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

@@ -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")
+endif()
+if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
   add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
-  endif()
 endif()
 
 option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
@@ -229,6 +257,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
     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})
@@ -567,6 +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)

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})
@@ -7,10 +8,17 @@ 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()
-    if (NOT DOWNLOAD_KIM)
-      message(WARNING "KIM-API package not found.  We will download and build our own")
+      set(DOWNLOAD_KIM_DEFAULT OFF)
+    endif()
+  else()
+    if ("${DOWNLOAD_KIM}" STREQUAL "")
+      message(WARNING "KIM-API package not found.  Default behavior set to download and build our own")
     endif()
     set(DOWNLOAD_KIM_DEFAULT ON)
   endif()
@@ -28,8 +36,8 @@ if(PKG_KIM)
       message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
     endif()
     ExternalProject_Add(kim_build
-      URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz
-      URL_MD5 6ac52e14ef52967fc7858220b208cba5
+      URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
+      URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
       BINARY_DIR build
       CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
                  -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
@@ -42,7 +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/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/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/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "2 August 2019" "2019-08-02"
+.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

@@ -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

@@ -120,7 +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
@@ -354,6 +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]:
 
@@ -366,6 +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
@@ -798,7 +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

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_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_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,

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_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/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_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/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="2 Aug 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
-2 Aug 2019 version :c,h2
+19 Sep 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -1191,7 +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/Tools.txt

@@ -76,6 +76,7 @@ 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) 
@@ -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
@@ -549,3 +565,4 @@ simulation.
 See the README file for details.
 
 These files were provided by Vikas Varshney (vv0210 at gmail.com)
+

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.

doc/src/compute.txt

@@ -217,6 +217,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "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
+"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

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_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_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/computes.txt

@@ -47,6 +47,7 @@ Computes :h1
    compute_gyration_shape
    compute_heat_flux
    compute_hexorder_atom
+   compute_hma
    compute_improper
    compute_improper_local
    compute_inertia_chunk

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:]

doc/src/dump.txt

@@ -21,7 +21,8 @@ dump ID group-ID style N file args :pre
 
 ID = user-assigned name for the dump :ulb,l
 group-ID = ID of the group of atoms to be dumped :l
-style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
+style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or
+{cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {local/gz} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
 N = dump every this many timesteps :l
 file = name of file to write dump info to :l
 args = list of arguments for a particular style :l

doc/src/dump_modify.txt

@@ -50,6 +50,7 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
   {sfactor} arg = coordinate scaling factor (> 0.0)
   {thermo} arg = {yes} or {no}
   {tfactor} arg = time scaling factor (> 0.0)
+  {units} arg = {yes} or {no}
   {sort} arg = {off} or {id} or N or -N
      off = no sorting of per-atom lines within a snapshot
      id = sort per-atom lines by atom ID
@@ -620,6 +621,21 @@ threshold criterion is met.  Otherwise it is not met.
 
 :line
 
+The {units} keyword only applies to the dump {atom}, {custom}, and
+{local} styles (and their COMPRESS package versions {atom/gz},
+{custom/gz} and {local/gz}). If set to {yes}, each individual dump
+file will contain two extra lines at the very beginning with:
+
+ITEM: UNITS
+\<units style\> :pre
+
+This will output the current selected "units"_units.html style
+to the dump file and thus allows visualization and post-processing
+tools to determine the choice of units of the data in the dump file.
+The default setting is {no}.
+
+:line
+
 The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
 If set to {yes}, coordinates will be written "unwrapped" by the image
 flags for each atom.  Unwrapped means that if the atom has passed through
@@ -924,6 +940,7 @@ scale = yes
 sort = off for dump styles {atom}, {custom}, {cfg}, and {local}
 sort = id for dump styles {dcd}, {xtc}, and {xyz}
 thresh = none
+units = no
 unwrap = no :ul
 
 acolor = * red/green/blue/yellow/aqua/cyan

doc/src/dynamical_matrix.txt

@@ -47,6 +47,9 @@ package"_Build_package.html doc page for more info.
 
 "fix phonon"_fix_phonon.html
 
+"compute hma"_compute_hma.html uses an analytic formulation of the hessian
+provided by Pair's single_hessian.
+
 [Default:]
 
 The default settings are file = "dynmat.dyn", binary = no

doc/src/fix.txt

@@ -244,7 +244,7 @@ accelerated styles exist.
 "mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
 "msst"_fix_msst.html - multi-scale shock technique (MSST) integration
 "mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
-"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm
+"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm
 "mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
 "neb"_fix_neb.html - nudged elastic band (NEB) spring forces
 "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
@@ -371,6 +371,7 @@ accelerated styles exist.
 "wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall
 "wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
 "wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall
+"wall/morse"_fix_wall.html - Morse potential wall
 "wall/piston"_fix_wall_piston.html - moving reflective piston wall
 "wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
 "wall/region"_fix_wall_region.html - use region surface as wall

doc/src/fix_bond_react.txt

@@ -186,20 +186,25 @@ reacting atoms.
 
 Some atoms in the pre-reacted template that are not reacting may have
 missing topology with respect to the simulation. For example, the
-pre-reacted template may contain an atom that would connect to the
-rest of a long polymer chain. These are referred to as edge atoms, and
-are also specified in the map file. When the pre-reaction template
-contains edge atoms, not all atoms, bonds, charges, etc. specified in
-the reaction templates will be updated. Specifically, topology that
-involves only atoms that are 'too near' to template edges will not be
-updated. The definition of 'too near the edge' depends on which
-interactions are defined in the simulation. If the simulation has
-defined dihedrals, atoms within two bonds of edge atoms are considered
-'too near the edge.' If the simulation defines angles, but not
-dihedrals, atoms within one bond of edge atoms are considered 'too
-near the edge.' If just bonds are defined, only edge atoms are
+pre-reacted template may contain an atom that, in the simulation, is
+currently connected to the rest of a long polymer chain. These are
+referred to as edge atoms, and are also specified in the map file. All
+pre-reaction template atoms should be linked to a bonding atom, via at
+least one path that does not involve edge atoms. When the pre-reaction
+template contains edge atoms, not all atoms, bonds, charges, etc.
+specified in the reaction templates will be updated. Specifically,
+topology that involves only atoms that are 'too near' to template
+edges will not be updated. The definition of 'too near the edge'
+depends on which interactions are defined in the simulation. If the
+simulation has defined dihedrals, atoms within two bonds of edge atoms
+are considered 'too near the edge.' If the simulation defines angles,
+but not dihedrals, atoms within one bond of edge atoms are considered
+'too near the edge.' If just bonds are defined, only edge atoms are
 considered 'too near the edge.'
 
+NOTE: Small molecules, i.e. ones that have all their atoms contained
+within the reaction templates, never have edge atoms.
+
 Note that some care must be taken when a building a molecule template
 for a given simulation. All atom types in the pre-reacted template
 must be the same as those of a potential reaction site in the
@@ -392,10 +397,11 @@ local command.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-No information about this fix is written to "binary restart
-files"_restart.html, aside from internally-created per-atom
-properties. None of the "fix_modify"_fix_modify.html options are
-relevant to this fix.
+Cumulative reaction counts for each reaction are written to "binary
+restart files"_restart.html. These values are associated with the
+reaction name (react-ID). Additionally, internally-created per-atom
+properties are stored to allow for smooth restarts. None of the
+"fix_modify"_fix_modify.html options are relevant to this fix.
 
 This fix computes one statistic for each {react} argument that it
 stores in a global vector, of length 'number of react arguments', that
@@ -406,8 +412,8 @@ These is 1 quantity for each react argument:
 
 (1) cumulative # of reactions occurred :ul
 
-No parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command.  This fix is not invoked during "energy
+No parameter of this fix can be used with the {start/stop} keywords
+of the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.
 
 When fix bond/react is 'unfixed,' all internally-created groups are
@@ -417,18 +423,20 @@ all other fixes that use any group created by fix bond/react.
 [Restrictions:]
 
 This fix 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.
+LAMMPS was built with that package.  See the
+"Build package"_Build_package.html doc page for more info.
 
 [Related commands:]
 
-"fix bond/create"_fix_bond_create.html, "fix
-bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
+"fix bond/create"_fix_bond_create.html,
+"fix bond/break"_fix_bond_break.html,
+"fix bond/swap"_fix_bond_swap.html,
 "dump local"_dump.html, "special_bonds"_special_bonds.html
 
 [Default:]
 
-The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none
+The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
+update_edges = none
 
 :line
 

doc/src/fix_controller.txt

@@ -31,7 +31,6 @@ cvar = name of control variable :l
 
 [Examples:]
 
-		
 fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
 fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
 fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol :pre

doc/src/fix_wall.txt

@@ -12,15 +12,17 @@ fix wall/lj126 command :h3
 fix wall/lj1043 command :h3
 fix wall/colloid command :h3
 fix wall/harmonic command :h3
+fix wall/morse command :h3
 
 [Syntax:]
 
 fix ID group-ID style face args ... keyword value ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
-style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} :l
+style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} or {wall/morse} :l
 one or more face/arg pairs may be appended :l
 face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
+  args for styles {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} :l
     args = coord epsilon sigma cutoff
     coord = position of wall = EDGE or constant or variable
       EDGE = current lo or hi edge of simulation box
@@ -31,6 +33,19 @@ face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
     sigma = size factor for wall-particle interaction (distance units)
       sigma can be a variable (see below)
     cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
+  args for style {morse} :l
+    args = coord D_0 alpha r_0 cutoff
+    coord = position of wall = EDGE or constant or variable
+      EDGE = current lo or hi edge of simulation box
+      constant = number like 0.0 or -30.0 (distance units)
+      variable = "equal-style variable"_variable.html like v_x or v_wiggle
+    D_0 = depth of the potential (energy units)
+      D_0 can be a variable (see below)
+    alpha = width factor for wall-particle interaction (1/distance units)
+      alpha can be a variable (see below)
+    r_0 = distance of the potential minimum from the face of region (distance units)
+      r_0 can be a variable (see below)
+    cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
 zero or more keyword/value pairs may be appended :l
 keyword = {units} or {fld} :l
   {units} value = {lattice} or {box}
@@ -48,6 +63,7 @@ keyword = {units} or {fld} :l
 
 fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
 fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
+fix wallhi all wall/morse xhi EDGE 1.0 1.0 1.0 2.5 units box
 fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
 fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre
 
@@ -80,6 +96,10 @@ potential:
 
 :c,image(Eqs/fix_wall_harmonic.jpg)
 
+For style {wall/morse}, the energy E is given by a Morse potential:
+
+:c,image(Eqs/pair_morse.jpg)
+
 In all cases, {r} is the distance from the particle to the wall at
 position {coord}, and Rc is the {cutoff} distance at which the
 particle and wall no longer interact.  The energy of the wall
@@ -147,7 +167,13 @@ constant K, and has units (energy/distance^2).  The input parameter
 spring is at the {cutoff}.  This is a repulsive-only spring since the
 interaction is truncated at the {cutoff}
 
-For any wall, the {epsilon} and/or {sigma} parameter can be specified
+For the {wall/morse} style, the three parameters are in this order:
+{D_0} the depth of the potential, {alpha} the width parameter, and
+{r_0} the location of the minimum.  {D_0} has energy units, {alpha}
+inverse distance units, and {r_0} distance units.
+
+For any wall, the {epsilon} and/or {sigma} and/or {alpha} parameter can
+be specified
 as an "equal-style variable"_variable.html, in which case it should be
 specified as v_name, where name is the variable name.  As with a
 variable wall position, the variable is evaluated each timestep and

doc/src/fix_wall_region.txt

@@ -10,19 +10,27 @@ fix wall/region command :h3
 
 [Syntax:]
 
-fix ID group-ID wall/region region-ID style epsilon sigma cutoff :pre
+fix ID group-ID wall/region region-ID style args ... cutoff :pre
 
-ID, group-ID are documented in "fix"_fix.html command
-wall/region = style name of this fix command
-region-ID = region whose boundary will act as wall
-style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic}
-epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
-sigma = size factor for wall-particle interaction (distance units)
-cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :ul
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+wall/region = style name of this fix command :l
+region-ID = region whose boundary will act as wall :l
+style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} or {morse} :l
+args for styles {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic} = :l
+   epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
+   sigma = size factor for wall-particle interaction (distance units) :pre
+args for style {morse} = :l
+   D_0 = depth of the potential (energy units)
+   alpha = width parameter (1/distance units)
+   r_0 = distance of the potential minimum from wall position (distance units) :pre
+cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l
+:ule
 
 [Examples:]
 
-fix wall all wall/region mySphere lj93 1.0 1.0 2.5 :pre
+fix wall all wall/region mySphere lj93 1.0 1.0 2.5
+fix wall all wall/region mySphere harmonic 1.0 0.0 2.5
+fix wall all wall/region box_top morse 1.0 1.0 1.5 3.0 :pre
 
 [Description:]
 
@@ -122,15 +130,22 @@ the "pair_style colloid"_pair_colloid.html potential:
 :c,image(Eqs/fix_wall_colloid.jpg)
 
 For style {wall/harmonic}, the energy E is given by a harmonic spring
-potential:
+potential (the distance parameter is ignored):
 
 :c,image(Eqs/fix_wall_harmonic.jpg)
 
+For style {wall/morse}, the energy E is given by the Morse potential:
+
+:c,image(Eqs/pair_morse.jpg)
+
+Unlike other styles, this requires three parameters ({D_0}, {alpha}, {r_0}
+in this order) instead of two like for the other wall styles.
+
 In all cases, {r} is the distance from the particle to the region
 surface, and Rc is the {cutoff} distance at which the particle and
-surface no longer interact.  The energy of the wall potential is
-shifted so that the wall-particle interaction energy is 0.0 at the
-cutoff distance.
+surface no longer interact.  The cutoff is always the last argument.
+The energy of the wall potential is shifted so that the wall-particle
+interaction energy is 0.0 at the cutoff distance.
 
 For a full description of these wall styles, see fix_style
 "wall"_fix_wall.html
@@ -179,7 +194,9 @@ option for this fix.
 
 "fix wall/lj93"_fix_wall.html,
 "fix wall/lj126"_fix_wall.html,
+"fix wall/lj1043"_fix_wall.html,
 "fix wall/colloid"_fix_wall.html,
+"fix wall/harmonic"_fix_wall.html,
 "fix wall/gran"_fix_wall_gran.html
 
 [Default:] none

doc/src/improper_fourier.txt

@@ -16,7 +16,7 @@ improper_style fourier :pre
 [Examples:]
 
 improper_style fourier
-improper_coeff 1 100.0 180.0 :pre
+improper_coeff 1 100.0 0.0 1.0 0.5 1 :pre
 
 [Description:]
 
@@ -24,12 +24,12 @@ The {fourier} improper style uses the following potential:
 
 :c,image(Eqs/improper_fourier.jpg)
 
-where K is the force constant and omega is the angle between the IL
-axis and the IJK plane:
+where K is the force constant, C0, C1, C2 are dimensionless coefficients,
+and omega is the angle between the IL axis and the IJK plane:
 
 :c,image(JPG/umbrella.jpg)
 
-If all parameter (see bellow) is not zero, the all the three possible angles will taken in account.
+If all parameter (see below) is not zero, the all the three possible angles will taken in account.
 
 The following coefficients must be defined for each improper type via
 the "improper_coeff"_improper_coeff.html command as in the example
@@ -38,10 +38,10 @@ above, or in the data file or restart files read by the
 commands:
 
 K (energy)
-C0 (real)
-C1 (real)
-C2 (real)
-all  (integer >= 0) :ul
+C0 (unitless)
+C1 (unitless)
+C2 (unitless)
+all  (0 or 1, optional) :ul
 
 :line
 

doc/src/kim_commands.txt

@@ -365,7 +365,7 @@ an array of one or more comma-separated items in brackets.
 The list of supported keywords and the type and format of their values
 depend on the query function used. The current list of query functions
 is available on the OpenKIM webpage at
-"https://openkim.org/doc/repository/kim-query"_https://openkim.org/doc/repository/kim-query.
+"https://openkim.org/doc/usage/kim-query"_https://openkim.org/doc/usage/kim-query.
 
 NOTE: All query functions require the {model} keyword, which identifies
 the IM whose predictions are being queried. This keyword is automatically

doc/src/lammps.book

@@ -569,6 +569,7 @@ pair_charmm.html
 pair_class2.html
 pair_colloid.html
 pair_comb.html
+pair_cosine_squared.html
 pair_coul.html
 pair_coul_diel.html
 pair_coul_shield.html
@@ -610,6 +611,7 @@ pair_lj_smooth.html
 pair_lj_smooth_linear.html
 pair_fep_soft.html
 pair_lj_switch3_coulgauss.html
+pair_local_density.html
 pair_lubricate.html
 pair_lubricateU.html
 pair_mdf.html

doc/src/min_style.txt

@@ -11,7 +11,7 @@ min_style command :h3
 
 min_style style :pre
 
-style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
+style = {cg} or {cg/kk} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
 
 [Examples:]
 
@@ -74,9 +74,34 @@ defined via the "timestep"_timestep.html command.  Often they will
 converge more quickly if you use a timestep about 10x larger than you
 would normally use for dynamics simulations.
 
-NOTE: The {quickmin}, {fire}, and {hftn} styles do not yet support the
-use of the "fix box/relax"_fix_box_relax.html command or minimizations
-involving the electron radius in "eFF"_pair_eff.html models.
+NOTE: The {quickmin}, {fire}, {hftn}, and {cg/kk} styles do not yet
+support the use of the "fix box/relax"_fix_box_relax.html command or
+minimizations involving the electron radius in "eFF"_pair_eff.html
+models.
+
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
 
 [Restrictions:] none
 

doc/src/minimize.txt

@@ -7,6 +7,7 @@
 :line
 
 minimize command :h3
+minimize/kk command :h3
 
 [Syntax:]
 
@@ -256,6 +257,28 @@ info in the Restrictions section below.
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 Features that are not yet implemented are listed here, in case someone

doc/src/pair_cosine_squared.txt

@@ -0,0 +1,108 @@
+"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
+
+pair_style cosine/squared command :h3
+
+[Syntax:]
+
+pair_style cosine/squared cutoff :pre
+
+cutoff = global cutoff for cosine-squared interactions (distance units) :ul
+
+pair_coeff i j eps sigma
+pair_coeff i j eps sigma cutoff
+pair_coeff i j eps sigma wca
+pair_coeff i j eps sigma cutoff wca :pre
+
+i,j = a particle type
+eps = interaction strength, i.e. the depth of the potential minimum (energy units)
+sigma = distance of the potential minimum from 0
+cutoff = the cutoff distance for this pair type, if different from global (distance units)
+wca = if specified a Weeks-Chandler-Andersen potential (with eps strength and minimum at sigma) is added, otherwise not :ul
+
+[Examples:]
+
+pair_style cosine/squared 3.0
+pair_coeff * * 1.0 1.3
+pair_coeff 1 3 1.0 1.3 2.0
+pair_coeff 1 3 1.0 1.3 wca
+pair_coeff 1 3 1.0 1.3 2.0 wca :pre
+
+[Description:]
+
+Style {cosine/squared} computes a potential of the form
+
+:c,image(Eqs/pair_cosine_squared.jpg)
+
+between two point particles, where (sigma, -epsilon) is the location of
+the (rightmost) minimum of the potential, as explained in the syntax
+section above.
+
+This potential was first used in (Cooke)_#CKD for a coarse-grained lipid
+membrane model.  It is generally very useful as a non-specific
+interaction potential because it is fully adjustable in depth and width
+while joining the minimum at (sigma, -epsilon) and zero at (cutoff, 0)
+smoothly, requiring no shifting and causing no related artifacts, tail
+energy calculations etc. This evidently requires {cutoff} to be larger
+than {sigma}.
+
+If the {wca} option is used then a Weeks-Chandler-Andersen potential
+(Weeks)_#WCA is added to the above specified cosine-squared potential,
+specifically the following:
+
+:c,image(Eqs/pair_cosine_squared_wca.jpg)
+
+In this case, and this case only, the {sigma} parameter can be equal to
+{cutoff} (sigma = cutoff) which will result in ONLY the WCA potential
+being used (and print a warning), so the minimum will be attained at
+(sigma, 0). This is a convenience feature that enables a purely
+repulsive potential to be used without a need to define an additional
+pair style and use the hybrid styles.
+
+The energy and force of this pair style for parameters epsilon = 1.0,
+sigma = 1.0, cutoff = 2.5, with and without the WCA potential, are shown
+in the graphs below:
+
+:c,image(JPG/pair_cosine_squared_graphs.jpg)
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+Mixing is not supported for this style.
+
+The {shift}, {table} and {tail} options are not relevant for this style.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These pair styles can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  They do not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+The {cosine/squared} style is part of the "USER-MISC" package. It is only
+enabled if LAMMPS is build with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html,
+"pair_style lj/cut"_pair_lj.html
+
+[Default:] none
+
+:link(CKD)
+[(Cooke)] "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)"
+
+:link(WCA)
+[(Weeks)] "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)"

doc/src/pair_local_density.txt

@@ -0,0 +1,207 @@
+"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
+
+pair_style local/density command :h3
+
+[Syntax:]
+
+pair_style style arg :pre
+
+style = {local/density}
+arg = name of file containing tabulated values of local density and the potential :ul
+
+[Examples:]
+
+pair_style local/density benzene_water.localdensity.table :pre
+
+pair_style hybrid/overlay table spline 500 local/density 
+pair_coeff * * local/density  benzene_water.localdensity.table :pre
+
+[Description:]
+
+The local density (LD) potential is a mean-field manybody potential, and, in some 
+sense,a generalization of embedded atom models (EAM). The name "local density 
+potential" arises from the fact that it assigns an energy to an atom depending 
+on the number of neighboring atoms of given type around it within a predefined 
+spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG)
+literature suggests that such potentials can be widely useful  in capturing 
+effective multibody forces in a computationally efficient manner so as to 
+improve the quality of CG models of implicit solvation"(Sanyal1)"_#Sanyal1 and 
+phase-segregation in liquid mixtures"(Sanyal2)"_#Sanyal2, and provide guidelines 
+to determine the extent of manybody correlations present in a CG 
+model."(Rosenberger)"_#Rosenberger The LD potential in LAMMPS is primarily 
+intended to be used as a corrective potential over traditional pair potentials 
+in bottom-up CG models, i.e., as a hybrid pair style with 
+other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.). 
+Because the LD potential is not a pair potential per se,  it is implemented 
+simply as a single auxiliary file with all specifications that will be read 
+upon initialization.
+
+NOTE: Thus when used as the only interaction in the system, there is no 
+corresponding pair_coeff command and when used with other pair styles using the 
+hybrid/overlay option, the corresponding pair_coeff command must be supplied
+*  * as placeholders for the atom types.
+
+:line
+
+[System with a single CG atom type:]
+
+A system of a single atom type (e.g., LJ argon) with a single local density (LD)
+potential would have an energy given by:
+
+:c,image(Eqs/pair_local_density_energy.jpg)
+
+where rho_i is the LD at atom i and F(rho) is similar in spirit to the 
+embedding function used in EAM potentials. The LD at atom i is given by the sum
+
+:c,image(Eqs/pair_local_density_ld.jpg)
+
+where phi is an indicator function that is one at r=0 and zero beyond a cutoff 
+distance R2. The choice of the functional form of phi is somewhat arbitrary, 
+but the following piecewise cubic function has proven sufficiently general: 
+"(Sanyal1)"_#Sanyal1, "(Sanyal2)"_#Sanyal2 "(Rosenberger)"_#Rosenberger
+
+:c,image(Eqs/pair_local_density_indicator_func.jpg)
+
+The constants {c} are chosen so that the indicator function smoothly 
+interpolates between 1 and 0 between the distances R1 and R2, which are 
+called the inner and outer cutoffs, respectively. Thus phi satisfies 
+phi(R1) = 1, phi(R2) = dphi/dr @ (r=R1) =  dphi/dr @ (r=R2) = 0. The embedding 
+function F(rho) may or may not have a closed-form expression. To maintain 
+generality, it is practically represented with a spline-interpolated table 
+over a predetermined range of rho. Outside of that range it simply adopts zero 
+values at the endpoints.
+
+It can be shown that the total force between two atoms due to the LD potential 
+takes the form of a pair force, which motivates its designation as a LAMMPS 
+pair style. Please see "(Sanyal1)"_#Sanyal1 for details of the derivation. 
+
+:line
+
+[Systems with arbitrary numbers of atom types:]
+
+The potential is easily generalized to systems involving multiple atom types:
+
+:c,image(Eqs/pair_local_density_energy_multi.jpg)
+
+with the LD expressed as
+
+:c,image(Eqs/pair_local_density_ld_multi.jpg)
+
+where alpha gives the type of atom i, beta the type of atom j, and the 
+coefficients a and b filter for atom types as specified by the user. a is 
+called the central atom filter as it determines to which atoms the 
+potential applies; a_alpha = 1 if the LD potential applies to atom type alpha 
+else zero. On the other hand, b is called the neighbor atom filter because it 
+specifies which atom types to use in the calculation of the LD; b_beta = 1 if 
+atom type beta contributes to the LD and zero otherwise.
+
+NOTE: Note that the potentials need not be symmetric with respect to atom types, 
+which is the reason for two distinct sets of coefficients a and b. An atom type 
+may contribute to the LD but not the potential, or to the potential but not the 
+LD. Such decisions are made by the user and should (ideally) be motivated on 
+physical grounds for the problem at hand.
+
+:line
+
+[General form for implementation in LAMMPS:]
+
+Of course, a system with many atom types may have many different possible LD 
+potentials, each with their own atom type filters, cutoffs, and embedding 
+functions. The most general form of this potential as implemented in the 
+pair_style local/density is:
+
+:c,image(Eqs/pair_local_density_energy_implement.jpg)
+
+where, k is an index that spans the (arbitrary) number of applied LD potentials 
+N_LD. Each LD is calculated as before with:
+
+:c,image(Eqs/pair_local_density_ld_implement.jpg)
+
+The superscript on the indicator function phi simply indicates that it is 
+associated with specific values of the cutoff distances R1(k) and R2(k). In 
+summary, there may be N_LD distinct LD potentials. With each potential type (k), 
+one must specify:
+
+the inner and outer cutoffs as R1 and R2
+the central type filter a(k), where k = 1,2,...N_LD
+the neighbor type filter b(k), where k = 1,2,...N_LD
+the LD potential function F(k)(rho), typically as a table that is later spline-interpolated :ul
+
+:line
+
+[Tabulated input file format:]
+
+Line 1:             comment or blank (ignored)
+Line 2:             comment or blank (ignored)
+Line 3:             N_LD N_rho (# of LD potentials and # of tabulated values, single space separated)
+Line 4:             blank (ignored)
+Line 5:             R1(k) R2(k) (lower and upper cutoffs, single space separated)
+Line 6:             central-types (central atom types, single space separated)
+Line 7:             neighbor-types (neighbor atom types single space separated)
+Line 8:             rho_min rho_max drho (min, max and diff. in tabulated rho values, single space separated)
+Line 9:             F(k)(rho_min + 0.drho)
+Line 10:            F(k)(rho_min + 1.drho)
+Line 11:            F(k)(rho_min + 2.drho)
+...
+Line 9+N_rho:       F(k)(rho_min + N_rho . drho)
+Line 10+N_rho:      blank (ignored) :pre
+
+Block 2 :pre
+
+Block 3 :pre
+
+Block N_LD :pre
+
+Lines 5 to 9+N_rho constitute the first block. Thus the input file is separated 
+(by blank lines) into N_LD blocks each representing a separate LD potential and 
+each specifying its own upper and lower cutoffs, central and neighbor atoms, 
+and potential.  In general, blank lines anywhere are ignored. 
+
+:line
+
+[Mixing, shift, table, tail correction, restart, info]:
+This pair style does not support automatic mixing. For atom type pairs alpha,
+beta and alpha != beta, even if LD potentials of type (alpha, alpha) and 
+(beta, beta) are provided, you will need to explicitly provide LD potential 
+types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha,
+beta) means that alpha is the central atom to which the LD potential is applied
+and beta is the neighbor atom which contributes to the LD potential on alpha).
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+The local/density pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in tabulated potential files.
+Thus, you need to re-specify the pair_style and pair_coeff commands in
+an input script that reads a restart file.
+
+:line
+
+[Restrictions:]
+
+The local/density pair style is a 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:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+
+:link(Sanyal1)
+[(Sanyal1)] Sanyal and Shell, Journal of Chemical Physics, 2016, 145 (3), 034109.
+:link(Sanyal2)
+[(Sanyal2)] Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.
+
+:link(Rosenberger)
+[(Rosenberger)] Rosenberger, Sanyal, Shell and van der Vegt,  Journal of Chemical Physics, 2019, 151 (4), 044111.

doc/src/pair_style.txt

@@ -129,6 +129,7 @@ accelerated styles exist.
 "colloid"_pair_colloid.html - integrated colloidal potential
 "comb"_pair_comb.html - charge-optimized many-body (COMB) potential
 "comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
+"cosine/squared"_pair_cosine_squared.html - Cooke-Kremer-Deserno membrane model potential
 "coul/cut"_pair_coul.html - cutoff Coulombic potential
 "coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core
 "coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
@@ -227,6 +228,7 @@ accelerated styles exist.
 "lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential
 "lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics
 "lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
+"local/density"_pair_local_density.html - generalized basic local density potential
 "lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
 "lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity
 "lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics

doc/src/pairs.txt

@@ -24,6 +24,7 @@ Pair Styles :h1
    pair_class2
    pair_colloid
    pair_comb
+   pair_cosine_squared
    pair_coul
    pair_coul_diel
    pair_coul_shield
@@ -65,6 +66,7 @@ Pair Styles :h1
    pair_lj_smooth
    pair_lj_smooth_linear
    pair_lj_switch3_coulgauss
+   pair_local_density
    pair_lubricate
    pair_lubricateU
    pair_mdf

doc/src/replicate.txt

@@ -14,7 +14,8 @@ replicate nx ny nz {keyword} :pre
 
 nx,ny,nz = replication factors in each dimension :ulb
 optional {keyword} = {bbox} :l
-  {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule
+  {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :pre
+:ule
 
 [Examples:]
 
@@ -45,11 +46,13 @@ file that crosses a periodic boundary should be between two atoms with
 image flags that differ by 1.  This will allow the bond to be
 unwrapped appropriately.
 
-The optional keyword {bbox} uses a bounding box to only check atoms
-in replicas that overlap with a processor's sub-domain when assigning
-atoms to processors, and thus can result in substantial speedups for
-calculations using a large number of processors. It does require
-temporarily using more memory.
+The optional keyword {bbox} uses a bounding box to only check atoms in
+replicas that overlap with a processor's sub-domain when assigning
+atoms to processors.  It typically results in a substantial speedup
+when using the replicate command on a large number of processors.  It
+does require temporary use of more memory, specifically that each
+processor can store all atoms in the entire system before it is
+replicated.
 
 [Restrictions:]
 

doc/src/temper.txt

@@ -110,7 +110,13 @@ the information from the log.lammps file.  E.g. you could produce one
 dump file with snapshots at 300K (from all replicas), another with
 snapshots at 310K, etc.  Note that these new dump files will not
 contain "continuous trajectories" for individual atoms, because two
-successive snapshots (in time) may be from different replicas.
+successive snapshots (in time) may be from different replicas. The 
+reorder_remd_traj python script can do the reordering for you 
+(and additionally also calculated configurational log-weights of 
+trajectory snapshots in the canonical ensemble). The script can be found
+in the tools/replica directory while instructions on how to use it is
+available in doc/Tools (in brief) and as a README file in tools/replica
+(in detail).
 
 The last argument {index} in the temper command is optional and is
 used when restarting a tempering run from a set of restart files (one

doc/utils/sphinx-config/false_positives.txt

@@ -45,6 +45,7 @@ Aidan
 aij
 airebo
 Aj
+ajs
 ajaramil
 akohlmey
 Aktulga
@@ -99,6 +100,7 @@ antisymmetry
 anton
 Antonelli
 api
+Apoorva
 Appl
 Apu
 arccos
@@ -303,6 +305,7 @@ Cavium
 Cawkwell
 cbecker
 ccache
+ccachepiecewise
 ccmake
 ccNspecies
 CCu
@@ -356,6 +359,7 @@ Cii
 Cij
 cis
 civ
+CKD
 Clang
 clearstore
 Cleary
@@ -421,6 +425,7 @@ coreshell
 cornflowerblue
 cornsilk
 corotate
+corotation
 corotational
 correlator
 cosineshifted
@@ -521,6 +526,7 @@ Dcut
 de
 dE
 De
+decorrelation
 debye
 Debye
 Decius
@@ -617,6 +623,7 @@ Doye
 dpd
 DPD
 dpdTheta
+dphi
 DPhil
 dr
 dR
@@ -1073,6 +1080,7 @@ Hilger
 histo
 histogrammed
 histogramming
+hma
 hmaktulga
 hoc
 Hochbruck
@@ -1329,6 +1337,8 @@ kmax
 Kmax
 Knizhnik
 knl
+Kofke
+kofke
 Kohlmeyer
 Kohn
 kokkos
@@ -1716,6 +1726,7 @@ Morteza
 Mosayebi
 Moseler
 Moskalev
+Moustafa
 mov
 mpi
 MPI
@@ -2035,7 +2046,6 @@ Otype
 Ouldridge
 outfile
 outmost
-outpur
 outputss
 Ouyang
 overlayed
@@ -2128,6 +2138,7 @@ picograms
 picosecond
 picoseconds
 pid
+piecewise
 Pieniazek
 Pieter
 pimd
@@ -2215,6 +2226,7 @@ PTM
 ptr
 pu
 purdue
+Purohit
 pushstore
 pvar
 pw
@@ -2229,6 +2241,7 @@ Py
 pydir
 pylammps
 PyLammps
+pymbar
 pymodule
 pymol
 pypar
@@ -2315,6 +2328,7 @@ reinit
 relink
 relTol
 remappings
+remd
 Ren
 Rendon
 reneighbor
@@ -2407,6 +2421,7 @@ Rodrigues
 Rohart
 Ronchetti
 Rosati
+Rosenberger
 Rossky
 rosybrown
 rotationally
@@ -2432,6 +2447,7 @@ Ryckaert
 Rycroft
 Rydbergs
 Rz
+Sabry
 saddlebrown
 Sadigh
 saed
@@ -2443,6 +2459,9 @@ Salles
 sandia
 Sandia
 sandybrown
+Sanitizer
+sanitizers
+Sanyal
 sc
 scafacos
 SCAFACOS
@@ -2467,6 +2486,7 @@ Scripta
 sdk
 sdpd
 SDPD
+se
 seagreen
 Secor
 sectoring
@@ -2560,6 +2580,7 @@ Snodin
 Sodani
 Soderlind
 solvated
+solvation
 Sorensen
 soundspeed
 Souza
@@ -2676,6 +2697,8 @@ Tajkhorshid
 Tamaskovics
 Tanaka
 tanh
+tanmoy
+Tanmoy
 Tartakovsky
 taskset
 taubi
@@ -2918,6 +2941,7 @@ vectorial
 vectorization
 Vectorization
 vectorized
+Vegt
 vel
 Verlag
 verlet
@@ -2989,6 +3013,7 @@ Waltham
 wavepacket
 wB
 Wbody
+wca
 webpage
 Weckner
 WeinanE

examples/COUPLE/python/example.py

@@ -0,0 +1,36 @@
+# this example requires the LAMMPS Python package (lammps.py) to be installed
+# and LAMMPS to be loadable as shared library in LD_LIBRARY_PATH
+
+import lammps
+
+def callback(caller, ntimestep, nlocal, tag, x, fext):
+    """
+    This callback receives a caller object that was setup when registering the callback
+
+    In addition to timestep and number of local atoms, the tag and x arrays are passed as
+    NumPy arrays. The fext array is a force array allocated for fix external, which
+    can be used to apply forces to all atoms. Simply update the value in the array,
+    it will be directly written into the LAMMPS C arrays
+    """
+    print("Data passed by caller (optional)", caller)
+    print("Timestep:", ntimestep)
+    print("Number of Atoms:", nlocal)
+    print("Atom Tags:", tag)
+    print("Atom Positions:", x)
+    print("Force Additions:", fext)
+    fext.fill(1.0)
+    print("Force additions after update:", fext)
+    print("="*40)
+
+L = lammps.lammps()
+L.file("in.fix_external")
+
+# you can pass an arbitrary Python object to the callback every time it is called
+# this can be useful if you need more state information such as the LAMMPS ptr to
+# make additional library calls
+custom_object = ["Some data", L]
+
+L.set_fix_external_callback("2", callback, custom_object)
+L.command("run 100")
+
+

examples/COUPLE/python/in.fix_external

@@ -0,0 +1,23 @@
+# LAMMPS input for coupling LAMMPS with Python via fix external
+
+units		metal
+dimension	3
+atom_style	atomic
+atom_modify	sort 0 0.0
+
+lattice		diamond 5.43
+region		box block 0 1 0 1 0 1
+create_box	1 box
+create_atoms	1 box
+mass		1 28.08
+
+velocity	all create 300.0 87293 loop geom
+
+fix		1 all nve
+fix		2 all external pf/callback 1 1
+
+#dump		2 all image 25 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3
+
+thermo		1

examples/README

@@ -99,12 +99,12 @@ pour:     pouring of granular particles into a 3d box, then chute flow
 prd:      parallel replica dynamics of vacancy diffusion in bulk Si
 python:   use of PYTHON package to invoke Python code from input script
 qeq:      use of QEQ package for charge equilibration
-reax:     RDX and TATB models using the ReaxFF
+reax:     RDX and TATB and several other models using ReaxFF
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void
-snap:     use of SNAP potential for Ta
+snap:     examples for using several bundled SNAP potentials
 srd:      stochastic rotation dynamics (SRD) particles as solvent
-snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
+steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
 streitz:  Streitz-Mintmire potential for Al2O3
 tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
 threebody: regression test input for a variety of manybody potentials

examples/USER/drude/toluene/data.toluene

@@ -79,10 +79,10 @@ Dihedral Coeffs
 
 Improper Coeffs
 
-   1    0.0000    2.1999    0.0000    0.0000 # CAO-CAO-CAT-CTT
-   2    0.0000    2.1999    0.0000    0.0000 # CAT-CAM-CAO-HAT
-   3    0.0000    2.1999    0.0000    0.0000 # CAO-CAP-CAM-HAT
-   4    0.0000    2.1999    0.0000    0.0000 # CAM-CAM-CAP-HAT
+   1    2.1999    0.0000    0.0000   -1.0000 0 # CAO-CAO-CAT-CTT
+   2    2.1999    0.0000    0.0000   -1.0000 0 # CAT-CAM-CAO-HAT
+   3    2.1999    0.0000    0.0000   -1.0000 0 # CAO-CAP-CAM-HAT
+   4    2.1999    0.0000    0.0000   -1.0000 0 # CAM-CAM-CAP-HAT
 
 Atoms
 

examples/USER/drude/toluene/in.toluene.lang

@@ -7,7 +7,7 @@ atom_style full
 bond_style harmonic
 angle_style harmonic
 dihedral_style opls
-improper_style opls
+improper_style fourier
 special_bonds lj/coul 0.0 0.0 0.5
 
 pair_style lj/cut/thole/long 2.600 8.0 8.0
@@ -109,7 +109,7 @@ fix fNPH all nve
 
 compute cTEMP all temp/drude
 
-thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
 thermo 50
 
 timestep 0.5

examples/USER/drude/toluene/in.toluene.nh

@@ -7,7 +7,7 @@ atom_style full
 bond_style harmonic
 angle_style harmonic
 dihedral_style opls
-improper_style opls
+improper_style fourier
 special_bonds lj/coul 0.0 0.0 0.5
 
 pair_style lj/cut/thole/long 2.600 8.0 8.0
@@ -115,7 +115,7 @@ fix fINVERSE all drude/transform/inverse
 
 fix fMOMENTUM all momentum 100 linear 1 1 1
 
-thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
 thermo 50
 
 timestep 0.5

examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1

@@ -1,14 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 250 toluene system for drude polarizability example (Langevin)
-
-units real
-boundary p p p
-
-atom_style full
-bond_style harmonic
-angle_style harmonic
-dihedral_style opls
-improper_style opls
-ERROR: Unknown improper style opls (src/force.cpp:634)
-Last command: improper_style opls

examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4

@@ -1,14 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 250 toluene system for drude polarizability example (Langevin)
-
-units real
-boundary p p p
-
-atom_style full
-bond_style harmonic
-angle_style harmonic
-dihedral_style opls
-improper_style opls
-ERROR: Unknown improper style opls (src/force.cpp:634)
-Last command: improper_style opls

examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1

@@ -1,14 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 250 toluene system for drude polarizability example (Nose-Hoover)
-
-units real
-boundary p p p
-
-atom_style full
-bond_style harmonic
-angle_style harmonic
-dihedral_style opls
-improper_style opls
-ERROR: Unknown improper style opls (src/force.cpp:634)
-Last command: improper_style opls

examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4

@@ -1,14 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 250 toluene system for drude polarizability example (Nose-Hoover)
-
-units real
-boundary p p p
-
-atom_style full
-bond_style harmonic
-angle_style harmonic
-dihedral_style opls
-improper_style opls
-ERROR: Unknown improper style opls (src/force.cpp:634)
-Last command: improper_style opls

examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.1

@@ -0,0 +1,254 @@
+LAMMPS (7 Aug 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Langevin)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style fourier
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+  special bonds CPU = 0.00199628 secs
+  read_data CPU = 0.0169649 secs
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+  find clusters CPU = 0.000807762 secs
+
+fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
+fix fNPH all nve
+
+compute cTEMP all temp/drude
+
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 103823 64000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50    4782.1702    4728.7435    328.28767    53.426722    1812.2203    685.37824    683.70917   -3277.1645    797.34329    1305983.2   -1306631.2    16874.358    48631.318    448.52419    116.25477 
+     100    2906.0879    3699.8031    256.85465    -793.7152    978.15364    778.36908    862.30899   -3270.1722    468.44888    1306096.8   -1306707.6    15631.384    48631.318    382.26408    35.748403 
+     150    2089.0918    3593.0499    249.44342   -1503.9581    751.32283    803.47802     668.4757   -3277.5983    128.17444    1306138.5   -1306716.3     15193.04    48631.318    384.75632    10.892446 
+     200    1547.3302     3248.639    225.53309   -1701.3089    699.65977    814.31164    692.83227   -3276.3957   -66.671816    1306160.9   -1306725.9    13787.676    48631.318    351.28242    3.8458668 
+     250    1177.9323     3095.949    214.93276   -1918.0167    688.87262    842.44531    615.89218   -3278.4465   -210.06178    1306154.3     -1306731    8808.5835    48631.318     335.8115    1.8330994 
+     300    895.90313    2870.3451    199.27046    -1974.442    734.95873    858.58147    624.00862   -3278.6022   -342.01951    1306163.6     -1306735    3388.4841    48631.318    311.56815    1.2987715 
+     350    669.25785    2764.9587    191.95413   -2095.7009    662.44028    860.79714    602.69567    -3278.776   -376.37081    1306172.3   -1306738.8    8494.9184    48631.318    300.19414    1.1358594 
+     400    531.21609    2722.6775    189.01881   -2191.4614    684.34049    868.77818    576.86096   -3280.1649   -459.66591      1306160   -1306741.6    6726.3087    48631.318    295.59622    1.1315427 
+     450    427.05425    2611.7588     181.3184   -2184.7046     719.2042    891.88178     591.2282    -3279.339   -534.65069    1306172.2   -1306745.2    2398.5394    48631.318    283.56126    1.0726045 
+     500    310.44891    2556.0967    177.45412   -2245.6477    720.86526    841.50195     586.3417   -3279.3029   -539.81715    1306169.5   -1306744.8     3028.595    48631.318    277.52314    1.0406334 
+     550    207.83114    2531.3051    175.73299   -2323.4739    674.71188     855.2132    555.53227   -3280.0378   -553.93222    1306171.9   -1306746.9    4609.4408    48631.318    274.80629    1.0748601 
+     600     88.81557    2459.9059    170.77619   -2371.0903     692.4485    834.47484    550.85905   -3280.9086   -595.31802    1306171.4     -1306744    2107.9995    48631.318    267.06312    1.0301965 
+     650    75.616307    2416.9747    167.79573   -2341.3584    703.57186    869.98959    564.81201   -3280.7522    -619.8016      1306168   -1306747.2    1236.4829    48631.318     262.3542    1.0968447 
+     700    49.832719    2415.7344    167.70963   -2365.9017    683.61663    882.67915    555.23571   -3280.7778   -615.06862    1306159.9   -1306751.4    2985.7048    48631.318    262.23095    1.0762424 
+     750    41.513638     2427.218    168.50687   -2385.7044    698.87619     863.2938    564.58197   -3280.0156   -637.29964    1306160.1   -1306755.3     1653.117    48631.318    263.49803    1.0451977 
+     800    109.53032    2481.9041    172.30339   -2372.3738    697.22709    897.36555    561.28745   -3280.6784   -651.29564      1306155   -1306751.3    1219.8761    48631.318    269.43698    1.0647792 
+     850    98.142203    2502.3132    173.72026    -2404.171     696.5382    878.83293    566.44302   -3280.2837   -663.94587    1306155.6   -1306757.4    1122.7487    48631.318    271.67716     1.030267 
+     900    62.992675    2409.7324    167.29295   -2346.7397    722.00541    896.64662    560.66083   -3279.4915   -644.05458    1306153.6   -1306756.1     1604.295    48631.318    261.58656    1.0609836 
+     950    5.6677468    2403.5067    166.86073    -2397.839    725.07222    891.00249    556.81977   -3279.7848   -672.66389      1306141   -1306759.2    1019.1694    48631.318    260.91187    1.0562387 
+    1000    38.526968      2444.97    169.73928   -2406.4431    704.72993    920.68493    534.59035   -3281.2673   -667.78091    1306141.1   -1306758.5    486.79846    48631.318    265.39928     1.098473 
+    1050    21.698026    2388.6306    165.82798   -2366.9326    712.15539    934.39244    546.92027   -3281.1469    -654.7449    1306137.4   -1306761.9    1556.1256    48631.318    259.28203    1.0760765 
+    1100   -26.971225    2433.8428    168.96678    -2460.814    710.11081    881.19212    524.51547   -3281.7925   -667.53202    1306137.1   -1306764.4    1203.8971    48631.318    264.20441    1.0706085 
+    1150   -49.171269    2375.9688    164.94895     -2425.14    729.78127    918.79575    518.21967   -3281.6542    -675.7239    1306130.4     -1306765    229.44016    48631.318    257.89845     1.086519 
+    1200   -53.421342    2422.0091    168.14524   -2475.4304    710.67274     884.2589    523.32524   -3282.2275   -674.49333    1306130.9   -1306767.9   -131.09655    48631.318    262.91124    1.0804821 
+    1250   -58.534776    2394.4031    166.22873   -2452.9378    680.27486    909.58096    532.81959   -3281.5551   -653.13731      1306127   -1306767.9    546.96357    48631.318    259.92916    1.0424914 
+    1300   -24.151217    2431.9902    168.83817   -2456.1414    681.27127    919.39245    536.41899   -3281.3717   -661.90875    1306121.6   -1306771.5    1455.7512    48631.318    264.00712    1.0630558 
+    1350   -38.973062    2438.6194     169.2984   -2477.5925    707.96118    912.62518    519.44533   -3281.6739   -687.67183    1306126.1   -1306774.4   -1470.4442    48631.318    264.70225    1.1091537 
+    1400    11.896539    2384.5407    165.54404   -2372.6442    719.03374    950.93261     550.5639   -3280.4581    -663.4921      1306122   -1306771.3    465.12854    48631.318    258.83564    1.0785364 
+    1450   -13.118691    2436.6246    169.15991   -2449.7433    661.04397    933.07103    561.29537   -3280.6997   -672.68495    1306123.9   -1306775.7   -108.46564    48631.318    264.50636    1.0718787 
+    1500   -38.151755    2417.4849    167.83116   -2455.6367    688.81484    892.35701    565.29013   -3279.6716    -662.1817    1306116.9   -1306777.2    517.89634    48631.318    262.44549    1.0338083 
+    1550   -71.663334    2405.7016    167.01311   -2477.3649    681.78925    876.31247      559.003    -3280.451   -649.16641    1306112.8   -1306777.7    925.49349    48631.318      261.148    1.0609731 
+    1600   -13.900431     2419.481    167.96973   -2433.3814    718.46559    909.67964    559.06779   -3280.8163    -667.6092      1306108   -1306780.2     13.95808    48631.318    262.63632     1.080229 
+    1650   -16.403222     2431.075    168.77464   -2447.4783    710.99509    907.65662    551.60307   -3279.8852   -661.52624    1306104.5   -1306780.8    726.89923    48631.318    263.91553    1.0489963 
+    1700   -18.555086    2438.2062    169.26971   -2456.7613    665.90475    943.02217    542.86579   -3280.9017   -657.99229      1306108   -1306777.7    801.41078    48631.318    264.67663    1.0750708 
+    1750   -6.9249446    2443.9707     169.6699   -2450.8956    733.23573    890.06857    560.83229    -3280.362   -670.93883    1306098.3   -1306782.1    47.037748    48631.318    265.30892    1.0661143 
+    1800   -21.686222    2434.3375    169.00113   -2456.0237    729.35297     899.9733    561.59516   -3280.4727   -680.98901    1306096.5     -1306782    495.63617    48631.318    264.25723    1.0723683 
+    1850   -72.916947    2408.8254    167.22998   -2481.7423    683.24984    904.13282    549.97726   -3279.6699   -652.63212    1306099.2     -1306786   -120.61674    48631.318    261.48504    1.0659808 
+    1900     -55.4099     2415.455    167.69023   -2470.8649     700.4473    904.72264     565.5266   -3280.4533   -673.23082    1306099.6   -1306787.4    202.15936    48631.318    262.20353    1.0709756 
+    1950   -79.877997    2409.2307    167.25812   -2489.1087     695.9536     894.4541     564.7034   -3279.3581   -680.33472    1306100.8   -1306785.3    213.72828    48631.318    261.52921    1.0658433 
+    2000   -102.20457    2399.4263    166.57746   -2501.6309    689.67819    894.58596    565.53233   -3280.7595   -680.39032    1306096.4   -1306786.6    1113.7499    48631.318    260.46311    1.0647045 
+Loop time of 68.4185 on 1 procs for 2000 steps with 5500 atoms
+
+Performance: 1.263 ns/day, 19.005 hours/ns, 29.232 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 48.825     | 48.825     | 48.825     |   0.0 | 71.36
+Bond    | 2.8852     | 2.8852     | 2.8852     |   0.0 |  4.22
+Kspace  | 13.795     | 13.795     | 13.795     |   0.0 | 20.16
+Neigh   | 1.0731     | 1.0731     | 1.0731     |   0.0 |  1.57
+Comm    | 0.27067    | 0.27067    | 0.27067    |   0.0 |  0.40
+Output  | 0.0031168  | 0.0031168  | 0.0031168  |   0.0 |  0.00
+Modify  | 1.5207     | 1.5207     | 1.5207     |   0.0 |  2.22
+Other   |            | 0.04541    |            |       |  0.07
+
+Nlocal:    5500 ave 5500 max 5500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    13157 ave 13157 max 13157 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.33822e+06 ave 1.33822e+06 max 1.33822e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1338215
+Ave neighs/atom = 243.312
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 32
+Dangerous builds = 0
+Total wall time: 0:01:08

examples/USER/drude/toluene/log.7Aug19.toluene.lang.g++.4

@@ -0,0 +1,254 @@
+LAMMPS (7 Aug 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Langevin)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style fourier
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+  special bonds CPU = 0.000747919 secs
+  read_data CPU = 0.0168228 secs
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+  find clusters CPU = 0.000355244 secs
+
+fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
+fix fNPH all nve
+
+compute cTEMP all temp/drude
+
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 34263 16000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50    4712.9507    4669.1606    324.15119    43.790082     1798.561    670.61319    690.16967   -3276.9493      811.643    1305983.2   -1306633.5    17164.771    48631.318    442.24313    116.13094 
+     100    2865.9139    3726.4166    258.70226   -860.50272    968.87546    749.70761    860.70151   -3270.7784    427.14745    1306104.7   -1306700.9    15017.273    48631.318    385.10628    35.845353 
+     150    1982.6673     3535.974      245.481   -1553.3068    764.86116    768.15837    658.70182   -3278.7906    108.49859    1306136.5   -1306711.2    16495.352    48631.318    378.64023    10.723986 
+     200    1440.0277    3240.5932    224.97452   -1800.5656    687.71813    791.29356    643.82915   -3276.9293   -99.549986    1306172.9   -1306719.8    13234.476    48631.318    350.46321    3.7468464 
+     250    1103.2915     3018.496    209.55567   -1915.2045    677.97905    825.32748    642.78891   -3278.0801    -226.1853    1306168.5   -1306725.5    8774.9103    48631.318    327.36313    1.8722119 
+     300    789.07159    2827.1716    196.27319      -2038.1    735.96101    852.72545    589.14167   -3280.0357   -374.66018      1306169   -1306730.2    2259.1028    48631.318    306.85585    1.3262598 
+     350    599.10023    2732.3739    189.69197   -2133.2737    677.67006    863.22888    565.41674   -3280.5231   -403.28794    1306177.4   -1306733.2     7989.222    48631.318    296.64126    1.1534418 
+     400    428.26436    2591.2884    179.89727   -2163.0241    676.18745    849.24505    612.34065   -3277.4703   -457.85799    1306173.6   -1306739.1    7282.1438    48631.318    281.34719    1.0502762 
+     450    307.26859    2534.2468    175.93722   -2226.9782    712.17636    853.98862    578.01327   -3279.7731   -533.87422    1306179.7   -1306737.2    1897.9643    48631.318    275.11317    1.0980929 
+     500    234.60959    2495.1082    173.22007   -2260.4987    707.43541    878.25753    547.08402   -3281.2756   -549.04991    1306176.5   -1306739.5    2683.0639    48631.318    270.85452    1.0984718 
+     550    203.34751    2445.6535    169.78673    -2242.306    669.03724    892.85034    599.20664   -3279.0757   -559.81157    1306175.9   -1306740.4    4512.9992    48631.318    265.49465    1.0628812 
+     600    205.63573    2526.5892     175.4056   -2320.9535    685.64073    887.97693    557.42296   -3280.0332   -597.34755    1306167.8   -1306742.5    2999.5823    48631.318    274.29935     1.064682 
+     650    176.23031    2526.3124    175.38638   -2350.0821    714.15285    895.42115    540.39191   -3280.8567   -636.27783    1306165.7   -1306748.6    871.68316    48631.318     274.2807    1.0442089 
+     700    106.97524    2441.1059    169.47101   -2334.1306    697.16018    905.51407    564.71847   -3279.6208   -631.62324    1306159.4   -1306749.6    1953.8241    48631.318    264.98935    1.0771037 
+     750    76.695104    2435.6635    169.09318   -2358.9684    672.01039    934.63351    545.64024   -3281.1075   -629.89722    1306152.4   -1306752.6    3044.0155    48631.318    264.39002    1.0932471 
+     800    57.614075     2456.928    170.56945   -2399.3139    720.76364    898.68013    534.10051   -3281.5897   -659.64354    1306145.5   -1306757.1    1691.9503    48631.318    266.72089    1.0622697 
+     850   -44.931126    2390.0608    165.92727   -2434.9919    708.70192    888.26851    537.13087    -3281.355   -665.17283    1306137.8   -1306760.3    123.07165    48631.318    259.45151    1.0516426 
+     900   -96.878205     2358.862    163.76133   -2455.7403    672.98976    868.41571    546.69492   -3280.6939   -636.80102    1306134.5   -1306760.9    1955.7005    48631.318    256.05598      1.05337 
+     950   -80.012575    2374.4497    164.84349   -2454.4623    679.59722    880.35157    548.35372   -3280.6061   -643.44517    1306125.8   -1306764.5    1510.9809    48631.318    257.72442    1.1017392 
+    1000   -21.440874    2440.6729    169.44096   -2462.1138    718.56593    868.65109    555.54643   -3279.8516   -686.71673    1306126.6     -1306765   -1148.6212    48631.318    264.92977    1.1019339 
+    1050     16.46903    2382.6961    165.41598   -2366.2271    712.51245    913.35848    579.81678   -3280.0559   -657.12122    1306129.3     -1306764    1004.5778    48631.318    258.64076    1.0684155 
+    1100    35.847247    2483.1985    172.39325   -2447.3513    685.05704    889.42278    553.73166   -3280.0177   -663.67201    1306134.3   -1306766.2     699.1824    48631.318    269.56773    1.0838094 
+    1150   -4.9817843    2431.4725    168.80223   -2436.4543    720.51056    868.17547    569.09902   -3280.5829   -677.99865    1306133.1   -1306768.7    435.19118    48631.318    263.96966    1.0303202 
+    1200   -23.907197    2443.6035    169.64441   -2467.5107    684.96437    887.58483    549.43666   -3280.3144   -679.46182    1306137.2   -1306766.9    367.11148    48631.318    265.28645    1.0344036 
+    1250   -16.904671    2389.9447    165.91921   -2406.8494    722.06959    902.90076    568.35616   -3280.6829   -683.32029    1306132.9   -1306769.1    76.759445    48631.318    259.41697    1.0908431 
+    1300   -1.7822102    2410.2768    167.33074   -2412.0591    706.98675    904.31941    551.23506   -3280.7552   -651.51211    1306127.3   -1306769.6    1659.1113    48631.318    261.64093    1.0701648 
+    1350    -3.569473    2446.3901    169.83786   -2449.9595    686.13971    894.85839    558.36242   -3279.9941   -664.59508      1306129   -1306773.7    783.32881    48631.318     265.5696    1.0709072 
+    1400   -33.385576     2400.262    166.63547   -2433.6476     709.5808    890.68408    571.13105   -3280.1428   -674.51247    1306123.4   -1306773.8   -751.38571    48631.318    260.54522     1.080234 
+    1450   -11.215152    2405.5409    167.00196    -2416.756    703.72038    913.21131    552.64196   -3280.9831   -649.19774    1306120.3   -1306776.4    1817.2174    48631.318    261.14741     1.031193 
+    1500   -25.974102    2435.8375    169.10527   -2461.8116    689.93174    900.70619    552.63711   -3280.1497   -671.17989      1306124   -1306777.8   -98.941796    48631.318    264.45069    1.0190784 
+    1550   -76.496407    2394.8126    166.25716    -2471.309    706.96953    886.06919     549.9101   -3280.8434   -659.57745    1306105.9   -1306779.7   -7.0989994    48631.318    259.95403    1.0772144 
+    1600   -79.549932    2395.1114     166.2779   -2474.6614    684.11692    888.93332    562.94522   -3280.1665   -665.21744    1306114.4   -1306779.6    320.58515    48631.318    260.00641    1.0425978 
+    1650   -99.702003    2360.5652    163.87957   -2460.2672    706.21244     900.9253    540.36599   -3280.2308   -655.96077    1306109.7   -1306781.3    307.35487    48631.318    256.23383    1.0666637 
+    1700   -69.422658    2372.1727    164.68541   -2441.5954    676.79347    913.90473    581.60658    -3279.997   -670.33218    1306115.7   -1306779.3   -204.22848    48631.318    257.50963    1.0434075 
+    1750   -80.889897    2425.3592    168.37782   -2506.2491    672.88937    911.52373    523.74733   -3280.4796   -673.90027      1306122     -1306782    965.12568    48631.318    263.26491    1.1001595 
+    1800   -82.419368     2361.798    163.96515   -2444.2173    716.51571     882.9729    577.92505   -3278.9279   -671.67438    1306111.6   -1306782.6   -44.954517    48631.318    256.36957    1.0636692 
+    1850   -93.715705    2373.3359    164.76616   -2467.0516    713.02466    907.03621    563.38626   -3280.2576   -693.30963    1306104.6   -1306781.5   -979.95945    48631.318    257.62543    1.0628288 
+    1900    -73.60945    2449.5873    170.05983   -2523.1967    683.65116    893.94251    539.90847   -3281.4318   -680.16358      1306108   -1306787.1    598.18213    48631.318    265.91405    1.0766352 
+    1950   -66.068291    2437.3691    169.21159   -2503.4374     672.5168    877.42934    573.56499    -3279.885   -668.54185    1306109.2   -1306787.7    733.05074    48631.318    264.61409    1.0224258 
+    2000   -91.043979    2374.4077    164.84057   -2465.4516    692.13299    909.46192    574.60109    -3279.837   -672.33599    1306102.4   -1306791.8   -665.61581    48631.318    257.76275    1.0263294 
+Loop time of 23.7656 on 4 procs for 2000 steps with 5500 atoms
+
+Performance: 3.636 ns/day, 6.602 hours/ns, 84.155 timesteps/s
+94.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.918     | 13.096     | 14.137     |  27.0 | 55.10
+Bond    | 0.74012    | 0.76511    | 0.79225    |   2.9 |  3.22
+Kspace  | 6.7821     | 7.8285     | 9.0172     |  35.4 | 32.94
+Neigh   | 0.37249    | 0.37262    | 0.37278    |   0.0 |  1.57
+Comm    | 0.70503    | 0.7188     | 0.72807    |   1.1 |  3.02
+Output  | 0.0018752  | 0.0047592  | 0.013386   |   7.2 |  0.02
+Modify  | 0.91164    | 0.91644    | 0.92123    |   0.5 |  3.86
+Other   |            | 0.06335    |            |       |  0.27
+
+Nlocal:    1375 ave 1381 max 1368 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Nghost:    7803.75 ave 7856 max 7755 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:    334465 ave 349504 max 315867 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 1337859
+Ave neighs/atom = 243.247
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 32
+Dangerous builds = 0
+Total wall time: 0:00:23

examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.1

@@ -0,0 +1,262 @@
+LAMMPS (7 Aug 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Nose-Hoover)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style fourier
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+  special bonds CPU = 0.0019815 secs
+  read_data CPU = 0.0168803 secs
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+  find clusters CPU = 0.000715256 secs
+
+compute cTEMP_CORE gCORES temp/com
+compute cTEMP all temp/drude
+
+fix fDIRECT all drude/transform/direct
+fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 260 100.0
+fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 1 20.0
+fix fINVERSE all drude/transform/inverse
+
+fix fMOMENTUM all momentum 100 linear 1 1 1
+
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 103823 64000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50    3563.3755    4630.6343    321.47655   -1067.2588    735.72049    604.78665    689.14827    -3277.411    815.58183    1306088.7   -1306723.8    17813.424    48631.318      503.827 0.0087118192 
+     100    3327.4724    4395.1107    305.12559   -1067.6382    597.93176    651.62645     945.4151   -3267.2851    584.58833    1306135.9   -1306715.8    17407.337    48631.318    478.20171 0.0075985539 
+     150    3036.9065    4740.2304    329.08513   -1703.3239    558.64983    619.91284    658.80687   -3278.7837    285.12462      1306173     -1306720    18448.248    48631.318    515.75286 0.0063215188 
+     200     2697.958    4559.3445    316.52733   -1861.3864    522.09334    593.89129    754.61446     -3273.49    87.660461    1306183.9     -1306730    17888.936    48631.318    496.07143 0.0068706164 
+     250    2348.7568     4410.585    306.19988   -2061.8283    506.05007    575.35171    715.55054   -3276.3261   -18.364473    1306177.3   -1306741.4     11592.05    48631.318    479.88562 0.0071741032 
+     300    2019.8258    4040.1415    280.48226   -2020.3157     604.3077    641.66689    693.93801   -3278.5312   -115.73641    1306183.2   -1306749.1    3631.3628    48631.318    439.57995 0.0069886387 
+     350    1699.5166    3944.9851    273.87613   -2245.4685    452.07416     638.0653    658.79117   -3279.6053   -157.07584    1306196.9   -1306754.6    13544.368    48631.318    429.22694 0.0062868111 
+     400    1399.2929     3726.098    258.68014   -2326.8051    457.91943    621.44726    639.39903   -3279.2395   -188.85914    1306185.4   -1306762.8    10792.274    48631.318    405.41134 0.0059340078 
+     450    1120.5249     3518.345    244.25712   -2397.8201    519.48856    584.65789    646.36689   -3278.6685   -289.59913    1306184.1   -1306764.2    2755.5598    48631.318    382.80716 0.0055707485 
+     500     868.0166    3359.8794    233.25583   -2491.8628     460.7393    581.49563    581.01731   -3281.5544   -252.20169    1306184.3   -1306765.7    6120.3639    48631.318    365.56528 0.0058756154 
+     550    637.01567    3214.9521    223.19441   -2577.9364    431.81483    578.87411    540.94047   -3281.5337   -266.36075    1306182.8   -1306764.5    8622.4334    48631.318    349.79661 0.0058589653 
+     600    418.04086    3113.4064    216.14472   -2695.3655    430.45935    538.68157    522.24598    -3283.456   -311.87901    1306174.3   -1306765.8    7068.9273    48631.318    338.74797 0.0059567598 
+     650     218.5966    2930.8439    203.47052   -2712.2473    514.47294    514.28379    551.52551   -3282.0904   -405.37401    1306164.5   -1306769.5   -13.553736    48631.318    318.88482 0.0052667842 
+     700     45.22721    2830.1443    196.47956    -2784.917    451.11156    498.26423    541.18835   -3282.1427   -375.95313    1306157.1   -1306774.4    3947.6276    48631.318    307.92741 0.0068019029 
+     750   -114.28621    2798.3153    194.26988   -2912.6016      412.753     503.2878    481.32173   -3284.3411   -393.53984      1306147   -1306779.1    7143.3414    48631.318    304.46466 0.0061596717 
+     800   -263.63817    2694.8084    187.08403   -2958.4466    455.67914    487.49754     476.8659   -3284.3133    -451.9578      1306145   -1306787.2    1185.9502    48631.318    293.20288 0.0058203332 
+     850   -397.71592    2559.1921    177.66902   -2956.9081    458.83317     481.2262    478.31241    -3284.068   -437.26503    1306138.6   -1306792.6    346.80209    48631.318    278.44745 0.0054921692 
+     900    -515.1823    2544.8753    176.67509   -3060.0576    395.00163    457.58988    446.68352    -3285.485   -423.56221      1306145   -1306795.3    3712.8598    48631.318    276.88864 0.0074054008 
+     950   -617.28259    2451.1723    170.16987   -3068.4549    383.64277    446.59877     434.4624   -3285.1348   -391.59344    1306142.3   -1306798.7    5429.2488    48631.318    266.69431 0.0057487316 
+    1000   -703.15534     2334.837    162.09342   -3037.9923    424.34948    462.21112    451.80809   -3284.3803   -426.53369    1306133.9   -1306799.3    1137.6145    48631.318    254.03675 0.0053914731 
+    1050    -771.1763     2303.837    159.94128   -3075.0133    426.21409    436.50718    435.09987   -3285.1939   -411.14054    1306125.6   -1306802.1    1636.9383    48631.318    250.66295 0.0069342505 
+    1100   -822.72236    2283.4196    158.52382    -3106.142    376.67684    447.77729    418.45768   -3286.5919   -377.48204    1306118.9   -1306803.8    4760.5163    48631.318    248.44119 0.0074025012 
+    1150   -857.06075    2259.0717     156.8335   -3116.1324    400.31523    431.65981    457.68066   -3285.1977   -430.47723    1306115.8   -1306805.9    3194.5161    48631.318    245.79223  0.007063589 
+    1200   -875.50848    2238.2637    155.38893   -3113.7722    445.38524    460.97125    432.10511   -3285.4238   -472.46606    1306114.7     -1306809   -653.49784    48631.318    243.52819 0.0071448738 
+    1250   -880.37572    2294.6889    159.30618   -3175.0646    411.35427    444.73793    420.06468   -3286.0366   -458.05371    1306104.4   -1306811.5    945.80793    48631.318    249.66481  0.011853487 
+    1300   -871.31064    2284.2298    158.58007   -3155.5405    404.97412    441.75285    426.34477   -3285.4859   -424.79609    1306094.9   -1306813.2    4406.6196    48631.318    248.48563  0.084424118 
+    1350   -816.70005    2325.9264    161.47481   -3142.6265    696.80296    442.50053    431.19923   -3285.7859    -450.2699    1305836.2   -1306813.3     593.8098    48631.318    251.40749    2.9297319 
+    1400   -794.25335    2263.5101    157.14163   -3057.7635    645.65165    466.22086    446.22268   -3285.1821   -420.65317    1305903.7   -1306813.8    1386.3633    48631.318    245.20554    1.8916154 
+    1450   -776.10866    2287.6575    158.81803   -3063.7661    427.03477    479.10627    439.67495   -3285.9537   -395.13186    1306087.6   -1306816.1    2936.7806    48631.318    248.87167  0.061343245 
+    1500   -725.48181     2371.413    164.63266   -3096.8948    390.03204    464.30903    446.91959   -3284.7809   -393.16613    1306095.4   -1306815.6      3544.25    48631.318    258.01286  0.011586563 
+    1550    -671.4904    2315.9297     160.7808   -2987.4201    457.04935    500.25282    464.76203   -3284.9311   -400.98103    1306091.7   -1306815.3    2052.6339    48631.318    251.97726 0.0094517862 
+    1600   -618.83633    2449.0918    170.02543   -3067.9281    425.47487    474.65876    471.99171   -3284.3677   -430.32107    1306091.3   -1306816.6    441.15682    48631.318    266.46311  0.014260935 
+    1650   -567.82245    2425.2238    168.36842   -2993.0462    421.01953    511.27133    463.22065    -3285.038   -377.24066    1306088.4   -1306814.7    5198.8565    48631.318    263.83185  0.074738268 
+    1700    -502.4486    2441.8554    169.52305    -2944.304    642.39962    512.90234    490.38297   -3283.9751   -417.39288    1305929.1   -1306817.7    1141.4411    48631.318    264.52393     2.043674 
+    1750   -459.52196    2499.0746    173.49543   -2958.5966    679.38259    505.31787    484.77659   -3284.6272   -384.27736    1305861.6   -1306820.8    1527.2046    48631.318    270.10074    3.1869342 
+    1800   -471.14403    2476.2266    171.90923   -2947.3706    442.47741    530.45656    474.03057   -3284.0954   -371.95117    1306084.3   -1306822.6    3392.2533    48631.318    269.36446   0.10416401 
+    1850   -462.80763    2536.7112    176.10831   -2999.5188    437.08241    525.07462     474.0838   -3283.7906   -422.23719    1306091.6   -1306821.3    1629.8629    48631.318    275.99502  0.016806806 
+    1900   -469.89289    2468.9765     171.4059   -2938.8694    446.77624    531.61059    496.01046   -3284.2338   -395.15325    1306085.7   -1306819.6    3119.5402    48631.318    268.62645  0.014601992 
+    1950   -491.08007    2445.5966    169.78278   -2936.6767    457.80452    527.23373    470.18125   -3283.9608   -391.86377    1306101.9     -1306818    1122.5275    48631.318    266.08018  0.018911601 
+    2000   -518.40811    2418.7208    167.91696   -2937.1289    415.93135     536.5973    480.44651   -3283.7881   -363.72783    1306096.2   -1306818.7    4475.7317    48631.318    263.09007   0.13504326 
+Loop time of 70.696 on 1 procs for 2000 steps with 5500 atoms
+
+Performance: 1.222 ns/day, 19.638 hours/ns, 28.290 timesteps/s
+97.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 48.367     | 48.367     | 48.367     |   0.0 | 68.42
+Bond    | 2.9191     | 2.9191     | 2.9191     |   0.0 |  4.13
+Kspace  | 14.266     | 14.266     | 14.266     |   0.0 | 20.18
+Neigh   | 1.5262     | 1.5262     | 1.5262     |   0.0 |  2.16
+Comm    | 0.27841    | 0.27841    | 0.27841    |   0.0 |  0.39
+Output  | 0.0035572  | 0.0035572  | 0.0035572  |   0.0 |  0.01
+Modify  | 3.2856     | 3.2856     | 3.2856     |   0.0 |  4.65
+Other   |            | 0.05018    |            |       |  0.07
+
+Nlocal:    5500 ave 5500 max 5500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    15317 ave 15317 max 15317 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.30285e+06 ave 1.30285e+06 max 1.30285e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1302849
+Ave neighs/atom = 236.882
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 44
+Dangerous builds = 0
+Total wall time: 0:01:10

examples/USER/drude/toluene/log.7Aug19.toluene.nh.g++.4

@@ -0,0 +1,262 @@
+LAMMPS (7 Aug 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Nose-Hoover)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style fourier
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+  special bonds CPU = 0.000718355 secs
+  read_data CPU = 0.0167146 secs
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+  find clusters CPU = 0.000344038 secs
+
+compute cTEMP_CORE gCORES temp/com
+compute cTEMP all temp/drude
+
+fix fDIRECT all drude/transform/direct
+fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 260 100.0
+fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 1 20.0
+fix fINVERSE all drude/transform/inverse
+
+fix fMOMENTUM all momentum 100 linear 1 1 1
+
+thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 34263 16000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
+Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50     3563.376    4630.6343    321.47655   -1067.2583    735.72048    604.78665    689.14826    -3277.411    815.58183    1306088.7   -1306723.8    17813.425    48631.318      503.827 0.0087118179 
+     100    3327.4722    4395.1107    305.12559   -1067.6385    597.93175    651.62645     945.4151   -3267.2851    584.58833    1306135.9   -1306715.8    17407.335    48631.318     478.2017 0.0075985638 
+     150    3036.9065    4740.2304    329.08513   -1703.3238    558.64983    619.91284    658.80686   -3278.7837    285.12462      1306173     -1306720    18448.248    48631.318    515.75286 0.0063215227 
+     200    2697.9581    4559.3445    316.52734   -1861.3864    522.09335     593.8913    754.61446     -3273.49    87.660464    1306183.9     -1306730    17888.937    48631.318    496.07143  0.006870622 
+     250    2348.7563     4410.585    306.19988   -2061.8288    506.05006    575.35172    715.55055   -3276.3261   -18.364482    1306177.3   -1306741.4    11592.049    48631.318    479.88562 0.0071741023 
+     300    2019.8256    4040.1415    280.48225   -2020.3159    604.30771    641.66688    693.93802   -3278.5312   -115.73639    1306183.2   -1306749.1    3631.3625    48631.318    439.57995 0.0069886424 
+     350    1699.5169    3944.9851    273.87613   -2245.4682    452.07416    638.06529    658.79116   -3279.6053   -157.07584    1306196.9   -1306754.6    13544.368    48631.318    429.22695 0.0062868216 
+     400    1399.2927     3726.098    258.68014   -2326.8053    457.91943    621.44727    639.39905   -3279.2395   -188.85912    1306185.4   -1306762.8    10792.273    48631.318    405.41133 0.0059340084 
+     450    1120.5246     3518.345    244.25712   -2397.8204    519.48859     584.6579    646.36688   -3278.6685   -289.59912    1306184.1   -1306764.2    2755.5597    48631.318    382.80717  0.005570751 
+     500    868.01643    3359.8794    233.25583    -2491.863    460.73928    581.49568    581.01732   -3281.5544   -252.20168    1306184.3   -1306765.7     6120.364    48631.318    365.56528 0.0058756204 
+     550    637.01646    3214.9521    223.19441   -2577.9356    431.81484    578.87415    540.94046   -3281.5337   -266.36074    1306182.8   -1306764.5    8622.4353    48631.318    349.79661 0.0058589476 
+     600    418.04028    3113.4063    216.14471   -2695.3661    430.45936    538.68158    522.24597    -3283.456   -311.87897    1306174.3   -1306765.8    7068.9275    48631.318    338.74796 0.0059567639 
+     650    218.59562    2930.8439    203.47052   -2712.2482    514.47296     514.2838    551.52551   -3282.0904   -405.37401    1306164.5   -1306769.5   -13.554086    48631.318    318.88481 0.0052667849 
+     700    45.227739    2830.1443    196.47957   -2784.9165    451.11157    498.26426    541.18833   -3282.1427   -375.95321    1306157.1   -1306774.4    3947.6268    48631.318    307.92741 0.0068018884 
+     750   -114.28676    2798.3154    194.26988   -2912.6022    412.75298    503.28782    481.32167   -3284.3411   -393.53987      1306147   -1306779.1    7143.3424    48631.318    304.46466 0.0061596613 
+     800   -263.63827    2694.8085    187.08403   -2958.4468    455.67916    487.49754    476.86576   -3284.3133   -451.95784      1306145   -1306787.2    1185.9474    48631.318    293.20289 0.0058203323 
+     850   -397.71592    2559.1922    177.66903   -2956.9082    458.83313    481.22619    478.31233    -3284.068   -437.26509    1306138.6   -1306792.6    346.80221    48631.318    278.44747 0.0054921238 
+     900   -515.18134    2544.8753    176.67509   -3060.0567     395.0016     457.5898    446.68361    -3285.485   -423.56234    1306145.1   -1306795.3    3712.8594    48631.318    276.88864 0.0074054726 
+     950   -617.28607    2451.1721    170.16985   -3068.4582     383.6428    446.59872    434.46241   -3285.1348   -391.59326    1306142.3   -1306798.7    5429.2191    48631.318    266.69429 0.0057487961 
+    1000   -703.15541    2334.8366    162.09339    -3037.992    424.34957    462.21115    451.80811   -3284.3803   -426.53346    1306133.9   -1306799.3    1137.6144    48631.318    254.03671 0.0053915025 
+    1050   -771.17572    2303.8364    159.94123   -3075.0121    426.21406    436.50744    435.10013   -3285.1938   -411.13999    1306125.6   -1306802.1    1636.9467    48631.318    250.66288 0.0069341736 
+    1100   -822.72317     2283.421    158.52392   -3106.1442    376.67703    447.77728    418.45763   -3286.5919   -377.48075    1306118.9   -1306803.8    4760.4718    48631.318    248.44134 0.0074024122 
+    1150   -857.06061    2259.0725    156.83355   -3116.1331    400.31517    431.65949    457.68078   -3285.1977   -430.47775    1306115.8   -1306805.9    3194.5159    48631.318    245.79231  0.007063706 
+    1200   -875.50971    2238.2632    155.38889   -3113.7729    445.38534    460.97161    432.10511   -3285.4238   -472.46582    1306114.7     -1306809   -653.49627    48631.318    243.52813 0.0071446561 
+    1250   -880.37609     2294.689    159.30619   -3175.0651    411.35498    444.73774    420.06429   -3286.0366   -458.05353    1306104.4   -1306811.5    945.79687    48631.318    249.66483  0.011854196 
+    1300   -871.31122    2284.2295    158.58005   -3155.5407    404.97869    441.75305    426.34479   -3285.4859   -424.79602    1306094.8   -1306813.2    4406.6128    48631.318     248.4856  0.084411062 
+    1350   -816.69657    2325.9211    161.47444   -3142.6176    696.85542    442.50059    431.19981   -3285.7859   -450.27129    1305836.1   -1306813.3    593.86622    48631.318    251.40736    2.9289249 
+    1400   -794.25213    2263.5122    157.14177   -3057.7643     645.6531     466.2204    446.22253   -3285.1821   -420.65316    1305903.7   -1306813.8    1386.3481    48631.318    245.20568    1.8917548 
+    1450    -776.1076    2287.6591    158.81814   -3063.7667     427.0331    479.10417    439.67675   -3285.9536   -395.13308    1306087.6   -1306816.1    2936.7117    48631.318    248.87185  0.061341392 
+    1500   -725.48032    2371.4108    164.63251   -3096.8911    390.03135    464.30817    446.91941   -3284.7808   -393.16302    1306095.4   -1306815.6    3544.3635    48631.318    258.01262  0.011585228 
+    1550   -671.48696    2315.9233    160.78035   -2987.4102    457.04771    500.26018     464.7623    -3284.931   -400.98142    1306091.7   -1306815.3    2052.6204    48631.318    251.97656 0.0094518433 
+    1600   -618.82679    2449.0893    170.02525   -3067.9161    425.47171    474.66369    471.99137   -3284.3677    -430.3224    1306091.3   -1306816.6    441.31257    48631.318    266.46283  0.014263201 
+    1650   -567.82233    2425.2281    168.36872   -2993.0504    421.02008    511.26686    463.22202   -3285.0378   -377.24205    1306088.4   -1306814.7    5198.6214    48631.318    263.83232  0.074728934 
+    1700   -502.46013    2441.8437    169.52224   -2944.3039    642.39863    512.90005    490.39655    -3283.975   -417.39351    1305929.1   -1306817.7    1141.2401    48631.318    264.52268    2.0436397 
+    1750   -459.52135    2499.0847    173.49613    -2958.606    679.34078    505.30943    484.78276   -3284.6269   -384.28217    1305861.7   -1306820.8    1527.0852    48631.318    270.10144    3.1876179 
+    1800   -471.14322    2476.2445    171.91047   -2947.3877    442.48278     530.4566     474.0343   -3284.0957   -371.97492    1306084.3   -1306822.6    3392.0306    48631.318    269.36641    0.1041603 
+    1850   -462.80151    2536.7173    176.10873   -2999.5188    437.07855    525.05914    474.07725   -3283.7908   -422.22641    1306091.6   -1306821.3    1630.1204    48631.318    275.99568  0.016808725 
+    1900    -469.8785    2468.9596    171.40473   -2938.8381     446.7879     531.6128    496.02681   -3284.2335   -395.17163    1306085.7   -1306819.6    3119.2384    48631.318    268.62462  0.014603394 
+    1950   -491.07182    2445.6794    169.78853   -2936.7512    457.80204    527.21208     470.1608   -3283.9622   -391.90163    1306101.9     -1306818    1122.0978    48631.318    266.08919  0.018903661 
+    2000   -518.41243     2418.604    167.90885   -2937.0165    415.92605    536.62844    480.48912   -3283.7876   -363.72641    1306096.2   -1306818.7    4474.8778    48631.318    263.07743   0.13492637 
+Loop time of 22.3198 on 4 procs for 2000 steps with 5500 atoms
+
+Performance: 3.871 ns/day, 6.200 hours/ns, 89.606 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.452     | 12.249     | 12.556     |  13.2 | 54.88
+Bond    | 0.71352    | 0.72923    | 0.74557    |   1.3 |  3.27
+Kspace  | 5.7189     | 6.0293     | 6.8195     |  18.6 | 27.01
+Neigh   | 0.44028    | 0.44044    | 0.44065    |   0.0 |  1.97
+Comm    | 0.39667    | 0.40817    | 0.41558    |   1.1 |  1.83
+Output  | 0.0019479  | 0.0032187  | 0.0068657  |   3.7 |  0.01
+Modify  | 2.413      | 2.4256     | 2.4347     |   0.5 | 10.87
+Other   |            | 0.0349     |            |       |  0.16
+
+Nlocal:    1375 ave 1407 max 1349 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Nghost:    8082.5 ave 8114 max 8047 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    325715 ave 343636 max 314954 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 1302860
+Ave neighs/atom = 236.884
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 44
+Dangerous builds = 0
+Total wall time: 0:00:22

examples/USER/misc/hma/README

@@ -0,0 +1,22 @@
+The example input script sets up a simple FCC crystal using the Lennard-Jones
+potential. The script sets up the HMA compute to calculate the energy, pressure
+and heat capacity.  The output columns are:
+
+1: timestep
+2: measured temperature
+3: potential energy
+4: HMA potential energy
+5: pressure
+6: HMA pressure
+7: HMA heat capacity contribution
+
+Averages of the potential energy (#3 and #4) agree although #4 (HMA) is more precise.
+
+Averages of the pressure (#5 and #6) agree once the ideal gas
+contribution is included; #6 (HMA) is more precise.
+
+The heat capacity can be computed from colume #3 (convential) as
+Cv = Var(#3)/(k T^2)
+
+With HMA, the heat capacity can be computed from column #4 and #7 as
+Cv = #7 + Var(#4)/(k T^2)

examples/USER/misc/hma/hma.in

@@ -0,0 +1,36 @@
+# Harmonically mapped average example
+
+units lj 
+dimension 3 
+boundary p p p 
+atom_style atomic 
+atom_modify map array
+# ---------- Create Atoms ----------------------------
+lattice 	fcc 1.0
+region	box block 0 4 0 4 0 4 units lattice
+create_box	1 box
+lattice	fcc 1.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1  
+create_atoms 1 region box
+# ---------- Define Interatomic Potential --------------------- 
+pair_style lj/smooth/linear 3
+pair_coeff * * 1.0 1.0 
+mass 1 1.0
+
+atom_modify sort 0 1
+velocity all create 0.1 45678 dist gaussian
+
+compute u all pe 
+  
+compute p all pressure NULL pair  
+
+compute hma all hma settemp u p 9.579586686264458 cv
+
+timestep 0.005
+
+fix settemp all nvt temp 1.0 1.0 0.5
+thermo_style custom elapsed temp c_u c_hma[1] c_p c_hma[2] c_hma[3]
+thermo_modify format float '%22.15e'
+thermo 500
+run 20000
+thermo 20
+run 200000

examples/USER/misc/local_density/benzene_water/benzene_water.in

@@ -0,0 +1,62 @@
+# LAMMPS input file for 26.5% benzene mole fraction solution
+# with 380 benzene and 1000 water molecules,
+# using all possible local density potentials
+# between benzene and water
+#
+# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
+#
+# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
+
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p 
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       benzene_water.data
+velocity        all create  3.0000e+02 16611 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1    table          benzene_water.pair.table      PairBB
+pair_coeff          1     2    table          benzene_water.pair.table      PairWW
+pair_coeff          2     2    table          benzene_water.pair.table      PairBW
+pair_coeff          *     *    local/density  benzene_water.localdensity.table
+
+# Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+# Thermostat & time integration
+timestep        2.0 
+thermo          100
+thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl
+
+# Minimization
+minimize        1.e-4 0.0 10000 10000
+
+# Set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890
+
+# Equilibration (for realistic results, run for 5000000 steps)
+reset_timestep  0
+run             5000
+
+# Turn off recentering during production phase
+unfix recentering
+
+# Setup trajectory output
+dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element B W
+dump_modify     myDump sort id
+
+# Production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+run             1000             
+
+