Addressing include conflict

.github/CODEOWNERS

@@ -115,6 +115,10 @@ src/min*                  @sjplimp @stanmoore1
 # tools
 tools/msi2lmp/*       @akohlmey
 tools/emacs/*         @HaoZeke
+tools/singularity/*   @akohlmey @rbberger
+
+# tests
+unittest/*            @akohlmey @rbberger
 
 # cmake
 cmake/*               @junghans @rbberger

cmake/CMakeLists.txt

@@ -3,16 +3,24 @@
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
 cmake_minimum_required(VERSION 3.10)
+# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
+if(POLICY CMP0074)
+  cmake_policy(SET CMP0074 NEW)
+endif()
+########################################
 
 project(lammps CXX)
 set(SOVERSION 0)
-get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE)
+
-get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE)
+get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
-get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
+
-get_filename_component(LAMMPS_TOOLS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tools ABSOLUTE)
+set(LAMMPS_SOURCE_DIR     ${LAMMPS_DIR}/src)
-get_filename_component(LAMMPS_PYTHON_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../python ABSOLUTE)
+set(LAMMPS_LIB_SOURCE_DIR ${LAMMPS_DIR}/lib)
-get_filename_component(LAMMPS_POTENTIALS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../potentials ABSOLUTE)
+set(LAMMPS_DOC_DIR        ${LAMMPS_DIR}/doc)
+set(LAMMPS_TOOLS_DIR      ${LAMMPS_DIR}/tools)
+set(LAMMPS_PYTHON_DIR     ${LAMMPS_DIR}/python)
+set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
 
 find_package(Git)
 
@@ -24,6 +32,12 @@ endif()
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
 
+# make sure LIBRARY_PATH is set if environment variable is set
+if (DEFINED ENV{LIBRARY_PATH})
+  list(APPEND CMAKE_LIBRARY_PATH "$ENV{LIBRARY_PATH}")
+  message(STATUS "Appending $ENV{LIBRARY_PATH} to CMAKE_LIBRARY_PATH: ${CMAKE_LIBRARY_PATH}")
+endif()
+
 include(LAMMPSUtils)
 
 get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)
@@ -57,11 +71,11 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
 endif()
 
 if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-  set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
+  set(CMAKE_TUNE_DEFAULT "-march=native")
 endif()
 
 if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
-  set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
+  set(CMAKE_TUNE_DEFAULT "-march=native")
 endif()
 
 # we require C++11 without extensions
@@ -491,7 +505,7 @@ execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HE
 # Generate lmpgitversion.h
 ######################################
 add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
-  -DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
+  -DLAMMPS_DIR="${LAMMPS_DIR}"
   -DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
   -DGIT_FOUND="${GIT_FOUND}"
   -DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
@@ -538,8 +552,6 @@ if(BUILD_SHARED_LIBS)
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
-  file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
-  install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
   include(CMakePackageConfigHelpers)
   configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
   write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)

cmake/LAMMPSConfig.cmake.in

@@ -1,11 +1,5 @@
-list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
 include(CMakeFindDependencyMacro)
 if(@BUILD_MPI@)
   find_dependency(MPI REQUIRED CXX)
 endif()
-if(@PKG_KSPACE@)
-  if(@FFT@ STREQUAL "FFTW3")
-    find_dependency(@FFTW@ REQUIRED MODULE)
-  endif()
-endif()
 include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")

cmake/Modules/CodeCoverage.cmake

@@ -15,14 +15,35 @@ if(ENABLE_COVERAGE)
             gen_coverage_xml
             COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-            COMMENT "Generating XML Coverage Report..."
+            COMMENT "Generating XML coverage report..."
         )
 
+        set(COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/coverage_html)
+
+        add_custom_target(coverage_html_folder
+            COMMAND ${CMAKE_COMMAND} -E make_directory ${COVERAGE_HTML_DIR})
+
         add_custom_target(
             gen_coverage_html
-            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html
+            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o ${COVERAGE_HTML_DIR}/index.html
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-            COMMENT "Generating HTML Coverage Report..."
+            COMMENT "Generating HTML coverage report..."
         )
+        add_dependencies(gen_coverage_html coverage_html_folder)
+
+        add_custom_target(clean_coverage_html
+            ${CMAKE_COMMAND} -E remove_directory ${COVERAGE_HTML_DIR}
+            COMMENT "Deleting HTML coverage report..."
+        )
+
+        add_custom_target(reset_coverage
+            ${CMAKE_COMMAND} -E remove -f */*.gcda */*/*.gcda */*/*/*.gcda
+                              */*/*/*/*.gcda */*/*/*/*/*.gcda */*/*/*/*/*/*.gcda
+                              */*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*.gcda
+                              */*/*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*/*/*.gcda
+            WORKIND_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Deleting coverage data files..."
+        )
+        add_dependencies(reset_coverage clean_coverage_html)
     endif()
 endif()

cmake/Modules/FindLATTE.cmake

@@ -1,27 +0,0 @@
-# - Find latte
-# Find the native LATTE libraries.
-#
-#  LATTE_LIBRARIES    - List of libraries when using latte.
-#  LATTE_FOUND        - True if latte found.
-#
-
-find_library(LATTE_LIBRARY NAMES latte)
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set LATTE_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(LATTE DEFAULT_MSG LATTE_LIBRARY)
-
-# Copy the results to the output variables and target.
-if(LATTE_FOUND)
-  set(LATTE_LIBRARIES ${LATTE_LIBRARY})
-
-  if(NOT TARGET LATTE::latte)
-    add_library(LATTE::latte UNKNOWN IMPORTED)
-    set_target_properties(LATTE::latte PROPERTIES
-      IMPORTED_LOCATION "${LATTE_LIBRARY}")
-  endif()
-endif()
-
-mark_as_advanced(LATTE_LIBRARY)

cmake/Modules/FindTBB_MALLOC.cmake

@@ -6,7 +6,6 @@
 #  TBB_MALLOC_FOUND        - True if tbb found.
 #
 
-
 ########################################################
 # TBB Malloc
 

cmake/Modules/FindYAML.cmake

@@ -0,0 +1,30 @@
+# - Find libyaml
+# Find the native Yaml headers and libraries.
+#
+#  YAML_INCLUDE_DIRS - where to find yaml.h
+#  YAML_LIBRARIES    - List of libraries when using libyaml
+#  YAML_FOUND        - True if libyaml is found.
+#
+
+find_path(YAML_INCLUDE_DIR yaml.h PATH_SUFFIXES yaml)
+find_library(YAML_LIBRARY NAMES yaml)
+
+# handle the QUIET and REQUIRED arguments and
+# set YAML_FOUND to TRUE if all variables are non-zero
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(YAML DEFAULT_MSG YAML_LIBRARY YAML_INCLUDE_DIR)
+
+# Copy the results to the output variables and target.
+if(YAML_FOUND)
+  set(YAML_LIBRARIES ${YAML_LIBRARY})
+  set(YAML_INCLUDE_DIRS ${YAML_INCLUDE_DIR})
+
+  if(NOT TARGET Yaml::Yaml)
+    add_library(Yaml::Yaml UNKNOWN IMPORTED)
+    set_target_properties(Yaml::Yaml PROPERTIES
+      IMPORTED_LOCATION "${YAML_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${YAML_INCLUDE_DIR}")
+  endif()
+endif()
+
+mark_as_advanced(YAML_INCLUDE_DIR YAML_LIBRARY)

cmake/Modules/GTest.cmake

@@ -0,0 +1,77 @@
+message(STATUS "Downloading and building Google Test library")
+
+if(CMAKE_BUILD_TYPE STREQUAL Debug)
+  set(GTEST_LIB_POSTFIX d)
+else()
+  set(GTEST_LIB_POSTFIX)
+endif()
+
+include(ExternalProject)
+ExternalProject_Add(googletest
+                    GIT_REPOSITORY  https://github.com/google/googletest.git
+                    GIT_TAG         release-1.10.0
+                    SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"
+                    BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"
+                    CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}
+                                    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                                    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                                    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+                                    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
+                    LOG_DOWNLOAD ON
+                    LOG_CONFIGURE ON
+                    LOG_BUILD ON
+                    INSTALL_COMMAND ""
+                    TEST_COMMAND    "")
+
+ExternalProject_Get_Property(googletest SOURCE_DIR)
+set(GTEST_INCLUDE_DIR ${SOURCE_DIR}/googletest/include)
+set(GMOCK_INCLUDE_DIR ${SOURCE_DIR}/googlemock/include)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
+file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
+
+ExternalProject_Get_Property(googletest BINARY_DIR)
+set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
+set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
+set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
+set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
+
+# Prevent GoogleTest from overriding our compiler/linker options
+# when building with Visual Studio
+set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
+
+find_package(Threads QUIET)
+
+add_library(GTest::GTest UNKNOWN IMPORTED)
+set_target_properties(GTest::GTest PROPERTIES
+        IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
+        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+add_dependencies(GTest::GTest googletest)
+
+add_library(GTest::GMock UNKNOWN IMPORTED)
+set_target_properties(GTest::GMock PROPERTIES
+        IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
+        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+add_dependencies(GTest::GMock googletest)
+
+add_library(GTest::GTestMain UNKNOWN IMPORTED)
+set_target_properties(GTest::GTestMain PROPERTIES
+        IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
+        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+add_dependencies(GTest::GTestMain googletest)
+
+add_library(GTest::GMockMain UNKNOWN IMPORTED)
+set_target_properties(GTest::GMockMain PROPERTIES
+        IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
+        IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+add_dependencies(GTest::GMockMain googletest)

cmake/Modules/Packages/GPU.cmake

@@ -40,6 +40,17 @@ if(GPU_API STREQUAL "CUDA")
 
   set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
+  # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
+  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
+  if (GPU_LIB_OLD_CUBIN_HEADERS)
+    message(FATAL_ERROR "########################################################################\n"
+      "Found file(s) generated by the make-based build system in lib/gpu\n"
+      "Please run\n"
+      "  make -C ${LAMMPS_LIB_SOURCE_DIR}/gpu -f Makefile.serial clean\n"
+      "to remove\n"
+      "########################################################################")
+  endif()
+
   file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
@@ -79,7 +90,7 @@ if(GPU_API STREQUAL "CUDA")
     string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
   endif()
 
-  cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+  cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
           -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}

cmake/Modules/Packages/KOKKOS.cmake

@@ -35,8 +35,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
   ExternalProject_Add(kokkos_build
-    URL https://github.com/kokkos/kokkos/archive/3.1.00.tar.gz
+    URL https://github.com/kokkos/kokkos/archive/3.1.01.tar.gz
-    URL_MD5 f638a6c786f748a602b26faa0e96ebab
+    URL_MD5 3ccb2100f7fc316891e7dad3bc33fa37
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )
@@ -50,10 +50,7 @@ if(DOWNLOAD_KOKKOS)
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
   add_dependencies(LAMMPS::KOKKOS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.1)
+  find_package(Kokkos 3.1.01 REQUIRED CONFIG)
-  if(NOT Kokkos_FOUND)
-    message(FATAL_ERROR "KOKKOS library version 3.1 or later not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
-  endif()
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

cmake/Modules/Packages/KSPACE.cmake

@@ -2,7 +2,7 @@ option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" O
 set(FFTW "FFTW3")
 if(FFT_SINGLE)
   set(FFTW "FFTW3F")
-  target_compile_definitions(lammps PUBLIC -DFFT_SINGLE)
+  target_compile_definitions(lammps PRIVATE -DFFT_SINGLE)
 endif()
 find_package(${FFTW} QUIET)
 if(${FFTW}_FOUND)
@@ -17,8 +17,8 @@ string(TOUPPER ${FFT} FFT)
 
 if(FFT STREQUAL "FFTW3")
   find_package(${FFTW} REQUIRED)
-  target_compile_definitions(lammps PUBLIC -DFFT_FFTW3)
+  target_compile_definitions(lammps PRIVATE -DFFT_FFTW3)
-  target_link_libraries(lammps PUBLIC ${FFTW}::${FFTW})
+  target_link_libraries(lammps PRIVATE ${FFTW}::${FFTW})
   if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
     option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
   else()

cmake/Modules/Packages/LATTE.cmake

@@ -6,7 +6,7 @@ if(TARGET LATTE::latte)
   return()
 endif()
 
-find_package(LATTE)
+find_package(LATTE 1.2.2 CONFIG)
 if(LATTE_FOUND)
   set(DOWNLOAD_LATTE_DEFAULT OFF)
 else()
@@ -17,8 +17,8 @@ if(DOWNLOAD_LATTE)
   message(STATUS "LATTE download requested - we will build our own")
   include(ExternalProject)
   ExternalProject_Add(latte_build
-    URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
+    URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz
-    URL_MD5 85ac414fdada2d04619c8f936344df14
+    URL_MD5 820e73a457ced178c08c71389a385de7
     SOURCE_SUBDIR cmake
     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
     -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
@@ -35,10 +35,6 @@ if(DOWNLOAD_LATTE)
   target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
   add_dependencies(LAMMPS::LATTE latte_build)
 else()
-  find_package(LATTE)
+  find_package(LATTE 1.2.2 REQUIRED CONFIG)
-  if(NOT LATTE_FOUND)
+  target_link_libraries(lammps PRIVATE LATTE::latte)
-    message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
-  endif()
-  # latte needs lapack
-  target_link_libraries(lammps PRIVATE LATTE::latte ${LAPACK_LIBRARIES})
 endif()

cmake/Modules/Packages/USER-H5MD.cmake

@@ -1,8 +1,5 @@
 enable_language(C)
 
-if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
-  cmake_policy(SET CMP0074 NEW)
-endif()
 find_package(HDF5 REQUIRED)
 target_link_libraries(h5md PRIVATE ${HDF5_LIBRARIES})
 target_include_directories(h5md PUBLIC ${HDF5_INCLUDE_DIRS})

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -1,8 +1,7 @@
 # USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
 # NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
-if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
+
-  cmake_policy(SET CMP0074 NEW)
+# may use NetCDF or PNetCDF with MPI, but must have NetCDF without
-endif()
 if(NOT BUILD_MPI)
   find_package(NetCDF REQUIRED)
 else()

cmake/Modules/Testing.cmake

@@ -4,48 +4,7 @@
 option(ENABLE_TESTING "Enable testing" OFF)
 if(ENABLE_TESTING)
   enable_testing()
-  option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
+  get_filename_component(LAMMPS_UNITTEST_DIR ${LAMMPS_SOURCE_DIR}/../unittest ABSOLUTE)
-  option(LAMMPS_TESTING_GIT_TAG    "Git tag of lammps-testing" "master")
+  get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
-  mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
+  add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
-
-  if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
-    include(FetchContent)
-
-    FetchContent_Declare(lammps-testing
-      GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
-      GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
-    )
-
-    FetchContent_GetProperties(lammps-testing)
-    if(NOT lammps-testing_POPULATED)
-      message(STATUS "Downloading tests...")
-      FetchContent_Populate(lammps-testing)
-    endif()
-
-    set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
-  elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
-    message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
-                    "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
-  endif()
-
-  add_test(NAME ShowHelp COMMAND $<TARGET_FILE:lmp> -help)
-
-  if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
-    message(STATUS "Running test discovery...")
-
-    file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
-    foreach(script_path ${TEST_SCRIPTS})
-      get_filename_component(TEST_NAME ${script_path} EXT)
-      get_filename_component(SCRIPT_NAME ${script_path} NAME)
-      get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
-      string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
-      string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
-      string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
-      set(TEST_NAME "test_core_${TEST_NAME}_serial")
-      add_test(NAME ${TEST_NAME} COMMAND $<TARGET_FILE:lmp> -in ${SCRIPT_NAME} WORKING_DIRECTORY ${PARENT_DIR})
-    endforeach()
-    list(LENGTH TEST_SCRIPTS NUM_TESTS)
-
-    message(STATUS "Found ${NUM_TESTS} tests.")
-  endif()
 endif()

cmake/Modules/generate_lmpgitversion.cmake

@@ -3,17 +3,19 @@ set(temp_git_commit "(unknown)")
 set(temp_git_branch "(unknown)")
 set(temp_git_describe "(unknown)")
 set(temp_git_info "false")
-if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
+
+message(STATUS "Git Directory: ${LAMMPS_DIR}/.git")
+if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
   set(temp_git_info "true")
-  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} rev-parse HEAD
     OUTPUT_VARIABLE temp_git_commit
     ERROR_QUIET
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} rev-parse --abbrev-ref HEAD
     OUTPUT_VARIABLE temp_git_branch
     ERROR_QUIET
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} describe --dirty=-modified
     OUTPUT_VARIABLE temp_git_describe
     ERROR_QUIET
     OUTPUT_STRIP_TRAILING_WHITESPACE)

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "5 May 2020" "2020-05-5"
+.TH LAMMPS "2 June 2020" "2020-06-02"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_cmake.rst

@@ -107,7 +107,7 @@ re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
 ``cmake .`` and then compile again. The included dependency tracking
 should make certain that only the necessary subset of files are
 re-compiled.  You can also delete compiled objects, libraries and
-executables with ``cmake --build . clean`` (or ``make clean``).
+executables with ``cmake --build . --target clean`` (or ``make clean``).
 
 After compilation, you may optionally install the LAMMPS executable into
 your system with:

doc/src/Build_development.rst

@@ -57,53 +57,252 @@ variable during configuration. Examples:
 
 .. _testing:
 
-Code Coverage and Testing
+Code Coverage and Unit Testing
----------------------------------------
+------------------------------
 
-We do extensive regression testing of the LAMMPS code base on a continuous
+The LAMMPS code is subject to multiple levels of automated testing
-basis. Some of the logic to do this has been added to the CMake build so
+during development: integration testing (i.e. whether the code compiles
-developers can run the tests directly on their workstation.
+on various platforms and with a variety of settings), unit testing
+(i.e. whether certain individual parts of the code produce the expected
+results for given inputs), run testing (whether selected complete input
+decks run without crashing for multiple configurations), and regression
+testing (i.e. whether selected input examples reproduce the same
+results over a given number of steps and operations within a given
+error margin).  The status of this automated testing can be viewed on
+`https://ci.lammps.org <https://ci.lammps.org>`_.
+
+The unit testing facility is integrated into the CMake build process
+of the LAMMPS source code distribution itself.  It can be enabled by
+setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
+It requires the `YAML <http://pyyaml.org/>`_ library and development
+headers to compile and will download and compile a recent version of the
+`Googletest <https://github.com/google/googletest/>`_ C++ test framework
+for implementing the tests.
+
+After compilation is complete, the unit testing is started in the build
+folder using the ``ctest`` command, which is part of the CMake software.
+The output of this command will be looking something like this::
+
+   [...]$ ctest
+   Test project /home/akohlmey/compile/lammps/build-testing
+         Start  1: MolPairStyle:hybrid-overlay
+    1/26 Test  #1: MolPairStyle:hybrid-overlay .........   Passed    0.02 sec
+         Start  2: MolPairStyle:hybrid
+    2/26 Test  #2: MolPairStyle:hybrid .................   Passed    0.01 sec
+         Start  3: MolPairStyle:lj_class2
+    [...]
+         Start 25: AngleStyle:harmonic
+   25/26 Test #25: AngleStyle:harmonic .................   Passed    0.01 sec
+         Start 26: AngleStyle:zero
+   26/26 Test #26: AngleStyle:zero .....................   Passed    0.01 sec
+   
+   100% tests passed, 0 tests failed out of 26
+   
+   Total Test time (real) =   0.27 sec
+
+
+The ``ctest`` command has many options, the most important ones are:
+
+.. list-table::
+
+   * - Option
+     - Function
+   * - -V
+     - verbose output: display output of individual test runs
+   * - -j <num>
+     - parallel run: run <num> tests in parallel
+   * - -R <regex>
+     - run subset of tests matching the regular expression <regex>
+   * - -E <regex>
+     - exclude subset of tests matching the regular expression <regex>
+   * - -N
+     - dry-run: display list of tests without running them
+
+In its full implementation, the unit test framework will consist of multiple
+kinds of tests implemented in different programming languages (C++, C, Python,
+Fortran) and testing different aspects of the LAMMPS software and its features.
+At the moment only tests for "force styles" are implemented. More on those
+in the next section.
 
 .. note::
 
-   this is incomplete and only represents a small subset of tests that we run
+   This unit test framework is new and still under development.
+   The coverage is only minimal and will be expanded over time.
+   Tests styles of the same kind of style (e.g. pair styles or
+   bond styles) are performed with the same executable using
+   different input files in YAML format.  So to add a test for
+   another pair style can be done by copying the YAML file and
+   editing the style settings and then running the individual test
+   program with a flag to update the computed reference data.
+   Detailed documentation about how to add new test program and
+   the contents of the YAML files for existing test programs
+   will be provided in time as well.
+
+Unit tests for force styles
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A large part of LAMMPS are different "styles" for computing non-bonded
+and bonded interactions selected through the :doc:`pair_style`,
+:doc:`bond_style`, :doc:`angle_style`, :doc:`dihedral_style`,
+:doc:`improper_style`, and :doc:`kspace_style`.  Since these all share
+common interfaces, it is possible to write generic test programs that
+will call those common interfaces for small test systems with less than
+100 atoms and compare the results with pre-recorded reference results.
+A test run is then a a collection multiple individual test runs each
+with many comparisons to reference results based on template input
+files, individual command settings, relative error margins, and
+reference data stored in a YAML format file with ``.yaml``
+suffix. Currently the programs ``pair_style``, ``bond_style``, and
+``angle_style`` are implemented.  They will compare forces, energies and
+(global) stress for all atoms after a ``run 0`` calculation and after a
+few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
+with different settings and also for multiple accelerated styles. If a
+prerequisite style or package is missing, the individual tests are
+skipped.  All tests will be executed on a single MPI process, so using
+the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
+since this will skip the MPI initialization for each test run.
+Below is an example command and output:
+
+.. parsed-literal::
+
+   [tests]$ pair_style mol-pair-lj_cut.yaml
+   [==========] Running 6 tests from 1 test suite.
+   [----------] Global test environment set-up.
+   [----------] 6 tests from PairStyle
+   [ RUN      ] PairStyle.plain
+   [       OK ] PairStyle.plain (24 ms)
+   [ RUN      ] PairStyle.omp
+   [       OK ] PairStyle.omp (18 ms)
+   [ RUN      ] PairStyle.intel
+   [       OK ] PairStyle.intel (6 ms)
+   [ RUN      ] PairStyle.opt
+   [  SKIPPED ] PairStyle.opt (0 ms)
+   [ RUN      ] PairStyle.single
+   [       OK ] PairStyle.single (7 ms)
+   [ RUN      ] PairStyle.extract
+   [       OK ] PairStyle.extract (6 ms)
+   [----------] 6 tests from PairStyle (62 ms total)
+
+   [----------] Global test environment tear-down
+   [==========] 6 tests from 1 test suite ran. (63 ms total)
+   [  PASSED  ] 5 tests.
+   [  SKIPPED ] 1 test, listed below:
+   [  SKIPPED ] PairStyle.opt
+
+In this particular case, 5 out of 6 sets of tests were conducted, the
+tests for the ``lj/cut/opt`` pair style was skipped, since the tests
+executable did not include it.  To learn what individual tests are performed,
+you (currently) need to read the source code.  You can use code coverage
+recording (see next section) to confirm how well the tests cover the individual
+source files.
+
+The force style test programs have a common set of options:
+
+.. list-table::
+
+   * - Option
+     - Function
+   * - -g <newfile>
+     - regenerate reference data in new YAML file
+   * - -u
+     - update reference data in the original YAML file
+   * - -s
+     - print error statistics for each group of comparisons
+   * - -v
+     - verbose output: also print the executed LAMMPS commands
+
+To add a test for a style that is not yet covered, it is usually best
+to copy a YAML file for a similar style to a new file, edit the details
+of the style (how to call it, how to set its coefficients) and then
+run test command with either the *-g* and the replace the initial
+test file with the regenerated one or the *-u* option.  The *-u* option
+will destroy the original file, if the generation run does not complete,
+so using *-g* is recommended unless the YAML file is fully tested
+and working.
+
+.. admonition:: Recommendations and notes for YAML files
+   :class: note
+
+   - The reference results should be recorded without any code
+     optimization or related compiler flags enabled.
+   - The ``epsilon`` parameter defines the relative precision with which
+     the reference results must be met.  The test geometries often have
+     high and low energy parts and thus a significant impact from
+     floating-point math truncation errors is to be expected. Some
+     functional forms and potentials are more noisy than others, so this
+     parameter needs to be adjusted. Typically a value around 1.0e-13
+     can be used, but it may need to be as large as 1.0e-8 in some
+     cases.
+   - The tests for pair styles from OPT, USER-OMP and USER-INTEL are
+     performed with automatically rescaled epsilon to account for
+     additional loss of precision from code optimizations and different
+     summation orders.
+   - When compiling with aggressive compiler optimization, some tests
+     are likely to fail.  It is recommended to inspect the individual
+     tests in detail to decide whether the specific error for a specific
+     property is acceptable (it often is), or this may be an indication
+     of mis-compiled code (or undesired large of precision due to
+     reordering of operations).
+
+Collect and visualize code coverage metrics
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can also collect code coverage metrics while running LAMMPS or the
+tests by enabling code coverage support during the CMake configuration:
 
 .. code-block:: bash
 
-   -D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
+   -D ENABLE_COVERAGE=on  # enable coverage measurements (off by default)
-   -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
 
-If you enable testing in the CMake build it will create an additional
+This will instrument all object files to write information about which
-target called "test". You can run them with:
+lines of code were accessed during execution in files next to the
+corresponding object files.  These can be post-processed to visually
+show the degree of coverage and which code paths are accessed and which
+are not taken.  When working on unit tests (see above), this can be
+extremely helpful to determine which parts of the code are not executed
+and thus what kind of tests are still missing. The coverage data is
+cumulative, i.e. new data is added with each new run.
+
+Enabling code coverage will also add the following build targets to
+generate coverage reports after running the LAMMPS executable or the
+unit tests:
 
 .. code-block:: bash
 
-   cmake --build . test
+   make gen_coverage_html   # generate coverage report in HTML format
+   make gen_coverage_xml    # generate coverage report in XML format
+   make clean_coverage_html # delete folder with HTML format coverage report
+   make reset_coverage      # delete all collected coverage data and HTML output
 
-The test cases used come from the lammps-testing repository. They are
+These reports require `GCOVR <https://gcovr.com/>`_ to be installed. The easiest way
-derivatives of the examples folder with some modifications to make the
+to do this to install it via pip:
-run faster.
-
-You can also collect code coverage metrics while running the tests by
-enabling coverage support during building.
-
-.. code-block:: bash
-
-   -D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes
-
-This will also add the following targets to generate coverage reports
-after running the LAMMPS executable:
-
-.. code-block:: bash
-
-   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
-
-These reports require GCOVR to be installed. The easiest way to do this
-to install it via pip:
 
 .. code-block:: bash
 
    pip install git+https://github.com/gcovr/gcovr.git
+
+After post-processing with ``gen_coverage_html`` the results are in
+a folder ``coverage_html`` and can be viewed with a web browser.
+The images below illustrate how the data is presented.
+
+.. list-table::
+
+      * - .. figure:: JPG/coverage-overview-top.png
+             :target: JPG/coverage-overview-top.png
+
+          Top of the overview page
+
+        - .. figure:: JPG/coverage-overview-manybody.png
+             :target: JPG/coverage-overview-manybody.png
+
+          Styles with good coverage
+
+        - .. figure:: JPG/coverage-file-top.png
+             :target: JPG/coverage-file-top.png
+
+          Top of individual source page
+
+        - .. figure:: JPG/coverage-file-branches.png
+             :target: JPG/coverage-file-branches.png
+
+          Source page with branches

doc/src/Build_extras.rst

@@ -132,6 +132,10 @@ Thus the GPU_ARCH setting is merely an optimization, to have code for
 the preferred GPU architecture directly included rather than having to wait
 for the JIT compiler of the CUDA driver to translate it.
 
+When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
+using the traditional build procedure. CMake will detect files generated by that
+process and will terminate with an error and a suggestion for how to remove them.
+
 If you are compiling with HIP, note that before running CMake you will have to
 set appropriate environment variables. Some variables such as
 :code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
@@ -320,12 +324,13 @@ to have an executable that will run on this and newer architectures.
 
 .. note::
 
-   If you run Kokkos on a newer GPU architecture than what LAMMPS was
+   If you run Kokkos on a different GPU architecture than what LAMMPS
-   compiled with, there will be a delay during device initialization
+   was compiled with, there will be a delay during device initialization
-   since the just-in-time compiler has to recompile all GPU kernels
+   while the just-in-time compiler is recompiling all GPU kernels for
-   for the new hardware.  This is, however, not possible when compiled
+   the new hardware.  This is, however, only supported for GPUs of the
-   for NVIDIA GPUs with CC 3.x (Kepler) for GPUs with CC 5.0 (Maxwell)
+   **same** major hardware version and different minor hardware versions,
-   and newer as they are not compatible.
+   e.g. 5.0 and 5.2 but not 5.2 and 6.0.  LAMMPS will abort with an
+   error message indicating a mismatch, if that happens.
 
 The settings discussed below have been tested with LAMMPS and are
 confirmed to work.  Kokkos is an active project with ongoing improvements
@@ -580,9 +585,14 @@ recommended when developing a Kokkos-enabled style in LAMMPS.
 
 The CMake option ``-DKokkos_ENABLE_CUDA_UVM=on`` or the makefile
 setting ``KOKKOS_CUDA_OPTIONS=enable_lambda,force_uvm`` enables the
-use of CUDA "Unified Virtual Memory" in Kokkos.  Please note, that
+use of CUDA "Unified Virtual Memory" (UVM) in Kokkos.  UVM allows to
-the LAMMPS KOKKOS package must **always** be compiled with the
+transparently use RAM on the host to supplement the memory used on the
-*enable_lambda* option when using GPUs.
+GPU (with some performance penalty) and thus enables running larger
+problems that would otherwise not fit into the RAM on the GPU.
+
+Please note, that the LAMMPS KOKKOS package must **always** be compiled
+with the *enable_lambda* option when using GPUs.  The CMake configuration
+will thus always enable it.
 
 ----------
 

doc/src/Commands_all.rst

@@ -94,6 +94,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`package <package>`
    * :doc:`pair_coeff <pair_coeff>`
    * :doc:`pair_modify <pair_modify>`
+   * :doc:`pair_style <pair_style>`
    * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
    * :doc:`prd <prd>`

doc/src/Commands_compute.rst

@@ -79,9 +79,6 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`ke/atom/eff <compute_ke_atom_eff>`
    * :doc:`ke/eff <compute_ke_eff>`
    * :doc:`ke/rigid <compute_ke_rigid>`
-   * :doc:`meso/e/atom <compute_meso_e_atom>`
-   * :doc:`meso/rho/atom <compute_meso_rho_atom>`
-   * :doc:`meso/t/atom <compute_meso_t_atom>`
    * :doc:`momentum <compute_momentum>`
    * :doc:`msd <compute_msd>`
    * :doc:`msd/chunk <compute_msd_chunk>`
@@ -133,6 +130,9 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`sna/atom <compute_sna_atom>`
    * :doc:`snad/atom <compute_sna_atom>`
    * :doc:`snav/atom <compute_sna_atom>`
+   * :doc:`sph/e/atom <compute_sph_e_atom>`
+   * :doc:`sph/rho/atom <compute_sph_rho_atom>`
+   * :doc:`sph/t/atom <compute_sph_t_atom>`
    * :doc:`spin <compute_spin>`
    * :doc:`stress/atom <compute_stress_atom>`
    * :doc:`stress/mop <compute_stress_mop>`

doc/src/Commands_fix.rst

@@ -95,9 +95,7 @@ OPT.
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
-   * :doc:`meso <fix_meso>`
    * :doc:`meso/move <fix_meso_move>`
-   * :doc:`meso/stationary <fix_meso_stationary>`
    * :doc:`momentum (k) <fix_momentum>`
    * :doc:`move <fix_move>`
    * :doc:`mscg <fix_mscg>`
@@ -149,6 +147,7 @@ OPT.
    * :doc:`oneway <fix_oneway>`
    * :doc:`orient/bcc <fix_orient>`
    * :doc:`orient/fcc <fix_orient>`
+   * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
@@ -202,6 +201,8 @@ OPT.
    * :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
    * :doc:`smd/setvel <fix_smd_setvel>`
    * :doc:`smd/wall_surface <fix_smd_wall_surface>`
+   * :doc:`sph <fix_sph>`
+   * :doc:`sph/stationary <fix_sph_stationary>`
    * :doc:`spring <fix_spring>`
    * :doc:`spring/chunk <fix_spring_chunk>`
    * :doc:`spring/rg <fix_spring_rg>`

doc/src/Commands_pair.rst

@@ -92,8 +92,8 @@ OPT.
    * :doc:`drip <pair_drip>`
    * :doc:`eam (gikot) <pair_eam>`
    * :doc:`eam/alloy (gikot) <pair_eam>`
-   * :doc:`eam/cd (o) <pair_eam>`
+   * :doc:`eam/cd <pair_eam>`
-   * :doc:`eam/cd/old (o) <pair_eam>`
+   * :doc:`eam/cd/old <pair_eam>`
    * :doc:`eam/fs (gikot) <pair_eam>`
    * :doc:`edip (o) <pair_edip>`
    * :doc:`edip/multi <pair_edip>`

doc/src/Howto_cmake.rst

@@ -415,8 +415,10 @@ This is particularly convenient, if you have set a custom build command
 via the ``CMAKE_MAKE_PROGRAM`` variable.
 
 When calling the build program, you can also select which "target" is to
-be build through appending the name of the target to the build command.
+be build through appending the ``--target`` flag and the name of the target
-Example: ``cmake --build . all``. The following abstract targets are available:
+to the build command.  When using ``make`` as build tool, you can just append
+the target name to the command. Example: ``cmake --build . --target all`` or
+``make all``.  The following abstract targets are available:
 
 .. list-table::
    :header-rows: 1
@@ -432,7 +434,7 @@ Example: ``cmake --build . all``. The following abstract targets are available:
    * - ``install``
      - install all target files into folders in ``CMAKE_INSTALL_PREFIX``
    * - ``test``
-     - run some simple tests (if configured with ``-D ENABLE_TESTING=on``)
+     - run some tests (if configured with ``-D ENABLE_TESTING=on``)
    * - ``clean``
      - remove all generated files
 

doc/src/Modify_atom.rst

@@ -3,115 +3,169 @@ Atom styles
 
 Classes that define an :doc:`atom style <atom_style>` are derived from
 the AtomVec class and managed by the Atom class.  The atom style
-determines what attributes are associated with an atom.  A new atom
+determines what attributes are associated with an atom and
-style can be created if one of the existing atom styles does not
+communicated when it is a ghost atom or migrates to a new processor.
-define all the attributes you need to store and communicate with
+A new atom style can be created if one of the existing atom styles
-atoms.
+does not define all the attributes you need to store and communicate
+with atoms.
 
-Atom_vec_atomic.cpp is a simple example of an atom style.
+Atom_vec_atomic.cpp is the simplest example of an atom style.
+Examining the code for others will make these instructions more clear.
 
-Here is a brief description of methods you define in your new derived
+Note that the :doc:`atom style hybrid <atom_style>` command can be
-class.  See atom_vec.h for details.
+used to define atoms or particles which have the union of properties
+of individual styles.  Also the :doc:`fix property/atom <fix_property_atom>`
+command can be used to add a single property (e.g. charge
+or a molecule ID) to a style that does not have it.  It can also be
+used to add custom properties to an atom, with options to communicate
+them with ghost atoms or read them from a data file.  Other LAMMPS
+commands can access these custom properties, as can new pair, fix,
+compute styles that are written to work with these properties.  For
+example, the :doc:`set <set>` command can be used to set the values of
+custom per-atom properties from an input script.  All of these methods
+are less work than writing code for a new atom style.
 
-+-------------------------+--------------------------------------------------------------------------------+
+If you follow these directions your new style will automatically work
-| init                    | one time setup (optional)                                                      |
+in tandem with others via the :doc:`atom_style hybrid <atom_style>`
-+-------------------------+--------------------------------------------------------------------------------+
+command.
-| grow                    | re-allocate atom arrays to longer lengths (required)                           |
-+-------------------------+--------------------------------------------------------------------------------+
-| grow_reset              | make array pointers in Atom and AtomVec classes consistent (required)          |
-+-------------------------+--------------------------------------------------------------------------------+
-| copy                    | copy info for one atom to another atom's array locations (required)            |
-+-------------------------+--------------------------------------------------------------------------------+
-| pack_comm               | store an atom's info in a buffer communicated every timestep (required)        |
-+-------------------------+--------------------------------------------------------------------------------+
-| pack_comm_vel           | add velocity info to communication buffer (required)                           |
-+-------------------------+--------------------------------------------------------------------------------+
-| pack_comm_hybrid        | store extra info unique to this atom style (optional)                          |
-+-------------------------+--------------------------------------------------------------------------------+
-| unpack_comm             | retrieve an atom's info from the buffer (required)                             |
-+-------------------------+--------------------------------------------------------------------------------+
-| unpack_comm_vel         | also retrieve velocity info (required)                                         |
-+-------------------------+--------------------------------------------------------------------------------+
-| unpack_comm_hybrid      | retrieve extra info unique to this atom style (optional)                       |
-+-------------------------+--------------------------------------------------------------------------------+
-| pack_reverse            | store an atom's info in a buffer communicating partial forces  (required)      |
-+-------------------------+--------------------------------------------------------------------------------+
-| pack_reverse_hybrid     | store extra info unique to this atom style (optional)                          |
-+-------------------------+--------------------------------------------------------------------------------+
-| unpack_reverse          | retrieve an atom's info from the buffer (required)                             |
-+-------------------------+--------------------------------------------------------------------------------+
-| unpack_reverse_hybrid   | retrieve extra info unique to this atom style (optional)                       |
-+-------------------------+--------------------------------------------------------------------------------+
-| pack_border             | store an atom's info in a buffer communicated on neighbor re-builds (required) |
-+-------------------------+--------------------------------------------------------------------------------+
-| pack_border_vel         | add velocity info to buffer (required)                                         |
-+-------------------------+--------------------------------------------------------------------------------+
-| pack_border_hybrid      | store extra info unique to this atom style (optional)                          |
-+-------------------------+--------------------------------------------------------------------------------+
-| unpack_border           | retrieve an atom's info from the buffer (required)                             |
-+-------------------------+--------------------------------------------------------------------------------+
-| unpack_border_vel       | also retrieve velocity info (required)                                         |
-+-------------------------+--------------------------------------------------------------------------------+
-| unpack_border_hybrid    | retrieve extra info unique to this atom style (optional)                       |
-+-------------------------+--------------------------------------------------------------------------------+
-| pack_exchange           | store all an atom's info to migrate to another processor (required)            |
-+-------------------------+--------------------------------------------------------------------------------+
-| unpack_exchange         | retrieve an atom's info from the buffer (required)                             |
-+-------------------------+--------------------------------------------------------------------------------+
-| size_restart            | number of restart quantities associated with proc's atoms (required)           |
-+-------------------------+--------------------------------------------------------------------------------+
-| pack_restart            | pack atom quantities into a buffer (required)                                  |
-+-------------------------+--------------------------------------------------------------------------------+
-| unpack_restart          | unpack atom quantities from a buffer (required)                                |
-+-------------------------+--------------------------------------------------------------------------------+
-| create_atom             | create an individual atom of this style (required)                             |
-+-------------------------+--------------------------------------------------------------------------------+
-| data_atom               | parse an atom line from the data file (required)                               |
-+-------------------------+--------------------------------------------------------------------------------+
-| data_atom_hybrid        | parse additional atom info unique to this atom style (optional)                |
-+-------------------------+--------------------------------------------------------------------------------+
-| data_vel                | parse one line of velocity information from data file (optional)               |
-+-------------------------+--------------------------------------------------------------------------------+
-| data_vel_hybrid         | parse additional velocity data unique to this atom style (optional)            |
-+-------------------------+--------------------------------------------------------------------------------+
-| memory_usage            | tally memory allocated by atom arrays (required)                               |
-+-------------------------+--------------------------------------------------------------------------------+
 
-The constructor of the derived class sets values for several variables
+The first step is to define a set of strings in the constructor of the
-that you must set when defining a new atom style, which are documented
+new derived class.  Each string will have zero or more space-separated
-in atom_vec.h.  New atom arrays are defined in atom.cpp.  Search for
+variable names which are identical to those used in the atom.h header
-the word "customize" and you will find locations you will need to
+file for per-atom properties.  Note that some represent per-atom
-modify.
+vectors (q, molecule) while other are per-atom arrays (x,v).  For all
+but the last 2 strings you do not need to specify any of
+(id,type,x,v,f).  Those are included automatically as needed in the
+other strings.
 
-.. note::
+.. list-table::
 
-   It is possible to add some attributes, such as a molecule ID, to
+   * - fields_grow
-   atom styles that do not have them via the :doc:`fix property/atom <fix_property_atom>` command.  This command also
+     - full list of properties which is allocated and stored
-   allows new custom attributes consisting of extra integer or
+   * - fields_copy
-   floating-point values to be added to atoms.  See the :doc:`fix property/atom <fix_property_atom>` doc page for examples of cases
+     - list of properties to copy atoms are rearranged on-processor
-   where this is useful and details on how to initialize, access, and
+   * - fields_comm
-   output the custom values.
+     - list of properties communicated to ghost atoms every step
+   * - fields_comm_vel
+     - additional properties communicated if :doc:`comm_modify vel <atom_style>` is used
+   * - fields_reverse
+     - list of properties summed from ghost atoms every step
+   * - fields_border
+     - list of properties communicated with ghost atoms every reneighboring step
+   * - fields_border_vel
+     - additional properties communicated if :doc:`comm_modify vel <atom_style>` is used
+   * - fields_exchange
+     - list of properties communicated when an atom migrates to another processor
+   * - fields_restart
+     - list of properties written/read to/from a restart file
+   * - fields_create
+     - list of properties defined when an atom is created by :doc:`create_atoms <create_atoms>`
+   * - fields_data_atom
+     - list of properties (in order) in the Atoms section of a data file, as read by :doc:`read_data <read_data>`
+   * - fields_data_vel
+     - list of properties (in order) in the Velocities section of a data file, as read by :doc:`read_data <read_data>`
 
-New :doc:`pair styles <pair_style>`, :doc:`fixes <fix>`, or
+In these strings you can list variable names which LAMMPS already
-:doc:`computes <compute>` can be added to LAMMPS, as discussed below.
+defines (in some other atom style), or you can create new variable
-The code for these classes can use the per-atom properties defined by
+names.  You should not re-use a LAMMPS variable for something with
-fix property/atom.  The Atom class has a find_custom() method that is
+different meaning in your atom style.  If the meaning is related, but
-useful in this context:
+interpreted differently by your atom style, then using the same
+variable name means a user should not use your style and the other
+style together in a :doc:`atom_style hybrid <atom_style>` command.
+Because there will only be one value of the variable and different
+parts of LAMMPS will then likely use it differently.  LAMMPS has
+no way of checking for this.
 
-.. code-block:: c++
+If you are defining new variable names then make them descriptive and
+unique to your new atom style.  For example choosing "e" for energy is
+a bad choice; it is too generic.  A better choice would be "e_foo",
+where "foo" is specific to your style.
 
-   int index = atom->find_custom(char *name, int &flag);
+If any of the variable names in your new atom style do not exist in
+LAMMPS, you need to add them to the src/atom.h and atom.cpp files.
 
-The "name" of a custom attribute, as specified in the :doc:`fix property/atom <fix_property_atom>` command, is checked to verify
+Search for the word "customize" or "customization" in these 2 files to
-that it exists and its index is returned.  The method also sets flag =
+see where to add your variable.  Adding a flag to the 2nd
-0/1 depending on whether it is an integer or floating-point attribute.
+customization section in atom.h is only necessary if your code (e.g. a
-The vector of values associated with the attribute can then be
+pair style) needs to check that a per-atom property is defined.  These
-accessed using the returned index as
+flags should also be set in the constructor of the atom style child
+class.
 
-.. code-block:: c++
+In atom.cpp, aside from the constructor and destructor, there are 3
+methods that a new variable name or flag needs to be added to.
 
-   int *ivector = atom->ivector[index];
+In Atom::peratom_create() when using the add_peratom() method, a
-   double *dvector = atom->dvector[index];
+final length argument of 0 is for per-atom vectors, a length > 1 is
+for per-atom arrays.  Note the use of an extra per-thread flag and the
+add_peratom_vary() method when last dimension of the array is
+variable-length.
 
-Ivector or dvector are vectors of length Nlocal = # of owned atoms,
+Adding the variable name to Atom::extract() enable the per-atom data
-which store the attributes of individual atoms.
+to be accessed through the :doc:`LAMMPS library interface
+<Howto_library>` by a calling code, including from :doc:`Python
+<Python_head>`.
+
+The constructor of the new atom style will also typically set a few
+flags which are defined at the top of atom_vec.h.  If these are
+unclear, see how other atom styles use them.
+
+The grow_pointers() method is also required to make
+a copy of peratom data pointers, as explained in the code.
+
+There are a number of other optional methods which your atom style can
+implement.  These are only needed if you need to do something
+out-of-the-ordinary which the default operation of the AtomVec parent
+class does not take care of.  The best way to figure out why they are
+sometimes useful is to look at how other atom styles use them.
+
+* process_args = use if the atom style has arguments
+* init = called before each run
+* force_clear = called before force computations each timestep
+
+A few atom styles define "bonus" data associated with some or all of
+their particles, such as :doc:`atom_style ellipsoid or tri
+<atom_style>`.  These methods work with that data:
+
+* copy_bonus
+* clear_bonus
+* pack_comm_bonus
+* unpack_comm_bonus
+* pack_border_bonus
+* unpack_border_bonus
+* pack_exchange_bonus
+* unpack_exchange_bonus
+* size_restart_bonus
+* pack_restart_bonus
+* unpack_restart_bonus
+* data_atom_bonus
+* memory_usage_bonus
+
+The :doc:`atom_style body <atom_style>` command can define a particle
+geometry with an arbitrary number of values.  This method reads it
+from a data file:
+
+* data_body
+
+These methods are called before or after operations handled by the
+parent AtomVec class.  They allow an atom style to do customized
+operations on the per-atom values.  For example :doc:`atom_style
+sphere <atom_style>` reads a diameter and density of each particle
+from a data file.  But these need to be converted internally to a
+radius and mass.  That operation is done in the data_atom_post()
+method.
+
+* pack_restart_pre
+* pack_restart_post
+* unpack_restart_init
+* create_atom_post
+* data_atom_post
+* pack_data_pre
+* pack_data_post
+
+These methods enable the :doc:`compute property/atom <compute_property_atom>`
+command to access per-atom variables it does not
+already define as arguments, so that they can be written to a dump
+file or used by other LAMMPS commands.
+
+* property_atom
+* pack_property_atom

doc/src/Modify_contribute.rst

@@ -1,37 +1,51 @@
 Submitting new features for inclusion in LAMMPS
 ===============================================
 
-We encourage users to submit new features or modifications for LAMMPS
+We encourage users to submit new features or modifications for LAMMPS to
-to `the core developers <https://lammps.sandia.gov/authors.html>`_ so they
+`the core developers <https://lammps.sandia.gov/authors.html>`_ so they
-can be added to the LAMMPS distribution. The preferred way to manage
+can be added to the LAMMPS distribution. The preferred way to manage and
-and coordinate this is as of Fall 2016 via the LAMMPS project on
+coordinate this is via the LAMMPS project on `GitHub
-`GitHub <https://github.com/lammps/lammps>`_. An alternative is to
+<https://github.com/lammps/lammps>`_.  Please see the :doc:`GitHub
-contact the LAMMPS developers or the indicated developer of a package
+Tutorial <Howto_github>` for a demonstration on how to do that.  An
-or feature directly and send in your contribution via e-mail.
+alternative is to contact the LAMMPS developers or the indicated
+developer of a package or feature directly and send in your contribution
+via e-mail, but that can add a significant delay on getting your
+contribution included, depending on how busy the developer is you
+contact, how complex a task it would be to integrate that code, and how
+many - if any - changes are required before the code can be included.
 
-For any larger modifications or programming project, you are
+For any larger modifications or programming project, you are encouraged
-encouraged to contact the LAMMPS developers ahead of time, in order to
+to contact the LAMMPS developers ahead of time, in order to discuss
-discuss implementation strategies and coding guidelines, that will
+implementation strategies and coding guidelines, that will make it
-make it easier to integrate your contribution and result in less work
+easier to integrate your contribution and result in less work for
-for everybody involved. You are also encouraged to search through the
+everybody involved. You are also encouraged to search through the list
-list of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_ and submit a new issue
+of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_
-for a planned feature, so you would not duplicate the work of others
+and submit a new issue for a planned feature, so you would not duplicate
-(and possibly get scooped by them) or have your work duplicated by
+the work of others (and possibly get scooped by them) or have your work
-others.
+duplicated by others.
 
-How quickly your contribution will be integrated depends largely on
+For informal communication with (some of) the LAMMPS developers you may
-how much effort it will cause to integrate and test it, how much it
+ask to join the `LAMMPS developers on Slack <https://lammps.slack.com>`_.
-requires changes to the core codebase, and of how much interest it is
+This slack work space is by invitation only. Thus for access, please
-to the larger LAMMPS community.  Please see below for a checklist of
+send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
-typical requirements. Once you have prepared everything, see the
+you are working on.  Only discussions related to LAMMPS development are
-:doc:`Using GitHub with LAMMPS Howto <Howto_github>` doc page for instructions on how to
+tolerated, so this is **NOT** for people that look for help with compiling,
-submit your changes or new files through a GitHub pull request. If you
+installing, or using LAMMPS. Please contact the `lammps-users mailing
-prefer to submit patches or full files, you should first make certain,
+list <https://lammps.sandia.gov>`_ for those purposes instead.
-that your code works correctly with the latest patch-level version of
+
-LAMMPS and contains all bug fixes from it. Then create a gzipped tar
+How quickly your contribution will be integrated depends largely on how
-file of all changed or added files or a corresponding patch file using
+much effort it will cause to integrate and test it, how much it requires
-'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip
+changes to the core codebase, and of how much interest it is to the
-compression, as this works well on all platforms.
+larger LAMMPS community.  Please see below for a checklist of typical
+requirements. Once you have prepared everything, see the :doc:`Using
+GitHub with LAMMPS Howto <Howto_github>` doc page for instructions on
+how to submit your changes or new files through a GitHub pull
+request. If you prefer to submit patches or full files, you should first
+make certain, that your code works correctly with the latest patch-level
+version of LAMMPS and contains all bug fixes from it. Then create a
+gzipped tar file of all changed or added files or a corresponding patch
+file using 'diff -u' or 'diff -c' and compress it with gzip. Please only
+use gzip compression, as this works well on all platforms.
 
 If the new features/files are broadly useful we may add them as core
 files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`.  Else we will add them as a

doc/src/Packages_details.rst

@@ -2064,7 +2064,7 @@ molecules, and chiral-sensitive reactions.
 * examples/USER/reaction
 * `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_
 * `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
-* disarmmd.org
+* reacter.org
 
 ----------
 

doc/src/atom_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    atom_style style args
 
-* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or         *dpd* or *edpd* or *mdpd* or *tdpd* or *electron* or *ellipsoid* or         *full* or *line* or *meso* or *molecular* or *peri* or *smd* or         *sphere* or *spin* or *tri* or *template* or *hybrid*
+* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *peri* or *smd* or *sph* or *sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
 
   .. parsed-literal::
 
@@ -18,7 +18,9 @@ Syntax
          *body* args = bstyle bstyle-args
            bstyle = style of body particles
            bstyle-args = additional arguments specific to the bstyle
-                         see the :doc:`Howto body <Howto_body>` doc page for details
+                         see the :doc:`Howto body <Howto_body>` doc
+                         page for details
+         *sphere* arg = 0/1 (optional) for static/dynamic particle radii
          *tdpd* arg = Nspecies
            Nspecies = # of chemical species
          *template* arg = template-ID
@@ -91,10 +93,6 @@ quantities.
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *edpd*       | temperature and heat capacity                       | eDPD particles                       |
 +--------------+-----------------------------------------------------+--------------------------------------+
-| *mdpd*       | density                                             | mDPD particles                       |
-+--------------+-----------------------------------------------------+--------------------------------------+
-| *tdpd*       | chemical concentration                              | tDPD particles                       |
-+--------------+-----------------------------------------------------+--------------------------------------+
 | *electron*   | charge and spin and eradius                         | electronic force field               |
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *ellipsoid*  | shape, quaternion, angular momentum                 | aspherical particles                 |
@@ -103,7 +101,7 @@ quantities.
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *line*       | end points, angular velocity                        | rigid bodies                         |
 +--------------+-----------------------------------------------------+--------------------------------------+
-| *meso*       | rho, e, cv                                          | SPH particles                        |
+| *mdpd*       | density                                             | mDPD particles                       |
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *molecular*  | bonds, angles, dihedrals, impropers                 | uncharged molecules                  |
 +--------------+-----------------------------------------------------+--------------------------------------+
@@ -111,10 +109,14 @@ quantities.
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *smd*        | volume, kernel diameter, contact radius, mass       | solid and fluid SPH particles        |
 +--------------+-----------------------------------------------------+--------------------------------------+
+| *sph*        | rho, esph, cv                                       | SPH particles                        |
++--------------+-----------------------------------------------------+--------------------------------------+
 | *sphere*     | diameter, mass, angular velocity                    | granular models                      |
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *spin*       | magnetic moment                                     | system with magnetic particles       |
 +--------------+-----------------------------------------------------+--------------------------------------+
+| *tdpd*       | chemical concentration                              | tDPD particles                       |
++--------------+-----------------------------------------------------+--------------------------------------+
 | *template*   | template index, template atom                       | small molecules with fixed topology  |
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *tri*        | corner points, angular momentum                     | rigid bodies                         |
@@ -144,9 +146,16 @@ basis.
 For the *sphere* style, the particles are spheres and each stores a
 per-particle diameter and mass.  If the diameter > 0.0, the particle
 is a finite-size sphere.  If the diameter = 0.0, it is a point
-particle.  Note that by use of the *disc* keyword with the :doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
+particle.  Note that by use of the *disc* keyword with the :doc:`fix
-:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>` commands, spheres can be effectively
+nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
-treated as 2d discs for a 2d simulation if desired.  See also the :doc:`set density/disc <set>` command.
+:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
+<fix_npt_sphere>` commands, spheres can be effectively treated as 2d
+discs for a 2d simulation if desired.  See also the :doc:`set
+density/disc <set>` command.  The *sphere* style takes an optional 0
+or 1 argument.  A value of 0 means the radius of each sphere is
+constant for the duration of the simulation.  A value of 1 means the
+radii may vary dynamically during the simulation, e.g. due to use of
+the :doc:`fix adapt <fix_adapt>` command.
 
 For the *ellipsoid* style, the particles are ellipsoids and each
 stores a flag which indicates whether it is a finite-size ellipsoid or
@@ -189,8 +198,8 @@ particles which store a set of chemical concentration. An integer
 "cc_species" is required to specify the number of chemical species
 involved in a tDPD system.
 
-The *meso* style is for smoothed particle hydrodynamics (SPH)
+The *sph* style is for smoothed particle hydrodynamics (SPH)
-particles which store a density (rho), energy (e), and heat capacity
+particles which store a density (rho), energy (esph), and heat capacity
 (cv).
 
 The *smd* style is for a general formulation of Smooth Particle
@@ -335,7 +344,7 @@ for energy-conserving dissipative particle dynamics (eDPD), many-body
 dissipative particle dynamics (mDPD), and transport dissipative particle
 dynamics (tDPD), respectively.
 
-The *meso* style is part of the USER-SPH package for smoothed particle
+The *sph* style is part of the USER-SPH package for smoothed particle
 hydrodynamics (SPH).  See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
 
 The *spin* style is part of the SPIN package.
@@ -351,7 +360,8 @@ Related commands
 Default
 """""""
 
-atom_style atomic
+The default atom style is atomic.  If atom_style sphere is used its
+default argument is 0.
 
 ----------
 

doc/src/compute.rst

@@ -225,9 +225,6 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
 * :doc:`ke/atom/eff <compute_ke_atom_eff>` - per-atom translational and radial kinetic energy in the electron force field model
 * :doc:`ke/eff <compute_ke_eff>` - kinetic energy of a group of nuclei and electrons in the electron force field model
 * :doc:`ke/rigid <compute_ke_rigid>` - translational kinetic energy of rigid bodies
-* :doc:`meso/e/atom <compute_meso_e_atom>` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
-* :doc:`meso/rho/atom <compute_meso_rho_atom>` - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
-* :doc:`meso/t/atom <compute_meso_t_atom>` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
 * :doc:`momentum <compute_momentum>` - translational momentum
 * :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms
 * :doc:`msd/chunk <compute_msd_chunk>` - mean-squared displacement for each chunk
@@ -279,6 +276,9 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
 * :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
 * :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum components for each atom
 * :doc:`snav/atom <compute_sna_atom>` - virial contribution from bispectrum components for each atom
+* :doc:`sph/e/atom <compute_sph_e_atom>` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
+* :doc:`sph/rho/atom <compute_sph_rho_atom>` - per-atom density of Smooth-Particle Hydrodynamics atoms
+* :doc:`sph/t/atom <compute_sph_t_atom>` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
 * :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
 * :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
 * :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes

doc/src/compute_gyration_shape_chunk.rst

@@ -37,7 +37,7 @@ and the relative shape anisotropy, k:
  b = & l_y - l_x \\
  k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2}
 
-where :math:`l_x` <= :math:`l_y` <= :math`l_z` are the three eigenvalues of the gyration tensor. A general description
+where :math:`l_x` <= :math:`l_y` <= :math:`l_z` are the three eigenvalues of the gyration tensor. A general description
 of these parameters is provided in :ref:`(Mattice) <Mattice2>` while an application to polymer systems
 can be found in :ref:`(Theodorou) <Theodorou2>`. The asphericity  is always non-negative and zero
 only when the three principal moments are equal. This zero condition is met when the distribution

doc/src/compute_property_atom.rst

@@ -67,8 +67,8 @@ Syntax
   .. parsed-literal::
 
            PERI package per-atom properties:
-           vfrac = ???
+           vfrac = volume fraction
-           s0 = ???
+           s0 = max stretch of any bond a particle is part of
 
   .. parsed-literal::
 
@@ -81,11 +81,11 @@ Syntax
   .. parsed-literal::
 
            USER-SPH package per-atom properties:
-           rho = ???
+           rho = density of SPH particles
-           drho = ???
+           drho = change in density
-           e = ???
+           e = energy
-           de = ???
+           de = change in thermal energy
-           cv = ???
+           cv = heat capacity
 
   .. parsed-literal::
 
@@ -108,13 +108,17 @@ Description
 
 Define a computation that simply stores atom attributes for each atom
 in the group.  This is useful so that the values can be used by other
-:doc:`output commands <Howto_output>` that take computes as inputs.  See
+:doc:`output commands <Howto_output>` that take computes as inputs.
-for example, the :doc:`compute reduce <compute_reduce>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/chunk <fix_ave_chunk>`, and :doc:`atom-style variable <variable>`
+See for example, the :doc:`compute reduce <compute_reduce>`, :doc:`fix
-commands.
+ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`,
+:doc:`fix ave/chunk <fix_ave_chunk>`, and :doc:`atom-style variable
+<variable>` commands.
 
-The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning, with some
+The list of possible attributes is the same as that used by the
-additional quantities that are only defined for certain :doc:`atom styles <atom_style>`.  Basically, this augmented list gives an
+:doc:`dump custom <dump>` command, which describes their meaning, with
-input script access to any per-atom quantity stored by LAMMPS.
+some additional quantities that are only defined for certain
+:doc:`atom styles <atom_style>`.  Basically, this augmented list gives
+an input script access to any per-atom quantity stored by LAMMPS.
 
 The values are stored in a per-atom vector or array as discussed
 below.  Zeroes are stored for atoms not in the specified group or for
@@ -132,8 +136,9 @@ particles and body particles and store the 4-vector quaternion
 representing the orientation of each particle.  See the :doc:`set <set>`
 command for an explanation of the quaternion vector.
 
-*End1x*\ , *end1y*\ , *end1z*\ , *end2x*\ , *end2y*\ , *end2z*\ , are defined for
+*End1x*\ , *end1y*\ , *end1z*\ , *end2x*\ , *end2y*\ , *end2z*\ , are
-line segment particles and define the end points of each line segment.
+defined for line segment particles and define the end points of each
+line segment.
 
 *Corner1x*\ , *corner1y*\ , *corner1z*\ , *corner2x*\ , *corner2y*\ ,
 *corner2z*\ , *corner3x*\ , *corner3y*\ , *corner3z*\ , are defined for
@@ -144,14 +149,14 @@ number of explicit bonds assigned to an atom.  Note that if the
 :doc:`newton bond <newton>` command is set to *on*\ , which is the
 default, then every bond in the system is assigned to only one of the
 two atoms in the bond.  Thus a bond between atoms I,J may be tallied
-for either atom I or atom J.  If :doc:`newton bond off <newton>` is set,
+for either atom I or atom J.  If :doc:`newton bond off <newton>` is
-it will be tallied with both atom I and atom J.
+set, it will be tallied with both atom I and atom J.
 
 The *i_name* and *d_name* attributes refer to custom integer and
 floating-point properties that have been added to each atom via the
-:doc:`fix property/atom <fix_property_atom>` command.  When that command
+:doc:`fix property/atom <fix_property_atom>` command.  When that
-is used specific names are given to each attribute which are what is
+command is used specific names are given to each attribute which are
-specified as the "name" portion of *i_name* or *d_name*.
+what is specified as the "name" portion of *i_name* or *d_name*.
 
 **Output info:**
 
@@ -160,8 +165,8 @@ on the number of input values.  If a single input is specified, a
 per-atom vector is produced.  If two or more inputs are specified, a
 per-atom array is produced where the number of columns = the number of
 inputs.  The vector or array can be accessed by any command that uses
-per-atom values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+per-atom values from a compute as input.  See the :doc:`Howto output
-options.
+<Howto_output>` doc page for an overview of LAMMPS output options.
 
 The vector or array values will be in whatever :doc:`units <units>` the
 corresponding attribute is in, e.g. velocity units for vx, charge
@@ -178,7 +183,8 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk <fix_ave_chunk>`,
+:doc:`dump custom <dump>`, :doc:`compute reduce <compute_reduce>`,
-:doc:`fix property/atom <fix_property_atom>`
+:doc::doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/chunk
+:doc:<fix_ave_chunk>`, `fix property/atom <fix_property_atom>`
 
 **Default:** none

doc/src/compute_sph_e_atom.rst

@@ -1,6 +1,6 @@
-.. index:: compute meso/e/atom
+.. index:: compute sph/e/atom
 
-compute meso/e/atom command
+compute sph/e/atom command
 ===========================
 
 Syntax
@@ -8,17 +8,17 @@ Syntax
 
 .. parsed-literal::
 
-   compute ID group-ID meso/e/atom
+   compute ID group-ID sph/e/atom
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
-* meso/e/atom = style name of this compute command
+* sph/e/atom = style name of this compute command
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   compute 1 all meso/e/atom
+   compute 1 all sph/e/atom
 
 Description
 """""""""""
@@ -27,8 +27,8 @@ Define a computation that calculates the per-atom internal energy
 for each atom in a group.
 
 The internal energy is the energy associated with the internal degrees
-of freedom of a mesoscopic particles, e.g. a Smooth-Particle
+of freedom of an SPH particle, i.e. a Smooth-Particle Hydrodynamics
-Hydrodynamics particle.
+particle.
 
 See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.

doc/src/compute_sph_rho_atom.rst

@@ -1,6 +1,6 @@
-.. index:: compute meso/rho/atom
+.. index:: compute sph/rho/atom
 
-compute meso/rho/atom command
+compute sph/rho/atom command
 =============================
 
 Syntax
@@ -8,32 +8,31 @@ Syntax
 
 .. parsed-literal::
 
-   compute ID group-ID meso/rho/atom
+   compute ID group-ID sph/rho/atom
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
-* meso/rho/atom = style name of this compute command
+* sph/rho/atom = style name of this compute command
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   compute 1 all meso/rho/atom
+   compute 1 all sph/rho/atom
 
 Description
 """""""""""
 
-Define a computation that calculates the per-atom mesoscopic density
+Define a computation that calculates the per-atom SPH density for each
-for each atom in a group.
+atom in a group, i.e. a Smooth-Particle Hydrodynamics density.
 
-The mesoscopic density is the mass density of a mesoscopic particle,
+The SPH density is the mass density of an SPH particle, calculated by
-calculated by kernel function interpolation using "pair style
+kernel function interpolation using "pair style sph/rhosum".
-sph/rhosum".
 
 See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
 
-The value of the mesoscopic density will be 0.0 for atoms not in the
+The value of the SPH density will be 0.0 for atoms not in the
 specified compute group.
 
 **Output info:**

doc/src/compute_sph_t_atom.rst

@@ -1,6 +1,6 @@
-.. index:: compute meso/t/atom
+.. index:: compute sph/t/atom
 
-compute meso/t/atom command
+compute sph/t/atom command
 ===========================
 
 Syntax
@@ -8,17 +8,17 @@ Syntax
 
 .. parsed-literal::
 
-   compute ID group-ID meso/t/atom
+   compute ID group-ID sph/t/atom
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
-* meso/t/atom = style name of this compute command
+* sph/t/atom = style name of this compute command
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   compute 1 all meso/t/atom
+   compute 1 all sph/t/atom
 
 Description
 """""""""""
@@ -27,8 +27,8 @@ Define a computation that calculates the per-atom internal temperature
 for each atom in a group.
 
 The internal temperature is the ratio of internal energy over the heat
-capacity associated with the internal degrees of freedom of a mesoscopic
+capacity associated with the internal degrees of freedom of an SPH
-particles, e.g. a Smooth-Particle Hydrodynamics particle.
+particles, i.e. a Smooth-Particle Hydrodynamics particle.
 
 .. math::
 

doc/src/dump_modify.rst

@@ -552,9 +552,9 @@ when writing to XTC files.  By default they are initialized for
 whatever :doc:`units <units>` style is being used, to write out
 coordinates in nanometers and time in picoseconds.  I.e. for *real*
 units, LAMMPS defines *sfactor* = 0.1 and *tfactor* = 0.001, since the
-Angstroms and fmsec used by *real* units are 0.1 nm and 0.001 psec
+Angstroms and fs used by *real* units are 0.1 nm and 0.001 ps
 respectively.  If you are using a units system with distance and time
-units far from nm and psec, you may wish to write XTC files with
+units far from nm and ps, you may wish to write XTC files with
 different units, since the compression algorithm used in XTC files is
 most effective when the typical magnitude of position data is between
 10.0 and 0.1.

doc/src/fix.rst

@@ -238,9 +238,7 @@ accelerated styles exist.
 * :doc:`lb/viscous <fix_lb_viscous>` -
 * :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
 * :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
-* :doc:`meso <fix_meso>` - time integration for SPH/DPDE particles
 * :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
-* :doc:`meso/stationary <fix_meso_stationary>` -
 * :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
 * :doc:`move <fix_move>` - move atoms in a prescribed fashion
 * :doc:`mscg <fix_mscg>` - apply MSCG method for force-matching to generate coarse grain models
@@ -292,6 +290,7 @@ accelerated styles exist.
 * :doc:`oneway <fix_oneway>` - constrain particles on move in one direction
 * :doc:`orient/bcc <fix_orient>` - add grain boundary migration force for BCC
 * :doc:`orient/fcc <fix_orient>` - add grain boundary migration force for FCC
+* :doc:`orient/eco <fix_orient_eco>` - add generalized grain boundary migration force
 * :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
 * :doc:`pimd <fix_pimd>` - Feynman path integral molecular dynamics
 * :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
@@ -345,6 +344,8 @@ accelerated styles exist.
 * :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>` -
 * :doc:`smd/setvel <fix_smd_setvel>` -
 * :doc:`smd/wall_surface <fix_smd_wall_surface>` -
+* :doc:`sph <fix_sph>` - time integration for SPH/DPDE particles
+* :doc:`sph/stationary <fix_sph_stationary>` -
 * :doc:`spring <fix_spring>` - apply harmonic spring force to group of atoms
 * :doc:`spring/chunk <fix_spring_chunk>` - apply harmonic spring force to each chunk of atoms
 * :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of group of atoms

doc/src/fix_bond_react.rst

@@ -300,7 +300,8 @@ either 'none' or 'charges.' Further details are provided in the
 discussion of the 'update_edges' keyword. The fifth optional section
 begins with the keyword 'Constraints' and lists additional criteria
 that must be satisfied in order for the reaction to occur. Currently,
-there are four types of constraints available, as discussed below.
+there are four types of constraints available, as discussed below:
+'distance', 'angle', 'dihedral', and 'arrhenius'.
 
 A sample map file is given below:
 
@@ -353,8 +354,9 @@ has syntax as follows:
    distance *ID1* *ID2* *rmin* *rmax*
 
 where 'distance' is the required keyword, *ID1* and *ID2* are
-pre-reaction atom IDs, and these two atoms must be separated by a
+pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
-distance between *rmin* and *rmax* for the reaction to occur.
+two atoms must be separated by a distance between *rmin* and *rmax*
+for the reaction to occur.
 
 The constraint of type 'angle' has the following syntax:
 
@@ -363,11 +365,11 @@ The constraint of type 'angle' has the following syntax:
    angle *ID1* *ID2* *ID3* *amin* *amax*
 
 where 'angle' is the required keyword, *ID1*\ , *ID2* and *ID3* are
-pre-reaction atom IDs, and these three atoms must form an angle
+pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
-between *amin* and *amax* for the reaction to occur (where *ID2* is
+three atoms must form an angle between *amin* and *amax* for the
-the central atom). Angles must be specified in degrees. This
+reaction to occur (where *ID2* is the central atom). Angles must be
-constraint can be used to enforce a certain orientation between
+specified in degrees. This constraint can be used to enforce a certain
-reacting molecules.
+orientation between reacting molecules.
 
 The constraint of type 'dihedral' has the following syntax:
 
@@ -376,15 +378,23 @@ The constraint of type 'dihedral' has the following syntax:
    dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2*
 
 where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3*
-and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in
+and *ID4* are pre-reaction atom IDs (or molecule-fragment IDs, see
-the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>`
+below). Dihedral angles are calculated in the interval (-180,180].
-documentation for further details on convention. If *amin* is less
+Refer to the :doc:`dihedral style <dihedral_style>` documentation for
-than *amax*, these four atoms must form a dihedral angle greater than
+further details on convention. If *amin* is less than *amax*, these
-*amin* **and** less than *amax* for the reaction to occur. If *amin*
+four atoms must form a dihedral angle greater than *amin* **and** less
-is greater than *amax*, these four atoms must form a dihedral angle
+than *amax* for the reaction to occur. If *amin* is greater than
-greater than *amin* **or** less than *amax* for the reaction to occur.
+*amax*, these four atoms must form a dihedral angle greater than
-Angles must be specified in degrees. Optionally, a second range of
+*amin* **or** less than *amax* for the reaction to occur. Angles must
-permissible angles *amin2*-*amax2* can be specified.
+be specified in degrees. Optionally, a second range of permissible
+angles *amin2*-*amax2* can be specified.
+
+For the 'distance', 'angle', and 'dihedral' constraints (explained
+above), atom IDs can be replaced by pre-reaction molecule-fragment
+IDs. The molecule-fragment ID must begin with a letter. The location
+of the ID is the geometric center of all atom positions in the
+fragment. The molecule fragment must have been defined in the
+:doc:`molecule <molecule>` command for the pre-reaction template.
 
 The constraint of type 'arrhenius' imposes an additional reaction
 probability according to the temperature-dependent Arrhenius equation:

doc/src/fix_deform.rst

@@ -154,8 +154,8 @@ specified in units of distance/time.  This is effectively a "constant
 engineering strain rate", where rate = V/L0 and L0 is the initial box
 length.  The distance can be in lattice or box distance units.  See
 the discussion of the units keyword below.  For example, if the
-initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
+initial box length is 100 Angstroms, and V is 10 Angstroms/ps, then
-after 10 psec, the box length will have doubled.  After 20 psec, it
+after 10 ps, the box length will have doubled.  After 20 ps, it
 will have tripled.
 
 The *erate* style changes a dimension of the box at a "constant
@@ -174,7 +174,7 @@ function of time will change as
 where dt is the elapsed time (in time units).  Thus if *erate* R is
 specified as 0.1 and time units are picoseconds, this means the box
 length will increase by 10% of its original length every picosecond.
-I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc.  R =
+I.e. strain after 1 ps = 0.1, strain after 2 ps = 0.2, etc.  R =
 -0.01 means the box length will shrink by 1% of its original length
 every picosecond.  Note that for an "engineering" rate the change is
 based on the original box length, so running with R = 1 for 10
@@ -201,7 +201,7 @@ The box length L as a function of time will change as
 where dt is the elapsed time (in time units).  Thus if *trate* R is
 specified as ln(1.1) and time units are picoseconds, this means the
 box length will increase by 10% of its current (not original) length
-every picosecond.  I.e. strain after 1 psec = 0.1, strain after 2 psec
+every picosecond.  I.e. strain after 1 ps = 0.1, strain after 2 ps
 = 0.21, etc.  R = ln(2) or ln(3) means the box length will double or
 triple every picosecond.  R = ln(0.99) means the box length will
 shrink by 1% of its current length every picosecond.  Note that for a
@@ -317,8 +317,8 @@ specified in units of distance/time.  This is effectively an
 initial box length perpendicular to the direction of shear.  The
 distance can be in lattice or box distance units.  See the discussion
 of the units keyword below.  For example, if the initial tilt factor
-is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the
+is 5 Angstroms, and the V is 10 Angstroms/ps, then after 1 ps, the
-tilt factor will be 15 Angstroms.  After 2 psec, it will be 25
+tilt factor will be 15 Angstroms.  After 2 ps, it will be 25
 Angstroms.
 
 The *erate* style changes a tilt factor at a "constant engineering
@@ -342,9 +342,9 @@ box perpendicular to the shear direction (e.g. y box length for xy
 deformation), and dt is the elapsed time (in time units).  Thus if
 *erate* R is specified as 0.1 and time units are picoseconds, this
 means the shear strain will increase by 0.1 every picosecond.  I.e. if
-the xy shear strain was initially 0.0, then strain after 1 psec = 0.1,
+the xy shear strain was initially 0.0, then strain after 1 ps = 0.1,
-strain after 2 psec = 0.2, etc.  Thus the tilt factor would be 0.0 at
+strain after 2 ps = 0.2, etc.  Thus the tilt factor would be 0.0 at
-time 0, 0.1\*ybox at 1 psec, 0.2\*ybox at 2 psec, etc, where ybox is the
+time 0, 0.1\*ybox at 1 ps, 0.2\*ybox at 2 ps, etc, where ybox is the
 original y box length.  R = 1 or 2 means the tilt factor will increase
 by 1 or 2 every picosecond.  R = -0.01 means a decrease in shear
 strain by 0.01 every picosecond.
@@ -373,7 +373,7 @@ where T0 is the initial tilt factor and dt is the elapsed time (in
 time units).  Thus if *trate* R is specified as ln(1.1) and time units
 are picoseconds, this means the shear strain or tilt factor will
 increase by 10% every picosecond.  I.e. if the xy shear strain was
-initially 0.1, then strain after 1 psec = 0.11, strain after 2 psec =
+initially 0.1, then strain after 1 ps = 0.11, strain after 2 ps =
 0.121, etc.  R = ln(2) or ln(3) means the tilt factor will double or
 triple every picosecond.  R = ln(0.99) means the tilt factor will
 shrink by 1% every picosecond.  Note that the change is continuous, so

doc/src/fix_heat.rst

@@ -57,7 +57,7 @@ its current value(s) used to determine the flux.
 
 If *eflux* is a numeric constant or equal-style variable which evaluates
 to a scalar value, then *eflux* determines the change in aggregate energy
-of the entire group of atoms per unit time, e.g. in eV/psec for
+of the entire group of atoms per unit time, e.g. in eV/ps for
 :doc:`metal units <units>`.  In this case it is an "extensive" quantity,
 meaning its magnitude should be scaled with the number of atoms in the
 group.  Note that since *eflux* also has per-time units (i.e. it is a

doc/src/fix_langevin_drude.rst

@@ -188,7 +188,7 @@ particles.
 *damp_com* is the characteristic time for reaching thermal equilibrium
 of the centers of mass.  For example, a value of 100.0 means to relax
 the temperature of the centers of mass in a timespan of (roughly) 100
-time units (tau or fmsec or psec - see the :doc:`units <units>`
+time units (tau or fs or ps - see the :doc:`units <units>`
 command).  *damp_drude* is the characteristic time for reaching
 thermal equilibrium of the dipoles. It is typically a few timesteps.
 

doc/src/fix_meso_move.rst

@@ -60,17 +60,19 @@ internal energy and extrapolated velocity are also updated.
 
 .. note::
 
-   The particles affected by this fix should not be time integrated
+   The particles affected by this fix should not be time integrated by
-   by other fixes (e.g. :doc:`fix meso <fix_meso>`, :doc:`fix meso/stationary <fix_meso_stationary>`), since that will change their
+   other fixes (e.g. :doc:`fix sph <fix_sph>`, :doc:`fix
+   sph/stationary <fix_sph_stationary>`), since that will change their
    positions and velocities twice.
 
 .. note::
 
    As particles move due to this fix, they will pass through periodic
    boundaries and be remapped to the other side of the simulation box,
-   just as they would during normal time integration (e.g. via the :doc:`fix meso <fix_meso>` command).  It is up to you to decide whether periodic
+   just as they would during normal time integration (e.g. via the
-   boundaries are appropriate with the kind of particle motion you are
+   :doc:`fix sph <fix_sph>` command).  It is up to you to decide
-   prescribing with this fix.
+   whether periodic boundaries are appropriate with the kind of
+   particle motion you are prescribing with this fix.
 
 .. note::
 
@@ -100,7 +102,7 @@ specified, *V* is the specified velocity vector with components
 specified.  This style also sets the velocity of each particle to V =
 (Vx,Vy,Vz).  If any of the velocity components is specified as NULL,
 then the position and velocity of that component is time integrated
-the same as the :doc:`fix meso <fix_meso>` command would perform, using
+the same as the :doc:`fix sph <fix_sph>` command would perform, using
 the corresponding force component on the particle.
 
 Note that the *linear* style is identical to using the *variable*
@@ -128,7 +130,7 @@ elapsed since the fix was specified.  This style also sets the
 velocity of each particle to the time derivative of this expression.
 If any of the amplitude components is specified as NULL, then the
 position and velocity of that component is time integrated the same as
-the :doc:`fix meso <fix_meso>` command would perform, using the
+the :doc:`fix sph <fix_sph>` command would perform, using the
 corresponding force component on the particle.
 
 Note that the *wiggle* style is identical to using the *variable*
@@ -180,21 +182,21 @@ particle.
 Any of the 6 variables can be specified as NULL.  If both the
 displacement and velocity variables for a particular x,y,z component
 are specified as NULL, then the position and velocity of that
-component is time integrated the same as the :doc:`fix meso <fix_meso>`
+component is time integrated the same as the :doc:`fix sph <fix_sph>`
 command would perform, using the corresponding force component on the
-particle.  If only the velocity variable for a component is specified as
+particle.  If only the velocity variable for a component is specified
-NULL, then the displacement variable will be used to set the position
+as NULL, then the displacement variable will be used to set the
-of the particle, and its velocity component will not be changed. If only
+position of the particle, and its velocity component will not be
-the displacement variable for a component is specified as NULL, then
+changed. If only the displacement variable for a component is
-the velocity variable will be used to set the velocity of the particle,
+specified as NULL, then the velocity variable will be used to set the
-and the position of the particle will be time integrated using that
+velocity of the particle, and the position of the particle will be
-velocity.
+time integrated using that velocity.
 
 The *units* keyword determines the meaning of the distance units used
 to define the *linear* velocity and *wiggle* amplitude and *rotate*
 origin.  This setting is ignored for the *variable* style.  A *box*
 value selects standard units as defined by the :doc:`units <units>`
-command, e.g. velocity in Angstroms/fmsec and amplitude and position
+command, e.g. velocity in Angstroms/fs and amplitude and position
 in Angstroms for units = real.  A *lattice* value means the velocity
 units are in lattice spacings per time and the amplitude and position
 are in lattice spacings.  The :doc:`lattice <lattice>` command must have
@@ -236,17 +238,18 @@ Restrictions
 """"""""""""
 
 This fix is part of the USER-SDPD package.  It is only enabled if
-LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 This fix requires that atoms store density and internal energy as
-defined by the :doc:`atom_style meso <atom_style>` command.
+defined by the :doc:`atom_style sph <atom_style>` command.
 
 All particles in the group must be mesoscopic SPH/SDPD particles.
 
 Related commands
 """"""""""""""""
 
-:doc:`fix move <fix_move>`, :doc:`fix meso <fix_meso>`,
+:doc:`fix move <fix_move>`, :doc:`fix sph <fix_sph>`,
 :doc:`displace_atoms <displace_atoms>`
 
 Default

doc/src/fix_move.rst

@@ -193,7 +193,7 @@ The *units* keyword determines the meaning of the distance units used
 to define the *linear* velocity and *wiggle* amplitude and *rotate*
 origin.  This setting is ignored for the *variable* style.  A *box*
 value selects standard units as defined by the :doc:`units <units>`
-command, e.g. velocity in Angstroms/fmsec and amplitude and position
+command, e.g. velocity in Angstroms/fs and amplitude and position
 in Angstroms for units = real.  A *lattice* value means the velocity
 units are in lattice spacings per time and the amplitude and position
 are in lattice spacings.  The :doc:`lattice <lattice>` command must have

doc/src/fix_nh.rst

@@ -46,7 +46,7 @@ Syntax
 
   .. parsed-literal::
 
-     keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update*
+     keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *ptemp* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update*
        *temp* values = Tstart Tstop Tdamp
          Tstart,Tstop = external temperature at start/end of run
          Tdamp = temperature damping parameter (time units)
@@ -69,6 +69,8 @@ Syntax
        *nreset* value = reset reference cell every this many timesteps
        *drag* value = Df
          Df = drag factor added to barostat/thermostat (0.0 = no drag)
+       *ptemp* value = Ttarget
+         Ttarget = target temperature for barostat
        *dilate* value = dilate-group-ID
          dilate-group-ID = only dilate atoms in this group due to barostat volume changes
        *scalexy* value = *yes* or *no* = scale xy with ly
@@ -137,8 +139,8 @@ description below.  The desired temperature at each timestep is a
 ramped value during the run from *Tstart* to *Tstop*\ .  The *Tdamp*
 parameter is specified in time units and determines how rapidly the
 temperature is relaxed.  For example, a value of 10.0 means to relax
-the temperature in a timespan of (roughly) 10 time units (e.g. tau or
+the temperature in a timespan of (roughly) 10 time units (e.g. :math:`\tau`
-fmsec or psec - see the :doc:`units <units>` command).  The atoms in the
+or fs or ps - see the :doc:`units <units>` command).  The atoms in the
 fix group are the only ones whose velocities and positions are updated
 by the velocity/position update portion of the integration.
 
@@ -195,8 +197,8 @@ simulation box must be triclinic, even if its initial tilt factors are
 For all barostat keywords, the *Pdamp* parameter operates like the
 *Tdamp* parameter, determining the time scale on which pressure is
 relaxed.  For example, a value of 10.0 means to relax the pressure in
-a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
+a timespan of (roughly) 10 time units (e.g. :math:`\tau` or fs or ps
-the :doc:`units <units>` command).
+- see the :doc:`units <units>` command).
 
 .. note::
 
@@ -208,6 +210,28 @@ the :doc:`units <units>` command).
    time units, and that timesteps are NOT the same as time units for most
    :doc:`units <units>` settings.
 
+The relaxation rate of the barostat is set by its inertia :math:`W`:
+
+.. math::
+
+   W = (N + 1) k T_{\rm target} P_{\rm damp}^2
+
+where :math:`N` is the number of atoms, :math:`k` is the Boltzmann constant,
+and :math:`T_{\rm target}` is the target temperature of the barostat :ref:`(Martyna) <nh-Martyna>`.
+If a thermostat is defined, :math:`T_{\rm target}` is the target temperature
+of the thermostat. If a thermostat is not defined, :math:`T_{\rm target}`
+is set to the current temperature of the system when the barostat is initialized.
+If this temperature is too low the simulation will quit with an error.
+Note: in previous versions of LAMMPS, :math:`T_{\rm target}` would default to
+a value of 1.0 for *lj* units and 300.0 otherwise if the system had a temperature
+of exactly zero.
+
+If a thermostat is not specified by this fix, :math:`T_{\rm target}` can be
+manually specified using the *Ptemp* parameter. This may be useful if the
+barostat is initialized when the current temperature does not reflect the
+steady state temperature of the system. This keyword may also be useful in
+athermal simulations where the temperature is not well defined.
+
 Regardless of what atoms are in the fix group (the only atoms which
 are time integrated), a global pressure or stress tensor is computed
 for all atoms.  Similarly, when the size of the simulation box is

doc/src/fix_npt_cauchy.rst

@@ -103,8 +103,8 @@ description below.  The desired temperature at each timestep is a
 ramped value during the run from *Tstart* to *Tstop*\ .  The *Tdamp*
 parameter is specified in time units and determines how rapidly the
 temperature is relaxed.  For example, a value of 10.0 means to relax
-the temperature in a timespan of (roughly) 10 time units (e.g. tau or
+the temperature in a timespan of (roughly) 10 time units (e.g. :math:`\tau`
-fmsec or psec - see the :doc:`units <units>` command).  The atoms in the
+or fs or ps - see the :doc:`units <units>` command).  The atoms in the
 fix group are the only ones whose velocities and positions are updated
 by the velocity/position update portion of the integration.
 
@@ -154,8 +154,8 @@ simulation box must be triclinic, even if its initial tilt factors are
 For all barostat keywords, the *Pdamp* parameter operates like the
 *Tdamp* parameter, determining the time scale on which pressure is
 relaxed.  For example, a value of 10.0 means to relax the pressure in
-a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
+a timespan of (roughly) 10 time units (e.g. :math:`\tau` or fs or ps
-the :doc:`units <units>` command).
+- see the :doc:`units <units>` command).
 
 .. note::
 

doc/src/fix_nve_dotc_langevin.rst

@@ -94,7 +94,7 @@ corresponds to T = 300 K.
 The *damp* parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 0.03
 means to relax the temperature in a timespan of (roughly) 0.03 time
-units tau (see the :doc:`units <units>` command).
+units :math:`\tau` (see the :doc:`units <units>` command).
 The damp factor can be thought of as inversely related to the
 viscosity of the solvent, i.e. a small relaxation time implies a
 high-viscosity solvent and vice versa.  See the discussion about gamma

doc/src/fix_orient.rst

@@ -6,6 +6,9 @@ fix orient/fcc command
 fix orient/bcc command
 ======================
 
+Syntax
+""""""
+
 .. parsed-literal::
 
    fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1

doc/src/fix_orient_eco.rst

@@ -0,0 +1,154 @@
+..  index:: fix orient/eco
+
+fix orient/eco command
+======================
+
+
+.. parsed-literal::
+
+   fix ID group-ID orient/eco u0 eta cutoff orientationsFile
+
+
+* ID, group-ID are documented in fix command
+* u0 = energy added to each atom (energy units)
+* eta = cutoff value (usually 0.25)
+* cutoff = cutoff radius for orientation parameter calculation
+* orientationsFile = file that specifies orientation of each grain
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix gb all orient/eco 0.08 0.25 3.524 sigma5.ori
+
+
+Description
+"""""""""""
+
+The fix applies a synthetic driving force to a grain boundary which can
+be used for the investigation of grain boundary motion. The affiliation
+of atoms to either of the two grains forming the grain boundary is
+determined from an orientation-dependent order parameter as described
+in :ref:`(Ulomek) <Ulomek>`. The potential energy of atoms is either increased by an amount
+of 0.5*\ *u0* or -0.5*\ *u0* according to the orientation of the surrounding
+crystal. This creates a potential energy gradient which pushes atoms near
+the grain boundary to orient according to the energetically favorable
+grain orientation. This fix is designed for applications in bicrystal system
+with one grain boundary and open ends, or two opposite grain boundaries in
+a periodic system. In either case, the entire system can experience a
+displacement during the simulation which needs to be accounted for in the
+evaluation of the grain boundary velocity. While the basic method is
+described in :ref:`(Ulomek) <Ulomek>`, the implementation follows the efficient
+implementation from :ref:`(Schratt & Mohles) <Schratt>`. The synthetic potential energy added to an
+atom j is given by the following formulas
+
+.. math::
+
+   w(|\vec{r}_{jk}|) = w_{jk} & = \left\{\begin{array}{lc} \frac{|\vec{r}_{jk}|^{4}}{r_{\mathrm{cut}}^{4}}
+     -2\frac{|\vec{r}_{jk}|^{2}}{r_{\mathrm{cut}}^{2}}+1, & |\vec{r}_{jk}|<r_{\mathrm{cut}} \\
+      0, & |\vec{r}_{jk}|\ge r_{\mathrm{cut}}
+      \end{array}\right. \\
+   \chi_{j} & = \frac{1}{N}\sum_{l=1}^{3}\left\lbrack\left\vert\psi_{l}^{\mathrm{I}}(\vec{r}_{j})\right\vert^{2}-\left\vert\psi_{l}^{\mathrm{II}}(\vec{r}_{j})\right\vert^{2}\right\rbrack \\
+   \psi_{l}^{\mathrm{X}}(\vec{r}_{j}) & = \sum_{k\in\mathit{\Gamma}_{j}}w_{jk}\exp\left(\mathrm{i}\vec{r}_{jk}\cdot\vec{q}_{l}^{\mathrm{X}}\right) \\
+   u(\chi_{j}) & = \frac{u_{0}}{2}\left\{\begin{array}{lc}
+   1, & \chi_{j}\ge\eta\\
+   \sin\left(\frac{\pi\chi_{j}}{2\eta}\right), &  -\eta<\chi_{j}<\eta\\
+   -1, & \chi_{j}\le-\eta
+   \end{array}\right.
+
+which are fully explained in :ref:`(Ulomek) <Ulomek>`
+and :ref:`(Schratt & Mohles) <Schratt>`.
+
+The force on each atom is the negative gradient of the synthetic potential energy. It
+depends on the surrounding of this atom. An atom far from the grain boundary does not
+experience a synthetic force as its surrounding is that of an oriented single crystal
+and thermal fluctuations are masked by the parameter *eta*\ . Near the grain boundary
+however, the gradient is nonzero and synthetic force terms are computed.
+The orientationsFile specifies the perfect oriented crystal basis vectors for the
+two adjoining crystals. The first three lines (line=row vector) for the energetically penalized and the
+last three lines for the energetically favored grain assuming *u0* is positive. For
+negative *u0*, this is reversed. With the *cutoff* parameter, the size of the region around
+each atom which is used in the order parameter computation is defined. The cutoff must be
+smaller than the interaction range of the MD potential. It should at
+least include the nearest neighbor shell. For high temperatures or low angle
+grain boundaries, it might be beneficial to increase the cutoff in order to get a more
+precise identification of the atoms surrounding. However, computation time will
+increase as more atoms are considered in the order parameter and force computation.
+It is also worth noting that the cutoff radius must not exceed the communication
+distance for ghost atoms in LAMMPS. With orientationsFile, the
+6 oriented crystal basis vectors is specified. Each line of the input file
+contains the three components of a primitive lattice vector oriented according to
+the grain orientation in the simulation box. The first (last) three lines correspond
+to the primitive lattice vectors of the first (second) grain. An example for
+a :math:`\Sigma\langle001\rangle` mis-orientation is given at the end.
+
+If no synthetic energy difference between the grains is created, :math:`u0=0`, the
+force computation is omitted. In this case, still, the order parameter of the
+driving force is computed and can be used to track the grain boundary motion throughout the
+simulation.
+
+
+
+**Restart, fix_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc: `binary restart files <restart>`.
+
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to
+add the potential energy of atom interactions with the grain boundary
+driving force to the system's potential energy as part of thermodynamic output.
+The total sum of added synthetic potential energy is computed and can be accessed
+by various output options. The order parameter as well as the thermally masked
+output parameter are stored in per-atom arrays and can also be accessed by various
+:doc:`output commands <Howto_output>`.
+
+No parameter of this fix can be used with the start/stop keywords of the run command. This fix is
+not invoked during energy minimization.
+
+
+
+Restrictions
+""""""""""""
+
+This fix is part of the USER-MISC package. It is only enabled if LAMMPS was
+built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+
+
+
+Related commands
+""""""""""""""""
+
+:doc:`fix_modify <fix_modify>`
+
+:doc:`fix_orient <fix_orient>`
+
+**Default:** none
+
+----------
+
+.. _Ulomek:
+
+**(Ulomek)** Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007
+
+.. _Schratt:
+
+**(Schratt & Mohles)** Schratt, Mohles. Comp. Mat. Sci. 182 (2020) 109774
+
+----------
+
+
+For illustration purposes, here is an example file that specifies a
+:math:`\Sigma=5 \langle 001 \rangle` tilt grain boundary. This is for a lattice constant of 3.52 Angstrom:
+
+.. parsed-literal::
+
+    sigma5.ori:
+
+    1.671685  0.557228  1.76212
+    0.557228 -1.671685  1.76212
+    2.228913 -1.114456  0.00000
+    0.557228  1.671685  1.76212
+    1.671685 -0.557228  1.76212
+    2.228913  1.114456  0.00000
+
+

doc/src/fix_poems.rst

@@ -3,7 +3,8 @@
 fix poems command
 =================
 
-Syntax:
+Syntax
+""""""
 
 .. parsed-literal::
 

doc/src/fix_press_berendsen.rst

@@ -90,7 +90,7 @@ although you have the option to change that dimension via the :doc:`fix deform <
 For all barostat keywords, the *Pdamp* parameter determines the time
 scale on which pressure is relaxed.  For example, a value of 10.0
 means to relax the pressure in a timespan of (roughly) 10 time units
-(tau or fmsec or psec - see the :doc:`units <units>` command).
+(tau or fs or ps - see the :doc:`units <units>` command).
 
 .. note::
 

doc/src/fix_rhok.rst

@@ -3,6 +3,9 @@
 fix rhok command
 ================
 
+Syntax
+""""""
+
 .. parsed-literal::
 
    fix ID group-ID rhok nx ny nz K a

doc/src/fix_rigid.rst

@@ -429,8 +429,8 @@ that dimension via the :doc:`fix deform <fix_deform>` command.
 For all barostat keywords, the *Pdamp* parameter operates like the
 *Tdamp* parameter, determining the time scale on which pressure is
 relaxed.  For example, a value of 10.0 means to relax the pressure in
-a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
+a timespan of (roughly) 10 time units (e.g. :math:`\tau` or fs or ps
-the :doc:`units <units>` command).
+- see the :doc:`units <units>` command).
 
 Regardless of what atoms are in the fix group (the only atoms which
 are time integrated), a global pressure or stress tensor is computed
@@ -514,7 +514,7 @@ desired temperature at each timestep is a ramped value during the run
 from *Tstart* to *Tstop*\ .  The *Tdamp* parameter is specified in time
 units and determines how rapidly the temperature is relaxed.  For
 example, a value of 100.0 means to relax the temperature in a timespan
-of (roughly) 100 time units (tau or fmsec or psec - see the
+of (roughly) 100 time units (:math:`\tau` or fs or ps - see the
 :doc:`units <units>` command).  The random # *seed* must be a positive
 integer.
 
@@ -539,7 +539,7 @@ timestep is a ramped value during the run from *Tstart* to *Tstop*\ .
 The *Tdamp* parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 100.0
 means to relax the temperature in a timespan of (roughly) 100 time
-units (tau or fmsec or psec - see the :doc:`units <units>` command).
+units (tau or fs or ps - see the :doc:`units <units>` command).
 
 Nose/Hoover chains are used in conjunction with this thermostat.  The
 *tparam* keyword can optionally be used to change the chain settings

doc/src/fix_rigid_meso.rst

@@ -75,19 +75,21 @@ internal energy and extrapolated velocity are also updated.
 .. note::
 
    You should not update the particles in rigid bodies via other
-   time-integration fixes (e.g. :doc:`fix meso <fix_meso>`,
+   time-integration fixes (e.g. :doc:`fix sph <fix_sph>`, :doc:`fix
-   :doc:`fix meso/stationary <fix_meso_stationary>`), or you will have conflicting
+   sph/stationary <fix_sph_stationary>`), or you will have conflicting
-   updates to positions and velocities resulting in unphysical behavior in most
+   updates to positions and velocities resulting in unphysical
-   cases. When performing a hybrid simulation with some atoms in rigid bodies,
+   behavior in most cases. When performing a hybrid simulation with
-   and some not, a separate time integration fix like :doc:`fix meso <fix_meso>`
+   some atoms in rigid bodies, and some not, a separate time
-   should be used for the non-rigid particles.
+   integration fix like :doc:`fix sph <fix_sph>` should be used for
+   the non-rigid particles.
 
 .. note::
 
-   These fixes are overkill if you simply want to hold a collection
+   These fixes are overkill if you simply want to hold a collection of
-   of particles stationary or have them move with a constant velocity. To
+   particles stationary or have them move with a constant velocity. To
-   hold particles stationary use :doc:`fix meso/stationary <fix_meso_stationary>` instead. If you would like to
+   hold particles stationary use :doc:`fix sph/stationary
-   move particles with a constant velocity use :doc:`fix meso/move <fix_meso_move>`.
+   <fix_sph_stationary>` instead. If you would like to move particles
+   with a constant velocity use :doc:`fix meso/move <fix_meso_move>`.
 
 .. warning::
 
@@ -346,7 +348,7 @@ package.  It is only enabled if LAMMPS was built with both packages. See
 the :doc:`Build package <Build_package>` doc page for more info.
 
 This fix requires that atoms store density and internal energy as
-defined by the :doc:`atom_style meso <atom_style>` command.
+defined by the :doc:`atom_style sph <atom_style>` command.
 
 All particles in the group must be mesoscopic SPH/SDPD particles.
 

doc/src/fix_sph.rst

@@ -1,6 +1,6 @@
-.. index:: fix meso
+.. index:: fix sph
 
-fix meso command
+fix sph command
 ================
 
 Syntax
@@ -8,25 +8,26 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID meso
+   fix ID group-ID sph
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* meso = style name of this fix command
+* sph = style name of this fix command
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   fix 1 all meso
+   fix 1 all sph
 
 Description
 """""""""""
 
 Perform time integration to update position, velocity, internal energy
 and local density for atoms in the group each timestep. This fix is
-needed to time-integrate mesoscopic systems where particles carry
+needed to time-integrate SPH systems where particles carry internal
-internal variables such as SPH or DPDE.
+variables such as internal energy.  SPH stands for Smoothed Particle
+Hydrodynamics.
 
 See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
@@ -48,6 +49,6 @@ LAMMPS was built with that package.  See the :doc:`Build package <Build_package>
 Related commands
 """"""""""""""""
 
-"fix meso/stationary"
+:doc:`fix sph/stationary <fix_sph_stationary>`
 
 **Default:** none

doc/src/fix_sph_stationary.rst

@@ -1,6 +1,6 @@
-.. index:: fix meso/stationary
+.. index:: fix sph/stationary
 
-fix meso/stationary command
+fix sph/stationary command
 ===========================
 
 Syntax
@@ -8,17 +8,17 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID meso/stationary
+   fix ID group-ID sph/stationary
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* meso = style name of this fix command
+* sph = style name of this fix command
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   fix 1 boundary meso/stationary
+   fix 1 boundary sph/stationary
 
 Description
 """""""""""
@@ -27,7 +27,7 @@ Perform time integration to update internal energy and local density,
 but not position or velocity for atoms in the group each timestep.
 This fix is needed for SPH simulations to correctly time-integrate
 fixed boundary particles which constrain a fluid to a given region in
-space.
+space.  SPH stands for Smoothed Particle Hydrodynamics.
 
 See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
 LAMMPS.
@@ -49,6 +49,6 @@ LAMMPS was built with that package.  See the :doc:`Build package <Build_package>
 Related commands
 """"""""""""""""
 
-"fix meso"
+:doc:`fix sph <fix_sph>`
 
 **Default:** none

doc/src/fix_temp_berendsen.rst

@@ -45,7 +45,7 @@ The desired temperature at each timestep is a ramped value during the
 run from *Tstart* to *Tstop*\ .  The *Tdamp* parameter is specified in
 time units and determines how rapidly the temperature is relaxed.  For
 example, a value of 100.0 means to relax the temperature in a timespan
-of (roughly) 100 time units (tau or fmsec or psec - see the
+of (roughly) 100 time units (tau or fs or ps - see the
 :doc:`units <units>` command).
 
 *Tstart* can be specified as an equal-style :doc:`variable <variable>`.

doc/src/fix_temp_csvr.rst

@@ -59,7 +59,7 @@ The desired temperature at each timestep is a ramped value during the
 run from *Tstart* to *Tstop*\ .  The *Tdamp* parameter is specified in
 time units and determines how rapidly the temperature is relaxed.  For
 example, a value of 100.0 means to relax the temperature in a timespan
-of (roughly) 100 time units (tau or fmsec or psec - see the
+of (roughly) 100 time units (tau or fs or ps - see the
 :doc:`units <units>` command).
 
 *Tstart* can be specified as an equal-style :doc:`variable <variable>`.

doc/src/fix_ti_spring.rst

@@ -88,7 +88,7 @@ time:
 
   \lambda(\tau) = \tau
 
-where tau is the scaled time variable *t/t_s*. The option *2* performs
+where :math:`\tau` is the scaled time variable *t/t_s*. The option *2* performs
 the lambda switching at a rate defined by the following switching
 function
 

doc/src/fix_wall_gran.rst

@@ -45,7 +45,7 @@ Syntax
          radius = cylinder radius (distance units)
 
 * zero or more keyword/value pairs may be appended to args
-* keyword = *wiggle* or *shear*
+* keyword = *wiggle* or *shear* or *contacts*
 
   .. parsed-literal::
 
@@ -56,6 +56,9 @@ Syntax
        *shear* values = dim vshear
          dim = *x* or *y* or *z*
          vshear = magnitude of shear velocity (velocity units)
+      *contacts* value = none
+         generate contact information for each particle
+
 
 Examples
 """"""""
@@ -68,6 +71,7 @@ Examples
    fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
    fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
    fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
+   fix 6 all wall/gran hooke  200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 contacts
 
 Description
 """""""""""
@@ -171,6 +175,7 @@ the clockwise direction for *vshear* > 0 or counter-clockwise for
 *vshear* < 0.  In this case, *vshear* is the tangential velocity of
 the wall at whatever *radius* has been defined.
 
+
 **Restart, fix_modify, output, run start/stop, minimize info:**
 
 This fix writes the shear friction state of atoms interacting with the
@@ -181,11 +186,37 @@ info on how to re-specify a fix in an input script that reads a
 restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
 
-None of the :doc:`fix_modify <fix_modify>` options are relevant to this
+If the :code:`contacts` option is used, this fix generates a per-atom array
-fix.  No global or per-atom quantities are stored by this fix for
+with 8 columns as output, containing the contact information for owned
-access by various :doc:`output commands <Howto_output>`.  No parameter
+particles (nlocal on each processor). All columns in this per-atom array will
-of this fix can be used with the *start/stop* keywords of the
+be zero if no contact has occurred.  The values of these columns are listed in
-:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the following table:
+
++-------+----------------------------------------------------+----------------+
+| Index | Value                                              | Units          |
++=======+====================================================+================+
+|     1 | 1.0 if particle is in contact with wall,           |                |
+|       | 0.0 otherwise                                      |                |
++-------+----------------------------------------------------+----------------+
+|     2 | Force :math:`f_x` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     3 | Force :math:`f_y` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     4 | Force :math:`f_z` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     5 | :math:`\Delta x` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     6 | :math:`\Delta y` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     7 | :math:`\Delta z` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     8 | Radius :math:`r` of atom                           | distance units |
++-------+----------------------------------------------------+----------------+
+
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
+No parameter of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command. This fix is not invoked during :doc:`energy
+minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_wall_gran_region.rst

@@ -8,7 +8,7 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID
+   fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID keyword values ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * wall/region = style name of this fix command
@@ -36,6 +36,12 @@ Syntax
 
 * wallstyle = region (see :doc:`fix wall/gran <fix_wall_gran>` for options for other kinds of walls)
 * region-ID = region whose boundary will act as wall
+* keyword = *contacts*
+
+  .. parsed-literal::
+
+      *contacts* value = none
+         generate contact information for each particle
 
 Examples
 """"""""
@@ -46,6 +52,7 @@ Examples
    fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
    fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
    fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone
+   fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone contacts
 
 Description
 """""""""""
@@ -215,11 +222,37 @@ uninterrupted fashion.
    use the same fix ID for fix wall/gran/region, but assign it a region
    with a different region ID.
 
-None of the :doc:`fix_modify <fix_modify>` options are relevant to this
+If the :code:`contacts` option is used, this fix generates a per-atom array
-fix.  No global or per-atom quantities are stored by this fix for
+with 8 columns as output, containing the contact information for owned
-access by various :doc:`output commands <Howto_output>`.  No parameter
+particles (nlocal on each processor). All columns in this per-atom array will
-of this fix can be used with the *start/stop* keywords of the
+be zero if no contact has occurred. The values of these columns are listed in
-:doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the following table:
+
++-------+----------------------------------------------------+----------------+
+| Index | Value                                              | Units          |
++=======+====================================================+================+
+|     1 | 1.0 if particle is in contact with wall,           |                |
+|       | 0.0 otherwise                                      |                |
++-------+----------------------------------------------------+----------------+
+|     2 | Force :math:`f_x` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     3 | Force :math:`f_y` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     4 | Force :math:`f_z` exerted on the wall              | force units    |
++-------+----------------------------------------------------+----------------+
+|     5 | :math:`\Delta x` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     6 | :math:`\Delta y` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     7 | :math:`\Delta z` between wall surface and particle | distance units |
++-------+----------------------------------------------------+----------------+
+|     8 | Radius :math:`r` of atom                           | distance units |
++-------+----------------------------------------------------+----------------+
+
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
+No parameter of this fix can be used with the *start/stop* keywords of the
+:doc:`run <run>` command. This fix is not invoked during :doc:`energy
+minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/kspace_modify.rst

@@ -145,16 +145,16 @@ parameters, see the :doc:`How-To <Howto_dispersion>` discussion.
 
 The *fftbench* keyword applies only to PPPM. It is off by default. If
 this option is turned on, LAMMPS will perform a short FFT benchmark
-computation and report its timings, and will thus finish a some seconds
+computation and report its timings, and will thus finish some seconds
 later than it would if this option were off.
 
 ----------
 
 The *force/disp/real* and *force/disp/kspace* keywords set the force
-accuracy for the real and space computations for the dispersion part
+accuracy for the real and reciprocal space computations for the dispersion
-of pppm/disp. As shown in :ref:`(Isele-Holder) <Isele-Holder1>`, optimal
+part of pppm/disp. As shown in :ref:`(Isele-Holder) <Isele-Holder1>`,
-performance and accuracy in the results is obtained when these values
+optimal performance and accuracy in the results is obtained when these
-are different.
+values are different.
 
 ----------
 
@@ -413,10 +413,10 @@ slab correction has also been extended to point dipole interactions
 ----------
 
 The *force/disp/real* and *force/disp/kspace* keywords set the force
-accuracy for the real and space computations for the dispersion part
+accuracy for the real and reciprocal space computations for the dispersion
-of pppm/disp. As shown in :ref:`(Isele-Holder) <Isele-Holder1>`, optimal
+part of pppm/disp. As shown in :ref:`(Isele-Holder) <Isele-Holder1>`,
-performance and accuracy in the results is obtained when these values
+optimal performance and accuracy in the results is obtained when these
-are different.
+values are different.
 
 The *disp/auto* option controls whether the pppm/disp is allowed to
 generate PPPM parameters automatically. If set to *no*\ , parameters

doc/src/pair_eam.rst

@@ -39,15 +39,9 @@ pair_style eam/alloy/opt command
 pair_style eam/cd command
 =========================
 
-pair_style eam/cd/omp command
-=============================
-
 pair_style eam/cd/old command
 =============================
 
-pair_style eam/cd/old/omp command
-=================================
-
 pair_style eam/fs command
 =========================
 

doc/src/pair_lubricate.rst

@@ -28,7 +28,9 @@ Syntax
 * flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions
 * flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
 
-**Examples:** (all assume radius = 1)
+Examples
+""""""""
+(all assume radius = 1)
 
 .. code-block:: LAMMPS
 

doc/src/pair_lubricateU.rst

@@ -22,7 +22,9 @@ Syntax
 * flagHI (optional) = 0/1 to exclude/include 1/r hydrodynamic interactions
 * flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
 
-**Examples:** (all assume radius = 1)
+Examples
+""""""""
+(all assume radius = 1)
 
 .. code-block:: LAMMPS
 

doc/src/read_data.rst

@@ -107,11 +107,11 @@ command, after the third read_data command is used.
 The *add*\ , *offset*\ , *shift*\ , *extra*\ , and *group* keywords are
 useful in this context.
 
-If a simulation box does not yet exist, the *add* keyword
+If a simulation box does not yet exist, the *add* keyword cannot be
-cannot be used; the read_data command is being used for the first
+used; the read_data command is being used for the first time.  If a
-time.  If a simulation box does exist, due to using the
+simulation box does exist, due to using the :doc:`create_box
-:doc:`create_box <create_box>` command, or a previous read_data command,
+<create_box>` command, or a previous read_data command, then the *add*
-then the *add* keyword must be used.
+keyword must be used.
 
 .. note::
 
@@ -571,68 +571,69 @@ appended to it, which indicate which image of a periodic simulation
 box the atom is in.  These may be important to include for some kinds
 of analysis.
 
-+------------+---------------------------------------------------------------------------+
+.. list-table::
-| angle      | atom-ID molecule-ID atom-type x y z                                       |
+
-+------------+---------------------------------------------------------------------------+
+   * - angle
-| atomic     | atom-ID atom-type x y z                                                   |
+     - atom-ID molecule-ID atom-type x y z
-+------------+---------------------------------------------------------------------------+
+   * - atomic
-| body       | atom-ID atom-type bodyflag mass x y z                                     |
+     - atom-ID atom-type x y z
-+------------+---------------------------------------------------------------------------+
+   * - body
-| bond       | atom-ID molecule-ID atom-type x y z                                       |
+     - atom-ID atom-type bodyflag mass x y z
-+------------+---------------------------------------------------------------------------+
+   * - bond
-| charge     | atom-ID atom-type q x y z                                                 |
+     - atom-ID molecule-ID atom-type x y z
-+------------+---------------------------------------------------------------------------+
+   * - charge
-| dipole     | atom-ID atom-type q x y z mux muy muz                                     |
+     - atom-type q x y z
-+------------+---------------------------------------------------------------------------+
+   * - dipole
-| dpd        | atom-ID atom-type theta x y z                                             |
+     - atom-ID atom-type q x y z mux muy muz
-+------------+---------------------------------------------------------------------------+
+   * - dpd
-| edpd       | atom-ID atom-type edpd_temp edpd_cv x y z                                 |
+     - atom-ID atom-type theta x y z
-+------------+---------------------------------------------------------------------------+
+   * - edpd
-| mdpd       | atom-ID atom-type rho x y z                                               |
+     - atom-ID atom-type edpd_temp edpd_cv x y z
-+------------+---------------------------------------------------------------------------+
+   * - electron
-| tdpd       | atom-ID atom-type x y z cc1 cc2 ... ccNspecies                            |
+     - atom-ID atom-type q spin eradius x y z
-+------------+---------------------------------------------------------------------------+
+   * - ellipsoid
-| electron   | atom-ID atom-type q spin eradius x y z                                    |
+     - atom-ID atom-type ellipsoidflag density x y z
-+------------+---------------------------------------------------------------------------+
+   * - full
-| ellipsoid  | atom-ID atom-type ellipsoidflag density x y z                             |
+     - atom-ID molecule-ID atom-type q x y z
-+------------+---------------------------------------------------------------------------+
+   * - line
-| full       | atom-ID molecule-ID atom-type q x y z                                     |
+     - atom-ID molecule-ID atom-type lineflag density x y z
-+------------+---------------------------------------------------------------------------+
+   * - mdpd
-| line       | atom-ID molecule-ID atom-type lineflag density x y z                      |
+     - atom-ID atom-type rho x y z
-+------------+---------------------------------------------------------------------------+
+   * - molecular
-| meso       | atom-ID atom-type rho e cv x y z                                          |
+     - atom-ID molecule-ID atom-type x y z
-+------------+---------------------------------------------------------------------------+
+   * - peri
-| molecular  | atom-ID molecule-ID atom-type x y z                                       |
+     - atom-ID atom-type volume density x y z
-+------------+---------------------------------------------------------------------------+
+   * - smd
-| peri       | atom-ID atom-type volume density x y z                                    |
+     - atom-ID atom-type molecule volume mass kernel-radius contact-radius x0 y0 z0 x y z
-+------------+---------------------------------------------------------------------------+
+   * - sph
-| smd        | atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z |
+     - atom-ID atom-type rho esph cv x y z
-+------------+---------------------------------------------------------------------------+
+   * - sphere
-| sphere     | atom-ID atom-type diameter density x y z                                  |
+     - atom-ID atom-type diameter density x y z
-+------------+---------------------------------------------------------------------------+
+   * - spin
-| spin       | atom-ID atom-type sp x y z spx spy spz                                    |
+     - atom-ID atom-type x y z spx spy spz sp
-+------------+---------------------------------------------------------------------------+
+   * - tdpd
-| template   | atom-ID molecule-ID template-index template-atom atom-type x y z          |
+     - atom-ID atom-type x y z cc1 cc2 ... ccNspecies
-+------------+---------------------------------------------------------------------------+
+   * - template
-| tri        | atom-ID molecule-ID atom-type triangleflag density x y z                  |
+     - atom-ID molecule-ID template-index template-atom atom-type x y z
-+------------+---------------------------------------------------------------------------+
+   * - tri
-| wavepacket | atom-ID atom-type charge spin eradius etag cs_re cs_im x y z              |
+     - atom-ID molecule-ID atom-type triangleflag density x y z
-+------------+---------------------------------------------------------------------------+
+   * - wavepacket
-| hybrid     | atom-ID atom-type x y z sub-style1 sub-style2 ...                         |
+     - atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
-+------------+---------------------------------------------------------------------------+
+   * - hybrid
+     - atom-ID atom-type x y z sub-style1 sub-style2 ...
 
 The per-atom values have these meanings and units, listed alphabetically:
 
 * atom-ID = integer ID of atom
 * atom-type = type of atom (1-Ntype)
 * bodyflag = 1 for body particles, 0 for point particles
-* cc = chemical concentration for tDPD particles for each species (mole/volume units)
+* ccN = chemical concentration for tDPD particles for each species (mole/volume units)
 * contact-radius = ??? (distance units)
 * cs_re,cs_im = real/imaginary parts of wave packet coefficients
 * cv = heat capacity (need units) for SPH particles
 * density = density of particle (mass/distance\^3 or mass/distance\^2 or mass/distance units, depending on dimensionality of particle)
 * diameter = diameter of spherical atom (distance units)
-* e = energy (need units) for SPH particles
+* esph = energy (need units) for SPH particles
 * edpd_temp = temperature for eDPD particles (temperature units)
 * edpd_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units)
 * ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
@@ -646,14 +647,15 @@ The per-atom values have these meanings and units, listed alphabetically:
 * q = charge on atom (charge units)
 * rho = density (need units) for SPH particles
 * spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
-* sp = norm of magnetic spin of atom (in number of Bohr magnetons)
+* sp = magnitude of magnetic spin of atom (Bohr magnetons)
-* spx,spy,spz = components of magnetic spin of atom (adim normalized vector)
+* spx,spy,spz = components of magnetic spin of atom (unit vector)
 * template-atom = which atom within a template molecule the atom is
 * template-index = which molecule within the molecule template the atom is part of
 * theta = internal temperature of a DPD particle
 * triangleflag = 1 for triangular particles, 0 for point or spherical particles
 * volume = volume of Peridynamic particle (distance\^3 units)
 * x,y,z = coordinates of atom (distance units)
+* x0,y0,z0 = original (strain-free) coordinates of atom (distance units)
 
 The units for these quantities depend on the unit style; see the
 :doc:`units <units>` command for details.
@@ -715,17 +717,18 @@ as spheres when converting density to mass.  However, they can also be
 modeled as 2d discs (circles) if the :doc:`set density/disc <set>`
 command is used to reset their mass after the read_data command is
 used.  A *disc* keyword can also be used with time integration fixes,
-such as :doc:`fix nve/sphere <fix_nve_sphere>` and :doc:`fix nvt/sphere <fix_nve_sphere>` to time integrate their motion as 2d
+such as :doc:`fix nve/sphere <fix_nve_sphere>` and :doc:`fix
+nvt/sphere <fix_nve_sphere>` to time integrate their motion as 2d
 discs (not 3d spheres), by changing their moment of inertia.
 
-For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
+For atom\_style hybrid, following the 5 initial values
-specific values for each sub-style must be listed.  The order of the
+(ID,type,x,y,z), specific values for each sub-style must be listed.
-sub-styles is the same as they were listed in the
+The order of the sub-styles is the same as they were listed in the
-:doc:`atom_style <atom_style>` command.  The sub-style specific values
+:doc:`atom_style <atom_style>` command.  The specific values for each
-are those that are not the 5 standard ones (ID,type,x,y,z).  For
+sub-style are those that are not the 5 standard ones (ID,type,x,y,z).
-example, for the "charge" sub-style, a "q" value would appear.  For
+For example, for the "charge" sub-style, a "q" value would appear.
-the "full" sub-style, a "molecule-ID" and "q" would appear.  These are
+For the "full" sub-style, a "molecule-ID" and "q" would appear.  These
-listed in the same order they appear as listed above.  Thus if
+are listed in the same order they appear as listed above.  Thus if
 
 .. parsed-literal::
 
@@ -738,12 +741,14 @@ were used in the input script, each atom line would have these fields:
    atom-ID atom-type x y z q diameter density
 
 Note that if a non-standard value is defined by multiple sub-styles,
-it must appear multiple times in the atom line.  E.g. the atom line
+it only appears once in the atom line.  E.g. the atom line for
-for atom_style hybrid dipole full would list "q" twice:
+atom_style hybrid dipole full would list "q" only once, with the
+dipole sub-style fields; "q" does not appear with the full sub-style
+fields.
 
 .. parsed-literal::
 
-   atom-ID atom-type x y z q mux muy myz molecule-ID q
+   atom-ID atom-type x y z q mux muy myz molecule-ID
 
 Atom lines specify the (x,y,z) coordinates of atoms.  These can be
 inside or outside the simulation box.  When the data file is read,
@@ -1176,9 +1181,9 @@ pair style.  See the :doc:`pair_style <pair_style>` and
 :doc:`pair_coeff <pair_coeff>` commands for details.  Since pair
 coefficients for types I != J are not specified, these will be
 generated automatically by the pair style's mixing rule.  See the
-individual pair_style doc pages and the :doc:`pair_modify mix <pair_modify>` command for details.  Pair coefficients can also
+individual pair_style doc pages and the :doc:`pair_modify mix
-be set via the :doc:`pair_coeff <pair_coeff>` command in the input
+<pair_modify>` command for details.  Pair coefficients can also be set
-script.
+via the :doc:`pair_coeff <pair_coeff>` command in the input script.
 
 ----------
 
@@ -1200,15 +1205,15 @@ script.
        3 3 0.022 2.35197 0.022 2.35197
        3 5 0.022 2.35197 0.022 2.35197
 
-This section must have N\*(N+1)/2 lines where N = # of atom types.  The
+This section must have N\*(N+1)/2 lines where N = # of atom types.
-number and meaning of the coefficients are specific to the defined
+The number and meaning of the coefficients are specific to the defined
 pair style.  See the :doc:`pair_style <pair_style>` and
 :doc:`pair_coeff <pair_coeff>` commands for details.  Since pair
 coefficients for types I != J are all specified, these values will
 turn off the default mixing rule defined by the pair style.  See the
-individual pair_style doc pages and the :doc:`pair_modify mix <pair_modify>` command for details.  Pair coefficients can also
+individual pair_style doc pages and the :doc:`pair_modify mix
-be set via the :doc:`pair_coeff <pair_coeff>` command in the input
+<pair_modify>` command for details.  Pair coefficients can also be set
-script.
+via the :doc:`pair_coeff <pair_coeff>` command in the input script.
 
 ----------
 

doc/src/run_style.rst

@@ -150,8 +150,8 @@ timestep, angle interactions computed 4x, pair interactions computed
 
 The :doc:`timestep <timestep>` command sets the large timestep for the
 outermost rRESPA level.  Thus if the 3 loop factors are "2 2 2" for
-4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the
+4-level rRESPA, and the outer timestep is set to 4.0 fs, then the
-inner timestep would be 8x smaller or 0.5 fmsec.  All other LAMMPS
+inner timestep would be 8x smaller or 0.5 fs.  All other LAMMPS
 commands that specify number of timesteps (e.g. :doc:`thermo <thermo>`
 for thermo output every N steps, :doc:`neigh_modify delay/every <neigh_modify>` parameters, :doc:`dump <dump>` every N
 steps, etc) refer to the outermost timesteps.
@@ -213,10 +213,10 @@ With that caveat, a few rules-of-thumb may be useful in selecting
 simulations using the CHARMM or a similar all-atom force field, but
 the concepts are adaptable to other problems.  Without SHAKE, bonds
 involving hydrogen atoms exhibit high-frequency vibrations and require
-a timestep on the order of 0.5 fmsec in order to conserve energy.  The
+a timestep on the order of 0.5 fs in order to conserve energy.  The
 relatively inexpensive force computations for the bonds, angles,
-impropers, and dihedrals can be computed on this innermost 0.5 fmsec
+impropers, and dihedrals can be computed on this innermost 0.5 fs
-step.  The outermost timestep cannot be greater than 4.0 fmsec without
+step.  The outermost timestep cannot be greater than 4.0 fs without
 risking energy drift.  Smooth switching of forces between the levels
 of the rRESPA hierarchy is also necessary to avoid drift, and a 1-2
 angstrom "healing distance" (the distance between the outer and inner
@@ -230,14 +230,14 @@ simulations:
    run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
 
 With these settings, users can expect good energy conservation and
-roughly a 2.5 fold speedup over the *verlet* style with a 0.5 fmsec
+roughly a 2.5 fold speedup over the *verlet* style with a 0.5 fs
 timestep.
 
 If SHAKE is used with the *respa* style, time reversibility is lost,
 but substantially longer time steps can be achieved.  For biomolecular
 simulations using the CHARMM or similar all-atom force field, bonds
 involving hydrogen atoms exhibit high frequency vibrations and require
-a time step on the order of 0.5 fmsec in order to conserve energy.
+a time step on the order of 0.5 fs in order to conserve energy.
 These high frequency modes also limit the outer time step sizes since
 the modes are coupled.  It is therefore desirable to use SHAKE with
 respa in order to freeze out these high frequency motions and increase
@@ -253,7 +253,7 @@ rRESPA:
 
 With these settings, users can expect good energy conservation and
 roughly a 1.5 fold speedup over the *verlet* style with SHAKE and a
-2.0 fmsec timestep.
+2.0 fs timestep.
 
 For non-biomolecular simulations, the *respa* style can be
 advantageous if there is a clear separation of time scales - fast and

doc/src/set.rst

@@ -13,7 +13,7 @@ Syntax
 * style = *atom* or *type* or *mol* or *group* or *region*
 * ID = atom ID range or type range or mol ID range or group ID or region ID
 * one or more keyword/value pairs may be appended
-* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset* or *mol* or *x* or *y* or *z* or           *charge* or *dipole* or *dipole/random* or *quat* or           *spin* or *spin/random* or *quat* or           *quat/random* or *diameter* or *shape* or           *length* or *tri* or *theta* or *theta/random* or           *angmom* or *omega* or           *mass* or *density* or *density/disc* or *volume* or *image* or           *bond* or *angle* or *dihedral* or *improper* or           *meso/e* or *meso/cv* or *meso/rho* or           *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or           *edpd/temp* or *edpd/cv* or *cc* or *i_name* or *d_name*
+* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset* or *mol* or *x* or *y* or *z* or           *charge* or *dipole* or *dipole/random* or *quat* or           *spin* or *spin/random* or *quat* or           *quat/random* or *diameter* or *shape* or           *length* or *tri* or *theta* or *theta/random* or           *angmom* or *omega* or           *mass* or *density* or *density/disc* or *volume* or *image* or           *bond* or *angle* or *dihedral* or *improper* or           *sph/e* or *sph/cv* or *sph/rho* or           *smd/contact/radius* or *smd/mass/density* or *dpd/theta* or           *edpd/temp* or *edpd/cv* or *cc* or *i_name* or *d_name*
 
   .. parsed-literal::
 
@@ -94,11 +94,11 @@ Syntax
        *angle* value = angle type for all angles between selected atoms
        *dihedral* value = dihedral type for all dihedrals between selected atoms
        *improper* value = improper type for all impropers between selected atoms
-       *meso/e* value = energy of SPH particles (need units)
+       *sph/e* value = energy of SPH particles (need units)
          value can be an atom-style variable (see below)
-       *meso/cv* value = heat capacity of SPH particles (need units)
+       *sph/cv* value = heat capacity of SPH particles (need units)
          value can be an atom-style variable (see below)
-       *meso/rho* value = density of SPH particles (need units)
+       *sph/rho* value = density of SPH particles (need units)
          value can be an atom-style variable (see below)
        *smd/contact/radius* = radius for short range interactions, i.e. contact and friction
          value can be an atom-style variable (see below)
@@ -299,29 +299,31 @@ for each particle set by this command.  This keyword does not allow
 use of an atom-style variable.
 
 Keyword *diameter* sets the size of the selected atoms.  The particles
-must be finite-size spheres as defined by the :doc:`atom_style sphere <atom_style>` command.  The diameter of a particle can be
+must be finite-size spheres as defined by the :doc:`atom_style sphere
-set to 0.0, which means they will be treated as point particles.  Note
+<atom_style>` command.  The diameter of a particle can be set to 0.0,
-that this command does not adjust the particle mass, even if it was
+which means they will be treated as point particles.  Note that this
-defined with a density, e.g. via the :doc:`read_data <read_data>`
+command does not adjust the particle mass, even if it was defined with
-command.
+a density, e.g. via the :doc:`read_data <read_data>` command.
 
 Keyword *shape* sets the size and shape of the selected atoms.  The
-particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid <atom_style>` command.  The *Sx*\ , *Sy*\ , *Sz* settings are
+particles must be ellipsoids as defined by the :doc:`atom_style
-the 3 diameters of the ellipsoid in each direction.  All 3 can be set
+ellipsoid <atom_style>` command.  The *Sx*\ , *Sy*\ , *Sz* settings
-to the same value, which means the ellipsoid is effectively a sphere.
+are the 3 diameters of the ellipsoid in each direction.  All 3 can be
-They can also all be set to 0.0 which means the particle will be
+set to the same value, which means the ellipsoid is effectively a
-treated as a point particle.  Note that this command does not adjust
+sphere.  They can also all be set to 0.0 which means the particle will
-the particle mass, even if it was defined with a density, e.g. via the
+be treated as a point particle.  Note that this command does not
-:doc:`read_data <read_data>` command.
+adjust the particle mass, even if it was defined with a density,
+e.g. via the :doc:`read_data <read_data>` command.
 
 Keyword *length* sets the length of selected atoms.  The particles
-must be line segments as defined by the :doc:`atom_style line <atom_style>` command.  If the specified value is non-zero the
+must be line segments as defined by the :doc:`atom_style line
-line segment is (re)set to a length = the specified value, centered
+<atom_style>` command.  If the specified value is non-zero the line
-around the particle position, with an orientation along the x-axis.
+segment is (re)set to a length = the specified value, centered around
-If the specified value is 0.0, the particle will become a point
+the particle position, with an orientation along the x-axis.  If the
-particle.  Note that this command does not adjust the particle mass,
+specified value is 0.0, the particle will become a point particle.
-even if it was defined with a density, e.g. via the
+Note that this command does not adjust the particle mass, even if it
-:doc:`read_data <read_data>` command.
+was defined with a density, e.g. via the :doc:`read_data <read_data>`
+command.
 
 Keyword *tri* sets the size of selected atoms.  The particles must be
 triangles as defined by the :doc:`atom_style tri <atom_style>` command.
@@ -335,7 +337,8 @@ does not adjust the particle mass, even if it was defined with a
 density, e.g. via the :doc:`read_data <read_data>` command.
 
 Keyword *theta* sets the orientation of selected atoms.  The particles
-must be line segments as defined by the :doc:`atom_style line <atom_style>` command.  The specified value is used to set the
+must be line segments as defined by the :doc:`atom_style line
+<atom_style>` command.  The specified value is used to set the
 orientation angle of the line segments with respect to the x axis.
 
 Keyword *theta/random* randomizes the orientation of theta for the
@@ -346,44 +349,47 @@ regardless of how many processors are being used.  This keyword does
 not allow use of an atom-style variable.
 
 Keyword *angmom* sets the angular momentum of selected atoms.  The
-particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid <atom_style>` command or triangles as defined by the
+particles must be ellipsoids as defined by the :doc:`atom_style
-:doc:`atom_style tri <atom_style>` command.  The angular momentum vector
+ellipsoid <atom_style>` command or triangles as defined by the
-of the particles is set to the 3 specified components.
+:doc:`atom_style tri <atom_style>` command.  The angular momentum
+vector of the particles is set to the 3 specified components.
 
 Keyword *omega* sets the angular velocity of selected atoms.  The
-particles must be spheres as defined by the
+particles must be spheres as defined by the :doc:`atom_style sphere
-:doc:`atom_style sphere <atom_style>` command.  The angular velocity
+<atom_style>` command.  The angular velocity vector of the particles
-vector of the particles is set to the 3 specified components.
+is set to the 3 specified components.
 
 Keyword *mass* sets the mass of all selected particles.  The particles
 must have a per-atom mass attribute, as defined by the
-:doc:`atom_style <atom_style>` command.  See the "mass" command for how
+:doc:`atom_style <atom_style>` command.  See the "mass" command for
-to set mass values on a per-type basis.
+how to set mass values on a per-type basis.
 
 Keyword *density* or *density/disc* also sets the mass of all selected
 particles, but in a different way.  The particles must have a per-atom
 mass attribute, as defined by the :doc:`atom_style <atom_style>`
-command.  If the atom has a radius attribute (see :doc:`atom_style sphere <atom_style>`) and its radius is non-zero, its mass is set
+command.  If the atom has a radius attribute (see :doc:`atom_style
-from the density and particle volume for 3d systems (the input density
+sphere <atom_style>`) and its radius is non-zero, its mass is set from
-is assumed to be in mass/distance\^3 units).  For 2d, the default is
+the density and particle volume for 3d systems (the input density is
-for LAMMPS to model particles with a radius attribute as spheres.
+assumed to be in mass/distance\^3 units).  For 2d, the default is for
+LAMMPS to model particles with a radius attribute as spheres.
 However, if the *density/disc* keyword is used, then they can be
 modeled as 2d discs (circles).  Their mass is set from the density and
 particle area (the input density is assumed to be in mass/distance\^2
 units).
 
-If the atom has a shape attribute (see :doc:`atom_style ellipsoid <atom_style>`) and its 3 shape parameters are non-zero,
+If the atom has a shape attribute (see :doc:`atom_style ellipsoid
-then its mass is set from the density and particle volume (the input
+<atom_style>`) and its 3 shape parameters are non-zero, then its mass
-density is assumed to be in mass/distance\^3 units).  The
+is set from the density and particle volume (the input density is
-*density/disc* keyword has no effect; it does not (yet) treat 3d
+assumed to be in mass/distance\^3 units).  The *density/disc* keyword
-ellipsoids as 2d ellipses.
+has no effect; it does not (yet) treat 3d ellipsoids as 2d ellipses.
 
-If the atom has a length attribute (see :doc:`atom_style line <atom_style>`) and its length is non-zero, then its mass is
+If the atom has a length attribute (see :doc:`atom_style line
-set from the density and line segment length (the input density is
+<atom_style>`) and its length is non-zero, then its mass is set from
-assumed to be in mass/distance units).  If the atom has an area
+the density and line segment length (the input density is assumed to
-attribute (see :doc:`atom_style tri <atom_style>`) and its area is
+be in mass/distance units).  If the atom has an area attribute (see
-non-zero, then its mass is set from the density and triangle area (the
+:doc:`atom_style tri <atom_style>`) and its area is non-zero, then its
-input density is assumed to be in mass/distance\^2 units).
+mass is set from the density and triangle area (the input density is
+assumed to be in mass/distance\^2 units).
 
 If none of these cases are valid, then the mass is set to the density
 value directly (the input density is assumed to be in mass units).
@@ -399,14 +405,15 @@ defined.  A value of 2 means add 2 box lengths to get the true value.
 A value of -1 means subtract 1 box length to get the true value.
 LAMMPS updates these flags as atoms cross periodic boundaries during
 the simulation.  The flags can be output with atom snapshots via the
-:doc:`dump <dump>` command.  If a value of NULL is specified for any of
+:doc:`dump <dump>` command.  If a value of NULL is specified for any
-nx,ny,nz, then the current image value for that dimension is unchanged.
+of nx,ny,nz, then the current image value for that dimension is
-For non-periodic dimensions only a value of 0 can be specified.
+unchanged.  For non-periodic dimensions only a value of 0 can be
-This command can be useful after a system has been equilibrated and
+specified.  This command can be useful after a system has been
-atoms have diffused one or more box lengths in various directions.
+equilibrated and atoms have diffused one or more box lengths in
-This command can then reset the image values for atoms so that they
+various directions.  This command can then reset the image values for
-are effectively inside the simulation box, e.g if a diffusion
+atoms so that they are effectively inside the simulation box, e.g if a
-coefficient is about to be measured via the :doc:`compute msd <compute_msd>` command.  Care should be taken not to reset the
+diffusion coefficient is about to be measured via the :doc:`compute
+msd <compute_msd>` command.  Care should be taken not to reset the
 image flags of two atoms in a bond to the same value if the bond
 straddles a periodic boundary (rather they should be different by +/-
 1).  This will not affect the dynamics of a simulation, but may mess
@@ -423,10 +430,10 @@ etc) was set by the *bond types* (\ *angle types*\ , etc) field in the
 header of the data file read by the :doc:`read_data <read_data>`
 command.  These keywords do not allow use of an atom-style variable.
 
-Keywords *meso/e*\ , *meso/cv*\ , and *meso/rho* set the energy, heat
+Keywords *sph/e*\ , *sph/cv*\ , and *sph/rho* set the energy, heat
 capacity, and density of smoothed particle hydrodynamics (SPH)
-particles.  See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to
+particles.  See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_
-using SPH in LAMMPS.
+to using SPH in LAMMPS.
 
 Keyword *smd/mass/density* sets the mass of all selected particles,
 but it is only applicable to the Smooth Mach Dynamics package

doc/src/special_bonds.rst

@@ -28,7 +28,8 @@ Syntax
        *angle* value = *yes* or *no*
        *dihedral* value = *yes* or *no*
 
-Examples:
+Examples
+""""""""
 
 .. code-block:: LAMMPS
 

doc/src/timestep.rst

@@ -46,22 +46,22 @@ Related commands
 Default
 """""""
 
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| choice of :doc:`units <units>` | time units | default timestep size |
+| choice of :doc:`units <units>` | time units    | default timestep size |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| lj                             | tau        | 0.005 tau             |
+| lj                             | :math:`\tau`  | 0.005 :math:`\tau`    |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| real                           | fmsec      | 1.0 fmsec             |
+| real                           | fs            | 1.0 fs                |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| metal                          | psec       | 0.001 psec            |
+| metal                          | ps            | 0.001 ps              |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| si                             | sec        | 1.0e-8 sec (10 nsec)  |
+| si                             | s             | 1.0e-8 s (10 ns)      |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| cgs                            | sec        | 1.0e-8 sec (10 nsec)  |
+| cgs                            | s             | 1.0e-8 s (10 ns)      |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| electron                       | fmsec      | 0.001 fmsec           |
+| electron                       | fs            | 0.001 fs              |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| micro                          | usec       | 2.0 usec              |
+| micro                          | :math:`\mu`\ s| 2.0 :math:`\mu`\ s    |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+
-| nano                           | nsec       | 0.00045 nsec          |
+| nano                           | ns            | 0.00045 ns            |
-+--------------------------------+------------+-----------------------+
++--------------------------------+---------------+-----------------------+

doc/src/units.rst

@@ -203,7 +203,7 @@ For style *nano*\ , these are the units:
 The units command also sets the timestep size and neighbor skin
 distance to default values for each style:
 
-* For style *lj* these are dt = 0.005 tau and skin = 0.3 sigma.
+* For style *lj* these are dt = 0.005 :math:`\tau` and skin = 0.3 :math:`\sigma`.
 * For style *real* these are dt = 1.0 femtoseconds and skin = 2.0 Angstroms.
 * For style *metal* these are dt = 0.001 picoseconds and skin = 2.0 Angstroms.
 * For style *si* these are dt = 1.0e-8 seconds and skin = 0.001 meters.

doc/src/velocity.rst

@@ -225,8 +225,8 @@ body defined by the fix, as described above.
 The *units* keyword is used by *set* and *ramp*\ .  If units = box,
 the velocities and coordinates specified in the velocity command are
 in the standard units described by the :doc:`units <units>` command
-(e.g. Angstroms/fmsec for real units).  If units = lattice, velocities
+(e.g. Angstroms/fs for real units).  If units = lattice, velocities
-are in units of lattice spacings per time (e.g. spacings/fmsec) and
+are in units of lattice spacings per time (e.g. spacings/fs) and
 coordinates are in lattice spacings.  The :doc:`lattice <lattice>`
 command must have been previously used to define the lattice spacing.
 

doc/utils/sphinx-config/false_positives.txt

@@ -135,6 +135,7 @@ atan
 atc
 AtC
 ATC
+athermal
 athomps
 atm
 atomeye
@@ -223,6 +224,7 @@ Bfrac
 bgq
 Bh
 Bialke
+bicrystal
 Biersack
 bigbig
 bigint
@@ -284,6 +286,7 @@ br
 Branduardi
 Branicio
 brennan
+Brien
 Brilliantov
 Broadwell
 Broglie
@@ -327,6 +330,7 @@ ccache
 ccachepiecewise
 ccl
 ccmake
+ccN
 ccNspecies
 CCu
 cd
@@ -593,6 +597,7 @@ Derjaguin
 Derlet
 Deserno
 Destree
+destructor
 detils
 Devanathan
 devel
@@ -627,7 +632,6 @@ dipolar
 dir
 Direc
 dirname
-disarmmd
 discoverable
 discretization
 discretized
@@ -719,6 +723,7 @@ ebook
 ebt
 ec
 Ec
+eco
 ecoul
 ecp
 Ecut
@@ -833,6 +838,7 @@ Espanol
 Eshelby
 eshelby
 eskm
+esph
 esu
 esub
 esw
@@ -940,7 +946,6 @@ fmackay
 fmag
 fmass
 fmm
-fmsec
 fmx
 fmy
 fmz
@@ -1821,6 +1826,7 @@ Modine
 mofff
 MOFFF
 Mohd
+Mohles
 mol
 Mol
 molfile
@@ -1983,6 +1989,7 @@ Neumann
 Nevent
 nevery
 Nevery
+newfile
 Newns
 newtype
 Neyts
@@ -2075,9 +2082,9 @@ Nroff
 nrun
 Ns
 Nsample
-nsec
 Nskip
 Nspecies
+ns
 nsq
 Nstart
 nstats
@@ -2161,6 +2168,7 @@ optimizations
 orangered
 organometallic
 orientational
+orientationsFile
 orientorder
 Orlikowski
 ornl
@@ -2350,7 +2358,6 @@ ps
 Ps
 pscreen
 pscrozi
-psec
 pseudodynamics
 pseudopotential
 Pstart
@@ -2455,6 +2462,7 @@ rdc
 rdf
 RDideal
 rdx
+reacter
 README
 realtime
 reamin
@@ -2626,6 +2634,7 @@ Schimansky
 Schiotz
 Schlitter
 Schmid
+Schratt
 Schoen
 Schotte
 Schulten
@@ -3038,6 +3047,7 @@ ul
 ulb
 Uleft
 uloop
+Ulomek
 ulsph
 uMech
 umin

examples/ASPHERE/line/in.line

@@ -10,7 +10,7 @@ velocity	all create 1.44 320984 loop geom
 
 neighbor	0.3 bin
 neigh_modify	delay 0 every 1 check yes
-neigh_modify	exclude molecule all
+neigh_modify	exclude molecule/intra all
 
 pair_style	line/lj 2.5
 pair_coeff	* * 1.0 1.0 1.0 0.25 2.5
@@ -33,8 +33,10 @@ compute		2 all ke
 compute		3 all pe
 variable	toteng equal (c_1+c_2+c_3)/atoms
 
+compute_modify  thermo_temp extra/dof -350
+
 thermo		1000
-thermo_style	custom step temp f_2 pe ke c_1 c_2 c_3 v_toteng
+thermo_style	custom step f_2 pe ke c_1 c_2 c_3 v_toteng
 
 run		10000
 

examples/ASPHERE/line/in.line.srd

@@ -36,7 +36,7 @@ velocity	small create 1.44 87287 loop geom
 
 neighbor	0.3 bin
 neigh_modify	delay 0 every 1 check yes
-neigh_modify	exclude molecule big include big
+neigh_modify	exclude molecule/intra big include big
 
 comm_modify	mode multi group big vel yes
 neigh_modify	include big
@@ -68,13 +68,15 @@ compute		tbig big temp
 variable	pebig equal pe*atoms/count(big)
 variable	ebig equal etotal*atoms/count(big)
 
+compute_modify  tbig extra/dof -350
+
 compute		1 big erotate/asphere
 compute		2 all ke
 compute		3 all pe
 variable	toteng equal (c_1+c_2+c_3)/atoms
 
 thermo		1000
-thermo_style	custom step temp c_tsmall f_2[9] c_1 etotal &
+thermo_style	custom step c_tsmall f_2[9] c_1 etotal &
 		v_pebig v_ebig press
 thermo_modify	temp tbig
 

examples/ASPHERE/tri/in.tri.srd

@@ -35,7 +35,7 @@ velocity	small create 1.44 87287 loop geom
 
 neighbor	0.3 bin
 neigh_modify	delay 0 every 1 check yes
-neigh_modify	exclude molecule big include big
+neigh_modify	exclude molecule/intra big include big
 
 comm_modify	mode multi group big vel yes
 neigh_modify	include big
@@ -66,6 +66,8 @@ compute		tbig big temp
 variable	pebig equal pe*atoms/count(big)
 variable	ebig equal etotal*atoms/count(big)
 
+compute_modify  tbig extra/dof -4500
+
 compute		1 big erotate/asphere
 compute		2 all ke
 compute		3 all pe

examples/USER/dpd/dpd-shardlow/in.dpd-shardlow

@@ -1,5 +1,5 @@
 # Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme
-log             log.dpd-shardlow
+
 boundary        p p p
 
 units           metal  

examples/USER/dpd/dpd-vv/in.dpd-vv

@@ -1,6 +1,5 @@
 # INPUT FILE FOR DPD_Fluid
 
-log             log.dpd-vv
 boundary        p p p
 
 units           metal  # ev, ps

examples/USER/dpd/dpde-shardlow/in.dpde-shardlow

@@ -1,5 +1,5 @@
 # Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme
-log             log.dpde-shardlow
+
 boundary        p p p
 
 units           metal  # ev, ps

examples/USER/dpd/dpde-vv/in.dpde-vv

@@ -1,6 +1,5 @@
 # INPUT FILE FOR DPD_Fluid
 
-log             log.dpde-vv
 boundary        p p p
 
 units           metal  # ev, ps

examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow

@@ -1,5 +1,5 @@
 # Input File for DPD fluid under isoenthalpic conditions using the VV-SSA integration scheme
-log             log.dpdh-shardlow
+
 boundary        p p p
 
 units           metal  # ev, ps

examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow

@@ -1,5 +1,5 @@
 # Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme
-log             log.dpdp-shardlow
+
 boundary        p p p
 
 units           metal

examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow

@@ -1,6 +1,5 @@
 # Example for running DPD-RX
 
-log             log.dpdrx-shardlow
 boundary        p p p
 units           metal  # ev, ps
 atom_style      dpd

examples/USER/dpd/multi-lucy/in.multi-lucy

@@ -1,5 +1,5 @@
 # RDX coarse-grain model
-log             log.multi-lucy
+
 units           metal  # ev, ps
 atom_style      dpd
 atom_modify     map array

examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve

@@ -1,5 +1,4 @@
 variable	sname index adamantane_ionized
-log		${sname}.nve.log
 
 units 		electron
 newton		on

examples/USER/eff/Be-solid/in.Be-solid.spe

@@ -1,5 +1,4 @@
 variable        sname index Be-solid
-log             ${sname}.spe.log
 
 units           electron
 newton          on

examples/USER/eff/CH4/in.ch4.dynamics

@@ -1,5 +1,4 @@
 variable	sname index ch4
-log		${sname}.nve.log
 
 units 		electron
 newton		on

examples/USER/eff/CH4/in.ch4.min

@@ -1,5 +1,4 @@
 variable	sname index ch4
-log		${sname}.nve.log
 
 units 		electron
 newton		on

examples/USER/eff/CH4/in.ch4_ionized.dynamics

@@ -1,5 +1,4 @@
 variable	sname index ch4_ionized
-log		${sname}.nvt.log
 
 units 		electron
 newton		on
@@ -15,6 +14,7 @@ pair_coeff	* *
 comm_modify	vel yes	
 
 # minimize
+
 min_style       cg
 min_modify      line quadratic 
 minimize        0 1.0e-6 10000 100000

examples/USER/eff/H/in.h_atom.spe.ang

@@ -1,5 +1,4 @@
 variable	sname index h_atom.ang
-log		${sname}.spe.log
 
 units 		real
 newton		on

examples/USER/eff/H/in.h_atom.spe.bohr

@@ -1,5 +1,4 @@
 variable	sname index h_atom.bohr
-log		${sname}.spe.log
 
 units 		electron
 newton		on

examples/USER/eff/H2/in.h2

@@ -1,5 +1,4 @@
 variable	sname index h2
-log		${sname}.spe.log
 
 units 		electron
 newton		on
@@ -47,4 +46,4 @@ unfix		3
 
 #fix		1 all nve/eff
 
-run 		100000
+run 		10000

examples/USER/eff/H_plasma/in.h2bulk.npt

@@ -1,5 +1,4 @@
 variable        sname index h2bulk
-log		${sname}.npt.log
 
 units 		electron
 newton		on
@@ -41,7 +40,8 @@ dump		2 all xyz 10000 ${sname}.npt.xyz
 compute         1 all property/atom spin eradius
 dump		3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2]
 
-run		10000000
+thermo          1
+run		10
 
 unfix		1
 undump		2

examples/USER/eff/H_plasma/in.h2bulk.nve

@@ -1,5 +1,4 @@
 variable        sname index h2bulk
-log		${sname}.nve.log
 
 units 		electron
 newton		on
@@ -18,13 +17,13 @@ comm_modify	vel yes
 
 compute		effTemp all temp/eff
 
-thermo          1000
+thermo          10
 thermo_style    custom step pe temp press
 thermo_modify	temp effTemp
 
 # structure minimization
 min_style	cg
-minimize 	0 1.0e-4 1000 10000
+minimize 	0 1.0e-4 10 10
 
 timestep	0.001
 
@@ -41,7 +40,7 @@ dump		2 all xyz 1000 ${sname}.nve.xyz
 compute         1 all property/atom spin eradius
 dump		3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
 
-run		100000
+run		10
 
 unfix		1
 #unfix		2

examples/USER/eff/H_plasma/in.h2bulk.nve.ang

@@ -1,5 +1,4 @@
 variable        sname index h2bulk.ang
-log		${sname}.nve.log
 
 units 		real
 newton		on
@@ -29,13 +28,13 @@ variable        epauli equal c_energies[2]
 variable        ecoul equal c_energies[3]
 variable        erres equal c_energies[4]
 
-thermo          100
+thermo          10
 thermo_style    custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
 thermo_modify   temp effTemp press effPress flush yes
 
 # structure minimization
 min_style	cg
-minimize 	0 1.0e-4 1000 10000
+minimize 	0 1.0e-4 10 10
 
 timestep	0.001
 
@@ -52,7 +51,7 @@ dump		2 all xyz 1000 ${sname}.nve.xyz
 compute         1 all property/atom spin eradius
 dump		3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
 
-run		100000
+run		10
 
 unfix		1
 #unfix		2

examples/USER/eff/Li-dendritic/in.Li-dendritic.min

@@ -1,5 +1,4 @@
 variable        sname index Li-dendritic
-log		${sname}.min.log
 
 units 		electron
 newton		on
@@ -7,8 +6,8 @@ boundary        p p p
 
 atom_style	electron
 
-#read_data  	data.${sname}
+read_data  	data.${sname}
-read_restart	${sname}.min.restart2
+#read_restart	${sname}.min.restart2
 
 pair_style      eff/cut 50.112 
 pair_coeff	* * 

examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt

@@ -1,5 +1,4 @@
 variable        sname index Li-dendritic
-log		${sname}.min.log
 
 units 		electron
 newton		on
@@ -29,7 +28,7 @@ compute         1 all property/atom spin eradius
 #dump            1 all custom 100 ${sname}.min.lammpstrj id type x y z q c_1[1] c_1[2]
 #dump            2 all xyz 100 ${sname}.min.xyz
 min_modify      line quadratic dmax 0.05
-minimize        0 1.0e-7 1000 2000
+minimize        0 1.0e-7 100 100
 
 write_restart	${sname}.min.restart
 
@@ -46,7 +45,7 @@ dump            1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1
 dump            2 all xyz 100 ${sname}.nvt.xyz
 restart		100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
 
-run		10000
+run		100
 
 undump		1
 undump		2