patch 17Jan18

Small character corrections to the file Developer.dox.lammps

cmake/CMakeLists.txt

@@ -37,6 +37,10 @@ enable_language(CXX)
 #####################################################################
 include(CheckCCompilerFlag)
 
+if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+endif()
+
 ########################################################################
 # User input options                                                   #
 ########################################################################
@@ -76,7 +80,7 @@ add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
 if(LAMMPS_EXCEPTIONS)
   add_definitions(-DLAMMPS_EXCEPTIONS)
-  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES -DLAMMPS_EXCEPTIONS")
+  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS")
 endif()
 
 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically")
@@ -101,7 +105,7 @@ set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
   USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
   USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
   USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
-  USER-SMTBQ USER-SPH USER-TALLY USER-VTK USER-QUIP USER-QMMM)
+  USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 foreach(PKG ${DEFAULT_PACKAGES})
   option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
@@ -194,14 +198,13 @@ if(ENABLE_PYTHON)
   add_definitions(-DLMP_PYTHON)
   include_directories(${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()
 
@@ -397,6 +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()
@@ -476,6 +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}")
@@ -483,6 +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 ${KOKKOS_PKG_SOURCES})
@@ -665,7 +685,9 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 ############################################
 add_library(lammps ${LIB_SOURCES})
 target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
-add_dependencies(lammps ${LAMMPS_DEPS})
+if(LAMMPS_DEPS)
+  add_dependencies(lammps ${LAMMPS_DEPS})
+endif()
 set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
 if(BUILD_SHARED_LIBS)
   set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})

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/Eqs/bond_gromos.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+$$
+   E = K (r^2 - r_0^2)^2
+$$
+
+\end{document}

doc/src/Eqs/fix_rhok.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ U &=&  \frac{1}{2} K (|\rho_{\vec{k}}| - a)^2 \\
+ \rho_{\vec{k}} &=& \sum_j^N \exp(-i\vec{k} \cdot \vec{r}_j )/\sqrt{N} \\
+ \vec{k} &=& (2\pi n_x /L_x , 2\pi n_y  /L_y , 2\pi n_z/L_z ) 
+\end{eqnarray*}
+
+\end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="22 Sep 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
-22 Sep 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,
@@ -720,17 +721,20 @@ package"_Section_start.html#start_3.
 "nve/eff"_fix_nve_eff.html,
 "nvt/eff"_fix_nh_eff.html,
 "nvt/sllod/eff"_fix_nvt_sllod_eff.html,
+"npt/uef"_fix_nh_uef.html,
+"nvt/uef"_fix_nh_uef.html,
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "qbmsst"_fix_qbmsst.html,
 "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,
-"rx"_fix_rx.html,
+"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/species (k)"_fix_reaxc_species.html,
+"rhok"_fix_rhok.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,
@@ -856,6 +860,7 @@ package"_Section_start.html#start_3.
 "meso/t/atom"_compute_meso_t_atom.html,
 "pe/tally"_compute_tally.html,
 "pe/mol/tally"_compute_tally.html,
+"pressure/uef"_compute_pressure_uef.html,
 "saed"_compute_saed.html,
 "smd/contact/radius"_compute_smd_contact_radius.html,
 "smd/damage"_compute_smd_damage.html,
@@ -884,6 +889,7 @@ package"_Section_start.html#start_3.
 "temp/deform/eff"_compute_temp_deform_eff.html,
 "temp/region/eff"_compute_temp_region_eff.html,
 "temp/rotate"_compute_temp_rotate.html,
+"temp/uef"_compute_temp_uef.html,
 "xrd"_compute_xrd.html :tb(c=6,ea=c)
 
 :line
@@ -901,7 +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,
@@ -915,11 +921,12 @@ KOKKOS, o = USER-OMP, t = OPT.
 "born/coul/long/cs"_pair_born.html,
 "born/coul/msm (o)"_pair_born.html,
 "born/coul/wolf (go)"_pair_born.html,
+"born/coul/wolf/cs"_pair_born.html,
 "brownian (o)"_pair_brownian.html,
 "brownian/poly (o)"_pair_brownian.html,
-"buck (gkio)"_pair_buck.html,
-"buck/coul/cut (gkio)"_pair_buck.html,
-"buck/coul/long (gkio)"_pair_buck.html,
+"buck (giko)"_pair_buck.html,
+"buck/coul/cut (giko)"_pair_buck.html,
+"buck/coul/long (giko)"_pair_buck.html,
 "buck/coul/long/cs"_pair_buck.html,
 "buck/coul/msm (o)"_pair_buck.html,
 "buck/long/coul/long (o)"_pair_buck_long.html,
@@ -934,12 +941,13 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (go)"_pair_dpd.html,
+"coul/wolf/cs"_pair_coul.html,
+"dpd (gio)"_pair_dpd.html,
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
-"eam (gkiot)"_pair_eam.html,
-"eam/alloy (gkiot)"_pair_eam.html,
-"eam/fs (gkiot)"_pair_eam.html,
+"eam (gikot)"_pair_eam.html,
+"eam/alloy (gikot)"_pair_eam.html,
+"eam/fs (gikot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
 "gauss (go)"_pair_gauss.html,
 "gayberne (gio)"_pair_gayberne.html,
@@ -953,9 +961,9 @@ KOKKOS, o = USER-OMP, t = OPT.
 "kim"_pair_kim.html,
 "lcbop"_pair_lcbop.html,
 "line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (kio)"_pair_charmm.html,
+"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (gkio)"_pair_charmm.html,
+"lj/charmm/coul/long (giko)"_pair_charmm.html,
 "lj/charmm/coul/msm"_pair_charmm.html,
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
 "lj/charmmfsw/coul/long"_pair_charmm.html,
@@ -1005,9 +1013,9 @@ KOKKOS, o = USER-OMP, t = OPT.
 "resquared (go)"_pair_resquared.html,
 "snap"_pair_snap.html,
 "soft (go)"_pair_soft.html,
-"sw (gkio)"_pair_sw.html,
+"sw (giko)"_pair_sw.html,
 "table (gko)"_pair_table.html,
-"tersoff (gkio)"_pair_tersoff.html,
+"tersoff (giko)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
 "tersoff/mod/c (o)"_pair_tersoff_mod.html,
 "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
@@ -1016,9 +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
@@ -1031,13 +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,
@@ -1063,7 +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,
@@ -1080,6 +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,
@@ -1087,7 +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,
@@ -1111,6 +1121,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "class2 (ko)"_bond_class2.html,
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
+"gromos (o)"_bond_gromos.html,
 "harmonic (ko)"_bond_harmonic.html,
 "morse (o)"_bond_morse.html,
 "nonlinear (o)"_bond_nonlinear.html,
@@ -1177,7 +1188,7 @@ USER-OMP, t = OPT.
 "none"_dihedral_none.html,
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
-"charmm (ko)"_dihedral_charmm.html,
+"charmm (iko)"_dihedral_charmm.html,
 "charmmfsw"_dihedral_charmm.html,
 "class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
@@ -1190,7 +1201,7 @@ used if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.
 
 "cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (o)"_dihedral_fourier.html,
+"fourier (io)"_dihedral_fourier.html,
 "nharmonic (o)"_dihedral_nharmonic.html,
 "quadratic (o)"_dihedral_quadratic.html,
 "spherical (o)"_dihedral_spherical.html,
@@ -1213,7 +1224,7 @@ USER-OMP, t = OPT.
 "hybrid"_improper_hybrid.html,
 "class2 (ko)"_improper_class2.html,
 "cvff (io)"_improper_cvff.html,
-"harmonic (ko)"_improper_harmonic.html,
+"harmonic (iko)"_improper_harmonic.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
 
 These are additional improper styles in USER packages, which can be
@@ -1241,7 +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

@@ -150,6 +150,7 @@ Package, Description, Doc page, Example, Library
 "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
 "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
 "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
+"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
 "USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
 
 :line
@@ -242,7 +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.
@@ -705,7 +706,7 @@ dynamics can be run with LAMMPS using density-functional tight-binding
 quantum forces calculated by LATTE.
 
 More information on LATTE can be found at this web site:
-"https://github.com/lanl/LATTE"_#latte_home.  A brief technical
+"https://github.com/lanl/LATTE"_latte_home.  A brief technical
 description is given with the "fix latte"_fix_latte.html command.
 
 :link(latte_home,https://github.com/lanl/LATTE)
@@ -728,11 +729,12 @@ make lib-latte args="-b"                # download and build in lib/latte/LATTE-
 make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
 make lib-latte args="-b -m gfortran"    # download and build in lib/latte and 
                                         #   copy Makefile.lammps.gfortran to Makefile.lammps
+: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
@@ -982,7 +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)
@@ -1779,7 +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.
@@ -2229,7 +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.
 
@@ -2493,7 +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.
 
@@ -2552,7 +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)
@@ -2770,13 +2772,44 @@ examples/USER/tally :ul
 
 :line
 
+USER-UEF package :link(USER-UEF),h4
+
+[Contents:]
+
+A fix style for the integration of the equations of motion under
+extensional flow with proper boundary conditions, as well as several
+supporting compute styles and an output option.
+
+[Author:] David Nicholson (MIT).
+
+[Install or un-install:]
+
+make yes-user-uef
+make machine :pre
+
+make no-user-uef
+make machine :pre
+
+[Supporting info:]
+
+src/USER-UEF: filenames -> commands
+src/USER-UEF/README
+"fix nvt/uef"_fix_nh_uef.html
+"fix npt/uef"_fix_nh_uef.html
+"compute pressure/uef"_compute_pressure_uef.html
+"compute temp/uef"_compute_temp_uef.html
+"dump cfg/uef"_dump_cfg_uef.html
+examples/uef :ul
+
+:line
+
 USER-VTK package :link(USER-VTK),h4
 
 [Contents:]
 
-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.
+A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
+"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
+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

@@ -25,14 +25,14 @@ LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
 [Currently Available USER-INTEL Styles:]
 
 Angle Styles: charmm, harmonic :ulb,l
-Bond Styles: fene, harmonic :l
+Bond Styles: fene, fourier, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
-Fixes: nve, npt, nvt, nvt/sllod :l
+Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l
 Improper Styles: cvff, harmonic :l
 Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long, 
-buck, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, 
-lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, rebo,
-sw, tersoff :l
+buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, 
+lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, 
+rebo, sw, tersoff :l
 K-Space Styles: pppm, pppm/disp :l
 :ule
 
@@ -54,11 +54,12 @@ warmup run (for use with offload benchmarks).
 :c,image(JPG/user_intel.png)
 
 Results are speedups obtained on Intel Xeon E5-2697v4 processors
-(code-named Broadwell) and Intel Xeon Phi 7250 processors
-(code-named Knights Landing) with "June 2017" LAMMPS built with
-Intel Parallel Studio 2017 update 2. Results are with 1 MPI task
-per physical core. See {src/USER-INTEL/TEST/README} for the raw
-simulation rates and instructions to reproduce.
+(code-named Broadwell), Intel Xeon Phi 7250 processors (code-named
+Knights Landing), and Intel Xeon Gold 6148 processors (code-named
+Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio
+2017 update 2. Results are with 1 MPI task per physical core. See
+{src/USER-INTEL/TEST/README} for the raw simulation rates and
+instructions to reproduce.
 
 :line
 
@@ -77,11 +78,16 @@ 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
 Vectorization can change the order for adding pairwise forces :l
+When using the -DLMP_USE_MKL_RNG define (all included intel optimized
+makefiles do) at build time, the random number generator for
+dissipative particle dynamics (pair style dpd/intel) uses the Mersenne
+Twister generator included in the Intel MKL library (that should be
+more robust than the default Masaglia random number generator) :l
 :ule
 
 The precision mode (described below) used with the USER-INTEL
@@ -108,7 +114,7 @@ $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
 For some of the simple 2-body potentials without long-range
 electrostatics, performance and scalability can be better with
 the "newton off" setting added to the input script :l
-For simulations on higher node counts, add "processors * * * grid 
+For simulations on higher node counts, add "processors * * * grid
 numa" to the beginning of the input script for better scalability :l
 If using {kspace_style pppm} in the input script, add
 "kspace_modify diff ad" for better performance :l
@@ -119,8 +125,8 @@ For Intel Xeon Phi CPUs:
 Runs should be performed using MCDRAM. :ulb,l
 :ule
 
-For simulations using {kspace_style pppm} on Intel CPUs
-supporting AVX-512:
+For simulations using {kspace_style pppm} on Intel CPUs supporting
+AVX-512:
 
 Add "kspace_modify diff ad" to the input script :ulb,l
 The command-line option should be changed to
@@ -237,14 +243,17 @@ However, if you do not have coprocessors on your system, building
 without offload support will produce a smaller binary.
 
 The general requirements for Makefiles with the USER-INTEL package
-are as follows. "-DLAMMPS_MEMALIGN=64" is required for CCFLAGS. When
-using Intel compilers, "-restrict" is required and "-qopenmp" is
-highly recommended for CCFLAGS and LINKFLAGS. LIB should include
-"-ltbbmalloc". For builds supporting offload, "-DLMP_INTEL_OFFLOAD"
-is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.
-Other recommended CCFLAG options for best performance are
-"-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
--no-prec-div".
+are as follows. When using Intel compilers, "-restrict" is required 
+and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. 
+CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads
+are not supported in the build environment) and "-DLMP_USE_MKL_RNG"
+(unless Intel Math Kernel Library (MKL) is not available in the build
+environment). For Intel compilers, LIB should include "-ltbbmalloc" 
+or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added
+to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is
+required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other
+recommended CCFLAG options for best performance are "-O2 -fno-alias
+-ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div".
 
 NOTE: The vectorization and math capabilities can differ depending on
 the CPU. For Intel compilers, the "-x" flag specifies the type of

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/atom_modify.txt

@@ -16,7 +16,7 @@ atom_modify keyword values ... :pre
 one or more keyword/value pairs may be appended :ulb,l
 keyword = {id} or {map} or {first} or {sort} :l
    {id} value = {yes} or {no}
-   {map} value = {array} or {hash}
+   {map} value = {yes} or {array} or {hash}
    {first} value = group-ID = group whose atoms will appear first in internal atom lists
    {sort} values = Nfreq binsize
      Nfreq = sort atoms spatially every this many time steps
@@ -25,8 +25,8 @@ keyword = {id} or {map} or {first} or {sort} :l
 
 [Examples:]
 
-atom_modify map hash
-atom_modify map array sort 10000 2.0
+atom_modify map yes
+atom_modify map hash sort 10000 2.0
 atom_modify first colloid :pre
 
 [Description:]
@@ -62,29 +62,33 @@ switch.  This is described in "Section 2.2"_Section_start.html#start_2
 of the manual.  If atom IDs are not used, they must be specified as 0
 for all atoms, e.g. in a data or restart file.
 
-The {map} keyword determines how atom ID lookup is done for molecular
-atom styles.  Lookups are performed by bond (angle, etc) routines in
-LAMMPS to find the local atom index associated with a global atom ID.
+The {map} keyword determines how atoms with specific IDs are found
+when required.  An example are the bond (angle, etc) methods which
+need to find the local index of an atom with a specific global ID
+which is a bond (angle, etc) partner.  LAMMPS performs this operation
+efficiently by creating a "map", which is either an {array} or {hash}
+table, as descibed below.
 
-When the {array} value is used, each processor stores a lookup table
-of length N, where N is the largest atom ID in the system.  This is a
+When the {map} keyword is not specified in your input script, LAMMPS
+only creates a map for "atom_styles"_atom_style.html for molecular
+systems which have permanent bonds (angles, etc).  No map is created
+for atomic systems, since it is normally not needed.  However some
+LAMMPS commands require a map, even for atomic systems, and will
+generate an error if one does not exist.  The {map} keyword thus
+allows you to force the creation of a map.  The {yes} value will
+create either an {array} or {hash} style map, as explained in the next
+paragraph.  The {array} and {hash} values create an atom-style or
+hash-style map respectively.
+
+For an {array}-style map, each processor stores a lookup table of
+length N, where N is the largest atom ID in the system.  This is a
 fast, simple method for many simulations, but requires too much memory
-for large simulations.  The {hash} value uses a hash table to perform
-the lookups.  This can be slightly slower than the {array} method, but
-its memory cost is proportional to the number of atoms owned by a
-processor, i.e. N/P when N is the total number of atoms in the system
-and P is the number of processors.
-
-When this setting is not specified in your input script, LAMMPS
-creates a map, if one is needed, as an array or hash.  See the
-discussion of default values below for how LAMMPS chooses which kind
-of map to build.  Note that atomic systems do not normally need to
-create a map.  However, even in this case some LAMMPS commands will
-create a map to find atoms (and then destroy it), or require a
-permanent map.  An example of the former is the "velocity loop
-all"_velocity.html command, which uses a map when looping over all
-atoms and insuring the same velocity values are assigned to an atom
-ID, no matter which processor owns it.
+for large simulations.  For a {hash}-style map, a hash table is
+created on each processor, which finds an atom ID in constant time
+(independent of the global number of atom IDs).  It can be slightly
+slower than the {array} map, but its memory cost is proportional to
+the number of atoms owned by a processor, i.e. N/P when N is the total
+number of atoms in the system and P is the number of processors.
 
 The {first} keyword allows a "group"_group.html to be specified whose
 atoms will be maintained as the first atoms in each processor's list

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/bond_gromos.txt

@@ -0,0 +1,73 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+bond_style gromos command :h3
+bond_style gromos/omp command :h3
+
+[Syntax:]
+
+bond_style gromos :pre
+
+[Examples:]
+
+bond_style gromos
+bond_coeff 5 80.0 1.2 :pre
+
+[Description:]
+
+The {gromos} bond style uses the potential
+
+:c,image(Eqs/bond_gromos.jpg)
+
+where r0 is the equilibrium bond distance.  Note that the usual 1/4
+factor is included in K.
+
+The following coefficients must be defined for each bond type via the
+"bond_coeff"_bond_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+K (energy/distance^4)
+r0 (distance) :ul
+
+: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 bond style can only be used if LAMMPS was built with the
+MOLECULE package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+[Related commands:]
+
+"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
+
+[Default:] none

doc/src/bonds.txt

@@ -8,6 +8,7 @@ Bond Styles :h1
    bond_class2
    bond_fene
    bond_fene_expand
+   bond_gromos
    bond_harmonic
    bond_harmonic_shift
    bond_harmonic_shift_cut

doc/src/commands.txt

@@ -32,6 +32,7 @@ Commands :h1
    dimension
    displace_atoms
    dump
+   dump_cfg_uef
    dump_h5md
    dump_image
    dump_modify

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

@@ -0,0 +1,61 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute pressure/uef command :h3
+
+[Syntax:]
+
+compute ID group-ID pressure/uef temp-ID keyword ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+pressure/uef = style name of this compute command
+temp-ID = ID of compute that calculates temperature, can be NULL if not needed
+zero or more keywords may be appended
+keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
+
+[Examples:]
+
+compute 1 all pressure/uef my_temp_uef
+compute 2 all pressure/uef my_temp_uef virial :pre
+
+[Description:]
+
+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.
+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
+"compute_pressure"_compute_pressure.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF package. It is only enabled if
+LAMMPS was built with that package. See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This 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 specified by {temp-ID} is a
+"compute temp/uef"_compute_temp_uef.html.
+
+[Related commands:]
+
+"compute pressure"_compute_pressure.html,
+"fix nvt/uef"_fix_nh_uef.html,
+"compute temp/uef"_compute_temp_uef.html
+
+[Default:] none
+
+

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/compute_temp_uef.txt

@@ -0,0 +1,52 @@
+"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
+
+compute temp/uef command :h3
+
+[Syntax:]
+
+compute ID group-ID temp/uef :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+temp/uef = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all temp/uef 
+compute 2 sel temp/uef :pre
+
+[Description:]
+
+This command is used to compute the kinetic energy 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.
+It is not necessary to use this command to compute the scalar
+value of the temperature. A "compute temp"_compute_temp.html 
+may be used for that purpose.
+
+Output information for this command can be found in the
+documentation for "compute temp"_compute_temp.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF package. It is only enabled if 
+LAMMPS was built with that package. See the 
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html 
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+[Related commands:]
+
+"compute temp"_compute_temp.html,
+"fix nvt/uef"_fix_nh_uef.html,
+"compute pressure/uef"_compute_pressure_uef.html
+
+
+[Default:] none

doc/src/computes.txt

@@ -65,6 +65,7 @@ Computes :h1
    compute_pe_atom
    compute_plasticity_atom
    compute_pressure
+   compute_pressure_uef
    compute_property_atom
    compute_property_chunk
    compute_property_local
@@ -114,6 +115,7 @@ Computes :h1
    compute_temp_region_eff
    compute_temp_rotate
    compute_temp_sphere
+   compute_temp_uef
    compute_ti
    compute_torque_chunk
    compute_vacf

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/dihedral_fourier.txt

@@ -7,6 +7,7 @@
 :line
 
 dihedral_style fourier command :h3
+dihedral_style fourier/intel command :h3
 dihedral_style fourier/omp command :h3
 
 [Syntax:]

doc/src/dump_cfg_uef.txt

@@ -0,0 +1,53 @@
+ "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
+
+dump cfg/uef command :h3
+
+[Syntax:]
+
+dump ID group-ID cfg/uef N file mass type xs ys zs args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be dumped :l
+N = dump every this many timesteps :l
+file = name of file to write dump info to :l
+args = same as args for "dump custom"_dump.html :pre
+
+:ule
+
+[Examples:]
+
+dump 1 all cfg/uef 10 dump.*.cfg mass type xs ys zs
+dump 2 all cfg/uef 100 dump.*.cfg mass type xs ys zs id c_stress :pre
+
+[Description:]
+
+This command is used to dump atomic coordinates 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 or is used. Only the atomic 
+coordinates and frame-invariant scalar quantities 
+will be in the flow frame. If velocities are selected
+as output, for example, they will not be in the same
+reference frame as the atomic positions.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF package. It is only enabled if
+LAMMPS was built with that package. See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+[Related commands:]
+
+"dump"_dump.html,
+"fix nvt/uef"_fix_nh_uef.html
+
+[Default:] none

doc/src/dump_modify.txt

@@ -15,8 +15,9 @@ dump_modify dump-ID keyword values ... :pre
 dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
-keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
-  {append} arg = {yes} or {no} or {at} N
+keyword = {append} or {at} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+  {append} arg = {yes} or {no}
+  {at} arg = N
     N = index of frame written upon first dump
   {buffer} arg = {yes} or {no}
   {element} args = E1 E2 ... EN, where N = # of atom types
@@ -141,13 +142,18 @@ and {dcd}.  It also applies only to text output files, not to binary
 or gzipped or image/movie files.  If specified as {yes}, then dump
 snapshots are appended to the end of an existing dump file.  If
 specified as {no}, then a new dump file will be created which will
-overwrite an existing file with the same name.  If the {at} option is present
-({netcdf} only), then the frame to append to can be specified.  Negative values
-are counted from the end of the file.  This keyword can only take effect if the
-dump_modify command is used after the "dump"_dump.html command, but before the
-first command that causes dump snapshots to be output, e.g. a "run"_run.html or
-"minimize"_minimize.html command.  Once the dump file has been opened, this
-keyword has no further effect.
+overwrite an existing file with the same name.
+
+:line
+
+The {at} keyword only applies to the {netcdf} dump style.  It can only
+be used if the {append yes} keyword is also used.  The {N} argument is
+the index of which frame to append to.  A negative value can be
+specified for {N}, which means a frame counted from the end of the
+file.  The {at} keyword can only be used if the dump_modify command is
+before the first command that causes dump snapshots to be output,
+e.g. a "run"_run.html or "minimize"_minimize.html command.  Once the
+dump file has been opened, this keyword has no further effect.
 
 :line
 

doc/src/dump_netcdf.txt

@@ -25,7 +25,8 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
 
 dump 1 all netcdf 100 traj.nc type x y z vx vy vz
 dump_modify 1 append yes at -1 thermo yes
-dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre
+dump 1 all netcdf/mpiio 1000 traj.nc id type x y z
+dump 1 all netcdf 1000 traj.*.nc id type x y z :pre
 
 [Description:]
 
@@ -73,4 +74,3 @@ section for more info.
 [Related commands:]
 
 "dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
-

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_deform.txt

@@ -86,11 +86,16 @@ Change the volume and/or shape of the simulation box during a dynamics
 run.  Orthogonal simulation boxes have 3 adjustable parameters
 (x,y,z).  Triclinic (non-orthogonal) simulation boxes have 6
 adjustable parameters (x,y,z,xy,xz,yz).  Any or all of them can be
-adjusted independently and simultaneously by this command.  This fix
-can be used to perform non-equilibrium MD (NEMD) simulations of a
-continuously strained system.  See the "fix
+adjusted independently and simultaneously by this command.  
+
+This fix can be used to perform non-equilibrium MD (NEMD) simulations
+of a continuously strained system.  See the "fix
 nvt/sllod"_fix_nvt_sllod.html and "compute
-temp/deform"_compute_temp_deform.html commands for more details.
+temp/deform"_compute_temp_deform.html commands for more details.  Note
+that simulation of a continuously extended system (extensional flow)
+can be modeled using the "USER-UEF
+package"_Section_packages.html#USER-UEF and its "fix
+commands"_fix_nh_uef.html.
 
 For the {x}, {y}, {z} parameters, the associated dimension cannot be
 shrink-wrapped.  For the {xy}, {yz}, {xz} parameters, the associated

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_latte.txt

@@ -66,7 +66,7 @@ reference charge of overlapping atom-centered densities and bond
 integrals are parameterized using a Slater-Koster tight-binding
 approach. This procedure, which usually is referred to as the DFTB
 method has been described in detail by ("Elstner"_#Elstner) and
-("Finnis"_#Finnis) and coworkers. 
+("Finnis"_#Finnis2) and coworkers. 
 
 The work of the LATTE developers follows that of Elstner closely with
 respect to the physical model.  However, the development of LATTE is
@@ -173,7 +173,7 @@ M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
 M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
 7260 (1998).
 
-:link(Finnis)
+:link(Finnis2)
 [(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van
 Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).
 
@@ -197,11 +197,11 @@ J. Sci. Comput. 36 (2), 147-170, (2014).
 [(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys.,
 141, 164123, (2014).
 
-:link(Niklasson2014)
+:link(Niklasson2017)
 [(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
 
-:link(Niklasson2012)
-[(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
+:link(Cawkwell2012)
+[(Cawkwell2012)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
 (17), 174308 (2012).
 
 :link(Negre2016)

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

@@ -93,7 +93,7 @@ intermediate replica with the previous and the next image:
 
 Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
 
-Note that in this case the specified {Kspring) is in force/distance
+Note that in this case the specified {Kspring} is in force/distance
 units.
 
 With a value of {ideal}, the spring force is computed as suggested in
@@ -105,7 +105,7 @@ where RD is the "reaction coordinate" see "neb"_neb.html section, and
 RDideal is the ideal RD for which all the images are equally spaced.
 I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
 I is the replica number).  The meanDist is the average distance
-between replicas.  Note that in this case the specified {Kspring) is
+between replicas.  Note that in this case the specified {Kspring} is
 in force units.
 
 Note that the {ideal} form of nudging can often be more effective at
@@ -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_nh.txt

@@ -393,32 +393,36 @@ thermostatting and barostatting.
 :line
 
 These fixes compute a temperature and pressure each timestep.  To do
-this, the fix creates its own computes of style "temp" and "pressure",
-as if one of these two sets of commands had been issued:
+this, the thermostat and barostat fixes create their own computes of
+style "temp" and "pressure", as if one of these sets of commands had
+been issued:
 
+For fix nvt:
 compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp :pre
 
+For fix npt and fix nph:
 compute fix-ID_temp all temp
 compute fix-ID_press all pressure fix-ID_temp :pre
 
-See the "compute temp"_compute_temp.html and "compute
-pressure"_compute_pressure.html commands for details.  Note that the
-IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
-+ underscore + "press".  For fix nvt, the group for the new computes
-is the same as the fix group.  For fix nph and fix npt, the group for
-the new computes is "all" since pressure is computed for the entire
-system.
+For fix nvt, the group for the new temperature compute is the same as
+the fix group.  For fix npt and fix nph, the group for both the new
+temperature and pressure compute is "all" since pressure is computed
+for the entire system.  In the case of fix nph, the temperature
+compute is not used for thermostatting, but just for a kinetic-energy
+contribution to the pressure.  See the "compute
+temp"_compute_temp.html and "compute pressure"_compute_pressure.html
+commands for details.  Note that the IDs of the new computes are the
+fix-ID + underscore + "temp" or fix_ID + underscore + "press".
 
 Note that these are NOT the computes used by thermodynamic output (see
 the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
-and {thermo_press}.  This means you can change the attributes of this
+and {thermo_press}.  This means you can change the attributes of these
 fix's temperature or pressure via the
-"compute_modify"_compute_modify.html command or print this temperature
-or pressure during thermodynamic output via the "thermo_style
-custom"_thermo_style.html command using the appropriate compute-ID.
-It also means that changing attributes of {thermo_temp} or
-{thermo_press} will have no effect on this fix.
+"compute_modify"_compute_modify.html command.  Or you can print this
+temperature or pressure during thermodynamic output via the
+"thermo_style custom"_thermo_style.html command using the appropriate
+compute-ID.  It also means that changing attributes of {thermo_temp}
+or {thermo_press} will have no effect on this fix.
 
 Like other fixes that perform thermostatting, fix nvt and fix npt can
 be used with "compute commands"_compute.html that calculate a

doc/src/fix_nh_uef.txt

@@ -0,0 +1,228 @@
+<"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 nvt/uef command :h3
+fix npt/uef command :h3
+
+[Syntax:]
+
+fix ID group-ID style_name erate edot_x edot_y temp Tstart Tstop Tdamp keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+style_name = {nvt/uef} or {npt/uef} :l
+{Tstart}, {Tstop}, and {Tdamp} are documented in the "fix npt"_fix_nh.html command :l
+{edot_x} and {edot_y} are the strain rates in the x and y directions (1/(time units)) :l
+one or more keyword/value pairs may be appended :l
+keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain} or {tloop} or {ploop} or {mtk}
+  {ext} value = {x} or {y} or {z} or {xy} or {yz} or {xz} = external dimensions
+    sets the external dimensions used to calculate the scalar pressure
+  {strain} values = e_x e_y = initial strain
+    usually not needed, but may be needed to resume a run with a data file.
+  {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, {mtk} keywords
+    documented by the "fix npt"_fix_nh.html command :pre
+:ule
+
+[Examples:]
+
+fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005
+fix biax_nvt all nvt/uef temp 400 400 100 erate 0.000005 0.000005
+fix uniax_npt all npt/uef temp 400 400 300 iso 1 1 3000 erate 0.00001 -0.000005 ext yz
+fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pre
+
+[Description:]
+
+This fix can be used to simulate non-equilibrium molecular dynamics
+(NEMD) under diagonal flow fields, including uniaxial and biaxial
+flow.  Simulations under continuous extensional flow may be carried
+out for an indefinite amount of time.  It is an implementation of the
+boundary conditions from "(Dobson)"_#Dobson, and also uses numerical
+lattice reduction as was proposed by "(Hunt)"_#Hunt. The lattice
+reduction algorithm is from "(Semaev)"_Semaev. The fix is intended for
+simulations of homogeneous flows, and integrates the SLLOD equations
+of motion, originally proposed by Hoover and Ladd (see "(Evans and
+Morriss)"_#Sllod).  Additional detail about this implementation can be
+found in "(Nicholson and Rutledge)"_#Nicholson.
+
+Note that NEMD simulations of a continuously strained system can be
+performed using the "fix deform"_fix_deform.html, "fix
+nvt/sllod"_fix_nvt_sllod.html, and "compute
+temp/deform"_compute_temp_deform.html commands.
+
+The applied flow field is set by the {eps} keyword. The values
+{edot_x} and {edot_y} correspond to the strain rates in the xx and yy
+directions.  It is implicitly assumed that the flow field is
+traceless, and therefore the strain rate in the zz direction is eqal
+to -({edot_x} + {edot_y}).
+
+NOTE: Due to an instability in the SLLOD equations under extension,
+"fix momentum"_fix_momentum.html should be used to regularly reset the
+linear momentum.
+
+The boundary conditions require a simulation box that does not have a
+consistent alignment relative to the applied flow field. Since LAMMPS
+utilizes an upper-triangular simulation box, it is not possible to
+express the evolving simulation box in the same coordinate system as
+the flow field.  This fix keeps track of two coordinate systems: the
+flow frame, and the upper triangular LAMMPS frame. The coordinate
+systems are related to each other through the QR decomposition, as is
+illustrated in the image below.
+
+:c,image(JPG/uef_frames.jpg)
+
+During most molecular dynamics operations, the system is represented
+in the LAMMPS frame. Only when the positions and velocities are
+updated is the system rotated to the flow frame, and it is rotated
+back to the LAMMPS frame immediately afterwards. For this reason, all
+vector-valued quantities (except for the tensors from
+"compute_pressure/uef"_compute_pressure_uef.html and
+"compute_temp/uef"_compute_temp_uef.html) will be computed in the
+LAMMPS frame. Rotationally invariant scalar quantities like the
+temperature and hydrostatic pressure are frame-invariant and will be
+computed correctly. Additionally, the system is in the LAMMPS frame
+during all of the output steps, and therefore trajectory files made
+using the dump command will be in the LAMMPS frame unless the
+"dump_cfg/uef"_dump_cfg_uef.html command is used.
+
+:line
+
+Temperature control is achieved with the default Nose-Hoover style
+thermostat documented in "fix npt"_fix_nh.html. When this fix is
+active, only the peculiar velocity of each atom is stored, defined as
+the velocity relative to the streaming velocity. This is in contrast
+to "fix nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame
+velocity, and removes the contribution from the streaming velocity in
+order to compute the temperature.
+
+Pressure control is achieved using the default Nose-Hoover barostat
+documented in "fix npt"_fix_nh.html. There are two ways to control the
+pressure using this fix. The first method involves using the {ext}
+keyword along with the {iso} pressure style. With this method, the
+pressure is controlled by scaling the simulation box isotropically to
+achieve the average pressure only in the directions specified by
+{ext}.  For example, if the {ext} value is set to {xy}, the average
+pressure (Pxx+Pyy)/2 will be controlled.
+
+This example command will control the total hydrostatic pressure under
+uniaxial tension:
+
+fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz :pre
+
+This example command will control the average stress in compression
+directions, which would typically correspond to free surfaces under
+drawing with uniaxial tension:
+
+fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy :pre
+
+The second method for pressure control involves setting the normal
+stresses using the {x}, {y} , and/or {z} keywords. When using this
+method, the same pressure must be specified via {Pstart} and {Pstop}
+for all dimensions controlled. Any choice of pressure conditions that
+would cause LAMMPS to compute a deviatoric stress are not permissible
+and will result in an error. Additionally, all dimensions with
+controlled stress must have the same applied strain rate. The {ext}
+keyword must be set to the default value ({xyz}) when using this
+method.
+
+For example, the following commands will work:
+
+fix f3 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 y 1 1 5 erate -0.5 -0.5
+fix f4 all npt/uef temp 0.7 0.7 0.5 z 1 1 5 erate 0.5 0.5 :pre
+
+The following commands will not work:
+
+fix f5 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 1 1 5 erate -0.5 -0.5
+fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5 :pre
+
+:line
+
+These fix computes a temperature and pressure each timestep.  To do
+this, it creates its own computes of style "temp/uef" and
+"pressure/uef", as if one of these two sets of commands had been
+issued:
+
+compute fix-ID_temp group-ID temp/uef
+compute fix-ID_press group-ID pressure/uef fix-ID_temp :pre
+
+compute fix-ID_temp all temp/uef
+compute fix-ID_press all pressure/uef fix-ID_temp :pre
+
+See the "compute temp/uef"_compute_temp_uef.html and "compute
+pressure/uef"_compute_pressure_uef.html commands for details.  Note
+that the IDs of the new computes are the fix-ID + underscore + "temp"
+or fix_ID + underscore + "press".
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+The fix writes the state of all the thermostat and barostat variables,
+as well as the cumulative strain applied, to "binary restart
+files"_restart.html.  See the "read_restart"_read_restart.html command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+NOTE: It is not necessary to set the {strain} keyword when resuming a
+run from a restart file. Only for resuming from data files, which do
+not contain the cumulative applied strain, will this keyword be
+necessary.
+
+This fix can be used with the "fix_modify"_fix_modify.html {temp} and
+{press} options. The temperature and pressure computes used must be of
+type {temp/uef} and {pressure/uef}.
+
+This fix computes the same global scalar and vecor quantities as "fix
+npt"_fix_nh.html.
+
+The fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF 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.
+
+Due to requirements of the boundary conditions, when the {strain}
+keyword is set to zero (or unset), the initial simulation box must be
+cubic and have style triclinic. If the box is initially of type ortho,
+use "change_box"_change_box.html before invoking the fix.
+
+NOTE: When resuming from restart files, you may need to use "box tilt
+large"_box.html since lammps has internal criteria from lattice
+reduction that are not the same as the criteria in the numerical
+lattice reduction algorithm.
+
+[Related commands:]
+
+"fix nvt"_fix_nh.html, "fix nvt/sllod"_fix_nvt_sllod.html, "compute
+temp/uef"_compute_temp_uef.html, "compute
+pressure/uef"_compute_pressure_uef.html, "dump
+cfg/uef"_dump_cfg_uef.html
+
+[Default:]
+
+The default keyword values specific to this fix are exy = xyz, strain
+= 0 0.  The remaining defaults are the same as for {fix
+npt}_fix_nh.html except tchain = 1.  The reason for this change is
+given in "fix nvt/sllod"_fix_nvt_sllod.html.
+
+:line
+
+:link(Dobson)
+[(Dobson)] Dobson, J Chem Phys, 141, 184103 (2014).
+
+:link(Hunt)
+[(Hunt)] Hunt, Mol Simul, 42, 347 (2016).
+
+:link(Semaev)
+[(Semaev)] Semaev, Cryptography and Lattices, 181 (2001).
+
+:link(Sllod)
+[(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984).
+
+:link(Nicholson)
+[(Nicholson and Rutledge)] Nicholson and Rutledge, J Chem Phys, 145,
+244903 (2016).

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_rhok.txt

@@ -0,0 +1,56 @@
+"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 rhok command :h3
+
+fix ID group-ID rhok nx ny nz K a :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nx, ny, nz = k-vektor of collective density field
+K = spring constant of bias potential
+a = anchor point of bias potential :ul
+
+[Examples:]
+
+fix bias all rhok 16 0 0 4.0 16.0
+fix 1 all npt temp 0.8 0.8 4.0 z 2.2 2.2 8.0
+# output of 4 values from fix rhok: U_bias rho_k_RE  rho_k_IM  |rho_k|
+thermo_style custom step temp pzz lz f_bias f_bias\[1\] f_bias\[2\] f_bias\[3\] :pre
+
+[Description:]
+
+The fix applies a force to atoms given by the potential
+
+:c,image(Eqs/fix_rhok.jpg)
+
+as described in "(Pedersen)"_#Pedersen.
+
+This field, which biases configurations with long-range order, can be
+used to study crystal-liquid interfaces and determine melting
+temperatures "(Pedersen)"_#Pedersen.
+
+An example of using the interface pinning method is located in the
+{examples/USER/misc/rhok} directory.
+
+[Restrictions:]
+
+This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"thermo_style"_thermo_style.html
+
+[Default:] none
+
+:line
+
+:link(Pedersen)
+[(Pedersen)] Pedersen, J. Chem. Phys., 139, 104102 (2013).
+

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
@@ -26,6 +32,9 @@ style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {
 bodystyle = {single} or {molecule} or {group} :l
   {single} args = none
   {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
   {group} args = N groupID1 groupID2 ...
     N = # of groups
     groupID1, groupID2, ... = list of N group IDs :pre
@@ -80,7 +89,17 @@ fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
 fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
 fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
 fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre
-	
+
+variable bodyid atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)
+fix 1 clump rigid custom v_bodyid :pre
+
+variable bodyid atomfile bodies.txt
+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
@@ -100,7 +119,7 @@ of a biomolecule such as a protein.
 
 Example of small rigid bodies are patchy nanoparticles, such as those
 modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of
-granular particles, lipid molecules consiting of one or more point
+granular particles, lipid molecules consisting of one or more point
 dipoles connected to other spheroids or ellipsoids, irregular
 particles built from line segments (2d) or triangles (3d), and
 coarse-grain models of nano or colloidal particles consisting of a
@@ -203,11 +222,11 @@ most one rigid body.  Which atoms are in which bodies can be defined
 via several options.
 
 NOTE: With the {rigid/small} styles, which require that {bodystyle} be
-specified as {molecule}, you can define a system that has no rigid
-bodies initially.  This is useful when you are using the {mol} keyword
-in conjunction with another fix that is adding rigid bodies on-the-fly
-as molecules, such as "fix deposit"_fix_deposit.html or "fix
-pour"_fix_pour.html.
+specified as {molecule} or {custom}, you can define a system that has
+no rigid bodies initially.  This is useful when you are using the {mol}
+keyword in conjunction with another fix that is adding rigid bodies
+on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
+"fix pour"_fix_pour.html.
 
 For bodystyle {single} the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for the {rigid} styles.
@@ -222,6 +241,15 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you
 want.  Thus you should be careful to use a fix group that only
 includes atoms you want to be part of rigid bodies.
 
+Bodystyle {custom} is similar to bodystyle {molecule}, however some
+custom properties are used to group atoms into rigid bodies. The
+special case for molecule/body ID = 0 is not available. Possible
+custom properties are an integer property associated with atoms through
+"fix property/atom"_fix_property_atom.html or an atom style variable
+or an atomfile style variable. For the latter two, the variable value
+will be rounded to an integer and then rigid bodies defined from
+those values.
+
 For bodystyle {group}, each of the listed groups is treated as a
 separate rigid body.  Only atoms that are also in the fix group are
 included in each rigid body.  This option is only allowed for the

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

@@ -59,6 +59,7 @@ Fixes :h1
    fix_langevin
    fix_langevin_drude
    fix_langevin_eff
+   fix_latte
    fix_lb_fluid
    fix_lb_momentum
    fix_lb_pc
@@ -76,6 +77,7 @@ Fixes :h1
    fix_neb
    fix_nh
    fix_nh_eff
+   fix_nh_uef
    fix_nph_asphere
    fix_nph_body
    fix_nph_sphere
@@ -113,7 +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
@@ -124,6 +127,7 @@ Fixes :h1
    fix_reaxc_species
    fix_recenter
    fix_restrain
+   fix_rhok
    fix_rigid
    fix_rx
    fix_saed_vtk
@@ -144,6 +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
@@ -62,6 +61,7 @@ dump_modify.html
 dump_molfile.html
 dump_netcdf.html
 dump_vtk.html
+dump_cfg_uef.html
 echo.html
 fix.html
 fix_modify.html
@@ -187,6 +187,7 @@ fix_ipi.html
 fix_langevin.html
 fix_langevin_drude.html
 fix_langevin_eff.html
+fix_latte.html
 fix_lb_fluid.html
 fix_lb_momentum.html
 fix_lb_pc.html
@@ -231,6 +232,7 @@ fix_nvt_manifold_rattle.html
 fix_nvt_sllod.html
 fix_nvt_sllod_eff.html
 fix_nvt_sphere.html
+fix_nh_uef.html
 fix_oneway.html
 fix_orient.html
 fix_phonon.html
@@ -241,7 +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
@@ -253,6 +256,7 @@ fix_reaxc_species.html
 fix_recenter.html
 fix_restrain.html
 fix_rigid.html
+fix_rhok.html
 fix_rx.html
 fix_saed_vtk.html
 fix_setforce.html
@@ -354,6 +358,7 @@ compute_pe.html
 compute_pe_atom.html
 compute_plasticity_atom.html
 compute_pressure.html
+compute_pressure_uef.html
 compute_property_atom.html
 compute_property_chunk.html
 compute_property_local.html
@@ -403,6 +408,7 @@ compute_temp_region.html
 compute_temp_region_eff.html
 compute_temp_rotate.html
 compute_temp_sphere.html
+compute_temp_uef.html
 compute_ti.html
 compute_torque_chunk.html
 compute_vacf.html
@@ -437,6 +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
@@ -514,7 +521,7 @@ pair_zero.html
 bond_class2.html
 bond_fene.html
 bond_fene_expand.html
-bond_oxdna.html
+bond_gromos.html
 bond_harmonic.html
 bond_harmonic_shift.html
 bond_harmonic_shift_cut.html
@@ -522,6 +529,7 @@ bond_hybrid.html
 bond_morse.html
 bond_none.html
 bond_nonlinear.html
+bond_oxdna.html
 bond_quartic.html
 bond_table.html
 bond_zero.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/package.txt

@@ -62,7 +62,7 @@ args = arguments specific to the style :l
       {no_affinity} values = none
   {kokkos} args = keyword value ...
     zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward}
+    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse}
       {neigh} value = {full} or {half}
         full = full neighbor list
         half = half neighbor list built in thread-safe manner
@@ -75,9 +75,10 @@ args = arguments specific to the style :l
       {binsize} value = size
         size = bin size for neighbor list construction (distance units)
       {comm} value = {no} or {host} or {device}
-        use value for both comm/exchange and comm/forward
+        use value for comm/exchange and comm/forward and comm/reverse
       {comm/exchange} value = {no} or {host} or {device}
       {comm/forward} value = {no} or {host} or {device}
+      {comm/reverse} value = {no} or {host} or {device}
         no = perform communication pack/unpack in non-KOKKOS mode
         host = perform pack/unpack on host (e.g. with OpenMP threading)
         device = perform pack/unpack on device (e.g. on GPU)
@@ -429,17 +430,18 @@ Coulombic solver"_kspace_style.html because the GPU is faster at
 performing pairwise interactions, then this rule of thumb may give too
 large a binsize.
 
-The {comm} and {comm/exchange} and {comm/forward} keywords determine
+The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} keywords determine
 whether the host or device performs the packing and unpacking of data
 when communicating per-atom data between processors.  "Exchange"
 communication happens only on timesteps that neighbor lists are
 rebuilt.  The data is only for atoms that migrate to new processors.
-"Forward" communication happens every timestep.  The data is for atom
+"Forward" communication happens every timestep. "Reverse" communication
+happens every timestep if the {newton} option is on.  The data is for atom
 coordinates and any other atom properties that needs to be updated for
 ghost atoms owned by each processor.
 
 The {comm} keyword is simply a short-cut to set the same value
-for both the {comm/exchange} and {comm/forward} keywords.
+for both the {comm/exchange} and {comm/forward} and {comm/reverse} keywords.
 
 The value options for all 3 keywords are {no} or {host} or {device}.
 A value of {no} means to use the standard non-KOKKOS method of

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_born.txt

@@ -17,6 +17,7 @@ pair_style born/coul/long/omp command :h3
 pair_style born/coul/msm command :h3
 pair_style born/coul/msm/omp command :h3
 pair_style born/coul/wolf command :h3
+pair_style born/coul/wolf/cs command :h3
 pair_style born/coul/wolf/gpu command :h3
 pair_style born/coul/wolf/omp command :h3
 pair_style born/coul/dsf command :h3
@@ -36,7 +37,7 @@ args = list of arguments for a particular style :ul
   {born/coul/msm} args = cutoff (cutoff2)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  {born/coul/wolf} args = alpha cutoff (cutoff2)
+  {born/coul/wolf} or {born/coul/wolf/cs} args = alpha cutoff (cutoff2)
     alpha = damping parameter (inverse distance units)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
@@ -65,6 +66,7 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
 pair_style born/coul/wolf 0.25 10.0
 pair_style born/coul/wolf 0.25 10.0 9.0
+pair_style born/coul/wolf/cs 0.25 10.0 9.0
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
@@ -106,8 +108,9 @@ damped shifted force model as in the "coul/dsf"_pair_coul.html style.
 Style {born/coul/long/cs} is identical to {born/coul/long} except that
 a term is added for the "core/shell model"_Section_howto.html#howto_25
 to allow charges on core and shell particles to be separated by r =
-0.0. The same correction is introduced for {born/coul/dsf/cs} style
-which is identical to {born/coul/dsf}.
+0.0.  The same correction is introduced for the {born/coul/dsf/cs}
+style which is identical to {born/coul/dsf}.  And likewise for
+{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.
 
 Note that these potentials are related to the "Buckingham
 potential"_pair_buck.html.

doc/src/pair_coul.txt

@@ -29,6 +29,7 @@ pair_style coul/streitz command :h3
 pair_style coul/wolf command :h3
 pair_style coul/wolf/kk command :h3
 pair_style coul/wolf/omp command :h3
+pair_style coul/wolf/cs command :h3
 pair_style tip4p/cut command :h3
 pair_style tip4p/long command :h3
 pair_style tip4p/cut/omp command :h3
@@ -43,6 +44,7 @@ pair_style coul/long cutoff
 pair_style coul/long/cs cutoff
 pair_style coul/long/gpu cutoff
 pair_style coul/wolf alpha cutoff
+pair_style coul/wolf/cs alpha cutoff
 pair_style coul/streitz cutoff keyword alpha
 pair_style tip4p/cut otype htype btype atype qdist cutoff
 pair_style tip4p/long otype htype btype atype qdist cutoff :pre
@@ -72,6 +74,7 @@ pair_style coul/msm 10.0
 pair_coeff * * :pre
 
 pair_style coul/wolf 0.2 9.0
+pair_style coul/wolf/cs 0.2 9.0
 pair_coeff * * :pre
 
 pair_style coul/streitz 12.0 ewald
@@ -202,7 +205,9 @@ interactions outside that distance are computed in reciprocal space.
 
 Style {coul/long/cs} is identical to {coul/long} except that a term is
 added for the "core/shell model"_Section_howto.html#howto_25 to allow
-charges on core and shell particles to be separated by r = 0.0.
+charges on core and shell particles to be separated by r = 0.0.  The
+same correction is introduced for the {coul/wolf/cs} style which is
+identical to {coul/wolf}.
 
 Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of
 the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces

doc/src/pair_cs.txt

@@ -9,12 +9,13 @@
 pair_style born/coul/long/cs command :h3
 pair_style buck/coul/long/cs command :h3
 pair_style born/coul/dsf/cs command :h3
+pair_style born/coul/wolf/cs command :h3
 
 [Syntax:]
 
 pair_style style args :pre
 
-style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs}
+style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} or {born/coul/wolf/cs}
 args = list of arguments for a particular style :ul
   {born/coul/long/cs} args = cutoff (cutoff2)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
@@ -26,6 +27,10 @@ args = list of arguments for a particular style :ul
     alpha = damping parameter (inverse distance units)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (distance units) :pre
+  {born/coul/wolf/cs} args = alpha cutoff (cutoff2)
+    alpha = damping parameter (inverse distance units)
+    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
 
 [Examples:]
 
@@ -41,6 +46,10 @@ pair_style born/coul/dsf/cs 0.1 10.0 12.0
 pair_coeff * *   0.0 1.00 0.00 0.00 0.00
 pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
 
+pair_style born/coul/wolf/cs 0.25 10.0 12.0
+pair_coeff * *   0.0 1.00 0.00 0.00 0.00
+pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
+
 [Description:]
 
 These pair styles are designed to be used with the adiabatic
@@ -73,13 +82,21 @@ the core and shell, epsilon is the dielectric constant and r_min is the
 minimal distance.
 
 The pair style {born/coul/dsf/cs} is identical to the
-"pair_style born/coul/dsf"_pair_born.html style, which uses the
+"pair_style born/coul/dsf"_pair_born.html style, which uses
 the damped shifted force model as in "coul/dsf"_pair_coul.html
 to compute the Coulomb contribution. This approach does not require
 a long-range solver, thus the only correction is the addition of a
 minimal distance to avoid the possible r = 0.0 case for a
 core/shell pair.
 
+The pair style {born/coul/wolf/cs} is identical to the
+"pair_style born/coul/wolf"_pair_born.html style, which uses
+the Wolf summation as in "coul/wolf"_pair_coul.html to compute
+the Coulomb contribution. This approach does not require
+a long-range solver, thus the only correction is the addition of a
+minimal distance to avoid the possible r = 0.0 case for a
+core/shell pair.
+
 [Restrictions:]
 
 These pair styles are part of the CORESHELL package.  They are only

doc/src/pair_dpd.txt

@@ -8,6 +8,7 @@
 
 pair_style dpd command :h3
 pair_style dpd/gpu command :h3
+pair_style dpd/intel command :h3
 pair_style dpd/omp command :h3
 pair_style dpd/tstat command :h3
 pair_style dpd/tstat/gpu command :h3

doc/src/pair_eam.txt

@@ -294,7 +294,7 @@ distribution have a ".cdeam" suffix.
 
 Style {eam/fs} computes pairwise interactions for metals and metal
 alloys using a generalized form of EAM potentials due to Finnis and
-Sinclair "(Finnis)"_#Finnis.  The total energy Ei of an atom I is
+Sinclair "(Finnis)"_#Finnis1.  The total energy Ei of an atom I is
 given by
 
 :c,image(Eqs/pair_eam_fs.jpg)
@@ -442,7 +442,7 @@ of Physics: Condensed Matter, 16, S2629 (2004).
 [(Daw)] Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
 Daw, Baskes, Phys Rev B, 29, 6443 (1984).
 
-:link(Finnis)
+:link(Finnis1)
 [(Finnis)] Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
 
 :link(Stukowski)

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/USER/misc/rhok/README.md

@@ -0,0 +1,74 @@
+# The Interface Pinning method for studying solid-liquid transitions
+
+In this example we will use the interface pinnig method to study a solid-liquid transition.
+This is done by adding a harmonic potential to the Hamiltonian 
+that bias the system towards two-phase configurations:
+
+  U_bias = 0.5*K*(Q-a)^2
+
+The bias field couple to an order-parameter of crystallinity Q. The implementation use long-range order:
+
+  Q=|rho_k|, 
+
+where rho_k is the collective density field of the wave-vector k. 
+For future reference we note that the structure factor S(k) is given by the variance of the collective density field: 
+
+  S(k)=|rho_k|^2.
+
+### About the method
+
+It is recommended to get familiar with the interface pinning method by reading:
+
+  [Ulf R. Pedersen, JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747)
+
+A detailed bibliography is provided at
+
+  <http://urp.dk/interface_pinning.htm>
+
+and a brief introduction can be found at YouTube:
+
+  [![Interface Pinning](http://img.youtube.com/vi/F_79JZNdyoQ/0.jpg)](http://www.youtube.com/watch?v=F_79JZNdyoQ)
+
+### Implimentation in LAMMPS
+
+For this example we will be using the rhok fix.
+
+   fix [name] [groupID] rhok [nx] [ny] [nz] [K] [a]
+
+This fix include a harmonic bias potential U_bias=0.5*K*(|rho_k|-a)^2 to the force calculation.
+The elements of the wave-vector k is given by the nx, ny and nz input: 
+
+  k_x = (2 pi / L_x) * n_x, k_y = (2 pi / L_y) * n_y and k_z = (2 pi / L_z) * n_z. 
+
+We will use a k vector that correspond to a Bragg peak.
+
+## Example: the Lennard-Jones (LJ) model
+
+We will use the interface pinning method to study melting of the LJ model
+at temperature 0.8 and pressure 2.185. This is a coexistence state-point, and the method
+can be used to show this. The present directory contains the input files that we will use:
+
+  in.crystal
+  in.setup
+  in.pinning
+
+1. First we will determine the density of the crystal with the LAMMPS input file in.crystal.
+  From the output we get that the average density after equilibration is 0.9731. 
+  We need this density to ensure hydrostatic pressure when in a two-phase simulation.
+
+2. Next, we setup a two-phase configuration using in.setup.
+
+3. Finally, we run a two-phase simulation with the bias-field applied using in.pinning.
+  The last column in the output show |rho_k|. We note that after a equilibration period
+  the value fluctuates around the anchor point (a) -- showing that this is indeed a coexistence
+  state point.
+
+The reference [JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points,
+and the reference [JCP 142, 044104 (2015)](http://dx.doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations.
+That method have been experienced to be most effective in the slightly super-heated regime above the melting temperature.
+
+## Contact
+
+  Ulf R. Pedersen;
+  <http://www.urp.dk>;
+  ulf AT urp.dk

examples/USER/misc/rhok/in.crystal

@@ -0,0 +1,36 @@
+units		lj
+dimension	3
+boundary	p p p
+atom_style  atomic
+
+# truncated and shifted LJ potential
+pair_style	lj/cut 2.5
+pair_modify	shift yes
+lattice	fcc 0.9731
+region	my_box block 0 8.0   0 8.0   0 20.0
+create_box 1 my_box
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify tail no
+pair_modify shift yes
+mass 1 1.0
+velocity all create 1.6 1 mom yes rot yes
+
+# simulation parameters
+neighbor	0.6 bin
+timestep	0.004
+run_style 	verlet
+fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32
+
+# computing long-range order (no bias is added since k=0)
+fix bias all rhok 16 0 0 0.0 0.0
+
+# output
+thermo 50
+thermo_style custom step temp press density f_bias[3]
+# dump dumpXYZ all xyz 2000 traj.xyz
+
+# NOTE: this is cut short to 5000 steps for demonstration purposes
+# run 100000
+run 5000

examples/USER/misc/rhok/in.pinning

@@ -0,0 +1,33 @@
+units       lj
+dimension   3
+boundary    p p p
+atom_style  atomic
+
+# truncated and shifted LJ potential
+pair_style  lj/cut 2.5
+pair_modify shift yes
+read_data   data.halfhalf
+pair_coeff  1 1 1.0 1.0 2.5
+mass        1 1.0
+
+# simulation parameters 
+neighbor	0.6 bin
+timestep	0.004
+run_style 	verlet
+
+velocity all create 0.8 1 mom yes rot yes
+fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0
+fix 100 all momentum 100 linear 1 1 1
+
+# harmonic rho_k bias-field 
+#                 nx ny nz K     a
+fix bias all rhok 16 0  0  4.0   26.00
+
+# output                                U_bias rho_k_RE  rho_k_IM |rho_k| 
+thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]
+thermo 50
+# dump dumpXYZ all xyz 500 traj.xyz
+
+# NOTE: run reduced for demonstration purposes
+# run 50000
+run 5000

examples/USER/misc/rhok/in.setup

@@ -0,0 +1,41 @@
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+
+# fcc lattice
+lattice	fcc 0.9731
+region my_box block 0 8.0   0 8.0   0 20.0
+create_box 1 my_box
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+pair_coeff 1 1 1.0 1.0 2.5
+mass 1 1.0
+change_box all z final 0.0 34 remap units box
+
+# select particles in one side of the elongated box
+region left plane 0 0 10 0 0 1
+group left region left
+
+velocity left create 6.0 1 mom yes rot yes
+
+# simulation parameters
+neighbor	0.6 bin
+timestep	0.004
+run_style 	verlet
+fix ensemble left nve     # Note: only move particle in left-hand side
+fix langevin left langevin 3.0 0.8 100.0 2017
+
+# outout
+thermo_style custom step temp pzz pe lz
+thermo 100
+# dump dumpXYZ all xyz 100 traj.xyz
+
+# run reduced for demonstration purposes
+# run 10000
+run 5000
+write_data data.halfhalf

examples/USER/misc/rhok/log.22Sep2017.crystal.g++.1

@@ -0,0 +1,187 @@
+LAMMPS (22 Sep 2017)
+  using 1 OpenMP thread(s) per MPI task
+units		lj
+dimension	3
+boundary	p p p
+atom_style  atomic
+
+# truncated and shifted LJ potential
+pair_style	lj/cut 2.5
+pair_modify	shift yes
+lattice	fcc 0.9731
+Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
+region	my_box block 0 8.0   0 8.0   0 20.0
+create_box 1 my_box
+Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
+  1 by 1 by 1 MPI processor grid
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+Created 5120 atoms
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify tail no
+pair_modify shift yes
+mass 1 1.0
+velocity all create 1.6 1 mom yes rot yes
+
+# simulation parameters
+neighbor	0.6 bin
+timestep	0.004
+run_style 	verlet
+fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32
+
+# computing long-range order (no bias is added since k=0)
+fix bias all rhok 16 0 0 0.0 0.0
+
+# output
+thermo 50
+thermo_style custom step temp press density f_bias[3]
+# dump dumpXYZ all xyz 2000 traj.xyz
+
+# NOTE: this is cut short to 5000 steps for demonstration purposes
+# run 100000
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.1
+  ghost atom cutoff = 3.1
+  binsize = 1.55, bins = 9 9 21
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.523 | 4.523 | 4.523 Mbytes
+Step Temp Press Density f_bias[3] 
+       0          1.6   -2.7568106       0.9731    71.554175 
+      50   0.78457786    3.1029192   0.97362639    54.327705 
+     100   0.85528971    2.4670259   0.97213457    55.189308 
+     150   0.85241818    2.3210306    0.9698027    56.138125 
+     200   0.82301385    2.3448692   0.96708227    55.735326 
+     250   0.83076383    2.0890816   0.96425763    55.320625 
+     300   0.81602823    2.0118796   0.96173925    54.095736 
+     350   0.81084006    1.9122192   0.95979392    54.526429 
+     400   0.80776593    1.8502174   0.95869117    54.434901 
+     450   0.80694697    1.8435873   0.95851085     53.20809 
+     500   0.81384248    1.8111331   0.95917305    53.419395 
+     550   0.81027072    1.9222272   0.96056019     54.36723 
+     600   0.81199582    2.0291945   0.96248486    54.888582 
+     650   0.82507964    2.0706462   0.96467227    55.807137 
+     700     0.832562    2.1471442    0.9668913    56.721267 
+     750   0.83358138    2.2674672     0.968984    56.723838 
+     800   0.83477542    2.3658275   0.97072603    56.234689 
+     850   0.84722921    2.3506233   0.97189674    56.262424 
+     900   0.83526965    2.4532068   0.97248856    56.219103 
+     950   0.83174583    2.4763958   0.97249527    56.409813 
+    1000   0.83022557    2.4334341   0.97194093    55.890858 
+    1050   0.83208978    2.3478416   0.97092452    54.934691 
+    1100   0.82789545     2.272404    0.9696152     54.90894 
+    1150   0.82678617    2.1798046   0.96819776    54.927782 
+    1200    0.8088841    2.1960256   0.96687735    54.914327 
+    1250   0.81512784    2.0736261   0.96579008    53.927291 
+    1300   0.81271067    2.0297138   0.96504188    54.289698 
+    1350    0.8201767    1.9493976   0.96464115    55.342131 
+    1400   0.80880489    2.0016987   0.96468463    55.757758 
+    1450    0.8114196    2.0282699   0.96514115    55.865676 
+    1500   0.81085664    2.0838361   0.96591869    56.553425 
+    1550   0.81257075    2.1283157   0.96694549    56.921544 
+    1600   0.82617645    2.1017986   0.96817075    56.858808 
+    1650   0.82616141    2.1885582   0.96941073    56.717917 
+    1700   0.81634174    2.2996967   0.97047447    56.453745 
+    1750   0.82447573    2.2924266   0.97128663    56.916813 
+    1800   0.83610432     2.236456   0.97178453    56.400752 
+    1850   0.82479203    2.3103493   0.97197318    55.891368 
+    1900   0.82298992    2.3059289   0.97181084    55.680563 
+    1950   0.82098556    2.2801003   0.97138609    55.754406 
+    2000    0.8181203    2.2480175   0.97078591    55.801363 
+    2050   0.82822293    2.1208884   0.97004107       55.687 
+    2100    0.7976818    2.2711199   0.96930169    55.459844 
+    2150   0.81817848    2.0680351   0.96860201    56.514731 
+    2200   0.80707457    2.1112141   0.96810519    55.504308 
+    2250   0.81651111    2.0077603   0.96781161    55.635702 
+    2300   0.80634534    2.0662241   0.96777177    56.051086 
+    2350   0.80892831    2.0619333   0.96799037    56.548711 
+    2400   0.82454203    1.9585394    0.9684672    56.695235 
+    2450   0.81517178     2.075283   0.96921622    56.613082 
+    2500   0.80969595    2.1624581   0.97010528     56.57516 
+    2550   0.80862964    2.2088622   0.97100774    57.072594 
+    2600   0.81468816    2.2293973   0.97192868    56.879212 
+    2650   0.82063107    2.2244887   0.97269715    55.454502 
+    2700   0.81691618    2.2789954   0.97319841    54.421943 
+    2750    0.8141787    2.2981247   0.97340453    54.469921 
+    2800   0.81973871    2.2422136    0.9733278    55.959235 
+    2850   0.82037399     2.201016   0.97302727    56.685826 
+    2900   0.80650164    2.2672955    0.9726128    56.574395 
+    2950   0.81752783    2.1317541   0.97207545    56.809412 
+    3000   0.80836945    2.1461483   0.97151192    57.205206 
+    3050   0.80785109    2.1189056   0.97103049    57.418763 
+    3100   0.79835058     2.146416   0.97069705    57.329383 
+    3150   0.79792089    2.1388267   0.97051679    57.279852 
+    3200   0.79934603    2.1049562   0.97046851    56.351494 
+    3250   0.79523232    2.1549779   0.97063956     56.00356 
+    3300    0.8004458    2.1145975   0.97096375    55.725509 
+    3350   0.79772742     2.166292   0.97143785    55.558075 
+    3400   0.80621087    2.1309217   0.97198456    55.816704 
+    3450   0.80540626    2.1727557   0.97263267    55.671283 
+    3500   0.80867606    2.1905129   0.97321538    55.390086 
+    3550   0.80917896    2.2144872   0.97370472    55.742085 
+    3600   0.80930722    2.2288938     0.974093     56.23064 
+    3650   0.80390523    2.2777327   0.97431886    56.084731 
+    3700   0.79620093    2.3143541   0.97435103    55.942797 
+    3750   0.80252393    2.2564638    0.9741875    56.042055 
+    3800   0.78981264    2.3156481    0.9739121    55.971352 
+    3850   0.80391951    2.1804938   0.97351088    55.855858 
+    3900   0.81268129    2.0855818   0.97308521    56.288315 
+    3950    0.7958182     2.175259   0.97273088    56.140141 
+    4000   0.80054484    2.1163279   0.97243129    56.366818 
+    4050   0.79760187     2.105362   0.97225308    56.684619 
+    4100   0.79283424    2.1357603     0.972206    56.203341 
+    4150   0.79543088    2.1036951   0.97227608    56.606315 
+    4200   0.79410999    2.1402049   0.97253758    56.277478 
+    4250    0.7985469    2.1285154   0.97293622    56.356076 
+    4300   0.79700387    2.1470614   0.97337091    56.722298 
+    4350   0.80479321    2.1403244   0.97384674    57.212574 
+    4400   0.79505512     2.224463   0.97434415    56.561877 
+    4450   0.78346648    2.3347865   0.97478611    56.681362 
+    4500   0.79811284     2.259123   0.97510069    57.365929 
+    4550   0.80015561    2.2345254   0.97523653     57.34799 
+    4600   0.79648318    2.2651869   0.97525975    57.502318 
+    4650   0.80524865    2.1943025   0.97507638    57.702488 
+    4700   0.80397778    2.1758629   0.97478268    57.162107 
+    4750   0.78914913    2.2470191    0.9744625    56.849565 
+    4800   0.79324889    2.2028993   0.97408817    57.572344 
+    4850   0.78993209     2.181763   0.97373372    57.683552 
+    4900   0.79041263    2.1604768   0.97348692    56.922312 
+    4950   0.79741332    2.1105901   0.97332545    57.488932 
+    5000    0.7891178     2.163416   0.97328963    57.365252 
+Loop time of 33.6467 on 1 procs for 5000 steps with 5120 atoms
+
+Performance: 51357.258 tau/day, 148.603 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    | 24.699     | 24.699     | 24.699     |   0.0 | 73.41
+Neigh   | 2.8894     | 2.8894     | 2.8894     |   0.0 |  8.59
+Comm    | 0.34907    | 0.34907    | 0.34907    |   0.0 |  1.04
+Output  | 0.0056     | 0.0056     | 0.0056     |   0.0 |  0.02
+Modify  | 5.5718     | 5.5718     | 5.5718     |   0.0 | 16.56
+Other   |            | 0.1319     |            |       |  0.39
+
+Nlocal:    5120 ave 5120 max 5120 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7594 ave 7594 max 7594 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    323081 ave 323081 max 323081 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 323081
+Ave neighs/atom = 63.1018
+Neighbor list builds = 248
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:33

examples/USER/misc/rhok/log.22Sep2017.crystal.g++.4

@@ -0,0 +1,187 @@
+LAMMPS (22 Sep 2017)
+  using 1 OpenMP thread(s) per MPI task
+units		lj
+dimension	3
+boundary	p p p
+atom_style  atomic
+
+# truncated and shifted LJ potential
+pair_style	lj/cut 2.5
+pair_modify	shift yes
+lattice	fcc 0.9731
+Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
+region	my_box block 0 8.0   0 8.0   0 20.0
+create_box 1 my_box
+Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
+  1 by 1 by 4 MPI processor grid
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+Created 5120 atoms
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify tail no
+pair_modify shift yes
+mass 1 1.0
+velocity all create 1.6 1 mom yes rot yes
+
+# simulation parameters
+neighbor	0.6 bin
+timestep	0.004
+run_style 	verlet
+fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32
+
+# computing long-range order (no bias is added since k=0)
+fix bias all rhok 16 0 0 0.0 0.0
+
+# output
+thermo 50
+thermo_style custom step temp press density f_bias[3]
+# dump dumpXYZ all xyz 2000 traj.xyz
+
+# NOTE: this is cut short to 5000 steps for demonstration purposes
+# run 100000
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.1
+  ghost atom cutoff = 3.1
+  binsize = 1.55, bins = 9 9 21
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.23 | 3.23 | 3.23 Mbytes
+Step Temp Press Density f_bias[3] 
+       0          1.6   -2.7568106       0.9731    71.554175 
+      50   0.78457786    3.1029192   0.97362639    54.327705 
+     100   0.85528971    2.4670259   0.97213457    55.189308 
+     150   0.85241818    2.3210306    0.9698027    56.138125 
+     200   0.82301385    2.3448692   0.96708227    55.735326 
+     250   0.83076383    2.0890816   0.96425763    55.320625 
+     300   0.81602823    2.0118796   0.96173925    54.095736 
+     350   0.81084006    1.9122192   0.95979392    54.526429 
+     400   0.80776593    1.8502174   0.95869117    54.434901 
+     450   0.80694697    1.8435873   0.95851085     53.20809 
+     500   0.81384248    1.8111331   0.95917305    53.419395 
+     550   0.81027072    1.9222272   0.96056019     54.36723 
+     600   0.81199582    2.0291945   0.96248486    54.888582 
+     650   0.82507964    2.0706462   0.96467227    55.807137 
+     700     0.832562    2.1471442    0.9668913    56.721267 
+     750   0.83358138    2.2674672     0.968984    56.723838 
+     800   0.83477542    2.3658275   0.97072603    56.234689 
+     850   0.84722921    2.3506233   0.97189674    56.262424 
+     900   0.83526965    2.4532068   0.97248856    56.219103 
+     950   0.83174583    2.4763958   0.97249527    56.409813 
+    1000   0.83022557    2.4334341   0.97194093    55.890858 
+    1050   0.83208978    2.3478416   0.97092452    54.934691 
+    1100   0.82789545     2.272404    0.9696152     54.90894 
+    1150   0.82678617    2.1798046   0.96819776    54.927782 
+    1200    0.8088841    2.1960256   0.96687735    54.914327 
+    1250   0.81512784    2.0736261   0.96579008    53.927291 
+    1300   0.81271067    2.0297138   0.96504188    54.289698 
+    1350    0.8201767    1.9493976   0.96464115    55.342131 
+    1400   0.80880489    2.0016987   0.96468463    55.757758 
+    1450    0.8114196    2.0282699   0.96514115    55.865676 
+    1500   0.81085664    2.0838361   0.96591869    56.553425 
+    1550   0.81257075    2.1283157   0.96694549    56.921544 
+    1600   0.82617645    2.1017986   0.96817075    56.858808 
+    1650   0.82616141    2.1885582   0.96941073    56.717917 
+    1700   0.81634174    2.2996967   0.97047447    56.453745 
+    1750   0.82447573    2.2924266   0.97128663    56.916813 
+    1800   0.83610432     2.236456   0.97178453    56.400752 
+    1850     0.824792    2.3103491   0.97197318    55.891368 
+    1900   0.82298989    2.3059287   0.97181084    55.680562 
+    1950   0.82098545    2.2801009   0.97138609    55.754404 
+    2000   0.81812031    2.2480166   0.97078591    55.801371 
+    2050   0.82822262    2.1208887   0.97004108    55.687001 
+    2100   0.79768162    2.2711186    0.9693017    55.459852 
+    2150   0.81817874    2.0680317   0.96860202    56.514744 
+    2200   0.80707412    2.1112032   0.96810521    55.504308 
+    2250   0.81650921    2.0077757   0.96781164    55.635717 
+    2300   0.80634656     2.066186   0.96777181    56.051088 
+    2350   0.80893174    2.0619084   0.96799042    56.548711 
+    2400   0.82453783    1.9585503   0.96846727    56.695111 
+    2450   0.81517275    2.0752617   0.96921631    56.614046 
+    2500   0.80969622    2.1624476    0.9701054    56.574846 
+    2550   0.80861922    2.2089505   0.97100787    57.072334 
+    2600   0.81468888    2.2293754   0.97192875    56.879416 
+    2650   0.82061239    2.2245462   0.97269723    55.442015 
+    2700   0.81687473    2.2792015   0.97319852    54.420301 
+    2750   0.81416567    2.2982988   0.97340467    54.469427 
+    2800   0.81978563    2.2418723   0.97332803    55.965451 
+    2850   0.82069759    2.1988948   0.97302752    56.686807 
+    2900   0.80631184    2.2684466   0.97261407    56.585682 
+    2950   0.81759744    2.1312328   0.97207888    56.812431 
+    3000   0.80748056     2.152676   0.97151807    57.178849 
+    3050   0.80789237     2.118162   0.97103728    57.433724 
+    3100   0.79882523    2.1414744   0.97070338     57.34686 
+    3150   0.79803949    2.1359043   0.97052875    57.382544 
+    3200   0.79170386    2.1548392   0.97049349    56.465806 
+    3250   0.78848813    2.1990144   0.97067557    55.929088 
+    3300   0.79820555    2.1304609   0.97101444    55.624487 
+    3350   0.79250565    2.1971235   0.97149233    55.933615 
+    3400   0.80584844    2.1417239   0.97206083     55.85922 
+    3450   0.80685744    2.1640501   0.97266047    55.135963 
+    3500   0.80751888    2.1858277   0.97318703    55.407581 
+    3550   0.79882754    2.2796452   0.97363149    55.392366 
+    3600   0.80219171    2.2715765   0.97392571    55.867887 
+    3650   0.79061794    2.3492866   0.97410985      56.0192 
+    3700    0.8058483    2.2327904   0.97411924    56.491303 
+    3750   0.79460746    2.2941868   0.97397764    55.929912 
+    3800   0.80447478    2.2018009   0.97367627    55.663208 
+    3850   0.80355335      2.17638   0.97333164    55.637261 
+    3900   0.80388417    2.1531434    0.9729647     56.03794 
+    3950   0.79557409    2.1853318    0.9726503    56.132348 
+    4000   0.79547396    2.1457051   0.97235244    55.552675 
+    4050    0.8058384    2.0637678   0.97213346    56.185416 
+    4100    0.7976931    2.1028246   0.97208255    56.050347 
+    4150   0.79555522     2.115473   0.97216375    56.868136 
+    4200   0.79324134    2.1510383   0.97246129    56.462635 
+    4250   0.80788167    2.0534887   0.97287821    55.650788 
+    4300   0.79389865    2.2019815   0.97337765    55.596846 
+    4350   0.79786309    2.1851119   0.97389825    57.000921 
+    4400   0.79986518    2.1997541   0.97443778    57.551564 
+    4450    0.8063901    2.1893874   0.97493151    57.236138 
+    4500   0.80005802     2.250364   0.97533075    57.341358 
+    4550   0.79707443    2.2995576   0.97557554    57.338713 
+    4600   0.79869949    2.2807889   0.97563277    57.084504 
+    4650   0.79694427    2.2673215   0.97544638    57.025663 
+    4700   0.79023986    2.2884131   0.97511483    57.131188 
+    4750   0.79566823    2.2215519   0.97464304    57.045676 
+    4800   0.78936986    2.2268037   0.97410626    57.384178 
+    4850   0.79025913    2.1836718     0.973616     57.78438 
+    4900   0.80138424    2.0657609    0.9732124    57.888266 
+    4950   0.77853735     2.207944   0.97296347    57.312213 
+    5000   0.79115984    2.1035893   0.97285578    57.109472 
+Loop time of 9.53489 on 4 procs for 5000 steps with 5120 atoms
+
+Performance: 181229.223 tau/day, 524.390 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.312      | 6.4238     | 6.5139     |   3.1 | 67.37
+Neigh   | 0.72062    | 0.73538    | 0.74531    |   1.1 |  7.71
+Comm    | 0.52697    | 0.64152    | 0.78688    |  14.1 |  6.73
+Output  | 0.0028393  | 0.0029888  | 0.0033851  |   0.4 |  0.03
+Modify  | 1.6249     | 1.669      | 1.7253     |   2.9 | 17.50
+Other   |            | 0.06221    |            |       |  0.65
+
+Nlocal:    1280 ave 1289 max 1266 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Nghost:    3346.25 ave 3379 max 3331 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Neighs:    80701.8 ave 81534 max 79755 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+
+Total # of neighbors = 322807
+Ave neighs/atom = 63.0482
+Neighbor list builds = 248
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:09

examples/USER/misc/rhok/log.22Sep2017.pinning.g++.1

@@ -0,0 +1,186 @@
+LAMMPS (22 Sep 2017)
+  using 1 OpenMP thread(s) per MPI task
+units       lj
+dimension   3
+boundary    p p p
+atom_style  atomic
+
+# truncated and shifted LJ potential
+pair_style  lj/cut 2.5
+pair_modify shift yes
+read_data   data.halfhalf
+  orthogonal box = (0 0 0) to (12.8152 12.8152 34)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  5120 atoms
+  reading velocities ...
+  5120 velocities
+pair_coeff  1 1 1.0 1.0 2.5
+mass        1 1.0
+
+# simulation parameters
+neighbor	0.6 bin
+timestep	0.004
+run_style 	verlet
+
+velocity all create 0.8 1 mom yes rot yes
+fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0
+fix 100 all momentum 100 linear 1 1 1
+
+# harmonic rho_k bias-field
+#                 nx ny nz k     a
+fix bias all rhok 16 0  0  4.0   26.00
+
+# output                                U_bias rho_k_RE  rho_k_IM |rho_k|
+thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]
+thermo 50
+dump dumpXYZ all xyz 500 traj.xyz
+
+# NOTE: run reduced for demonstration purposes
+# run 50000
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.1
+  ghost atom cutoff = 3.1
+  binsize = 1.55, bins = 9 9 22
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, 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) = 5.723 | 5.723 | 5.723 Mbytes
+Step Temp Pzz PotEng Lz f_bias f_bias[1] f_bias[2] f_bias[3] 
+       0          0.8    5.1566801   -4.8556711           34    179.52419    35.473155   -0.2832763    35.474286 
+      50     1.072533    3.8158392   -5.2704532    34.024206  0.010596224    25.927135 -0.063106738    25.927212 
+     100    1.1093231    3.6703116   -5.3380965    34.094814    1.8552612    26.958236  -0.51403326    26.963136 
+     150    1.1080721    3.8202601   -5.3568368    34.207473   0.39188605    26.420755   -1.0759575    26.442655 
+     200    1.1435287    3.3445987   -5.4365298    34.354119    3.0758718    27.239465  -0.19115251    27.240135 
+     250    1.1203046    3.4669456   -5.4293867    34.511473    0.8543814    26.652785  -0.20818214    26.653598 
+     300    1.1012709    3.4583154   -5.4281803    34.664509    2.4837156    27.097674    0.9518628    27.114387 
+     350    1.0439632    3.8953869    -5.368619    34.810399   0.55385719    26.518391   0.64525272     26.52624 
+     400    1.0083878    4.0523864   -5.3418278    34.957669   0.34806057    26.404011   0.83368604    26.417169 
+     450    0.9675244     4.310087   -5.3089468    35.114208    0.7921285    26.607512     1.077889    26.629336 
+     500   0.94605476    4.1050097   -5.3062273    35.284018   0.87757754    26.639125    1.1140858    26.662411 
+     550   0.92662323    3.9299063   -5.3062927    35.458565    1.3746441    26.773494    1.7256603    26.829049 
+     600   0.89723165    3.7683555    -5.289725    35.629881   0.46692943    26.372973    2.4135502    26.483182 
+     650   0.90612566    3.1098837   -5.3267851    35.788537  0.032662126    25.918784    3.2982102    26.127793 
+     700    0.9152508    2.6527976   -5.3597799    35.923343  0.014621588    25.834591    3.6093492    26.085503 
+     750   0.90156356    2.3474851   -5.3545938    36.031813   0.75225637    26.307204    4.0247215    26.613293 
+     800   0.89748513    1.9825103   -5.3610202    36.113888   0.33402511    26.261326    2.7858039    26.408672 
+     850   0.89496343    1.8906342   -5.3673514    36.169424   0.85431557    26.534648    2.5150347    26.653573 
+     900   0.89463983    1.5654217   -5.3753283     36.20181    1.5689239    26.764737    2.5474794    26.885699 
+     950   0.88663832    1.4399476   -5.3703322    36.209971  0.044436903    25.818418    1.2963356    25.850941 
+    1000   0.87407208     1.485718   -5.3572665    36.195386    1.4405611    26.828072    1.0520795    26.848693 
+    1050   0.87580489     1.163155   -5.3647269    36.160279   0.15319559    26.234791    1.4845964    26.276763 
+    1100   0.86978111    1.3743181   -5.3594907    36.104958    1.1313537     25.19895    1.5711793    25.247885 
+    1150   0.86987861    1.3212927   -5.3628503    36.035486  0.039865678    25.841762   0.93898962    25.858816 
+    1200   0.87142486    1.3293818   -5.3676854    35.954411   0.16827389     25.70952  -0.14639427    25.709936 
+    1250   0.87582265    1.3203803   -5.3764058     35.86575   0.25946652    25.639682  0.082696867    25.639815 
+    1300   0.87371627    1.4680294    -5.375151    35.772824   0.17697069    25.701417    0.2397926    25.702535 
+    1350   0.88617453    1.5923057   -5.3954912    35.681046 0.00049155526    25.973634  -0.74521794    25.984323 
+    1400   0.87809636    1.5821707   -5.3850722    35.594706  0.024050814    26.107395  -0.34393685     26.10966 
+    1450   0.87912192    1.7820174   -5.3885842    35.514722   0.20999914    25.667238  -0.66933655    25.675964 
+    1500   0.88293618    2.0295275   -5.3963602    35.443445   0.60232374    25.376395   -1.9501461    25.451218 
+    1550   0.90012542    1.9476472   -5.4249456    35.382791    0.4488038    26.448928   -1.1452474    26.473711 
+    1600   0.89155063    2.2462603   -5.4153432    35.332095  0.039621687    26.138157  -0.36825239    26.140751 
+    1650    0.8942624     2.343747   -5.4233433    35.294954 0.0089980332    26.064277   0.38189192    26.067075 
+    1700   0.90047841     2.451289   -5.4376312     35.27234   0.86985171    26.646438   0.83408084    26.659489 
+    1750   0.87586052    2.6381221   -5.4067182    35.264564     6.346204    27.652722    2.6699692     27.78132 
+    1800   0.87392582    2.6338176   -5.4109056    35.270073  0.046414129    26.016188    2.6651053    26.152339 
+    1850   0.86540415    2.5434301   -5.4058587    35.285902  0.054615472    26.074279    2.1799787    26.165251 
+    1900   0.87043082    2.5776772   -5.4216997    35.309062   0.68978148     26.38648    3.2614091    26.587274 
+    1950   0.86281992    2.3107762   -5.4188978    35.338501 0.0072672577    25.736893    3.2375012     25.93972 
+    2000   0.85905576    2.2894047   -5.4215995     35.36787  0.095633435    26.072085    2.7685848     26.21867 
+    2050   0.85793751    2.2382039   -5.4279351    35.395213   0.13602344    25.598457    2.6881027    25.739209 
+    2100   0.85585253    2.0765811   -5.4324511    35.418877 0.0059888115    25.754128    3.1436222    25.945279 
+    2150   0.86701057    1.8449875   -5.4562208    35.436124  0.097328618    25.413697    4.3268293      25.7794 
+    2200   0.85168154    1.9024923   -5.4395776     35.44246   0.20764576    25.094788    5.4406104    25.677784 
+    2250    0.8429719     1.870335   -5.4320586    35.438363   0.34419961    24.998478    5.4475709    25.585151 
+    2300   0.84176891    1.7100228   -5.4351472    35.422863   0.76036958    24.697018    5.8629967    25.383409 
+    2350   0.84601588    1.8539039   -5.4456629    35.395979   0.38437531    25.647986    6.4163366    26.438392 
+    2400   0.84637647    1.6299091   -5.4498948     35.36125  0.074236719    24.995872    7.8269968    26.192661 
+    2450   0.85650449    1.6828907   -5.4683101    35.316669    0.3671827    25.280669    7.7040329    26.428476 
+    2500   0.84963707    1.7305222   -5.4605394    35.265508    0.1406965    25.236741    7.2780025    26.265232 
+    2550   0.84084365    1.8758368   -5.4497083    35.208725   0.33937687    24.544376    7.2334512    25.588067 
+    2600   0.85317342    1.7781674   -5.4702734    35.149747   0.60378248    24.046307    8.3370138    25.450554 
+    2650   0.85487644    2.0065374   -5.4747643    35.090431   0.22483651    24.937101    8.4669004    26.335288 
+    2700   0.84550083    1.9363031   -5.4628401    35.034349   0.43442577    24.250196    7.9943738    25.533939 
+    2750   0.85843419    2.0473138    -5.484528    34.980671   0.45959294     24.17438     8.179356    25.520629 
+    2800   0.86047607    2.0754522   -5.4899966    34.932466 0.00038123477    24.619856    8.3153434    25.986194 
+    2850   0.86375793    2.2751324   -5.4977459    34.892337 0.0016455263    24.927259     7.289789    25.971316 
+    2900   0.84438986    2.3790377   -5.4721407    34.863512    1.2372354    25.819445     7.132603    26.786523 
+    2950    0.8551438    2.2721926   -5.4925958     34.84473    1.5405388    25.956466     6.976385     26.87765 
+    3000   0.83737707    2.4009609   -5.4707188    34.834171   0.28507766    25.643879    6.1778846    26.377543 
+    3050   0.84923235    2.4187994   -5.4938573    34.830836  0.036512025    25.139252    7.1457857    26.135115 
+    3100   0.83872396    2.3811576   -5.4838787    34.833673     0.246984     24.21358    8.4588719    25.648586 
+    3150   0.83957817    2.3901421   -5.4913118     34.84163   0.20477984    24.309852    10.088243    26.319984 
+    3200   0.84283033      2.17292   -5.5025459    34.853975    1.3367154    24.581685     10.72011    26.817531 
+    3250   0.84002379    2.1247709   -5.5044955    34.866106   0.11434509    24.463842    9.4874246    26.239108 
+    3300   0.83311101    2.1492058   -5.5000847    34.875625 0.0053284993    23.815298    10.560222    26.051616 
+    3350   0.83216701    1.9587594   -5.5043446    34.881623   0.58985562    23.934253    11.475462    26.543073 
+    3400   0.82396039    2.1914951   -5.4971506    34.881199  0.098206955    23.393402     10.82936    25.778407 
+    3450   0.83483253    1.9783612   -5.5182844    34.877327 7.6571212e-05    23.675355    10.761012    26.006188 
+    3500   0.82712062    1.9718522   -5.5111818    34.869214  0.014836125    23.314122    11.312845    25.913872 
+    3550    0.8342927    1.9114357   -5.5259968    34.855179    1.4050442    22.442758    11.377192    25.161834 
+    3600   0.82631637    1.9836457   -5.5176244    34.835738  0.084637609    23.413286    10.824194    25.794285 
+    3650   0.82425697    1.9218541   -5.5178548    34.811901   0.11000071    22.788707    12.022258    25.765478 
+    3700   0.82491437    1.9624493    -5.521738    34.782417  0.034984027    23.011433    12.384217    26.132257 
+    3750   0.82758167    2.0856442   -5.5283493    34.748872  0.001362163    23.030662    12.122144    26.026098 
+    3800   0.81891108    1.9858824   -5.5177774    34.714618   0.17075993     23.21344    12.345683    26.292199 
+    3850   0.83392227    2.1631514   -5.5426333    34.681146   0.82106473    22.510204    11.678329    25.359272 
+    3900   0.82230654    2.0017132   -5.5276756    34.650221   0.48735732    23.444809    12.339117    26.493638 
+    3950   0.81929288    2.1749936   -5.5256673     34.61976  0.089219805    23.540062    11.527925    26.211211 
+    4000   0.83415169    2.0446791   -5.5506187    34.591266   0.15593937    23.742282     11.26508    26.279231 
+    4050   0.82362522    2.1998083   -5.5375157    34.563164   0.25405351    23.913834    11.081011    26.356408 
+    4100   0.82589505    2.3074345    -5.543718    34.537763  0.080213125     24.03253    10.435108    26.200266 
+    4150   0.83855297    2.2424199   -5.5658171    34.517758   0.62913338    23.974257    8.5079223    25.439138 
+    4200   0.82522111    2.2622619   -5.5493275    34.502472    1.8756517    25.754617    7.9996898    26.968414 
+    4250   0.82083124    2.4135193   -5.5464932      34.4919    1.1217436      25.8944    6.7070444    26.748914 
+    4300   0.83059704    2.1375109   -5.5653245    34.487366   0.53623038     26.05979    4.9072346    26.517798 
+    4350   0.82755047    2.1159821   -5.5650889    34.484506   0.10017723    25.405936    4.3532342    25.776195 
+    4400   0.83192877     2.180851   -5.5759565    34.480909  0.053664012    25.993034    2.9844338    26.163805 
+    4450   0.81860572    2.2333381   -5.5602138    34.477183  0.037864077    25.792233    1.9038859    25.862406 
+    4500   0.82821762    2.1142023   -5.5788682    34.474784  0.088221344     26.20329   0.59417897    26.210025 
+    4550    0.8205154    2.0896984   -5.5715531    34.472405  0.016076192    26.083166  -0.58187024    26.089655 
+    4600   0.81294948    2.2274108   -5.5642678    34.469014  0.033774986    25.869616   0.14951307    25.870048 
+    4650   0.80890532    2.1556346   -5.5622407    34.465277   0.67402048    25.413229  -0.56341819    25.419474 
+    4700   0.82070227    1.9852605    -5.583747    34.460206  0.052623237    26.158394  -0.44673492    26.162209 
+    4750   0.81451857    2.1097726   -5.5779782    34.451438   0.12221733    25.733718   -0.9911436    25.752798 
+    4800   0.81300453    2.0211325   -5.5790076    34.439504   0.34536082    26.358606   -1.7335167    26.415548 
+    4850   0.82035497    1.9489595   -5.5929886    34.424097   0.70899626    26.575865   -1.0191012    26.595397 
+    4900    0.8127066    2.1312269    -5.584271    34.405998  0.087959314    26.185217   -1.1329105    26.209713 
+    4950   0.81252621    2.1094866   -5.5866296    34.387869   0.79067667    26.564722   -1.8456354    26.628759 
+    5000   0.80575936    2.1875995    -5.579054    34.370679  0.031787364    26.027557   -2.2666774     26.12607 
+Loop time of 32.2397 on 1 procs for 5000 steps with 5120 atoms
+
+Performance: 53598.557 tau/day, 155.088 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 22.967     | 22.967     | 22.967     |   0.0 | 71.24
+Neigh   | 2.9914     | 2.9914     | 2.9914     |   0.0 |  9.28
+Comm    | 0.37485    | 0.37485    | 0.37485    |   0.0 |  1.16
+Output  | 0.064337   | 0.064337   | 0.064337   |   0.0 |  0.20
+Modify  | 5.7143     | 5.7143     | 5.7143     |   0.0 | 17.72
+Other   |            | 0.1281     |            |       |  0.40
+
+Nlocal:    5120 ave 5120 max 5120 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7962 ave 7962 max 7962 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    296101 ave 296101 max 296101 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 296101
+Ave neighs/atom = 57.8322
+Neighbor list builds = 283
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:32

examples/USER/misc/rhok/log.22Sep2017.pinning.g++.4

@@ -0,0 +1,186 @@
+LAMMPS (22 Sep 2017)
+  using 1 OpenMP thread(s) per MPI task
+units       lj
+dimension   3
+boundary    p p p
+atom_style  atomic
+
+# truncated and shifted LJ potential
+pair_style  lj/cut 2.5
+pair_modify shift yes
+read_data   data.halfhalf
+  orthogonal box = (0 0 0) to (12.8152 12.8152 34)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  5120 atoms
+  reading velocities ...
+  5120 velocities
+pair_coeff  1 1 1.0 1.0 2.5
+mass        1 1.0
+
+# simulation parameters
+neighbor	0.6 bin
+timestep	0.004
+run_style 	verlet
+
+velocity all create 0.8 1 mom yes rot yes
+fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0
+fix 100 all momentum 100 linear 1 1 1
+
+# harmonic rho_k bias-field
+#                 nx ny nz k     a
+fix bias all rhok 16 0  0  4.0   26.00
+
+# output                                U_bias rho_k_RE  rho_k_IM |rho_k|
+thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]
+thermo 50
+dump dumpXYZ all xyz 500 traj.xyz
+
+# NOTE: run reduced for demonstration purposes
+# run 50000
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.1
+  ghost atom cutoff = 3.1
+  binsize = 1.55, bins = 9 9 22
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.023 | 4.027 | 4.03 Mbytes
+Step Temp Pzz PotEng Lz f_bias f_bias[1] f_bias[2] f_bias[3] 
+       0          0.8    5.1872229   -4.8361269           34    152.02869    34.711006  -0.72709593     34.71862 
+      50    1.0819371    3.9250728   -5.2655842     34.02563   0.51385908    26.505979    0.2187864    26.506882 
+     100    1.1182271    3.5397251   -5.3331401    34.100753    2.1059904    27.025883  -0.12127124    27.026156 
+     150    1.1121434    3.7845571   -5.3440494    34.213993    1.7206575    26.894862   -1.3261751    26.927539 
+     200    1.1446439    3.4114364   -5.4199119    34.358914     2.383615    27.054401   -1.4211151    27.091699 
+     250    1.1115073    3.5603047   -5.3988013    34.517397   0.60819391     26.51404   -1.4089688     26.55145 
+     300    1.0828478    3.7411116   -5.3842818    34.673948   0.73987465    26.528178    -2.062382    26.608225 
+     350    1.0342597    3.9206217   -5.3384367    34.825105   0.99965014    26.657737   -1.6211152    26.706983 
+     400    1.0064356    3.9929044    -5.324003     34.97579   0.41927007    26.402623   -1.7087432    26.457859 
+     450   0.96799277    4.2764255   -5.2947175    35.133839   0.77739461    26.503753   -2.5217998    26.623456 
+     500   0.94691076    4.1007962   -5.2922124    35.301893   0.17015805    26.212252   -2.0421698    26.291683 
+     550   0.93675297    3.7404088   -5.3056917    35.474301   0.56247039    26.335926    -3.205722    26.530316 
+     600   0.92707577    3.5439822   -5.3176094    35.641282   0.04054693    25.679461   -3.0301039    25.857615 
+     650   0.91828226    3.1833648   -5.3278237    35.794766    0.8427054      26.4003   -3.6331211    26.649117 
+     700    0.9084826    2.8374306   -5.3327944    35.928138    1.5635222    26.605971   -3.8575939    26.884173 
+     750   0.91219559      2.46172   -5.3548299    36.039156    6.3772911    27.350725   -4.8971146    27.785678 
+     800   0.90000337    2.2187716   -5.3499181    36.126451    4.9080838    27.085156   -5.1291678    27.566538 
+     850    0.9003432    1.8634244   -5.3614648    36.189019 0.0081092188    25.497333   -5.4038153    26.063676 
+     900   0.89741573    1.5697398   -5.3660799    36.226074  0.011155479    25.312724   -6.2574069    26.074684 
+     950   0.88871454    1.4427205   -5.3604669    36.237407    0.3287078    25.659237    -6.232896    26.405406 
+    1000   0.88606353    1.3088636   -5.3626576    36.226015   0.30068168    24.554896   -7.2832017    25.612262 
+    1050   0.88527541    1.3194263   -5.3666773     36.19311   0.10646314    24.514921   -7.9419424     25.76928 
+    1100   0.87522001    1.2852124   -5.3556811    36.143056   0.13675329    24.865981    -8.446822    26.261489 
+    1150    0.8805978     1.246973   -5.3671716      36.0781 0.00043275463    24.187039   -9.4985495     25.98529 
+    1200   0.85711495     1.376588   -5.3346243    36.002427   0.47623639    23.691349   -9.4648541    25.512026 
+    1250   0.88116805    1.3562001   -5.3731036    35.919289   0.32797055    23.322103    -10.54448    25.595049 
+    1300   0.87178482    1.5046564   -5.3610798    35.831278   0.17704849    24.190231   -10.314689     26.29753 
+    1350   0.87022621    1.6830825   -5.3603618    35.743318 0.0052854997    23.731157   -10.747465    26.051408 
+    1400   0.89019669    1.6144812   -5.3921986    35.659687    1.4152796      22.8393   -10.551347    25.158787 
+    1450   0.88852819    1.7587964   -5.3918592    35.580319   0.63560961    23.599033      -12.195    26.563742 
+    1500   0.89029085    1.8772498   -5.3966098    35.509232   0.20895386    23.055083   -12.703366    26.323229 
+    1550   0.88639722    2.2284824   -5.3933288    35.449043   0.44413965    22.448774   -12.156068    25.528757 
+    1600   0.88816451    2.2167704   -5.3994757    35.401661   0.12210235    23.108351    -12.44643    26.247085 
+    1650   0.89154791    2.3397824   -5.4086923    35.365815    0.4820208    23.090699   -12.984179    26.490928 
+    1700   0.88518032    2.5351236   -5.4041601    35.343757  0.080806002    22.749825    -12.99762    26.201005 
+    1750   0.86848721    2.5527491   -5.3851928    35.336433  0.045102165    22.357111   -13.564328     26.15017 
+    1800   0.88501061    2.5215825   -5.4169341    35.340849   0.27488483    22.086584   -14.408273    26.370732 
+    1850    0.8716061    2.5809558   -5.4045854    35.355038  0.042909785    21.270956   -14.695278    25.853525 
+    1900   0.85672517    2.4836326   -5.3902797    35.375469   0.72877764    21.639909   -15.474764    26.603646 
+    1950   0.85133731    2.3141629   -5.3902573    35.398523 0.0016908803    21.106617   -15.132733    25.970924 
+    2000   0.86152109    2.1562002   -5.4132601    35.419851     0.371016    21.325237   -15.614625    26.430706 
+    2050   0.86243551     2.019931   -5.4220349    35.436069  0.017935421      20.4131   -16.255418    26.094698 
+    2100   0.87417672    1.8083823   -5.4464117    35.445091   0.18429432     19.75625   -17.365705    26.303558 
+    2150   0.85872128    1.7608768   -5.4293103     35.44341   0.91209166    20.149648   -17.480387    26.675312 
+    2200   0.86615373    1.8372778   -5.4458315    35.430616   0.10151993    18.559234   -17.885469      25.7747 
+    2250   0.85053605    1.7198437   -5.4272104    35.408688   0.96154548    17.200861   -18.562206    25.306622 
+    2300   0.85400281    1.7939644   -5.4364682    35.377708   0.12283263    18.759325   -18.358539    26.247823 
+    2350   0.85495278    1.5856029   -5.4417321    35.337987   0.20564329    18.967923   -18.248149    26.320658 
+    2400   0.84606771    1.7782708   -5.4315646    35.287411   0.10063977    19.185527   -17.878215    26.224321 
+    2450   0.85210051    1.8190391   -5.4432116    35.232321   0.69988647    19.268861   -18.325448     26.59156 
+    2500   0.85304715    1.7466204   -5.4470889    35.175245 0.0048314937     18.09176    -18.74157     26.04915 
+    2550   0.85401123    1.8601945   -5.4509309    35.115748   0.99467901    17.170045   -18.574587    25.294777 
+    2600   0.85778606     1.974012   -5.4586742    35.058013 0.0026599702    17.438966   -19.333395    26.036469 
+    2650    0.8521239    2.0606329   -5.4526006    35.003616  0.091056354     17.16363   -19.244738    25.786627 
+    2700   0.85918482    2.0766792   -5.4658947    34.954171   0.89590606     15.77108   -19.822153    25.330707 
+    2750   0.85786577     2.225549   -5.4667773    34.911468   0.26577575    15.769018   -21.128817    26.364538 
+    2800   0.86764664    2.2325018   -5.4849414    34.877604   0.47167555    14.950515   -20.675229    25.514369 
+    2850   0.85209564    2.3434319    -5.465734    34.852715    2.7350296     13.51553   -20.829996    24.830592 
+    2900   0.85757283    2.3512971   -5.4786051    34.836138   0.14816492     14.06033   -21.545946    25.727819 
+    2950   0.86098926    2.3480431   -5.4890615    34.826408   0.26401534    13.381395   -22.714827    26.363329 
+    3000   0.85413421    2.3243973   -5.4844129    34.823242  0.024244334    12.739486   -22.538687    25.889899 
+    3050   0.85015323    2.5479266   -5.4844303    34.825228    0.4463147    12.990582   -21.975063    25.527605 
+    3100    0.8530523    2.3643505    -5.495343    34.834883   0.12144265    12.844293   -22.321989    25.753583 
+    3150   0.85098478    2.2521299   -5.4990526    34.848419   0.33194916    12.747856   -23.126671      26.4074 
+    3200   0.84391449    2.2650057    -5.495222    34.862626  0.031888328    12.788845   -22.782174     26.12627 
+    3250   0.84807155    2.1715388   -5.5080873    34.877548  0.082426694    13.316219    -22.09441    25.796989 
+    3300   0.83028242     2.242889   -5.4878846     34.89175    1.1334975    14.326678   -22.593363    26.752827 
+    3350   0.82924001    2.0324002   -5.4924558    34.903232   0.35473989    14.354166   -22.181868    26.421153 
+    3400   0.83032841    2.0003371   -5.4997142    34.908733  0.041677437    14.528378   -21.735998    26.144356 
+    3450   0.82908891    1.8683902   -5.5029185    34.907936   0.02365857    15.069507   -21.053887    25.891237 
+    3500   0.82842914    1.9165344   -5.5064218    34.898681   0.17663531     15.27043   -20.674834    25.702817 
+    3550   0.82735822      1.98221   -5.5088197     34.88272    1.5607134    14.915228   -20.208431    25.116622 
+    3600   0.82642915    1.8422766   -5.5110752      34.8611    1.1861112    15.312314   -20.051953    25.229899 
+    3650   0.82556781    1.9351408   -5.5130349    34.833406     1.018872    16.152478   -19.454871    25.286252 
+    3700   0.82360651    1.9791184   -5.5128431    34.802021   0.14080727    16.907104   -19.401616    25.734663 
+    3750   0.83017793    1.9855734   -5.5253254    34.768644   0.15311334    16.969506   -19.331958    25.723311 
+    3800   0.82362926    2.1029656   -5.5179624    34.734178   0.10807487    17.892584   -18.542426     25.76754 
+    3850   0.82313508    2.0781681   -5.5196175     34.70093   0.13343085    19.072706    -17.28778    25.741707 
+    3900   0.83643385    2.0570262   -5.5421224    34.669761 0.00022792038    19.551677     -17.1548    26.010675 
+    3950   0.82346174    2.0842322   -5.5252757    34.640849 0.0093759386    20.892792   -15.590263    26.068469 
+    4000   0.83485868    2.1196669   -5.5451736    34.612396   0.31198053    21.630258   -15.126984    26.394956 
+    4050   0.82729429    2.2033274   -5.5365945    34.585721   0.53752252    21.283533   -14.011497    25.481578 
+    4100   0.82040242    2.1757309   -5.5292269    34.562271   0.36031984    22.047609   -12.961927    25.575548 
+    4150   0.81932521     2.285666   -5.5307807    34.542102   0.84343149    22.486289    -11.70555    25.350604 
+    4200   0.83819319     2.231174   -5.5625532    34.526447   0.47190752    23.311855    -12.57189    26.485751 
+    4250   0.82542274    2.1874789   -5.5472057    34.513795   0.70518398    23.411553   -12.614639    26.593795 
+    4300   0.81971158     2.241167   -5.5424504    34.503969   0.26707612    23.089805   -12.727793    26.365429 
+    4350   0.83255377    2.1295532   -5.5657895    34.496326  0.072548591    23.003138    -12.52181    26.190458 
+    4400    0.8128474    2.3327845   -5.5402264    34.490126 0.0013023434    23.020811   -12.029795    25.974482 
+    4450   0.82013491    2.3069915   -5.5554953    34.488039  0.041123896    23.632908   -11.178674    26.143394 
+    4500   0.81411544    2.2247193   -5.5509183    34.488014   0.54440601    23.010678   -10.938506    25.478269 
+    4550   0.82814624    2.1142779   -5.5763482    34.487885    0.1518945    23.696817   -11.351972    26.275585 
+    4600   0.82929492     2.090881   -5.5823492    34.486698 0.0045520899    23.538527   -10.929741    25.952292 
+    4650   0.81061417    1.9818043   -5.5584018    34.484038  0.012526806    23.993543   -10.219174    26.079142 
+    4700   0.81816105    1.9605811   -5.5735005    34.476764    1.2079835    25.151166   -9.1888856    26.777169 
+    4750   0.81657042    2.0064313   -5.5744795    34.465784    1.2045017    25.487486   -8.2063886    26.776048 
+    4800   0.81789335    2.0838696   -5.5796632    34.451996   0.27642542    24.647157    -7.023095     25.62823 
+    4850   0.80649339    1.9892413   -5.5654796    34.436067  0.024697945     25.09823   -6.3492244    25.888874 
+    4900   0.81673441    2.0125635   -5.5835037    34.416236 0.0011188576    25.446818   -5.2182483    25.976348 
+    4950   0.82250033    1.9770391   -5.5946082    34.394723   0.72696707     26.37002   -3.5122842    26.602896 
+    5000   0.80762758     2.075517   -5.5746076    34.371696   0.12796344    26.102184   -2.8094827    26.252946 
+Loop time of 10.3394 on 4 procs for 5000 steps with 5120 atoms
+
+Performance: 167127.370 tau/day, 483.586 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.029      | 6.0128     | 7.1918     |  35.0 | 58.15
+Neigh   | 0.65673    | 0.75825    | 0.88597    |  10.3 |  7.33
+Comm    | 0.43982    | 1.5284     | 2.4112     |  60.5 | 14.78
+Output  | 0.022835   | 0.023039   | 0.023453   |   0.2 |  0.22
+Modify  | 1.7294     | 1.9472     | 2.5687     |  25.7 | 18.83
+Other   |            | 0.06978    |            |       |  0.67
+
+Nlocal:    1280 ave 1404 max 1214 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost:    3521.25 ave 3581 max 3426 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Neighs:    73872.2 ave 87973 max 64161 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 295489
+Ave neighs/atom = 57.7127
+Neighbor list builds = 278
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:10

examples/USER/misc/rhok/log.22Sep2017.setup.g++.1

@@ -0,0 +1,141 @@
+LAMMPS (22 Sep 2017)
+  using 1 OpenMP thread(s) per MPI task
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+
+# fcc lattice
+lattice	fcc 0.9731
+Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
+region my_box block 0 8.0   0 8.0   0 20.0
+create_box 1 my_box
+Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
+  1 by 1 by 1 MPI processor grid
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+Created 5120 atoms
+pair_coeff 1 1 1.0 1.0 2.5
+mass 1 1.0
+change_box all z final 0.0 34 remap units box
+  orthogonal box = (0 0 0) to (12.8152 12.8152 34)
+
+# select particles in one side of the elongated box
+region left plane 0 0 10 0 0 1
+group left region left
+2688 atoms in group left
+
+velocity left create 6.0 1 mom yes rot yes
+
+# simulation parameters
+neighbor	0.6 bin
+timestep	0.004
+run_style 	verlet
+fix ensemble left nve     # Note: only move particle in left-hand side
+fix langevin left langevin 3.0 0.8 100.0 2017
+
+# outout
+thermo_style custom step temp pzz pe lz
+thermo 100
+# dump dumpXYZ all xyz 100 traj.xyz
+
+# run reduced for demonstration purposes
+# run 10000
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.1
+  ghost atom cutoff = 3.1
+  binsize = 1.55, bins = 9 9 22
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.524 | 4.524 | 4.524 Mbytes
+Step Temp Pzz PotEng Lz 
+       0    3.1494433   -3.4735106   -6.8707307           34 
+     100    1.7727555    6.5330255   -4.8035477           34 
+     200    1.7462368    7.0070325   -4.7646426           34 
+     300    1.7564888    6.6190123   -4.7894637           34 
+     400    1.7641186     6.609684   -4.8064772           34 
+     500    1.7383511    6.7304936   -4.7708095           34 
+     600     1.731708    6.8574656   -4.7612918           34 
+     700    1.7332167    6.6530919   -4.7670014           34 
+     800    1.7487537    6.5644963   -4.7907458           34 
+     900    1.7353648    6.7115188   -4.7772149           34 
+    1000     1.728878    6.4175719   -4.7797216           34 
+    1100    1.7471488    6.5346083    -4.813376           34 
+    1200    1.7188149    6.2502104   -4.7822235           34 
+    1300    1.7151194     6.792534   -4.7781701           34 
+    1400    1.7406603    6.6639592   -4.8170174           34 
+    1500    1.7090537    6.4677579    -4.770701           34 
+    1600    1.7014954    6.2853535   -4.7679742           34 
+    1700    1.7064354    6.4352857   -4.7812978           34 
+    1800    1.7169971    6.5808758    -4.799426           34 
+    1900    1.6822712    6.3746758   -4.7522464           34 
+    2000    1.7126546     6.534969   -4.8091595           34 
+    2100    1.7086108    6.4679932   -4.8146664           34 
+    2200    1.6974952    6.3802129   -4.8052505           34 
+    2300    1.6868035    6.4009243   -4.7935769           34 
+    2400    1.7107125    6.2318869   -4.8358765           34 
+    2500     1.660241    6.4891487   -4.7661183           34 
+    2600    1.6801816    6.1988356   -4.8024291           34 
+    2700    1.6940298    6.1328187   -4.8290053           34 
+    2800    1.6755061    6.4150693   -4.8145473           34 
+    2900    1.6749928    6.4248792   -4.8213509           34 
+    3000    1.6310737    6.6491291   -4.7673027           34 
+    3100    1.6559915    6.2726719   -4.8109181           34 
+    3200    1.6574579    5.7132029   -4.8189484           34 
+    3300    1.6816136    5.7697439   -4.8652811           34 
+    3400    1.6489483    6.4463349   -4.8247812           34 
+    3500    1.6557974    5.9763333   -4.8383712           34 
+    3600    1.6215459    6.2806534   -4.7954657           34 
+    3700    1.6484987    6.0671609   -4.8470777           34 
+    3800    1.6473922    5.8688108   -4.8555351           34 
+    3900    1.6435957     5.930425   -4.8562076           34 
+    4000    1.6514434    6.1962122    -4.872998           34 
+    4100    1.6138337    6.4808124   -4.8219373           34 
+    4200    1.6215239    5.9467966   -4.8412146           34 
+    4300    1.6129295    5.9377323   -4.8414596           34 
+    4400    1.6020549    6.1104301   -4.8395939           34 
+    4500    1.6047738    6.0816222   -4.8538151           34 
+    4600    1.6053565     6.183466   -4.8686817           34 
+    4700    1.6088152    5.7416542    -4.894114           34 
+    4800    1.5954309     5.694319   -4.8840198           34 
+    4900    1.5582564    6.1199614   -4.8429998           34 
+    5000    1.5786672    5.8813574   -4.8907344           34 
+Loop time of 28.3867 on 1 procs for 5000 steps with 5120 atoms
+
+Performance: 60873.483 tau/day, 176.139 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 22.269     | 22.269     | 22.269     |   0.0 | 78.45
+Neigh   | 4.7222     | 4.7222     | 4.7222     |   0.0 | 16.64
+Comm    | 0.40821    | 0.40821    | 0.40821    |   0.0 |  1.44
+Output  | 0.0042329  | 0.0042329  | 0.0042329  |   0.0 |  0.01
+Modify  | 0.88231    | 0.88231    | 0.88231    |   0.0 |  3.11
+Other   |            | 0.1005     |            |       |  0.35
+
+Nlocal:    5120 ave 5120 max 5120 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7768 ave 7768 max 7768 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    297167 ave 297167 max 297167 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 297167
+Ave neighs/atom = 58.0404
+Neighbor list builds = 474
+Dangerous builds = 246
+write_data data.halfhalf
+Total wall time: 0:00:28

examples/USER/misc/rhok/log.22Sep2017.setup.g++.4

@@ -0,0 +1,141 @@
+LAMMPS (22 Sep 2017)
+  using 1 OpenMP thread(s) per MPI task
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+
+# fcc lattice
+lattice	fcc 0.9731
+Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
+region my_box block 0 8.0   0 8.0   0 20.0
+create_box 1 my_box
+Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
+  1 by 1 by 4 MPI processor grid
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+Created 5120 atoms
+pair_coeff 1 1 1.0 1.0 2.5
+mass 1 1.0
+change_box all z final 0.0 34 remap units box
+  orthogonal box = (0 0 0) to (12.8152 12.8152 34)
+
+# select particles in one side of the elongated box
+region left plane 0 0 10 0 0 1
+group left region left
+2688 atoms in group left
+
+velocity left create 6.0 1 mom yes rot yes
+
+# simulation parameters
+neighbor	0.6 bin
+timestep	0.004
+run_style 	verlet
+fix ensemble left nve     # Note: only move particle in left-hand side
+fix langevin left langevin 3.0 0.8 100.0 2017
+
+# outout
+thermo_style custom step temp pzz pe lz
+thermo 100
+# dump dumpXYZ all xyz 100 traj.xyz
+
+# run reduced for demonstration purposes
+# run 10000
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.1
+  ghost atom cutoff = 3.1
+  binsize = 1.55, bins = 9 9 22
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.23 | 3.23 | 3.23 Mbytes
+Step Temp Pzz PotEng Lz 
+       0    3.1494433   -3.4735106   -6.8707307           34 
+     100    1.7914373    6.4805818   -4.8420353           34 
+     200     1.740256    6.6108149   -4.7672571           34 
+     300    1.7663827    6.5188941   -4.8103672           34 
+     400    1.7440644    6.5156543   -4.7769467           34 
+     500    1.7471724    6.5208992   -4.7843928           34 
+     600    1.7320106    6.6557835   -4.7654637           34 
+     700    1.6839043    6.7689759   -4.7045352           34 
+     800    1.7216746      6.66436   -4.7601673           34 
+     900    1.7342542    6.3242367   -4.7790803           34 
+    1000    1.7338566    6.5803438   -4.7854529           34 
+    1100    1.7328856    6.3846366   -4.7902625           34 
+    1200    1.7546906    6.5048137   -4.8213443           34 
+    1300    1.7163891    6.3903221   -4.7665145           34 
+    1400    1.7011627    6.5782672   -4.7517875           34 
+    1500    1.7105234    6.5811813   -4.7677748           34 
+    1600    1.7334403    6.5032837   -4.8067749           34 
+    1700    1.7252102    6.5443871   -4.8058994           34 
+    1800     1.721958    6.3378188   -4.8150073           34 
+    1900    1.6797892    6.6780506   -4.7538618           34 
+    2000    1.7001774    6.3578192   -4.7894018           34 
+    2100    1.7127784    6.3219105   -4.8161059           34 
+    2200     1.696825     6.536793   -4.7946902           34 
+    2300    1.6704578    6.7186933   -4.7609628           34 
+    2400    1.6772498    6.3432817   -4.7778471           34 
+    2500    1.7073862    6.2153226   -4.8299181           34 
+    2600    1.6951557    6.4397257   -4.8156787           34 
+    2700    1.6845984    6.0123544   -4.8136864           34 
+    2800    1.6550565    6.2489392   -4.7829639           34 
+    2900    1.6892315     6.158499   -4.8423004           34 
+    3000    1.6814436      6.07976   -4.8400696           34 
+    3100    1.6387025     6.330166   -4.7878978           34 
+    3200    1.6747855    6.0767043   -4.8481995           34 
+    3300    1.6508768    6.2749233   -4.8181888           34 
+    3400    1.6426364    6.3934935   -4.8223824           34 
+    3500    1.6576512    6.0638185   -4.8559078           34 
+    3600    1.6444173    6.1376573   -4.8463113           34 
+    3700    1.6480039    5.9943705   -4.8601776           34 
+    3800    1.6467212    6.0556591   -4.8722719           34 
+    3900    1.6271804     6.116738   -4.8547278           34 
+    4000    1.6158134    5.9089534   -4.8477829           34 
+    4100    1.6388157    5.9890465   -4.8920284           34 
+    4200    1.6182368    6.0639887   -4.8724963           34 
+    4300     1.647633    5.6333906   -4.9267536           34 
+    4400    1.5856411    6.2675475   -4.8471239           34 
+    4500    1.5773417    6.1789163   -4.8469057           34 
+    4600    1.6181445    5.7988068    -4.922419           34 
+    4700    1.5876712    5.7398111   -4.8853849           34 
+    4800    1.5708353    6.2204997   -4.8718872           34 
+    4900    1.5514708    5.9782256   -4.8523812           34 
+    5000     1.553347    5.9286523     -4.86582           34 
+Loop time of 8.10259 on 4 procs for 5000 steps with 5120 atoms
+
+Performance: 213265.164 tau/day, 617.087 timesteps/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.2964     | 5.6236     | 5.8982     |   9.0 | 69.40
+Neigh   | 1.0562     | 1.1907     | 1.3257     |   8.7 | 14.70
+Comm    | 0.43963    | 0.98786    | 1.5968     |  42.5 | 12.19
+Output  | 0.0023124  | 0.004741   | 0.0090873  |   4.0 |  0.06
+Modify  | 0.018652   | 0.22213    | 0.39884    |  36.4 |  2.74
+Other   |            | 0.07357    |            |       |  0.91
+
+Nlocal:    1280 ave 1337 max 1211 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Nghost:    3416.25 ave 3549 max 3297 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:    74269.8 ave 77932 max 69612 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+
+Total # of neighbors = 297079
+Ave neighs/atom = 58.0232
+Neighbor list builds = 474
+Dangerous builds = 247
+write_data data.halfhalf
+Total wall time: 0:00:08

examples/USER/uef/README

@@ -0,0 +1,19 @@
+This directory contains two short example scripts for the USER-UEF
+package.
+
+
+nvt_uniaxial:
+  A simulation of a WCA fluid under constant volume uniaxial strain
+  with stretching in the z direction, compression in the x and y
+  directions.The xx, yy and zz components of the pressure tensor are 
+  written to the log file. The simulation conditions are the same 
+  used in the paper by Thomas Hunt [http://arxiv.org/abs/1310.3905]
+  and should yield an zz pressure near 5 and xx/yy pressures near 10.
+
+npt_biaxial:
+  A simulation of a WCA fluid under stress-controlled biaxial strain 
+  with stretching in the x and y directions, compression in the z 
+  direction. The zz stress is controlled using the ext keyword in fix
+  npt/uef. The xx yy and zz components of the pressure tensor are 
+  written to the log file. The simulations conditions should yield 
+  xx/yy pressures near 5 and zz pressure near 10

examples/USER/uef/npt_biaxial/in.npt_biaxial

@@ -0,0 +1,31 @@
+# biaxial NPT deformation of WCA fluid
+
+units		lj
+atom_style	atomic
+
+
+pair_style	lj/cut 1.122562
+read_data       data.wca
+pair_coeff	1 1 1.0 1.0
+pair_modify     shift yes
+
+neighbor	0.5 bin
+neigh_modify	delay 0
+
+change_box      all triclinic
+
+# these commads show the different methods that may be used to impose
+# a constant stress through isotropic or anisotropic coupling
+fix		1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z
+#fix		1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5  erate 0.5 0.5 ext xyz
+
+fix             2 all momentum 100 linear 1 1 1
+
+#dump		1 all atom 25 dump.lammpstrj
+
+#dump		2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
+
+thermo_style    custom step c_1_press[1] c_1_press[2] c_1_press[3]
+
+thermo		50
+run		10000

examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1

@@ -0,0 +1,284 @@
+LAMMPS (22 Sep 2017)
+# biaxial NPT deformation of WCA fluid
+
+units		lj
+atom_style	atomic
+
+
+pair_style	lj/cut 1.122562
+read_data       data.wca
+  orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  500 atoms
+  reading velocities ...
+  500 velocities
+pair_coeff	1 1 1.0 1.0
+pair_modify     shift yes
+
+neighbor	0.5 bin
+neigh_modify	delay 0
+
+change_box      all triclinic
+  triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0)
+
+# these commads show the different methods that may be used to impose
+# a constant stress through isotropic or anisotropic coupling
+fix		1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z
+#fix		1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5  erate 0.5 0.5 ext xyz
+
+fix             2 all momentum 100 linear 1 1 1
+
+#dump		1 all atom 25 dump.lammpstrj
+
+#dump		2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
+
+thermo_style    custom step c_1_press[1] c_1_press[2] c_1_press[3]
+
+thermo		50
+run		10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.62256
+  ghost atom cutoff = 1.62256
+  binsize = 0.811281, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton/tri
+      stencil: half/bin/3d/newton/tri
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes
+Step c_1_press[1] c_1_press[2] c_1_press[3] 
+       0    6.3937851    7.0436438    6.4461087 
+      50    7.9020345     7.303289    14.733929 
+     100    8.3214325     8.385843    13.166247 
+     150    5.7168419    5.6083988    9.7224198 
+     200    3.8875348    4.0840705    7.9912973 
+     250    4.2933724    4.2410519    7.7200953 
+     300    4.5452314    4.2434949    8.6709832 
+     350     5.446489    5.6166962    11.300536 
+     400    6.0682558    5.7787878    12.106852 
+     450    5.3884296    5.5066688    9.9100012 
+     500    4.8046418    4.7115986    9.9769201 
+     550    4.9043933    4.6240966     9.319336 
+     600    4.6843238    4.9571246    9.5325487 
+     650    5.1952989     5.195648    9.6187047 
+     700    5.4163364    5.2938289    10.136655 
+     750    5.6723178    5.0670261    11.415221 
+     800    5.9379901    5.6402916    10.815209 
+     850    5.0695389    5.3021432    10.742859 
+     900    4.6498962    4.7111912    9.8453523 
+     950    4.4811641     5.170132     9.421765 
+    1000    4.7501483    4.2420772    9.3510803 
+    1050    4.5973379    5.2046799    9.8632975 
+    1100    4.7879562    4.9051316    9.8658626 
+    1150    5.0528771    5.5048545    10.110913 
+    1200    4.9926563    5.2482081    9.9610863 
+    1250    4.8476232    4.8498859    9.5752989 
+    1300    5.2932038    5.0594534    10.869545 
+    1350    5.4720421    5.0830442     10.69386 
+    1400    4.8175566    4.9863651    10.041898 
+    1450    4.6307145    4.5615459     9.231299 
+    1500    5.0296259    4.5433558    8.7180513 
+    1550    4.8708444    5.1601014    10.256791 
+    1600    5.5098593     5.316773    10.224386 
+    1650    5.5055907    5.0516814    10.272037 
+    1700    4.6965552    5.2436628    9.8272905 
+    1750    5.0212307     4.740601    8.9738802 
+    1800    4.7756351     5.199734    9.9929449 
+    1850    4.7107092     5.177203    10.580427 
+    1900    5.0935608    4.5286844    9.3036832 
+    1950    4.8035855     4.894359    9.4423987 
+    2000    4.5643937    4.7480477    9.4384251 
+    2050    4.9314701     4.990414    10.151815 
+    2100    5.9828824    5.8188026    12.262691 
+    2150    5.5337303    5.4598468    10.136112 
+    2200     4.892172    4.8699674    9.1629905 
+    2250    4.5680591    4.5740533    9.5633545 
+    2300    5.0023535    4.3948659    8.9645774 
+    2350    5.2533056    4.9803884    10.255653 
+    2400    5.3330196    5.3888322    10.021617 
+    2450    5.2095527    4.8765336    10.135381 
+    2500     5.221153    5.2974568      10.2493 
+    2550     5.385331    5.0801192    10.490479 
+    2600    5.3274988    5.0253548    10.147587 
+    2650     4.718677    5.2710337    9.7549521 
+    2700    4.5811521    4.6083971    8.1923164 
+    2750    4.4743752    4.3319737    8.8690805 
+    2800    5.0215013    5.2262961    9.8627954 
+    2850    6.1005107    5.5994942    11.170661 
+    2900    5.9673524     5.362124    10.401699 
+    2950    5.5400849    5.7523993    10.292536 
+    3000    4.9202636    5.1210431    10.125839 
+    3050    4.5286487    5.3586164    9.8634322 
+    3100    4.5719961    5.1615414    9.8027972 
+    3150    5.4091919    4.8581943      9.96938 
+    3200     5.522125    5.3564838    9.7638407 
+    3250    4.9019062    5.2514758    9.2993079 
+    3300    5.2375918    5.1439012    9.4313575 
+    3350     4.750235    4.8692016     10.54193 
+    3400    5.5793211    5.4184157    11.021389 
+    3450    4.9022614    5.3166498    9.4629659 
+    3500    4.6348617    4.4650979    9.0665548 
+    3550    4.7922405    4.8961269    10.255446 
+    3600    4.8914457    5.1158894    9.4736084 
+    3650     5.062771    4.6725475    10.263484 
+    3700    5.4842823    5.7793971    10.342915 
+    3750    5.3136012     5.063065    10.398307 
+    3800    4.9372149    4.9270414    9.5304748 
+    3850    5.2144752    5.1716455    9.7575725 
+    3900    5.0892665    5.1697057     9.918052 
+    3950    5.1124507     5.354702     9.791366 
+    4000    5.1255084    5.1143653    10.913101 
+    4050    5.1891698    4.9913681    9.6871728 
+    4100    4.7663368    4.2435014    8.3815668 
+    4150    4.8060033    4.3415868    9.6553386 
+    4200    4.8548303    4.8006768    9.5995801 
+    4250    5.0976366    5.2683175    10.386444 
+    4300    5.8921937    5.5134696    10.788143 
+    4350    5.8323871    5.5255869    11.199128 
+    4400    5.2464655    5.0005905    10.311055 
+    4450    4.9264849    5.2499854     10.26702 
+    4500    4.4431895     4.536981    8.7489096 
+    4550    4.5180914    4.2080277    8.6525529 
+    4600    5.1782188    5.1224059    10.683341 
+    4650    5.4156233    4.8714464    10.473939 
+    4700    5.3107669     5.224614    10.569391 
+    4750    4.9538022    5.2509475    10.288918 
+    4800    4.6976945    4.8107142    9.8299772 
+    4850    5.1227936    5.0737571    10.440452 
+    4900    4.7580514    4.6375995    9.1971008 
+    4950    5.0647601    4.6470735     9.583131 
+    5000     5.196231    5.7531491    10.409807 
+    5050    5.6691323    5.7163652    12.335701 
+    5100    5.3603738    5.4887106    10.961712 
+    5150     4.455028    4.6494465    9.8096968 
+    5200    4.7596912    4.4804896    9.3762885 
+    5250    5.3144927    5.0113772     9.553101 
+    5300    5.3445266    4.8262035    9.1220802 
+    5350    5.1540657    5.5982676    10.765178 
+    5400    5.1773418    5.2684381    10.452351 
+    5450    4.8946859    5.3283747    9.8015564 
+    5500    5.2009608    4.7183522    9.4558009 
+    5550    5.4158589    5.5005458    10.539505 
+    5600    4.7196831    5.4181991    9.6439249 
+    5650    4.8333571    4.8601728    8.9350189 
+    5700    5.4395698    4.9730096    10.669681 
+    5750    5.2947443    5.6973259    10.020539 
+    5800    5.4391993    5.5255143    10.264969 
+    5850    4.9921388    5.2643827    10.217028 
+    5900    5.0048643    4.7952641    8.9718929 
+    5950    5.1843818    4.5987295    9.6858944 
+    6000    5.0343993     4.946933    9.7436708 
+    6050    4.6202714    5.3502658    10.752915 
+    6100    5.6914422    5.3621964    10.281827 
+    6150    5.1928763    5.9652686    10.923881 
+    6200    5.0030409    5.2013891    10.056308 
+    6250    4.9699876    5.2363753    9.9964211 
+    6300    4.9129606    4.4558458    9.0419952 
+    6350    4.6623958    4.4078264     8.528649 
+    6400    4.9811441    5.1183207    10.261751 
+    6450    5.3644017    5.5153937    10.401295 
+    6500    5.6674981    5.7427566    11.928777 
+    6550    5.1622364    5.3212928    10.067198 
+    6600    4.5954278    5.1645397     10.16724 
+    6650    4.9192712    5.0413326      9.95656 
+    6700    4.6179845    4.5656214    9.3798952 
+    6750    4.7287495    4.5071148    8.7890116 
+    6800    4.8600442    4.8083512    10.245595 
+    6850    5.0515531    5.1609272    10.553855 
+    6900    5.1159742    5.1359869    10.594699 
+    6950    4.8908884    5.0592418    9.5698704 
+    7000    4.7654136    4.7530776    8.9439321 
+    7050     4.779293    4.7534957    9.7244349 
+    7100    5.2265831    5.6869073     10.32717 
+    7150    5.4019177      5.15174    10.457567 
+    7200    4.9817102    5.0596098    10.337574 
+    7250    5.1836654    5.6065238    10.723108 
+    7300    4.2916569     4.457143    8.5419099 
+    7350    4.3906104    4.5439294    9.0805415 
+    7400     4.998572    5.3386063    10.491418 
+    7450    5.1109022    5.0506801    10.636116 
+    7500    5.0248381     5.019932    10.217023 
+    7550    5.0109265    5.1438717    9.9032426 
+    7600    4.6628614    4.6204146    8.9459669 
+    7650    4.8930717    5.0650009    10.049331 
+    7700    4.9373454    5.6265835    10.210644 
+    7750    5.5001067    5.3133253    10.667995 
+    7800    5.0816102    5.0125753    10.591986 
+    7850    4.9638046    5.1969015    9.9728333 
+    7900    4.8438207    4.9217213    8.9978809 
+    7950    4.7318805    4.6248537    8.6806596 
+    8000    5.2808543    5.2892613    10.932535 
+    8050    5.9609722      5.87087     10.47602 
+    8100    5.2190231    5.6693244    11.244536 
+    8150    5.3481127    5.2849903    10.222845 
+    8200    4.7833053    4.7404657    9.2034474 
+    8250    4.5461994     4.510467    10.294452 
+    8300    4.6025175    4.8332817    8.7967546 
+    8350    5.0389897    5.6642908    10.243402 
+    8400    4.8414338    4.8925143    9.3653631 
+    8450    5.5087429    4.7830361    10.831666 
+    8500    5.2678146    5.1697789    9.9105782 
+    8550    5.1211843    4.9097801    9.4165956 
+    8600    5.8239149    5.0821022    10.803261 
+    8650    5.3620154    5.5831747     11.16202 
+    8700    5.1625813    4.8791404    10.537681 
+    8750    4.5622461    5.0157549    10.013227 
+    8800    4.4051517    5.0224553    9.6364273 
+    8850    4.1711629     4.635617    8.5470244 
+    8900    4.7049907    5.2458435    10.100728 
+    8950    4.8568883    5.2360772    9.2306469 
+    9000    5.0091899    5.2203574    10.718541 
+    9050    5.1037824    4.9022451     10.24271 
+    9100    5.0789015    4.9331454     9.173614 
+    9150    5.3865455    5.3427553     11.40199 
+    9200    5.5089482    5.9423232    10.976063 
+    9250    5.1353552    5.0650262    10.040607 
+    9300    4.6761948    4.9155175    9.6413722 
+    9350    4.4780834    4.3934708    8.7049819 
+    9400    4.2561799    4.7906324     9.046134 
+    9450    5.6162819    5.2881846    9.9040868 
+    9500    5.7554547    5.6111262     10.23849 
+    9550    5.4230462    5.5656045    10.908006 
+    9600    5.5045685    4.9818892    9.8929535 
+    9650    5.0541481    5.0183351    9.5226021 
+    9700    4.9712829    5.2395398    9.9996693 
+    9750    5.0960017    5.4419775    10.914719 
+    9800    5.0790688    5.6378474     10.00789 
+    9850    4.9661747     5.114502    9.4585052 
+    9900    5.0133498    4.7456254    9.4572653 
+    9950    5.3318846    4.6643122    10.096292 
+   10000    5.2227687    4.8924305    9.5894615 
+Loop time of 4.78247 on 1 procs for 10000 steps with 500 atoms
+
+Performance: 903298.340 tau/day, 2090.968 timesteps/s
+99.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.73894    | 0.73894    | 0.73894    |   0.0 | 15.45
+Neigh   | 2.9092     | 2.9092     | 2.9092     |   0.0 | 60.83
+Comm    | 0.32306    | 0.32306    | 0.32306    |   0.0 |  6.76
+Output  | 0.003392   | 0.003392   | 0.003392   |   0.0 |  0.07
+Modify  | 0.6959     | 0.6959     | 0.6959     |   0.0 | 14.55
+Other   |            | 0.112      |            |       |  2.34
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    905 ave 905 max 905 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3340 ave 3340 max 3340 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3340
+Ave neighs/atom = 6.68
+Neighbor list builds = 4580
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04