Merge pull request #1687 from akohlmey/next_patch_release

Step version string for next patch release

bench/POTENTIALS/CH.airebo

@@ -0,0 +1 @@
+../../potentials/CH.airebo

bench/POTENTIALS/CdTe.bop.table

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+../../potentials/CdTe.bop.table

bench/POTENTIALS/Cu_u3.eam

@@ -1,305 +0,0 @@
-Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
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-  1.0802032746662471e-02  1.0602811831688208e-02  1.0407756070544782e-02  1.0216725810699157e-02  1.0029589433467268e-02
-  9.8462227798860602e-03  9.6665086187306404e-03  9.4903361536790021e-03  9.3176005668363371e-03  9.1482025960089031e-03
-  8.9820481433065535e-03  8.8190479128032462e-03  8.6591170751522117e-03  8.5021749571883021e-03  8.3481447546937537e-03
-  8.1969532666261724e-03  8.0485306492223962e-03  7.9028101885199598e-03  7.7597280899136256e-03  7.6192232834934315e-03
-  7.4812372439735375e-03  7.3457138241272979e-03  7.2125991007052359e-03  7.0818412319012813e-03  6.9533903254870300e-03
-  6.8271983168139705e-03  6.7032188559211503e-03  6.5814072030662141e-03  6.4617201320263939e-03  6.3441158405819764e-03
-  6.2285538676237207e-03  6.1149950163802147e-03  6.0034012832899109e-03  5.8937357920846312e-03  5.7859627326801166e-03
-  5.6800473044990030e-03  5.5759556638887986e-03  5.4736548753111791e-03  5.3731128660109428e-03  5.2742983838981461e-03
-  5.1771809583849582e-03  5.0817308639591330e-03  4.9879190862693046e-03  4.8957172905357560e-03  4.8050977921015592e-03
-  4.7160335289582467e-03  4.6284980360953021e-03  4.5424654215287241e-03  4.4579103438822931e-03  4.3748079913988880e-03
-  4.2931340622749670e-03  4.2128647462132407e-03  4.1339767071033873e-03  4.0564470667446839e-03  3.9802533895282599e-03
-  3.9053736680121076e-03  3.8317863093158128e-03  3.7594701222811860e-03  3.6884043053326127e-03  3.6185684349951674e-03
-  3.5499424550168301e-03  3.4825066660512660e-03  3.4162417158645347e-03  3.3511285900229004e-03  3.2871486030347646e-03
-  3.2242833899080170e-03  3.1625148980992668e-03  3.1018253798278661e-03  3.0421973847258310e-03  2.9836137528083811e-03
-  2.9260576077371064e-03  2.8695123503632708e-03  2.8139616525287708e-03  2.7593894511106498e-03  2.7057799422959966e-03
-  2.6531175760685227e-03  2.6013870509009052e-03  2.5505733086344240e-03  2.5006615295404683e-03  2.4516371275501436e-03
-  2.4034857456453340e-03  2.3561932514012535e-03  2.3097457326723414e-03  2.2641294934160616e-03  2.2193310496436136e-03
-  2.1753371254977782e-03  2.1321346494441173e-03  2.0897107505768314e-03  2.0480527550303662e-03  2.0071481824917164e-03
-  1.9669847428123305e-03  1.9275503327108034e-03  1.8888330325659355e-03  1.8508211032951805e-03  1.8135029833145980e-03
-  1.7768672855772646e-03  1.7409027946878666e-03  1.7055984640891586e-03  1.6709434133182904e-03  1.6369269253308227e-03
-  1.6035384438881917e-03  1.5707675710093030e-03  1.5386040644797400e-03  1.5070378354209296e-03  1.4760589459142243e-03
-  1.4456576066784674e-03  1.4158241748004133e-03  1.3865491515145517e-03  1.3578231800324136e-03  1.3296370434173130e-03
-  1.3019816625059188e-03  1.2748480938728074e-03  1.2482275278369870e-03  1.2221112865106742e-03  1.1964908218862064e-03
-  1.1713577139624703e-03  1.1467036689077198e-03  1.1225205172586891e-03  1.0988002121543120e-03  1.0755348276031765e-03
-  1.0527165567835728e-03  1.0303377103750150e-03  1.0083907149206553e-03  9.8686811121878604e-04  9.6576255274356815e-04
-  9.4506680409354657e-04  9.2477373946662708e-04  9.0487634116191706e-04  8.8536769810608137e-04  8.6624100440530968e-04
-  8.4748955791986991e-04  8.2910675886310736e-04  8.1108610842155551e-04  7.9342120739794852e-04  7.7610575487466887e-04
-  7.5913354689786591e-04  7.4249847518158968e-04  7.2619452583109687e-04  7.1021577808524222e-04  6.9455640307671332e-04
-  6.7921066261025093e-04  6.6417290795844214e-04  6.4943757867335500e-04  6.3499920141575628e-04  6.2085238879914031e-04
-  6.0699183824991856e-04  5.9341233088238896e-04  5.8010873038847818e-04  5.6707598194186137e-04  5.5430911111587280e-04
-  5.4180322281523891e-04  5.2955350022104025e-04  5.1755520374872563e-04  5.0580367001857793e-04  4.9429431083891986e-04
-  4.8302261220136561e-04  4.7198413328763435e-04  4.6117450548847222e-04  4.5058943143359842e-04  4.4022468403297037e-04
-  4.3007610552883886e-04  4.2013960655883260e-04  4.1041116522908330e-04  4.0088682619821882e-04  3.9156269977118005e-04
-  3.8243496100300207e-04  3.7349984881274514e-04  3.6475366510662147e-04  3.5619277391102898e-04  3.4781360051482253e-04
-  3.3961263062063513e-04  3.3158640950565685e-04  3.2373154119109092e-04  3.1604468762060252e-04  3.0852256784754707e-04
-  3.0116195723081836e-04  2.9395968663908575e-04  2.8691264166377101e-04  2.8001776184017647e-04  2.7327203987681688e-04
-  2.6667252089326854e-04  2.6021630166557681e-04  2.5390052988028163e-04  2.4772240339593181e-04  2.4167916951265550e-04
-  2.3576812424967210e-04  2.2998661163024531e-04  2.2433202297460642e-04  2.1880179620031078e-04  2.1339341513026532e-04
-  2.0810440880823181e-04  2.0293235082175821e-04  1.9787485863260665e-04  1.9292959291436311e-04  1.8809425689761319e-04
-  1.8336659572205580e-04  1.7874439579616125e-04  1.7422548416372047e-04  1.6980772787763936e-04  1.6548903338088530e-04
-  1.6126734589430591e-04  1.5714064881157744e-04  1.5310696310104604e-04  1.4916434671449329e-04  1.4531089400280153e-04
-  1.4154473513841234e-04  1.3786403554466153e-04  1.3426699533172857e-04  1.3075184873951283e-04  1.2731686358694039e-04
-  1.2396034072819674e-04  1.2068061351527565e-04  1.1747604726729168e-04  1.1434503874632306e-04  1.1128601563955686e-04
-  1.0829743604811193e-04  1.0537778798212988e-04  1.0252558886227753e-04  9.9739385027582898e-05  9.7017751249615057e-05
-  9.4359290252773662e-05  9.1762632240957511e-05  8.9226434430383569e-05  8.6749380588361721e-05  8.4330180578390864e-05
-  8.1967569911181246e-05  7.9660309301724484e-05  7.7407184232279429e-05  7.5207004521348451e-05  7.3058603898526649e-05
-  7.0960839585107720e-05  6.8912591880629977e-05  6.6912763755002085e-05  6.4960280446513426e-05  6.3054089065330086e-05
-  6.1193158202771814e-05  5.9376477546041213e-05  5.7603057498502742e-05  5.5871928805544500e-05  5.4182142185708361e-05
-  5.2532767967318744e-05  5.0922895730446966e-05  4.9351633954125953e-05  4.7818109668823321e-05  4.6321468114150300e-05
-  4.4860872401664663e-05  4.3435503182825573e-05  4.2044558321957873e-05  4.0687252574273750e-05  3.9362817268785450e-05
-  3.8070499996214428e-05  3.6809564301621984e-05  3.5579289382025496e-05  3.4378969788611451e-05  3.3207915133769052e-05
-  3.2065449802711312e-05  3.0950912669766876e-05  2.9863656819185611e-05  2.8803049270468119e-05  2.7768470708167169e-05
-  2.6759315216115260e-05  2.5774990015931323e-05  2.4814915209964844e-05  2.3878523528387922e-05  2.2965260080560611e-05
-  2.2074582110528148e-05  2.1205958756658535e-05  2.0358870815317476e-05  1.9532810508535560e-05  1.8727281255713447e-05
-  1.7941797449145505e-05  1.7175884233475961e-05  1.6429077288930018e-05  1.5700922618341645e-05  1.4990976337865471e-05
-  1.4298804471386687e-05  1.3623982748522034e-05  1.2966096406226424e-05  1.2324739993882115e-05  1.1699517181902770e-05
-  1.1090040573734860e-05  1.0495931521266495e-05  9.9168199435395021e-06  9.3523441487842465e-06  8.8021506596591475e-06
-  8.2658940417265321e-06  7.7432367350197678e-06  7.2338488887770244e-06  6.7374081991923703e-06  6.2535997501888662e-06
-  5.7821158571569505e-06  5.3226559136389283e-06  4.8749262408651290e-06  4.4386399401326240e-06  4.0135167480073166e-06
-  3.5992828942305738e-06  3.1956709623667747e-06  2.8024197531120341e-06  2.4192741502208947e-06  2.0459849890155880e-06
-  1.6823089274468580e-06  1.3280083196495871e-06  9.8285109196557868e-07  6.4661062138351467e-07  3.1906561636122974e-07
-  0.                      0.                      0.                      0.                      0.
-
-

bench/POTENTIALS/Cu_u3.eam

@@ -0,0 +1 @@
+../../potentials/Cu_u3.eam

bench/POTENTIALS/Ni.adp

@@ -0,0 +1 @@
+../../potentials/Ni.adp

cmake/CMakeLists.txt

@@ -37,7 +37,7 @@ include(PreventInSourceBuilds)
 
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
   #release comes with -O3 by default
-  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
+  set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
 endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
 string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
 
@@ -52,10 +52,17 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckCCompilerFlag)
 include(CheckIncludeFileCXX)
 
-if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
 endif()
 
+option(DISABLE_CXX11_REQUIREMENT "Disable check that requires C++11 for compiling LAMMPS" OFF)
+if(DISABLE_CXX11_REQUIREMENT)
+  add_definitions(-DLAMMPS_CXX98)
+else()
+  set(CMAKE_CXX_STANDARD 11)
+endif()
+
 # GNU compiler features
 if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
   option(ENABLE_COVERAGE "Enable code coverage" OFF)
@@ -133,6 +140,24 @@ foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
+######################################################
+# download and unpack support binaries for compilation
+# of windows binaries.
+######################################################
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
+  file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
+          EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
+  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+  if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
+    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
+  elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
+    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
+  endif()
+  set(OpenCL_INCLUDE_DIR "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
+endif()
+
+######################################################
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
@@ -148,6 +173,7 @@ if(PKG_USER-ADIOS)
 endif()
 
 # do MPI detection after language activation, if MPI for these language is required
+set(MPI_CXX_SKIP_MPICXX TRUE)
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 if(BUILD_MPI)
@@ -175,11 +201,13 @@ add_definitions(-DLAMMPS_${LAMMPS_SIZES})
 set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}")
 
 # posix_memalign is not available on Windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
+else()
   set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
-  if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
-    add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
-  endif()
+endif()
+if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
+  add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 endif()
 
 option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
@@ -219,8 +247,7 @@ if(BUILD_OMP)
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
 endif()
 
-
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -230,6 +257,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUI
     enable_language(Fortran)
     file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
     add_library(linalg STATIC ${LAPACK_SOURCES})
+    set(BLAS_LIBRARIES linalg)
     set(LAPACK_LIBRARIES linalg)
   else()
     list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
@@ -303,6 +331,7 @@ include(Packages/USER-QUIP)
 include(Packages/USER-QMMM)
 include(Packages/USER-VTK)
 include(Packages/KIM)
+include(Packages/LATTE)
 include(Packages/MESSAGE)
 include(Packages/MSCG)
 include(Packages/COMPRESS)
@@ -496,10 +525,43 @@ if(BUILD_LIB)
   if(LAMMPS_DEPS)
     add_dependencies(lammps ${LAMMPS_DEPS})
   endif()
+  set(LAMMPS_CXX_HEADERS
+    ${LAMMPS_SOURCE_DIR}/angle.h
+    ${LAMMPS_SOURCE_DIR}/atom.h
+    ${LAMMPS_SOURCE_DIR}/bond.h
+    ${LAMMPS_SOURCE_DIR}/citeme.h
+    ${LAMMPS_SOURCE_DIR}/comm.h
+    ${LAMMPS_SOURCE_DIR}/compute.h
+    ${LAMMPS_SOURCE_DIR}/dihedral.h
+    ${LAMMPS_SOURCE_DIR}/domain.h
+    ${LAMMPS_SOURCE_DIR}/error.h
+    ${LAMMPS_SOURCE_DIR}/fix.h
+    ${LAMMPS_SOURCE_DIR}/force.h
+    ${LAMMPS_SOURCE_DIR}/group.h
+    ${LAMMPS_SOURCE_DIR}/improper.h
+    ${LAMMPS_SOURCE_DIR}/input.h
+    ${LAMMPS_SOURCE_DIR}/kspace.h
+    ${LAMMPS_SOURCE_DIR}/lammps.h
+    ${LAMMPS_SOURCE_DIR}/lattice.h
+    ${LAMMPS_SOURCE_DIR}/lmppython.h
+    ${LAMMPS_SOURCE_DIR}/memory.h
+    ${LAMMPS_SOURCE_DIR}/modify.h
+    ${LAMMPS_SOURCE_DIR}/neighbor.h
+    ${LAMMPS_SOURCE_DIR}/neigh_list.h
+    ${LAMMPS_SOURCE_DIR}/output.h
+    ${LAMMPS_SOURCE_DIR}/pair.h
+    ${LAMMPS_SOURCE_DIR}/pointers.h
+    ${LAMMPS_SOURCE_DIR}/region.h
+    ${LAMMPS_SOURCE_DIR}/timer.h
+    ${LAMMPS_SOURCE_DIR}/universe.h
+    ${LAMMPS_SOURCE_DIR}/update.h
+    ${LAMMPS_SOURCE_DIR}/variable.h)
+
   set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
   set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
   install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
   install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
@@ -534,6 +596,7 @@ if(BUILD_TOOLS)
     enable_language(Fortran)
     add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
     target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+    install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
   endif()
 
   enable_language(C)
@@ -550,11 +613,11 @@ include(Documentation)
 ###############################################################################
 # Install potential and force field files in data directory
 ###############################################################################
-set(LAMMPS_INSTALL_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
-install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_POTENTIALS_DIR})
-
-set(LAMMPS_INSTALL_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files)
-install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files/ DESTINATION ${LAMMPS_INSTALL_FRC_FILES_DIR})
+set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)
+install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
+if(BUILD_TOOLS)
+  install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
+endif()
 
 configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
 configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
@@ -672,5 +735,10 @@ if(PKG_KOKKOS)
   message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
 endif()
 if(PKG_KSPACE)
-  message(STATUS "Using ${FFT} as FFT")
+  message(STATUS "Using ${FFT} as primary FFT library")
+  if(FFT_SINGLE)
+    message(STATUS "Using single precision FFTs")
+  else()
+    message(STATUS "Using double precision FFTs")
+  endif()
 endif()

cmake/Modules/FindKIM-API.cmake

@@ -37,6 +37,26 @@
 # KIM-API-CMAKE_Fortran_COMPILER
 #
 
+function(_KIMAPI_GET_VERSION _OUT_ver _version_hdr)
+  if(NOT EXISTS ${_version_hdr})
+    message(FATAL_ERROR "Header file ${_version_hdr} not found (check value of KIM-API_INCLUDE_DIR)")
+  endif()
+  foreach(_var KIM_VERSION_MAJOR KIM_VERSION_MINOR KIM_VERSION_PATCH)  
+    file(STRINGS ${_version_hdr} _contents REGEX "#define ${_var}[ \t]+")
+    if(_contents)
+      string(REGEX REPLACE ".*#define ${_var}[ \t]+([0-9]+).*" "\\1" _${_var} "${_contents}")
+      if(${_${_var}} STREQUAL "")
+        message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, got empty return!")
+      elseif(NOT ${_${_var}} MATCHES "^[0-9]+$")
+        message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, excepted a number but got ${_${_var}}!")
+      endif()
+    else()
+      message(FATAL_ERROR "No ${_var} line found in include file ${_version_hdr}")
+    endif()
+  endforeach()
+  set(${_OUT_ver} ${_KIM_VERSION_MAJOR}.${_KIM_VERSION_MINOR}.${_KIM_VERSION_PATCH} PARENT_SCOPE)
+endfunction()
+
 if(KIM-API_FIND_QUIETLY)
   set(REQ_OR_QUI "QUIET")
 else()
@@ -54,6 +74,12 @@ if(KIM-API_FOUND)
   pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
 endif()
 
+if(KIM-API_INCLUDEDIR)
+  _KIMAPI_GET_VERSION(KIM-API_VERSION ${KIM-API_INCLUDEDIR}/KIM_Version.h)
+else()
+  set(KIM-API_VERSION 0)
+endif()
+
 # handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
 # if all listed variables are TRUE
-find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)
+find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES VERSION_VAR KIM-API_VERSION)

cmake/Modules/Packages/KIM.cmake

@@ -1,4 +1,5 @@
 if(PKG_KIM)
+  set(KIM-API_MIN_VERSION 2.1)
   find_package(CURL)
   if(CURL_FOUND)
     include_directories(${CURL_INCLUDE_DIRS})
@@ -7,8 +8,18 @@ if(PKG_KIM)
   endif()
   find_package(KIM-API QUIET)
   if(KIM-API_FOUND)
-    set(DOWNLOAD_KIM_DEFAULT OFF)
+    if (KIM-API_VERSION VERSION_LESS ${KIM-API_MIN_VERSION})
+      if ("${DOWNLOAD_KIM}" STREQUAL "")
+        message(WARNING "Unsuitable KIM-API version \"${KIM-API_VERSION}\" found, but required is at least \"${KIM-API_MIN_VERSION}\".  Default behavior set to download and build our own.")
+      endif()
+      set(DOWNLOAD_KIM_DEFAULT ON)
+    else()
+      set(DOWNLOAD_KIM_DEFAULT OFF)
+    endif()
   else()
+    if ("${DOWNLOAD_KIM}" STREQUAL "")
+      message(WARNING "KIM-API package not found.  Default behavior set to download and build our own")
+    endif()
     set(DOWNLOAD_KIM_DEFAULT ON)
   endif()
   option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
@@ -17,12 +28,16 @@ if(PKG_KIM)
       message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
     endif()
     message(STATUS "KIM-API download requested - we will build our own")
-    enable_language(C)
-    enable_language(Fortran)
+    include(CheckLanguage)
     include(ExternalProject)
+    enable_language(C)
+    check_language(Fortran)
+    if(NOT CMAKE_Fortran_COMPILER)
+      message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
+    endif()
     ExternalProject_Add(kim_build
-      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
-      URL_MD5 537d9c0abd30f85b875ebb584f9143fa
+      URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
+      URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
       BINARY_DIR build
       CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
                  -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
@@ -35,7 +50,7 @@ if(PKG_KIM)
     set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
     list(APPEND LAMMPS_DEPS kim_build)
   else()
-    find_package(KIM-API REQUIRED)
+    find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED)
   endif()
   list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
   include_directories(${KIM-API_INCLUDE_DIRS})

cmake/Modules/Packages/KOKKOS.cmake

@@ -17,12 +17,15 @@ if(PKG_KOKKOS)
                          ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
                          ${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}/npair_halffull_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
 
@@ -38,6 +41,7 @@ if(PKG_KOKKOS)
   # register kokkos-only styles
   RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
   RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
 
   if(PKG_USER-DPD)
     get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)

cmake/Modules/Packages/KSPACE.cmake

@@ -1,5 +1,5 @@
 if(PKG_KSPACE)
-  option(FFT_SINGLE "Use single precision FFT instead of double" OFF)
+  option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
   set(FFTW "FFTW3")
   if(FFT_SINGLE)
     set(FFTW "FFTW3F")
@@ -7,26 +7,30 @@ if(PKG_KSPACE)
   endif()
   find_package(${FFTW} QUIET)
   if(${FFTW}_FOUND)
-    set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")
+    set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
   else()
     set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
   endif()
-  set(FFT_VALUES KISS ${FFTW} MKL)
+  set(FFT_VALUES KISS FFTW3 MKL)
   set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
   validate_option(FFT FFT_VALUES)
   string(TOUPPER ${FFT} FFT)
-  if(NOT FFT STREQUAL "KISS")
-    find_package(${FFT} REQUIRED)
-    if(NOT FFT STREQUAL "FFTW3F")
-      add_definitions(-DFFT_FFTW)
-    else()
-      add_definitions(-DFFT_${FFT})
-    endif()
-    include_directories(${${FFT}_INCLUDE_DIRS})
-    list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
+
+  if(FFT STREQUAL "FFTW3")
+    find_package(${FFTW} REQUIRED)
+    add_definitions(-DFFT_FFTW3)
+    include_directories(${${FFTW}_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
+  elseif(FFT STREQUAL "MKL")
+    find_package(MKL REQUIRED)
+    add_definitions(-DFFT_MKL)
+    include_directories(${MKL_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
   else()
+    # last option is KISSFFT
     add_definitions(-DFFT_KISS)
   endif()
+
   set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
   set(FFT_PACK_VALUES array pointer memcpy)
   set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -1,11 +1,23 @@
 if(PKG_USER-PLUMED)
-  find_package(GSL REQUIRED)
   set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
   set(PLUMED_MODE_VALUES static shared runtime)
   set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
   validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
   string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
 
+  set(PLUMED_LINK_LIBS "")
+  if(PLUMED_MODE STREQUAL "STATIC")
+    find_package(LAPACK REQUIRED)
+    find_package(BLAS REQUIRED)
+    find_package(GSL REQUIRED)
+    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
+    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})
+    find_package(ZLIB QUIET)
+    if(ZLIB_FOUND)
+      list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})
+    endif()
+  endif()
+
   find_package(PkgConfig QUIET)
   set(DOWNLOAD_PLUMED_DEFAULT ON)
   if(PKG_CONFIG_FOUND)
@@ -37,8 +49,8 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz
-      URL_MD5 c2a7b519e32197a120cdf47e0f194f81
+      URL https://github.com/plumed/plumed2/releases/download/v2.5.2/plumed-src-2.5.2.tgz
+      URL_MD5 bd2f18346c788eb54e1e52f4f6acf41a
       BUILD_IN_SOURCE 1
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                                ${CONFIGURE_REQUEST_PIC}
@@ -53,11 +65,11 @@ if(PKG_USER-PLUMED)
     list(APPEND LAMMPS_DEPS plumed_build)
     if(PLUMED_MODE STREQUAL "STATIC")
       add_definitions(-D__PLUMED_WRAPPER_CXX=1)
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "SHARED")
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
       list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
     endif()
     set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
@@ -70,7 +82,7 @@ if(PKG_USER-PLUMED)
     elseif(PLUMED_MODE STREQUAL "SHARED")
       include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so)
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
       include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
     endif()
     list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})

cmake/Modules/Packages/VORONOI.cmake

@@ -18,8 +18,12 @@ if(PKG_VORONOI)
     else()
       set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
     endif()
-    string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS})
-    set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    if(APPLE)
+      get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
+      set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
+    else()
+      set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    endif()
 
     ExternalProject_Add(voro_build
       URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz

cmake/README.md

@@ -33,12 +33,17 @@ tasks, act as a reference and provide examples of typical use cases.
       * [Package-Specific Configuration Options](#package-specific-configuration-options)
          * [KSPACE Package](#kspace-package)
          * [MKL](#mkl)
-         * [FFTW2](#fftw2)
          * [FFTW3](#fftw3)
+         * [BLAS](#blas)
          * [LAPACK](#lapack)
          * [PYTHON Package](#python-package)
          * [GPU Package](#gpu-package)
+         * [MESSAGE Package](#message-package)
+         * [MSCG Package](#mscg-package)
          * [VORONOI Package](#voronoi-package)
+         * [USER-LATTE Package](#user-latte-package)
+         * [USER-PLUMED Package](#user-plumed-package)
+         * [USER-SCAFACOS Package](#user-scafacos-package)
          * [USER-SMD Package](#user-smd-package)
       * [Optional Features](#optional-features)
          * [zlib support](#zlib-support)
@@ -50,8 +55,6 @@ tasks, act as a reference and provide examples of typical use cases.
          * [Building with GNU Compilers](#building-with-gnu-compilers)
          * [Building with Intel Compilers](#building-with-intel-compilers)
          * [Building with LLVM/Clang Compilers](#building-with-llvmclang-compilers)
-      * [Examples](#examples)
-
 
 ## Quick Start for the Impatient
 If you want to skip ahead and just run the compilation using `cmake`, please
@@ -205,8 +208,10 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   <td>Controls if debugging symbols are added to the generated binaries</td>
   <td>
   <dl>
-  <dt><code>Release</code> (default)</dt>
+  <dt><code>RelWithDebInfo (default)</code></dt>
+  <dt><code>Release</code></dt>
   <dt><code>Debug</code></dt>
+  <dt><code>MinSizeRel</code></dt>
   </dl>
   </td>
 </tr>
@@ -249,6 +254,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
+  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>LAMMPS_MEMALIGN</code></td>
   <td>controls the alignment of blocks of memory allocated by LAMMPS</td>
@@ -271,7 +286,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
 </tr>
 <tr>
   <td><code>LAMMPS_MACHINE</code></td>
-  <td>allows appending a machine suffix to the generate LAMMPS binary</td>
+  <td>allows appending a machine suffix to the generated LAMMPS binary</td>
+  <td>
+  <dl>
+    <dt>*none*  (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_LIB_SUFFIX</code></td>
+  <td>allows appending a suffix to the generated LAMMPS library</td>
   <td>
   <dl>
     <dt>*none*  (default)</dt>
@@ -319,8 +343,8 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </td>
 </tr>
 <tr>
-  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
-  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
+  <td><code>BUILD_TOOLS</code></td>
+  <td>control whether to build LAMMPS tools</td>
   <td>
   <dl>
     <dt><code>off</code> (default)</dt>
@@ -561,23 +585,6 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </dl>
   </td>
 </tr>
-<tr>
-  <td><code>PKG_MEAM</code></td>
-  <td>
-<p>A pair style for the modified embedded atom (MEAM) potential.</p>
-
-<p><strong>Please note that the MEAM package has been superseded by the USER-MEAMC package,
-which is a direct translation of the MEAM package to C++. USER-MEAMC contains
-additional optimizations making it run faster than MEAM on most machines, while
-providing the identical features and USER interface.</strong></p>
-  </td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_MISC</code></td>
   <td>
@@ -634,21 +641,6 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
-<tr>
-  <td><code>PKG_REAX</code></td>
-  <td>
-  A pair style which wraps a Fortran library which implements the ReaxFF
-  potential, which is a universal reactive force field. See the USER-REAXC
-  package for an alternate implementation in C/C++. Also a fix reax/bonds
-  command for monitoring molecules as bonds are created and destroyed.
-  </td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_REPLICA</code></td>
   <td>
@@ -695,6 +687,16 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_SPIN</code></td>
+  <td>Model atomic magnetic spins classically, coupled to atoms moving in the usual manner via MD. Various pair, fix, and compute styles.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_SNAP</code></td>
   <td>
@@ -757,6 +759,16 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_MESSAGE</code></td>
+  <td>Commands to use LAMMPS as either a client or server and couple it to another application.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_MSCG</code></td>
   <td>
@@ -811,6 +823,18 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_VORONOI</code></td>
+  <td>
+  A compute command which calculates the Voronoi tesselation of a collection of atoms by wrapping the Voro++ library. This can be used to calculate the local volume or each atoms or its near neighbors.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -825,6 +849,16 @@ providing the identical features and USER interface.</strong></p>
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>PKG_USER-ADIOS</code></td>
+  <td>ADIOS is a high-performance I/O library. This package implements the dump “atom/adios” and dump “custom/adios” commands to write data using the ADIOS library.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-ATC</code></td>
   <td>
@@ -853,6 +887,18 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-BOCS</code></td>
+  <td>
+  This package provides fix bocs, a modified version of fix npt which includes the pressure correction to the barostat as outlined in: N. J. H. Dunn and W. G. Noid, “Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids,” J. Chem. Phys. 143, 243148 (2015).
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-CGDNA</code></td>
   <td>
@@ -1142,6 +1188,30 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-PLUMED</code></td>
+  <td>
+  The fix plumed command allows you to use the PLUMED free energy plugin for molecular dynamics to analyze and bias your LAMMPS trajectory on the fly. The PLUMED library is called from within the LAMMPS input script by using the <code>fix plumed</code> command.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PKG_USER-PTM</code></td>
+  <td>
+  A <code>compute ptm/atom</code> command that calculates local structure characterization using the Polyhedral Template Matching methodology.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-QTB</code></td>
   <td>
@@ -1197,6 +1267,33 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-SCAFACOS</code></td>
+  <td>
+  A KSpace style which wraps the ScaFaCoS Coulomb solver library to compute long-range Coulombic interactions.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PKG_USER-SDPD</code></td>
+  <td>
+  A pair style for smoothed dissipative particle dynamics (SDPD), which is an
+  extension of smoothed particle hydrodynamics (SPH) to mesoscale where thermal
+  fluctuations are important (see the USER-SPH package). Also two fixes for
+  moving and rigid body integration of SPH/SDPD particles (particles of
+  <code>atom_style meso</code>).</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-SMD</code></td>
   <td>
@@ -1280,6 +1377,23 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-YAFF</code></td>
+  <td>
+  Some potentials that are also implemented in the Yet Another Force Field (YAFF) code.
+  The expressions and their use are discussed in the following papers:
+  <ul>
+    <li><a href="http://dx.doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li>
+    <li><a href="http://dx.doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
+  </ul>
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -1300,14 +1414,27 @@ providing the identical features and USER interface.</strong></p>
   <td><code>FFT</code></td>
   <td>
     <p>FFT library for KSPACE package</p>
-    <p>If either MKL or FFTW is selected <code>cmake</code> will try to locate these libraries automatically. To control which one should be used please see the options below for each FFT library.</p>
+    <p>If either MKL or FFTW is selected <code>cmake</code> will try to locate
+    these libraries automatically. To control which one should be used please see
+    the options below for each FFT library.  Otherwise it will default to KISS
+    FFT.</p>
   </td>
   <td>
   <dl>
-    <dt><code>KISS</code></dt>
     <dt><code>FFTW3</code></dt>
     <dt><code>FFTW2</code></dt>
     <dt><code>MKL</code></dt>
+    <dt><code>KISS</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>FFT_SINGLE</code></td>
+  <td>Use single-precision floating-point in FFT</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default = double precision)</dt>
+    <dt><code>on</code></dt>
   </dl>
   </td>
 </tr>
@@ -1325,60 +1452,6 @@ providing the identical features and USER interface.</strong></p>
 </tbody>
 </table>
 
-### MKL
-
-<table>
-<thead>
-<tr>
-  <th>Option</th>
-  <th>Description</th>
-  <th>Values</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-  <td><code>MKL_INCLUDE_DIRS</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-<tr>
-  <td><code>MKL_LIBRARIES</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-</tbody>
-</table>
-
-TODO static vs dynamic linking
-
-### FFTW2
-
-<table>
-<thead>
-<tr>
-  <th>Option</th>
-  <th>Description</th>
-  <th>Values</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-  <td><code>FFTW2_INCLUDE_DIRS</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-<tr>
-  <td><code>FFTW2_LIBRARIES</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-</tbody>
-</table>
-
 ### FFTW3
 
 <table>
@@ -1392,24 +1465,57 @@ TODO static vs dynamic linking
 <tbody>
 <tr>
   <td><code>FFTW3_INCLUDE_DIRS</code></td>
-  <td></td>
+  <td>path to FFTW3 include files</td>
   <td>
   </td>
 </tr>
 <tr>
   <td><code>FFTW3_LIBRARIES</code></td>
-  <td></td>
+  <td>list of paths to FFTW3 libraries</td>
   <td>
   </td>
 </tr>
 </tbody>
 </table>
 
+### MKL
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>MKL_INCLUDE_DIRS</code></td>
+  <td>path to MKL include files</td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>MKL_LIBRARIES</code></td>
+  <td>list of paths to MKL libraries</td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### BLAS
+
+See [FindBLAS documentation](https://cmake.org/cmake/help/latest/module/FindBLAS.html)
+
 ### LAPACK
-TODO
+
+See [FindLAPACK documentation](https://cmake.org/cmake/help/latest/module/FindLAPACK.html)
 
 ### PYTHON Package
 
+See [FindPYTHON documentation](https://cmake.org/cmake/help/latest/module/FindPython.html)
+
 ### USER-INTEL Package
 
 <table>
@@ -1499,10 +1605,11 @@ target API.
   <td>
   <dl>
     <dt><code>sm_20</code> (Fermi)</dt>
-    <dt><code>sm_30</code> (Kepler)</dt>
+    <dt><code>sm_30</code> (Kepler) (default)</dt>
     <dt><code>sm_50</code> (Maxwell)</dt>
     <dt><code>sm_60</code> (Pascal)</dt>
     <dt><code>sm_70</code> (Volta)</dt>
+    <dt><code>sm_75</code> (Turing)</dt>
   </dl>
   </td>
 </tr>
@@ -1534,13 +1641,14 @@ target API.
 </tbody>
 </table>
 
-### VORONOI Package
+### KIM Package
 
-TODO
+Requires installation of the KIM library with API v2
 
-### USER-SMD Package
-
-Requires a Eigen3 installation
+If `DOWNLOAD_KIM` is set, the KIM library will be downloaded and built inside
+the CMake build directory. If the KIM library is already on your system (in a
+location CMake cannot find it), set the `PKG_CONFIG_PATH` environment variable
+so that `libkim-api` can be found.
 
 <table>
 <thead>
@@ -1551,9 +1659,323 @@ Requires a Eigen3 installation
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>DOWNLOAD_KIM</code></td>
+  <td>Download KIM API v2 and compile it as part of the build.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### MESSAGE Package
+
+This package can optionally include support for messaging via sockets, using the open-source [ZeroMQ library](http://zeromq.org/), which must be installed on your system.
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>MESSAGE_ZMQ</code></td>
+  <td>Build with ZeroMQ support</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ZMQ_LIBRARY</code></td>
+  <td>
+    ZMQ library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>ZMG_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing ZMQ installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### MSCG Package
+
+Requires installation of the MSCG library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_MSCG</code></td>
+  <td>Download MSCG and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>MSCG_LIBRARY</code></td>
+  <td>
+    MSCG library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>MSCG_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing MSCG installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### VORONOI Package
+
+Requires installation of the Voro++ library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_VORO</code></td>
+  <td>Download Voro++ and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>VORO_LIBRARY</code></td>
+  <td>
+    Voro++ library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>VORO_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing Voro++ installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-LATTE Package
+
+Requires installation of the LATTE library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_LATTE</code></td>
+  <td>Download LATTE and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LATTE_LIBRARY</code></td>
+  <td>
+    LATTE library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-PLUMED Package
+
+Requires installation of the PLUMED library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_PLUMED</code></td>
+  <td>Download PLUMED and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PLUMED_MODE</code></td>
+  <td>
+    Determines the linkage mode for the PLUMED library.
+  </td>
+  <td>
+  <dl>
+    <dt><code>static</code> (default)</dt>
+    <dt><code>shared</code></dt>
+    <dt><code>runtime</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-LATTE Package
+
+Requires installation of the LATTE library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_LATTE</code></td>
+  <td>Download LATTE and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LATTE_LIBRARY</code></td>
+  <td>
+    LATTE library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-SMD Package
+
+Requires installation of the Eigen3 library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_EIGEN3</code></td>
+  <td>Download Eigen3 and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>EIGEN3_INCLUDE_DIR</code></td>
-  <td></td>
+  <td>
+    Provide include directory of existing Eigen3 installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+
+### USER-SCAFACOS Package
+
+To build with this package, you must download and build the [ScaFaCoS Coulomb solver library](http://www.scafacos.de/)
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_SCAFACOS</code></td>
+  <td>Download SCAFACOS and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>SCAFACOS_LIBRARY</code></td>
+  <td>
+    SCAFACOS library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>SCAFACOS_INCLUDE_DIR</code></td>
+  <td>
+    SCAFACOS include directory (only needed if at custom location)
+  </td>
   <td>
   </td>
 </tr>
@@ -1791,5 +2213,82 @@ cmake -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc -D CMAKE_Fortran_COMPIL
 cmake -D CMAKE_C_COMPILER=clang -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_Fortran_COMPILER=flang ../cmake
 ```
 
+## LAMMPS Developer Options
 
-## Examples
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>ENABLE_TESTING</code></td>
+  <td>Control wheather to add tests via CTest</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_TESTING_SOURCE_DIR</code></td>
+  <td>Custom location of lammps-testing repository (optional). If not specified it will download it via Git</td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_TESTING_GIT_TAG</code></td>
+  <td>If lammps-testing repository is cloned, this is the tag/commit that will be checked out</td>
+  <td>
+  <dl>
+    <dt><code>master</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_COVERAGE</code></td>
+  <td>Enables code coverage support via gcov and adds a gcovr build target to generate a coverage report.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_ADDRESS</code></td>
+  <td>Enables Address Sanitizer support when compiling using GCC or Clang for detecting memory leaks in binaries while running them. See https://clang.llvm.org/docs/AddressSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_UNDEFINED</code></td>
+  <td>Enables Undefined Behavior Sanitizer support when compiling using GCC or Clang for detecting code that is running into undefined behavior of the language. See https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_THREAD</code></td>
+  <td>Enables Thread Sanitizer support when compiling using GCC or Clang for detecting data races in binaries while running them. See https://clang.llvm.org/docs/ThreadSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>

cmake/etc/profile.d/lammps.csh.in

@@ -1,4 +1,4 @@
 # set environment for LAMMPS and msi2lmp executables
 # to find potential and force field files
-if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@
-if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@
+if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_INSTALL_DATADIR@/potentials
+if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_INSTALL_DATADIR@/frc_files

cmake/etc/profile.d/lammps.sh.in

@@ -1,5 +1,5 @@
 # set environment for LAMMPS and msi2lmp executables
 # to find potential and force field files
-LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
-MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@}
+LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_INSTALL_DATADIR@/potentials}
+MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_INSTALL_DATADIR@/frc_files}
 export LAMMPS_POTENTIALS MSI2LMP_LIBRARY

cmake/presets/mingw-cross.cmake

@@ -3,9 +3,9 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
                  REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
                  USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
                  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
-                 USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-MOLFILE USER-OMP
-                 USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD USER-SMD
-                 USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
+                 USER-MEAMC USER-MESO USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE
+                 USER-OMP USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD
+                 USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
 
 foreach(PKG ${WIN_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -14,4 +14,4 @@ endforeach()
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
-set(INTEL_LRT_MODE "none" CACHE STRING "" FORCE)
+set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")

doc/include-file-conventions.md

@@ -0,0 +1,133 @@
+# Outline of include file conventions in LAMMPS
+
+This purpose of this document is to provide a point of reference
+for LAMMPS developers and contributors as to what include files
+and definitions to put where into LAMMPS source.
+Last change 2019-07-05
+
+## Table of Contents
+
+  * [Motivation](#motivation)
+  * [Rules](#rules)
+  * [Tools](#tools)
+  * [Legacy Code](#legacy-code)
+
+## Motivation
+
+The conventions outlined in this document are supposed to help make
+maintenance of the LAMMPS software easier.  By trying to achieve
+consistency across files contributed by different developers, it will
+become easier for the code maintainers to modify and adjust files and,
+overall, the chance for errors or portability issues will be reduced.
+The rules employed are supposed to minimize naming conflicts and
+simplify dependencies between files and thus speed up compilation. They
+may, as well, make otherwise hidden dependencies visible.
+
+## Rules
+
+Below are the various rules that are applied.  Not all are enforced
+strictly and automatically.  If there are no significant side effects,
+exceptions may be possible for cases where a full compliance to the
+rules may require a large effort compared to the benefit.
+
+### Core Files Versus Package Files
+
+All rules listed below are most strictly observed for core LAMMPS files,
+which are the files that are not part of a package, and the files of the
+packages MOLECULE, MANYBODY, KSPACE, and RIGID.  On the other end of
+the spectrum are USER packages and legacy packages that predate these
+rules and thus may not be fully compliant.  Also, new contributions
+will be checked more closely, while existing code will be incrementally
+adapted to the rules as time and required effort permits.
+
+### System Versus Local Header Files
+
+All system- or library-provided include files are included with angular
+brackets (examples: `#include <cstring>` or `#include <mpi.h>`) while
+include files provided with LAMMPS are included with double quotes
+(examples: `#include "pointers.h"` or `#include "compute_temp.h"`).
+
+For headers declaring functions of the C-library, the corresponding
+C++ versions should be included (examples: `#include <cstdlib>` or
+`#include <cctypes>`).  However, these includes are limited to those defined
+in the C++98 standard.  Some files thus must use the older style until
+the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
+even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
+or `#include <inttypes.h>` versus `#include <cinttypes>`).
+
+### C++ Standard Compliance
+
+LAMMPS core files currently correspond to the C++98 standard. Files
+requiring C++11 or later are only permitted in (optional) packages
+and particularly packages that are not part of the list of commonly
+used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
+
+Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.
+Since using both at the same time can cause problems, iostreams should
+be avoided where possible.
+
+### Lean Header Files
+
+Header files will typically contain the definition of a (single) class.
+These header files should have as few include statements as possible.
+This is particularly important for classes that implement a "style" and
+thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
+all be included in the auto-generated `"some_style.h"` files which 
+results in a high potential for direct or indirect symbol name clashes.
+
+In the ideal case, the header would only include one file defining the
+parent class. That would typically be either `#include "pointers.h"` for
+the `Pointers` class, or a header of a class derived from it like
+`#include "pair.h"` for the `Pair` class and so on.  References to other
+classes inside the class should be make through pointers, for which forward
+declarations (inside the `LAMMPS_NS` or the new class' namespace) can
+be employed.  The full definition will then be included into the corresponding
+implementation file.  In the given example from above, the header file
+would be called `some_name.h` and the implementation `some_name.cpp` (all
+lower case with underscores, while the class itself would be in camel case
+and no underscores `SomeName`, and the style name with lower case names separated by
+a forward slash).
+
+### Implementation Files
+
+In the implementation files (typically, those would have the same base name
+as the corresponding header with a .cpp extension instead of .h) include
+statements should follow the "include what you use" principle.
+
+### Order of Include Statements
+
+Include files should be included in this order:
+* the header matching the implementation (`some_class.h` for file `some_class.cpp`)
+* mpi.h
+* system and library headers (anything that is using angular brackets; C-library headers first, then C++)
+* LAMMPS local headers (preferably in alphabetical order)
+
+### Special Cases and Exceptions
+
+#### pointers.h
+
+The `pointer.h` header file also includes `cstdio` and `lmptype.h`
+(and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`).
+This means any header including `pointers.h` can assume that `FILE`,
+`NULL`, `INT_MAX` are defined.
+
+## Tools
+
+The [Include What You Use tool](https://include-what-you-use.org/)
+can be used to provide supporting information about compliance with
+the rules listed here.  There are some limitations and the IWYU tool
+may give incorrect advice.  The tools is activated by setting the
+CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the
+path of the `include-what-you-use` command.  When activated, the
+tool will be run after each compilation and provide suggestions for
+which include files should be added or removed.
+
+## Legacy Code
+
+A lot of code predates the application of the rules in this document
+and the rules themselves are a moving target.  So there are going to be
+significant chunks of code that do not fully comply.  This applies
+for example to the USER-REAXC, or the USER-ATC package.  The LAMMPS
+developers are dedicated to make an effort to improve the compliance
+and welcome volunteers wanting to help with the process.
+

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "18 June 2019" "2019-06-18"
+.TH LAMMPS "19 September 2019" "2019-09-19"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build.txt

@@ -29,6 +29,7 @@ as described on the "Install"_Install.html doc page.
    Build_package
    Build_extras
    Build_windows
+   Build_development
 
 END_RST -->
 
@@ -41,7 +42,8 @@ END_RST -->
 "Optional build settings"_Build_settings.html
 "Include packages in build"_Build_package.html
 "Packages with extra build options"_Build_extras.html
-"Notes for building LAMMPS on Windows"_Build_windows.html  :all(b)
+"Notes for building LAMMPS on Windows"_Build_windows.html
+"Development build options (CMake only)"_Build_development.html  :all(b)
 
 If you have problems building LAMMPS, it is often due to software
 issues on your local machine.  If you can, find a local expert to

doc/src/Build_basics.txt

@@ -51,7 +51,7 @@ Serial build (see src/MAKE/Makefile.serial):
 
 MPI_INC =       -I../STUBS
 MPI_PATH =      -L../STUBS
-MPI_LIB =	-lmpi_stubs :pre
+MPI_LIB =       -lmpi_stubs :pre
 
 For a parallel build, if MPI is installed on your system in the usual
 place (e.g. under /usr/local), you do not need to specify the 3
@@ -183,17 +183,17 @@ want.
 
 Parallel build (see src/MAKE/Makefile.mpi):
 
-CC =		mpicxx
-CCFLAGS =	-g -O3
-LINK =		mpicxx
-LINKFLAGS =	-g -O :pre
+CC =            mpicxx
+CCFLAGS =       -g -O3
+LINK =          mpicxx
+LINKFLAGS =     -g -O :pre
 
 Serial build (see src/MAKE/Makefile.serial):
 
-CC =		g++
-CCFLAGS =	-g -O3
-LINK =		g++
-LINKFLAGS =	-g -O :pre
+CC =            g++
+CCFLAGS =       -g -O3
+LINK =          g++
+LINKFLAGS =     -g -O :pre
 
 The "compiler/linker settings" section of a Makefile.machine lists
 compiler and linker settings for your C++ compiler, including
@@ -235,12 +235,16 @@ running LAMMPS from Python via its library interface.
 
 -D BUILD_EXE=value           # yes (default) or no
 -D BUILD_LIB=value           # yes or no (default)
--D BUILD_SHARED_LIBS=value   # yes or no (default) :pre
+-D BUILD_SHARED_LIBS=value   # yes or no (default)
+-D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc
+                             # no default value :pre
+
 
 Setting BUILD_EXE=no will not produce an executable.  Setting
 BUILD_LIB=yes will produce a static library named liblammps.a.
 Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a
-shared library named liblammps.so.
+shared library named liblammps.so. If LAMMPS_LIB_SUFFIX is set the generated
+libraries will be named liblammps_name.a or liblammps_name.so instead.
 
 [Traditional make]:
 
@@ -310,6 +314,30 @@ current LAMMPS version (HTML and PDF files), from the website
 
 :line
 
+Build LAMMPS tools :h4,link(tools)
+
+Some tools described in "Auxiliary tools"_Tools.html can be built directly
+using CMake or Make.
+
+[CMake variable]:
+
+-D BUILD_TOOLS=value       # yes or no (default) :pre
+
+The generated binaries will also become part of the LAMMPS installation (see below)
+
+[Traditional make]:
+
+cd lammps/tools
+make all              # build all binaries of tools
+make binary2txt       # build only binary2txt tool
+make chain            # build only chain tool
+make micelle2d        # build only micelle2d tool
+make thermo_extract   # build only thermo_extract tool
+:pre
+
+:line
+
+
 Install LAMMPS after a build :h4,link(install)
 
 After building LAMMPS, you may wish to copy the LAMMPS executable of

doc/src/Build_cmake.txt

@@ -52,11 +52,17 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
 ccache (= Compiler Cache) software may speed up repeated compilation
 even more.
 
-After compilation, you can optionally copy the LAMMPS executable and
-library into your system folders (by default under $HOME/.local) with:
+After compilation, you may optionally install the LAMMPS executable into
+your system with:
 
 make install    # optional, copy LAMMPS executable & library elsewhere :pre
 
+This will install the lammps executable and library (if requested), some
+tools (if configured) and additional files like library API headers,
+manpages, potential and force field files. The location of the installation
+tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults
+to $\{HOME\}/.local
+
 :line
 
 There are 3 variants of CMake: a command-line version (cmake), a text mode
@@ -114,7 +120,7 @@ The argument can be preceeded or followed by various CMake
 command-line options.  Several useful ones are:
 
 -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
--D CMAKE_BUILD_TYPE=type      # type = Release or Debug
+-D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
 -G output                     # style of output CMake generates
 -DVARIABLE=value              # setting for a LAMMPS feature to enable
 -D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir

doc/src/Build_development.txt

@@ -0,0 +1,86 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Development build options (CMake only) :h3
+
+The CMake build of LAMMPS has a few extra options which are useful during
+development,  testing or debugging.
+
+:line
+
+Verify compilation flags :h4,link(compilation)
+
+Sometimes it is necessary to verify the complete sequence of compilation flags
+generated by the CMake build. To enable a more verbose output during
+compilation you can use the following option.
+
+-D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes :pre
+
+Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+
+make VERBOSE=1 :pre
+
+:line
+
+Address, Undefined Behavior, and Thread Sanitizer Support :h4,link(sanitizer)
+
+Compilers such as GCC and Clang support generating binaries which use different
+sanitizers to detect problems in code during run-time. They can detect "memory leaks"_https://clang.llvm.org/docs/AddressSanitizer.html,
+code that runs into "undefined behavior"_https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html of the
+language and "data races"_https://clang.llvm.org/docs/ThreadSanitizer.html in threaded code.
+
+The following settings allow you enable these features if your compiler supports
+it. Please note that they come with a performance hit. However, they are
+usually faster than using tools like Valgrind.
+
+-D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
+-D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
+-D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes
+:pre
+
+:line
+
+Code Coverage and Testing :h4,link(testing)
+
+We do extensive regression testing of the LAMMPS code base on a continuous
+basis. Some of the logic to do this has been added to the CMake build so
+developers can run the tests directly on their workstation.
+
+NOTE: this is incomplete and only represents a small subset of tests that we run
+
+-D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
+-D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
+-D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
+:pre
+
+If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
+
+make test
+:pre
+
+The test cases used come from the lammps-testing repository. They are
+derivatives of the examples folder with some modifications to make the run
+faster.
+
+You can also collect code coverage metrics while running the tests by enabling
+coverage support during building.
+
+-D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes :pre
+
+This will also add the following targets to generate coverage reports after running the LAMMPS executable:
+
+make test               # run tests first!
+make gen_coverage_html  # generate coverage report in HTML format
+make gen_coverage_xml   # generate coverage report in XML format
+:pre
+
+These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
+
+pip install git+https://github.com/gcovr/gcovr.git :pre
+:pre

doc/src/Build_extras.txt

@@ -88,7 +88,7 @@ which GPU hardware to build for.
                           # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
 -D GPU_ARCH=value         # primary GPU hardware choice for GPU_API=cuda
                           # value = sm_XX, see below
-                          # default is Cuda-compiler dependent, but typically sm_20
+                          # default is sm_30
 -D CUDPP_OPT=value        # optimization setting for GPU_API=cuda
                           # enables CUDA Performance Primitives Optimizations
                           # value = yes (default) or no
@@ -172,22 +172,17 @@ KIM package :h4,link(kim)
 
 To build with this package, the KIM library with API v2 must be downloaded
 and built on your system.  It must include the KIM models that you want to
-use with LAMMPS. If you want to use the "kim_query"_kim_query.html
+use with LAMMPS. If you want to use the "kim_query"_kim_commands.html
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
-Note that in LAMMPS lingo, a KIM model driver is a pair style
-(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
-element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file.  Also note that downloading and installing
-the KIM API library with all its models, may take a long time (10s of
-minutes to hours) to build.  Of course you only need to do that once.
+See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to
+learn how to install a pre-build binary of the OpenKIM Repository of Models.
+See the list of all KIM models here: https://openkim.org/browse/models
 
-See the list of KIM model drivers here:
-https://openkim.org/browse/model-drivers/alphabetical
-
-See the list of all KIM models here:
-https://openkim.org/browse/models/by-model-drivers
+(Also note that when downloading and installing from source
+the KIM API library with all its models, may take a long time (tens of
+minutes to hours) to build.  Of course you only need to do that once.)
 
 [CMake build]:
 
@@ -307,7 +302,7 @@ files.
 
 KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
 export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
-CC =		mpicxx :pre
+CC =            mpicxx :pre
 
 :line
 
@@ -359,6 +354,9 @@ be installed on your system.
 [CMake build]:
 
 -D MESSAGE_ZMQ=value    # build with ZeroMQ support, value = no (default) or yes
+-D ZMQ_LIBRARY=path     # ZMQ library file (only needed if a custom location)
+-D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)
+:pre
 
 [Traditional make]:
 
@@ -371,6 +369,7 @@ simply invoke the lib/message/Install.py script with the specified args:
 make lib-message               # print help message
 make lib-message args="-m -z"  # build with MPI and socket (ZMQ) support
 make lib-message args="-s"     # build as serial lib with no ZMQ support
+:pre
 
 The build should produce two files: lib/message/cslib/src/libmessage.a
 and lib/message/Makefile.lammps.  The latter is copied from an
@@ -803,7 +802,7 @@ dir, using a command like these, which simply invoke the
 lib/h5md/Install.py script with the specified args:
 
 make lib-h5md                     # print help message
-make lib-hm5d args="-m h5cc"      # build with h5cc compiler :pre
+make lib-h5md args="-m h5cc"      # build with h5cc compiler :pre
 
 The build should produce two files: lib/h5md/libch5md.a and
 lib/h5md/Makefile.lammps.  The latter is copied from an existing
@@ -850,15 +849,15 @@ additional information.
 For CPUs:
 
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
-CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
-LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
+CCFLAGS =       -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+LINKFLAGS =     -g -qopenmp $(OPTFLAGS)
 LIB =           -ltbbmalloc :pre
 
 For KNLs:
 
 OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
-CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
-LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
+CCFLAGS =       -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+LINKFLAGS =     -g -qopenmp $(OPTFLAGS)
 LIB =           -ltbbmalloc :pre
 
 :line

doc/src/Build_settings.txt

@@ -12,6 +12,7 @@ Optional build settings :h3
 LAMMPS can be built with several optional settings.  Each sub-section
 explain how to do this for building both with CMake and make.
 
+"C++11 standard compliance test"_#cxx11 when building all of LAMMPS
 "FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command
 "Size of LAMMPS data types"_#size
 "Read or write compressed files"_#gzip
@@ -23,6 +24,28 @@ explain how to do this for building both with CMake and make.
 
 :line
 
+C++11 standard compliance test :h4,link(cxx11)
+
+The LAMMPS developers plan to transition to make the C++11 standard the
+minimum requirement for compiling LAMMPS.  Currently this only applies to
+some packages like KOKKOS while the rest aims to be compatible with the C++98
+standard.  Most currently used compilers are compatible with C++11; some need
+to set extra flags to switch.  To determine the impact of requiring C++11,
+we have added a simple compliance test to the source code, that will cause
+the compilation to abort, if C++11 compliance is not available or enabled.
+To bypass this check, you need to change a setting in the makefile or
+when calling CMake.
+
+[CMake variable]:
+
+-D DISABLE_CXX11_REQUIREMENT=yes
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_CXX98
+
+:line
+
 FFT library :h4,link(fft)
 
 When the KSPACE package is included in a LAMMPS build, the

doc/src/Commands_all.txt

@@ -50,11 +50,11 @@ An alphabetic list of all general LAMMPS commands.
 "dump"_dump.html,
 "dump adios"_dump_adios.html,
 "dump image"_dump_image.html,
-"dump_modify"_dump_modify.html,
 "dump movie"_dump_image.html,
 "dump netcdf"_dump_netcdf.html,
 "dump netcdf/mpiio"_dump_netcdf.html,
 "dump vtk"_dump_vtk.html,
+"dump_modify"_dump_modify.html,
 "dynamical_matrix"_dynamical_matrix.html,
 "echo"_echo.html,
 "fix"_fix.html,
@@ -68,7 +68,9 @@ An alphabetic list of all general LAMMPS commands.
 "improper_style"_improper_style.html,
 "include"_include.html,
 "jump"_jump.html,
-"kim_query"_kim_query.html,
+"kim_init"_kim_commands.html,
+"kim_interactions"_kim_commands.html,
+"kim_query"_kim_commands.html,
 "kspace_modify"_kspace_modify.html,
 "kspace_style"_kspace_style.html,
 "label"_label.html,

doc/src/Commands_bond.txt

@@ -108,7 +108,7 @@ OPT.
 "class2 (ko)"_dihedral_class2.html,
 "cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
 "fourier (io)"_dihedral_fourier.html,
-"harmonic (io)"_dihedral_harmonic.html,
+"harmonic (iko)"_dihedral_harmonic.html,
 "helix (o)"_dihedral_helix.html,
 "multi/harmonic (o)"_dihedral_multi_harmonic.html,
 "nharmonic (o)"_dihedral_nharmonic.html,

doc/src/Commands_compute.txt

@@ -66,6 +66,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
 "gyration/chunk"_compute_gyration_chunk.html,
+"gyration/shape"_compute_gyration_shape.html,
 "heat/flux"_compute_heat_flux.html,
 "heat/flux/tally"_compute_tally.html,
 "hexorder/atom"_compute_hexorder_atom.html,
@@ -80,6 +81,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "meso/e/atom"_compute_meso_e_atom.html,
 "meso/rho/atom"_compute_meso_rho_atom.html,
 "meso/t/atom"_compute_meso_t_atom.html,
+"momentum"_compute_momentum.html,
 "msd"_compute_msd.html,
 "msd/chunk"_compute_msd_chunk.html,
 "msd/nongauss"_compute_msd_nongauss.html,

doc/src/Commands_fix.txt

@@ -232,6 +232,7 @@ OPT.
 "wall/lj1043"_fix_wall.html,
 "wall/lj126"_fix_wall.html,
 "wall/lj93 (k)"_fix_wall.html,
+"wall/morse"_fix_wall.html,
 "wall/piston"_fix_wall_piston.html,
 "wall/reflect (k)"_fix_wall_reflect.html,
 "wall/region"_fix_wall_region.html,

doc/src/Commands_pair.txt

@@ -65,6 +65,7 @@ OPT.
 "colloid (go)"_pair_colloid.html,
 "comb (o)"_pair_comb.html,
 "comb3"_pair_comb.html,
+"cosine/squared"_pair_cosine_squared.html,
 "coul/cut (gko)"_pair_coul.html,
 "coul/cut/soft (o)"_pair_fep_soft.html,
 "coul/debye (gko)"_pair_coul.html,
@@ -165,6 +166,7 @@ OPT.
 "lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
 "lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
 "lj96/cut (go)"_pair_lj96.html,
+"local/density"_pair_local_density.html,
 "lubricate (o)"_pair_lubricate.html,
 "lubricate/poly (o)"_pair_lubricate.html,
 "lubricateU"_pair_lubricateU.html,
@@ -222,6 +224,8 @@ OPT.
 "sph/rhosum"_pair_sph_rhosum.html,
 "sph/taitwater"_pair_sph_taitwater.html,
 "sph/taitwater/morris"_pair_sph_taitwater_morris.html,
+"spin/dipole/cut"_pair_spin_dipole.html,
+"spin/dipole/long"_pair_spin_dipole.html,
 "spin/dmi"_pair_spin_dmi.html,
 "spin/exchange"_pair_spin_exchange.html,
 "spin/magelec"_pair_spin_magelec.html,

doc/src/Eqs/angle_class2_p6.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/angle_cosine_buck6d.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E = K \left[ 1 + \cos(n\theta - \theta_0)\right]
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/compute_shape_parameters.tex

@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+ c = l_z - 0.5(l_y+l_x) \\
+ b = l_y - l_x \\
+ k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} 
+\end{eqnarray*}
+
+\end{document}
+

doc/src/Eqs/improper_inversion_harmonic.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E = K \left(\theta - \theta_0\right)^2
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/pair_agni.tex

@@ -0,0 +1,18 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+  F_i^u & = & \sum_t^{N_t}\alpha_t \cdot \exp\left[-\frac{\left(d_{i,t}^u\right)^2}{2l^2}\right] \\
+  d_{i,t}^u & = & \left|\left| V_i^u(\eta) - V_t^u(\eta) \right|\right| \\
+  V_i^u(\eta) & = & \sum_{j \neq i}\frac{r^u_{ij}}{r_{ij}} \cdot e^{-\left(\frac{r_{ij}}{\eta} \right)^2} \cdot f_d\left(r_{ij}\right) \\
+  f_d\left(r_{ij}\right) & = & \frac{1}{2} \left[\cos\left(\frac{\pi r_{ij}}{R_c}\right) + 1 \right]
+\end{eqnarray*}
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/pair_buck6d.tex

@@ -1,6 +1,7 @@
 \documentclass[12pt]{article}
 
 \begin{document}
+\pagestyle{empty}
 
 \begin{eqnarray*}
   E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\

doc/src/Eqs/pair_cosine_squared.tex

@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+\begin{align*}
+E = 
+\begin{cases}
+-\epsilon& \quad r < \sigma \\
+-\epsilon\cos\left(\frac{\pi\left(r - \sigma\right)}{2\left(r_c - \sigma\right)}\right)&\quad \sigma \leq r < r_c \\
+0& \quad r \geq r_c
+\end{cases}
+\end{align*}
+
+\end{document}

doc/src/Eqs/pair_cosine_squared_wca.tex

@@ -0,0 +1,11 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
+                       2\left(\frac{\sigma}{r}\right)^6 + 1\right]
+                       , \quad r < \sigma
+$$
+
+\end{document}

doc/src/Eqs/pair_coul_gauss.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+$$
+  E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c
+$$
+
+\end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:

doc/src/Eqs/pair_kolmogorov_crespi_full.tex

@@ -27,7 +27,7 @@
   V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\
   \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt]
   \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot  {\bf n}_{j})^2 \\[15pt]
-  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
+  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n}
 \end{eqnarray*}
 \endgroup
 \end{document}

doc/src/Eqs/pair_local_density_energy.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+ U_{LD} = \sum_i F(\rho_i)
+$$
+
+
+\end{document}
+~                  

doc/src/Eqs/pair_local_density_energy_implement.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+U_{LD} = \sum_k U_{LD}^{(k)} = \sum_i \left[ \sum_k a_\alpha^{(k)} F^{(k)} \left(\rho_i^{(k)}\right) \right] 
+$$
+
+\end{document}

doc/src/Eqs/pair_local_density_energy_multi.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+U_{LD} = \sum_i a_\alpha F(\rho_i)
+$$
+
+\end{document}

doc/src/Eqs/pair_local_density_indicator_func.tex

@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+\usepackage[utf8]{inputenc}
+\usepackage{amsmath}
+\usepackage{amsfonts}
+
+\begin{document}
+\[
+  \varphi(r) = 
+    \begin{cases}
+       1 & r \le R_1 \\
+       c_0 + c_2r^2 + c_4r^4 + c_6r^6  & r \in (R_1, R_2) \\
+       0 & r \ge R_2
+  \end{cases}
+\]
+
+\end{document}

doc/src/Eqs/pair_local_density_ld.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+
+$$
+\rho_i = \sum_{j \neq i} \varphi(r_{ij})
+$$
+
+\end{document}

doc/src/Eqs/pair_local_density_ld_implement.tex

@@ -0,0 +1,10 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+
+$$
+\rho_i^{(k)} = \sum_j b_\beta^{(k)} \varphi^{(k)} (r_{ij})
+$$
+
+\end{document}

doc/src/Eqs/pair_local_density_ld_multi.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+
+$$
+\rho_i = \sum_{j \neq i} b_\beta \varphi(r_{ij})
+$$
+
+\end{document}

doc/src/Errors_messages.txt

@@ -2438,6 +2438,14 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Compute gyration ID does not exist for compute gyration/shape} :dt
+
+Self-explanatory. Provide a valid compute ID. :dd
+
+{Compute gyration/shape compute ID does not point to a gyration compute} :dt
+
+Self-explanatory. Provide and ID of a compute gyration command. :dd
+
 {Compute ID for compute reduce does not exist} :dt
 
 Self-explanatory. :dd
@@ -5777,6 +5785,16 @@ definitions. :dd
 
 The data file header lists improper but no improper types. :dd
 
+{Incompatible KIM Simulator Model} :dt
+
+The requested KIM Simulator Model was defined for a different MD code
+and thus is not compatible with LAMMPS. :dd
+
+{Incompatible units for KIM Simulator Model} :dt
+
+The selected unit style is not compatible with the requested KIM
+Simulator Model. :dd
+
 {Incomplete use of variables in create_atoms command} :dt
 
 The var and set options must be used together. :dd
@@ -5890,6 +5908,11 @@ The element names in the ADP file do not match those requested. :dd
 
 The element names in the EAM file do not match those requested. :dd
 
+{Incorrect format of ... section in data file} :dt
+
+Number or type of values per line in the given section of the data file
+is not consistent with the requirements for this section. :dd
+
 {Incorrect format in COMB potential file} :dt
 
 Incorrect number of words per line in the potential file. :dd
@@ -7042,6 +7065,12 @@ The atom style defined does not have this attribute. :dd
 
 The atom style defined does not have these attributes. :dd
 
+{KIM Simulator Model has no Model definition} :dt
+
+There is no model definition (key: model-defn) in the KIM Simulator
+Model.  Please contact the OpenKIM database maintainers to verify
+and potentially correct this. :dd
+
 {KOKKOS package does not yet support comm_style tiled} :dt
 
 Self-explanatory. :dd
@@ -7546,6 +7575,18 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Must use 'kim_style init' command before simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Must use 'kim_style define' command after simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Must use 'kim_style init' command before 'kim_style define'} :dt
+
+Self-explanatory. :dd
+
 {Must use 'kspace_modify pressure/scalar no' for rRESPA with kspace_style MSM} :dt
 
 The kspace scalar pressure option cannot (yet) be used with rRESPA. :dd
@@ -9489,6 +9530,11 @@ See the "read_data extra/special/per/atom" command
 for info on how to leave space in the special bonds
 list to allow for additional bonds to be formed. :dd
 
+{Species XXX is not supported by this KIM Simulator Model} :dt
+
+The kim_style define command was referencing a species that is not
+present in the requested KIM Simulator Model. :dd
+
 {Specified processors != physical processors} :dt
 
 The 3d grid of processors defined by the processors command does not

doc/src/Errors_warnings.txt

@@ -129,6 +129,16 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost} :dt
+
+The communication cutoff defaults to the maximum of what is inferred from
+pair and bond styles (will be zero, if none are defined) and what is specified
+via "comm_modify cutoff"_comm_modify.html (defaults to 0.0).  If this results
+to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use
+incorrect periodic images of atoms in interaction lists.  To avoid, either use
+"pair style zero"_pair_zero.html with a suitable cutoff or use "comm_modify
+cutoff"_comm_modify.html. :dd
+
 {Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt
 
 Self-explanatory. :dd

doc/src/Examples.txt

@@ -73,7 +73,7 @@ granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
 hyper:    global and local hyperdynamics of diffusion on Pt surface
 indent:   spherical indenter into a 2d solid
-kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
+kim:      use of potentials from the "OpenKIM Repository"_openkim
 latte:    examples for using fix latte for DFTB via the LATTE library
 meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
@@ -153,3 +153,5 @@ illustrate how to use the command(s) provided in that package.  Many
 of the sub-directories have their own README files which give further
 instructions.  See the "Packages_details"_Packages_details.html doc
 page for more info on specific USER packages.
+
+:link(openkim,https://openkim.org)

doc/src/Howto_chunk.txt

@@ -136,7 +136,9 @@ The "compute chunk/spread/atom"_compute_chunk_spread_atom.html command
 spreads per-chunk values to each atom in the chunk, producing per-atom
 values as its output.  This can be useful for outputting per-chunk
 values to a per-atom "dump file"_dump.html.  Or for using an atom's
-associated chunk value in an "atom-style variable"_variable.html.
+associated chunk value in an "atom-style variable"_variable.html.  Or
+as input to the "fix ave/chunk"_fix_ave_chunk.html command to
+spatially average per-chunk values calculated by a per-chunk compute.
 
 The "compute reduce/chunk"_compute_reduce_chunk.html command reduces a
 peratom value across the atoms in each chunk to produce a value per
@@ -184,12 +186,20 @@ compute cc1 all chunk/atom c_cluster compress yes
 compute size all property/chunk cc1 count
 fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre
 
-(6) An example of using a per-chunk value to apply per-atom forces to
+(6) An example for using a per-chunk value to apply per-atom forces to
 compress individual polymer chains (molecules) in a mixture, is
 explained on the "compute
 chunk/spread/atom"_compute_chunk_spread_atom.html command doc page.
 
-(7) An example of using one set of per-chunk values for molecule
+(7) An example for using one set of per-chunk values for molecule
 chunks, to create a 2nd set of micelle-scale chunks (clustered
 molecules, due to hydrophobicity), is explained on the "compute
 chunk/reduce"_compute_reduce_chunk.html command doc page.
+
+(8) An example for using one set of per-chunk values (dipole moment
+vectors) for molecule chunks, spreading the values to each atom in
+each chunk, then defining a second set of chunks as spatial bins, and
+using the "fix ave/chunk"_fix_ave_chunk.html command to calculate an
+average dipole moment vector for each bin.  This example is explained
+on the "compute chunk/spread/atom"_compute_chunk_spread_atom.html
+command doc page.

doc/src/Howto_spins.txt

@@ -43,19 +43,19 @@ langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
 the thermal energy of the Langevin thermostat, or to perform a
 relaxation of the magnetic configuration toward an equilibrium state.
 
-The command "fix setforce/spin"_fix_setforce.html allows to set the 
-components of the magnetic precession vectors (while erasing and 
-replacing the previously computed magnetic precession vectors on 
-the atom). 
-This command can be used to freeze the magnetic moment of certain 
-atoms in the simulation by zeroing their precession vector. 
+The command "fix setforce/spin"_fix_setforce.html allows to set the
+components of the magnetic precession vectors (while erasing and
+replacing the previously computed magnetic precession vectors on
+the atom).
+This command can be used to freeze the magnetic moment of certain
+atoms in the simulation by zeroing their precession vector.
 
 The command "fix nve/spin"_fix_nve_spin.html can be used to
-perform a symplectic integration of the combined dynamics of spins 
+perform a symplectic integration of the combined dynamics of spins
 and atomic motions.
 
 The minimization style "min/spin"_min_spin.html can be applied
-to the spins to perform a minimization of the spin configuration. 
+to the spins to perform a minimization of the spin configuration.
 
 
 All the computed magnetic properties can be output by two main

doc/src/Howto_walls.txt

@@ -59,14 +59,15 @@ granular particles; all the other commands create smooth walls.
 "fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential
 "fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential
 "fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential
+"fix wall/morse"_fix_wall.html - flat walls, with Morse potential
 "fix wall/region"_fix_wall_region.html - use region surface as wall
 "fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul
 
-The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the
-flat walls to move with a constant velocity, or oscillate in time.
-The "fix wall/region"_fix_wall_region.html command offers the most
-generality, since the region surface is treated as a wall, and the
-geometry of the region can be a simple primitive volume (e.g. a
+The {lj93}, {lj126}, {colloid}, {harmonic}, and {morse} styles all
+allow the flat walls to move with a constant velocity, or oscillate in
+time.  The "fix wall/region"_fix_wall_region.html command offers the
+most generality, since the region surface is treated as a wall, and
+the geometry of the region can be a simple primitive volume (e.g. a
 sphere, or cube, or plane), or a complex volume made from the union
 and intersection of primitive volumes.  "Regions"_region.html can also
 specify a volume "interior" or "exterior" to the specified primitive

doc/src/Install_linux.txt

@@ -15,7 +15,8 @@ Binaries are available for different versions of Linux:
 "Pre-built Fedora Linux executables"_#fedora
 "Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
 "Pre-built OpenSuse Linux executables"_#opensuse
-"Gentoo Linux executable"_#gentoo :all(b)
+"Gentoo Linux executable"_#gentoo
+"Arch Linux build-script"_#arch :all(b)
 
 :line
 
@@ -168,3 +169,31 @@ for details.
 
 Thanks to Nicolas Bock and Christoph Junghans (LANL) for setting up
 this Gentoo capability.
+
+:line
+
+Archlinux build-script :h4,link(arch)
+
+LAMMPS is available via Arch's unofficial Arch User repository (AUR).
+
+There are three scripts available, named lammps, lammps-beta and lammps-git.
+They respectively package the stable, patch and git releases.
+
+To install, you will need to have the git package installed. You may use
+any of the above names in-place of lammps.
+
+$ git clone https://aur.archlinux.org/lammps.git :pre
+$ cd lammps :pre
+$ makepkg -s :pre
+# makepkg -i :pre
+
+To update, you may repeat the above, or change into the cloned directory,
+and execute the following, after which, if there are any changes, you may
+use makepkg as above.
+
+$ git pull :pre
+
+Alternatively, you may use an AUR helper to install these packages.
+
+Note that the AUR provides build-scripts that download the source and
+the build the package on your machine.

doc/src/Install_mac.txt

@@ -10,47 +10,34 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 Download an executable for Mac :h3
 
 LAMMPS can be downloaded, built, and configured for OS X on a Mac with
-"Homebrew"_homebrew.  Only four of the LAMMPS packages are unavailable
-at this time because of additional needs not yet met: KIM, GPU,
-USER-INTEL, USER-ATC.
+"Homebrew"_homebrew.  The following LAMMPS packages are unavailable at this
+time because of additional needs not yet met: GPU, KOKKOS, LATTE, MSCG,
+MESSAGE, MPIIO POEMS VORONOI.
 
 After installing Homebrew, you can install LAMMPS on your system with
 the following commands:
 
-% brew tap homebrew/science
-% brew install lammps              # serial version
-% brew install lammps --with-mpi   # mpi support :pre
+% brew install lammps :pre
 
-This will install the executable "lammps", a python module named
-"lammps", and additional resources with all the standard packages.  To
-get the location of the additional resources type this:
-
-% brew info lammps :pre
-
-This command also tells you additional installation options available.
-The user-packages are available as options, just install them like
-this example for the USER-OMP package:
-
-% brew install lammps --enable-user-omp :pre
-
-It is usually best to install LAMMPS with the most up to date source
-files, which can be done with the "--HEAD" option:
-
-% brew install lammps --HEAD :pre
-
-To re-install the LAMMPS HEAD, run this command occasionally (make sure
-to use the desired options).
-
-% brew install --force lammps --HEAD $\{options\} :pre
+This will install the executables "lammps_serial" and "lammps_mpi", as well as
+the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
 
 Once LAMMPS is installed, you can test the installation with the
 Lennard-Jones benchmark file:
 
 % brew test lammps -v :pre
 
+The LAMMPS binary is built with the "KIM package"_Build_extras#kim which
+results in Homebrew also installing the `kim-api` binaries when LAMMPS is
+installed.  In order to use potentials from "openkim.org"_openkim, you can
+install the `openkim-models` package
+
+% brew install openkim-models :pre
+
 If you have problems with the installation you can post issues to
 "this link"_homebrew.
 
 Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
 up the Homebrew capability.
-:link(homebrew,https://github.com/Homebrew/homebrew-science/issues)
+:link(homebrew,https://github.com/Homebrew/homebrew-core/issues)
+:link(openkim,https://openkim.org)

doc/src/Intro_features.txt

@@ -92,8 +92,8 @@ commands)
   implicit solvent potentials: hydrodynamic lubrication, Debye
   force-field compatibility with common CHARMM, AMBER, DREIDING, \
     OPLS, GROMACS, COMPASS options
-  access to "KIM archive"_http://openkim.org of potentials via \
-    "pair kim"_pair_kim.html
+  access to the "OpenKIM Repository"_http://openkim.org of potentials via \
+    "kim_init, kim_interactions, and kim_query"_kim_commands.html commands
   hybrid potentials: multiple pair, bond, angle, dihedral, improper \
     potentials can be used in one simulation
   overlaid potentials: superposition of multiple pair potentials :ul

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="18 Jun 2019 version">
+<META NAME="docnumber" CONTENT="19 Sep 2019 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 @@
 :line
 
 LAMMPS Documentation :c,h1
-18 Jun 2019 version :c,h2
+19 Sep 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -338,22 +338,37 @@ KIM package :link(PKG-KIM),h4
 
 [Contents:]
 
-A "pair_style kim"_pair_kim.html command which is a wrapper on the
-Knowledge Base for Interatomic Models (KIM) repository of interatomic
-potentials, enabling any of them to be used in LAMMPS simulations.
-Also a "kim_query"_kim_query.html command, which allows to query
-the OpenKIM database for stored properties.
+This package contains a set of commands that serve as a wrapper on the
+"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org
+repository of interatomic models (IMs)
+enabling compatible ones to be used in LAMMPS simulations.
+This includes "kim_init and kim_interactions"_kim_commands.html
+commands to select, initialize and instantiate the IM, and a
+"kim_query"_kim_commands.html command to perform web queries
+for material property predictions of OpenKIM IMs.
+Support for KIM IMs that conform to the
+"KIM Application Programming Interface (API)"_https://openkim.org/kim-api/
+is provided by the "pair_style kim"_pair_kim.html command.
 
-To use this package you must have the KIM library available on your
-system.
+NOTE: The command {pair_style kim} is called by {kim_interactions} and
+is not recommended to be directly used in input scripts.
+
+To use this package you must have the KIM API library available on your
+system. The KIM API is available for download on the
+"OpenKIM website"_https://openkim.org/kim-api/.
+When installing LAMMPS from binary, the kim-api package
+is a dependency that is automatically downloaded and installed.
 
 Information about the KIM project can be found at its website:
-https://openkim.org.  The KIM project is led by Ellad Tadmor and Ryan
-Elliott (U Minnesota).
+"https://openkim.org"_https://openkim.org.
+The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota)
+and is funded by the "National Science Foundation"_https://www.nsf.gov/.
 
 [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
-API which the "pair_style kim"_pair_kim.html command uses.  He
-developed the pair style.
+API and the {pair_style kim} command. Axel Kohlmeyer (Temple U) and
+Ellad Tadmor (U Minnesota) contributed to the "kim_commands"_kim_commands.html
+interface in close collaboration with Ryan Elliott.
+
 
 [Install:]
 
@@ -363,10 +378,11 @@ extras"_Build_extras.html doc page.
 
 [Supporting info:]
 
+"kim_commands"_kim_commands.html
+"pair_style kim"_pair_kim.html
 src/KIM: filenames -> commands
 src/KIM/README
 lib/kim/README
-"pair_style kim"_pair_kim.html
 examples/kim :ul
 
 :line
@@ -911,6 +927,8 @@ the usual manner via MD.  Various pair, fix, and compute styles.
 
 src/SPIN: filenames -> commands
 "Howto spins"_Howto_spins.html
+"pair_style spin/dipole/cut"_pair_spin_dipole.html
+"pair_style spin/dipole/long"_pair_spin_dipole.html
 "pair_style spin/dmi"_pair_spin_dmi.html
 "pair_style spin/exchange"_pair_spin_exchange.html
 "pair_style spin/magelec"_pair_spin_magelec.html
@@ -982,9 +1000,9 @@ USER-ADIOS package :link(PKG-USER-ADIOS),h4
 
 [Contents:]
 
-ADIOS is a high-performance I/O library. This package implements the 
+ADIOS is a high-performance I/O library. This package implements the
 dump "atom/adios" and dump "custom/adios" commands to write data using
-the ADIOS library. 
+the ADIOS library.
 
 [Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
 
@@ -1173,7 +1191,7 @@ USER-PLUMED package :link(PKG-USER-PLUMED),h4
 The fix plumed command allows you to use the PLUMED free energy plugin
 for molecular dynamics to analyze and bias your LAMMPS trajectory on
 the fly.  The PLUMED library is called from within the LAMMPS input
-script by using the "fix plumed _fix_plumed.html command.
+script by using the "fix plumed"_fix_plumed.html command.
 
 [Authors:] The "PLUMED library"_#PLUMED is written and maintained by
 Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth

doc/src/Run_options.txt

@@ -126,9 +126,10 @@ are intended for computational work like running LAMMPS.  By default
 Ng = 1 and Ns is not set.
 
 Depending on which flavor of MPI you are running, LAMMPS will look for
-one of these 3 environment variables
+one of these 4 environment variables
 
 SLURM_LOCALID (various MPI variants compiled with SLURM support)
+MPT_LRANK (HPE MPI)
 MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
 OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) :pre
 

doc/src/Speed_kokkos.txt

@@ -46,16 +46,15 @@ software version 7.5 or later must be installed on your system. See
 the discussion for the "GPU package"_Speed_gpu.html for details of how
 to check and do this.
 
-NOTE: Kokkos with CUDA currently implicitly assumes that the MPI
-library is CUDA-aware and has support for GPU-direct. This is not
-always the case, especially when using pre-compiled MPI libraries
-provided by a Linux distribution. This is not a problem when using
-only a single GPU and a single MPI rank on a desktop. When running
-with multiple MPI ranks, you may see segmentation faults without
-GPU-direct support.  These can be avoided by adding the flags "-pk
-kokkos gpu/direct off"_Run_options.html to the LAMMPS command line or
-by using the command "package kokkos gpu/direct off"_package.html in
-the input file.
+NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library
+is CUDA-aware. This is not always the case, especially when using
+pre-compiled MPI libraries provided by a Linux distribution. This is not
+a problem when using only a single GPU with a single MPI rank. When
+running with multiple MPI ranks, you may see segmentation faults without
+CUDA-aware MPI support. These can be avoided by adding the flags "-pk
+kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by
+using the command "package kokkos cuda/aware off"_package.html in the
+input file.
 
 [Building LAMMPS with the KOKKOS package:]
 
@@ -111,10 +110,10 @@ Makefile.kokkos_mpi_only) will give better performance than the OpenMP
 back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
 the code thread-safe is removed.
 
-NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html 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: 
+NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html 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 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
 
@@ -184,15 +183,15 @@ 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 when 
-running on KNL is to use "half" neighbor lists and set the Newton flag 
-to "on" for both pairwise and bonded interactions. This will typically 
-be best for many-body potentials. For simpler pair-wise potentials, it 
-may be faster to use a "full" neighbor list with Newton flag to "off". 
-Use the "-pk kokkos" "command-line switch"_Run_options.html 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: 
+NOTE: The default for the "package kokkos"_package.html command when
+running on KNL is to use "half" neighbor lists and set the Newton flag
+to "on" for both pairwise and bonded interactions. This will typically
+be best for many-body potentials. For simpler pair-wise potentials, it
+may be faster to use a "full" neighbor list with Newton flag to "off".
+Use the "-pk kokkos" "command-line switch"_Run_options.html 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 host -in in.reax      #  Newton on, half neighbor list, threaded comm
 mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj      # Newton off, full neighbor list, non-threaded comm :pre
@@ -207,20 +206,19 @@ supports.
 
 [Running on GPUs:]
 
-Use the "-k" "command-line switch"_Run_options.html 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 number 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 some 
-portions of the input script have not been ported to use Kokkos. In this 
-case, also packing/unpacking communication buffers on the host may give 
-speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS 
+Use the "-k" "command-line switch"_Run_options.html 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 number 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 some
+portions of the input script have not been ported to use Kokkos. In this
+case, also packing/unpacking communication buffers on the host may give
+speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS
 is recommended in this scenario.
 
-Using a CUDA-aware MPI library with 
-support for GPU-direct is highly recommended. GPU-direct use can be 
-avoided by using "-pk kokkos gpu/direct no"_package.html. As above for 
-multi-core CPUs (and no GPU), if N is the number of physical cores/node, 
+Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
+avoided by using "-pk kokkos cuda/aware no"_package.html. 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
@@ -231,18 +229,18 @@ 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 when 
-running on GPUs 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 twice the CPU default value will 
-give speedup, which is the default when running on GPUs. Use the "-pk 
-kokkos" "command-line switch"_Run_options.html 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: 
+NOTE: The default for the "package kokkos"_package.html command when
+running on GPUs 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 twice the CPU default value will
+give speedup, which is the default when running on GPUs. Use the "-pk
+kokkos" "command-line switch"_Run_options.html 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 newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre
 

doc/src/Tools.txt

@@ -76,9 +76,10 @@ Post-processing tools :h3
 "pymol_asphere"_#pymol,
 "python"_#pythontools,
 "reax"_#reax_tool,
+"replica"_#replica,
 "smd"_#smd,
 "spin"_#spin,
-"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
+"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l) 
 
 Miscellaneous tools :h3
 
@@ -485,6 +486,21 @@ README for more info on Pizza.py and how to use these scripts.
 
 :line
 
+replica tool :h4,link(replica)
+
+The tools/replica directory contains the reorder_remd_traj python script which
+can be used to reorder the replica trajectories (resulting from the use of the 
+temper command) according to temperature. This will produce discontinuous
+trajectories with all frames at the same temperature in each trajectory.
+Additional options can be used to calculate the canonical configurational
+log-weight for each frame at each temperature using the pymbar package. See
+the README.md file for further details. Try out the peptide example provided.
+
+This tool was written by (and is maintained by) Tanmoy Sanyal, 
+while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com) 
+
+:line
+
 reax tool :h4,link(reax_tool)
 
 The reax sub-directory contains stand-alone codes that can
@@ -515,13 +531,13 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
 spin tool :h4,link(spin)
 
 The spin sub-directory contains a C file interpolate.c which can
-be compiled and used to perform a cubic polynomial interpolation of 
+be compiled and used to perform a cubic polynomial interpolation of
 the MEP following a GNEB calculation.
 
 See the README file in tools/spin/interpolate_gneb for more details.
 
 This tool was written by the SPIN package author, Julien
-Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei 
+Tranchida at Sandia National Labs (jtranch at sandia.gov, and by Aleksei
 Ivanov, at University of Iceland (ali5 at hi.is).
 
 :line
@@ -549,3 +565,4 @@ simulation.
 See the README file for details.
 
 These files were provided by Vikas Varshney (vv0210 at gmail.com)
+

doc/src/angle_table.txt

@@ -143,6 +143,16 @@ instructions on how to use the accelerated styles effectively.
 
 :line
 
+[Restart info:]
+
+This angle style writes the settings for the "angle_style table"
+command to "binary restart files"_restart.html, so a angle_style
+command does not need to specified in an input script that reads a
+restart file.  However, the coefficient information is not stored in
+the restart file, since it is tabulated in the potential files.  Thus,
+angle_coeff commands do need to be specified in the restart input
+script.
+
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the

doc/src/bond_table.txt

@@ -140,6 +140,16 @@ instructions on how to use the accelerated styles effectively.
 
 :line
 
+[Restart info:]
+
+This bond style writes the settings for the "bond_style table"
+command to "binary restart files"_restart.html, so a bond_style
+command does not need to specified in an input script that reads a
+restart file.  However, the coefficient information is not stored in
+the restart file, since it is tabulated in the potential files.  Thus,
+bond_coeff commands do need to be specified in the restart input
+script.
+
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the MOLECULE

doc/src/comm_modify.txt

@@ -40,11 +40,12 @@ coordinates and other properties are exchanged between neighboring
 processors and stored as properties of ghost atoms.
 
 NOTE: These options apply to the currently defined comm style.  When
-you specify a "comm_style"_comm_style.html command, all communication
-settings are restored to their default values, including those
+you specify a "comm_style"_comm_style.html or
+"read_restart"_read_restart.html command, all communication settings
+are restored to their default or stored values, including those
 previously reset by a comm_modify command.  Thus if your input script
-specifies a comm_style command, you should use the comm_modify command
-after it.
+specifies a comm_style or read_restart command, you should use the
+comm_modify command after it.
 
 The {mode} keyword determines whether a single or multiple cutoff
 distances are used to determine which atoms to communicate.
@@ -69,9 +70,15 @@ processors.  By default the ghost cutoff = neighbor cutoff = pairwise
 force cutoff + neighbor skin.  See the "neighbor"_neighbor.html command
 for more information about the skin distance.  If the specified Rcut is
 greater than the neighbor cutoff, then extra ghost atoms will be acquired.
-If the provided cutoff is smaller, the provided value will be ignored
-and the ghost cutoff is set to the neighbor cutoff. Specifying a
-cutoff value of 0.0 will reset any previous value to the default.
+If the provided cutoff is smaller, the provided value will be ignored,
+the ghost cutoff is set to the neighbor cutoff and a warning will be
+printed. Specifying a cutoff value of 0.0 will reset any previous value
+to the default. If bonded interactions exist and equilibrium bond length
+information is available, then also a heuristic based on that bond length
+is computed. It is used as communication cutoff, if there is no pair
+style present and no {comm_modify cutoff} command used. Otherwise a
+warning is printed, if this bond based estimate is larger than the
+communication cutoff used. A
 
 The {cutoff/multi} option is equivalent to {cutoff}, but applies to
 communication mode {multi} instead. Since in this case the communication

doc/src/commands_list.txt

@@ -53,7 +53,7 @@ Commands :h1
    include
    info
    jump
-   kim_query
+   kim_commands
    kspace_modify
    kspace_style
    label

doc/src/compute.txt

@@ -171,42 +171,40 @@ The individual style names on the "Commands
 compute"_Commands_compute.html doc page are followed by one or more of
 (g,i,k,o,t) to indicate which accelerated styles exist.
 
-"ackland/atom"_compute_ackland_atom.html -
+"ackland/atom"_compute_ackland_atom.html - determines the local lattice structure based on the Ackland formulation
 "adf"_compute_adf.html - angular distribution function of triples of atoms
 "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
-"angle"_compute_angle.html -
-"angle/local"_compute_angle_local.html -
-"angle/local"_compute_bond_local.html - theta and energy of each angle
+"angle"_compute_angle.html - energy of each angle sub-style
+"angle/local"_compute_angle_local.html - theta and energy of each angle
 "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
-"basal/atom"_compute_basal_atom.html -
+"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed "c" lattice vector of each atom
 "body/local"_compute_body_local.html - attributes of body sub-particles
-"bond"_compute_bond.html - values computed by a bond style
+"bond"_compute_bond.html - energy of each bond sub-style
 "bond/local"_compute_bond_local.html - distance and energy of each bond
 "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
 "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
 "chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
 "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
 "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
-"cnp/atom"_compute_cnp_atom.html -
+"cnp/atom"_compute_cnp_atom.html - common neighborhood parameter (CNP) for each atom
 "com"_compute_com.html - center-of-mass of group of atoms
 "com/chunk"_compute_com_chunk.html - center-of-mass for each chunk
 "contact/atom"_compute_contact_atom.html - contact count for each spherical particle
 "coord/atom"_compute_coord_atom.html - coordination number for each atom
 "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom
-"dihedral"_compute_dihedral.html -
+"dihedral"_compute_dihedral.html - energy of each dihedral sub-style
 "dihedral/local"_compute_dihedral_local.html - angle of each dihedral
 "dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom
-"dipole/chunk"_compute_dipole_chunk.html -
+"dipole/chunk"_compute_dipole_chunk.html - dipole vector and total dipole for each chunk
 "displace/atom"_compute_displace_atom.html - displacement of each atom
 "dpd"_compute_dpd.html -
 "dpd/atom"_compute_dpd_atom.html -
-"edpd/temp/atom"_compute_edpd_temp_atom.html -
-"entropy/atom"_compute_entropy_atom.html -
+"edpd/temp/atom"_compute_edpd_temp_atom.html - per-atom temperature for each eDPD particle in a group
+"entropy/atom"_compute_entropy_atom.html - pair entropy fingerprint of each atom
 "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
 "erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies
 "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
-"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
-"erotate/sphere/atom"_compute_erotate_sphere_atom.html -
+"erotate/sphere/atom"_compute_erotate_sphere_atom.html - rotational energy for each spherical particle
 "event/displace"_compute_event_displace.html - detect event on atom displacement
 "fep"_compute_fep.html -
 "force/tally"_compute_tally.html -
@@ -215,20 +213,23 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "group/group"_compute_group_group.html - energy/force between two groups of atoms
 "gyration"_compute_gyration.html - radius of gyration of group of atoms
 "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
+"gyration/shape"_compute_gyration_shape.html - compute shape parameters from radius of gyration tensor
 "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
 "heat/flux/tally"_compute_tally.html -
 "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
-"improper"_compute_improper.html -
+"hma"_compute_hma.html - harmonically mapped averaging for atomic crystals
+"improper"_compute_improper.html - energy of each improper sub-style
 "improper/local"_compute_improper_local.html - angle of each improper
 "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
 "ke"_compute_ke.html - translational kinetic energy
 "ke/atom"_compute_ke_atom.html - kinetic energy for each atom
-"ke/atom/eff"_compute_ke_atom_eff.html -
-"ke/eff"_compute_ke_eff.html -
+"ke/atom/eff"_compute_ke_atom_eff.html - per-atom translational and radial kinetic energy in the electron force field model
+"ke/eff"_compute_ke_eff.html - kinetic energy of a group of nuclei and electrons in the electron force field model
 "ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies
-"meso/e/atom"_compute_meso_e_atom.html -
-"meso/rho/atom"_compute_meso_rho_atom.html -
-"meso/t/atom"_compute_meso_t_atom.html -
+"meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
+"meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
+"meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
+"momentum"_compute_momentum.html - translational momentum
 "msd"_compute_msd.html - mean-squared displacement of group of atoms
 "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
 "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms
@@ -242,73 +243,72 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "pe/tally"_compute_tally.html -
 "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
 "pressure"_compute_pressure.html - total pressure and pressure tensor
-"pressure/cylinder"_compute_pressure_cylinder.html -
-"pressure/uef"_compute_pressure_uef.html -
+"pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates
+"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field
 "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
 "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
 "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
-"ptm/atom"_compute_ptm_atom.html -
+"ptm/atom"_compute_ptm_atom.html - determines the local lattice structure based on the Polyhedral Template Matching method
 "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
 "reduce"_compute_reduce.html - combine per-atom quantities into a single global value
 "reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
 "reduce/region"_compute_reduce.html - same as compute reduce, within a region
 "rigid/local"_compute_rigid_local.html - extract rigid body attributes
-"saed"_compute_saed.html -
+"saed"_compute_saed.html - electron diffraction intensity on a mesh of reciprocal lattice nodes
 "slice"_compute_slice.html - extract values from global vector or array
 "smd/contact/radius"_compute_smd_contact_radius.html -
-"smd/damage"_compute_smd_damage.html -
+"smd/damage"_compute_smd_damage.html - damage status of SPH particles in Smooth Mach Dynamics
 "smd/hourglass/error"_compute_smd_hourglass_error.html -
-"smd/internal/energy"_compute_smd_internal_energy.html -
-"smd/plastic/strain"_compute_smd_plastic_strain.html -
-"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html -
-"smd/rho"_compute_smd_rho.html -
-"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html -
-"smd/tlsph/dt"_compute_smd_tlsph_dt.html -
+"smd/internal/energy"_compute_smd_internal_energy.html - per-particle enthalpy in Smooth Mach Dynamics
+"smd/plastic/strain"_compute_smd_plastic_strain.html - equivalent plastic strain per particle in Smooth Mach Dynamics
+"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - time rate of the equivalent plastic strain in Smooth Mach Dynamics
+"smd/rho"_compute_smd_rho.html - per-particle mass density in Smooth Mach Dynamics
+"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - deformation gradient in Smooth Mach Dynamics
+"smd/tlsph/dt"_compute_smd_tlsph_dt.html - CFL-stable time increment per particle in Smooth Mach Dynamics
 "smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html -
 "smd/tlsph/shape"_compute_smd_tlsph_shape.html -
 "smd/tlsph/strain"_compute_smd_tlsph_strain.html -
 "smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html -
-"smd/tlsph/stress"_compute_smd_tlsph_stress.html -
-"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
+"smd/tlsph/stress"_compute_smd_tlsph_stress.html - per-particle Cauchy stress tensor for SPH particles
 "smd/triangle/vertices"_compute_smd_triangle_vertices.html -
 "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html -
 "smd/ulsph/strain"_compute_smd_ulsph_strain.html -
 "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
-"smd/ulsph/stress"_compute_smd_ulsph_stress.html -
-"smd/vol"_compute_smd_vol.html -
+"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
+"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics
 "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
 "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
 "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
-"spin"_compute_spin.html -
+"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins
 "stress/atom"_compute_stress_atom.html - stress tensor for each atom
-"stress/mop"_compute_stress_mop.html -
-"stress/mop/profile"_compute_stress_mop.html -
+"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
+"stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes
 "stress/tally"_compute_tally.html -
-"tdpd/cc/atom"_compute_tdpd_cc_atom.html -
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle
 "temp"_compute_temp.html - temperature of group of atoms
 "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
 "temp/body"_compute_temp_body.html - temperature of body particles
 "temp/chunk"_compute_temp_chunk.html - temperature of each chunk
 "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
-"temp/cs"_compute_temp_cs.html -
+"temp/cs"_compute_temp_cs.html - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other
 "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
-"temp/deform/eff"_compute_temp_deform_eff.html -
-"temp/drude"_compute_temp_drude.html -
-"temp/eff"_compute_temp_eff.html -
+"temp/deform/eff"_compute_temp_deform_eff.html - temperature excluding box deformation velocity in the electron force field model
+"temp/drude"_compute_temp_drude.html - temperature of Core-Drude pairs
+"temp/eff"_compute_temp_eff.html - temperature of a group of nuclei and electrons in the electron force field model
 "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
 "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
 "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
 "temp/region"_compute_temp_region.html - temperature of a region of atoms
-"temp/region/eff"_compute_temp_region_eff.html -
-"temp/rotate"_compute_temp_rotate.html -
+"temp/region/eff"_compute_temp_region_eff.html - temperature of a region of nuclei and electrons in the electron force field model
+"temp/rotate"_compute_temp_rotate.html - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities
 "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
-"temp/uef"_compute_temp_uef.html -
+"temp/uef"_compute_temp_uef.html - kinetic energy tensor in the reference frame of an applied flow field
 "ti"_compute_ti.html - thermodynamic integration free energy values
 "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
 "vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms
 "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
 "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom
-"xrd"_compute_xrd.html - :ul
+"xrd"_compute_xrd.html - x-ray diffraction intensity on a mesh of reciprocal lattice nodes :ul
 
 [Restrictions:] none
 

doc/src/compute_bond_local.txt

@@ -15,10 +15,11 @@ compute ID group-ID bond/local value1 value2 ... keyword args ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 bond/local = style name of this compute command :l
 one or more values may be appended :l
-value = {dist} or {engpot} or {force} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
+value = {dist} or {engpot} or {force} or {fx} or {fy} or {fz} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
   {dist} = bond distance
   {engpot} = bond potential energy
   {force} = bond force :pre
+  {fx},{fy},{fz} = components of bond force
   {engvib} = bond kinetic energy of vibration
   {engrot} = bond kinetic energy of rotation
   {engtrans} = bond kinetic energy of translation
@@ -38,6 +39,7 @@ keyword = {set} :l
 
 compute 1 all bond/local engpot
 compute 1 all bond/local dist engpot force :pre
+compute 1 all bond/local dist fx fy fz :pre
 compute 1 all angle/local dist v_distsq set dist d :pre
 
 [Description:]
@@ -59,6 +61,9 @@ based on the current separation of the pair of atoms in the bond.
 The value {force} is the magnitude of the force acting between the
 pair of atoms in the bond.
 
+The values {fx}, {fy}, and {fz} are the xyz components of
+{force} between the pair of atoms in the bond.
+
 The remaining properties are all computed for motion of the two atoms
 relative to the center of mass (COM) velocity of the 2 atoms in the
 bond.

doc/src/compute_chunk_spread_atom.txt

@@ -30,11 +30,18 @@ compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre
 [Description:]
 
 Define a calculation that "spreads" one or more per-chunk values to
-each atom in the chunk.  This can be useful for creating a "dump
-file"_dump.html where each atom lists info about the chunk it is in,
-e.g. for post-processing purposes.  It can also be used in "atom-style
-variables"_variable.html that need info about the chunk each atom is
-in.  Examples are given below.
+each atom in the chunk.  This can be useful in several scenarios:
+
+For creating a "dump file"_dump.html where each atom lists info about
+the chunk it is in, e.g. for post-processing purposes. :ulb,l
+
+To access chunk value in "atom-style variables"_variable.html that
+need info about the chunk each atom is in. :l
+
+To use the "fix ave/chunk"_fix_ave_chunk.html command to spatially
+average per-chunk values calculated by a per-chunk compute. :l,ule
+
+Examples are given below.
 
 In LAMMPS, chunks are collections of atoms defined by a "compute
 chunk/atom"_compute_chunk_atom.html command, which assigns each atom
@@ -148,6 +155,28 @@ thermo_style    custom step etotal press v_ave :pre
 
 :line
 
+Here is an example for using one set of chunks, defined for molecules,
+to compute the dipole moment vector for each chunk.  E.g. for water
+molecules. Then spreading those values to each atom in each chunk.
+Then defining a second set of chunks based on spatial bins.  And
+finally, using the "fix ave/chunk"_fix_ave_chunk.html command to
+calculate an average dipole moment vector per spatial bin.
+
+compute       cmol all chunk/atom molecule
+compute       dipole all dipole/chunk cmol
+compute       spread all chunk/spread/atom cmol c_dipole\[1\] c_dipole\[2\] c_dipole\[3\]
+compute       cspatial all chunk/atom bin/1d z lower 0.1 units reduced
+fix           ave all ave/chunk 100 10 1000 cspatial c_spread\[*\] :pre
+
+Note that the "fix ave/chunk"_fix_ave_chunk.html command requires
+per-atom values as input.  That is why the compute chunk/spread/atom
+command is used to assign per-chunk values to each atom in the chunk.
+If a molecule straddles bin boundaries, each of its atoms contributes
+in a weighted manner to the average dipole moment of the spatial bin
+it is in.
+
+:line
+
 [Output info:]
 
 This compute calculates a per-atom vector or array, which can be

doc/src/compute_coord_atom.txt

@@ -47,7 +47,7 @@ neighboring atoms, unless selected by type, type range, or group option,
 are included in the coordination number tally.
 
 The optional {group} keyword allows to specify from which group atoms
-contribute to the coordination number. Default setting is group 'all'. 
+contribute to the coordination number. Default setting is group 'all'.
 
 The {typeN} keywords allow specification of which atom types
 contribute to each coordination number.  One coordination number is

doc/src/compute_gyration.txt

@@ -67,6 +67,7 @@ distance^2 "units"_units.html respectively.
 
 [Related commands:]
 
-"compute gyration/chunk"_compute_gyration_chunk.html
+"compute gyration/chunk"_compute_gyration_chunk.html,
+"compute gyration/shape"_compute_gyration_shape.html
 
 [Default:] none

doc/src/compute_gyration_shape.txt

@@ -0,0 +1,86 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+compute gyration/shape command :h3
+
+[Syntax:]
+
+compute ID group-ID gyration compute-ID :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+gyration/shape = style name of this compute command
+compute-ID = ID of "compute gyration"_compute_gyration.html command :ul
+
+[Examples:]
+
+compute 1 molecule gyration/shape pe :pre
+
+[Description:]
+
+Define a computation that calculates the eigenvalues of the gyration tensor of a
+group of atoms and three shape parameters. The computation includes all effects
+due to atoms passing thru periodic boundaries.
+
+The three computed shape parameters are the asphericity, b, the acylindricity, c,
+and the relative shape anisotropy, k:
+
+:c,image(Eqs/compute_shape_parameters.jpg)
+
+where lx <= ly <= lz are the three eigenvalues of the gyration tensor.
+The asphericity  is always non-negative and zero only when the three principal
+moments are equal. This zero condition is met when the distribution of particles
+is spherically symmetric (hence the name asphericity) but also whenever the particle
+distribution is symmetric with respect to the three coordinate axes, e.g.,
+when the particles are distributed uniformly on a cube, tetrahedron or other Platonic
+solid. The acylindricity is always non-negative and zero only when the two principal
+moments are equal. This zero condition is met when the distribution of particles is
+cylindrically symmetric (hence the name, acylindricity), but also whenever the particle
+distribution is symmetric with respect to the two coordinate axes, e.g., when the
+particles are distributed uniformly on a regular prism. the relative shape anisotropy
+is bounded between zero (if all points are spherically symmetric) and one
+(if all points lie on a line).
+
+NOTE: The coordinates of an atom contribute to the gyration tensor in
+"unwrapped" form, by using the image flags associated with each atom.
+See the "dump custom"_dump.html command for a discussion of "unwrapped"
+coordinates. See the Atoms section of the "read_data"_read_data.html
+command for a discussion of image flags and how they are set for each
+atom.  You can reset the image flags (e.g. to 0) before invoking this
+compute by using the "set image"_set.html command.
+
+[Output info:]
+
+This compute calculates a global vector of
+length 6, which can be accessed by indices 1-6. The first three values are the
+eigenvalues of the gyration tensor followed by the asphericity, the acylindricity
+and the relative shape anisotropy.  The computed values can be used by any command
+that uses global  vector values from a compute as input.  See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
+options.
+
+The vector values calculated by this compute are
+"intensive".  The first five vector values will be in
+distance^2 "units"_units.html while the sixth one is dimensionless.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"compute gyration"_compute_gyration.html
+
+[Default:] none
+
+:line
+
+:link(Theodorou)
+[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).
+

doc/src/compute_hexorder_atom.txt

@@ -65,7 +65,7 @@ In an isotropic liquid, local neighborhoods may still exhibit
 weak hexagonal symmetry, but because the orientational correlation
 decays quickly with distance, the value of phi will be different for
 different atoms, and so when {q}6 is averaged over all the atoms
-in the system, \|<{q}6>\| << 1.
+in the system, |<{q}6>| << 1.
 
 The value of {qn} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than

doc/src/compute_hma.txt

@@ -0,0 +1,184 @@
+"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 hma command :h3
+
+[Syntax:]
+
+compute ID group-ID hma temp-ID keyword ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :l
+hma = style name of this compute command :l
+temp-ID = ID of fix that specifies the set temperature during canonical simulation :l
+keyword = {anharmonic} {u} {p Pharm} {cv} :l
+  {anharmonic} = compute will return anharmonic property values
+  {u} = compute will return potential energy
+  {p} = compute will return pressure.  the following keyword must be the difference between the harmonic pressure and lattice pressure as described below
+  {cv} = compute will return the heat capacity :pre
+:ule
+
+[Examples:]
+
+compute 2 all hma 1 u
+compute 2 all hma 1 anharmonic u p 0.9
+compute 2 all hma 1 u cv :pre
+
+
+
+[Description:]
+
+Define a computation that calculates the properties of a solid (potential
+energy, pressure or heat capacity), using the harmonically-mapped averaging
+(HMA) method.
+This command yields much higher precision than the equivalent compute commands
+("compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html, etc.)
+commands during a canonical simulation of an atomic crystal. Specifically,
+near melting HMA can yield averages of a given precision an order of magnitude
+faster than conventional methods, and this only improves as the temperatures is
+lowered.  This is particularly important for evaluating the free energy by
+thermodynamic integration, where the low-temperature contributions are the
+greatest source of statistical uncertainty.  Moreover, HMA has other
+advantages, including smaller potential-truncation effects, finite-size
+effects, smaller timestep inaccuracy, faster equilibration and shorter
+decorrelation time.
+
+HMA should not be used if atoms are expected to diffuse.  It is also
+restricted to simulations in the NVT ensemble.  While this compute may be
+used with any potential in LAMMPS, it will provide inaccurate results
+for potentials that do not go to 0 at the truncation distance;
+"pair_lj_smooth_linear"_pair_lj_smooth_linear.html and Ewald summation should
+work fine, while "pair_lj"_pair_lj.html will perform poorly unless
+the potential is shifted (via "pair_modify"_pair_modify.html shift) or the cutoff is large.  Furthermore, computation of the heat capacity with
+this compute is restricted to those that implement the single_hessian method
+in Pair.  Implementing single_hessian in additional pair styles is simple.
+Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at
+buffalo.edu) if your desired pair style does not have this method.  This is
+the list of pair styles that currently implement pair_hessian:
+
+"lj_smooth_linear"_pair_lj_smooth_linear.html :l
+:ule
+
+In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble
+averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination
+by noise produced by the already-known harmonic behavior.
+A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa). The potential energy is computed by the formula:
+
+\begin\{equation\}
+\left< U\right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B T  + \left< U + \frac\{1\}\{2\} F\bullet\Delta r \right>
+\end\{equation\}
+
+where \(N\) is the number of atoms in the system, \(k_B\) is Boltzmann's
+constant, \(T\) is the temperature, \(d\) is the
+dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the
+atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of
+pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies.
+
+The pressure is computed by the formula:
+
+\begin\{equation\}
+\left< P\right>_\{HMA\} = \Delta \hat P + \left< P_\{vir\} + \frac\{\beta \Delta \hat P - \rho\}\{d(N-1)\} F\bullet\Delta r \right>
+\end\{equation\}
+
+where \(\rho\) is the number density of the system, \(\Delta \hat P\) is the
+difference between the harmonic and lattice pressure, \(P_\{vir\}\) is
+the virial pressure computed as the sum of pair, bond, angle, dihedral,
+improper, kspace (long-range), and fix contributions to the force on each
+atom, and \(k_B=1/k_B T\).  Although the method will work for any value of \(\Delta \hat P\)
+specified (use pressure "units"_units.html), the precision of the resultant
+pressure is sensitive to \(\Delta \hat P\); the precision tends to be
+best when \(\Delta \hat P\) is the actual the difference between the lattice
+pressure and harmonic pressure.
+
+\begin\{equation\}
+\left<C_V \right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B + \frac\{1\}\{k_B T^2\} \left( \left<
+U_\{HMA\}^2 \right> - \left<U_\{HMA\}\right>^2 \right) + \frac\{1\}\{4 T\}
+\left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right>
+\end\{equation\}
+
+where \(\Phi\) is the Hessian matrix. The compute hma command
+computes the full expression for \(C_V\) except for the
+\(\left<U_\{HMA\}^2\right>^2\) in the variance term, which can be obtained by
+passing the {u} keyword; you must add this extra contribution to the \(C_V\)
+value reported by this compute.  The variance term can cause significant
+round-off error when computing \(C_V\).  To address this, the {anharmonic}
+keyword can be passed and/or the output format can be specified with more
+digits.
+
+thermo_modify format float '%22.15e' :pre
+
+The {anharmonic} keyword will instruct the compute to return anharmonic
+properties rather than the full properties, which include lattice, harmonic
+and anharmonic contributions.
+When using this keyword, the compute must be first active (it must be included
+via a "thermo_style custom"_thermo_style.html command) while the atoms are
+still at their lattice sites (before equilibration).
+
+The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or
+Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat
+("fix langevin"_fix_langevin.html)
+should be avoided as its extra forces interfere with the HMA implementation.
+
+
+
+NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites.
+The simulation should not be started before this command has been used in the input script.
+
+
+The following example illustrates the placement of this command in the input script:
+
+
+min_style cg
+minimize 1e-35 1e-15 50000 500000
+compute 1 all hma thermostatid u
+fix thermostatid all nvt temp 600.0 600.0 100.0 :pre
+
+
+
+NOTE: Compute hma should be used when the atoms of the solid do not diffuse. Diffusion will reduce the precision in the potential energy computation.
+
+
+NOTE: The "fix_modify energy yes"_fix_modify.html command must also be specified if a fix is to contribute potential energy to this command.
+
+An example input script that uses this compute is included in
+examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA
+properties fluctuate less than the corresponding conventional properties.
+
+[Output info:]
+
+This compute calculates a global vector that includes the n properties
+requested as arguments to the command (the potential energy, pressure and/or heat
+capacity).  The elements of the vector can be accessed by indices 1-n by any
+command that uses global vector values as input.  See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output options.
+
+The vector values calculated by this compute are "extensive".  The
+scalar value will be in energy "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is enabled only
+if LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+Usage restricted to canonical (NVT) ensemble simulation only.
+
+[Related commands:]
+
+"compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html
+
+"dynamical matrix"_dynamical_matrix.html provides a finite difference
+formulation of the hessian provided by Pair's single_hessian, which is used by
+this compute.
+
+[Default:] none
+
+:line
+
+:link(hma-Moustafa)
+[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation},
+"Phys. Rev. E \[92\], 043303 (2015)"_https://link.aps.org/doi/10.1103/PhysRevE.92.043303

doc/src/compute_momentum.txt

@@ -0,0 +1,49 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+compute momentum command :h3
+
+[Syntax:]
+
+compute ID group-ID momentum :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+momentum = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all momentum :pre
+
+[Description:]
+
+Define a computation that calculates the translational momentum
+of a group of particles.
+
+The momentum of each particles is computed as m v, where m and v are
+the mass and velocity of the particle.
+
+[Output info:]
+
+This compute calculates a global vector (the summed momentum) of
+length 3. This value can be used by any command that uses a global
+vector value from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
+options.
+
+The vector value calculated by this compute is "extensive". The vector
+value will be in mass*velocity "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+[Default:] none

doc/src/compute_orientorder_atom.txt

@@ -19,6 +19,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
   {cutoff} value = distance cutoff
   {nnn} value = number of nearest neighbors
   {degrees} values = nlvalues, l1, l2,...
+  {wl} value = yes or no
+  {wl/hat} value = yes or no
   {components} value = ldegree  :pre
 
 :ule
@@ -27,7 +29,8 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
 
 compute 1 all orientorder/atom
 compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
-compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre
+compute 1 all orientorder/atom wl/hat yes
+compute 1 all orientorder/atom components 6 :pre
 
 [Description:]
 
@@ -48,7 +51,7 @@ neighbors of the central atom.
 The angles theta and phi are the standard spherical polar angles
 defining the direction of the bond vector {rij}.
 The second equation defines {Ql}, which is a
-rotationally invariant scalar quantity obtained by summing
+rotationally invariant non-negative amplitude obtained by summing
 over all the components of degree {l}.
 
 The optional keyword {cutoff} defines the distance cutoff
@@ -63,7 +66,7 @@ specified distance cutoff are used.
 
 The optional keyword {degrees} defines the list of order parameters to
 be computed.  The first argument {nlvalues} is the number of order
-parameters. This is followed by that number of integers giving the
+parameters. This is followed by that number of non-negative 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,
@@ -71,7 +74,20 @@ parameters are zero for atoms in cubic crystals (see
 = sqrt(7/3)/8 = 0.19094....  The numerical values of all order
 parameters up to {Q}12 for a range of commonly encountered
 high-symmetry structures are given in Table I of "Mickel et
-al."_#Mickel.
+al."_#Mickel, and these can be reproduced with this compute
+
+The optional keyword {wl} will output the third-order invariants {Wl}
+(see Eq. 1.4 in "Steinhardt"_#Steinhardt) for the same degrees as
+for the {Ql} parameters. For the FCC crystal with {nnn} =12,
+{W}4 = -sqrt(14/143).(49/4096)/Pi^1.5 = -0.0006722136...
+
+The optional keyword {wl/hat} will output the normalized third-order
+invariants {Wlhat} (see Eq. 2.2 in "Steinhardt"_#Steinhardt)
+for the same degrees as for the {Ql} parameters. For the FCC crystal
+with {nnn} =12, {W}4hat = -7/3*sqrt(2/429) = -0.159317...The numerical
+values of {Wlhat} for a range of commonly encountered high-symmetry
+structures are given in Table I of "Steinhardt"_#Steinhardt, and these
+can be reproduced with this keyword.
 
 The optional keyword {components} will output the components of the
 normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
@@ -82,7 +98,7 @@ particles, as discussed in "ten Wolde"_#tenWolde2.
 
 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
-{nnn} neighbors within the distance cutoff.
+{nnn} neighbors within the distance cutoff, unless {nnn} is NULL.
 
 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@@ -108,6 +124,12 @@ This compute calculates a per-atom array with {nlvalues} columns,
 giving the {Ql} values for each atom, which are real numbers on the
 range 0 <= {Ql} <= 1.
 
+If the keyword {wl} is set to yes, then the {Wl} values for each
+atom will be added to the output array, which are real numbers.
+
+If the keyword {wl/hat} is set to yes, then the {Wl_hat}
+values for each atom will be added to the output array, which are real numbers.
+
 If the keyword {components} is set, then the real and imaginary parts
 of each component of (normalized) {Ybar_lm} will be added to the
 output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
@@ -130,7 +152,8 @@ hexorder/atom"_compute_hexorder_atom.html
 [Default:]
 
 The option defaults are {cutoff} = pair style cutoff, {nnn} = 12,
-{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12,
+{wl} = no, {wl/hat} = no, and {components} off
 
 :line
 

doc/src/compute_pair_local.txt

@@ -64,6 +64,23 @@ which calculate the tangential force between two particles and return
 its components and magnitude acting on atom I for N = 1,2,3,4.  See
 individual pair styles for details.
 
+When using {pN} with pair style {hybrid}, the output will be the Nth
+quantity from the sub-style that computes the pairwise interaction
+(based on atom types).  If that sub-style does not define a {pN},
+the output will be 0.0.  The maximum allowed N is the maximum number
+of quantities provided by any sub-style.
+
+When using {pN} with pair style {hybrid/overlay} the quantities
+from all sub-styles that provide them are concatenated together
+into one long list. For example, if there are 3 sub-styles and
+2 of them have additional output (with 3 and 4 quantities,
+respectively), then 7 values ({p1} up to {p7}) are defined.
+The values {p1} to {p3} refer to quantities defined by the first
+of the two sub-styles.  Values {p4} to {p7} refer to quantities
+from the second of the two sub-styles.  If the referenced {pN}
+is not computed for the specific pairwise interaction (based on
+atom types), then the output will be 0.0.
+
 The value {dist} will be in distance "units"_units.html.  The value
 {eng} will be in energy "units"_units.html.  The values {force}, {fx},
 {fy}, and {fz} will be in force "units"_units.html.  The values {pN}
@@ -126,7 +143,7 @@ options.
 The output for {dist} will be in distance "units"_units.html.  The
 output for {eng} will be in energy "units"_units.html.  The output for
 {force}, {fx}, {fy}, and {fz} will be in force "units"_units.html.
-The outpur for {pN} will be in whatever units the pair style defines.
+The output for {pN} will be in whatever units the pair style defines.
 
 [Restrictions:] none
 

doc/src/compute_pressure.txt

@@ -16,12 +16,13 @@ ID, group-ID are documented in "compute"_compute.html command
 pressure = 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
+keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} or {pair/hybrid} :ul
 
 [Examples:]
 
 compute 1 all pressure thermo_temp
-compute 1 all pressure NULL pair bond :pre
+compute 1 all pressure NULL pair bond
+compute 1 all pressure NULL pair/hybrid lj/cut :pre
 
 [Description:]
 
@@ -67,6 +68,9 @@ extra keywords are listed, then only those components are summed to
 compute temperature or ke and/or the virial.  The {virial} keyword
 means include all terms except the kinetic energy {ke}.
 
+The {pair/hybrid} keyword means to only include contribution
+from a sub-style in a {hybrid} or {hybrid/overlay} pair style.
+
 Details of how LAMMPS computes the virial efficiently for the entire
 system, including for many-body potentials and accounting for the
 effects of periodic boundary conditions are discussed in

doc/src/compute_sna_atom.txt

@@ -196,7 +196,7 @@ for j1 in range(0,twojmax+1):
             if (j>=j1): print j1/2.,j2/2.,j/2. :pre
 
 NOTE: the {diagonal} keyword allowing other possible choices
-for the number of bispectrum components was removed in 2019, 
+for the number of bispectrum components was removed in 2019,
 since all potentials use the value of 3, corresponding to the
 above set of bispectrum components.
 

doc/src/compute_spin.txt

@@ -40,14 +40,14 @@ The simplest way to output the results of the compute spin calculation
 is to define some of the quantities as variables, and to use the thermo and
 thermo_style commands, for example:
 
-compute out_mag		all spin :pre
+compute out_mag         all spin :pre
 
-variable mag_z      	equal c_out_mag\[3\]
-variable mag_norm	equal c_out_mag\[4\]
-variable temp_mag      	equal c_out_mag\[6\] :pre
+variable mag_z          equal c_out_mag\[3\]
+variable mag_norm       equal c_out_mag\[4\]
+variable temp_mag       equal c_out_mag\[6\] :pre
 
-thermo          	10
-thermo_style    	custom step v_mag_z v_mag_norm v_temp_mag :pre
+thermo                  10
+thermo_style            custom step v_mag_z v_mag_norm v_temp_mag :pre
 
 This series of commands evaluates the total magnetization along z, the norm of
 the total magnetization, and the magnetic temperature. Three variables are

doc/src/computes.txt

@@ -44,8 +44,10 @@ Computes :h1
    compute_group_group
    compute_gyration
    compute_gyration_chunk
+   compute_gyration_shape
    compute_heat_flux
    compute_hexorder_atom
+   compute_hma
    compute_improper
    compute_improper_local
    compute_inertia_chunk
@@ -57,6 +59,7 @@ Computes :h1
    compute_meso_e_atom
    compute_meso_rho_atom
    compute_meso_t_atom
+   compute_momentum
    compute_msd
    compute_msd_chunk
    compute_msd_nongauss

doc/src/create_atoms.txt

@@ -242,9 +242,8 @@ write_dump      all atom sinusoid.lammpstrj :pre
 
 :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
 
-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
+The {rotate} keyword allows specification of the orientation
+at which molecules are 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

doc/src/dihedral_harmonic.txt

@@ -8,6 +8,7 @@
 
 dihedral_style harmonic command :h3
 dihedral_style harmonic/intel command :h3
+dihedral_style harmonic/kk command :h3
 dihedral_style harmonic/omp command :h3
 
 [Syntax:]