threads/core.  Note that with the KOKKOS package you do not need to
-specify how many Phi coprocessors there are per node; each
-coprocessors is simply treated as running some number of MPI tasks.
+mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj        # 1 node, 16 MPI tasks/node, no multi-threading
+mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj  # 2 nodes, 1 MPI task/node, 16 threads/task
+mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj          # 1 node,  2 MPI tasks/node, 8 threads/task
+mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj  # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
 
+To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk kokkos" "command-line switches"_Section_start.html#start_7 in your mpirun command.
 You must use the "-k on" "command-line
-switch"_Section_start.html#start_6 to enable the KOKKOS package.  It
+switch"_Section_start.html#start_7 to enable the KOKKOS package. It
 takes additional arguments for hardware settings appropriate to your
-system.  Those arguments are "documented
-here"_Section_start.html#start_6.  The two most commonly used
-options are:
+system. Those arguments are "documented
+here"_Section_start.html#start_7. For OpenMP use:
 
--k on t Nt g Ng :pre
-
-The "t Nt" option applies to host=OMP (even if device=CUDA) and
-host=MIC.  For host=OMP, it specifies how many OpenMP threads per MPI
-task to use with a node.  For host=MIC, it specifies how many Xeon Phi
-threads per MPI task to use within a node.  The default is Nt = 1.
-Note that for host=OMP this is effectively MPI-only mode which may be
-fine.  But for host=MIC you will typically end up using far less than
-all the 240 available threads, which could give very poor performance.
-
-The "g Ng" option applies to device=CUDA.  It specifies how many GPUs
-per compute node to use.  The default is 1, so this only needs to be
-specified is you have 2 or more GPUs per compute node.
+-k on t Nt :pre
 
+The "t Nt" option specifies how many OpenMP threads per MPI
+task to use with a node. The default is Nt = 1, which is MPI-only mode.
+Note that the product of MPI tasks * OpenMP
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer. If hyperthreading is enabled, then
+the product of MPI tasks * OpenMP threads/task should not exceed the
+physical number of cores * hardware threads.
 The "-k on" switch also issues a "package kokkos" command (with no
 additional arguments) which sets various KOKKOS options to default
 values, as discussed on the "package"_package.html command doc page.
 
-Use the "-sf kk" "command-line switch"_Section_start.html#start_6,
-which will automatically append "kk" to styles that support it.  Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_6 if
-you wish to change any of the default "package kokkos"_package.html
-optionns set by the "-k on" "command-line
-switch"_Section_start.html#start_6.
+The "-sf kk" "command-line switch"_Section_start.html#start_7
+will automatically append the "/kk" suffix to styles that support it.
+In this manner no modification to the input script is needed. Alternatively,
+one can run with the KOKKOS package by editing the input script as described below.
 
-
-
-Note that the default for the "package kokkos"_package.html command is
+NOTE: The default for the "package kokkos"_package.html command is
 to use "full" neighbor lists and set the Newton flag to "off" for both
-pairwise and bonded interactions.  This typically gives fastest
-performance.  If the "newton"_newton.html command is used in the input
-script, it can override the Newton flag defaults.
-
-However, when running in MPI-only mode with 1 thread per MPI task, it
+pairwise and bonded interactions. However, when running on CPUs, it
 will typically be faster to use "half" neighbor lists and set the
 Newton flag to "on", just as is the case for non-accelerated pair
-styles.  You can do this with the "-pk" "command-line
-switch"_Section_start.html#start_6.
+styles. It can also be faster to use non-threaded communication.
+Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html
+options. See its doc page for details and default settings. Experimenting with
+its options can provide a speed-up for specific calculations. For example:
 
-[Or run with the KOKKOS package by editing an input script:]
+mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm :pre
 
-The discussion above for the mpirun/mpiexec command and setting
-appropriate thread and GPU values for host=OMP or host=MIC or
-device=CUDA are the same.
+If the "newton"_newton.html command is used in the input
+script, it can also override the Newton flag defaults.
+
+[Core and Thread Affinity:]
+
+When using multi-threading, it is important for
+performance to bind both MPI tasks to physical cores, and threads to
+physical cores, so they do not migrate during a simulation.
+
+If you are not certain MPI tasks are being bound (check the defaults
+for your MPI installation), binding can be forced with these flags:
+
+OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
+Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... :pre
+
+For binding threads with KOKKOS OpenMP, 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. In general, for best performance
+with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads.
+For binding threads with the
+KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
+as described below.
+
+[Running on Knight's Landing (KNL) Intel Xeon Phi:]
+
+Here is a quick overview of how to use the KOKKOS package
+for the Intel Knight's Landing (KNL) Xeon Phi:
+
+KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores
+are reserved for the OS, and only 64 or 66 cores are used. Each core
+has 4 hyperthreads,so there are effectively N = 256 (4*64) or
+N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit,
+otherwise performance will suffer. Note that with the KOKKOS package you do not need to
+specify how many KNLs there are per node; each
+KNL is simply treated as running some number of MPI tasks.
+
+Examples of mpirun commands that follow these rules are shown below.
+
+Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 64 MPI tasks/node, 4 threads/task
+mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 66 MPI tasks/node, 4 threads/task
+mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj      # 1 node, 32 MPI tasks/node, 8 threads/task
+mpirun -np 512 -ppn 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj  # 8 nodes, 64 MPI tasks/node, 4 threads/task :pre
+
+The -np setting of the mpirun command sets the number of MPI
+tasks/node. The "-k on t Nt" command-line switch sets the number of
+threads/task as Nt. The product of these two values should be N, i.e.
+256 or 264.
+
+NOTE: The default for the "package kokkos"_package.html command is
+to use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions. When running on KNL, this
+will typically be best for pair-wise potentials. For manybody potentials,
+using "half" neighbor lists and setting the
+Newton flag to "on" may be faster. It can also be faster to use non-threaded communication.
+Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html
+options. See its doc page for details and default settings. Experimenting with
+its options can provide a speed-up for specific calculations. For example:
+
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj      #  Newton off, full neighbor list, non-threaded comm
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax      # Newton on, half neighbor list, non-threaded comm :pre
+
+NOTE: MPI tasks and threads should be bound to cores as described above for CPUs.
+
+NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors such as Knight's Corner (KNC), your
+system must be configured to use them in "native" mode, not "offload"
+mode like the USER-INTEL package supports.
+
+[Running on GPUs:]
+
+Use the "-k" "command-line switch"_Section_commands.html#start_7 to
+specify the number of GPUs per node. Typically the -np setting
+of the mpirun command should set the number of MPI
+tasks/node to be equal to the # of physical GPUs on the node.
+You can assign multiple MPI tasks to the same GPU with the
+KOKKOS package, but this is usually only faster if significant portions
+of the input script have not been ported to use Kokkos. Using CUDA MPS
+is recommended in this scenario. As above for multi-core CPUs (and no GPU), if N is the number
+of physical cores/node, then the number of MPI tasks/node should not exceed N.
+
+-k on g Ng :pre
+
+Here are examples of how to use the KOKKOS package for GPUs,
+assuming one or more nodes, each with two GPUs:
+
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node
+mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
+
+NOTE: The default for the "package kokkos"_package.html command is
+to use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions, along with threaded communication.
+When running on Maxwell or Kepler GPUs, this will typically be best. For Pascal GPUs,
+using "half" neighbor lists and setting the
+Newton flag to "on" may be faster. For many pair styles, setting the neighbor binsize
+equal to the ghost atom cutoff will give speedup.
+Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html
+options. See its doc page for details and default settings. Experimenting with
+its options can provide a speed-up for specific calculations. For example:
+
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj      # Set binsize = neighbor ghost cutoff
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
+
+NOTE: For good performance of the KOKKOS package on GPUs, you must
+have Kepler generation GPUs (or later). The Kokkos library exploits
+texture cache options not supported by Telsa generation GPUs (or
+older).
+
+NOTE: When using a GPU, you will achieve the best performance if your
+input script does not use fix or compute styles which are not yet
+Kokkos-enabled. This allows data to stay on the GPU for multiple
+timesteps, without being copied back to the host CPU. Invoking a
+non-Kokkos fix or compute, or performing I/O for
+"thermo"_thermo_style.html or "dump"_dump.html output will cause data
+to be copied back to the CPU incurring a performance penalty.
+
+NOTE: To get an accurate timing breakdown between time spend in pair,
+kspace, etc., you must set the environment variable CUDA_LAUNCH_BLOCKING=1.
+However, this will reduce performance and is not recommended for production runs.
+
+[Run with the KOKKOS package by editing an input script:]
+
+Alternatively the effect of the "-sf" or "-pk" switches can be
+duplicated by adding the "package kokkos"_package.html or "suffix
+kk"_suffix.html commands to your input script.
+
+The discussion above for building LAMMPS with the KOKKOS package, the mpirun/mpiexec command, and setting
+appropriate thread are the same.
 
 You must still use the "-k on" "command-line
-switch"_Section_start.html#start_6 to enable the KOKKOS package, and
+switch"_Section_start.html#start_7 to enable the KOKKOS package, and
 specify its additional arguments for hardware options appropriate to
 your system, as documented above.
 
-Use the "suffix kk"_suffix.html command, or you can explicitly add a
+You can use the "suffix kk"_suffix.html command, or you can explicitly add a
 "kk" suffix to individual styles in your input script, e.g.
 
 pair_style lj/cut/kk 2.5 :pre
 
 You only need to use the "package kokkos"_package.html command if you
 wish to change any of its option defaults, as set by the "-k on"
-"command-line switch"_Section_start.html#start_6.
+"command-line switch"_Section_start.html#start_7.
+
+[Using OpenMP threading and CUDA together (experimental):]
+
+With the KOKKOS package, both OpenMP multi-threading and GPUs can be used
+together in a few special cases. In the Makefile, the KOKKOS_DEVICES variable must
+include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
+
+KOKKOS_DEVICES=Cuda,OpenMP :pre
+
+The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
+using the "-sf kk" in the command line gives the default CUDA version everywhere.
+However, if the "/kk/host" suffix is added to a specific style in the input
+script, the Kokkos OpenMP (CPU) version of that specific style will be used instead.
+Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng"
+
+-k on t Nt g Ng :pre
+
+For example, the command to run with 1 GPU and 8 OpenMP threads is then:
+
+mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre
+
+Conversely, if the "-sf kk/host" is used in the command line and then the
+"/kk" or "/kk/device" suffix is added to a specific style in your input script,
+then only that specific style will run on the GPU while everything else will
+run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU
+styles will NOT overlap, except for a special case:
+
+A kspace style and/or molecular topology (bonds, angles, etc.) running on
+the host CPU can overlap with a pair style running on the GPU. First compile
+with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile.
+Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc.
+in the input file and the "kk" suffix (equal to "kk/device") on the command line.
+Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
+so CPU/GPU overlap can occur.
 
 [Speed-ups to expect:]
 
@@ -353,7 +363,7 @@ Generally speaking, the following rules of thumb apply:
 When running on CPUs only, with a single thread per MPI task,
 performance of a KOKKOS style is somewhere between the standard
 (un-accelerated) styles (MPI-only mode), and those provided by the
-USER-OMP package.  However the difference between all 3 is small (less
+USER-OMP package. However the difference between all 3 is small (less
 than 20%). :ulb,l
 
 When running on CPUs only, with multiple threads per MPI task,
@@ -363,7 +373,7 @@ package. :l
 When running large number of atoms per GPU, KOKKOS is typically faster
 than the GPU package. :l
 
-When running on Intel Xeon Phi, KOKKOS is not as fast as
+When running on Intel hardware, KOKKOS is not as fast as
 the USER-INTEL package, which is optimized for that hardware. :l
 :ule
 
@@ -371,123 +381,78 @@ See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
 LAMMPS web site for performance of the KOKKOS package on different
 hardware.
 
-[Guidelines for best performance:]
+[Advanced Kokkos options:]
 
-Here are guidline for using the KOKKOS package on the different
-hardware configurations listed above.
+There are other allowed options when building with the KOKKOS package.
+As above, they can be set either as variables on the make command line
+or in Makefile.machine. This is the full list of options, including
+those discussed above. Each takes a value shown below. The
+default value is listed, which is set in the
+/lib/kokkos/Makefile.kokkos file.
 
-Many of the guidelines use the "package kokkos"_package.html command
-See its doc page for details and default settings.  Experimenting with
-its options can provide a speed-up for specific calculations.
+KOKKOS_DEVICES, values = {Serial}, {OpenMP}, {Pthreads}, {Cuda}, default = {OpenMP}
+KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {Pascal60}, {Pascal61}, {ARMv80}, {ARMv81}, {ARMv81}, {ARMv8-ThunderX}, {BGQ}, {Power7}, {Power8}, {Power9}, {KNL}, {BDW}, {SKX}, default = {none}
+KOKKOS_DEBUG, values = {yes}, {no}, default = {no}
+KOKKOS_USE_TPLS, values = {hwloc}, {librt}, {experimental_memkind}, default = {none}
+KOKKOS_CXX_STANDARD, values = {c++11}, {c++1z}, default = {c++11}
+KOKKOS_OPTIONS, values = {aggressive_vectorization}, {disable_profiling}, default = {none}
+KOKKOS_CUDA_OPTIONS, values = {force_uvm}, {use_ldg}, {rdc}, {enable_lambda}, default = {enable_lambda} :ul
 
-[Running on a multi-core CPU:]
+KOKKOS_DEVICES sets the parallelization method used for Kokkos code
+(within LAMMPS). KOKKOS_DEVICES=Serial means that no threading will be used.
+KOKKOS_DEVICES=OpenMP means that OpenMP threading will be
+used. KOKKOS_DEVICES=Pthreads means that pthreads will be used.
+KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.
 
-If N is the number of physical cores/node, then the number of MPI
-tasks/node * number of threads/task should not exceed N, and should
-typically equal N.  Note that the default threads/task is 1, as set by
-the "t" keyword of the "-k" "command-line
-switch"_Section_start.html#start_6.  If you do not change this, no
-additional parallelism (beyond MPI) will be invoked on the host
-CPU(s).
+KOKKOS_ARCH enables compiler switches needed when compiling for a
+specific hardware:
 
-You can compare the performance running in different modes:
+ARMv80 = ARMv8.0 Compatible CPU
+ARMv81 = ARMv8.1 Compatible CPU
+ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
+SNB = Intel Sandy/Ivy Bridge CPUs
+HSW = Intel Haswell CPUs
+BDW = Intel Broadwell Xeon E-class CPUs
+SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
+KNC = Intel Knights Corner Xeon Phi
+KNL = Intel Knights Landing Xeon Phi
+Kepler30 = NVIDIA Kepler generation CC 3.0
+Kepler32 = NVIDIA Kepler generation CC 3.2
+Kepler35 = NVIDIA Kepler generation CC 3.5
+Kepler37 = NVIDIA Kepler generation CC 3.7
+Maxwell50 = NVIDIA Maxwell generation CC 5.0
+Maxwell52 = NVIDIA Maxwell generation CC 5.2
+Maxwell53 = NVIDIA Maxwell generation CC 5.3
+Pascal60 = NVIDIA Pascal generation CC 6.0
+Pascal61 = NVIDIA Pascal generation CC 6.1
+BGQ = IBM Blue Gene/Q CPUs
+Power8 = IBM POWER8 CPUs
+Power9 = IBM POWER9 CPUs :ul
 
-run with 1 MPI task/node and N threads/task
-run with N MPI tasks/node and 1 thread/task
-run with settings in between these extremes :ul
+KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
+migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
+used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
+necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
+provides alternative methods via environment variables for binding
+threads to hardware cores. More info on binding threads to cores is
+given in "Section 5.3"_Section_accelerate.html#acc_3.
 
-Examples of mpirun commands in these modes are shown above.
+KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
+on most Unix platforms. This library is not available on all
+platforms.
 
-When using KOKKOS to perform multi-threading, it is important for
-performance to bind both MPI tasks to physical cores, and threads to
-physical cores, so they do not migrate during a simulation.
+KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
+within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
+debugging information that can be useful. It also enables runtime
+bounds checking on Kokkos data structures.
 
-If you are not certain MPI tasks are being bound (check the defaults
-for your MPI installation), binding can be forced with these flags:
+KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when building LAMMPS.
 
-OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
-Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ... :pre
-
-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
-(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_packages.html#KOKKOS of the manual for
-details).
-
-The -np setting of the mpirun command should set the number of MPI
-tasks/node to be equal to the # of physical GPUs on the node.
-
-Use the "-k" "command-line switch"_Section_commands.html#start_6 to
-specify the number of GPUs per node, and the number of threads per MPI
-task.  As above for multi-core CPUs (and no GPU), if N is the number
-of physical cores/node, then the number of MPI tasks/node * number of
-threads/task should not exceed N.  With one GPU (and one MPI task) it
-may be faster to use less than all the available cores, by setting
-threads/task to a smaller value.  This is because using all the cores
-on a dual-socket node will incur extra cost to copy memory from the
-2nd socket to the GPU.
-
-Examples of mpirun commands that follow these rules are shown above.
-
-NOTE: When using a GPU, you will achieve the best performance if your
-input script does not use any fix or compute styles which are not yet
-Kokkos-enabled.  This allows data to stay on the GPU for multiple
-timesteps, without being copied back to the host CPU.  Invoking a
-non-Kokkos fix or compute, or performing I/O for
-"thermo"_thermo_style.html or "dump"_dump.html output will cause data
-to be copied back to the CPU.
-
-You cannot yet assign multiple MPI tasks to the same GPU with the
-KOKKOS package.  We plan to support this in the future, similar to the
-GPU package in LAMMPS.
-
-You cannot yet use both the host (multi-threaded) and device (GPU)
-together to compute pairwise interactions with the KOKKOS package.  We
-hope to support this in the future, similar to the GPU package in
-LAMMPS.
-
-[Running on an Intel Phi:]
-
-Kokkos only uses Intel Phi processors in their "native" mode, i.e.
-not hosted by a CPU.
-
-As illustrated above, build LAMMPS with OMP=yes (the default) and
-MIC=yes.  The latter insures code is correctly compiled for the Intel
-Phi.  The OMP setting means OpenMP will be used for parallelization on
-the Phi, which is currently the best option within Kokkos.  In the
-future, other options may be added.
-
-Current-generation Intel Phi chips have either 61 or 57 cores.  One
-core should be excluded for running the OS, leaving 60 or 56 cores.
-Each core is hyperthreaded, so there are effectively N = 240 (4*60) or
-N = 224 (4*56) cores to run on.
-
-The -np setting of the mpirun command sets the number of MPI
-tasks/node.  The "-k on t Nt" command-line switch sets the number of
-threads/task as Nt.  The product of these 2 values should be N, i.e.
-240 or 224.  Also, the number of threads/task should be a multiple of
-4 so that logical threads from more than one MPI task do not run on
-the same physical core.
-
-Examples of mpirun commands that follow these rules are shown above.
+KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS package must be compiled
+with the {enable_lambda} option when using GPUs.
 
 [Restrictions:]
 
-As noted above, if using GPUs, the number of MPI tasks per compute
-node should equal to the number of GPUs per compute node.  In the
-future Kokkos will support assigning multiple MPI tasks to a single
-GPU.
-
-Currently Kokkos does not support AMD GPUs due to limits in the
-available backend programming models.  Specifically, Kokkos requires
-extensive C++ support from the Kernel language.  This is expected to
-change in the future.
+Currently, there are no precision options with the KOKKOS
+package. All compilation and computation is performed in double
+precision.

doc/src/body.txt

@@ -261,7 +261,7 @@ For images created by the "dump image"_dump_image.html command, if the
 polygon consisting of N line segments.  Note that the line segments
 are drawn between the N vertices, which does not correspond exactly to
 the physical extent of the body (because the "pair_style
-rounded/polygon"_pair_body_rounded_polygon.cpp defines finite-size
+rounded/polygon"_pair_body_rounded_polygon.html defines finite-size
 spheres at those point and the line segments between the spheres are
 tangent to the spheres).  The drawn diameter of each line segment is
 determined by the {bflag1} parameter for the {body} keyword.  The

doc/src/compute_cluster_atom.txt

@@ -28,7 +28,7 @@ compute 1 all aggregate/atom 3.5 :pre
 
 [Description:]
 
-Define a computation that assigns each atom a cluster, fragement,
+Define a computation that assigns each atom a cluster, fragment,
 or aggregate ID.
 
 A cluster is defined as a set of atoms, each of which is within the
@@ -53,7 +53,7 @@ like micelles.
 Only atoms in the compute group are clustered and assigned cluster
 IDs. Atoms not in the compute group are assigned a cluster ID = 0.
 For fragments, only bonds where [both] atoms of the bond are included
-in the compute group are assigned to fragments, so that only fragmets
+in the compute group are assigned to fragments, so that only fragments
 are detected where [all] atoms are in the compute group. Thus atoms
 may be included in the compute group, yes still have a fragment ID of 0.
 

doc/src/compute_dihedral_local.txt

@@ -27,8 +27,8 @@ compute 1 all dihedral/local phi :pre
 
 Define a computation that calculates properties of individual dihedral
 interactions.  The number of datums generated, aggregated across all
-processors, equals the number of angles in the system, modified by the
-group parameter as explained below.
+processors, equals the number of dihedral angles in the system, modified
+by the group parameter as explained below.
 
 The value {phi} is the dihedral angle, as defined in the diagram on
 the "dihedral_style"_dihedral_style.html doc page.

doc/src/compute_orientorder_atom.txt

@@ -67,7 +67,7 @@ parameters. This is followed by that number of integers giving the
 degree of each order parameter. Because {Q}2 and all odd-degree order
 parameters are zero for atoms in cubic crystals (see
 "Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
-{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn}=12, {Q}4
+{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn} =12, {Q}4
 = sqrt(7/3)/8 = 0.19094....  The numerical values of all order
 parameters up to {Q}12 for a range of commonly encountered
 high-symmetry structures are given in Table I of "Mickel et

doc/src/compute_pressure_uef.txt

@@ -25,15 +25,15 @@ compute 2 all pressure/uef my_temp_uef virial :pre
 
 [Description:]
 
-This command is used to compute the pressure tensor in  
+This command is used to compute the pressure tensor in
 the reference frame of the applied flow field when
-"fix nvt/uef"_fix_nh_uef.html" or 
-"fix npt/uef"_fix_nh_uef.html" is used. 
+"fix nvt/uef"_fix_nh_uef.html" or
+"fix npt/uef"_fix_nh_uef.html" is used.
 It is not necessary to use this command to compute the scalar
 value of the pressure. A "compute pressure"_compute_pressure.html
 may be used for that purpose.
 
-The keywords and output information are documented in 
+The keywords and output information are documented in
 "compute_pressure"_compute_pressure.html.
 
 [Restrictions:]
@@ -46,8 +46,8 @@ This command can only be used when "fix nvt/uef"_fix_nh_uef.html
 or "fix npt/uef"_fix_nh_uef.html is active.
 
 The kinetic contribution to the pressure tensor
-will be accurate only when 
-the compute specificed by {temp-ID} is a 
+will be accurate only when
+the compute specified by {temp-ID} is a
 "compute temp/uef"_compute_temp_uef.html.
 
 [Related commands:]

doc/src/compute_sna_atom.txt

@@ -224,7 +224,7 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz},
 notation.  Each of these sub-blocks contains one column for each
 bispectrum component, the same as for compute {sna/atom}
 
-For example, if {K}=30 and ntypes=1, the number of columns in the per-atom
+For example, if {K} =30 and ntypes=1, the number of columns in the per-atom
 arrays generated by {sna/atom}, {snad/atom}, and {snav/atom}
 are 30, 90, and 180, respectively. With {quadratic} value=1,
 the numbers of columns are 930, 2790, and 5580, respectively.

doc/src/create_atoms.txt

@@ -36,9 +36,9 @@ keyword = {mol} or {basis} or {remap} or {var} or {set} or {units} :l
   {set} values = dim name
     dim = {x} or {y} or {z}
     name = name of variable to set with x, y, or z atom position
-  {rotate} values = Rx Ry Rz theta
-    Rx,Ry,Rz = rotation vector for single molecule
+  {rotate} values = theta Rx Ry Rz
     theta = rotation angle for single molecule (degrees)
+    Rx,Ry,Rz = rotation vector for single molecule
   {units} value = {lattice} or {box}
     {lattice} = the geometry is defined in lattice units
     {box} = the geometry is defined in simulation box units :pre
@@ -227,28 +227,30 @@ the sinusoid would appear to be "smoother".  Also note the use of the
 converts lattice spacings to distance.  Click on the image for a
 larger version.
 
+dimension       2
 variable        x equal 100
 variable        y equal 25
 lattice         hex 0.8442
 region          box block 0 $x 0 $y -0.5 0.5
 create_box      1 box :pre
 
-variable        xx equal 0.0
-variable        yy equal 0.0
+variable        xx internal 0.0
+variable        yy internal 0.0
 variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
-create_atoms    1 box var v set x xx set y yy :pre
+create_atoms    1 box var v set x xx set y yy
+write_dump      all atom sinusoid.lammpstrj :pre
 
 :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
 
-The {rotate} keyword can be used with the {single} style, when adding
-a single molecule to specify the orientation at which the molecule is
-inserted.  The axis of rotation is determined by the rotation vector
-(Rx,Ry,Rz) that goes through the insertion point.  The specified
-{theta} determines the angle of rotation around that axis.  Note that
-the direction of rotation for the atoms around the rotation axis is
-consistent with the right-hand rule: if your right-hand's thumb points
-along {R}, then your fingers wrap around the axis in the direction of
-rotation.
+The {rotate} keyword can only be used with the {single} style and
+when adding a single molecule. It allows to specify the orientation
+at which the molecule is inserted.  The axis of rotation is
+determined by the rotation vector (Rx,Ry,Rz) that goes through the
+insertion point.  The specified {theta} determines the angle of
+rotation around that axis.  Note that the direction of rotation for
+the atoms around the rotation axis is consistent with the right-hand
+rule: if your right-hand's thumb points along {R}, then your fingers
+wrap around the axis in the direction of rotation.
 
 The {units} keyword determines the meaning of the distance units used
 to specify the coordinates of the one particle created by the {single}

doc/src/create_bonds.txt

@@ -18,7 +18,7 @@ style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
     group2-ID = ID of second group, bonds will be between atoms in the 2 groups
     btype = bond type of created bonds
     rmin = minimum distance between pair of atoms to bond together
-    rmax = minimum distance between pair of atoms to bond together
+    rmax = maximum distance between pair of atoms to bond together
   {single/bond} args = btype batom1 batom2
     btype = bond type of new bond
     batom1,batom2 = atom IDs for two atoms in bond

doc/src/fix_controller.txt

@@ -83,7 +83,7 @@ the following dynamic equation:
 :c,image(Eqs/fix_controller1.jpg)
 
 where {c} is the continuous time analog of the control variable,
-{e}={pvar}-{setpoint} is the error in the process variable, and
+{e} ={pvar}-{setpoint} is the error in the process variable, and
 {alpha}, {Kp}, {Ki}, and {Kd} are constants set by the corresponding
 keywords described above. The discretized version of this equation is:
 
@@ -106,10 +106,10 @@ the value of {alpha} to reflect this, while leaving {Kp}, {Ki}, and
 When choosing the values of the four constants, it is best to first
 pick a value and sign for {alpha} that is consistent with the
 magnitudes and signs of {pvar} and {cvar}.  The magnitude of {Kp}
-should then be tested over a large positive range keeping {Ki}={Kd}=0.
+should then be tested over a large positive range keeping {Ki} = {Kd} =0.
 A good value for {Kp} will produce a fast response in {pvar}, without
 overshooting the {setpoint}.  For many applications, proportional
-feedback is sufficient, and so {Ki}={Kd}=0 can be used. In cases where
+feedback is sufficient, and so {Ki} = {Kd} =0 can be used. In cases where
 there is a substantial lag time in the response of {pvar} to a change
 in {cvar}, this can be counteracted by increasing {Kd}. In situations
 where {pvar} plateaus without reaching {setpoint}, this can be

doc/src/fix_halt.txt

@@ -64,10 +64,10 @@ not performed once every {N} steps by this command.  Instead it is
 performed (typically) only a small number of times and the elapsed
 times are used to predict when the end-of-the-run will be.  Both of
 these attributes can be useful when performing benchmark calculations
-for a desired length of time with minmimal overhead.  For example, if
+for a desired length of time with minimal overhead.  For example, if
 a run is performing 1000s of timesteps/sec, the overhead for syncing
 the timer frequently across a large number of processors may be
-non-negligble.
+non-negligible.
 
 Equal-style variables evaluate to a numeric value.  See the
 "variable"_variable.html command for a description.  They calculate
@@ -125,7 +125,7 @@ to the screen and logfile when the halt condition is triggered.  If
 {message} is set to yes, a one line message with the values that
 triggered the halt is printed.  If {message} is set to no, no message
 is printed; the run simply exits.  The latter may be desirable for
-post-processing tools that extract thermodyanmic information from log
+post-processing tools that extract thermodynamic information from log
 files.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]

doc/src/fix_mvv_dpd.txt

@@ -44,7 +44,7 @@ the velocity for the force evaluation:
 
 where the parameter <font size="4">&lambda;</font> depends on the
 specific choice of DPD parameters, and needs to be tuned on a
-case-by-case basis.  Specification of a {lambda} value is opttional.
+case-by-case basis.  Specification of a {lambda} value is optional.
 If specified, the setting must be from 0.0 to 1.0.  If not specified,
 a default value of 0.5 is used, which effectively reproduces the
 standard velocity-Verlet (VV) scheme.  For more details, see

doc/src/fix_neb.txt

@@ -113,9 +113,9 @@ keeping the replicas equally spaced.
 
 :line
 
-The keyword {perp} specifies if and how a perpendicual nudging force
+The keyword {perp} specifies if and how a perpendicular nudging force
 is computed.  It adds a spring force perpendicular to the path in
-order to prevent the path from becoming too kinky.  It can
+order to prevent the path from becoming too strongly kinked.  It can
 significantly improve the convergence of the NEB calculation when the
 resolution is poor.  I.e. when few replicas are used; see
 "(Maras)"_#Maras1 for details.
@@ -138,17 +138,17 @@ By default, no additional forces act on the first and last replicas
 during the NEB relaxation, so these replicas simply relax toward their
 respective local minima.  By using the key word {end}, additional
 forces can be applied to the first and/or last replicas, to enable
-them to relax toward a MEP while constraining their energy.
+them to relax toward a MEP while constraining their energy E to the
+target energy ETarget.
 
-The interatomic force Fi for the specified replica becomes:
+If ETarget>E, the interatomic force Fi for the specified replica becomes:
 
 Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)*Kspring3) T',  {when} Grad(V) dot T' < 0
 Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)*Kspring3) T', {when} Grad(V) dot T' > 0
 :pre
 
-where E is the current energy of the replica and ETarget is the target
-energy.  The "spring" constant on the difference in energies is the
-specified {Kspring3} value.
+The "spring" constant on the difference in energies is the specified
+{Kspring3} value.
 
 When {estyle} is specified as {first}, the force is applied to the
 first replica.  When {estyle} is specified as {last}, the force is
@@ -183,10 +183,9 @@ After converging a NEB calculation using an {estyle} of
 have a larger energy than the first replica. If this is not the case,
 the path is probably not a MEP.
 
-Finally, note that if the last replica converges toward a local
-minimum which has a larger energy than the energy of the first
-replica, a NEB calculation using an {estyle} of {last/efirst} or
-{last/efirst/middle} cannot reach final convergence.
+Finally, note that the last replica may never reach the target energy
+if it is stuck in a local minima which has a larger energy than the
+target energy.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 

doc/src/fix_property_atom.txt

@@ -111,6 +111,10 @@ need to communicate their new values to/from ghost atoms, an operation
 that can be invoked from within a "pair style"_pair_style.html or
 "fix"_fix.html or "compute"_compute.html that you write.
 
+NOTE: If this fix is defined [after] the simulation box is created,
+a 'run 0' command should be issued to properly initialize the storage
+created by this fix.
+
 :line
 
 This fix is one of a small number that can be defined in an input
@@ -155,7 +159,7 @@ these commands could be used:
 
 fix prop all property/atom mol
 variable cluster atom ((id-1)/10)+1
-set id * mol v_cluster :pre
+set atom * mol v_cluster :pre
 
 The "atom-style variable"_variable.html will create values for atoms
 with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9.  When the

doc/src/fix_python_invoke.txt

@@ -6,14 +6,14 @@
 
 :line
 
-fix python command :h3
+fix python/invoke command :h3
 
 [Syntax:]
 
-fix ID group-ID python N callback function_name :pre
+fix ID group-ID python/invoke N callback function_name :pre
 
 ID, group-ID are ignored by this fix :ulb,l
-python = style name of this fix command :l
+python/invoke = 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
@@ -36,8 +36,8 @@ def end_of_step_callback(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
+fix pf  all python/invoke 50 post_force post_force_callback
+fix eos all python/invoke 50 end_of_step end_of_step_callback :pre
 
 [Description:]
 

doc/src/fix_python_move.txt

@@ -0,0 +1,102 @@
+"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/move command :h3
+
+[Syntax:]
+
+fix python/move pymodule.CLASS :pre
+
+pymodule.CLASS = use class [CLASS] in module/file [pymodule] to compute how to move atoms
+
+[Examples:]
+
+fix  1 all python/move py_nve.NVE
+fix  1 all python/move py_nve.NVE_OPT :pre
+
+[Description:]
+
+The {python/move} fix style provides a way to define ways how particles
+are moved during an MD run from python script code, that is loaded from
+a file into LAMMPS and executed at the various steps where other fixes
+can be executed. This python script must contain specific python class
+definitions.
+
+This allows to implement complex position updates and also modified
+time integration methods. Due to python being an interpreted language,
+however, the performance of this fix can be moderately to significantly
+slower than the corresponding C++ code. For specific cases, this
+performance penalty can be limited through effective use of NumPy.
+
+:line
+
+The python module file has to start with the following code:
+
+from __future__ import print_function
+import lammps
+import ctypes
+import traceback
+import numpy as np
+#
+class LAMMPSFix(object):
+    def __init__(self, ptr, group_name="all"):
+        self.lmp = lammps.lammps(ptr=ptr)
+        self.group_name = group_name
+#
+class LAMMPSFixMove(LAMMPSFix):
+    def __init__(self, ptr, group_name="all"):
+        super(LAMMPSFixMove, self).__init__(ptr, group_name)
+#
+    def init(self):
+        pass
+#
+    def initial_integrate(self, vflag):
+        pass
+#
+    def final_integrate(self):
+        pass
+#
+    def initial_integrate_respa(self, vflag, ilevel, iloop):
+        pass
+#
+    def final_integrate_respa(self, ilevel, iloop):
+        pass
+#
+    def reset_dt(self):
+        pass :pre
+
+Any classes implementing new atom motion functionality have to be
+derived from the [LAMMPSFixMove] class, overriding the available
+methods as needed.
+
+Examples for how to do this are in the {examples/python} folder.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output
+commands"_Section_howto.html#howto_15.  No parameter of this fix can
+be used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[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:]
+
+"fix nve"_fix_nve.html, "fix python/invoke"_fix_python_invoke.html
+
+[Default:] none
+

doc/src/fix_rigid.txt

@@ -7,11 +7,17 @@
 :line
 
 fix rigid command :h3
+fix rigid/omp command :h3
 fix rigid/nve command :h3
+fix rigid/nve/omp command :h3
 fix rigid/nvt command :h3
+fix rigid/nvt/omp command :h3
 fix rigid/npt command :h3
+fix rigid/npt/omp command :h3
 fix rigid/nph command :h3
+fix rigid/nph/omp command :h3
 fix rigid/small command :h3
+fix rigid/small/omp command :h3
 fix rigid/nve/small command :h3
 fix rigid/nvt/small command :h3
 fix rigid/npt/small command :h3
@@ -28,7 +34,7 @@ bodystyle = {single} or {molecule} or {group} :l
   {molecule} args = none
   {custom} args = {i_propname} or {v_varname}
     i_propname = an integer property defined via fix property/atom
-    v_varname  = an atom-style or atomfile-style variable 
+    v_varname  = an atom-style or atomfile-style variable
   {group} args = N groupID1 groupID2 ...
     N = # of groups
     groupID1, groupID2, ... = list of N group IDs :pre
@@ -93,7 +99,7 @@ fix 1 clump rigid custom v_bodyid :pre
 fix 0 all property/atom i_bodyid
 read_restart data.rigid fix 0 NULL Bodies
 fix 1 clump rigid/small custom i_bodyid :pre
-	
+
 [Description:]
 
 Treat one or more sets of atoms as independent rigid bodies.  This

doc/src/fix_shake.txt

@@ -58,7 +58,7 @@ required in order to eliminate velocity components along the bonds
 In order to formulate individual constraints for SHAKE and RATTLE,
 focus on a single molecule whose bonds are constrained.  Let Ri and Vi
 be the position and velocity of atom {i} at time {n}, for
-{i}=1,...,{N}, where {N} is the number of sites of our reference
+{i} =1,...,{N}, where {N} is the number of sites of our reference
 molecule. The distance vector between sites {i} and {j} is given by
 
 :c,image(Eqs/fix_rattle_rij.jpg)

doc/src/fix_smd_integrate_tlsph.txt

@@ -14,15 +14,12 @@ fix ID group-ID smd/integrate_tlsph keyword values :pre
 
 ID, group-ID are documented in "fix"_fix.html command
 smd/integrate_tlsph = style name of this fix command
-zero or more keyword/value pairs may be appended :ul
-
-keyword = {limit_velocity}  :l
+zero or more keyword/value pairs may be appended
+keyword = {limit_velocity}  :ul
 
   {limit_velocity} value = max_vel
     max_vel = maximum allowed velocity :pre
 
-:ule
-
 [Examples:]
 
 fix 1 all smd/integrate_tlsph

doc/src/fix_smd_integrate_ulsph.txt

@@ -14,9 +14,8 @@ fix ID group-ID smd/integrate_ulsph keyword :pre
 
 ID, group-ID are documented in "fix"_fix.html command
 smd/integrate_ulsph = style name of this fix command
-zero or more keyword/value pairs may be appended :ul
-
-keyword = adjust_radius or limit_velocity
+zero or more keyword/value pairs may be appended
+keyword = adjust_radius or limit_velocity :ul
 
 adjust_radius values = adjust_radius_factor min_nn max_nn
       adjust_radius_factor = factor which scale the smooth/kernel radius
@@ -28,7 +27,7 @@ limit_velocity values = max_velocity
 
 [Examples:]
 
-fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 :pre
+fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
 fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre
 
 [Description:]
@@ -38,7 +37,7 @@ See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics
 
 The {adjust_radius} keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
 within the interval {min_nn} to {max_nn}. The parameter {adjust_radius_factor} determines the amount of adjustment per timestep. Typical values are
-{adjust_radius_factor}=1.02, {min_nn}=15, and {max_nn}=20.
+{adjust_radius_factor} =1.02, {min_nn} =15, and {max_nn} =20.
 
 The {limit_velocity} keyword will control the velocity, scaling the norm of
 the velocity vector to max_vel in case it exceeds this velocity limit.

doc/src/fix_surface_global.txt

@@ -0,0 +1,19 @@
+"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 wall/surface/globale command :h3
+
+[Description:]
+
+This feature is not yet implemented.
+
+[Related commands:]
+
+"dump image"_dump_image.html
+
+

doc/src/fixes.txt

@@ -115,7 +115,8 @@ Fixes :h1
    fix_press_berendsen
    fix_print
    fix_property_atom
-   fix_python
+   fix_python_invoke
+   fix_python_move
    fix_qbmsst
    fix_qeq
    fix_qeq_comb
@@ -147,6 +148,7 @@ Fixes :h1
    fix_srd
    fix_store_force
    fix_store_state
+   fix_surface_global
    fix_temp_berendsen
    fix_temp_csvr
    fix_temp_rescale

doc/src/info.txt

@@ -12,7 +12,7 @@ info command :h3
 
 info args :pre
 
-args = one or more of the following keywords: {out}, {all}, {system}, {memory}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {styles}, {time}, or {configuration}
+args = one or more of the following keywords: {out}, {all}, {system}, {memory}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {coeffs}, {styles}, {time}, or {configuration}
      {out} values = {screen}, {log}, {append} filename, {overwrite} filename
      {styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {pair}, {region} :ul
 
@@ -81,6 +81,11 @@ The {variables} category prints a list of all currently defined
 variables, their names, styles, definition and last computed value, if
 available.
 
+The {coeffs} category prints a list for each defined force style
+(pair, bond, angle, dihedral, improper) indicating which of the
+corresponding coefficients have been set. This can be very helpful
+to debug error messages like "All pair coeffs are not set".
+
 The {styles} category prints the list of styles available in the
 current LAMMPS binary. It supports one of the following options
 to control which category of styles is printed out:

doc/src/lammps.book

@@ -1,6 +1,5 @@
-#HTMLDOC 1.8.27
--t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=1 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont helvetica --bodyfont times --headfootsize 11.0 --headfootfont helvetica --charset iso-8859-1 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all  --owner-password ""  --user-password "" --browserwidth 680 --no-strict --no-overflow
-
+#HTMLDOC 1.8.28
+-t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all  --owner-password ""  --user-password "" --browserwidth 680 --no-strict --no-overflow
 Manual.html
 Section_intro.html
 Section_start.html
@@ -244,7 +243,8 @@ fix_pour.html
 fix_press_berendsen.html
 fix_print.html
 fix_property_atom.html
-fix_python.html
+fix_python_invoke.html
+fix_python_move.html
 fix_qbmsst.html
 fix_qeq.html
 fix_qeq_comb.html
@@ -443,6 +443,7 @@ pair_edip.html
 pair_eff.html
 pair_eim.html
 pair_exp6_rx.html
+pair_extep.html
 pair_gauss.html
 pair_gayberne.html
 pair_gran.html

doc/src/neb.txt

@@ -322,9 +322,9 @@ the fix neb command.
 The forward (reverse) energy barrier is the potential energy of the
 highest replica minus the energy of the first (last) replica.
 
-Supplementary informations for all replicas can be printed out to the
-screen and master log.lammps file by adding the verbose keyword. These
-informations include the following.  The "path angle" (pathangle) for
+Supplementary information for all replicas can be printed out to the
+screen and master log.lammps file by adding the verbose keyword. This
+information include the following.  The "path angle" (pathangle) for
 the replica i which is the angle between the 3N-length vectors (Ri-1 -
 Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
 i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
@@ -339,8 +339,8 @@ energy gradient of image i.  ReplicaForce is the two-norm of the
 3N-length force vector (including nudging forces) for replica i.
 MaxAtomForce is the maximum force component of any atom in replica i.
 
-When a NEB calculation does not converge properly, these suplementary
-informations can help understanding what is going wrong. For instance
+When a NEB calculation does not converge properly, the suplementary
+information can help understanding what is going wrong. For instance
 when the path angle becomes accute the definition of tangent used in
 the NEB calculation is questionable and the NEB cannot may diverge
 "(Maras)"_#Maras2.

doc/src/pair_body_rounded_polygon.txt

@@ -0,0 +1,19 @@
+"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 body/rounded/polygon command :h3
+
+[Description:]
+
+Note: This feature is not yet implemented.
+
+[Related commands:]
+
+"pair_style body"_pair_body.html
+
+[Default:] none

doc/src/pair_extep.txt

@@ -0,0 +1,40 @@
+"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 extep command :h3
+
+[Syntax:]
+
+pair_style extep :pre
+
+[Examples:]
+
+pair_style extep
+pair_coeff * * BN.extep B N :pre
+
+[Description:]
+
+Style {extep} computes the Extended Tersoff Potential (ExTeP)
+interactions as described in "(Los2017)"_#Los2017.
+
+:line
+
+[Restrictions:] none
+
+[Related commands:]
+
+"pair_tersoff" pair_tersoff.html
+
+[Default:] none
+
+:line
+
+:link(Los2017)
+[(Los2017)] J. H. Los et al. "Extended Tersoff potential for boron nitride: 
+Energetics and elastic properties of pristine and defective h-BN", 
+Phys. Rev. B 96 (184108), 2017.

doc/src/pair_smd_hertz.txt

@@ -28,7 +28,7 @@ The parameter <contact_stiffness> has units of pressure and should equal roughly
 of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.
 
 The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
-particles can approach each other. Usually, {scale_factor}=1.0.
+particles can approach each other. Usually, {scale_factor} =1.0.
 
 :line
 

doc/src/pair_smd_triangulated_surface.txt

@@ -29,7 +29,7 @@ The parameter <contact_stiffness> has units of pressure and should equal roughly
 of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle
 
 The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
-particles can approach the triangulated surface. Usually, {scale_factor}=1.0.
+particles can approach the triangulated surface. Usually, {scale_factor} =1.0.
 
 :line
 

doc/src/pair_smd_ulsph.txt

@@ -12,8 +12,8 @@ pair_style smd/ulsph command :h3
 
 pair_style smd/ulsph args :pre
 
-these keywords must be given :l
-keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT} or {*NO_VELOCITY_GRADIENT} and {*GRADIENT_CORRECTION} or {*NO_GRADIENT_CORRECTION}
+these keywords must be given :ul
+keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT} or {*NO_VELOCITY_GRADIENT} and {*GRADIENT_CORRECTION} or {*NO_GRADIENT_CORRECTION} :pre
 
 [Examples:]
 

doc/src/pair_snap.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style snap command :h3
+pair_style snap/kk command :h3
 
 [Syntax:]
 
@@ -171,6 +172,29 @@ This pair style can only be used via the {pair} keyword of the
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This style is part of the SNAP package.  It is only enabled if

doc/src/pair_yukawa.txt

@@ -9,6 +9,7 @@
 pair_style yukawa command :h3
 pair_style yukawa/gpu command :h3
 pair_style yukawa/omp command :h3
+pair_style yukawa/kk command :h3
 
 [Syntax:]
 

doc/src/pair_zbl.txt

@@ -8,6 +8,7 @@
 
 pair_style zbl command :h3
 pair_style zbl/gpu command :h3
+pair_style zbl/kk command :h3
 pair_style zbl/omp command :h3
 
 [Syntax:]

doc/src/pairs.txt

@@ -11,6 +11,7 @@ Pair Styles :h1
    pair_awpmd
    pair_beck
    pair_body
+   pair_body_rounded_polygon
    pair_bop
    pair_born
    pair_brownian
@@ -32,6 +33,7 @@ Pair Styles :h1
    pair_eff
    pair_eim
    pair_exp6_rx
+   pair_extep
    pair_gauss
    pair_gayberne
    pair_gran

doc/src/print.txt

@@ -14,10 +14,11 @@ print string keyword value :pre
 
 string = text string to print, which may contain variables :ulb,l
 zero or more keyword/value pairs may be appended :l
-keyword = {file} or {append} or {screen} :l
+keyword = {file} or {append} or {screen} or {universe} :l
   {file} value = filename
   {append} value = filename
-  {screen} value = {yes} or {no} :pre
+  {screen} value = {yes} or {no}
+  {universe} value = {yes} or {no} :pre
 :ule
 
 [Examples:]
@@ -26,6 +27,7 @@ print "Done with equilibration" file info.dat
 print Vol=$v append info.dat screen no
 print "The system volume is now $v"
 print 'The system volume is now $v'
+print "NEB calculation 1 complete" screen no universe yes
 print """
 System volume = $v
 System temperature = $t
@@ -49,6 +51,11 @@ it does not exist.
 If the {screen} keyword is used, output to the screen and logfile can
 be turned on or off as desired.
 
+If the {universe} keyword is used, output to the global screen and
+logfile can be turned on or off as desired. In multi-partition
+calculations, the {screen} option and the corresponding output only
+apply to the screen and logfile of the individual partition.
+
 If you want the print command to be executed multiple times (with
 changing variable values), there are 3 options.  First, consider using
 the "fix print"_fix_print.html command, which will print a string
@@ -74,4 +81,4 @@ thermodynamic properties, global values calculated by a
 
 [Default:]
 
-The option defaults are no file output and screen = yes.
+The option defaults are no file output, screen = yes, and universe = no.

doc/src/python.txt

@@ -406,7 +406,7 @@ 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.
+each time step using "fix python/invoke"_fix_python_invoke.html.
 
 :line
 
@@ -493,6 +493,6 @@ different source files, problems may occur.
 
 [Related commands:]
 
-"shell"_shell.html, "variable"_variable.html, "fix python"_fix_python.html
+"shell"_shell.html, "variable"_variable.html, "fix python/invoke"_fix_python_invoke.html
 
 [Default:] none

doc/src/replicate.txt

@@ -10,9 +10,11 @@ replicate command :h3
 
 [Syntax:]
 
-replicate nx ny nz :pre
+replicate nx ny nz {keyword} :pre
 
-nx,ny,nz = replication factors in each dimension :ul
+nx,ny,nz = replication factors in each dimension :ulb
+optional {keyword} = {bbox} :l
+  {bbox} = only check atoms in replicas that overlap with a processor's subdomain :ule
 
 [Examples:]
 
@@ -43,6 +45,12 @@ file that crosses a periodic boundary should be between two atoms with
 image flags that differ by 1.  This will allow the bond to be
 unwrapped appropriately.
 
+The optional keyword {bbox} uses a bounding box to only check atoms
+in replicas that overlap with a processor's subdomain when assigning
+atoms to processors, and thus can result in substantial speedups for
+calculations using a large number of processors. It does require
+temporarily using more memory.
+
 [Restrictions:]
 
 A 2d simulation cannot be replicated in the z dimension.

doc/utils/converters/lammpsdoc/txt2rst.py

@@ -67,7 +67,8 @@ class RSTMarkup(Markup):
         text = text.replace('*', '\\*')
         text = text.replace('^', '\\^')
         text = text.replace('|', '\\|')
-        text = re.sub(r'([^"])_', r'\1\\_', text)
+        text = re.sub(r'([^"])_([ \t\n\r\f])', r'\1\\\\_\2', text)
+        text = re.sub(r'([^"])_([^ \t\n\r\f])', r'\1\\_\2', text)
         return text
 
     def unescape_rst_chars(self, text):
@@ -148,15 +149,18 @@ class RSTFormatting(Formatting):
         return "\n----------\n\n" + content.strip()
 
     def image(self, content, file, link=None):
-        if link and (link.lower().endswith('.jpg') or
-                         link.lower().endswith('.jpeg') or
-                         link.lower().endswith('.png') or
-                         link.lower().endswith('.gif')):
-            converted = ".. thumbnail:: " + self.markup.unescape_rst_chars(link) + "\n"
-        else:
-            converted = ".. image:: " + self.markup.unescape_rst_chars(file) + "\n"
-            if link:
-                converted += "   :target: " + self.markup.unescape_rst_chars(link) + "\n"
+        # 2017-12-07: commented out to disable thumbnail processing due to dropping
+        #             support for obsolete sphinxcontrib.images extension
+        #
+        #if link and (link.lower().endswith('.jpg') or
+        #                 link.lower().endswith('.jpeg') or
+        #                 link.lower().endswith('.png') or
+        #                 link.lower().endswith('.gif')):
+        #    converted = ".. thumbnail:: " + self.markup.unescape_rst_chars(link) + "\n"
+        #else:
+        converted = ".. image:: " + self.markup.unescape_rst_chars(file) + "\n"
+        if link:
+            converted += "   :target: " + self.markup.unescape_rst_chars(link) + "\n"
 
         if "c" in self.current_command_list:
             converted += "   :align: center\n"

doc/utils/sphinx-config/conf.py

@@ -31,8 +31,11 @@ import os
 # ones.
 extensions = [
     'sphinx.ext.mathjax',
-    'sphinxcontrib.images',
 ]
+# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
+#             yet we can no longer use Sphinx 15.x, since that breaks with
+#             newer version of the multiprocessor module.
+#    'sphinxcontrib.images',
 
 images_config = {
   'default_image_width' : '25%',

examples/COUPLE/simple/README

@@ -17,33 +17,36 @@ additional wrapper library that interfaces the C interface of the
 LAMMPS library to Fortran and also translates the MPI communicator
 from Fortran to C.
 
-Once you have built LAMMPS as a library (see examples/COUPLE/README),
-you can then build any of the driver codes with compile lines like
-these, which include paths to the LAMMPS library interface, MPI (an
-installed MPICH in this case), and FFTW (assuming you built LAMMPS as
-a library with its PPPM solver).
+First build LAMMPS as a library (see examples/COUPLE/README), e.g. 
 
-This builds the C++ driver with the LAMMPS library using a C++ compiler:
+make mode=shlib mpi
 
-g++ -I/home/sjplimp/lammps/src -c simple.cpp
-g++ -L/home/sjplimp/lammps/src simple.o \
-    -llammps -lfftw -lmpich -lmpl -lpthread -o simpleCC
+You can then build any of the driver codes with compile lines like
+these, which include paths to the LAMMPS library interface, and
+linking with FFTW (only needed if you built LAMMPS as a library with
+its PPPM solver).
 
-This builds the C driver with the LAMMPS library using a C compiler:
+This builds the C++ driver with the LAMMPS library using the mpiCC
+(C++) compiler:
 
-gcc -I/home/sjplimp/lammps/src -c simple.c
-gcc -L/home/sjplimp/lammps/src simple.o \
-    -llammps -lfftw -lmpich -lmpl -lpthread -lstdc++ -o simpleC
+mpiCC -I/home/sjplimp/lammps/src -c simple.cpp
+mpiCC -L/home/sjplimp/lammps/src simple.o -llammps -lfftw -o simpleCC
+
+This builds the C driver with the LAMMPS library using the mpicc (C)
+compiler:
+
+mpicc -I/home/sjplimp/lammps/src -c simple.c
+mpicc -L/home/sjplimp/lammps/src simple.o -llammps -lfftw -o simpleC
 
 This builds the Fortran wrapper and driver with the LAMMPS library
-using a Fortran and C compiler, using the wrapper in the fortran
-directory:
+using the mpicc (C) and mpifort (Fortran) compilers, using the wrapper
+in the fortran directory:
 
 cp ../fortran/libfwrapper.c .
-gcc -I/home/sjplimp/lammps/src -c libfwrapper.c
-gfortran -I/home/sjplimp/lammps/src -c simple.f90
-gfortran -L/home/sjplimp/lammps/src simple.o libfwrapper.o \
-    -llammps -lfftw -lfmpich -lmpich -lpthread -lstdc++ -o simpleF
+mpicc -I/home/sjplimp/lammps/src -c libfwrapper.c
+mpifort -c simple.f90
+mpifort -L/home/sjplimp/lammps/src simple.o libfwrapper.o \
+    -llammps -lfftw -o simpleF
 
 You then run simpleCC, simpleC, or simpleF on a parallel machine
 on some number of processors Q with 2 arguments:

examples/COUPLE/simple/simple.c

@@ -145,7 +145,7 @@ int main(int narg, char **arg)
     for (i = 0; i < natoms; i++) type[i] = 1;
 
     lammps_command(lmp,"delete_atoms group all");
-    lammps_create_atoms(lmp,natoms,NULL,type,x,v);
+    lammps_create_atoms(lmp,natoms,NULL,type,x,v,NULL,0);
     lammps_command(lmp,"run 10");
   }
 

examples/COUPLE/simple/simple.cpp

@@ -109,11 +109,11 @@ int main(int narg, char **arg)
     int natoms = static_cast<int> (lmp->atom->natoms);
     x = new double[3*natoms];
     v = new double[3*natoms];
-    lammps_gather_atoms(lmp,"x",1,3,x);
-    lammps_gather_atoms(lmp,"v",1,3,v);
+    lammps_gather_atoms(lmp,(char *) "x",1,3,x);
+    lammps_gather_atoms(lmp,(char *) "v",1,3,v);
     double epsilon = 0.1;
     x[0] += epsilon;
-    lammps_scatter_atoms(lmp,"x",1,3,x);
+    lammps_scatter_atoms(lmp,(char *) "x",1,3,x);
 
     // these 2 lines are the same
 
@@ -124,21 +124,22 @@ int main(int narg, char **arg)
   // extract force on single atom two different ways
 
   if (lammps == 1) {
-    double **f = (double **) lammps_extract_atom(lmp,"f");
+    double **f = (double **) lammps_extract_atom(lmp,(char *) "f");
     printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
 
-    double *fx = (double *) lammps_extract_variable(lmp,"fx","all");
+    double *fx = (double *) 
+      lammps_extract_variable(lmp,(char *) "fx",(char *) "all");
     printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
   }
 
   // use commands_string() and commands_list() to invoke more commands
 
-  char *strtwo = "run 10\nrun 20";
+  char *strtwo = (char *) "run 10\nrun 20";
   if (lammps == 1) lammps_commands_string(lmp,strtwo);
 
   char *cmds[2];
-  cmds[0] = "run 10";
-  cmds[1] = "run 20";
+  cmds[0] = (char *) "run 10";
+  cmds[1] = (char *) "run 20";
   if (lammps == 1) lammps_commands_list(lmp,2,cmds);
 
   // delete all atoms

examples/COUPLE/simple/simple.f90

@@ -115,9 +115,12 @@ PROGRAM f_driver
      CALL lammps_get_natoms(ptr,natoms)
      ALLOCATE(x(3*natoms))
 
-     CALL lammps_gather_atoms(ptr,'x',1,3,x);
-     x(1) = x(1) + epsilon
-     CALL lammps_scatter_atoms(ptr,'x',1,3,x);
+     ! these calls are commented out, b/c libfwrapper.c
+     ! needs to be updated to use gather_atoms and scatter_atoms
+
+     !CALL lammps_gather_atoms(ptr,'x',1,3,x);
+     !x(1) = x(1) + epsilon
+     !CALL lammps_scatter_atoms(ptr,'x',1,3,x);
 
      DEALLOCATE(x)
 

examples/USER/misc/extep/BN.data

@@ -0,0 +1,116 @@
+info: BN sample with r_BN=1.45
+
+100 atoms
+2 atom types
+
+0.0  21.75000000 xlo xhi
+0.0  12.55736835 ylo yhi
+0.0  50.00000000 zlo zhi
+
+Masses
+
+1 10.811
+2 14.0067
+
+Atoms
+
+  1 1  0.00000000   0.00000000   0.00000000
+  2 2  1.45000000   0.00000000   0.00000000
+  3 1  2.17500000   1.25573684   0.00000000
+  4 2  3.62500000   1.25573684   0.00000000
+  5 1  0.00000000   2.51147367   0.00000000
+  6 2  1.45000000   2.51147367   0.00000000
+  7 1  2.17500000   3.76721051   0.00000000
+  8 2  3.62500000   3.76721051   0.00000000
+  9 1  0.00000000   5.02294734   0.00000000
+ 10 2  1.45000000   5.02294734   0.00000000
+ 11 1  2.17500000   6.27868418   0.00000000
+ 12 2  3.62500000   6.27868418   0.00000000
+ 13 1  0.00000000   7.53442101   0.00000000
+ 14 2  1.45000000   7.53442101   0.00000000
+ 15 1  2.17500000   8.79015785   0.00000000
+ 16 2  3.62500000   8.79015785   0.00000000
+ 17 1  0.00000000  10.04589468   0.00000000
+ 18 2  1.45000000  10.04589468   0.00000000
+ 19 1  2.17500000  11.30163152   0.00000000
+ 20 2  3.62500000  11.30163152   0.00000000
+ 21 1  4.35000000   0.00000000   0.00000000
+ 22 2  5.80000000   0.00000000   0.00000000
+ 23 1  6.52500000   1.25573684   0.00000000
+ 24 2  7.97500000   1.25573684   0.00000000
+ 25 1  4.35000000   2.51147367   0.00000000
+ 26 2  5.80000000   2.51147367   0.00000000
+ 27 1  6.52500000   3.76721051   0.00000000
+ 28 2  7.97500000   3.76721051   0.00000000
+ 29 1  4.35000000   5.02294734   0.00000000
+ 30 2  5.80000000   5.02294734   0.00000000
+ 31 1  6.52500000   6.27868418   0.00000000
+ 32 2  7.97500000   6.27868418   0.00000000
+ 33 1  4.35000000   7.53442101   0.00000000
+ 34 2  5.80000000   7.53442101   0.00000000
+ 35 1  6.52500000   8.79015785   0.00000000
+ 36 2  7.97500000   8.79015785   0.00000000
+ 37 1  4.35000000  10.04589468   0.00000000
+ 38 2  5.80000000  10.04589468   0.00000000
+ 39 1  6.52500000  11.30163152   0.00000000
+ 40 2  7.97500000  11.30163152   0.00000000
+ 41 1  8.70000000   0.00000000   0.00000000
+ 42 2 10.15000000   0.00000000   0.00000000
+ 43 1 10.87500000   1.25573684   0.00000000
+ 44 2 12.32500000   1.25573684   0.00000000
+ 45 1  8.70000000   2.51147367   0.00000000
+ 46 2 10.15000000   2.51147367   0.00000000
+ 47 1 10.87500000   3.76721051   0.00000000
+ 48 2 12.32500000   3.76721051   0.00000000
+ 49 1  8.70000000   5.02294734   0.00000000
+ 50 2 10.15000000   5.02294734   0.00000000
+ 51 1 10.87500000   6.27868418   0.00000000
+ 52 2 12.32500000   6.27868418   0.00000000
+ 53 1  8.70000000   7.53442101   0.00000000
+ 54 2 10.15000000   7.53442101   0.00000000
+ 55 1 10.87500000   8.79015785   0.00000000
+ 56 2 12.32500000   8.79015785   0.00000000
+ 57 1  8.70000000  10.04589468   0.00000000
+ 58 2 10.15000000  10.04589468   0.00000000
+ 59 1 10.87500000  11.30163152   0.00000000
+ 60 2 12.32500000  11.30163152   0.00000000
+ 61 1 13.05000000   0.00000000   0.00000000
+ 62 2 14.50000000   0.00000000   0.00000000
+ 63 1 15.22500000   1.25573684   0.00000000
+ 64 2 16.67500000   1.25573684   0.00000000
+ 65 1 13.05000000   2.51147367   0.00000000
+ 66 2 14.50000000   2.51147367   0.00000000
+ 67 1 15.22500000   3.76721051   0.00000000
+ 68 2 16.67500000   3.76721051   0.00000000
+ 69 1 13.05000000   5.02294734   0.00000000
+ 70 2 14.50000000   5.02294734   0.00000000
+ 71 1 15.22500000   6.27868418   0.00000000
+ 72 2 16.67500000   6.27868418   0.00000000
+ 73 1 13.05000000   7.53442101   0.00000000
+ 74 2 14.50000000   7.53442101   0.00000000
+ 75 1 15.22500000   8.79015785   0.00000000
+ 76 2 16.67500000   8.79015785   0.00000000
+ 77 1 13.05000000  10.04589468   0.00000000
+ 78 2 14.50000000  10.04589468   0.00000000
+ 79 1 15.22500000  11.30163152   0.00000000
+ 80 2 16.67500000  11.30163152   0.00000000
+ 81 1 17.40000000   0.00000000   0.00000000
+ 82 2 18.85000000   0.00000000   0.00000000
+ 83 1 19.57500000   1.25573684   0.00000000
+ 84 2 21.02500000   1.25573684   0.00000000
+ 85 1 17.40000000   2.51147367   0.00000000
+ 86 2 18.85000000   2.51147367   0.00000000
+ 87 1 19.57500000   3.76721051   0.00000000
+ 88 2 21.02500000   3.76721051   0.00000000
+ 89 1 17.40000000   5.02294734   0.00000000
+ 90 2 18.85000000   5.02294734   0.00000000
+ 91 1 19.57500000   6.27868418   0.00000000
+ 92 2 21.02500000   6.27868418   0.00000000
+ 93 1 17.40000000   7.53442101   0.00000000
+ 94 2 18.85000000   7.53442101   0.00000000
+ 95 1 19.57500000   8.79015785   0.00000000
+ 96 2 21.02500000   8.79015785   0.00000000
+ 97 1 17.40000000  10.04589468   0.00000000
+ 98 2 18.85000000  10.04589468   0.00000000
+ 99 1 19.57500000  11.30163152   0.00000000
+100 2 21.02500000  11.30163152   0.00000000

examples/USER/misc/extep/in.extep-bn

@@ -0,0 +1,29 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      atomic
+processors      * * 1
+
+# System and atom definition
+read_data       BN.data     # read lammps data file
+
+# Neighbor update settings 
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+# Potential
+pair_style      extep
+pair_coeff      * * ../../../../potentials/BN.extep B N
+
+# Output 
+thermo          10
+thermo_style    custom step time etotal pe temp lx ly lz pxx pyy pzz
+thermo_modify   line one format float %14.8g
+
+# Setup NPT MD run
+timestep        0.0001 # ps
+velocity        all create 300.0 12345
+fix             thermos all npt temp 300 300 1.0 x 0 0 1.0 y 0 0 1.0
+run 1000

examples/USER/misc/extep/log.23Oct17.extep-bn.g++.1

@@ -0,0 +1,180 @@
+LAMMPS (23 Oct 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      atomic
+processors      * * 1
+
+# System and atom definition
+read_data       BN.data     # read lammps data file
+  orthogonal box = (0 0 0) to (21.75 12.5574 50)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  100 atoms
+
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+# Potential
+pair_style      extep
+pair_coeff      * * ../../../../potentials/BN.extep B N
+Reading potential file ../../../../potentials/BN.extep with DATE: 2017-11-28
+
+# Output
+thermo          10
+thermo_style    custom step time etotal pe temp lx ly lz pxx pyy pzz
+thermo_modify   line one format float %14.8g
+
+# Setup NPT MD run
+timestep        0.0001 # ps
+velocity        all create 300.0 12345
+fix             thermos all npt temp 300 300 1.0 x 0 0 1.0 y 0 0 1.0
+run 1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.2
+  ghost atom cutoff = 4.2
+  binsize = 2.1, bins = 11 6 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair extep, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.97 | 2.97 | 2.97 Mbytes
+Step Time TotEng PotEng Temp Lx Ly Lz Pxx Pyy Pzz 
+       0              0     -665.11189     -668.95092            300          21.75      12.557368             50     -1638.8315     -1636.7368      321.73163 
+      10          0.001     -665.11194     -668.81065      289.03491      21.749944      12.557333             50     -1391.3771     -1841.1723      316.66669 
+      20          0.002      -665.1121      -668.4273      259.06599      21.749789      12.557222             50     -1137.0171     -1980.5977      301.79466 
+      30          0.003     -665.11237     -667.90117      217.93027      21.749552      12.557029             50     -912.51949      -2055.822      278.00774 
+      40          0.004     -665.11278     -667.36471      175.97662       21.74925      12.556752             50     -755.38643     -2078.0669      246.62816 
+      50          0.005     -665.11333     -666.94254      142.94321      21.748894      12.556389             50     -694.93153     -2062.1349      209.26356 
+      60          0.006     -665.11405     -666.71476      125.08741      21.748487       12.55594             50      -744.6962     -2019.9093      167.70563 
+      70          0.007     -665.11494     -666.69555      123.51632      21.748026      12.555408             50     -898.67863     -1956.2845      123.88845 
+      80          0.008       -665.116     -666.83408      134.25892        21.7475      12.554796             50     -1132.5952      -1868.738       79.87581 
+      90          0.009      -665.1172     -667.03647      149.98053      21.746893      12.554106             50     -1409.6896     -1750.4875      37.821017 
+     100           0.01     -665.11853     -667.20002      162.65705      21.746185      12.553344             50     -1689.1599     -1595.9411    -0.14399002 
+     110          0.011     -665.11997     -667.24752      166.25742      21.745356      12.552516             50     -1934.6334     -1406.3665     -32.091026 
+     120          0.012     -665.12148     -667.15088      158.58671      21.744389       12.55163             50     -2120.4014     -1193.6117      -56.50543 
+     130          0.013     -665.12306     -666.93754       141.7922      21.743271      12.550694             50     -2234.0841     -980.32815      -72.45885 
+     140          0.014      -665.1247     -666.67903       121.4631      21.741993      12.549719             50     -2275.5656     -796.26701     -79.693692 
+     150          0.015      -665.1264     -666.46562      104.65306      21.740553       12.54871             50       -2253.08      -671.5409     -78.603431 
+     160          0.016      -665.1282     -666.37541      97.462619      21.738952      12.547674             50     -2178.0108     -628.83531     -70.130423 
+     170          0.017     -665.13011     -666.44775      102.96665      21.737195      12.546611             50     -2060.2073     -677.02227     -55.623931 
+     180          0.018     -665.13215     -666.67004      120.17784      21.735292       12.54552             50       -1905.36     -808.22824     -36.699042 
+     190          0.019     -665.13431     -666.98201      144.38814      21.733253      12.544396             50     -1715.2526      -999.2481     -15.117617 
+     200           0.02     -665.13656     -667.29591      168.74214      21.731091      12.543231             50     -1490.6934      -1216.735      7.3107732 
+     210          0.021     -665.13885     -667.52511      186.47391      21.728823      12.542015             50     -1235.9283     -1424.4324      28.822782 
+     220          0.022     -665.14112     -667.61153       193.0492      21.726467      12.540741             50     -962.70697     -1590.2885      47.801678 
+     230          0.023     -665.14332     -667.54317      187.53534      21.724043      12.539402             50     -692.12856     -1691.6537      62.881768 
+     240          0.024      -665.1454     -667.35665      172.79772       21.72157      12.537993             50     -453.02755     -1717.6064      73.041858 
+     250          0.025     -665.14735     -667.12424      154.48373      21.719064      12.536514             50     -276.81709     -1668.3598      77.670868 
+     260          0.026     -665.14918     -666.92939      139.11409      21.716539      12.534967             50     -190.03656     -1552.4049       76.59734 
+     270          0.027     -665.15091     -666.83859      131.88391         21.714      12.533357             50     -206.85537     -1382.4915      70.085105 
+     280          0.028     -665.15258     -666.87889      134.90214      21.711446       12.53169             50     -324.01795     -1171.7578      58.801327 
+     290          0.029     -665.15421     -667.02881      146.49028      21.708869      12.529975             50      -520.0146     -931.26466      43.758636 
+     300           0.03      -665.1558     -667.22646      161.81084      21.706255      12.528222             50     -758.87113     -669.74523      26.225956 
+     310          0.031     -665.15734     -667.39183      174.61368      21.703587      12.526442             50     -997.42782     -395.56111       7.601897 
+     320          0.032     -665.15878     -667.45546      179.47345      21.700849      12.524646             50     -1193.9402     -119.86797     -10.744258 
+     330          0.033     -665.16008     -667.38312      173.71901      21.698026      12.522846             50     -1315.6446       140.7451     -27.638433 
+     340          0.034     -665.16118     -667.18792      158.37888      21.695112      12.521051             50     -1343.5396      363.95099     -42.231049 
+     350          0.035     -665.16207     -666.92571      137.81938      21.692103      12.519271             50     -1273.6625      524.73453     -54.046178 
+     360          0.036     -665.16274     -666.67543      118.20885      21.689004      12.517514             50     -1115.1514      601.37143     -62.932702 
+     370          0.037      -665.1632      -666.5115      105.36258      21.685827      12.515781             50     -886.11568      582.42087     -68.942158 
+     380          0.038     -665.16348     -666.47849      102.76116      21.682589      12.514072             50     -608.71321      472.04732     -72.193259 
+     390          0.039      -665.1636     -666.57728      110.47178      21.679308      12.512382             50     -304.85697      291.41908     -72.787214 
+     400           0.04     -665.16356     -666.76741      125.33244      21.676006      12.510704             50      6.3732307      75.407852     -70.806087 
+     410          0.041     -665.16336     -666.98363      142.24457      21.672705       12.50903             50      309.23046     -134.40319     -66.378966 
+     420          0.042     -665.16298     -667.15939      156.00935      21.669426      12.507351             50      590.16982     -298.16702     -59.767469 
+     430          0.043     -665.16239     -667.24843      163.01313       21.66619       12.50566             50      836.19535     -385.22443     -51.420249 
+     440          0.044     -665.16157     -667.23746       162.2204      21.663014      12.503955             50       1033.943      -378.7816     -41.969885 
+     450          0.045      -665.1605     -667.14707      155.24066      21.659911      12.502234             50      1170.3399     -277.11556     -32.175503 
+     460          0.046     -665.15917      -667.0218      145.55489      21.656891      12.500503             50      1234.9026     -91.620499     -22.833423 
+     470          0.047     -665.15761     -666.91366      137.22578       21.65396      12.498768             50      1222.9519      157.31306     -14.680548 
+     480          0.048     -665.15585     -666.86462      133.53159      21.651114      12.497041             50      1138.5551       445.2926     -8.3071781 
+     490          0.049     -665.15393     -666.89359       135.9458       21.64835      12.495333             50      996.00682      748.51842     -4.0872169 
+     500           0.05     -665.15188     -666.99142      143.75058      21.645657      12.493655             50      819.08561      1046.9785     -2.1306918 
+     510          0.051     -665.14975     -667.12519      154.36991      21.643022       12.49202             50      637.99022      1325.7112     -2.2650822 
+     520          0.052     -665.14756        -667.25      164.29491      21.640432       12.49044             50      484.54509      1574.1916     -4.0528391 
+     530          0.053     -665.14531     -667.32459      170.29969      21.637878      12.488923             50      386.77357      1784.4858     -6.8479114 
+     540          0.054       -665.143     -667.32552      170.55254      21.635352       12.48748             50      364.14599      1949.2189     -9.8841824 
+     550          0.055     -665.14064     -667.25527      165.24765      21.632853      12.486117             50       424.6565      2060.4607      -12.37851 
+     560          0.056     -665.13822     -667.14127      156.52756      21.630385      12.484837             50       564.3912      2110.2547      -13.62742 
+     570          0.057     -665.13576      -667.0259      147.70502      21.627958      12.483643             50      769.54354      2092.8157     -13.082914 
+     580          0.058     -665.13327     -666.95107      142.05154      21.625586      12.482535             50      1020.1218      2007.6508     -10.405617 
+     590          0.059     -665.13079     -666.94279      141.59877      21.623287      12.481508             50      1294.1274      1862.3568     -5.5031153 
+     600           0.06     -665.12832     -667.00189      146.40928      21.621079      12.480557             50      1570.9478      1673.8456      1.4410957 
+     610          0.061     -665.12591     -667.10417      154.59072      21.618982      12.479674             50      1833.1388      1467.2639      9.9561573 
+     620          0.062     -665.12355     -667.20973      163.02368      21.617015      12.478851             50      2066.4951      1272.6732      19.310607 
+     630          0.063     -665.12128     -667.27744      168.49239      21.615193       12.47808             50      2259.0193      1120.2758       28.59477 
+     640          0.064     -665.11911     -667.27898       168.7823      21.613531      12.477355             50       2399.792      1035.3525        36.8539 
+     650          0.065     -665.11707     -667.20773      163.37438      21.612037      12.476673             50      2478.6675      1034.0481      43.239368 
+     660          0.066     -665.11518      -667.0802      153.55598      21.610718      12.476033             50      2487.2505      1120.8274      47.131883 
+     670          0.067     -665.11345     -666.93026      141.97434      21.609573      12.475439             50      2420.9786      1288.0136      48.201717 
+     680          0.068     -665.11191     -666.79864      131.80955      21.608598      12.474897             50      2281.6131      1517.4002      46.399066 
+     690          0.069     -665.11056     -666.72065      125.82027      21.607784      12.474418             50      2079.2055      1783.5346      41.895586 
+     700           0.07     -665.10941     -666.71578       125.5291      21.607116      12.474011             50      1832.7039      2057.9076      35.011051 
+     710          0.071     -665.10848     -666.78203      130.77932      21.606577      12.473687             50      1568.7275      2313.0601      26.153491 
+     720          0.072     -665.10776     -666.89681      139.80468      21.606148      12.473458             50      1318.5189      2525.6808      15.783637 
+     730          0.073     -665.10727      -667.0243      149.80574      21.605812       12.47333             50      1113.5537      2678.1859      4.3967762 
+     740          0.074     -665.10701     -667.12698      157.85016      21.605555      12.473311             50        980.633      2758.9123     -7.4930622 
+     750          0.075     -665.10697     -667.17729      161.78497      21.605368      12.473404             50      937.45086      2761.5936     -19.376492 
+     760          0.076     -665.10714      -667.1654      160.84249      21.605247      12.473609             50       989.5724      2684.9256     -30.776106 
+     770          0.077      -665.1075     -667.10061      155.75086      21.605196      12.473922             50      1129.4775      2532.7048     -41.263677 
+     780          0.078     -665.10803     -667.00654      148.35835      21.605226      12.474338             50      1337.8663      2314.4556     -50.455407 
+     790          0.079     -665.10869     -666.91242       140.9515      21.605349      12.474848             50      1586.9099      2045.9808     -57.988114 
+     800           0.08     -665.10946     -666.84375      135.52533      21.605585      12.475441             50      1844.7038      1749.1281     -63.495405 
+     810          0.081     -665.11032     -666.81538      133.24173       21.60595      12.476105             50      2079.9601      1450.3113      -66.60795 
+     820          0.082     -665.11127     -666.82877      134.21424      21.606461      12.476828             50      2266.0059      1177.7937     -66.990929 
+     830          0.083      -665.1123     -666.87353       137.6312      21.607131      12.477599             50      2383.4351      958.19752     -64.411861 
+     840          0.084     -665.11343     -666.93214      142.12323      21.607968      12.478409             50      2421.1969      812.91475     -58.816538 
+     850          0.085     -665.11467     -666.98597       146.2321      21.608975      12.479253             50      2376.3483      755.06052     -50.389393 
+     860          0.086     -665.11603     -667.02075      148.84448      21.610149      12.480128             50      2252.9811      787.43069     -39.585062 
+     870          0.087      -665.1175     -667.03045      149.48743      21.611481      12.481034             50       2060.884      901.76342     -27.129117 
+     880          0.088     -665.11907     -667.01838      148.42091      21.612958      12.481978             50      1814.3354      1079.4855     -13.988401 
+     890          0.089     -665.12073     -666.99552      146.50471      21.614562      12.482966             50      1531.1565      1293.9709      -1.305884 
+     900           0.09     -665.12247     -666.97639      144.87389      21.616275      12.484007             50      1231.9005      1514.0741      9.7083525 
+     910          0.091     -665.12426     -666.97371      144.52455      21.618074      12.485109             50      938.90089       1708.364      17.929974 
+     920          0.092     -665.12609     -666.99389      145.95889       21.61994      12.486281             50      674.90767      1849.2415      22.497207 
+     930          0.093     -665.12794     -667.03498      149.02559      21.621853      12.487528             50      461.18604      1916.1468      22.971745 
+     940          0.094     -665.12977     -667.08777      153.00718        21.6238      12.488852             50      315.19601      1897.3867       19.43758 
+     950          0.095     -665.13156     -667.13925       156.8903       21.62577      12.490254             50      248.20946      1790.5667      12.504818 
+     960          0.096     -665.13326     -667.17668      159.68273      21.627757      12.491728             50      263.35912      1601.9528      3.2123256 
+     970          0.097     -665.13485     -667.19079       160.6611      21.629764      12.493267             50      354.58496      1345.1489     -7.1487162 
+     980          0.098     -665.13628     -667.17758       159.5175      21.631796      12.494862             50       506.7626       1039.346     -17.249179 
+     990          0.099     -665.13753     -667.13942      156.43758      21.633864      12.496499             50      697.06054      707.26671      -25.92737 
+    1000            0.1     -665.13859      -667.0853      152.12472      21.635982      12.498164             50      897.38498      372.94791     -32.344697 
+Loop time of 0.463574 on 1 procs for 1000 steps with 100 atoms
+
+Performance: 18.638 ns/day, 1.288 hours/ns, 2157.152 timesteps/s
+99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.44776    | 0.44776    | 0.44776    |   0.0 | 96.59
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0023057  | 0.0023057  | 0.0023057  |   0.0 |  0.50
+Output  | 0.0015752  | 0.0015752  | 0.0015752  |   0.0 |  0.34
+Modify  | 0.010602   | 0.010602   | 0.010602   |   0.0 |  2.29
+Other   |            | 0.001331   |            |       |  0.29
+
+Nlocal:    100 ave 100 max 100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    360 ave 360 max 360 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:  1800 ave 1800 max 1800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1800
+Ave neighs/atom = 18
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/USER/misc/extep/log.23Oct17.extep-bn.g++.4

@@ -0,0 +1,180 @@
+LAMMPS (23 Oct 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      atomic
+processors      * * 1
+
+# System and atom definition
+read_data       BN.data     # read lammps data file
+  orthogonal box = (0 0 0) to (21.75 12.5574 50)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  100 atoms
+
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+# Potential
+pair_style      extep
+pair_coeff      * * ../../../../potentials/BN.extep B N
+Reading potential file ../../../../potentials/BN.extep with DATE: 2017-11-28
+
+# Output
+thermo          10
+thermo_style    custom step time etotal pe temp lx ly lz pxx pyy pzz
+thermo_modify   line one format float %14.8g
+
+# Setup NPT MD run
+timestep        0.0001 # ps
+velocity        all create 300.0 12345
+fix             thermos all npt temp 300 300 1.0 x 0 0 1.0 y 0 0 1.0
+run 1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.2
+  ghost atom cutoff = 4.2
+  binsize = 2.1, bins = 11 6 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair extep, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.943 | 2.943 | 2.943 Mbytes
+Step Time TotEng PotEng Temp Lx Ly Lz Pxx Pyy Pzz 
+       0              0     -665.11189     -668.95092            300          21.75      12.557368             50     -1638.8315     -1636.7368      321.73163 
+      10          0.001     -665.11194     -668.81065      289.03491      21.749944      12.557333             50     -1391.3771     -1841.1723      316.66669 
+      20          0.002      -665.1121      -668.4273      259.06599      21.749789      12.557222             50     -1137.0171     -1980.5977      301.79466 
+      30          0.003     -665.11237     -667.90117      217.93027      21.749552      12.557029             50     -912.51949      -2055.822      278.00774 
+      40          0.004     -665.11278     -667.36471      175.97662       21.74925      12.556752             50     -755.38643     -2078.0669      246.62816 
+      50          0.005     -665.11333     -666.94254      142.94321      21.748894      12.556389             50     -694.93153     -2062.1349      209.26356 
+      60          0.006     -665.11405     -666.71476      125.08741      21.748487       12.55594             50      -744.6962     -2019.9093      167.70563 
+      70          0.007     -665.11494     -666.69555      123.51632      21.748026      12.555408             50     -898.67863     -1956.2845      123.88845 
+      80          0.008       -665.116     -666.83408      134.25892        21.7475      12.554796             50     -1132.5952      -1868.738       79.87581 
+      90          0.009      -665.1172     -667.03647      149.98053      21.746893      12.554106             50     -1409.6896     -1750.4875      37.821017 
+     100           0.01     -665.11853     -667.20002      162.65705      21.746185      12.553344             50     -1689.1599     -1595.9411    -0.14399002 
+     110          0.011     -665.11997     -667.24752      166.25742      21.745356      12.552516             50     -1934.6334     -1406.3665     -32.091026 
+     120          0.012     -665.12148     -667.15088      158.58671      21.744389       12.55163             50     -2120.4014     -1193.6117      -56.50543 
+     130          0.013     -665.12306     -666.93754       141.7922      21.743271      12.550694             50     -2234.0841     -980.32815      -72.45885 
+     140          0.014      -665.1247     -666.67903       121.4631      21.741993      12.549719             50     -2275.5656     -796.26701     -79.693692 
+     150          0.015      -665.1264     -666.46562      104.65306      21.740553       12.54871             50       -2253.08      -671.5409     -78.603431 
+     160          0.016      -665.1282     -666.37541      97.462619      21.738952      12.547674             50     -2178.0108     -628.83531     -70.130423 
+     170          0.017     -665.13011     -666.44775      102.96665      21.737195      12.546611             50     -2060.2073     -677.02227     -55.623931 
+     180          0.018     -665.13215     -666.67004      120.17784      21.735292       12.54552             50       -1905.36     -808.22824     -36.699042 
+     190          0.019     -665.13431     -666.98201      144.38814      21.733253      12.544396             50     -1715.2526      -999.2481     -15.117617 
+     200           0.02     -665.13656     -667.29591      168.74214      21.731091      12.543231             50     -1490.6934      -1216.735      7.3107732 
+     210          0.021     -665.13885     -667.52511      186.47391      21.728823      12.542015             50     -1235.9283     -1424.4324      28.822782 
+     220          0.022     -665.14112     -667.61153       193.0492      21.726467      12.540741             50     -962.70697     -1590.2885      47.801678 
+     230          0.023     -665.14332     -667.54317      187.53534      21.724043      12.539402             50     -692.12856     -1691.6537      62.881768 
+     240          0.024      -665.1454     -667.35665      172.79772       21.72157      12.537993             50     -453.02755     -1717.6064      73.041858 
+     250          0.025     -665.14735     -667.12424      154.48373      21.719064      12.536514             50     -276.81709     -1668.3598      77.670868 
+     260          0.026     -665.14918     -666.92939      139.11409      21.716539      12.534967             50     -190.03656     -1552.4049       76.59734 
+     270          0.027     -665.15091     -666.83859      131.88391         21.714      12.533357             50     -206.85537     -1382.4915      70.085105 
+     280          0.028     -665.15258     -666.87889      134.90214      21.711446       12.53169             50     -324.01795     -1171.7578      58.801327 
+     290          0.029     -665.15421     -667.02881      146.49028      21.708869      12.529975             50      -520.0146     -931.26466      43.758636 
+     300           0.03      -665.1558     -667.22646      161.81084      21.706255      12.528222             50     -758.87113     -669.74523      26.225956 
+     310          0.031     -665.15734     -667.39183      174.61368      21.703587      12.526442             50     -997.42782     -395.56111       7.601897 
+     320          0.032     -665.15878     -667.45546      179.47345      21.700849      12.524646             50     -1193.9402     -119.86797     -10.744258 
+     330          0.033     -665.16008     -667.38312      173.71901      21.698026      12.522846             50     -1315.6446       140.7451     -27.638433 
+     340          0.034     -665.16118     -667.18792      158.37888      21.695112      12.521051             50     -1343.5396      363.95099     -42.231049 
+     350          0.035     -665.16207     -666.92571      137.81938      21.692103      12.519271             50     -1273.6625      524.73453     -54.046178 
+     360          0.036     -665.16274     -666.67543      118.20885      21.689004      12.517514             50     -1115.1514      601.37143     -62.932702 
+     370          0.037      -665.1632      -666.5115      105.36258      21.685827      12.515781             50     -886.11568      582.42087     -68.942158 
+     380          0.038     -665.16348     -666.47849      102.76116      21.682589      12.514072             50     -608.71321      472.04732     -72.193259 
+     390          0.039      -665.1636     -666.57728      110.47178      21.679308      12.512382             50     -304.85697      291.41908     -72.787214 
+     400           0.04     -665.16356     -666.76741      125.33244      21.676006      12.510704             50      6.3732307      75.407852     -70.806087 
+     410          0.041     -665.16336     -666.98363      142.24457      21.672705       12.50903             50      309.23046     -134.40319     -66.378966 
+     420          0.042     -665.16298     -667.15939      156.00935      21.669426      12.507351             50      590.16982     -298.16702     -59.767469 
+     430          0.043     -665.16239     -667.24843      163.01313       21.66619       12.50566             50      836.19535     -385.22443     -51.420249 
+     440          0.044     -665.16157     -667.23746       162.2204      21.663014      12.503955             50       1033.943      -378.7816     -41.969885 
+     450          0.045      -665.1605     -667.14707      155.24066      21.659911      12.502234             50      1170.3399     -277.11556     -32.175503 
+     460          0.046     -665.15917      -667.0218      145.55489      21.656891      12.500503             50      1234.9026     -91.620499     -22.833423 
+     470          0.047     -665.15761     -666.91366      137.22578       21.65396      12.498768             50      1222.9519      157.31306     -14.680548 
+     480          0.048     -665.15585     -666.86462      133.53159      21.651114      12.497041             50      1138.5551       445.2926     -8.3071781 
+     490          0.049     -665.15393     -666.89359       135.9458       21.64835      12.495333             50      996.00682      748.51842     -4.0872169 
+     500           0.05     -665.15188     -666.99142      143.75058      21.645657      12.493655             50      819.08561      1046.9785     -2.1306918 
+     510          0.051     -665.14975     -667.12519      154.36991      21.643022       12.49202             50      637.99022      1325.7112     -2.2650822 
+     520          0.052     -665.14756        -667.25      164.29491      21.640432       12.49044             50      484.54509      1574.1916     -4.0528391 
+     530          0.053     -665.14531     -667.32459      170.29969      21.637878      12.488923             50      386.77357      1784.4858     -6.8479114 
+     540          0.054       -665.143     -667.32552      170.55254      21.635352       12.48748             50      364.14599      1949.2189     -9.8841824 
+     550          0.055     -665.14064     -667.25527      165.24765      21.632853      12.486117             50       424.6565      2060.4607      -12.37851 
+     560          0.056     -665.13822     -667.14127      156.52756      21.630385      12.484837             50       564.3912      2110.2547      -13.62742 
+     570          0.057     -665.13576      -667.0259      147.70502      21.627958      12.483643             50      769.54354      2092.8157     -13.082914 
+     580          0.058     -665.13327     -666.95107      142.05154      21.625586      12.482535             50      1020.1218      2007.6508     -10.405617 
+     590          0.059     -665.13079     -666.94279      141.59877      21.623287      12.481508             50      1294.1274      1862.3568     -5.5031153 
+     600           0.06     -665.12832     -667.00189      146.40928      21.621079      12.480557             50      1570.9478      1673.8456      1.4410957 
+     610          0.061     -665.12591     -667.10417      154.59072      21.618982      12.479674             50      1833.1388      1467.2639      9.9561573 
+     620          0.062     -665.12355     -667.20973      163.02368      21.617015      12.478851             50      2066.4951      1272.6732      19.310607 
+     630          0.063     -665.12128     -667.27744      168.49239      21.615193       12.47808             50      2259.0193      1120.2758       28.59477 
+     640          0.064     -665.11911     -667.27898       168.7823      21.613531      12.477355             50       2399.792      1035.3525        36.8539 
+     650          0.065     -665.11707     -667.20773      163.37438      21.612037      12.476673             50      2478.6675      1034.0481      43.239368 
+     660          0.066     -665.11518      -667.0802      153.55598      21.610718      12.476033             50      2487.2505      1120.8274      47.131883 
+     670          0.067     -665.11345     -666.93026      141.97434      21.609573      12.475439             50      2420.9786      1288.0136      48.201717 
+     680          0.068     -665.11191     -666.79864      131.80955      21.608598      12.474897             50      2281.6131      1517.4002      46.399066 
+     690          0.069     -665.11056     -666.72065      125.82027      21.607784      12.474418             50      2079.2055      1783.5346      41.895586 
+     700           0.07     -665.10941     -666.71578       125.5291      21.607116      12.474011             50      1832.7039      2057.9076      35.011051 
+     710          0.071     -665.10848     -666.78203      130.77932      21.606577      12.473687             50      1568.7275      2313.0601      26.153491 
+     720          0.072     -665.10776     -666.89681      139.80468      21.606148      12.473458             50      1318.5189      2525.6808      15.783637 
+     730          0.073     -665.10727      -667.0243      149.80574      21.605812       12.47333             50      1113.5537      2678.1859      4.3967762 
+     740          0.074     -665.10701     -667.12698      157.85016      21.605555      12.473311             50        980.633      2758.9123     -7.4930622 
+     750          0.075     -665.10697     -667.17729      161.78497      21.605368      12.473404             50      937.45086      2761.5936     -19.376492 
+     760          0.076     -665.10714      -667.1654      160.84249      21.605247      12.473609             50       989.5724      2684.9256     -30.776106 
+     770          0.077      -665.1075     -667.10061      155.75086      21.605196      12.473922             50      1129.4775      2532.7048     -41.263677 
+     780          0.078     -665.10803     -667.00654      148.35835      21.605226      12.474338             50      1337.8663      2314.4556     -50.455407 
+     790          0.079     -665.10869     -666.91242       140.9515      21.605349      12.474848             50      1586.9099      2045.9808     -57.988114 
+     800           0.08     -665.10946     -666.84375      135.52533      21.605585      12.475441             50      1844.7038      1749.1281     -63.495405 
+     810          0.081     -665.11032     -666.81538      133.24173       21.60595      12.476105             50      2079.9601      1450.3113      -66.60795 
+     820          0.082     -665.11127     -666.82877      134.21424      21.606461      12.476828             50      2266.0059      1177.7937     -66.990929 
+     830          0.083      -665.1123     -666.87353       137.6312      21.607131      12.477599             50      2383.4351      958.19752     -64.411861 
+     840          0.084     -665.11343     -666.93214      142.12323      21.607968      12.478409             50      2421.1969      812.91475     -58.816538 
+     850          0.085     -665.11467     -666.98597       146.2321      21.608975      12.479253             50      2376.3483      755.06052     -50.389393 
+     860          0.086     -665.11603     -667.02075      148.84448      21.610149      12.480128             50      2252.9811      787.43069     -39.585062 
+     870          0.087      -665.1175     -667.03045      149.48743      21.611481      12.481034             50       2060.884      901.76342     -27.129117 
+     880          0.088     -665.11907     -667.01838      148.42091      21.612958      12.481978             50      1814.3354      1079.4855     -13.988401 
+     890          0.089     -665.12073     -666.99552      146.50471      21.614562      12.482966             50      1531.1565      1293.9709      -1.305884 
+     900           0.09     -665.12247     -666.97639      144.87389      21.616275      12.484007             50      1231.9005      1514.0741      9.7083525 
+     910          0.091     -665.12426     -666.97371      144.52455      21.618074      12.485109             50      938.90089       1708.364      17.929974 
+     920          0.092     -665.12609     -666.99389      145.95889       21.61994      12.486281             50      674.90767      1849.2415      22.497207 
+     930          0.093     -665.12794     -667.03498      149.02559      21.621853      12.487528             50      461.18604      1916.1468      22.971745 
+     940          0.094     -665.12977     -667.08777      153.00718        21.6238      12.488852             50      315.19601      1897.3867       19.43758 
+     950          0.095     -665.13156     -667.13925       156.8903       21.62577      12.490254             50      248.20946      1790.5667      12.504818 
+     960          0.096     -665.13326     -667.17668      159.68273      21.627757      12.491728             50      263.35912      1601.9528      3.2123256 
+     970          0.097     -665.13485     -667.19079       160.6611      21.629764      12.493267             50      354.58496      1345.1489     -7.1487162 
+     980          0.098     -665.13628     -667.17758       159.5175      21.631796      12.494862             50       506.7626       1039.346     -17.249179 
+     990          0.099     -665.13753     -667.13942      156.43758      21.633864      12.496499             50      697.06054      707.26671      -25.92737 
+    1000            0.1     -665.13859      -667.0853      152.12472      21.635982      12.498164             50      897.38498      372.94791     -32.344697 
+Loop time of 0.174508 on 4 procs for 1000 steps with 100 atoms
+
+Performance: 49.511 ns/day, 0.485 hours/ns, 5730.393 timesteps/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.12409    | 0.12834    | 0.13408    |   1.1 | 73.54
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.016369   | 0.021358   | 0.025324   |   2.7 | 12.24
+Output  | 0.0023892  | 0.0025101  | 0.0028272  |   0.4 |  1.44
+Modify  | 0.01733    | 0.018302   | 0.018958   |   0.5 | 10.49
+Other   |            | 0.003995   |            |       |  2.29
+
+Nlocal:    25 ave 26 max 24 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    179 ave 180 max 178 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  450 ave 468 max 432 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 1800
+Ave neighs/atom = 18
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/gcmc/in.gcmc.co2

@@ -67,6 +67,15 @@ variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
 fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
 
+# atom counts
+
+variable 	carbon atom "type==1"
+variable        oxygen atom "type==2"
+group 		carbon dynamic all var carbon
+group 	        oxygen dynamic all var oxygen
+variable        nC equal count(carbon)
+variable        nO equal count(oxygen)
+
 # output
 
 variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@@ -74,7 +83,7 @@ variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
 variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
 compute_modify  thermo_temp dynamic/dof yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
 thermo          1000
 
 # run

examples/gcmc/in.gcmc.h2o

@@ -72,6 +72,15 @@ variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
 fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
                 h2omol tfac_insert ${tfac} group h2o shake wshake
 
+# atom counts
+
+variable 	oxygen atom "type==1"
+variable 	hydrogen atom "type==2"
+group 	        oxygen dynamic all var oxygen
+group 		hydrogen dynamic all var hydrogen
+variable        nO equal count(oxygen)
+variable        nH equal count(hydrogen)
+
 # output
 
 variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@@ -79,7 +88,7 @@ variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
 variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
 compute_modify  thermo_temp dynamic/dof yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
 thermo          1000
 
 # run

examples/gcmc/in.gcmc.lj

@@ -33,6 +33,12 @@ mass		* 1.0
 
 fix             mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
 
+# atom count
+
+variable 	type1 atom "type==1"
+group 		type1 dynamic all var type1
+variable        n1 equal count(type1)
+
 # averaging
 
 variable	rho equal density
@@ -40,10 +46,11 @@ variable	p equal press
 variable	nugget equal 1.0e-8
 variable        lambda equal 1.0
 variable     	muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
-fix 		ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
+fix 		ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
 variable	rhoav equal f_ave[1]
 variable	pav equal f_ave[2]
 variable	muexav equal f_ave[3]
+variable	n1av equal f_ave[4]
 
 # output
 
@@ -51,7 +58,7 @@ variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
 variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
 compute_modify  thermo_temp dynamic yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
 thermo          1000
 
 # run

examples/gcmc/log.23Oct17.gcmc.co2.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (6 Jul 2017)
+LAMMPS (23 Oct 2017)
   using 1 OpenMP thread(s) per MPI task
 # GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
 # Rigid CO2 TraPPE model
@@ -46,6 +46,7 @@ Read molecule co2mol:
   0 impropers with 0 types
 create_atoms   	0 box mol co2mol 464563 units box
 Created 24 atoms
+  Time spent = 0.00196958 secs
 
 # rigid CO2 TraPPE model
 
@@ -87,6 +88,17 @@ fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
 fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
 fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
 
+# atom counts
+
+variable 	carbon atom "type==1"
+variable        oxygen atom "type==2"
+group 		carbon dynamic all var carbon
+dynamic group carbon defined
+group 	        oxygen dynamic all var oxygen
+dynamic group oxygen defined
+variable        nC equal count(carbon)
+variable        nO equal count(oxygen)
+
 # output
 
 variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@@ -94,7 +106,7 @@ variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
 variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
 compute_modify  thermo_temp dynamic/dof yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
 thermo          1000
 
 # run
@@ -124,45 +136,45 @@ Neighbor list info ...
       stencil: half/bin/3d/newton
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc 
-       0    364.27579    4238.8631   -9.6809388    13.391989    0.5846359       24            0            0            0            0 
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 
+       0    364.27579    4238.8631   -9.6809388    13.391989    0.5846359       24            0            0            0            0            8           16 
 WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
-    1000    420.43475    1722.4052   -9.6956123    15.456579    0.5846359       24   0.20879341   0.20713005            0            0 
-    2000    302.29516   -547.83641   -22.017674     14.11699   0.73079488       30    0.1742478    0.1678018            0            0 
-    3000     316.6934   -1080.2672   -8.2218891    10.069364   0.51155641       21   0.13544917   0.13720634            0            0 
-    4000    246.81618   -679.83642   -14.577244     10.29997   0.65771539       27    0.1568939   0.15860229            0            0 
-    5000    260.22849   -896.29914   -16.097593    10.859684   0.65771539       27   0.13138744   0.13547049            0            0 
-    6000    291.70796     -1521.99   -22.303136    13.622574   0.73079488       30   0.12615476   0.12717694            0            0 
-    7000    236.02638   -599.92186   -27.580831    13.367447   0.87695385       36     0.119703   0.12145398            0            0 
-    8000    321.45341    688.10577    -10.09204    11.817696    0.5846359       24   0.10917411   0.11032646            0            0 
-    9000    502.85382   -302.31056  -0.22330142   0.99927447  0.073079488        3    0.1254105   0.12905828            0            0 
-   10000    249.98239    -510.0091   -32.815145    15.399767   0.95003334       39    0.1274504   0.12875623            0            0 
-   11000    247.59424   -1129.0274   -25.320205    12.792544   0.80387436       33   0.11739076   0.11916784            0            0 
-   12000            0    -20.39554  -0.14872889           -0            0        0    0.1254933   0.12920375            0            0 
-   13000    1272.2738   -474.79484  -0.29450485    8.8489483   0.14615898        6   0.13767133   0.14112496            0            0 
-   14000    516.54246   -36.296516   -5.0012009    11.291243   0.36539744       15   0.15632744   0.15955377            0            0 
-   15000    307.09233    1951.9301   -14.820362    12.815375   0.65771539       27   0.15393544   0.15716192            0            0 
-   16000    198.31989   -559.48443   -30.459487    11.231925   0.87695385       36    0.1482565   0.15025652            0            0 
-   17000    246.99311    657.85683   -18.579206     11.53442   0.73079488       30   0.14143958   0.14375423            0            0 
-   18000    467.13468    167.03738   -1.0945268     5.569759   0.21923846        9   0.13847359   0.14098533            0            0 
-   19000    359.54027   -1413.5407   -12.156233    13.217895    0.5846359       24   0.15169146   0.15294205            0            0 
-   20000    227.79597   -1204.5652    -23.24144    10.637925   0.73079488       30   0.14917199   0.15022946            0            0 
-Loop time of 20.153 on 1 procs for 20000 steps with 30 atoms
+    1000    420.43475    1722.4052   -9.6956123    15.456579    0.5846359       24   0.20879341   0.20713005            0            0            8           16 
+    2000    302.29516   -547.83641   -22.017674     14.11699   0.73079488       30    0.1742478    0.1678018            0            0           10           20 
+    3000     316.6934   -1080.2672   -8.2218891    10.069364   0.51155641       21   0.13544917   0.13720634            0            0            7           14 
+    4000    246.81618   -679.83642   -14.577244     10.29997   0.65771539       27    0.1568939   0.15860229            0            0            9           18 
+    5000    260.22849   -896.29914   -16.097593    10.859684   0.65771539       27   0.13138744   0.13547049            0            0            9           18 
+    6000    291.70796     -1521.99   -22.303136    13.622574   0.73079488       30   0.12615476   0.12717694            0            0           10           20 
+    7000    236.02638   -599.92186   -27.580831    13.367447   0.87695385       36     0.119703   0.12145398            0            0           12           24 
+    8000    321.45341    688.10577    -10.09204    11.817696    0.5846359       24   0.10917411   0.11032646            0            0            8           16 
+    9000    502.85382   -302.31056  -0.22330142   0.99927447  0.073079488        3    0.1254105   0.12905828            0            0            1            2 
+   10000    249.98239    -510.0091   -32.815145    15.399767   0.95003334       39    0.1274504   0.12875623            0            0           13           26 
+   11000    247.59424   -1129.0274   -25.320205    12.792544   0.80387436       33   0.11739076   0.11916784            0            0           11           22 
+   12000            0    -20.39554  -0.14872889           -0            0        0    0.1254933   0.12920375            0            0            0            0 
+   13000    1272.2738   -474.79484  -0.29450485    8.8489483   0.14615898        6   0.13767133   0.14112496            0            0            2            4 
+   14000    516.54246   -36.296516   -5.0012009    11.291243   0.36539744       15   0.15632744   0.15955377            0            0            5           10 
+   15000    307.09233    1951.9301   -14.820362    12.815375   0.65771539       27   0.15393544   0.15716192            0            0            9           18 
+   16000    198.31989   -559.48443   -30.459487    11.231925   0.87695385       36    0.1482565   0.15025652            0            0           12           24 
+   17000    246.99311    657.85683   -18.579206     11.53442   0.73079488       30   0.14143958   0.14375423            0            0           10           20 
+   18000    467.13468    167.03738   -1.0945268     5.569759   0.21923846        9   0.13847359   0.14098533            0            0            3            6 
+   19000    359.54027   -1413.5407   -12.156233    13.217895    0.5846359       24   0.15169146   0.15294205            0            0            8           16 
+   20000    227.79597   -1204.5652    -23.24144    10.637925   0.73079488       30   0.14917199   0.15022946            0            0           10           20 
+Loop time of 20.6928 on 1 procs for 20000 steps with 30 atoms
 
-Performance: 85.744 ns/day, 0.280 hours/ns, 992.408 timesteps/s
-99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 83.507 ns/day, 0.287 hours/ns, 966.519 timesteps/s
+99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.5352     | 2.5352     | 2.5352     |   0.0 | 12.58
-Bond    | 0.026112   | 0.026112   | 0.026112   |   0.0 |  0.13
-Kspace  | 0.25       | 0.25       | 0.25       |   0.0 |  1.24
-Neigh   | 0.10364    | 0.10364    | 0.10364    |   0.0 |  0.51
-Comm    | 0.22907    | 0.22907    | 0.22907    |   0.0 |  1.14
-Output  | 0.0013065  | 0.0013065  | 0.0013065  |   0.0 |  0.01
-Modify  | 16.957     | 16.957     | 16.957     |   0.0 | 84.14
-Other   |            | 0.05061    |            |       |  0.25
+Pair    | 2.5462     | 2.5462     | 2.5462     |   0.0 | 12.30
+Bond    | 0.029783   | 0.029783   | 0.029783   |   0.0 |  0.14
+Kspace  | 0.26167    | 0.26167    | 0.26167    |   0.0 |  1.26
+Neigh   | 0.10705    | 0.10705    | 0.10705    |   0.0 |  0.52
+Comm    | 0.23409    | 0.23409    | 0.23409    |   0.0 |  1.13
+Output  | 0.0013416  | 0.0013416  | 0.0013416  |   0.0 |  0.01
+Modify  | 17.458     | 17.458     | 17.458     |   0.0 | 84.37
+Other   |            | 0.05433    |            |       |  0.26
 
 Nlocal:    30 ave 30 max 30 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/gcmc/log.23Oct17.gcmc.co2.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (6 Jul 2017)
+LAMMPS (23 Oct 2017)
   using 1 OpenMP thread(s) per MPI task
 # GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
 # Rigid CO2 TraPPE model
@@ -46,6 +46,7 @@ Read molecule co2mol:
   0 impropers with 0 types
 create_atoms   	0 box mol co2mol 464563 units box
 Created 24 atoms
+  Time spent = 0.00261331 secs
 
 # rigid CO2 TraPPE model
 
@@ -87,6 +88,17 @@ fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
 fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
 fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
 
+# atom counts
+
+variable 	carbon atom "type==1"
+variable        oxygen atom "type==2"
+group 		carbon dynamic all var carbon
+dynamic group carbon defined
+group 	        oxygen dynamic all var oxygen
+dynamic group oxygen defined
+variable        nC equal count(carbon)
+variable        nO equal count(oxygen)
+
 # output
 
 variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@@ -94,7 +106,7 @@ variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
 variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
 compute_modify  thermo_temp dynamic/dof yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
 thermo          1000
 
 # run
@@ -124,45 +136,45 @@ Neighbor list info ...
       stencil: half/bin/3d/newton
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 15.41 | 15.41 | 15.41 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc 
-       0    386.52184    23582.465   -3.2433417    14.209828    0.5846359       24            0            0            0            0 
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 
+       0    386.52184    23582.465   -3.2433417    14.209828    0.5846359       24            0            0            0            0            8           16 
 WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
-    1000    335.66829   -3.7743052   -4.6268612    7.3374649   0.36539744       15   0.20601899   0.20787963            0            0 
-    2000    459.73529    238.91592  -0.42937831    5.4815343   0.21923846        9   0.30392058   0.30105616            0            0 
-    3000    255.47773   -479.67802   -36.850434    15.738299   0.95003334       39   0.22220744    0.2197582            0            0 
-    4000    182.70803   -1059.2262   -43.044833    12.163134    1.0231128       42   0.16781689   0.16716177            0            0 
-    5000    234.00907   -1821.0444    -46.04795    15.578317    1.0231128       42   0.13498091   0.13704201            0            0 
-    6000    163.42759   -774.67294   -49.686261    11.691518    1.0961923       45   0.11401677   0.11296973            0            0 
-    7000    171.64616   -355.23516   -49.323434     12.27947    1.0961923       45  0.098302308  0.098552065            0            0 
-    8000    251.29791   -905.47863   -37.841209    15.480807   0.95003334       39  0.086856972   0.08638658            0            0 
-    9000    143.69498   -849.95393   -49.073188    10.279858    1.0961923       45  0.078261061  0.077955243            0            0 
-   10000    239.35727   -1158.1879   -43.562047    15.934355    1.0231128       42  0.070789792  0.070807529            0            0 
-   11000    169.51213   -1574.7885   -51.125228    12.126803    1.0961923       45  0.065008734   0.06498871            0            0 
-   12000    181.39739    160.11631   -46.850937    12.977068    1.0961923       45  0.059648717  0.059514803            0            0 
-   13000    164.14601   -1107.7629   -50.726722    11.742914    1.0961923       45  0.055207333  0.055097701            0            0 
-   14000    287.26285    418.51463   -41.664766    19.123497    1.0231128       42  0.051346789  0.051222285            0            0 
-   15000    256.94593   -532.36615   -41.651618    17.105257    1.0231128       42  0.047870301  0.047861685            0            0 
-   16000    166.92132    151.15933   -39.957018     11.11219    1.0231128       42  0.045205599  0.045042211            0            0 
-   17000    163.22452   -1299.8119   -42.677558    10.866089    1.0231128       42  0.043122086  0.042993687            0            0 
-   18000    158.01154    475.77329   -48.803162    11.304057    1.0961923       45  0.041016683  0.040647229            0            0 
-   19000    138.49297   -1585.1508   -47.517099    9.9077098    1.0961923       45  0.038929287  0.038436764            0            0 
-   20000    173.84439   -1362.6301   -53.002743    12.436731    1.0961923       45  0.036973919  0.036523816            0            0 
-Loop time of 31.8386 on 4 procs for 20000 steps with 45 atoms
+    1000    335.66829   -3.7743052   -4.6268612    7.3374649   0.36539744       15   0.20601899   0.20787963            0            0            5           10 
+    2000    459.73529    238.91592  -0.42937831    5.4815343   0.21923846        9   0.30392058   0.30105616            0            0            3            6 
+    3000    255.47773   -479.67802   -36.850434    15.738299   0.95003334       39   0.22220744    0.2197582            0            0           13           26 
+    4000    182.70803   -1059.2262   -43.044833    12.163134    1.0231128       42   0.16781689   0.16716177            0            0           14           28 
+    5000    234.00907   -1821.0444    -46.04795    15.578317    1.0231128       42   0.13498091   0.13704201            0            0           14           28 
+    6000    163.42759   -774.67294   -49.686261    11.691518    1.0961923       45   0.11401677   0.11296973            0            0           15           30 
+    7000    171.64616   -355.23516   -49.323434     12.27947    1.0961923       45  0.098302308  0.098552065            0            0           15           30 
+    8000    251.29791   -905.47863   -37.841209    15.480807   0.95003334       39  0.086856972   0.08638658            0            0           13           26 
+    9000    143.69498   -849.95393   -49.073188    10.279858    1.0961923       45  0.078261061  0.077955243            0            0           15           30 
+   10000    239.35727   -1158.1879   -43.562047    15.934355    1.0231128       42  0.070789792  0.070807529            0            0           14           28 
+   11000    169.51213   -1574.7885   -51.125228    12.126803    1.0961923       45  0.065008734   0.06498871            0            0           15           30 
+   12000    181.39739    160.11631   -46.850937    12.977068    1.0961923       45  0.059648717  0.059514803            0            0           15           30 
+   13000    164.14601   -1107.7629   -50.726722    11.742914    1.0961923       45  0.055207333  0.055097701            0            0           15           30 
+   14000    287.26285    418.51463   -41.664766    19.123497    1.0231128       42  0.051346789  0.051222285            0            0           14           28 
+   15000    256.94593   -532.36615   -41.651618    17.105257    1.0231128       42  0.047870301  0.047861685            0            0           14           28 
+   16000    166.92132    151.15933   -39.957018     11.11219    1.0231128       42  0.045205599  0.045042211            0            0           14           28 
+   17000    163.22452   -1299.8119   -42.677558    10.866089    1.0231128       42  0.043122086  0.042993687            0            0           14           28 
+   18000    158.01154    475.77329   -48.803162    11.304057    1.0961923       45  0.041016683  0.040647229            0            0           15           30 
+   19000    138.49297   -1585.1508   -47.517099    9.9077098    1.0961923       45  0.038929287  0.038436764            0            0           15           30 
+   20000    173.84439   -1362.6301   -53.002743    12.436731    1.0961923       45  0.036973919  0.036523816            0            0           15           30 
+Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms
 
-Performance: 54.274 ns/day, 0.442 hours/ns, 628.168 timesteps/s
-98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 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    | 1.1546     | 1.6687     | 2.1338     |  29.5 |  5.24
-Bond    | 0.019769   | 0.020369   | 0.02132    |   0.4 |  0.06
-Kspace  | 0.53392    | 0.99911    | 1.5116     |  37.8 |  3.14
-Neigh   | 0.06737    | 0.067842   | 0.068412   |   0.2 |  0.21
-Comm    | 1.9408     | 1.9582     | 1.9733     |   1.1 |  6.15
-Output  | 0.0019503  | 0.0020472  | 0.0022476  |   0.3 |  0.01
-Modify  | 26.974     | 26.99      | 27.001     |   0.2 | 84.77
-Other   |            | 0.1322     |            |       |  0.42
+Pair    | 1.1687     | 1.6702     | 2.1864     |  30.8 |  5.15
+Bond    | 0.018828   | 0.020035   | 0.020975   |   0.6 |  0.06
+Kspace  | 0.57506    | 1.0931     | 1.5898     |  37.7 |  3.37
+Neigh   | 0.068863   | 0.069524   | 0.070128   |   0.2 |  0.21
+Comm    | 2.0735     | 2.0865     | 2.0979     |   0.7 |  6.43
+Output  | 0.0025017  | 0.0025966  | 0.0027781  |   0.2 |  0.01
+Modify  | 27.335     | 27.344     | 27.363     |   0.2 | 84.27
+Other   |            | 0.1621     |            |       |  0.50
 
 Nlocal:    11.25 ave 14 max 8 min
 Histogram: 1 0 0 0 0 1 1 0 0 1
@@ -177,4 +189,4 @@ Ave special neighs/atom = 2
 Neighbor list builds = 20394
 Dangerous builds = 0
 
-Total wall time: 0:00:31
+Total wall time: 0:00:32

examples/gcmc/log.23Oct17.gcmc.h2o.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (6 Jul 2017)
+LAMMPS (23 Oct 2017)
   using 1 OpenMP thread(s) per MPI task
 # fix gcmc example with fix shake
 
@@ -51,6 +51,7 @@ Read molecule h2omol:
   0 impropers with 0 types
 create_atoms   	0 box mol h2omol 464563 units box
 Created 24 atoms
+  Time spent = 0.00201297 secs
 
 # rigid SPC/E water model
 
@@ -100,9 +101,9 @@ Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          338   -4.1890564 9.2628112e-06     18.98377    739.06991 
      100          338   -30.182886   0.85607237   -6.1539961   -2535.3207 
-Loop time of 0.0525794 on 1 procs for 100 steps with 24 atoms
+Loop time of 0.0507543 on 1 procs for 100 steps with 24 atoms
 
-99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
@@ -116,14 +117,14 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.044199   | 0.044199   | 0.044199   |   0.0 | 84.06
-Bond    | 0.00049019 | 0.00049019 | 0.00049019 |   0.0 |  0.93
-Kspace  | 0.0031631  | 0.0031631  | 0.0031631  |   0.0 |  6.02
-Neigh   | 0.00046444 | 0.00046444 | 0.00046444 |   0.0 |  0.88
-Comm    | 0.0034101  | 0.0034101  | 0.0034101  |   0.0 |  6.49
-Output  | 1.9073e-05 | 1.9073e-05 | 1.9073e-05 |   0.0 |  0.04
+Pair    | 0.042597   | 0.042597   | 0.042597   |   0.0 | 83.93
+Bond    | 0.00047708 | 0.00047708 | 0.00047708 |   0.0 |  0.94
+Kspace  | 0.0031135  | 0.0031135  | 0.0031135  |   0.0 |  6.13
+Neigh   | 0.00045919 | 0.00045919 | 0.00045919 |   0.0 |  0.90
+Comm    | 0.0032997  | 0.0032997  | 0.0032997  |   0.0 |  6.50
+Output  | 1.359e-05  | 1.359e-05  | 1.359e-05  |   0.0 |  0.03
 Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.0008333  |            |       |  1.58
+Other   |            | 0.0007946  |            |       |  1.57
 
 Nlocal:    24 ave 24 max 24 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -164,22 +165,22 @@ Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0    518.26667   -30.182886            0   -7.0100684     993.1985 
     1000     326.9865   -62.258445            0   -47.638175   -5.3440813 
-Loop time of 0.14263 on 1 procs for 1000 steps with 24 atoms
+Loop time of 0.141449 on 1 procs for 1000 steps with 24 atoms
 
-Performance: 605.764 ns/day, 0.040 hours/ns, 7011.155 timesteps/s
-99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 610.819 ns/day, 0.039 hours/ns, 7069.663 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    | 0.10849    | 0.10849    | 0.10849    |   0.0 | 76.07
-Bond    | 0.00015426 | 0.00015426 | 0.00015426 |   0.0 |  0.11
-Kspace  | 0.01205    | 0.01205    | 0.01205    |   0.0 |  8.45
-Neigh   | 0.0046577  | 0.0046577  | 0.0046577  |   0.0 |  3.27
-Comm    | 0.011531   | 0.011531   | 0.011531   |   0.0 |  8.08
-Output  | 1.6212e-05 | 1.6212e-05 | 1.6212e-05 |   0.0 |  0.01
-Modify  | 0.0037699  | 0.0037699  | 0.0037699  |   0.0 |  2.64
-Other   |            | 0.001957   |            |       |  1.37
+Pair    | 0.10788    | 0.10788    | 0.10788    |   0.0 | 76.27
+Bond    | 0.00018954 | 0.00018954 | 0.00018954 |   0.0 |  0.13
+Kspace  | 0.011867   | 0.011867   | 0.011867   |   0.0 |  8.39
+Neigh   | 0.0045254  | 0.0045254  | 0.0045254  |   0.0 |  3.20
+Comm    | 0.011277   | 0.011277   | 0.011277   |   0.0 |  7.97
+Output  | 1.5497e-05 | 1.5497e-05 | 1.5497e-05 |   0.0 |  0.01
+Modify  | 0.00383    | 0.00383    | 0.00383    |   0.0 |  2.71
+Other   |            | 0.001868   |            |       |  1.32
 
 Nlocal:    24 ave 24 max 24 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -201,6 +202,17 @@ fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
 fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
 fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert 1.66666666666667 group h2o shake wshake
 
+# atom counts
+
+variable 	oxygen atom "type==1"
+variable 	hydrogen atom "type==2"
+group 	        oxygen dynamic all var oxygen
+dynamic group oxygen defined
+group 		hydrogen dynamic all var hydrogen
+dynamic group hydrogen defined
+variable        nO equal count(oxygen)
+variable        nH equal count(hydrogen)
+
 # output
 
 variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@@ -208,7 +220,7 @@ variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
 variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
 compute_modify  thermo_temp dynamic/dof yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
 thermo          1000
 
 # run
@@ -226,44 +238,44 @@ WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
 Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc 
-    1000     326.9865   -4.3509713   -62.258445     14.62027   0.23910963       24            0            0            0            0 
-    2000    116.99793   -5344.1527   -286.61595    17.088682   0.74721761       75  0.048183096  0.013941446            0            0 
-    3000    106.86746   -3920.4926   -361.60598    18.794545   0.89666113       90  0.035637919  0.012768883            0            0 
-    4000    75.002668    540.46846    -414.8511    14.531966   0.98632724       99  0.025963651 0.0093451705            0            0 
-    5000    79.924788   -2131.1173   -437.21216    15.962121    1.0162159      102  0.019879728 0.0070418993            0            0 
-    6000    95.552773   -3647.0233   -438.24276    19.083253    1.0162159      102  0.015753613 0.0056885133            0            0 
-    7000    79.501736   -2071.5369   -440.77351    15.877631    1.0162159      102   0.01326216 0.0046915318            0            0 
-    8000    62.567091   -3102.9616   -442.21884    12.495541    1.0162159      102  0.011305503 0.0040437885            0            0 
-    9000    68.324047   -3812.7866   -440.46835    13.645287    1.0162159      102 0.0099549538 0.0035157329            0            0 
-   10000    83.857631   -2158.2659    -444.8183    16.747566    1.0162159      102 0.0088200922 0.0031354281            0            0 
-   11000    68.350984   -2084.0789   -440.14081    13.650667    1.0162159      102 0.0081331455 0.0030247424            0            0 
-   12000    76.867315   -1585.6723   -443.36199      15.3515    1.0162159      102 0.0073845932 0.0027532534            0            0 
-   13000     59.74266   -2211.0211   -446.07791    11.931462    1.0162159      102 0.0067756276 0.0025213898            0            0 
-   14000    81.154979    -907.0176   -441.53368    16.207808    1.0162159      102 0.0062527642 0.0023280719            0            0 
-   15000    66.814346   -2804.5134   -455.80704      13.7421    1.0461046      105 0.0059590528 0.0021576214            0            0 
-   16000     71.42983   -3930.4004   -458.43218    14.691394    1.0461046      105 0.0055547473 0.0020163729            0            0 
-   17000    89.624855   -3569.8136   -455.18164    18.433672    1.0461046      105 0.0052173265 0.0018867687            0            0 
-   18000    63.519962   -1882.8157   -456.58939    13.064525    1.0461046      105 0.0049082049 0.0017765986            0            0 
-   19000    71.872698   -2243.5046   -454.93359    14.782481    1.0461046      105 0.0046439115 0.0016748361            0            0 
-   20000    73.660765   -2285.3173   -476.35473    15.589381    1.0759934      108 0.0045124933 0.0015837653            0            0 
-   21000    95.675868    987.92089   -475.46736    20.248603    1.0759934      108  0.004285814 0.0015049513            0            0 
-Loop time of 226.155 on 1 procs for 20000 steps with 108 atoms
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH 
+    1000     326.9865   -4.3509713   -62.258445     14.62027   0.23910963       24            0            0            0            0            8           16 
+    2000    116.99793   -5344.1527   -286.61595    17.088682   0.74721761       75  0.048183096  0.013941446            0            0           25           50 
+    3000    106.86746   -3920.4926   -361.60598    18.794545   0.89666113       90  0.035637919  0.012768883            0            0           30           60 
+    4000    75.002668    540.46846    -414.8511    14.531966   0.98632724       99  0.025963651 0.0093451705            0            0           33           66 
+    5000    79.924788   -2131.1173   -437.21216    15.962121    1.0162159      102  0.019879728 0.0070418993            0            0           34           68 
+    6000    95.552773   -3647.0233   -438.24276    19.083253    1.0162159      102  0.015753613 0.0056885133            0            0           34           68 
+    7000    79.501736   -2071.5369   -440.77351    15.877631    1.0162159      102   0.01326216 0.0046915318            0            0           34           68 
+    8000    62.567091   -3102.9616   -442.21884    12.495541    1.0162159      102  0.011305503 0.0040437885            0            0           34           68 
+    9000    68.324047   -3812.7866   -440.46835    13.645287    1.0162159      102 0.0099549538 0.0035157329            0            0           34           68 
+   10000    83.857631   -2158.2659    -444.8183    16.747566    1.0162159      102 0.0088200922 0.0031354281            0            0           34           68 
+   11000    68.350984   -2084.0789   -440.14081    13.650667    1.0162159      102 0.0081331455 0.0030247424            0            0           34           68 
+   12000    76.867315   -1585.6723   -443.36199      15.3515    1.0162159      102 0.0073845932 0.0027532534            0            0           34           68 
+   13000     59.74266   -2211.0211   -446.07791    11.931462    1.0162159      102 0.0067756276 0.0025213898            0            0           34           68 
+   14000    81.154979    -907.0176   -441.53368    16.207808    1.0162159      102 0.0062527642 0.0023280719            0            0           34           68 
+   15000    66.814346   -2804.5134   -455.80704      13.7421    1.0461046      105 0.0059590528 0.0021576214            0            0           35           70 
+   16000     71.42983   -3930.4004   -458.43218    14.691394    1.0461046      105 0.0055547473 0.0020163729            0            0           35           70 
+   17000    89.624855   -3569.8136   -455.18164    18.433672    1.0461046      105 0.0052173265 0.0018867687            0            0           35           70 
+   18000    63.519962   -1882.8157   -456.58939    13.064525    1.0461046      105 0.0049082049 0.0017765986            0            0           35           70 
+   19000    71.872698   -2243.5046   -454.93359    14.782481    1.0461046      105 0.0046439115 0.0016748361            0            0           35           70 
+   20000    73.660765   -2285.3173   -476.35473    15.589381    1.0759934      108 0.0045124933 0.0015837653            0            0           36           72 
+   21000    95.675868    987.92089   -475.46736    20.248603    1.0759934      108  0.004285814 0.0015049513            0            0           36           72 
+Loop time of 220.662 on 1 procs for 20000 steps with 108 atoms
 
-Performance: 7.641 ns/day, 3.141 hours/ns, 88.435 timesteps/s
-99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 7.831 ns/day, 3.065 hours/ns, 90.637 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    | 38.053     | 38.053     | 38.053     |   0.0 | 16.83
-Bond    | 0.089673   | 0.089673   | 0.089673   |   0.0 |  0.04
-Kspace  | 0.92778    | 0.92778    | 0.92778    |   0.0 |  0.41
-Neigh   | 1.2619     | 1.2619     | 1.2619     |   0.0 |  0.56
-Comm    | 0.97483    | 0.97483    | 0.97483    |   0.0 |  0.43
-Output  | 0.0013306  | 0.0013306  | 0.0013306  |   0.0 |  0.00
-Modify  | 184.68     | 184.68     | 184.68     |   0.0 | 81.66
-Other   |            | 0.171      |            |       |  0.08
+Pair    | 37.459     | 37.459     | 37.459     |   0.0 | 16.98
+Bond    | 0.087067   | 0.087067   | 0.087067   |   0.0 |  0.04
+Kspace  | 0.90234    | 0.90234    | 0.90234    |   0.0 |  0.41
+Neigh   | 1.2299     | 1.2299     | 1.2299     |   0.0 |  0.56
+Comm    | 0.95437    | 0.95437    | 0.95437    |   0.0 |  0.43
+Output  | 0.0010636  | 0.0010636  | 0.0010636  |   0.0 |  0.00
+Modify  | 179.85     | 179.85     | 179.85     |   0.0 | 81.51
+Other   |            | 0.1754     |            |       |  0.08
 
 Nlocal:    108 ave 108 max 108 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -278,4 +290,4 @@ Ave special neighs/atom = 2
 Neighbor list builds = 20439
 Dangerous builds = 0
 
-Total wall time: 0:03:46
+Total wall time: 0:03:40

examples/gcmc/log.23Oct17.gcmc.h2o.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (6 Jul 2017)
+LAMMPS (23 Oct 2017)
   using 1 OpenMP thread(s) per MPI task
 # fix gcmc example with fix shake
 
@@ -51,6 +51,7 @@ Read molecule h2omol:
   0 impropers with 0 types
 create_atoms   	0 box mol h2omol 464563 units box
 Created 24 atoms
+  Time spent = 0.00174451 secs
 
 # rigid SPC/E water model
 
@@ -100,9 +101,9 @@ Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          338   -4.9610706 9.2628112e-06    18.211756    730.90791 
      100          338   -15.742442   0.14954269     7.579918   -637.49568 
-Loop time of 0.0828406 on 4 procs for 100 steps with 24 atoms
+Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms
 
-98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
@@ -116,14 +117,14 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.012844   | 0.025471   | 0.047008   |   8.1 | 30.75
-Bond    | 0.00038934 | 0.00046468 | 0.00054336 |   0.0 |  0.56
-Kspace  | 0.0061138  | 0.027556   | 0.04014    |   7.8 | 33.26
+Pair    | 0.0085177  | 0.016083   | 0.026787   |   5.3 | 28.41
+Bond    | 0.00022459 | 0.00031394 | 0.00037575 |   0.0 |  0.55
+Kspace  | 0.0049062  | 0.014122   | 0.02044    |   5.0 | 24.94
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.023276   | 0.023636   | 0.023804   |   0.1 | 28.53
-Output  | 3.171e-05  | 3.3557e-05 | 3.8147e-05 |   0.0 |  0.04
+Comm    | 0.018515   | 0.02086    | 0.023246   |   1.2 | 36.84
+Output  | 2.4796e-05 | 2.6047e-05 | 2.9802e-05 |   0.0 |  0.05
 Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.00568    |            |       |  6.86
+Other   |            | 0.005213   |            |       |  9.21
 
 Nlocal:    6 ave 8 max 3 min
 Histogram: 1 0 0 0 1 0 0 0 0 2
@@ -164,22 +165,22 @@ Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0    518.26667   -15.742442            0    7.4303753    -613.0781 
     1000    369.81793   -54.202686            0   -37.667331    294.98823 
-Loop time of 0.199641 on 4 procs for 1000 steps with 24 atoms
+Loop time of 0.154891 on 4 procs for 1000 steps with 24 atoms
 
-Performance: 432.777 ns/day, 0.055 hours/ns, 5008.996 timesteps/s
-98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 557.810 ns/day, 0.043 hours/ns, 6456.135 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    | 0.017161   | 0.034988   | 0.05833    |   8.0 | 17.53
-Bond    | 0.00017357 | 0.00021374 | 0.00027347 |   0.0 |  0.11
-Kspace  | 0.018025   | 0.044624   | 0.065613   |   8.4 | 22.35
-Neigh   | 0.0029755  | 0.0033154  | 0.0036366  |   0.6 |  1.66
-Comm    | 0.059933   | 0.06537    | 0.070709   |   1.5 | 32.74
-Output  | 3.4571e-05 | 3.6657e-05 | 4.22e-05   |   0.0 |  0.02
-Modify  | 0.043458   | 0.045628   | 0.04767    |   0.9 | 22.86
-Other   |            | 0.005465   |            |       |  2.74
+Pair    | 0.0154     | 0.028993   | 0.040525   |   5.5 | 18.72
+Bond    | 0.00016999 | 0.0001902  | 0.00023293 |   0.0 |  0.12
+Kspace  | 0.019093   | 0.028112   | 0.038976   |   4.3 | 18.15
+Neigh   | 0.0020263  | 0.0022184  | 0.002408   |   0.4 |  1.43
+Comm    | 0.04947    | 0.053627   | 0.058009   |   1.4 | 34.62
+Output  | 2.5749e-05 | 2.7537e-05 | 3.2187e-05 |   0.0 |  0.02
+Modify  | 0.035275   | 0.036815   | 0.038425   |   0.7 | 23.77
+Other   |            | 0.004909   |            |       |  3.17
 
 Nlocal:    6 ave 8 max 3 min
 Histogram: 1 0 0 0 0 0 1 0 1 1
@@ -201,6 +202,17 @@ fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol
 fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
 fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert 1.66666666666667 group h2o shake wshake
 
+# atom counts
+
+variable 	oxygen atom "type==1"
+variable 	hydrogen atom "type==2"
+group 	        oxygen dynamic all var oxygen
+dynamic group oxygen defined
+group 		hydrogen dynamic all var hydrogen
+dynamic group hydrogen defined
+variable        nO equal count(oxygen)
+variable        nH equal count(hydrogen)
+
 # output
 
 variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
@@ -208,7 +220,7 @@ variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
 variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
 compute_modify  thermo_temp dynamic/dof yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
 thermo          1000
 
 # run
@@ -226,44 +238,44 @@ WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
 Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc 
-    1000    369.81793    295.32434   -54.202686    16.535355   0.23910963       24            0            0            0            0 
-    2000    84.544466   -2810.9047   -344.81664    14.364627   0.86677242       87  0.052198354 0.0099581757            0            0 
-    3000    75.188527    -3688.256   -425.02228    14.567977   0.98632724       99  0.030546787 0.0049111089            0            0 
-    4000    75.019396   -5669.3063   -427.69454    14.535207   0.98632724       99  0.019972039 0.0033375609            0            0 
-    5000    90.415371   -2141.7596   -434.65925    17.518218   0.98632724       99  0.014909796  0.002514964            0            0 
-    6000    78.212628   -943.75125   -428.80584    15.153904   0.98632724       99   0.01181521 0.0020316119            0            0 
-    7000    71.754139   -2028.5122    -435.2139    13.902555   0.98632724       99 0.0099466198 0.0016755471            0            0 
-    8000    84.446231   -1969.1657   -428.27313    16.361681   0.98632724       99 0.0084791272 0.0014442102            0            0 
-    9000    70.952348   -2476.9812   -446.33824    14.170197    1.0162159      102 0.0077150892 0.0012556189            0            0 
-   10000    71.418543   -1875.7083    -443.7214    14.263302    1.0162159      102 0.0068355714 0.0011197957            0            0 
-   11000    86.094994   -4508.7581   -444.82687    17.194399    1.0162159      102 0.0061494515 0.0010082475            0            0 
-   12000    81.906091   -1547.8105   -442.36719    16.357815    1.0162159      102 0.0055834729 0.00091775114            0            0 
-   13000    57.221548   -4607.6222   -448.30939     11.42796    1.0162159      102 0.0051230355 0.00084046326            0            0 
-   14000    61.288344   -2518.1779   -445.70636    12.240157    1.0162159      102 0.0047276997 0.00077602396            0            0 
-   15000    85.787669   -2407.7111    -443.3834    17.133022    1.0162159      102 0.0043983485 0.00071920715            0            0 
-   16000    74.845939   -3288.3403    -445.8247    14.947802    1.0162159      102 0.0042321884 0.00080654918            0            0 
-   17000    73.835431   -1926.9566   -445.67476    14.745989    1.0162159      102 0.0039751059 0.00075470749            0            0 
-   18000    72.634985    -3997.552    -447.2351    14.506243    1.0162159      102 0.0037395847 0.00071063946            0            0 
-   19000    96.776472   -714.44132   -453.65552    19.904587    1.0461046      105 0.0036487876 0.00066993446            0            0 
-   20000    75.470786    183.16972   -464.04688    15.522521    1.0461046      105 0.0034630763 0.00063350614            0            0 
-   21000    65.658309   -773.41266   -466.27068    13.504331    1.0461046      105  0.003289113 0.00060198052            0            0 
-Loop time of 93.8859 on 4 procs for 20000 steps with 105 atoms
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH 
+    1000    369.81793    295.32434   -54.202686    16.535355   0.23910963       24            0            0            0            0            8           16 
+    2000    84.544466   -2810.9047   -344.81664    14.364627   0.86677242       87  0.052198354 0.0099581757            0            0           29           58 
+    3000    75.188527    -3688.256   -425.02228    14.567977   0.98632724       99  0.030546787 0.0049111089            0            0           33           66 
+    4000    75.019396   -5669.3063   -427.69454    14.535207   0.98632724       99  0.019972039 0.0033375609            0            0           33           66 
+    5000    90.415371   -2141.7596   -434.65925    17.518218   0.98632724       99  0.014909796  0.002514964            0            0           33           66 
+    6000    78.212628   -943.75125   -428.80584    15.153904   0.98632724       99   0.01181521 0.0020316119            0            0           33           66 
+    7000    71.754139   -2028.5122    -435.2139    13.902555   0.98632724       99 0.0099466198 0.0016755471            0            0           33           66 
+    8000    84.446231   -1969.1657   -428.27313    16.361681   0.98632724       99 0.0084791272 0.0014442102            0            0           33           66 
+    9000    70.952348   -2476.9812   -446.33824    14.170197    1.0162159      102 0.0077150892 0.0012556189            0            0           34           68 
+   10000    71.418543   -1875.7083    -443.7214    14.263302    1.0162159      102 0.0068355714 0.0011197957            0            0           34           68 
+   11000    86.094994   -4508.7581   -444.82687    17.194399    1.0162159      102 0.0061494515 0.0010082475            0            0           34           68 
+   12000    81.906091   -1547.8105   -442.36719    16.357815    1.0162159      102 0.0055834729 0.00091775114            0            0           34           68 
+   13000    57.221548   -4607.6222   -448.30939     11.42796    1.0162159      102 0.0051230355 0.00084046326            0            0           34           68 
+   14000    61.288344   -2518.1779   -445.70636    12.240157    1.0162159      102 0.0047276997 0.00077602396            0            0           34           68 
+   15000    85.787669   -2407.7111    -443.3834    17.133022    1.0162159      102 0.0043983485 0.00071920715            0            0           34           68 
+   16000    74.845939   -3288.3403    -445.8247    14.947802    1.0162159      102 0.0042321884 0.00080654918            0            0           34           68 
+   17000    73.835431   -1926.9566   -445.67476    14.745989    1.0162159      102 0.0039751059 0.00075470749            0            0           34           68 
+   18000    72.634985    -3997.552    -447.2351    14.506243    1.0162159      102 0.0037395847 0.00071063946            0            0           34           68 
+   19000    96.776472   -714.44132   -453.65552    19.904587    1.0461046      105 0.0036487876 0.00066993446            0            0           35           70 
+   20000    75.470786    183.16972   -464.04688    15.522521    1.0461046      105 0.0034630763 0.00063350614            0            0           35           70 
+   21000    65.658309   -773.41266   -466.27068    13.504331    1.0461046      105  0.003289113 0.00060198052            0            0           35           70 
+Loop time of 84.4085 on 4 procs for 20000 steps with 105 atoms
 
-Performance: 18.405 ns/day, 1.304 hours/ns, 213.024 timesteps/s
+Performance: 20.472 ns/day, 1.172 hours/ns, 236.943 timesteps/s
 98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 6.7882     | 10.264     | 14.758     |  93.2 | 10.93
-Bond    | 0.028286   | 0.034218   | 0.039038   |   2.5 |  0.04
-Kspace  | 0.57255    | 5.2227     | 8.8493     | 133.8 |  5.56
-Neigh   | 0.3635     | 0.36915    | 0.37473    |   0.9 |  0.39
-Comm    | 2.9961     | 3.2542     | 3.509      |  11.4 |  3.47
-Output  | 0.0011675  | 0.0012342  | 0.001375   |   0.2 |  0.00
-Modify  | 74.428     | 74.499     | 74.571     |   0.7 | 79.35
-Other   |            | 0.2411     |            |       |  0.26
+Pair    | 6.3571     | 9.7574     | 13.984     |  90.7 | 11.56
+Bond    | 0.026374   | 0.031321   | 0.035482   |   2.1 |  0.04
+Kspace  | 0.57402    | 4.7894     | 8.1754     | 129.0 |  5.67
+Neigh   | 0.34952    | 0.34987    | 0.35021    |   0.1 |  0.41
+Comm    | 2.4028     | 2.4228     | 2.4372     |   0.9 |  2.87
+Output  | 0.0012269  | 0.0012826  | 0.0014355  |   0.2 |  0.00
+Modify  | 66.819     | 66.828     | 66.837     |   0.1 | 79.17
+Other   |            | 0.2281     |            |       |  0.27
 
 Nlocal:    26.25 ave 31 max 22 min
 Histogram: 1 0 1 0 0 0 1 0 0 1
@@ -278,4 +290,4 @@ Ave special neighs/atom = 2
 Neighbor list builds = 20428
 Dangerous builds = 0
 
-Total wall time: 0:01:34
+Total wall time: 0:01:24

examples/gcmc/log.23Oct17.gcmc.lj.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (6 Jul 2017)
+LAMMPS (23 Oct 2017)
   using 1 OpenMP thread(s) per MPI task
 # GCMC for LJ simple fluid, no dynamics
 # T = 2.0
@@ -43,6 +43,13 @@ fix             mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
 fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
 fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
 
+# atom count
+
+variable 	type1 atom "type==1"
+group 		type1 dynamic all var type1
+dynamic group type1 defined
+variable        n1 equal count(type1)
+
 # averaging
 
 variable	rho equal density
@@ -54,10 +61,11 @@ variable     	muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
 variable     	muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
 variable     	muex equal -1.25-2.0*ln(density*1+${nugget})
 variable     	muex equal -1.25-2.0*ln(density*1+1e-08)
-fix 		ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
+fix 		ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
 variable	rhoav equal f_ave[1]
 variable	pav equal f_ave[2]
 variable	muexav equal f_ave[3]
+variable	n1av equal f_ave[4]
 
 # output
 
@@ -68,7 +76,7 @@ variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
 compute_modify  thermo_temp dynamic yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
 thermo          1000
 
 # run
@@ -87,32 +95,32 @@ Neighbor list info ...
       stencil: half/bin/3d/newton
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav 
-       0            0            0            0           -0            0        0            0            0            0            0            0            0 
-    1000    2.4038954    2.1735585   -2.7041368    3.5476844        0.496       62  0.064790036   0.06313096    0.1081294      0.54304    1.4513524 -0.025479219 
-    2000    2.0461168    1.1913842   -2.9880181    3.0212194        0.512       64  0.067416408  0.066335853   0.11306166      0.52736    1.3274665  0.034690004 
-    3000    1.7930436    1.3788681   -3.2212667    2.6505861        0.552       69  0.067733191  0.066877836    0.1133516       0.5344    1.3834744 0.0070582537 
-    4000     1.981449    1.2541054   -2.8222868    2.9217977        0.472       59  0.068546991  0.067856412   0.11442807      0.52504    1.3815629  0.043309657 
-    5000    2.0946818    1.0701629   -3.5213291    3.0977688        0.568       71   0.06813743  0.067567891   0.11342906      0.53824    1.4049567 -0.0054539777 
-    6000    1.9793484   0.68224187    -3.410211    2.9247088        0.536       67  0.067797628  0.067420108   0.11295333       0.5384     1.401683 -0.0066894359 
-    7000    2.1885798    1.6745012    -3.185499    3.2345922        0.544       68  0.068630201  0.068261832   0.11403705       0.5244     1.449239  0.045987399 
-    8000    2.2175324    1.5897263    -3.078898    3.2759002        0.528       66  0.068180395  0.067899629   0.11332691      0.53928    1.5488388  -0.01075766 
-    9000    1.8610779    1.0396231    -2.923262    2.7465908        0.496       62  0.068346453  0.068028117    0.1134132      0.52912    1.4352871  0.027082544 
-   10000    2.1079271    1.1746643   -2.9112062    3.1091925         0.48       60  0.068352878  0.068054948   0.11335434       0.5316    1.4462327  0.018503094 
-Loop time of 20.6892 on 1 procs for 10000 steps with 60 atoms
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av 
+       0            0            0            0           -0            0        0            0            0            0            0            0            0            0 
+    1000    2.4038954    2.1735585   -2.7041368    3.5476844        0.496       62  0.064790036   0.06313096    0.1081294      0.54304    1.4513524 -0.025479219        64.98 
+    2000    2.0461168    1.1913842   -2.9880181    3.0212194        0.512       64  0.067416408  0.066335853   0.11306166      0.52736    1.3274665  0.034690004        62.97 
+    3000    1.7930436    1.3788681   -3.2212667    2.6505861        0.552       69  0.067733191  0.066877836    0.1133516       0.5344    1.3834744 0.0070582537         63.5 
+    4000     1.981449    1.2541054   -2.8222868    2.9217977        0.472       59  0.068546991  0.067856412   0.11442807      0.52504    1.3815629  0.043309657        62.17 
+    5000    2.0946818    1.0701629   -3.5213291    3.0977688        0.568       71   0.06813743  0.067567891   0.11342906      0.53824    1.4049567 -0.0054539777        64.15 
+    6000    1.9793484   0.68224187    -3.410211    2.9247088        0.536       67  0.067797628  0.067420108   0.11295333       0.5384     1.401683 -0.0066894359        64.37 
+    7000    2.1885798    1.6745012    -3.185499    3.2345922        0.544       68  0.068630201  0.068261832   0.11403705       0.5244     1.449239  0.045987399        62.33 
+    8000    2.2175324    1.5897263    -3.078898    3.2759002        0.528       66  0.068180395  0.067899629   0.11332691      0.53928    1.5488388  -0.01075766        64.29 
+    9000    1.8610779    1.0396231    -2.923262    2.7465908        0.496       62  0.068346453  0.068028117    0.1134132      0.52912    1.4352871  0.027082544        62.87 
+   10000    2.1079271    1.1746643   -2.9112062    3.1091925         0.48       60  0.068352878  0.068054948   0.11335434       0.5316    1.4462327  0.018503094         63.2 
+Loop time of 20.4081 on 1 procs for 10000 steps with 60 atoms
 
-Performance: 208804.611 tau/day, 483.344 timesteps/s
-99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 211680.375 tau/day, 490.001 timesteps/s
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.47227    | 0.47227    | 0.47227    |   0.0 |  2.28
-Neigh   | 1.1729     | 1.1729     | 1.1729     |   0.0 |  5.67
-Comm    | 0.17133    | 0.17133    | 0.17133    |   0.0 |  0.83
-Output  | 0.00028253 | 0.00028253 | 0.00028253 |   0.0 |  0.00
-Modify  | 18.852     | 18.852     | 18.852     |   0.0 | 91.12
-Other   |            | 0.02063    |            |       |  0.10
+Pair    | 0.46484    | 0.46484    | 0.46484    |   0.0 |  2.28
+Neigh   | 1.1447     | 1.1447     | 1.1447     |   0.0 |  5.61
+Comm    | 0.1696     | 0.1696     | 0.1696     |   0.0 |  0.83
+Output  | 0.000319   | 0.000319   | 0.000319   |   0.0 |  0.00
+Modify  | 18.607     | 18.607     | 18.607     |   0.0 | 91.17
+Other   |            | 0.02194    |            |       |  0.11
 
 Nlocal:    60 ave 60 max 60 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/gcmc/log.23Oct17.gcmc.lj.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (6 Jul 2017)
+LAMMPS (23 Oct 2017)
   using 1 OpenMP thread(s) per MPI task
 # GCMC for LJ simple fluid, no dynamics
 # T = 2.0
@@ -43,6 +43,13 @@ fix             mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
 fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
 fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
 
+# atom count
+
+variable 	type1 atom "type==1"
+group 		type1 dynamic all var type1
+dynamic group type1 defined
+variable        n1 equal count(type1)
+
 # averaging
 
 variable	rho equal density
@@ -54,10 +61,11 @@ variable     	muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
 variable     	muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
 variable     	muex equal -1.25-2.0*ln(density*1+${nugget})
 variable     	muex equal -1.25-2.0*ln(density*1+1e-08)
-fix 		ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
+fix 		ave all ave/time 10 100 1000 v_rho v_p v_muex v_n1 ave one file rho_vs_p.dat
 variable	rhoav equal f_ave[1]
 variable	pav equal f_ave[2]
 variable	muexav equal f_ave[3]
+variable	n1av equal f_ave[4]
 
 # output
 
@@ -68,7 +76,7 @@ variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
 compute_modify  thermo_temp dynamic yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av
 thermo          1000
 
 # run
@@ -87,32 +95,32 @@ Neighbor list info ...
       stencil: half/bin/3d/newton
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav 
-       0            0            0            0           -0            0        0            0            0            0            0            0            0 
-    1000     1.956397    1.7699101   -2.7889468    2.8864874        0.488       61  0.068894746  0.067229075    0.1141726      0.53288    1.3832798  0.013392866 
-    2000     2.040943   0.56060899   -2.8001647    3.0077055        0.456       57  0.069858594  0.068831934   0.11629114       0.5232    1.3587174  0.049995794 
-    3000    2.0004866    1.5736515   -3.3098044    2.9572411        0.552       69  0.069594029  0.068727791   0.11592543      0.53096    1.4129434  0.020022578 
-    4000    2.1127942     2.642809   -2.8865084    3.1211733        0.528       66  0.070268697  0.069533235   0.11693806      0.52424    1.3444615  0.046884078 
-    5000    2.3663648     1.354269   -3.1917346    3.4957662        0.528       66  0.070519633  0.069960064   0.11710321      0.52688    1.3595814  0.036270867 
-    6000    1.9224136   0.82756699      -3.1965     2.839257         0.52       65   0.06985018  0.069474645   0.11628632        0.536      1.47062   0.00141549 
-    7000    2.0266192    1.5593811   -2.9972341    2.9931606         0.52       65  0.070244693  0.069880791   0.11666541      0.52528    1.3246332  0.040754793 
-    8000    1.7790467    1.8680568   -2.8028819    2.6275151         0.52       65  0.070454494  0.070172368   0.11736806        0.524    1.4213649  0.047985191 
-    9000    1.7968847    1.3195587    -3.261001    2.6550983        0.536       67  0.069952011  0.069618327   0.11650087      0.53904    1.4624201  -0.01069837 
-   10000    2.1566109    1.1015729   -3.4999837    3.1880335        0.552       69  0.069603309  0.069284134   0.11625548      0.53128    1.3587249   0.02075238 
-Loop time of 24.9916 on 4 procs for 10000 steps with 69 atoms
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av 
+       0            0            0            0           -0            0        0            0            0            0            0            0            0            0 
+    1000     1.956397    1.7699101   -2.7889468    2.8864874        0.488       61  0.068894746  0.067229075    0.1141726      0.53288    1.3832798  0.013392866        63.44 
+    2000     2.040943   0.56060899   -2.8001647    3.0077055        0.456       57  0.069858594  0.068831934   0.11629114       0.5232    1.3587174  0.049995794        62.19 
+    3000    2.0004866    1.5736515   -3.3098044    2.9572411        0.552       69  0.069594029  0.068727791   0.11592543      0.53096    1.4129434  0.020022578        63.23 
+    4000    2.1127942     2.642809   -2.8865084    3.1211733        0.528       66  0.070268697  0.069533235   0.11693806      0.52424    1.3444615  0.046884078        62.57 
+    5000    2.3663648     1.354269   -3.1917346    3.4957662        0.528       66  0.070519633  0.069960064   0.11710321      0.52688    1.3595814  0.036270867        62.56 
+    6000    1.9224136   0.82756699      -3.1965     2.839257         0.52       65   0.06985018  0.069474645   0.11628632        0.536      1.47062   0.00141549        63.76 
+    7000    2.0266192    1.5593811   -2.9972341    2.9931606         0.52       65  0.070244693  0.069880791   0.11666541      0.52528    1.3246332  0.040754793         62.2 
+    8000    1.7790467    1.8680568   -2.8028819    2.6275151         0.52       65  0.070454494  0.070172368   0.11736806        0.524    1.4213649  0.047985191        62.03 
+    9000    1.7968847    1.3195587    -3.261001    2.6550983        0.536       67  0.069952011  0.069618327   0.11650087      0.53904    1.4624201  -0.01069837        64.36 
+   10000    2.1566109    1.1015729   -3.4999837    3.1880335        0.552       69  0.069603309  0.069284134   0.11625548      0.53128    1.3587249   0.02075238        63.24 
+Loop time of 23.8213 on 4 procs for 10000 steps with 69 atoms
 
-Performance: 172857.936 tau/day, 400.134 timesteps/s
-98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 181350.388 tau/day, 419.793 timesteps/s
+97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.11696    | 0.12516    | 0.1321     |   1.7 |  0.50
-Neigh   | 0.34874    | 0.35644    | 0.36545    |   1.2 |  1.43
-Comm    | 0.48531    | 0.51366    | 0.54755    |   3.8 |  2.06
-Output  | 0.0005362  | 0.00069767 | 0.00076008 |   0.0 |  0.00
-Modify  | 23.956     | 23.972     | 23.988     |   0.3 | 95.92
-Other   |            | 0.02376    |            |       |  0.10
+Pair    | 0.10935    | 0.11844    | 0.12741    |   2.1 |  0.50
+Neigh   | 0.33       | 0.33945    | 0.35091    |   1.6 |  1.42
+Comm    | 0.49249    | 0.51745    | 0.53856    |   2.7 |  2.17
+Output  | 0.00053334 | 0.0007208  | 0.0007906  |   0.0 |  0.00
+Modify  | 22.82      | 22.822     | 22.825     |   0.0 | 95.81
+Other   |            | 0.02289    |            |       |  0.10
 
 Nlocal:    17.25 ave 23 max 10 min
 Histogram: 1 0 0 0 0 0 2 0 0 1
@@ -125,4 +133,4 @@ Total # of neighbors = 2823
 Ave neighs/atom = 40.913
 Neighbor list builds = 10000
 Dangerous builds = 0
-Total wall time: 0:00:24
+Total wall time: 0:00:23

examples/python/README.fix_python_move

@@ -0,0 +1,16 @@
+This folder contains several LAMMPS input scripts and a python module
+file py_nve.py to demonstrate the use of the fix style python/move
+to reimplement NVE using Python.
+
+in.fix_python_move_nve_melt:
+This is a version of the melt example which replaces the default NVE integrator
+with a Python implementation. Fix python/move is used to create an
+instance of the py_nve.NVE class which implements the required interface.
+It demonstrates how to access LAMMPS data as numpy arrays. This gives direct
+access to memory owned by the C++ code, allows easy manipulation through numpy
+operations and avoids unnecessary copies.
+
+in.fix_python_move_nve_melt_opt:
+This version of melt example uses NVE_Opt instead of NVE. While this Python
+implementation is still much slower than the native version, it shows that
+simple code transformations can lead to speedups.

examples/python/funcs.py

@@ -8,17 +8,21 @@ def loop(N,cut0,thresh,lmpptr):
   from lammps import lammps
   lmp = lammps(ptr=lmpptr)
   natoms = lmp.get_natoms()
-  
-  for i in range(N):
-    cut = cut0 + i*0.1
 
-    lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
+  try:
+    for i in range(N):
+      cut = cut0 + i*0.1
 
-    lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
-    #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option
+      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)
+      if pe/natoms < thresh: return
+  except Exception as e:
+    print("LOOP error:", e)
 
-    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)
-    if pe/natoms < thresh: return

examples/python/in.fix_python_invoke

@@ -33,8 +33,8 @@ def post_force_callback(lmp, v):
 """
 
 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
+fix     2 all python/invoke 50 end_of_step end_of_step_callback
+fix     3 all python/invoke 50 post_force post_force_callback
 
 #dump		id all atom 50 dump.melt
 

examples/python/in.fix_python_move_nve_melt

@@ -0,0 +1,23 @@
+# 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	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 python/move py_nve.NVE
+
+thermo		50
+run		250

examples/python/in.fix_python_move_nve_melt_opt

@@ -0,0 +1,23 @@
+# 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	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 python/move py_nve.NVE_Opt
+
+thermo		50
+run		250

examples/python/in.python

@@ -28,6 +28,7 @@ python          simple here """
 from __future__ import print_function
 
 def simple():
+  foo = 0
   print("Inside simple function")
   try:
     foo += 1

examples/python/py_nve.py

@@ -0,0 +1,118 @@
+from __future__ import print_function
+import lammps
+import ctypes
+import traceback
+import numpy as np
+
+class LAMMPSFix(object):
+    def __init__(self, ptr, group_name="all"):
+        self.lmp = lammps.lammps(ptr=ptr)
+        self.group_name = group_name
+
+class LAMMPSFixMove(LAMMPSFix):
+    def __init__(self, ptr, group_name="all"):
+        super(LAMMPSFixMove, self).__init__(ptr, group_name)
+
+    def init(self):
+        pass
+
+    def initial_integrate(self, vflag):
+        pass
+
+    def final_integrate(self):
+        pass
+
+    def initial_integrate_respa(self, vflag, ilevel, iloop):
+        pass
+
+    def final_integrate_respa(self, ilevel, iloop):
+        pass
+
+    def reset_dt(self):
+        pass
+
+
+class NVE(LAMMPSFixMove):
+    """ Python implementation of fix/nve """
+    def __init__(self, ptr, group_name="all"):
+        super(NVE, self).__init__(ptr)
+        assert(self.group_name == "all")
+
+    def init(self):
+        dt = self.lmp.extract_global("dt", 1)
+        ftm2v = self.lmp.extract_global("ftm2v", 1)
+        self.ntypes = self.lmp.extract_global("ntypes", 0)
+        self.dtv = dt
+        self.dtf = 0.5 * dt * ftm2v
+
+    def initial_integrate(self, vflag):
+        nlocal = self.lmp.extract_global("nlocal", 0)
+        mass = self.lmp.numpy.extract_atom_darray("mass", self.ntypes+1)
+        atype = self.lmp.numpy.extract_atom_iarray("type", nlocal)
+        x = self.lmp.numpy.extract_atom_darray("x", nlocal, dim=3)
+        v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3)
+        f = self.lmp.numpy.extract_atom_darray("f", nlocal, dim=3)
+
+        for i in range(x.shape[0]):
+            dtfm = self.dtf / mass[int(atype[i])]
+            v[i,:]+= dtfm * f[i,:]
+            x[i,:] += self.dtv * v[i,:]
+
+    def final_integrate(self):
+        nlocal = self.lmp.extract_global("nlocal", 0)
+        mass = self.lmp.numpy.extract_atom_darray("mass", self.ntypes+1)
+        atype = self.lmp.numpy.extract_atom_iarray("type", nlocal)
+        v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3)
+        f = self.lmp.numpy.extract_atom_darray("f", nlocal, dim=3)
+
+        for i in range(v.shape[0]):
+            dtfm = self.dtf / mass[int(atype[i])]
+            v[i,:] += dtfm * f[i,:]
+
+
+class NVE_Opt(LAMMPSFixMove):
+    """ Performance-optimized Python implementation of fix/nve """
+    def __init__(self, ptr, group_name="all"):
+        super(NVE_Opt, self).__init__(ptr)
+        assert(self.group_name == "all")
+
+    def init(self):
+        dt = self.lmp.extract_global("dt", 1)
+        ftm2v = self.lmp.extract_global("ftm2v", 1)
+        self.ntypes = self.lmp.extract_global("ntypes", 0)
+        self.dtv = dt
+        self.dtf = 0.5 * dt * ftm2v
+        self.mass = self.lmp.numpy.extract_atom_darray("mass", self.ntypes+1)
+
+    def initial_integrate(self, vflag):        
+        nlocal = self.lmp.extract_global("nlocal", 0)
+        atype = self.lmp.numpy.extract_atom_iarray("type", nlocal)
+        x = self.lmp.numpy.extract_atom_darray("x", nlocal, dim=3)
+        v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3)
+        f = self.lmp.numpy.extract_atom_darray("f", nlocal, dim=3)
+        dtf = self.dtf
+        dtv = self.dtv
+        mass = self.mass
+
+        dtfm = dtf / np.take(mass, atype)
+        dtfm.reshape((nlocal, 1))
+
+        for d in range(x.shape[1]):
+            v[:,d] += dtfm[:,0] * f[:,d]
+            x[:,d] += dtv * v[:,d]
+
+    def final_integrate(self):
+        nlocal = self.lmp.extract_global("nlocal", 0)
+        mass = self.lmp.numpy.extract_atom_darray("mass", self.ntypes+1)
+        atype = self.lmp.numpy.extract_atom_iarray("type", nlocal)
+        v = self.lmp.numpy.extract_atom_darray("v", nlocal, dim=3)
+        f = self.lmp.numpy.extract_atom_darray("f", nlocal, dim=3)
+        dtf = self.dtf
+        dtv = self.dtv
+        mass = self.mass
+
+        dtfm = dtf / np.take(mass, atype)
+        dtfm.reshape((nlocal, 1))
+
+        for d in range(v.shape[1]):
+            v[:,d] += dtfm[:,0] * f[:,d]

examples/reax/HNS/README.txt

@@ -0,0 +1,49 @@
+# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
+
+Authors: Mitchell Wood, Stan Moore, and Aidan Thompson, Sandia National Labs
+Date: 2017-10-17
+Questions: Mitchell Wood, mitwood@sandia.gov
+
+---------ReaxFF Benchmark Files---------
+1) in.reaxc.hns
+2) data.hns-equil
+3) ffield.reax.hns
+
+---------File Description---------
+
+1) LAMMPS input file for this test. 
+  The file is read line by line looking for keywords to set up this run. 
+  It will read in the configuration given by the argument of the read_data command, which is supplied in this distribution.
+  The type of simulation is set by the 'fix' commands, dynamic charges are controlled with 'fix qeq' and the integration style is given as 'fix nve' here.
+  More information about each of the individual commands can be found online at lammps.sandia.gov in the user manual section.
+
+  *There are four free varaibles in this file, three of which control the size of the simulation and the last will dictate how many MD time steps are taken.
+  *The size of the system is controlled by the 'replicate' command given the values of $x, $y and $z.
+  *The number of timesteps taken is controlled by the 'run' command given the value of $t
+
+  It is worth noting that these four free variables can be set at the command line when the simulation is invoked rather than editing the file by hand prior to each run.
+
+  Example syntax:
+    lmp_serial -in in.reaxc.hns -v x 2 -v y 2 -v z 2 -v t 100
+
+2) LAMMPS Data file for crystalline HNS
+  This file matches the LAMMPS data format, more information about this data structure can be found at lammps.sandia.gov
+  
+  This particular data file is of the energetic material Hexanitrostilbene (HNS) with atom_style charge (id type q x y z).
+  The file contains eight molecules (2 unit cells).
+
+    Chemical Name: Hexanitrostilbene
+    Molecule Composition:  C14H6N6O12
+    IUPAC Name: 1,3,5-Trinitro-2-[2-(2,4,6-trinitrophenyl)ethenyl]benzene    
+    
+    Phyical Properties (Gerard F., Hardy A. Acta Cryst. (1988) 1283-1287)
+    Density: 1.741 g/cc
+    Crystal Structure: Monoclinic P2(1)/c
+    Molecules per Unit Cell: 4
+    Lattice Constants: a=22.326
+           b=5.5706
+           c=14.667
+           beta=110.04 deg
+
+3) ReaxFF force field file.
+  Details about this particular parameterization can be found in T.-R. Shan, R. R. Wixom, A. P. Thompson, "Atomistic Simulation of Nanoscale Void-Enhanced Initiation in Hexanitrostilbene", Proc. 15th International Detonation Symposium, pp. 962-969, SAND Number: SAND2014-15518J

examples/reax/HNS/data.hns-equil

@@ -0,0 +1,631 @@
+# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
+# See README for more info
+
+304 atoms
+4 atom types
+
+0.0000000000000000e+00 2.2326000000000001e+01 xlo xhi
+0.0000000000000000e+00 1.1141200000000000e+01 ylo yhi
+0.0000000000000000e+00 1.3778966000000000e+01 zlo zhi
+0.0000000000000000e+00 -5.0260300000000004e+00 0.0000000000000000e+00 xy xz yz
+
+Masses
+
+1 12
+2 1.008
+3 15.999
+4 14
+
+Atoms
+
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+276 -1.0986838142969923e-03 5.4315792533420901e-03 5.0077081054951244e-03
+244 -1.2183665223623778e-03 -4.2193410981771198e-03 -2.7354288515525696e-03
+280 1.3552010403368481e-03 6.3132429381080192e-04 1.7031901341229926e-04
+256 -2.2077829342060304e-03 1.6772588023449473e-03 2.2350654447874461e-04
+216 1.2254364422878230e-03 2.0994512158283556e-03 -2.0172376558553222e-03
+272 2.1464441432257797e-03 -1.8486660410473694e-04 1.9014747511050384e-03
+240 3.1573950446869229e-04 -3.7605367960744638e-04 2.3191303881599541e-04
+289 -1.2039974662100633e-02 2.6395586163545951e-03 -2.8478645629107940e-02
+177 6.1157082891864691e-03 6.9161818478923455e-04 -3.0081137643864736e-03
+96 -3.1669072586457290e-03 -6.3737086224948253e-03 1.5172924185041878e-03
+285 -1.2188701008670824e-02 -1.7123376677445068e-02 2.0830072814090890e-02

examples/reax/HNS/ffield.reax.hns

@@ -0,0 +1,168 @@
+Reactive MD-force field: c/h/o/s/f/cl Jan30_2012
+ 39       ! Number of general parameters                                        
+   50.0000 !p(boc1)                                                             
+    9.5469 !p(boc2)                                                             
+   26.5405 !p(coa2)                                                             
+    1.5105 !p(trip4)                                                            
+    6.6630 !p(trip3)                                                            
+   70.0000 !kc2                                                                 
+    1.0588 !p(ovun6)                                                            
+    4.6000 !p(trip2)                                                            
+   12.1176 !p(ovun7)                                                            
+   13.3056 !p(ovun8)                                                            
+  -60.1292 !p(trip1)                                                            
+    0.0000 !Lower Taper-radius (swa)                                            
+   10.0000 !Upper Taper-radius (swb)                                            
+    0.0000 !not used                                                            
+   33.8667 !p(val7)                                                             
+    6.0891 !p(lp1)                                                              
+    1.0563 !p(val9)                                                             
+    2.0384 !p(val10)                                                            
+    6.1431 !not used                                                            
+    6.9290 !p(pen2)                                                             
+    0.3989 !p(pen3)                                                             
+    3.9954 !p(pen4)                                                             
+    0.0000 !not used                                                            
+    5.7796 !p(tor2)                                                             
+   10.0000 !p(tor3)                                                             
+    1.9487 !p(tor4)                                                             
+    0.0000 !not used                                                            
+    2.1645 !p(cot2)                                                             
+    1.5591 !p(vdW1)                                                             
+    0.1000 !Cutoff for bond order*100 (cutoff)                                  
+    2.1365 !p(coa4)                                                             
+    0.6991 !p(ovun4)                                                            
+   50.0000 !p(ovun3)                                                            
+    1.8512 !p(val8)                                                             
+    0.0000 !not used                                                            
+    0.0000 !not used                                                            
+    0.0000 !not used                                                            
+    0.0000 !not used                                                            
+    2.6962 !p(coa3)                                                             
+  4    ! Nr of atoms; atomID;ro(sigma); Val;atom mass;Rvdw;Dij;gamma            
+            alfa;gamma(w);Val(angle);p(ovun5);n.u.;chiEEM;etaEEM;n.u.           
+            ro(pipi);p(lp2);Heat increment;p(boc4);p(boc3);p(boc5),n.u.;n.u.    
+            p(ovun2);p(val3);n.u.;Val(boc);p(val5);n.u.;n.u.;n.u.               
+ C    1.3825   4.0000  12.0000   1.9133   0.1853   0.9000   1.1359   4.0000     
+      9.7602   2.1346   4.0000  33.2433  79.5548   5.8678   7.0000   0.0000     
+      1.2104   0.0000 199.0303   8.6991  34.7289  13.3894   0.8563   0.0000     
+     -2.8983   2.5000   1.0564   4.0000   2.9663   0.0000   0.0000   0.0000     
+ H    0.7853   1.0000   1.0080   1.5904   0.0419   1.0206  -0.1000   1.0000     
+      9.3557   5.0518   1.0000   0.0000 121.1250   5.3200   7.4366   1.0000     
+     -0.1000   0.0000  55.0000   1.9771   3.3517   0.7571   1.0698   0.0000     
+    -15.7683   2.1488   1.0338   1.0000   2.8793   0.0000   0.0000   0.0000     
+ O    1.2477   2.0000  15.9990   1.9236   0.0904   1.0503   1.0863   6.0000     
+     10.2127   7.7719   4.0000  36.9573 116.0768   8.5000   8.9989   2.0000     
+      0.9088   1.0003  60.8726  20.4140   3.3754   0.2702   0.9745   0.0000     
+     -3.6141   2.7025   1.0493   4.0000   2.9225   0.0000   0.0000   0.0000     
+ N    1.6157   3.0000  14.0000   1.9376   0.1203   1.0000   1.2558   5.0000     
+      9.4267  26.8500   4.0000   8.6294 100.0000   7.6099   7.7500   2.0000     
+      1.0439   0.1000 119.9837   1.7640   2.7409   2.3814   0.9745   0.0000     
+     -6.5798   4.4843   1.0183   4.0000   2.8793   0.0000   0.0000   0.0000     
+ 10      ! Nr of bonds; at1;at2;De(sigma);De(pi);De(pipi);p(be1);p(b            
+                      p(be2);p(bo3);p(bo4);n.u.;p(bo1);p(bo2)                   
+  1  1 156.5953 100.0397  80.0000  -0.8157  -0.4591   1.0000  37.7369   0.4235  
+         0.4527  -0.1000   9.2605   1.0000  -0.0750   6.8316   1.0000   0.0000  
+  1  2 170.2316   0.0000   0.0000  -0.5931   0.0000   1.0000   6.0000   0.7140  
+         5.2267   1.0000   0.0000   1.0000  -0.0500   6.8315   0.0000   0.0000  
+  2  2 156.0973   0.0000   0.0000  -0.1377   0.0000   1.0000   6.0000   0.8240  
+         2.9907   1.0000   0.0000   1.0000  -0.0593   4.8358   0.0000   0.0000  
+  1  3 160.4802 105.1693  23.3059  -0.3873  -0.1613   1.0000  10.8851   1.0000  
+         0.5341  -0.3174   7.0303   1.0000  -0.1463   5.2913   0.0000   0.0000  
+  3  3  60.1463 176.6202  51.1430  -0.2802  -0.1244   1.0000  29.6439   0.9114  
+         0.2441  -0.1239   7.6487   1.0000  -0.1302   6.2919   1.0000   0.0000  
+  2  3 180.4373   0.0000   0.0000  -0.8074   0.0000   1.0000   6.0000   0.5514  
+         1.2490   1.0000   0.0000   1.0000  -0.0657   5.0451   0.0000   0.0000  
+  1  4 175.7446 131.3190 132.3859  -0.5827  -0.2709   1.0000  29.9009   0.8400  
+         1.9511  -0.2103   7.4487   1.0000  -0.1150   5.8717   1.0000   0.0000  
+  2  4 161.1063   0.0000   0.0000  -0.1387   0.0000   1.0000   6.0000   0.7276  
+         0.6127   1.0000   0.0000   1.0000  -0.0395   7.2218   0.0000   0.0000  
+  3  4  86.0536 180.5864  40.0000   1.0000  -0.4462   1.0000  34.9336   0.2000  
+         0.8154  -0.2175   7.0255   1.0000  -0.1937   5.2140   1.0000   0.0000  
+  4  4 134.6492  66.2329 149.2707  -0.7228  -0.1000   1.0000  19.0850   1.0000  
+         0.6060  -0.2050   9.7308   1.0000  -0.1791   5.8008   1.0000   0.0000  
+  6    ! Nr of off-diagonal terms. at1;at2;Dij;RvdW;alfa;ro(sigma);r            
+  1  2   0.1219   1.4000   9.8442   1.1203  -1.0000  -1.0000                    
+  2  3   0.0344   1.6800  10.3247   0.9013  -1.0000  -1.0000                    
+  1  3   0.1131   1.8523   9.8442   1.2775   1.1342   1.0621                    
+  1  4   0.1398   1.9263  10.1847   1.4778   1.1446   1.1216                    
+  2  4   0.0480   2.3000   9.0050   1.0156  -1.0000  -1.0000                    
+  3  4   0.0942   1.9531  10.3265   1.3018   1.0984   1.0125                    
+ 40    ! Nr of angles. at1;at2;at3;Thetao,o;p(val1);p(val2);p(coa1);            
+  1  1  1  67.2326  22.0695   1.6286   0.0000   1.7959  15.4141   1.8089        
+  1  1  2  65.2527  14.3185   6.2977   0.0000   0.5645   0.0000   1.1530        
+  2  1  2  70.0840  25.3540   3.4508   0.0000   0.0050   0.0000   3.0000        
+  1  2  2   0.0000   0.0000   6.0000   0.0000   0.0000   0.0000   1.0400        
+  1  2  1   0.0000   3.4110   7.7350   0.0000   0.0000   0.0000   1.0400        
+  2  2  2   0.0000  27.9213   5.8635   0.0000   0.0000   0.0000   1.0400        
+  1  1  3  49.5561   7.3771   4.9568   0.0000   0.7533  15.9906   1.0010        
+  3  1  3  77.1171  39.8746   2.5403 -24.3902   1.7740 -42.9758   2.1240        
+  2  1  3  65.0000  14.2057   4.8649   0.0000   0.3504   0.0000   1.7185        
+  1  3  1  74.3994  44.7500   0.7982   0.0000   3.0000   0.0000   1.0528        
+  1  3  3  77.9854  36.6201   2.0201   0.0000   0.7434  67.0264   3.0000        
+  3  3  3  80.7324  30.4554   0.9953   0.0000   1.6310  50.0000   1.0783        
+  1  3  2  71.5018  21.7062   0.4735   0.0000   0.5186   0.0000   1.1793        
+  2  3  3  84.9468  23.3540   1.5057   0.0000   2.6374   0.0000   1.3023        
+  2  3  2  77.0645  10.4737   1.2895   0.0000   0.9924   0.0000   1.1043        
+  1  2  3   0.0000  25.0000   3.0000   0.0000   1.0000   0.0000   1.0400        
+  3  2  3   0.0000   0.0148   6.0000   0.0000   0.0000   0.0000   1.0400        
+  2  2  3   0.0000   9.7025   6.0000   0.0000   0.0000   0.0000   1.0400        
+  1  1  4  61.6894   9.9742   3.5920   0.0000   5.0000  50.0000   2.2098        
+  3  1  4  67.5853  29.6915   1.8611   0.0000   3.0000   0.0000   1.5926        
+  4  1  4  53.0437  35.9280   1.7824   0.0000   5.0000   0.0000   4.0000        
+  2  1  4  66.9313  25.8025   3.5718   0.0000   0.0600   0.0000   1.0946        
+  1  3  4  71.7246  38.5022   1.1738   0.0000   1.6310   0.0000   1.2782        
+  3  3  4  83.0764  35.5413   1.4072   0.0000   1.6310   0.0000   1.1439        
+  4  3  4  79.3317  40.0000   2.3424   0.0000   1.6310   0.0000   1.0061        
+  2  3  4  81.0695  40.0000   2.0285   0.0000   0.1218   0.0000   1.4477        
+  1  4  1  68.9764  14.3404   1.9702   0.0000   1.3606   0.0000   1.0000        
+  1  4  3  76.1086  35.0355   1.0724   0.0000   1.6777   0.0000   1.6071        
+  1  4  4  81.8917  25.7475   0.7287   0.0000   2.0100   0.0000   1.9350        
+  3  4  3  80.1274  24.7547   1.7946 -10.0963   1.6777   0.0000   3.2815        
+  3  4  4  83.6527  36.3627   1.0967  -0.9193   1.6777   0.0000   1.0000        
+  4  4  4  90.0000  44.3028   1.6659   0.0000   0.7529   0.0000   1.2398        
+  1  4  2  76.9847  29.2262   0.9407   0.0000   0.0300   0.0000   2.6196        
+  2  4  3  85.4080  40.0000   1.7549   0.0000   0.0222   0.0000   1.0774        
+  2  4  4  83.5658  40.0000   1.3540   0.0000   0.0222   0.0000   2.6397        
+  2  4  2  58.0387   1.1862   3.9770   0.0000   0.0222   0.0000   1.0000        
+  1  2  4   0.0000   0.0019   6.3000   0.0000   0.0000   0.0000   1.0400        
+  2  2  4   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400        
+  3  2  4   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400        
+  4  2  4   0.0000   0.0019   6.0000   0.0000   0.0000   0.0000   1.0400        
+ 31    ! Nr of torsions. at1;at2;at3;at4;;V1;V2;V3;p(tor1);p(cot1);n            
+  1  1  1  1  -0.2500  11.5822   0.1879  -4.7057  -2.2047   0.0000   0.0000     
+  1  1  1  2  -0.2500  31.2596   0.1709  -4.6391  -1.9002   0.0000   0.0000     
+  2  1  1  2  -0.1770  30.0252   0.4340  -5.0019  -2.0697   0.0000   0.0000     
+  1  1  1  3  -0.7098  22.2951   0.0060  -2.5000  -2.1688   0.0000   0.0000     
+  2  1  1  3  -0.3568  22.6472   0.6045  -4.0088  -1.0000   0.0000   0.0000     
+  3  1  1  3  -0.0528   6.8150   0.7498  -5.0913  -1.0000   0.0000   0.0000     
+  1  1  3  1   2.0007  25.5641  -0.0608  -2.6456  -1.1766   0.0000   0.0000     
+  1  1  3  2  -1.1953  42.1545  -1.0000  -8.0821  -1.0000   0.0000   0.0000     
+  2  1  3  1  -0.9284  34.3952   0.7285  -2.5440  -2.4641   0.0000   0.0000     
+  2  1  3  2  -2.5000  79.6980   1.0000  -3.5697  -2.7501   0.0000   0.0000     
+  1  1  3  3  -0.0179   5.0603  -0.1894  -2.5000  -2.0399   0.0000   0.0000     
+  2  1  3  3  -0.5583  80.0000   1.0000  -4.4000  -3.0000   0.0000   0.0000     
+  3  1  3  1  -2.5000  76.0427  -0.0141  -3.7586  -2.9000   0.0000   0.0000     
+  3  1  3  2   0.0345  78.9586  -0.6810  -4.1777  -3.0000   0.0000   0.0000     
+  3  1  3  3  -2.5000  66.3525   0.3986  -3.0293  -3.0000   0.0000   0.0000     
+  1  3  3  1   2.5000  -0.5332   1.0000  -3.5096  -2.9000   0.0000   0.0000     
+  1  3  3  2  -2.5000   3.3219   0.7180  -5.2021  -2.9330   0.0000   0.0000     
+  2  3  3  2   2.2500  -6.2288   1.0000  -2.6189  -1.0000   0.0000   0.0000     
+  1  3  3  3   0.0531 -17.3983   1.0000  -2.5000  -2.1584   0.0000   0.0000     
+  2  3  3  3   0.4723 -12.4144  -1.0000  -2.5000  -1.0000   0.0000   0.0000     
+  3  3  3  3  -2.5000 -25.0000   1.0000  -2.5000  -1.0000   0.0000   0.0000     
+  0  1  2  0   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000     
+  0  2  2  0   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000     
+  0  2  3  0   0.0000   0.1000   0.0200  -2.5415   0.0000   0.0000   0.0000     
+  0  1  1  0   0.0000  50.0000   0.3000  -4.0000  -2.0000   0.0000   0.0000     
+  0  3  3  0   0.5511  25.4150   1.1330  -5.1903  -1.0000   0.0000   0.0000     
+  0  1  4  0  -0.5473  25.3808   0.9931  -4.3407  -3.0000   0.0000   0.0000     
+  0  2  4  0   0.0000   0.1000   0.0200  -2.5415   0.0000   0.0000   0.0000     
+  0  3  4  0   2.0000  71.9948  -0.8805  -6.1274  -2.7831   0.0000   0.0000     
+  0  4  4  0   2.0000  90.0000  -0.7837  -9.0000  -2.0000   0.0000   0.0000     
+  4  1  4  4  -2.0000  90.0000  -0.0279  -7.5866  -0.1000   0.0000   0.0000     
+  4    ! Nr of hydrogen bonds. at1;at2;at3;r(hb);p(hb1);p(hb2);p(hb3            
+  3  2  3   2.0000  -2.0000   1.5000  19.5000                                   
+  3  2  4   1.9000  -2.0000   1.7976  19.0000                                   
+  4  2  3   1.9000  -2.0000   1.7976  19.0000                                   
+  4  2  4   1.9000  -2.0000   1.7976  19.0000                                   

examples/reax/HNS/in.reaxc.hns

@@ -0,0 +1,34 @@
+# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
+# See README for more info
+
+units             real
+atom_style        charge
+atom_modify sort  100 0.0 # optional
+dimension         3
+boundary          p p p
+box               tilt large
+
+read_data         data.hns-equil
+replicate         $x $y $z bbox
+
+
+pair_style        reax/c NULL
+pair_coeff        * * ffield.reax.hns C H O N
+
+compute           reax all pair reax/c
+
+neighbor          1.0 bin
+neigh_modify      every 20 delay 0 check no
+
+timestep          0.1
+
+thermo_style      custom step temp pe press evdwl ecoul vol
+thermo_modify     norm yes
+thermo            100
+
+velocity          all create 300.0 41279 loop geom
+
+fix               1 all nve
+fix               2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
+
+run               100

examples/reax/ci-reaxFF/CH4.dat

@@ -0,0 +1,649 @@
+LAMMPS data file via write_data, version 23 Oct 2017, timestep = 100000
+
+315 atoms
+2 atom types
+
+0.0000000000000000e+00 2.0000000000000000e+01 xlo xhi
+0.0000000000000000e+00 2.0000000000000000e+01 ylo yhi
+0.0000000000000000e+00 2.0000000000000000e+01 zlo zhi
+
+Masses
+
+1 12.011
+2 1.008
+
+Atoms # charge
+
+175 2 0.0000000000000000e+00 5.3453687209469996e+00 5.5862726787962940e+00 4.0849785930715354e+00 1 0 0
+103 2 0.0000000000000000e+00 1.3073645814185417e+00 3.7206017715158937e+00 3.8524713056132751e+00 0 0 -1
+275 2 0.0000000000000000e+00 4.5600071648073301e+00 3.2329990023327824e+00 1.4821360978767673e+00 1 0 0
+271 1 0.0000000000000000e+00 4.5843986967581722e+00 3.9176387402395871e+00 5.8099831361575494e-01 1 0 0
+272 2 0.0000000000000000e+00 5.4182317432033766e+00 3.6898398009502156e+00 1.9965991602287605e+01 1 0 -1
+273 2 0.0000000000000000e+00 3.6051023956156447e+00 3.8873287655431406e+00 1.9973105836472126e+01 1 0 -1
+274 2 0.0000000000000000e+00 4.7919672477150748e+00 4.9286774621912297e+00 9.6215228549394083e-01 1 0 0
+1 1 0.0000000000000000e+00 1.0949422771872639e+01 1.1263564251882920e+00 4.5818433826058058e+00 2 -1 0
+4 2 0.0000000000000000e+00 1.1062078869518452e+01 1.8180370241226866e+00 3.7056441784637810e+00 2 -1 0
+2 2 0.0000000000000000e+00 1.0128614847702552e+01 4.0521961508372545e-01 4.3443871852431215e+00 2 -1 0
+49 2 0.0000000000000000e+00 9.5420250978384704e+00 3.6748811076174732e+00 6.9923624106878846e-01 0 -3 -1
+5 2 0.0000000000000000e+00 1.1895921213727425e+01 5.9644887079656606e-01 4.8275121519683699e+00 2 -1 0
+156 1 0.0000000000000000e+00 1.5350436635040626e+01 3.4944682618464196e+00 1.7820227892005359e+01 0 0 -1
+158 2 0.0000000000000000e+00 1.6234885135644735e+01 4.1073565210303551e+00 1.8057804919138462e+01 0 0 -1
+3 2 0.0000000000000000e+00 1.0638740127309621e+01 1.8737956827951723e+00 5.3939971205730135e+00 2 -1 0
+54 2 0.0000000000000000e+00 1.7052455149295493e+01 6.1908001655126670e+00 3.8576008358326090e+00 -3 2 -3
+159 2 0.0000000000000000e+00 1.4499107646573572e+01 3.7948767230433833e+00 1.8431013979305458e+01 0 0 -1
+174 2 0.0000000000000000e+00 4.2023079102565521e+00 6.1554910639166103e+00 5.3707953997810565e+00 1 0 0
+110 2 0.0000000000000000e+00 5.9228298978270466e+00 7.2826855552171832e+00 1.7589830768160732e+00 1 1 0
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+57 -2.9042456936939399e-02 6.2743816133522274e-03 1.1686513268136620e-02
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+150 -1.2023262083111609e-02 1.2775249595154581e-02 -4.0634835881225795e-02
+60 1.7557898280791597e-02 2.4376215248477891e-02 1.1758538347152450e-02
+58 1.8144992057570124e-02 -7.5702843234868675e-03 -1.4923629995870002e-02
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+13 1.9137045428760239e-03 8.9875474076530435e-03 -9.6156675976183999e-04
+12 -1.7227019616086664e-02 -1.2548485558094287e-03 -1.7605743351882273e-02
+14 -6.5469806850148235e-03 1.5603731904149499e-02 1.9379213254520373e-02
+11 3.4021735315404480e-03 -1.4732629503099006e-02 -1.8387894210675133e-03
+15 6.6797251992020462e-04 3.0865198998886196e-02 2.3887987113380628e-03
+47 -9.5048600550045759e-03 -2.3464057334906328e-02 1.3777084230302550e-03
+46 3.2157418933077791e-03 3.9493646679240263e-03 1.3047481022319314e-02
+50 1.1645344227592129e-03 3.0412923736907820e-03 4.2707643455573305e-02
+154 3.4168366668140590e-02 -1.9036765580252253e-02 1.8131624915819520e-02
+151 -3.3072286903951718e-03 8.7648710297958570e-04 -6.5782652677157721e-03
+155 -6.1680563882888602e-03 -1.0497735177604228e-02 1.9450379799624801e-02
+160 -1.7349898337797182e-03 2.1359907178594897e-02 -2.2464567848825313e-02
+205 -1.5623743135857664e-02 -1.7620923464120024e-02 1.3038901242119249e-02
+201 3.4115069176382067e-03 3.1389139355505473e-03 1.4288076224225500e-02
+202 2.4222754326574891e-02 -1.3489556718246623e-02 2.1163756388853386e-02
+203 -1.1595039481442856e-03 -7.4102913106757014e-04 4.5462822628578540e-03
+212 7.3935859008519662e-03 4.8226922649550735e-03 1.8869381529652517e-02
+211 -4.3960341535625161e-03 -6.0861360973294535e-05 -1.4952919349255620e-03
+214 4.3428210510383222e-03 -5.7906399923477537e-03 3.0942525621017947e-02
+213 1.5215939043494105e-02 -2.7902659887590931e-02 1.5816722811721345e-02
+48 -3.5077816781627887e-03 -3.2333124504558386e-02 -2.0454521813995038e-02
+195 -7.4689898202003622e-03 -3.4393994553156719e-02 9.5646117774240130e-03
+191 7.7439226193524377e-03 -1.6749714198483069e-03 -6.6151343864332502e-06
+192 2.4463864491014845e-02 2.2614803437104033e-02 3.3890821685470522e-02
+37 -8.9568894218416961e-03 1.2792918581938388e-03 -1.5471001358254778e-02
+215 1.9578246142917431e-04 3.0762244364193399e-02 -1.6498990559322031e-02
+200 2.2542526933536308e-02 4.2199096064752445e-02 2.2077373881583519e-02
+198 3.5778288054771831e-03 5.0482035751054396e-04 -6.5716247893242291e-03
+196 -9.8419792498795743e-03 2.7419078925250018e-03 -2.6038068222809106e-03
+197 -1.5089375859679781e-02 2.2046092191812455e-02 -2.7059575962908280e-02
+199 -2.1714227606551884e-02 6.4731847272046870e-03 -2.7308574260460093e-02
+292 5.2200250189205532e-03 -3.5583672736965023e-03 -3.8669973002571710e-02
+193 -2.7565971198342479e-02 3.3670688856475457e-02 -8.5250838280123281e-03
+222 3.7605718668314823e-02 -2.4346327009190323e-02 1.7456599656632692e-02
+225 -9.9510518223425142e-03 -8.7062067334547737e-03 -1.9168305625664527e-02
+221 -1.8762639766564139e-03 -2.2718227061860651e-03 -4.2361460647047490e-03
+223 6.3985564466709950e-03 4.0948349441623205e-02 -2.0062674414098799e-03
+224 -9.4998995917320757e-03 -4.1774686424660918e-03 -2.5519386468900784e-02
+39 8.4596247618711779e-03 1.0616795164921563e-02 2.3657858473230930e-02
+122 -1.4968464286657639e-02 -1.0871390032076086e-02 -1.8167519395605201e-02
+291 1.3883634609707012e-03 4.0790427863098642e-03 -2.1697404837098112e-03
+295 2.0264615856771768e-02 5.3307640197827492e-03 -1.3852908987409937e-02
+294 7.1603455916708150e-03 5.0285897843204619e-03 7.3241166431432738e-04
+153 3.0076738303306889e-02 2.4298999351012863e-02 -1.2607136131303244e-02
+152 4.8236632932468042e-03 5.2217071221687963e-02 5.9123414621807264e-04
+283 -5.8039400887170125e-03 5.0704532701600765e-03 -1.4112642821927698e-02
+281 -9.8195026779512255e-03 2.6380048577205636e-03 9.0530689248384671e-03
+284 3.3924632555861422e-03 4.2116137610867660e-03 2.2206053317133925e-03
+64 6.9103638123651535e-03 1.4460305245499955e-02 -1.1337529684205920e-02
+62 -1.5026973746144957e-02 -1.4229612681198415e-02 2.9749430352746346e-02
+63 1.3416625499363493e-02 -1.3681352134066847e-02 -2.7443459813718808e-02
+61 3.3033012398804508e-03 1.6556859169437473e-03 -7.8539529573181839e-03
+65 -2.5121974420729800e-02 -2.3099061980316700e-02 5.2735737931542709e-02
+204 1.4575953419115398e-02 -3.8575307452158376e-02 -1.5289570845150143e-02
+293 1.1695533411766636e-02 3.1524287197995153e-02 1.2872141480690781e-02

examples/reax/ci-reaxFF/control

@@ -0,0 +1 @@
+tabulate_long_range 30000

examples/reax/ci-reaxFF/ffield.ci-reax.CH

@@ -0,0 +1,78 @@
+DATE: 2017-11-20 CONTRIBUTOR: Michal Kanski michal.kanski@uj.edu.pl CITATION: Michal Kanski, Dawid Maciazek, Zbigniew Postawa, Adri C.T. van Duin, Chowdhury Ashraf, and Barbara J. Garrison Development of a Charge-Implicit ReaxFF Potential for Hydrocarbon Systems, J. Phys. Chem. Lett., 2018, 9, pp 359–363,  DOI: 10.1021/acs.jpclett.7b03155
+ 39       ! Number of general parameters                                        
+   50.0000 !p(boc1)                                                             
+    9.5469 !p(boc2)                                                             
+   26.5405 !p(coa2)                                                             
+    1.5105 !p(trip4)                                                            
+    6.6630 !p(trip3)                                                            
+   70.0000 !kc2                                                                 
+    1.0588 !p(ovun6)                                                            
+    4.6000 !p(trip2)                                                            
+   12.1176 !p(ovun7)                                                            
+   13.3056 !p(ovun8)                                                            
+  -70.1292 !p(trip1)                                                            
+    0.0000 !Lower Taper-radius (swa)                                            
+    7.0000 !Upper Taper-radius (swb)                                            
+    0.0000 !not used                                                            
+   33.8667 !p(val7)                                                             
+    6.0891 !p(lp1)                                                              
+    1.0563 !p(val9)                                                             
+    2.0384 !p(val10)                                                            
+    6.1431 !not used                                                            
+    6.9290 !p(pen2)                                                             
+    0.3989 !p(pen3)                                                             
+    3.9954 !p(pen4)                                                             
+    0.0000 !not used                                                            
+    5.7796 !p(tor2)                                                             
+   10.0000 !p(tor3)                                                             
+    1.9487 !p(tor4)                                                             
+    0.0000 !not used                                                            
+    2.1645 !p(cot2)                                                             
+    1.5591 !p(vdW1)                                                             
+    0.1000 !Cutoff for bond order*100 (cutoff)                                  
+    2.1365 !p(coa4)                                                             
+    0.6991 !p(ovun4)                                                            
+   50.0000 !p(ovun3)                                                            
+    1.8512 !p(val8)                                                             
+    0.0000 !not used                                                            
+    0.0000 !not used                                                            
+    0.0000 !not used                                                            
+    0.0000 !not used                                                            
+    2.6962 !p(coa3)                                                             
+  2    ! Nr of atoms; atomID;ro(sigma); Val;atom mass;Rvdw;Dij;gamma            
+            alfa;gamma(w);Val(angle);p(ovun5);n.u.;chiEEM;etaEEM;n.u.           
+            ro(pipi);p(lp2);Heat increment;p(boc4);p(boc3);p(boc5),n.u.;n.u.    
+            p(ovun2);p(val3);n.u.;Val(boc);p(val5);n.u.;n.u.;n.u.               
+ C    1.5807   4.0000  12.0000   2.1339   0.2705   0.9000   1.3561   4.0000     
+      7.0578   2.2030   4.0000  33.2433  79.5548   1.0000   7.0000   0.0000     
+      1.2857   0.0000 199.0303  25.5946  34.7987  33.8858   0.8563   0.0000     
+     -3.2763   4.0000   1.0564   4.0000   1.1829   1.8737   0.9340  10.7610     
+ H    0.8431   1.0000   1.0080   1.7993   0.0531   1.0206  -0.1000   1.0000     
+      5.1365   2.3597   1.0000   0.0000 121.1250   1.0000   7.0000   1.0000     
+     -0.1000   0.0000  62.4879   1.7831  10.0956   1.5343   1.0698   0.0000     
+    -39.1433   2.0000   1.0338   1.0000   1.4937   1.4730   0.2395   9.1813     
+  3      ! Nr of bonds; at1;at2;De(sigma);De(pi);De(pipi);p(be1);p(b            
+                      p(be2);p(bo3);p(bo4);n.u.;p(bo1);p(bo2)                   
+  1  1 143.8966  78.5316  96.1991  -0.6337  -1.0884   1.0000  19.6513   0.4644  
+         1.0466  -0.6287   8.3354   1.0000  -0.1410   7.4059   1.0000   0.0000  
+  1  2 142.2786   0.0000   0.0000  -0.7910   0.0000   1.0000   7.6804   0.6354  
+         8.9091   1.0000   0.0000   1.0000  -0.1759   9.1526   0.0000   0.0000  
+  2  2 166.9928   0.0000   0.0000  -0.2894   0.0000   1.0000   9.0000   0.7986  
+        22.4216   1.0000   0.0000   1.0000  -0.1025   5.0250   0.0000   0.0000  
+  1    ! Nr of off-diagonal terms. at1;at2;Dij;RvdW;alfa;ro(sigma);r            
+  1  2   0.0384   1.4571   8.0036   1.4872  -1.0000  -1.0000                    
+  6   ! Nr of angles. at1;at2;at3;Thetao,o;p(val1);p(val2);p(coa1);             
+  1  1  1  66.9930  26.8666   1.3549  -0.9012   4.6851  18.8775   1.8087        
+  1  1  2  65.9137   8.8776   9.1600   0.0000   0.3144   0.0000   4.3449        
+  2  1  2  70.6653  32.2568   1.7885   0.0000   2.1528   0.0000   9.9760        
+  1  2  2   0.0000  40.0000   1.0000   0.0000   3.2849   0.0000   9.0719        
+  1  2  1   0.0000  33.4427   5.0679   0.0000   1.1188   0.0000  10.0000        
+  2  2  2   0.0000  27.9213   5.8635   0.0000   0.0000   0.0000   1.0400        
+  6    ! Nr of torsions. at1;at2;at3;at4;;V1;V2;V3;p(tor1);p(cot1);n            
+  1  1  1  1   0.0500  17.1779   0.1145  -3.7630  -1.4900   0.0000   0.0000     
+  1  1  1  2  -0.4619  27.8830   0.2611  -3.8205  -2.0485   0.0000   0.0000     
+  2  1  1  2   0.1629  22.7282   0.3893  -2.9569  -7.8729   0.0000   0.0000     
+  0  1  2  0   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000     
+  0  2  2  0   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000     
+  0  1  1  0   0.0000  50.0000   0.3000  -4.0000  -2.0000   0.0000   0.0000     
+  0    ! Nr of hydrogen bonds. at1;at2;at3;r(hb);p(hb1);p(hb2);p(hb3            

examples/reax/ci-reaxFF/input.in

@@ -0,0 +1,19 @@
+#ci-reax potential for CH systems with tabulated ZBL correction
+atom_style      charge
+units           real
+
+read_data       CH4.dat
+
+pair_style      hybrid/overlay reax/c control checkqeq no table linear 11000
+pair_coeff      * * reax/c ffield.ci-reax.CH C H
+pair_coeff      1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF 
+pair_coeff      1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF 
+pair_coeff      2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
+
+timestep        0.25
+fix             1 all nve
+fix             2 all temp/berendsen 500.0 500.0 100.0
+
+#dump           1 all atom 30 dump.ci-reax.lammpstrj
+
+run             3000

examples/reax/ci-reaxFF/log.23Oct17.g++.1

@@ -0,0 +1,84 @@
+LAMMPS (23 Oct 2017)
+#ci-reax potential for CH systems with tabulated ZBL correction
+atom_style      charge
+units           real
+
+read_data       CH4.dat
+  orthogonal box = (0 0 0) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  315 atoms
+  reading velocities ...
+  315 velocities
+
+pair_style      hybrid/overlay reax/c control checkqeq no table linear 11000
+pair_coeff      * * reax/c ffield.ci-reax.CH C H
+Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
+pair_coeff      1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
+WARNING: 2 of 10000 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:481)
+pair_coeff      1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
+WARNING: 2 of 11000 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:481)
+pair_coeff      2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
+WARNING: 2 of 6000 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:481)
+
+timestep        0.25
+fix             1 all nve
+fix             2 all temp/berendsen 500.0 500.0 100.0
+
+#dump           1 all atom 30 dump.ci-reax.lammpstrj
+
+run             3000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9.5
+  ghost atom cutoff = 9.5
+  binsize = 4.75, bins = 5 5 5
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair reax/c, perpetual
+      attributes: half, newton off, ghost
+      pair build: half/bin/newtoff/ghost
+      stencil: half/ghost/bin/3d/newtoff
+      bin: standard
+  (2) pair table, 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) = 43.46 | 43.46 | 43.46 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    508.42043   -28736.654            0   -28260.785    1678.3276 
+    3000    480.41333   -28707.835            0   -28258.181   -3150.0762 
+Loop time of 21.5509 on 1 procs for 3000 steps with 315 atoms
+
+Performance: 3.007 ns/day, 7.982 hours/ns, 139.205 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 21.315     | 21.315     | 21.315     |   0.0 | 98.91
+Neigh   | 0.17846    | 0.17846    | 0.17846    |   0.0 |  0.83
+Comm    | 0.028676   | 0.028676   | 0.028676   |   0.0 |  0.13
+Output  | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 |   0.0 |  0.00
+Modify  | 0.018969   | 0.018969   | 0.018969   |   0.0 |  0.09
+Other   |            | 0.009438   |            |       |  0.04
+
+Nlocal:    315 ave 315 max 315 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2056 ave 2056 max 2056 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    32754 ave 32754 max 32754 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 32754
+Ave neighs/atom = 103.981
+Neighbor list builds = 37
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:21

lib/atc/Matrix.h

@@ -356,7 +356,7 @@ DenseMatrix<T> Matrix<T>::pow(double n) const
   int sz=this->size(); for(INDEX i=0; i<sz; i++)
   {
     double val = R[i];
-    R[i] = pow(val,n);
+    R[i] = std::pow(val,n);
   }
   return R;
 }

lib/gpu/lal_lj_expand_ext.cpp

@@ -92,7 +92,7 @@ int lje_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
 // ---------------------------------------------------------------------------
 // Copy updated coeffs from host to device
 // ---------------------------------------------------------------------------
-int lje_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
+void lje_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1,
                    double **host_lj2, double **host_lj3, double **host_lj4,
                    double **offset, double **shift) {
   int world_me=LJEMF.device->world_me();

lib/kokkos/CHANGELOG.md

@@ -1,5 +1,75 @@
 # Change Log
 
+## [2.5.00](https://github.com/kokkos/kokkos/tree/2.5.00) (2017-12-15)
+[Full Changelog](https://github.com/kokkos/kokkos/compare/2.04.11...2.5.00)
+
+**Part of the Kokkos C++ Performance Portability Programming EcoSystem 2.5**      
+
+**Implemented enhancements:**
+
+- Provide Makefile.kokkos logic for CMake and TriBITS [\#878](https://github.com/kokkos/kokkos/issues/878)
+- Add Scatter View [\#825](https://github.com/kokkos/kokkos/issues/825)
+- Drop gcc 4.7 and intel 14 from supported compiler list [\#603](https://github.com/kokkos/kokkos/issues/603)
+- Enable construction of unmanaged view using common\_view\_alloc\_prop [\#1170](https://github.com/kokkos/kokkos/issues/1170)
+- Unused Function Warning with XL [\#1267](https://github.com/kokkos/kokkos/issues/1267)
+- Add memory pool parameter check [\#1218](https://github.com/kokkos/kokkos/issues/1218)
+- CUDA9: Fix warning for unsupported long double [\#1189](https://github.com/kokkos/kokkos/issues/1189)
+- CUDA9: fix warning on defaulted function marking [\#1188](https://github.com/kokkos/kokkos/issues/1188)
+- CUDA9: fix warnings for deprecated warp level functions [\#1187](https://github.com/kokkos/kokkos/issues/1187)
+- Add CUDA 9.0 nightly testing [\#1174](https://github.com/kokkos/kokkos/issues/1174)
+- {OMPI,MPICH}\_CXX hack breaks nvcc\_wrapper use case [\#1166](https://github.com/kokkos/kokkos/issues/1166)
+- KOKKOS\_HAVE\_CUDA\_LAMBDA became KOKKOS\_CUDA\_USE\_LAMBDA [\#1274](https://github.com/kokkos/kokkos/issues/1274)
+
+**Fixed bugs:**
+
+- MinMax Reducer with tagged operator doesn't compile [\#1251](https://github.com/kokkos/kokkos/issues/1251)
+- Reducers for Tagged operators give wrong answer [\#1250](https://github.com/kokkos/kokkos/issues/1250)
+- Kokkos not Compatible with Big Endian Machines? [\#1235](https://github.com/kokkos/kokkos/issues/1235)
+- Parallel Scan hangs forever on BG/Q [\#1234](https://github.com/kokkos/kokkos/issues/1234)
+- Threads backend doesn't compile with Clang on OS X [\#1232](https://github.com/kokkos/kokkos/issues/1232)
+- $\(shell date\) needs quote [\#1264](https://github.com/kokkos/kokkos/issues/1264)
+- Unqualified parallel\_for call conflicts with user-defined parallel\_for [\#1219](https://github.com/kokkos/kokkos/issues/1219)
+- KokkosAlgorithms: CMake issue in unit tests [\#1212](https://github.com/kokkos/kokkos/issues/1212)
+- Intel 18 Error: "simd pragma has been deprecated" [\#1210](https://github.com/kokkos/kokkos/issues/1210)
+- Memory leak in Kokkos::initialize [\#1194](https://github.com/kokkos/kokkos/issues/1194)
+- CUDA9: compiler error with static assert template arguments [\#1190](https://github.com/kokkos/kokkos/issues/1190)
+- Kokkos::Serial::is\_initialized returns always true [\#1184](https://github.com/kokkos/kokkos/issues/1184)
+- Triple nested parallelism still fails on bowman [\#1093](https://github.com/kokkos/kokkos/issues/1093)
+- OpenMP openmp.range on Develop Runs Forever on POWER7+ with RHEL7 and GCC4.8.5 [\#995](https://github.com/kokkos/kokkos/issues/995)
+- Rendezvous performance at global scope [\#985](https://github.com/kokkos/kokkos/issues/985)
+
+
+## [2.04.11](https://github.com/kokkos/kokkos/tree/2.04.11) (2017-10-28)
+[Full Changelog](https://github.com/kokkos/kokkos/compare/2.04.04...2.04.11)
+
+**Implemented enhancements:**
+
+- Add Subview pattern. [\#648](https://github.com/kokkos/kokkos/issues/648)
+- Add Kokkos "global" is\_initialized [\#1060](https://github.com/kokkos/kokkos/issues/1060)
+- Add create\_mirror\_view\_and\_copy [\#1161](https://github.com/kokkos/kokkos/issues/1161)
+- Add KokkosConcepts SpaceAccessibility function [\#1092](https://github.com/kokkos/kokkos/issues/1092)
+- Option to Disable Initialize Warnings [\#1142](https://github.com/kokkos/kokkos/issues/1142)
+- Mature task-DAG capability [\#320](https://github.com/kokkos/kokkos/issues/320)
+- Promote Work DAG from experimental [\#1126](https://github.com/kokkos/kokkos/issues/1126)
+- Implement new WorkGraph push/pop [\#1108](https://github.com/kokkos/kokkos/issues/1108)
+- Kokkos\_ENABLE\_Cuda\_Lambda should default ON [\#1101](https://github.com/kokkos/kokkos/issues/1101)
+- Add multidimensional parallel for example and improve unit test [\#1064](https://github.com/kokkos/kokkos/issues/1064)
+- Fix ROCm:  Performance tests not building [\#1038](https://github.com/kokkos/kokkos/issues/1038)
+- Make KOKKOS\_ALIGN\_SIZE a configure-time option [\#1004](https://github.com/kokkos/kokkos/issues/1004)
+- Make alignment consistent [\#809](https://github.com/kokkos/kokkos/issues/809)
+- Improve subview construction on Cuda backend [\#615](https://github.com/kokkos/kokkos/issues/615)
+
+**Fixed bugs:**
+
+- Kokkos::vector fixes for application [\#1134](https://github.com/kokkos/kokkos/issues/1134)
+- DynamicView non-power of two value\_type [\#1177](https://github.com/kokkos/kokkos/issues/1177)
+- Memory pool bug [\#1154](https://github.com/kokkos/kokkos/issues/1154)
+- Cuda launch bounds performance regression bug [\#1140](https://github.com/kokkos/kokkos/issues/1140)
+- Significant performance regression in LAMMPS after updating Kokkos [\#1139](https://github.com/kokkos/kokkos/issues/1139)
+- CUDA compile error [\#1128](https://github.com/kokkos/kokkos/issues/1128)
+- MDRangePolicy neg idx test failure in debug mode [\#1113](https://github.com/kokkos/kokkos/issues/1113)
+- subview construction on Cuda backend [\#615](https://github.com/kokkos/kokkos/issues/615)
+
 ## [2.04.04](https://github.com/kokkos/kokkos/tree/2.04.04) (2017-09-11)
 [Full Changelog](https://github.com/kokkos/kokkos/compare/2.04.00...2.04.04)
 

lib/kokkos/CMakeLists.txt

@@ -1,3 +1,5 @@
+# Is this a build as part of Trilinos?
+
 IF(COMMAND TRIBITS_PACKAGE_DECL)
   SET(KOKKOS_HAS_TRILINOS ON CACHE BOOL "")
 ELSE()
@@ -6,13 +8,57 @@ ENDIF()
 
 IF(NOT KOKKOS_HAS_TRILINOS)
   cmake_minimum_required(VERSION 3.1 FATAL_ERROR)
-  project(Kokkos CXX)
 
-  INCLUDE(cmake/kokkos.cmake)
+  # Define Project Name if this is a standalone build
+  IF(NOT DEFINED ${PROJECT_NAME})
+    project(Kokkos CXX) 
+  ENDIF()
+
+  # Basic initialization (Used in KOKKOS_SETTINGS)
+  set(KOKKOS_SRC_PATH ${Kokkos_SOURCE_DIR})
+  set(KOKKOS_PATH ${KOKKOS_SRC_PATH})
+
+  #------------ COMPILER AND FEATURE CHECKS ------------------------------------
+  include(${KOKKOS_SRC_PATH}/cmake/kokkos_functions.cmake)
+  set_kokkos_cxx_compiler()
+  set_kokkos_cxx_standard()
+  
+  #------------ GET OPTIONS AND KOKKOS_SETTINGS --------------------------------
+  # Add Kokkos' modules to CMake's module path.
+  set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${Kokkos_SOURCE_DIR}/cmake/Modules/")
+
+  set(KOKKOS_CMAKE_VERBOSE True)
+  include(${KOKKOS_SRC_PATH}/cmake/kokkos_options.cmake)
+
+  include(${KOKKOS_SRC_PATH}/cmake/kokkos_settings.cmake)
+
+  #------------ GENERATE HEADER AND SOURCE FILES -------------------------------
+  execute_process(
+    COMMAND ${KOKKOS_SETTINGS} make -f ${KOKKOS_SRC_PATH}/cmake/Makefile.generate_cmake_settings CXX=${CMAKE_CXX_COMPILER} generate_build_settings
+    WORKING_DIRECTORY "${Kokkos_BINARY_DIR}"
+    OUTPUT_FILE ${Kokkos_BINARY_DIR}/core_src_make.out
+    RESULT_VARIABLE res
+  )
+  include(${Kokkos_BINARY_DIR}/kokkos_generated_settings.cmake)
+  set_kokkos_srcs(KOKKOS_SRC ${KOKKOS_SRC})
+
+  #------------ NOW BUILD ------------------------------------------------------
+  include(${KOKKOS_SRC_PATH}/cmake/kokkos_build.cmake)
+
+  #------------ Add in Fake Tribits Handling to allow unit test builds- --------
+
+  include(${KOKKOS_SRC_PATH}/cmake/tribits.cmake)
+
+  TRIBITS_PACKAGE_DECL(Kokkos)
+
+  ADD_SUBDIRECTORY(core)
+  ADD_SUBDIRECTORY(containers)
+  ADD_SUBDIRECTORY(algorithms)
+
 ELSE()
 #------------------------------------------------------------------------------
 #
-# A) Forward delcare the package so that certain options are also defined for
+# A) Forward declare the package so that certain options are also defined for
 # subpackages
 #
 
@@ -21,178 +67,28 @@ TRIBITS_PACKAGE_DECL(Kokkos) # ENABLE_SHADOWING_WARNINGS)
 
 #------------------------------------------------------------------------------
 #
-# B) Define the common options for Kokkos first so they can be used by
-# subpackages as well.
+# B) Install Kokkos' build files
 #
+# If using the Makefile-generated files, then need to set things up.
+# Here, assume that TriBITS has been run from ProjectCompilerPostConfig.cmake
+# and already generated KokkosCore_config.h and kokkos_generated_settings.cmake
+# in the previously define Kokkos_GEN_DIR
+# We need to copy them over to the correct place and source the cmake file
 
-# mfh 01 Aug 2016: See Issue #61:
-#
-# https://github.com/kokkos/kokkos/issues/61
-#
-# Don't use TRIBITS_ADD_DEBUG_OPTION() here, because that defines
-# HAVE_KOKKOS_DEBUG.  We define KOKKOS_HAVE_DEBUG here instead,
-# for compatibility with Kokkos' Makefile build system.
+if(NOT KOKKOS_LEGACY_TRIBITS)
+  set(Kokkos_GEN_DIR ${CMAKE_BINARY_DIR})
+  file(COPY "${Kokkos_GEN_DIR}/KokkosCore_config.h"
+    DESTINATION "${CMAKE_CURRENT_BINARY_DIR}" USE_SOURCE_PERMISSIONS)
+  install(FILES "${Kokkos_GEN_DIR}/KokkosCore_config.h"
+    DESTINATION include)
+  file(COPY "${Kokkos_GEN_DIR}/kokkos_generated_settings.cmake"
+    DESTINATION "${CMAKE_CURRENT_BINARY_DIR}" USE_SOURCE_PERMISSIONS)
 
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_DEBUG
-  KOKKOS_HAVE_DEBUG
-  "Enable run-time debug checks.  These checks may be expensive, so they are disabled by default in a release build."
-  ${${PROJECT_NAME}_ENABLE_DEBUG}
-)
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_SIERRA_BUILD
-  KOKKOS_FOR_SIERRA
-  "Configure Kokkos for building within the Sierra build system."
-  OFF
-  )
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_Cuda
-  KOKKOS_HAVE_CUDA
-  "Enable CUDA support in Kokkos."
-  "${TPL_ENABLE_CUDA}"
-  )
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_Cuda_UVM
-  KOKKOS_USE_CUDA_UVM
-  "Enable CUDA Unified Virtual Memory as the default in Kokkos."
-  OFF
-  )
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_Cuda_RDC
-  KOKKOS_HAVE_CUDA_RDC
-  "Enable CUDA Relocatable Device Code support in Kokkos."
-  OFF
-  )
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_Cuda_Lambda
-  KOKKOS_HAVE_CUDA_LAMBDA
-  "Enable CUDA LAMBDA support in Kokkos."
-  OFF
-  )
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_Pthread
-  KOKKOS_HAVE_PTHREAD
-  "Enable Pthread support in Kokkos."
-  OFF
-  )
-
-ASSERT_DEFINED(TPL_ENABLE_Pthread)
-IF(Kokkos_ENABLE_Pthread AND NOT TPL_ENABLE_Pthread)
-  MESSAGE(FATAL_ERROR "You set Kokkos_ENABLE_Pthread=ON, but Trilinos' support for Pthread(s) is not enabled (TPL_ENABLE_Pthread=OFF).  This is not allowed.  Please enable Pthreads in Trilinos before attempting to enable Kokkos' support for Pthreads.")
-ENDIF()
-IF(NOT TPL_ENABLE_Pthread)
-  ADD_DEFINITIONS(-DGTEST_HAS_PTHREAD=0)
-ENDIF()
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_OpenMP
-  KOKKOS_HAVE_OPENMP
-  "Enable OpenMP support in Kokkos."
-  "${${PROJECT_NAME}_ENABLE_OpenMP}"
-  )
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_QTHREAD
-  KOKKOS_HAVE_QTHREADS
-  "Enable Qthreads support in Kokkos."
-  "${TPL_ENABLE_QTHREAD}"
-  )
-
-# TODO: No longer an option in Kokkos.  Needs to be removed.
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_CXX11
-  KOKKOS_HAVE_CXX11
-  "Enable C++11 support in Kokkos."
-  "${${PROJECT_NAME}_ENABLE_CXX11}"
-  )
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_HWLOC
-  KOKKOS_HAVE_HWLOC
-  "Enable HWLOC support in Kokkos."
-  "${TPL_ENABLE_HWLOC}"
-  )
-
-# TODO: This is currently not used in Kokkos.  Should it be removed?
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_MPI
-  KOKKOS_HAVE_MPI
-  "Enable MPI support in Kokkos."
-  "${TPL_ENABLE_MPI}"
-  )
-
-# Set default value of Kokkos_ENABLE_Debug_Bounds_Check option
-#
-# CMake is case sensitive.  The Kokkos_ENABLE_Debug_Bounds_Check
-# option (defined below) is annoyingly not all caps, but we need to
-# keep it that way for backwards compatibility.  If users forget and
-# try using an all-caps variable, then make it count by using the
-# all-caps version as the default value of the original, not-all-caps
-# option.  Otherwise, the default value of this option comes from
-# Kokkos_ENABLE_DEBUG (see Issue #367).
-
-ASSERT_DEFINED(${PACKAGE_NAME}_ENABLE_DEBUG)
-IF(DEFINED Kokkos_ENABLE_DEBUG_BOUNDS_CHECK)
-  IF(Kokkos_ENABLE_DEBUG_BOUNDS_CHECK)
-    SET(Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT ON)
-  ELSE()
-    SET(Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT "${${PACKAGE_NAME}_ENABLE_DEBUG}")
-  ENDIF()
-ELSE()
-  SET(Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT "${${PACKAGE_NAME}_ENABLE_DEBUG}")
-ENDIF()
-ASSERT_DEFINED(Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT)
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_Debug_Bounds_Check
-  KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK
-  "Enable Kokkos::View run-time bounds checking."
-  "${Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT}"
-  )
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_Debug_DualView_Modify_Check
-  KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK
-  "Enable abort when Kokkos::DualView modified on host and device without sync."
-  "${Kokkos_ENABLE_DEBUG}"
-  )
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_Profiling
-  KOKKOS_ENABLE_PROFILING
-  "Enable KokkosP profiling support for kernel data collections."
-  "${TPL_ENABLE_DLlib}"
-  )
-
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_Profiling_Load_Print
-  KOKKOS_ENABLE_PROFILING_LOAD_PRINT
-  "Print to standard output which profiling library was loaded."
-  OFF
-  )
-
-# placeholder for future device...
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_ENABLE_Winthread
-  KOKKOS_HAVE_WINTHREAD
-  "Enable Winthread support in Kokkos."
-  "${TPL_ENABLE_Winthread}"
-  )
-
-# TODO: No longer an option in Kokkos.  Needs to be removed.
-# use new/old View
-TRIBITS_ADD_OPTION_AND_DEFINE(
-  Kokkos_USING_DEPRECATED_VIEW
-  KOKKOS_USING_DEPRECATED_VIEW
-  "Choose whether to use the old, deprecated Kokkos::View"
-  OFF
-  )
+  include(${CMAKE_CURRENT_BINARY_DIR}/kokkos_generated_settings.cmake)
+  # Sources come from makefile-generated kokkos_generated_settings.cmake file
+  # Enable using the individual sources if needed
+  set_kokkos_srcs(KOKKOS_SRC ${KOKKOS_SRC})
+endif ()
 
 
 #------------------------------------------------------------------------------
@@ -226,10 +122,6 @@ TRIBITS_PACKAGE_DEF()
 
 TRIBITS_EXCLUDE_AUTOTOOLS_FILES()
 
-TRIBITS_EXCLUDE_FILES(
-  classic/doc
-  classic/LinAlg/doc/CrsRefactorNotesMay2012
-  )
-
 TRIBITS_PACKAGE_POSTPROCESS()
+
 ENDIF()

lib/kokkos/Makefile.kokkos

@@ -28,33 +28,39 @@ KOKKOS_OPTIONS ?= ""
 # Options: force_uvm,use_ldg,rdc,enable_lambda
 KOKKOS_CUDA_OPTIONS ?= "enable_lambda"
 
+# Return a 1 if a string contains a substring and 0 if not
+# Note the search string should be without '"'
+# Example: $(call kokkos_has_string,"hwloc,librt",hwloc)
+#   Will return a 1
+kokkos_has_string=$(if $(findstring $2,$1),1,0)
+
 # Check for general settings.
-KOKKOS_INTERNAL_ENABLE_DEBUG := $(strip $(shell echo $(KOKKOS_DEBUG) | grep "yes" | wc -l))
-KOKKOS_INTERNAL_ENABLE_CXX11 := $(strip $(shell echo $(KOKKOS_CXX_STANDARD) | grep "c++11" | wc -l))
-KOKKOS_INTERNAL_ENABLE_CXX1Z := $(strip $(shell echo $(KOKKOS_CXX_STANDARD) | grep "c++1z" | wc -l))
+KOKKOS_INTERNAL_ENABLE_DEBUG := $(call kokkos_has_string,$(KOKKOS_DEBUG),yes)
+KOKKOS_INTERNAL_ENABLE_CXX11 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++11)
+KOKKOS_INTERNAL_ENABLE_CXX1Z := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++1z)
 
 # Check for external libraries.
-KOKKOS_INTERNAL_USE_HWLOC := $(strip $(shell echo $(KOKKOS_USE_TPLS) | grep "hwloc" | wc -l))
-KOKKOS_INTERNAL_USE_LIBRT := $(strip $(shell echo $(KOKKOS_USE_TPLS) | grep "librt" | wc -l))
-KOKKOS_INTERNAL_USE_MEMKIND := $(strip $(shell echo $(KOKKOS_USE_TPLS) | grep "experimental_memkind" | wc -l))
+KOKKOS_INTERNAL_USE_HWLOC := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),hwloc)
+KOKKOS_INTERNAL_USE_LIBRT := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),librt)
+KOKKOS_INTERNAL_USE_MEMKIND := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),experimental_memkind)
 
 # Check for advanced settings.
-KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "compiler_warnings" | wc -l))
-KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "aggressive_vectorization" | wc -l))
-KOKKOS_INTERNAL_DISABLE_PROFILING := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "disable_profiling" | wc -l))
-KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "disable_dualview_modify_check" | wc -l))
-KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "enable_profile_load_print" | wc -l))
-KOKKOS_INTERNAL_CUDA_USE_LDG := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "use_ldg" | wc -l))
-KOKKOS_INTERNAL_CUDA_USE_UVM := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "force_uvm" | wc -l))
-KOKKOS_INTERNAL_CUDA_USE_RELOC := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "rdc" | wc -l))
-KOKKOS_INTERNAL_CUDA_USE_LAMBDA := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "enable_lambda" | wc -l))
+KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),compiler_warnings)
+KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION := $(call kokkos_has_string,$(KOKKOS_OPTIONS),aggressive_vectorization)
+KOKKOS_INTERNAL_DISABLE_PROFILING := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_profiling)
+KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_dualview_modify_check)
+KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_profile_load_print)
+KOKKOS_INTERNAL_CUDA_USE_LDG := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),use_ldg)
+KOKKOS_INTERNAL_CUDA_USE_UVM := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),force_uvm)
+KOKKOS_INTERNAL_CUDA_USE_RELOC := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),rdc)
+KOKKOS_INTERNAL_CUDA_USE_LAMBDA := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),enable_lambda)
 
 
 # Check for Kokkos Host Execution Spaces one of which must be on.
-KOKKOS_INTERNAL_USE_OPENMP := $(strip $(shell echo $(subst OpenMPTarget,,$(KOKKOS_DEVICES)) | grep OpenMP | wc -l))
-KOKKOS_INTERNAL_USE_PTHREADS := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Pthread | wc -l))
-KOKKOS_INTERNAL_USE_QTHREADS := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Qthreads | wc -l))
-KOKKOS_INTERNAL_USE_SERIAL := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Serial | wc -l))
+KOKKOS_INTERNAL_USE_OPENMP := $(call kokkos_has_string,$(subst OpenMPTarget,,$(KOKKOS_DEVICES)),OpenMP)
+KOKKOS_INTERNAL_USE_PTHREADS := $(call kokkos_has_string,$(KOKKOS_DEVICES),Pthread)
+KOKKOS_INTERNAL_USE_QTHREADS := $(call kokkos_has_string,$(KOKKOS_DEVICES),Qthreads)
+KOKKOS_INTERNAL_USE_SERIAL := $(call kokkos_has_string,$(KOKKOS_DEVICES),Serial)
 
 ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 0)
   ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 0)
@@ -65,9 +71,9 @@ ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 0)
 endif
 
 # Check for other Execution Spaces.
-KOKKOS_INTERNAL_USE_CUDA := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Cuda | wc -l))
-KOKKOS_INTERNAL_USE_ROCM := $(strip $(shell echo $(KOKKOS_DEVICES) | grep ROCm | wc -l))
-KOKKOS_INTERNAL_USE_OPENMPTARGET := $(strip $(shell echo $(KOKKOS_DEVICES) | grep OpenMPTarget | wc -l))
+KOKKOS_INTERNAL_USE_CUDA := $(call kokkos_has_string,$(KOKKOS_DEVICES),Cuda)
+KOKKOS_INTERNAL_USE_ROCM := $(call kokkos_has_string,$(KOKKOS_DEVICES),ROCm)
+KOKKOS_INTERNAL_USE_OPENMPTARGET := $(call kokkos_has_string,$(KOKKOS_DEVICES),OpenMPTarget)
 
 ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
   KOKKOS_INTERNAL_NVCC_PATH := $(shell which nvcc)
@@ -77,25 +83,20 @@ endif
 
 # Check OS.
 KOKKOS_OS                      := $(strip $(shell uname -s))
-KOKKOS_INTERNAL_OS_CYGWIN      := $(strip $(shell uname -s | grep CYGWIN | wc -l))
-KOKKOS_INTERNAL_OS_LINUX       := $(strip $(shell uname -s | grep Linux  | wc -l))
-KOKKOS_INTERNAL_OS_DARWIN      := $(strip $(shell uname -s | grep Darwin | wc -l))
+KOKKOS_INTERNAL_OS_CYGWIN      := $(call kokkos_has_string,$(KOKKOS_OS),CYGWIN)
+KOKKOS_INTERNAL_OS_LINUX       := $(call kokkos_has_string,$(KOKKOS_OS),Linux)
+KOKKOS_INTERNAL_OS_DARWIN      := $(call kokkos_has_string,$(KOKKOS_OS),Darwin)
 
 # Check compiler.
-KOKKOS_INTERNAL_COMPILER_INTEL       := $(strip $(shell $(CXX) --version       2>&1 | grep "Intel Corporation" | wc -l))
-KOKKOS_INTERNAL_COMPILER_PGI         := $(strip $(shell $(CXX) --version       2>&1 | grep PGI                 | wc -l))
+KOKKOS_CXX_VERSION                   := $(strip $(shell $(CXX) --version       2>&1))
+KOKKOS_INTERNAL_COMPILER_INTEL       := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),Intel Corporation)
+KOKKOS_INTERNAL_COMPILER_PGI         := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),PGI)
 KOKKOS_INTERNAL_COMPILER_XL          := $(strip $(shell $(CXX) -qversion       2>&1 | grep XL                  | wc -l))
 KOKKOS_INTERNAL_COMPILER_CRAY        := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep "CC-"               | wc -l))
-KOKKOS_INTERNAL_COMPILER_NVCC        := $(strip $(shell $(CXX) --version       2>&1 | grep nvcc                | wc -l))
-ifneq ($(OMPI_CXX),)
-  KOKKOS_INTERNAL_COMPILER_NVCC      := $(strip $(shell $(OMPI_CXX) --version       2>&1 | grep nvcc                | wc -l))
-endif
-ifneq ($(MPICH_CXX),)
-  KOKKOS_INTERNAL_COMPILER_NVCC      := $(strip $(shell $(MPICH_CXX) --version       2>&1 | grep nvcc                | wc -l))
-endif
-KOKKOS_INTERNAL_COMPILER_CLANG       := $(strip $(shell $(CXX) --version       2>&1 | grep clang               | wc -l))
-KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(strip $(shell $(CXX) --version       2>&1 | grep "apple-darwin"      | wc -l))
-KOKKOS_INTERNAL_COMPILER_HCC         := $(strip $(shell $(CXX) --version       2>&1 | grep HCC                 | wc -l))
+KOKKOS_INTERNAL_COMPILER_NVCC        := $(strip $(shell export OMPI_CXX=$(OMPI_CXX); export MPICH_CXX=$(MPICH_CXX); $(CXX) --version       2>&1 | grep nvcc                | wc -l))
+KOKKOS_INTERNAL_COMPILER_CLANG       := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),clang)
+KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),apple-darwin)
+KOKKOS_INTERNAL_COMPILER_HCC         := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),HCC)
 
 ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 2)
   KOKKOS_INTERNAL_COMPILER_CLANG = 1
@@ -209,47 +210,48 @@ endif
 # Check for Kokkos Architecture settings.
 
 # Intel based.
-KOKKOS_INTERNAL_USE_ARCH_KNC := $(strip $(shell echo $(KOKKOS_ARCH) | grep KNC | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_WSM := $(strip $(shell echo $(KOKKOS_ARCH) | grep WSM | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_SNB := $(strip $(shell echo $(KOKKOS_ARCH) | grep SNB | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_HSW := $(strip $(shell echo $(KOKKOS_ARCH) | grep HSW | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_BDW := $(strip $(shell echo $(KOKKOS_ARCH) | grep BDW | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_SKX := $(strip $(shell echo $(KOKKOS_ARCH) | grep SKX | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_KNL := $(strip $(shell echo $(KOKKOS_ARCH) | grep KNL | wc -l))
+KOKKOS_INTERNAL_USE_ARCH_KNC := $(call kokkos_has_string,$(KOKKOS_ARCH),KNC)
+KOKKOS_INTERNAL_USE_ARCH_WSM := $(call kokkos_has_string,$(KOKKOS_ARCH),WSM)
+KOKKOS_INTERNAL_USE_ARCH_SNB := $(call kokkos_has_string,$(KOKKOS_ARCH),SNB)
+KOKKOS_INTERNAL_USE_ARCH_HSW := $(call kokkos_has_string,$(KOKKOS_ARCH),HSW)
+KOKKOS_INTERNAL_USE_ARCH_BDW := $(call kokkos_has_string,$(KOKKOS_ARCH),BDW)
+KOKKOS_INTERNAL_USE_ARCH_SKX := $(call kokkos_has_string,$(KOKKOS_ARCH),SKX)
+KOKKOS_INTERNAL_USE_ARCH_KNL := $(call kokkos_has_string,$(KOKKOS_ARCH),KNL)
 
 # NVIDIA based.
 NVCC_WRAPPER := $(KOKKOS_PATH)/bin/nvcc_wrapper
-KOKKOS_INTERNAL_USE_ARCH_KEPLER30 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler30 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_KEPLER32 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler32 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_KEPLER35 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler35 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_KEPLER37 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler37 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_MAXWELL50 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Maxwell50 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_MAXWELL52 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Maxwell52 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_MAXWELL53 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Maxwell53 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_PASCAL61 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Pascal61 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_PASCAL60 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Pascal60 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30)  \
-                                                      + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32)  \
-                                                      + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35)  \
-                                                      + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37)  \
-                                                      + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61)  \
-                                                      + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60)  \
-                                                      + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
-                                                      + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
-                                                      + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53) | bc))
+KOKKOS_INTERNAL_USE_ARCH_KEPLER30 := $(call kokkos_has_string,$(KOKKOS_ARCH),Kepler30)
+KOKKOS_INTERNAL_USE_ARCH_KEPLER32 := $(call kokkos_has_string,$(KOKKOS_ARCH),Kepler32)
+KOKKOS_INTERNAL_USE_ARCH_KEPLER35 := $(call kokkos_has_string,$(KOKKOS_ARCH),Kepler35)
+KOKKOS_INTERNAL_USE_ARCH_KEPLER37 := $(call kokkos_has_string,$(KOKKOS_ARCH),Kepler37)
+KOKKOS_INTERNAL_USE_ARCH_MAXWELL50 := $(call kokkos_has_string,$(KOKKOS_ARCH),Maxwell50)
+KOKKOS_INTERNAL_USE_ARCH_MAXWELL52 := $(call kokkos_has_string,$(KOKKOS_ARCH),Maxwell52)
+KOKKOS_INTERNAL_USE_ARCH_MAXWELL53 := $(call kokkos_has_string,$(KOKKOS_ARCH),Maxwell53)
+KOKKOS_INTERNAL_USE_ARCH_PASCAL61 := $(call kokkos_has_string,$(KOKKOS_ARCH),Pascal61)
+KOKKOS_INTERNAL_USE_ARCH_PASCAL60 := $(call kokkos_has_string,$(KOKKOS_ARCH),Pascal60)
+KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30)  \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32)  \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35)  \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37)  \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61)  \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60)  \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
+                                              + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53))
 
+#SEK: This seems like a bug to me
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0)
-  KOKKOS_INTERNAL_USE_ARCH_MAXWELL50 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Maxwell | wc -l))
-  KOKKOS_INTERNAL_USE_ARCH_KEPLER35 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler | wc -l))
-  KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30)  \
-                                                        + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32)  \
-                                                        + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35)  \
-                                                        + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37)  \
-                                                        + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61)  \
-                                                        + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60)  \
-                                                        + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
-                                                        + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
-                                                        + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53) | bc))
+  KOKKOS_INTERNAL_USE_ARCH_MAXWELL50 := $(call kokkos_has_string,$(KOKKOS_ARCH),Maxwell)
+  KOKKOS_INTERNAL_USE_ARCH_KEPLER35 := $(call kokkos_has_string,$(KOKKOS_ARCH),Kepler)
+  KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30)  \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32)  \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35)  \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37)  \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61)  \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60)  \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
+                                                + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53))
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 1)
@@ -262,43 +264,43 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 1)
   endif
 endif
 # ARM based.
-KOKKOS_INTERNAL_USE_ARCH_ARMV80 := $(strip $(shell echo $(KOKKOS_ARCH) | grep ARMv80 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_ARMV81 := $(strip $(shell echo $(KOKKOS_ARCH) | grep ARMv81 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX := $(strip $(shell echo $(KOKKOS_ARCH) | grep ARMv8-ThunderX | wc -l))
+KOKKOS_INTERNAL_USE_ARCH_ARMV80 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv80)
+KOKKOS_INTERNAL_USE_ARCH_ARMV81 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv81)
+KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8-ThunderX)
 KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX) | bc))
 
 # IBM based.
-KOKKOS_INTERNAL_USE_ARCH_BGQ := $(strip $(shell echo $(KOKKOS_ARCH) | grep BGQ | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_POWER7 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Power7 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_POWER8 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Power8 | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_POWER9 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Power9 | wc -l))
+KOKKOS_INTERNAL_USE_ARCH_BGQ := $(call kokkos_has_string,$(KOKKOS_ARCH),BGQ)
+KOKKOS_INTERNAL_USE_ARCH_POWER7 := $(call kokkos_has_string,$(KOKKOS_ARCH),Power7)
+KOKKOS_INTERNAL_USE_ARCH_POWER8 := $(call kokkos_has_string,$(KOKKOS_ARCH),Power8)
+KOKKOS_INTERNAL_USE_ARCH_POWER9 := $(call kokkos_has_string,$(KOKKOS_ARCH),Power9)
 KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_BGQ)+$(KOKKOS_INTERNAL_USE_ARCH_POWER7)+$(KOKKOS_INTERNAL_USE_ARCH_POWER8)+$(KOKKOS_INTERNAL_USE_ARCH_POWER9) | bc))
 
 # AMD based.
-KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(strip $(shell echo $(KOKKOS_ARCH) | grep AMDAVX | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_RYZEN := $(strip $(shell echo $(KOKKOS_ARCH) | grep Ryzen | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_EPYC := $(strip $(shell echo $(KOKKOS_ARCH) | grep Epyc | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_KAVERI := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kaveri | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_CARRIZO := $(strip $(shell echo $(KOKKOS_ARCH) | grep Carrizo | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_FIJI := $(strip $(shell echo $(KOKKOS_ARCH) | grep Fiji | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_VEGA := $(strip $(shell echo $(KOKKOS_ARCH) | grep Vega | wc -l))
-KOKKOS_INTERNAL_USE_ARCH_GFX901 := $(strip $(shell echo $(KOKKOS_ARCH) | grep gfx901 | wc -l))
+KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(call kokkos_has_string,$(KOKKOS_ARCH),AMDAVX)
+KOKKOS_INTERNAL_USE_ARCH_RYZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Ryzen)
+KOKKOS_INTERNAL_USE_ARCH_EPYC := $(call kokkos_has_string,$(KOKKOS_ARCH),Epyc)
+KOKKOS_INTERNAL_USE_ARCH_KAVERI := $(call kokkos_has_string,$(KOKKOS_ARCH),Kaveri)
+KOKKOS_INTERNAL_USE_ARCH_CARRIZO := $(call kokkos_has_string,$(KOKKOS_ARCH),Carrizo)
+KOKKOS_INTERNAL_USE_ARCH_FIJI := $(call kokkos_has_string,$(KOKKOS_ARCH),Fiji)
+KOKKOS_INTERNAL_USE_ARCH_VEGA := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega)
+KOKKOS_INTERNAL_USE_ARCH_GFX901 := $(call kokkos_has_string,$(KOKKOS_ARCH),gfx901)
 
 # Any AVX?
-KOKKOS_INTERNAL_USE_ARCH_SSE42      := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_WSM) | bc ))
-KOKKOS_INTERNAL_USE_ARCH_AVX        := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_SNB)+$(KOKKOS_INTERNAL_USE_ARCH_AMDAVX) | bc ))
-KOKKOS_INTERNAL_USE_ARCH_AVX2       := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_HSW)+$(KOKKOS_INTERNAL_USE_ARCH_BDW) | bc ))
-KOKKOS_INTERNAL_USE_ARCH_AVX512MIC  := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_KNL) | bc ))
-KOKKOS_INTERNAL_USE_ARCH_AVX512XEON := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_SKX) | bc ))
+KOKKOS_INTERNAL_USE_ARCH_SSE42      := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM))
+KOKKOS_INTERNAL_USE_ARCH_AVX        := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_AMDAVX))
+KOKKOS_INTERNAL_USE_ARCH_AVX2       := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW))
+KOKKOS_INTERNAL_USE_ARCH_AVX512MIC  := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNL))
+KOKKOS_INTERNAL_USE_ARCH_AVX512XEON := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SKX))
 
 # Decide what ISA level we are able to support.
-KOKKOS_INTERNAL_USE_ISA_X86_64    := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_WSM)+$(KOKKOS_INTERNAL_USE_ARCH_SNB)+$(KOKKOS_INTERNAL_USE_ARCH_HSW)+$(KOKKOS_INTERNAL_USE_ARCH_BDW)+$(KOKKOS_INTERNAL_USE_ARCH_KNL)+$(KOKKOS_INTERNAL_USE_ARCH_SKX) | bc ))
-KOKKOS_INTERNAL_USE_ISA_KNC       := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_KNC) | bc ))
-KOKKOS_INTERNAL_USE_ISA_POWERPCLE := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_POWER8)+$(KOKKOS_INTERNAL_USE_ARCH_POWER9) | bc ))
-KOKKOS_INTERNAL_USE_ISA_POWERPCBE := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_POWER7) | bc ))
+KOKKOS_INTERNAL_USE_ISA_X86_64    := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX))
+KOKKOS_INTERNAL_USE_ISA_KNC       := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNC))
+KOKKOS_INTERNAL_USE_ISA_POWERPCLE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER8) + $(KOKKOS_INTERNAL_USE_ARCH_POWER9))
+KOKKOS_INTERNAL_USE_ISA_POWERPCBE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER7))
 
 # Decide whether we can support transactional memory
-KOKKOS_INTERNAL_USE_TM            := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_BDW)+$(KOKKOS_INTERNAL_USE_ARCH_SKX) | bc ))
+KOKKOS_INTERNAL_USE_TM            := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_SKX))
 
 # Incompatible flags?
 KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_SSE42)+$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_ARM)>1" | bc ))
@@ -320,94 +322,100 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS), 1)
   KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_WARNINGS)
 endif
 
-KOKKOS_LIBS = -lkokkos -ldl
+KOKKOS_LIBS = -ldl
 KOKKOS_LDFLAGS = -L$(shell pwd)
 KOKKOS_SRC =
 KOKKOS_HEADERS =
 
 # Generating the KokkosCore_config.h file.
 
+KOKKOS_INTERNAL_CONFIG_TMP=KokkosCore_config.tmp
+KOKKOS_CONFIG_HEADER=KokkosCore_config.h
+# Functions for generating config header file
+kokkos_append_header = $(shell echo $1 >> $(KOKKOS_INTERNAL_CONFIG_TMP))
+
+# Do not append first line
 tmp := $(shell echo "/* ---------------------------------------------" > KokkosCore_config.tmp)
-tmp := $(shell echo "Makefile constructed configuration:" >> KokkosCore_config.tmp)
-tmp := $(shell date >> KokkosCore_config.tmp)
-tmp := $(shell echo "----------------------------------------------*/" >> KokkosCore_config.tmp)
+tmp := $(call kokkos_append_header,"Makefile constructed configuration:")
+tmp := $(call kokkos_append_header,"$(shell date)")
+tmp := $(call kokkos_append_header,"----------------------------------------------*/")
 
-tmp := $(shell echo '\#if !defined(KOKKOS_MACROS_HPP) || defined(KOKKOS_CORE_CONFIG_H)' >> KokkosCore_config.tmp)
-tmp := $(shell echo '\#error "Do not include KokkosCore_config.h directly; include Kokkos_Macros.hpp instead."' >> KokkosCore_config.tmp)
-tmp := $(shell echo '\#else' >> KokkosCore_config.tmp)
-tmp := $(shell echo '\#define KOKKOS_CORE_CONFIG_H' >> KokkosCore_config.tmp)
-tmp := $(shell echo '\#endif' >> KokkosCore_config.tmp)
-
-tmp := $(shell echo "/* Execution Spaces */" >> KokkosCore_config.tmp)
+tmp := $(call kokkos_append_header,'\#if !defined(KOKKOS_MACROS_HPP) || defined(KOKKOS_CORE_CONFIG_H)')
+tmp := $(call kokkos_append_header,'\#error "Do not include $(KOKKOS_CONFIG_HEADER) directly; include Kokkos_Macros.hpp instead."')
+tmp := $(call kokkos_append_header,'\#else')
+tmp := $(call kokkos_append_header,'\#define KOKKOS_CORE_CONFIG_H')
+tmp := $(call kokkos_append_header,'\#endif')
+	
+tmp := $(call kokkos_append_header,"/* Execution Spaces */")
 
 ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
-  tmp := $(shell echo "\#define KOKKOS_HAVE_CUDA 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_CUDA")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1)
-  tmp := $(shell echo '\#define KOKKOS_ENABLE_ROCM 1' >> KokkosCore_config.tmp)
+  tmp := $(call kokkos_append_header,'\#define KOKKOS_ENABLE_ROCM')
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
-  tmp := $(shell echo '\#define KOKKOS_ENABLE_OPENMPTARGET 1' >> KokkosCore_config.tmp)
+  tmp := $(call kokkos_append_header,'\#define KOKKOS_ENABLE_OPENMPTARGET')
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
-  tmp := $(shell echo '\#define KOKKOS_HAVE_OPENMP 1' >> KokkosCore_config.tmp)
+  tmp := $(call kokkos_append_header,'\#define KOKKOS_HAVE_OPENMP')
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
-  tmp := $(shell echo "\#define KOKKOS_HAVE_PTHREAD 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_PTHREAD")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_QTHREADS), 1)
-  tmp := $(shell echo "\#define KOKKOS_HAVE_QTHREADS 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_QTHREADS")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
-  tmp := $(shell echo "\#define KOKKOS_HAVE_SERIAL 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_SERIAL")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_TM), 1)
-  tmp := $(shell echo "\#ifndef __CUDA_ARCH__" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#define KOKKOS_ENABLE_TM" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#endif" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#ifndef __CUDA_ARCH__")
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_TM")
+  tmp := $(call kokkos_append_header,"\#endif")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ISA_X86_64), 1)
-  tmp := $(shell echo "\#ifndef __CUDA_ARCH__" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#define KOKKOS_USE_ISA_X86_64" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#endif" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#ifndef __CUDA_ARCH__")
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_ISA_X86_64")
+  tmp := $(call kokkos_append_header,"\#endif")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ISA_KNC), 1)
-  tmp := $(shell echo "\#ifndef __CUDA_ARCH__" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#define KOKKOS_USE_ISA_KNC" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#endif" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#ifndef __CUDA_ARCH__")
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_ISA_KNC")
+  tmp := $(call kokkos_append_header,"\#endif")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ISA_POWERPCLE), 1)
-  tmp := $(shell echo "\#ifndef __CUDA_ARCH__" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#define KOKKOS_USE_ISA_POWERPCLE" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#endif" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#ifndef __CUDA_ARCH__")
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_ISA_POWERPCLE")
+  tmp := $(call kokkos_append_header,"\#endif")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ISA_POWERPCBE), 1)
-  tmp := $(shell echo "\#ifndef __CUDA_ARCH__" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#define KOKKOS_USE_ISA_POWERPCBE" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#endif" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#ifndef __CUDA_ARCH__")
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_ISA_POWERPCBE")
+  tmp := $(call kokkos_append_header,"\#endif")
 endif
 
-tmp := $(shell echo "/* General Settings */" >> KokkosCore_config.tmp)
+tmp := $(call kokkos_append_header,"/* General Settings */")
 ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX11), 1)
   KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX11_FLAG)
-  tmp := $(shell echo "\#define KOKKOS_HAVE_CXX11 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_CXX11")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX1Z), 1)
   KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX1Z_FLAG)
-  tmp := $(shell echo "\#define KOKKOS_HAVE_CXX11 1" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#define KOKKOS_HAVE_CXX1Z 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_CXX11")
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_CXX1Z")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1)
@@ -417,26 +425,26 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1)
 
   KOKKOS_CXXFLAGS += -g
   KOKKOS_LDFLAGS += -g -ldl
-  tmp := $(shell echo "\#define KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK 1" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#define KOKKOS_HAVE_DEBUG 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK")
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_DEBUG")
   ifeq ($(KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK), 0)
-    tmp := $(shell echo "\#define KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK")
   endif
 endif
 
 ifeq ($(KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT), 1)
-  tmp := $(shell echo "\#define KOKKOS_ENABLE_PROFILING_LOAD_PRINT 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_PROFILING_LOAD_PRINT")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1)
   KOKKOS_CPPFLAGS += -I$(HWLOC_PATH)/include
   KOKKOS_LDFLAGS += -L$(HWLOC_PATH)/lib
   KOKKOS_LIBS += -lhwloc
-  tmp := $(shell echo "\#define KOKKOS_HAVE_HWLOC 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_HWLOC")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_LIBRT), 1)
-  tmp := $(shell echo "\#define KOKKOS_USE_LIBRT 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_LIBRT")
   KOKKOS_LIBS += -lrt
 endif
 
@@ -444,36 +452,36 @@ ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1)
   KOKKOS_CPPFLAGS += -I$(MEMKIND_PATH)/include
   KOKKOS_LDFLAGS += -L$(MEMKIND_PATH)/lib
   KOKKOS_LIBS += -lmemkind -lnuma
-  tmp := $(shell echo "\#define KOKKOS_HAVE_HBWSPACE 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_HBWSPACE")
 endif
 
 ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 0)
-  tmp := $(shell echo "\#define KOKKOS_ENABLE_PROFILING" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_PROFILING")
 endif
 
-tmp := $(shell echo "/* Optimization Settings */" >> KokkosCore_config.tmp)
+tmp := $(call kokkos_append_header,"/* Optimization Settings */")
 
 ifeq ($(KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION), 1)
-  tmp := $(shell echo "\#define KOKKOS_OPT_RANGE_AGGRESSIVE_VECTORIZATION 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_OPT_RANGE_AGGRESSIVE_VECTORIZATION")
 endif
 
-tmp := $(shell echo "/* Cuda Settings */" >> KokkosCore_config.tmp)
+tmp := $(call kokkos_append_header,"/* Cuda Settings */")
 
 ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
   ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LDG), 1)
-    tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LDG_INTRINSIC 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_LDG_INTRINSIC")
   else
     ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
-      tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LDG_INTRINSIC 1" >> KokkosCore_config.tmp )
+      tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_LDG_INTRINSIC")
     endif
   endif
 
   ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1)
-    tmp := $(shell echo "\#define KOKKOS_CUDA_USE_UVM 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_UVM")
   endif
 
   ifeq ($(KOKKOS_INTERNAL_CUDA_USE_RELOC), 1)
-    tmp := $(shell echo "\#define KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE")
     KOKKOS_CXXFLAGS += --relocatable-device-code=true
     KOKKOS_LDFLAGS += --relocatable-device-code=true
   endif
@@ -481,7 +489,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
   ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LAMBDA), 1)
     ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1)
       ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -gt 70; echo $$?),0)
-        tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LAMBDA 1" >> KokkosCore_config.tmp )
+        tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_LAMBDA")
         KOKKOS_CXXFLAGS += -expt-extended-lambda
       else
         $(warning Warning: Cuda Lambda support was requested but NVCC version is too low. This requires NVCC for Cuda version 7.5 or higher. Disabling Lambda support now.)
@@ -489,19 +497,19 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
     endif
 
     ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
-      tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LAMBDA 1" >> KokkosCore_config.tmp )
+      tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_LAMBDA")
     endif
   endif
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
-    tmp := $(shell echo "\#define KOKKOS_CUDA_CLANG_WORKAROUND" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_CLANG_WORKAROUND")
   endif
 endif
 
 # Add Architecture flags.
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV80), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_ARMV80 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV80")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
     KOKKOS_CXXFLAGS +=
@@ -518,7 +526,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV80), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV81), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_ARMV81 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV81")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
     KOKKOS_CXXFLAGS +=
@@ -535,8 +543,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV81), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_ARMV80 1" >> KokkosCore_config.tmp )
-  tmp := $(shell echo "\#define KOKKOS_ARCH_ARMV8_THUNDERX 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV80")
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV8_THUNDERX")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
     KOKKOS_CXXFLAGS +=
@@ -553,7 +561,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_SSE42), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_SSE42 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_SSE42")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
     KOKKOS_CXXFLAGS += -xSSE4.2
@@ -575,7 +583,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_SSE42), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_AVX 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AVX")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
     KOKKOS_CXXFLAGS += -mavx
@@ -597,7 +605,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER7), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_POWER7 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_POWER7")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
 
@@ -609,7 +617,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER7), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER8), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_POWER8 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_POWER8")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
 
@@ -630,7 +638,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER8), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER9), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_POWER9 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_POWER9")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
 
@@ -651,7 +659,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER9), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_HSW), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_AVX2 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AVX2")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
     KOKKOS_CXXFLAGS += -xCORE-AVX2
@@ -673,7 +681,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_HSW), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_BDW), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_AVX2 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AVX2")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
     KOKKOS_CXXFLAGS += -xCORE-AVX2
@@ -695,7 +703,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_BDW), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_AVX512MIC 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AVX512MIC")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
     KOKKOS_CXXFLAGS += -xMIC-AVX512
@@ -716,7 +724,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_AVX512XEON 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AVX512XEON")
 
   ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
     KOKKOS_CXXFLAGS += -xCORE-AVX512
@@ -737,7 +745,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON), 1)
 endif
 
 ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KNC), 1)
-  tmp := $(shell echo "\#define KOKKOS_ARCH_KNC 1" >> KokkosCore_config.tmp )
+  tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KNC")
   KOKKOS_CXXFLAGS += -mmic
   KOKKOS_LDFLAGS += -mmic
 endif
@@ -753,48 +761,48 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
   endif
 
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER30), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER30 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER30")
     KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_30
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER32), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER32 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER32")
     KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_32
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER35), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER35 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER35")
     KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_35
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER37), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER37 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER37")
     KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_37
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL50 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL50")
     KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_50
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL52 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL52")
     KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_52
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL53 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL53")
     KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_53
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL60), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL60 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_PASCAL")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_PASCAL60")
     KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_60
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL61), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL61 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_PASCAL")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_PASCAL61")
     KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_61
   endif
 
@@ -811,28 +819,28 @@ endif
 ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1)
   # Lets start with adding architecture defines
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KAVERI), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_ROCM 701" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_KAVERI 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ROCM 701")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KAVERI")
     KOKKOS_INTERNAL_ROCM_ARCH_FLAG := --amdgpu-target=gfx701 
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_CARRIZO), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_ROCM 801" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_CARRIZO 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ROCM 801")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_CARRIZO")
     KOKKOS_INTERNAL_ROCM_ARCH_FLAG := --amdgpu-target=gfx801 
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_FIJI), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_ROCM 803" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_FIJI 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ROCM 803")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_FIJI")
     KOKKOS_INTERNAL_ROCM_ARCH_FLAG := --amdgpu-target=gfx803
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VEGA), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_ROCM 900" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_VEGA 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ROCM 900")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VEGA")
     KOKKOS_INTERNAL_ROCM_ARCH_FLAG := --amdgpu-target=gfx900 
   endif
   ifeq ($(KOKKOS_INTERNAL_USE_ARCH_GFX901), 1)
-    tmp := $(shell echo "\#define KOKKOS_ARCH_ROCM 901" >> KokkosCore_config.tmp )
-    tmp := $(shell echo "\#define KOKKOS_ARCH_GFX901 1" >> KokkosCore_config.tmp )
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ROCM 901")
+    tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_GFX901")
     KOKKOS_INTERNAL_ROCM_ARCH_FLAG := --amdgpu-target=gfx901 
   endif
  
@@ -952,6 +960,10 @@ ifeq ($(KOKKOS_INTERNAL_OS_CYGWIN), 1)
   KOKKOS_CXXFLAGS += -U__STRICT_ANSI__
 endif
 
+# Set KokkosExtraLibs and add -lkokkos to link line
+KOKKOS_EXTRA_LIBS := ${KOKKOS_LIBS}
+KOKKOS_LIBS := -lkokkos ${KOKKOS_LIBS}
+
 # Setting up dependencies.
 
 KokkosCore_config.h:

lib/kokkos/Makefile.targets

@@ -22,8 +22,8 @@ Kokkos_HostThreadTeam.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokk
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostThreadTeam.cpp
 Kokkos_Spinwait.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Spinwait.cpp
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Spinwait.cpp
-Kokkos_Rendezvous.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Rendezvous.cpp
-	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Rendezvous.cpp
+Kokkos_HostBarrier.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HostBarrier.cpp
+	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostBarrier.cpp
 Kokkos_Profiling_Interface.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Profiling_Interface.cpp
 	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Profiling_Interface.cpp
 Kokkos_SharedAlloc.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_SharedAlloc.cpp

lib/kokkos/README

@@ -41,48 +41,44 @@ hcedwar(at)sandia.gov and crtrott(at)sandia.gov
 ============================================================================
 
 Primary tested compilers on X86 are:
-  GCC 4.7.2
   GCC 4.8.4
-  GCC 4.9.2
+  GCC 4.9.3
   GCC 5.1.0
-  GCC 5.2.0
-  Intel 14.0.4
+  GCC 5.3.0
+  GCC 6.1.0
   Intel 15.0.2
   Intel 16.0.1
-  Intel 17.0.098
-  Intel 17.1.132
+  Intel 17.1.043
+  Intel 17.4.196
+  Intel 18.0.128
   Clang 3.5.2
   Clang 3.6.1
   Clang 3.7.1
   Clang 3.8.1
   Clang 3.9.0
-  PGI 17.1
+  Clang 4.0.0
+  Clang 4.0.0 for CUDA (CUDA Toolkit 8.0.44)
+  PGI 17.10
+  NVCC 7.0 for CUDA (with gcc 4.8.4)
+  NVCC 7.5 for CUDA (with gcc 4.8.4)
+  NVCC 8.0.44 for CUDA (with gcc 5.3.0)
 
 Primary tested compilers on Power 8 are:
   GCC 5.4.0 (OpenMP,Serial)
-  IBM XL 13.1.3 (OpenMP, Serial) (There is a workaround in place to avoid a compiler bug)
+  IBM XL 13.1.5 (OpenMP, Serial) (There is a workaround in place to avoid a compiler bug)
+  NVCC 8.0.44 for CUDA (with gcc 5.4.0)
+  NVCC 9.0.103 for CUDA (with gcc 6.3.0)
 
 Primary tested compilers on Intel KNL are:
    GCC 6.2.0
-   Intel 16.2.181 (with gcc 4.7.2)
-   Intel 17.0.098 (with gcc 4.7.2)
-   Intel 17.1.132 (with gcc 4.9.3)
+   Intel 16.4.258 (with gcc 4.7.2)
    Intel 17.2.174 (with gcc 4.9.3)
-   Intel 18.0.061 (beta) (with gcc 4.9.3)
-
-Secondary tested compilers are:
-  CUDA 7.0 (with gcc 4.8.4)
-  CUDA 7.5 (with gcc 4.8.4)
-  CUDA 8.0 (with gcc 5.3.0 on X86 and gcc 5.4.0 on Power8)
-  CUDA/Clang 8.0 using Clang/Trunk compiler
+   Intel 18.0.128 (with gcc 4.9.3)
 
 Other compilers working:
   X86:
    Cygwin 2.1.0 64bit with gcc 4.9.3
 
-Limited testing of the following compilers on POWER7+ systems:
-  GCC 4.8.5 (on RHEL7.1 POWER7+)
-
 Known non-working combinations:
   Power8:
    Pthreads backend
@@ -96,8 +92,8 @@ GCC:   -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits
        -Wignored-qualifiers -Wempty-body -Wclobbered -Wuninitialized
 Intel: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wuninitialized
 Clang: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wuninitialized
+NVCC: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wuninitialized
 
-Secondary compilers are passing without -Werror.
 Other compilers are tested occasionally, in particular when pushing from develop to 
 master branch, without -Werror and only for a select set of backends.
 

lib/kokkos/algorithms/CMakeLists.txt

@@ -2,7 +2,9 @@
 
 TRIBITS_SUBPACKAGE(Algorithms)
 
-ADD_SUBDIRECTORY(src)
+IF(KOKKOS_HAS_TRILINOS)
+  ADD_SUBDIRECTORY(src)
+ENDIF()
 
 TRIBITS_ADD_TEST_DIRECTORIES(unit_tests)
 #TRIBITS_ADD_TEST_DIRECTORIES(performance_tests)

lib/kokkos/algorithms/unit_tests/CMakeLists.txt

@@ -3,6 +3,32 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
 INCLUDE_DIRECTORIES(REQUIRED_DURING_INSTALLATION_TESTING ${CMAKE_CURRENT_SOURCE_DIR})
 INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/../src )
 
+IF(NOT KOKKOS_HAS_TRILINOS)
+  IF(KOKKOS_SEPARATE_LIBS)
+    set(TEST_LINK_TARGETS kokkoscore)
+  ELSE()
+    set(TEST_LINK_TARGETS kokkos)
+  ENDIF()
+ENDIF()
+
+SET(GTEST_SOURCE_DIR ${${PARENT_PACKAGE_NAME}_SOURCE_DIR}/tpls/gtest)
+INCLUDE_DIRECTORIES(${GTEST_SOURCE_DIR})
+
+# mfh 03 Nov 2017: The gtest library used here must have a different
+# name than that of the gtest library built in KokkosCore.  We can't
+# just refer to the library in KokkosCore's tests, because it's
+# possible to build only (e.g.,) KokkosAlgorithms tests, without
+# building KokkosCore tests.
+
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DGTEST_HAS_PTHREAD=0")
+
+TRIBITS_ADD_LIBRARY(
+  kokkosalgorithms_gtest
+  HEADERS ${GTEST_SOURCE_DIR}/gtest/gtest.h
+  SOURCES ${GTEST_SOURCE_DIR}/gtest/gtest-all.cc
+  TESTONLY
+  )
+
 SET(SOURCES
   UnitTestMain.cpp 
   TestCuda.cpp
@@ -34,5 +60,5 @@ TRIBITS_ADD_EXECUTABLE_AND_TEST(
   COMM serial mpi
   NUM_MPI_PROCS 1
   FAIL_REGULAR_EXPRESSION "  FAILED  "
-  TESTONLYLIBS kokkos_gtest
+  TESTONLYLIBS kokkosalgorithms_gtest ${TEST_LINK_TARGETS}
   )

lib/kokkos/algorithms/unit_tests/Makefile

@@ -15,7 +15,8 @@ endif
 
 CXXFLAGS = -O3
 LINK ?= $(CXX)
-LDFLAGS ?= -lpthread
+LDFLAGS ?=
+override LDFLAGS += -lpthread
 
 include $(KOKKOS_PATH)/Makefile.kokkos
 

lib/kokkos/algorithms/unit_tests/TestSort.hpp

@@ -211,12 +211,15 @@ void test_dynamic_view_sort(unsigned int n )
 
   const size_t upper_bound = 2 * n ;
 
+  const size_t total_alloc_size = n * sizeof(KeyType) * 1.2 ;
+  const size_t superblock_size  = std::min(total_alloc_size, size_t(1000000));
+
   typename KeyDynamicViewType::memory_pool
     pool( memory_space()
         , n * sizeof(KeyType) * 1.2
         ,     500 /* min block size in bytes */
         ,   30000 /* max block size in bytes */
-        , 1000000 /* min superblock size in bytes */
+        , superblock_size
         );
 
   KeyDynamicViewType keys("Keys",pool,upper_bound);
@@ -271,8 +274,10 @@ void test_sort(unsigned int N)
 {
   test_1D_sort<ExecutionSpace,KeyType>(N*N*N, true);
   test_1D_sort<ExecutionSpace,KeyType>(N*N*N, false);
+#if !defined(KOKKOS_ENABLE_ROCM)
   test_3D_sort<ExecutionSpace,KeyType>(N);
   test_dynamic_view_sort<ExecutionSpace,KeyType>(N*N);
+#endif
 }
 
 }

lib/kokkos/benchmarks/atomic/Makefile

@@ -0,0 +1,44 @@
+KOKKOS_PATH = ${HOME}/kokkos
+KOKKOS_DEVICES = "OpenMP"
+KOKKOS_ARCH = "SNB"
+EXE_NAME = "test"
+
+SRC = $(wildcard *.cpp)
+
+default: build
+	echo "Start Build"
+
+
+ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
+CXX = ${KOKKOS_PATH}/config/nvcc_wrapper
+EXE = ${EXE_NAME}.cuda
+KOKKOS_CUDA_OPTIONS = "enable_lambda"
+else
+CXX = g++
+EXE = ${EXE_NAME}.host
+endif
+
+CXXFLAGS = -O3
+
+LINK = ${CXX}
+LINKFLAGS = -O3
+
+DEPFLAGS = -M
+
+OBJ = $(SRC:.cpp=.o)
+LIB =
+
+include $(KOKKOS_PATH)/Makefile.kokkos
+
+build: $(EXE)
+
+$(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
+	$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
+
+clean: kokkos-clean 
+	rm -f *.o *.cuda *.host
+
+# Compilation rules
+
+%.o:%.cpp $(KOKKOS_CPP_DEPENDS)
+	$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<

lib/kokkos/benchmarks/atomic/main.cpp

@@ -0,0 +1,124 @@
+#include<Kokkos_Core.hpp>
+#include<impl/Kokkos_Timer.hpp>
+#include<Kokkos_Random.hpp>
+
+template<class Scalar>
+double test_atomic(int L, int N, int M,int K,int R,Kokkos::View<const int*> offsets) {
+  Kokkos::View<Scalar*> output("Output",N);
+  Kokkos::Impl::Timer timer;
+
+  for(int r = 0; r<R; r++)
+  Kokkos::parallel_for(L, KOKKOS_LAMBDA (const int&i) {
+    Scalar s = 2;
+    for(int m=0;m<M;m++) {
+      for(int k=0;k<K;k++)
+        s=s*s+s;
+      const int idx = (i+offsets(i,m))%N;
+      Kokkos::atomic_add(&output(idx),s);
+    }
+  }); 
+  Kokkos::fence();
+  double time = timer.seconds();
+ 
+  return time;
+}
+
+template<class Scalar>
+double test_no_atomic(int L, int N, int M,int K,int R,Kokkos::View<const int*> offsets) {
+  Kokkos::View<Scalar*> output("Output",N);
+  Kokkos::Impl::Timer timer;
+  for(int r = 0; r<R; r++)
+  Kokkos::parallel_for(L, KOKKOS_LAMBDA (const int&i) {
+    Scalar s = 2;
+    for(int m=0;m<M;m++) {
+      for(int k=0;k<K;k++)
+        s=s*s+s;
+      const int idx = (i+offsets(i,m))%N;
+      output(idx) += s;
+    }
+  });
+  Kokkos::fence();
+  double time =  timer.seconds();
+  return time;
+}
+
+int main(int argc, char* argv[]) {
+  Kokkos::initialize(argc,argv);
+{
+  if(argc<8) {
+    printf("Arguments: L N M D K R T\n");
+    printf("  L:   Number of iterations to run\n");
+    printf("  N:   Length of array to do atomics into\n");
+    printf("  M:   Number of atomics per iteration to do\n");
+    printf("  D:   Distance from index i to do atomics into (randomly)\n");
+    printf("  K:   Number of FMAD per atomic\n");
+    printf("  R:   Number of repeats of the experiments\n");
+    printf("  T:   Type of atomic\n");
+    printf("       1 - int\n");
+    printf("       2 - long\n");
+    printf("       3 - float\n");
+    printf("       4 - double\n");
+    printf("       5 - complex<double>\n");
+    printf("Example Input GPU:\n");
+    printf("  Histogram : 1000000 1000 1 1000 1 10 1\n");
+    printf("  MD Force : 100000 100000 100 1000 20 10 4\n");
+    printf("  Matrix Assembly : 100000 1000000 50 1000 20 10 4\n");
+    Kokkos::finalize();
+    return 0;
+  }
+
+
+  int L = atoi(argv[1]);
+  int N = atoi(argv[2]);
+  int M = atoi(argv[3]);
+  int D = atoi(argv[4]); 
+  int K = atoi(argv[5]);
+  int R = atoi(argv[6]); 
+  int type = atoi(argv[7]);
+ 
+  Kokkos::View<int*> offsets("Offsets",L,M);
+  Kokkos::Random_XorShift64_Pool<> pool(12371);
+  Kokkos::fill_random(offsets,pool,D);
+  double time = 0;
+  if(type==1)
+    time  = test_atomic<int>(L,N,M,K,R,offsets);
+  if(type==2)
+    time = test_atomic<long>(L,N,M,K,R,offsets);
+  if(type==3)
+    time = test_atomic<float>(L,N,M,K,R,offsets);
+  if(type==4)
+    time = test_atomic<double>(L,N,M,K,R,offsets);
+  if(type==5)
+    time = test_atomic<Kokkos::complex<double> >(L,N,M,K,R,offsets);
+
+  double time2 = 1;
+  if(type==1)
+    time2 = test_no_atomic<int>(L,N,M,K,R,offsets);
+  if(type==2)
+    time2 = test_no_atomic<long>(L,N,M,K,R,offsets);
+  if(type==3)
+    time2 = test_no_atomic<float>(L,N,M,K,R,offsets);
+  if(type==4)
+    time2 = test_no_atomic<double>(L,N,M,K,R,offsets);
+  if(type==5)
+    time2 = test_no_atomic<Kokkos::complex<double> >(L,N,M,K,R,offsets);
+
+  int size = 0;
+  if(type==1) size = sizeof(int);
+  if(type==2) size = sizeof(long);
+  if(type==3) size = sizeof(float);
+  if(type==4) size = sizeof(double);
+  if(type==5) size = sizeof(Kokkos::complex<double>);
+
+  printf("%i\n",size);
+  printf("Time: %s %i %i %i %i %i %i (t_atomic: %e t_nonatomic: %e ratio: %lf )( GUpdates/s: %lf GB/s: %lf )\n",
+    (type==1)?"int": (
+    (type==2)?"long": (
+    (type==3)?"float": (
+    (type==4)?"double":"complex"))),
+    L,N,M,D,K,R,time,time2,time/time2,
+    1.e-9*L*R*M/time, 1.0*L*R*M*2*size/time/1024/1024/1024);
+}
+  Kokkos::finalize();
+}
+

lib/kokkos/benchmarks/benchmark_suite/scripts/build_code.bash

@@ -0,0 +1,84 @@
+#!/bin/bash
+
+# ---- Default Settings -----
+
+# Paths
+KOKKOS_PATH=${PWD}/kokkos
+KOKKOS_KERNELS_PATH=${PWD}/kokkos-kernels
+MINIMD_PATH=${PWD}/miniMD/kokkos
+MINIFE_PATH=${PWD}/miniFE/kokkos
+
+# Kokkos Configure Options
+KOKKOS_DEVICES=OpenMP
+KOKKOS_ARCH=SNB
+
+# Compiler Options
+CXX=mpicxx
+OPT_FLAG="-O3"
+
+while [[ $# > 0 ]]
+do
+  key="$1"
+
+  case $key in
+    --kokkos-path*)
+      KOKKOS_PATH="${key#*=}"
+      ;;
+    --kokkos-kernels-path*)
+      KOKKOS_KERNELS_PATH="${key#*=}"
+      ;;
+    --minimd-path*)
+      MINIMD_PATH="${key#*=}"
+      ;;
+    --minife-path*)
+      MINIFE_PATH="${key#*=}"
+      ;;
+    --device-list*)
+      KOKKOS_DEVICES="${key#*=}"
+      ;;
+    --arch*)
+      KOKKOS_ARCH="--arch=${key#*=}"
+      ;;
+    --opt-flag*)
+      OPT_FLAG="${key#*=}"
+      ;;
+    --compiler*)
+      CXX="${key#*=}"
+      ;;
+    --with-cuda-options*)
+      KOKKOS_CUDA_OPTIONS="--with-cuda-options=${key#*=}"
+      ;;
+    --help*)
+      PRINT_HELP=True
+      ;;
+    *)
+      # args, just append
+      ARGS="$ARGS $1"
+      ;;
+  esac
+
+  shift
+done
+
+mkdir build
+
+# Build BytesAndFlops
+mkdir build/bytes_and_flops
+cd build/bytes_and_flops
+make KOKKOS_ARCH=${KOKKOS_ARCH} KOKKOS_DEVICES=${KOKKOS_DEVICES} CXX=${CXX} KOKKOS_PATH=${KOKKOS_PATH}\
+     CXXFLAGS=${OPT_FLAG} -f ${KOKKOS_PATH}/benchmarks/bytes_and_flops/Makefile -j 16
+cd ../..
+
+mkdir build/miniMD
+cd build/miniMD
+make KOKKOS_ARCH=${KOKKOS_ARCH} KOKKOS_DEVICES=${KOKKOS_DEVICES} CXX=${CXX} KOKKOS_PATH=${KOKKOS_PATH} \
+     CXXFLAGS=${OPT_FLAG} -f ${MINIMD_PATH}/Makefile -j 16
+cd ../../
+
+mkdir build/miniFE
+cd build/miniFE
+make KOKKOS_ARCH=${KOKKOS_ARCH} KOKKOS_DEVICES=${KOKKOS_DEVICES} CXX=${CXX} KOKKOS_PATH=${KOKKOS_PATH} \
+     CXXFLAGS=${OPT_FLAG} -f ${MINIFE_PATH}/src/Makefile -j 16
+cd ../../
+
+

lib/kokkos/benchmarks/benchmark_suite/scripts/checkout_repos.bash

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+# Kokkos
+if [ ! -d "kokkos" ]; then
+  git clone https://github.com/kokkos/kokkos
+fi
+cd kokkos
+git checkout develop
+git pull
+cd ..
+
+# KokkosKernels
+if [ ! -d "kokkos-kernels" ]; then
+git clone https://github.com/kokkos/kokkos-kernels
+fi
+cd kokkos-kernels
+git pull
+cd ..
+
+# MiniMD
+if [ ! -d "miniMD" ]; then
+  git clone https://github.com/mantevo/miniMD
+fi
+cd miniMD
+git pull
+cd ..
+
+# MiniFE
+if [ ! -d "miniFE" ]; then
+  git clone https://github.com/mantevo/miniFE
+fi
+cd miniFE
+git pull
+cd ..
+
+
+

lib/kokkos/benchmarks/benchmark_suite/scripts/run_benchmark.bash

@@ -0,0 +1,14 @@
+#!/bin/bash
+SCRIPT_PATH=$1
+KOKKOS_DEVICES=$2
+KOKKOS_ARCH=$3
+COMPILER=$4
+if [[ $# < 4 ]]; then
+  echo "Usage: ./run_benchmark.bash PATH_TO_SCRIPTS KOKKOS_DEVICES KOKKOS_ARCH COMPILER"
+else
+
+${SCRIPT_PATH}/checkout_repos.bash
+${SCRIPT_PATH}/build_code.bash --arch=${KOKKOS_ARCH} --device-list=${KOKKOS_DEVICES} --compiler=${COMPILER}
+${SCRIPT_PATH}/run_tests.bash
+
+fi