flag as update 4

Thanks to @joshuakempfert. See issue #4210

.github/CODEOWNERS

@@ -151,12 +151,12 @@ tools/vim/*           @hammondkd
 unittest/*            @akohlmey
 
 # cmake
-cmake/*               @rbberger
+cmake/*               @akohlmey
 cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
 cmake/Modules/MPI4WIN.cmake @akohlmey
 cmake/Modules/OpenCLLoader.cmake @akohlmey
-cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
-cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
+cmake/Modules/Packages/COLVARS.cmake @giacomofiorin
+cmake/Modules/Packages/KIM.cmake @ellio167
 cmake/presets/*.cmake @akohlmey
 
 # python

.github/workflows/unittest-macos.yml

@@ -15,7 +15,7 @@ jobs:
   build:
     name: MacOS Unit Test
     if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: macos-latest
+    runs-on: macos-13
     env:
       CCACHE_DIR: ${{ github.workspace }}/.ccache
 
@@ -43,6 +43,8 @@ jobs:
       working-directory: build
       run: |
         ccache -z
+        python3 -m venv macosenv
+        source macosenv/bin/activate
         python3 -m pip install numpy
         python3 -m pip install pyyaml
         cmake -C ../cmake/presets/clang.cmake \

cmake/CMakeLists.txt

@@ -1,7 +1,7 @@
+# -*- CMake -*- master configuration file for building LAMMPS
 ########################################
 # CMake build system
 # 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
@@ -12,11 +12,6 @@ endif()
 if(POLICY CMP0075)
   cmake_policy(SET CMP0075 NEW)
 endif()
-# set policy to silence warnings about missing executable permissions in
-# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
-if(POLICY CMP0109)
-  cmake_policy(SET CMP0109 OLD)
-endif()
 # set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
 if(POLICY CMP0135)
   cmake_policy(SET CMP0135 OLD)
@@ -34,6 +29,7 @@ project(lammps CXX)
 set(SOVERSION 0)
 get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 
+include(GNUInstallDirs)
 get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 # collect all executables and shared libs in the top level build folder
@@ -116,7 +112,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
       set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
+      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
     endif()
   endif()
 endif()
@@ -131,6 +127,19 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
   set(CMAKE_TUNE_DEFAULT "-Minform=severe")
 endif()
 
+# this hack is required to compile fmt lib with CrayClang version 15.0.2
+# CrayClang is only directly recognized by version 3.28 and later
+if(CMAKE_VERSION VERSION_LESS 3.28)
+  get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
+    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+  endif()
+else()
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
+    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+  endif()
+endif()
+
 # silence nvcc warnings
 if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
   set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
@@ -155,11 +164,28 @@ if(MSVC)
     add_compile_options(/Zc:__cplusplus)
     add_compile_options(/wd4244)
     add_compile_options(/wd4267)
+    add_compile_options(/wd4250)
     add_compile_options(/EHsc)
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
+# warn about potentially problematic GCC compiler versions
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+  if (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
+      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
+        "with C++17 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 9.x or later")
+    endif()
+  endif()
+  if (CMAKE_CXX_STANDARD GREATER_EQUAL 11)
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
+      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
+        "with C++11 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
+    endif()
+  endif()
+endif()
+
 # export all symbols when building a .dll file on windows
 if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
   set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@@ -202,7 +228,6 @@ else()
   unset(CMAKE_CXX_CLANG_TIDY CACHE)
 endif()
 
-include(GNUInstallDirs)
 file(GLOB ALL_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
 file(GLOB MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
@@ -216,6 +241,10 @@ endif()
 add_executable(lmp ${MAIN_SOURCES})
 target_link_libraries(lmp PRIVATE lammps)
 set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
+# re-export all symbols for plugins
+if(PKG_PLUGIN AND (NOT ((CMAKE_SYSTEM_NAME STREQUAL "Windows"))))
+  set_target_properties(lmp PROPERTIES ENABLE_EXPORTS TRUE)
+endif()
 install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
@@ -404,6 +433,7 @@ pkg_depends(CG-DNA MOLECULE)
 pkg_depends(CG-DNA ASPHERE)
 pkg_depends(ELECTRODE KSPACE)
 pkg_depends(EXTRA-MOLECULE MOLECULE)
+pkg_depends(MESONT MOLECULE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -429,6 +459,7 @@ if(BUILD_OMP)
       (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
     # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
@@ -441,6 +472,18 @@ if(BUILD_OMP)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
+# lower C++ standard for fmtlib sources when using Intel classic compiler
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
+    AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 2021.10))
+  message(STATUS "Lowering C++ standard for compiling fmtlib sources with Intel Classic compiler")
+  get_filename_component(LMP_UTILS_SRC "${LAMMPS_SOURCE_DIR}/utils.cpp" ABSOLUTE)
+  get_filename_component(LMP_VARIABLE_SRC "${LAMMPS_SOURCE_DIR}/variable.cpp" ABSOLUTE)
+  get_filename_component(FMT_FORMAT_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_format.cpp" ABSOLUTE)
+  get_filename_component(FMT_OS_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_os.cpp" ABSOLUTE)
+  set_source_files_properties("${FMT_FORMAT_SRC}" "${FMT_OS_SRC}" "${LMP_VARIABLE_SRC}" "${LMP_UTILS_SRC}"
+          PROPERTIES COMPILE_OPTIONS "-std=c++14")
+endif()
+
 if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
   enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
@@ -893,13 +936,23 @@ else()
 endif()
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
+if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
+  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
+    OUTPUT_VARIABLE GIT_DESCRIBE
+    ERROR_QUIET
+    WORKING_DIRECTORY ${LAMMPS_DIR}
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+endif()
 message(STATUS "<<< Build configuration >>>
-   LAMMPS Version:   ${PROJECT_VERSION}
+   LAMMPS Version:   ${PROJECT_VERSION} ${GIT_DESCRIBE}
    Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
    CMake Version:    ${CMAKE_VERSION}
    Build type:       ${LAMMPS_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
+if(CMAKE_CROSSCOMPILING)
+  message(STATUS "Cross compiling on ${CMAKE_HOST_SYSTEM}")
+endif()
 ###############################################################################
 # Print package summary
 ###############################################################################
@@ -1028,6 +1081,14 @@ endif()
 if(BUILD_LAMMPS_SHELL)
   message(STATUS "<<< Building LAMMPS Shell >>>")
 endif()
+if(BUILD_LAMMPS_GUI)
+  message(STATUS "<<< Building LAMMPS GUI >>>")
+  if(LAMMPS_GUI_USE_PLUGIN)
+    message(STATUS "Loading LAMMPS library as plugin at run time")
+  else()
+    message(STATUS "Linking LAMMPS library at compile time")
+  endif()
+endif()
 if(ENABLE_TESTING)
   message(STATUS "<<< Building Unit Tests >>>")
   if(ENABLE_COVERAGE)

cmake/Modules/ExternalCMakeProject.cmake

@@ -43,5 +43,5 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
       "${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/CMakeLists.txt")
   endif()
   add_subdirectory("${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}"
-    "${CMAKE_BINARY_DIR}/_deps/${target}-build")
+    "${CMAKE_BINARY_DIR}/_deps/${target}-build" EXCLUDE_FROM_ALL)
 endfunction(ExternalCMakeProject)

cmake/Modules/FindClangFormat.cmake

@@ -1,5 +1,7 @@
 # Find clang-format
 find_program(ClangFormat_EXECUTABLE NAMES clang-format
+                                          clang-format-17.0
+                                          clang-format-16.0
                                           clang-format-15.0
                                           clang-format-14.0
                                           clang-format-13.0
@@ -19,7 +21,7 @@ if(ClangFormat_EXECUTABLE)
                   OUTPUT_VARIABLE clang_format_version
                   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-  if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
+  if(clang_format_version MATCHES "^(Ubuntu |Debian |)clang-format version .*")
     # Arch Linux output:
     # clang-format version 10.0.0
     #
@@ -32,9 +34,15 @@ if(ClangFormat_EXECUTABLE)
     # Ubuntu 22.04 LTS output:
     # Ubuntu clang-format version 14.0.0-1ubuntu1
     #
+    # Debian 11 output:
+    # Debian clang-format version 11.0.1-2
+    #
+    # Debian 12 output:
+    # Debian clang-format version 14.0.6
+    #
     # Fedora 36 output:
     # clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
-    string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
+    string(REGEX REPLACE "^(Ubuntu |Debian |)clang-format version ([0-9.]+).*"
                          "\\2"
                          ClangFormat_VERSION
                          "${clang_format_version}")

cmake/Modules/LAMMPSUtils.cmake

@@ -83,17 +83,17 @@ function(check_for_autogen_files source_dir)
     file(GLOB SRC_AUTOGEN_FILES ${CONFIGURE_DEPENDS} ${source_dir}/style_*.h)
     file(GLOB SRC_AUTOGEN_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
-    list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
+    list(APPEND SRC_AUTOGEN_FILES ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
     foreach(_SRC ${SRC_AUTOGEN_FILES})
       get_filename_component(FILENAME "${_SRC}" NAME)
       if(EXISTS ${source_dir}/${FILENAME})
         message(FATAL_ERROR "\n########################################################################\n"
-                              "Found header file(s) generated by the make-based build system\n"
-                              "\n"
-                              "Please run\n"
-                              "make -C ${source_dir} purge\n"
-                              "to remove\n"
-                              "########################################################################")
+                            "Found header file ${source_dir}/${FILENAME} generated by the make-based build system\n"
+                            "\n"
+                            "Please run\n"
+                            "make -C ${source_dir} purge\n"
+                            "to remove\n"
+                            "########################################################################")
       endif()
     endforeach()
 endfunction()

cmake/Modules/Packages/KOKKOS.cmake

@@ -132,8 +132,12 @@ if(PKG_KSPACE)
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
   if(Kokkos_ENABLE_CUDA)
     if(NOT (FFT STREQUAL "KISS"))
+      find_library(CUFFT_LIBRARY cufft)
+      if (CUFFT_LIBRARY STREQUAL "CUFFT_LIBRARY-NOTFOUND")
+        message(FATAL_ERROR "Required cuFFT library not found. Check your environment or set CUFFT_LIBRARY to its location")
+      endif()
       target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
-      target_link_libraries(lammps PRIVATE cufft)
+      target_link_libraries(lammps PRIVATE ${CUFFT_LIBRARY})
     endif()
   elseif(Kokkos_ENABLE_HIP)
     if(NOT (FFT STREQUAL "KISS"))

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "3124bb85259471e2a53a891f04bf697a" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   GetFallbackURL(MDI_URL MDI_FALLBACK)

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,6 +1,6 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.10.04.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "70ff79f4e59af175e55d24f3243ad1ff" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)

cmake/Modules/Packages/ML-QUIP.cmake

@@ -18,14 +18,14 @@ if(DOWNLOAD_QUIP)
     set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
     set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
   elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
-    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
+    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}} -fmax-stack-var-size=6553600\n")
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
     set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
     set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
   else()
     message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
   endif()
-  set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
+  set(temp "${temp}CFLAGS += -fPIC -Wno-return-mismatch \nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
   set(temp "${temp}MATH_LINKOPTS=")
   foreach(flag ${BLAS_LIBRARIES})
     set(temp "${temp} ${flag}")
@@ -41,6 +41,11 @@ if(DOWNLOAD_QUIP)
   set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
   set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n")
   set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\nHAVE_SCALAPACK=0\n")
+  # for gfortran, the -std= flag, if present, *must* be -std=gnu or else the compilation will fail.
+  if(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
+    string(REGEX REPLACE -std=f[0-9]+ -std=gnu newtemp "${temp}")
+    set(temp "${newtemp}")
+  endif()
   file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
 
   message(STATUS "QUIP download via git requested - we will build our own")
@@ -56,7 +61,7 @@ if(DOWNLOAD_QUIP)
     GIT_SUBMODULES "src/fox;src/GAP"
     PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
     CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
-    BUILD_COMMAND env QUIP_ARCH=lammps make libquip
+    BUILD_COMMAND env QUIP_ARCH=lammps make -j1 libquip
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE YES
     BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}

cmake/Modules/Packages/PLUMED.cmake

@@ -21,9 +21,11 @@ else()
   set(PLUMED_CONFIG_OMP "--disable-openmp")
 endif()
 
-set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz"
+# Note: must also adjust check for supported API versions in
+# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.1/plumed-src-2.9.1.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)

cmake/packaging/build_windows_cross_zip.sh

@@ -1,26 +1,64 @@
-#!/bin/bash -vx
+#!/bin/bash
 
 APP_NAME=lammps-gui
-DESTDIR=${PWD}/../LAMMPS_GUI
+DESTDIR=${PWD}/LAMMPS_GUI
+SYSROOT="$1"
 
 echo "Delete old files, if they exist"
-rm -rvf ${DESTDIR} LAMMPS-Win10-amd64.zip
+rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64.zip
 
 echo "Create staging area for deployment and populate"
 DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
 
-echo "Add required dependencies for Qt"
-for dll in Qt5Core.dll Qt5Gui.dll Qt5Widgets.dll
+# no static libs needed
+rm -rvf ${DESTDIR}/lib
+# but the LAMMPS lib
+
+echo "Copying required DLL files"
+for dll in $(objdump -p *.exe *.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
 do \
-    cp /usr/x86_64-w64-mingw32/sys-root/mingw/bin/${dll} ${DESTDIR}/bin/
-done
-for dir in styles platforms imageformats
-do \
-    mkdir -p ${DESTDIR}/${dir}
-    cp -r /usr/x86_64-w64-mingw32/sys-root/mingw/lib/qt5/plugins/${dir}/*.dll ${DESTDIR}/${dir}
+    doskip=0
+    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
+    do \
+        test ${dll} = ${skip}.dll && doskip=1
+    done
+    test ${doskip} -eq 1 && continue
+    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
 done
 
-pushd ..
-zip -9rv LAMMPS-Win10-amd64.zip LAMMPS_GUI
-popd
-exit 0
+echo "Copy required Qt plugins"
+mkdir -p ${DESTDIR}/qt5plugins
+for plugin in imageformats platforms styles
+do \
+    cp -r ${SYSROOT}/lib/qt5/plugins/${plugin} ${DESTDIR}/qt5plugins/
+done
+
+echo "Check dependencies of DLL files"
+for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
+do \
+    doskip=0
+    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
+    do \
+        test ${dll} = ${skip}.dll && doskip=1
+    done
+    test ${doskip} -eq 1 && continue
+    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
+done
+
+for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
+do \
+    doskip=0
+    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
+    do \
+        test ${dll} = ${skip}.dll && doskip=1
+    done
+    test ${doskip} -eq 1 && continue
+    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
+done
+
+cat > ${DESTDIR}/bin/qt.conf <<EOF
+[Paths]
+Plugins = ../qt5plugins
+EOF
+zip -9rvD LAMMPS-Win10-amd64.zip LAMMPS_GUI
+

cmake/packaging/linux_wrapper.sh

@@ -1,6 +1,9 @@
 #!/bin/sh
 # wrapper for bundled executables
 
+# reset locale to avoid problems with decimal numbers
+export LC_ALL=C
+
 BASEDIR=$(dirname "$0")
 EXENAME=$(basename "$0")
 

cmake/presets/kokkos-cuda.cmake

@@ -6,6 +6,8 @@ set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
+get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
+set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
 
 # hide deprecation warnings temporarily for stable release
 set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -32,7 +32,6 @@ set(WIN_PACKAGES
   FEP
   GPU
   GRANULAR
-  INTEL
   INTERLAYER
   KSPACE
   LEPTON

cmake/presets/oneapi.cmake

@@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icx" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

cmake/presets/windows.cmake

@@ -32,6 +32,7 @@ set(WIN_PACKAGES
   INTERLAYER
   KSPACE
   LEPTON
+  MACHDYN
   MANIFOLD
   MANYBODY
   MC
@@ -45,6 +46,7 @@ set(WIN_PACKAGES
   MOLECULE
   MOLFILE
   OPENMP
+  OPT
   ORIENT
   PERI
   PHONON

doc/Makefile

@@ -63,6 +63,7 @@ help:
 	@echo "  anchor_check  scan for duplicate anchor labels"
 	@echo "  style_check   check for complete and consistent style lists"
 	@echo "  package_check check for complete and consistent package lists"
+	@echo "  role_check    check for misformatted role keywords"
 	@echo "  spelling      spell-check the manual"
 
 # ------------------------------------------
@@ -98,6 +99,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -179,6 +181,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -227,6 +230,7 @@ char_check :
 role_check :
 	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\

doc/src/Build_basics.rst

@@ -489,8 +489,9 @@ using CMake or Make.
 
       .. code-block:: bash
 
-         -D BUILD_TOOLS=value         # yes or no (default)
-         -D BUILD_LAMMPS_SHELL=value  # yes or no (default)
+         -D BUILD_TOOLS=value         # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt
+         -D BUILD_LAMMPS_SHELL=value  # yes or no (default). Build lammps-shell
+         -D BUILD_LAMMPS_GUI=value    # yes or no (default). Build lammps-gui
 
       The generated binaries will also become part of the LAMMPS installation
       (see below).
@@ -504,7 +505,6 @@ using CMake or Make.
          make binary2txt       # build only binary2txt tool
          make chain            # build only chain tool
          make micelle2d        # build only micelle2d tool
-         make thermo_extract   # build only thermo_extract tool
 
          cd lammps/tools/lammps-shell
          make                  # build LAMMPS shell

doc/src/Build_extras.rst

@@ -881,6 +881,50 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder.
 
 ----------
 
+.. _machdyn:
+
+MACHDYN package
+-------------------------------
+
+To build with this package, you must download the Eigen3 library.
+Eigen3 is a template library, so you do not need to build it.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
+         -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location)
+
+      If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
+      downloaded and inside the CMake build directory.  If the Eigen3
+      library is already on your system (in a location where CMake
+      cannot find it), set ``EIGEN3_INCLUDE_DIR`` to the directory the
+      ``Eigen3`` include file is in.
+
+   .. tab:: Traditional make
+
+      You can download the Eigen3 library manually if you prefer; follow
+      the instructions in ``lib/machdyn/README``.  You can also do it in one
+      step from the ``lammps/src`` dir, using a command like these,
+      which simply invokes the ``lib/machdyn/Install.py`` script with the
+      specified args:
+
+      .. code-block:: bash
+
+         make lib-machdyn                         # print help message
+         make lib-machdyn args="-b"               # download to lib/machdyn/eigen3
+         make lib-machdyn args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
+
+      Note that a symbolic (soft) link named ``includelink`` is created
+      in ``lib/machdyn`` to point to the Eigen dir.  When LAMMPS builds it
+      will use this link.  You should not need to edit the
+      ``lib/machdyn/Makefile.lammps`` file.
+
+----------
+
 .. _mliap:
 
 ML-IAP package
@@ -1479,6 +1523,55 @@ ML-POD package
 
 ----------
 
+.. _ml-quip:
+
+ML-QUIP package
+---------------------------------
+
+To build with this package, you must download and build the QUIP
+library.  It can be obtained from GitHub.  For support of GAP
+potentials, additional files with specific licensing conditions need
+to be downloaded and configured.  The automatic download will from
+within CMake will download the non-commercial use version.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_QUIP=value       # download QUIP library for build, value = no (default) or yes
+         -D QUIP_LIBRARY=path         # path to libquip.a (only needed if a custom location)
+         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
+                                      #   value = no (default) or yes
+
+      CMake will try to download and build the QUIP library from GitHub,
+      if it is not found on the local machine. This requires to have git
+      installed. It will use the same compilers and flags as used for
+      compiling LAMMPS.  Currently this is only supported for the GNU
+      and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
+      want to use a previously compiled and installed QUIP library and
+      CMake cannot find it.
+
+      The QUIP library requires LAPACK (and BLAS) and CMake can identify
+      their locations and pass that info to the QUIP build script. But
+      on some systems this triggers a (current) limitation of CMake and
+      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
+      those cases to use the bundled linear algebra library and work around
+      the limitation.
+
+   .. tab:: Traditional make
+
+      The download/build procedure for the QUIP library, described in
+      ``lib/quip/README`` file requires setting two environment
+      variables, ``QUIP_ROOT`` and ``QUIP_ARCH``.  These are accessed by
+      the ``lib/quip/Makefile.lammps`` file which is used when you
+      compile and link LAMMPS with this package.  You should only need
+      to edit ``Makefile.lammps`` if the LAMMPS build can not use its
+      settings to successfully build on your system.
+
+----------
+
 .. _plumed:
 
 PLUMED package
@@ -2000,55 +2093,6 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
 ----------
 
-.. _ml-quip:
-
-ML-QUIP package
----------------------------------
-
-To build with this package, you must download and build the QUIP
-library.  It can be obtained from GitHub.  For support of GAP
-potentials, additional files with specific licensing conditions need
-to be downloaded and configured.  The automatic download will from
-within CMake will download the non-commercial use version.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D DOWNLOAD_QUIP=value       # download QUIP library for build, value = no (default) or yes
-         -D QUIP_LIBRARY=path         # path to libquip.a (only needed if a custom location)
-         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
-                                      #   value = no (default) or yes
-
-      CMake will try to download and build the QUIP library from GitHub,
-      if it is not found on the local machine. This requires to have git
-      installed. It will use the same compilers and flags as used for
-      compiling LAMMPS.  Currently this is only supported for the GNU
-      and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
-      want to use a previously compiled and installed QUIP library and
-      CMake cannot find it.
-
-      The QUIP library requires LAPACK (and BLAS) and CMake can identify
-      their locations and pass that info to the QUIP build script. But
-      on some systems this triggers a (current) limitation of CMake and
-      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
-      those cases to use the bundled linear algebra library and work around
-      the limitation.
-
-   .. tab:: Traditional make
-
-      The download/build procedure for the QUIP library, described in
-      ``lib/quip/README`` file requires setting two environment
-      variables, ``QUIP_ROOT`` and ``QUIP_ARCH``.  These are accessed by
-      the ``lib/quip/Makefile.lammps`` file which is used when you
-      compile and link LAMMPS with this package.  You should only need
-      to edit ``Makefile.lammps`` if the LAMMPS build can not use its
-      settings to successfully build on your system.
-
-----------
-
 .. _scafacos:
 
 SCAFACOS package
@@ -2096,50 +2140,6 @@ To build with this package, you must download and build the
 
 ----------
 
-.. _machdyn:
-
-MACHDYN package
--------------------------------
-
-To build with this package, you must download the Eigen3 library.
-Eigen3 is a template library, so you do not need to build it.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
-         -D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location)
-
-      If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
-      downloaded and inside the CMake build directory.  If the Eigen3
-      library is already on your system (in a location where CMake
-      cannot find it), set ``EIGEN3_INCLUDE_DIR`` to the directory the
-      ``Eigen3`` include file is in.
-
-   .. tab:: Traditional make
-
-      You can download the Eigen3 library manually if you prefer; follow
-      the instructions in ``lib/smd/README``.  You can also do it in one
-      step from the ``lammps/src`` dir, using a command like these,
-      which simply invokes the ``lib/smd/Install.py`` script with the
-      specified args:
-
-      .. code-block:: bash
-
-         make lib-smd                         # print help message
-         make lib-smd args="-b"               # download to lib/smd/eigen3
-         make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
-
-      Note that a symbolic (soft) link named ``includelink`` is created
-      in ``lib/smd`` to point to the Eigen dir.  When LAMMPS builds it
-      will use this link.  You should not need to edit the
-      ``lib/smd/Makefile.lammps`` file.
-
-----------
-
 .. _vtk:
 
 VTK package

doc/src/Howto.rst

@@ -100,6 +100,7 @@ Tutorials howto
 
    Howto_cmake
    Howto_github
+   Howto_lammps_gui
    Howto_pylammps
    Howto_wsl
 

doc/src/Howto_lammps_gui.rst

@@ -0,0 +1,402 @@
+Using the LAMMPS GUI
+====================
+
+LAMMPS GUI is a simple graphical text editor that is linked to the
+:ref:`LAMMPS C-library interface <lammps_c_api>` and thus can run LAMMPS
+directly using the contents of the editor's text buffer as input.
+
+This is similar to what people traditionally would do to run LAMMPS:
+using a regular text editor to edit the input and run the necessary
+commands, possibly including the text editor, too, from a command line
+terminal window.  That is quite effective when running LAMMPS on
+high-performance computing facilities and when you are very proficient
+in using the command line.  The main benefit of a GUI application is
+that this integrates well with graphical desktop environments and many
+basic tasks can be done directly from within the GUI without switching
+to a text console or requiring external programs or scripts to extract
+data from the generated output.  This makes it easier for beginners to
+get started running simple LAMMPS simulations and thus very suitable for
+tutorials on LAMMPS.  But also makes it easier to switch to a full
+featured text editor and more sophisticated visualization and analysis
+tools.
+
+-----
+
+The following text provides a detailed tour of the features and
+functionality of the LAMMPS GUI.  This document describes LAMMPS GUI
+version 1.2.
+
+Main window
+-----------
+
+When LAMMPS GUI starts, it will show the main window with either an
+empty buffer, or have a file loaded. In the latter case it may look like
+the following:
+
+.. image:: JPG/lammps-gui-main.png
+   :align: center
+   :scale: 50%
+
+There is the menu bar at the top, then the main editor buffer with the
+input file contents in the center with line numbers on the left and the
+input colored according to the LAMMPS input file syntax.  At the bottom
+is the status bar, which shows the status of LAMMPS execution on the
+left ("Ready." when idle) and the current working directory on the
+right.  The size of the main window will be stored when exiting and
+restored when starting again.  The name of the current file in the
+buffer is shown in the window title and the text `*modified*` is added
+in case the buffer has modifications that are not yet saved to a file.
+
+Opening Files
+^^^^^^^^^^^^^
+
+The LAMMPS GUI application will try to open the first command line
+argument as input file, further arguments are ignored.  When no
+argument is given LAMMPS GUI will start with an empty buffer.
+Files can also be opened via the ``File`` menu or by drag-and-drop
+of a file from a file manager to the editor window.  Only one
+file can be open at a time, so opening a new file with a filled
+buffer will close this buffer and in case the buffer has unsaved
+modifications will ask to either cancel the load, discard the
+changes or save them.
+
+
+Running LAMMPS
+^^^^^^^^^^^^^^
+
+From within the LAMMPS GUI main window LAMMPS can be started either from
+the ``Run`` menu, by the hotkey `Ctrl-Enter` (`Command-Enter` on macOS),
+or by clicking on the green button in the status bar.  LAMMPS runs in a
+separate thread, so the GUI stays responsive and thus it is able to
+interact with the calculation and access its data.  It is important to
+note, that LAMMPS is using the contents of the input buffer for the run,
+**not** the file it was read from. If there are unsaved changes in the
+buffer, they *will* be used.
+
+.. image:: JPG/lammps-gui-running.png
+   :align: center
+   :scale: 75%
+
+While LAMMPS is running, the contents of the status bar change: on the
+left side there is a text indicating that LAMMPS is running, which will
+contain the selected number of threads, if thread-parallel acceleration
+was selected in the ``Preferences`` dialog.  On the right side, a
+progress bar is shown that displays the estimated progress on the
+current :doc:`run command <run>`.  Additionally, two windows will open:
+the log window with the captured screen output and the chart window with
+a line graph created from the thermodynamic output of the run.
+
+The run can be stopped cleanly by using either the ``Stop LAMMPS`` entry
+in the ``Run`` menu, the hotkey `Ctrl-/` (`Command-/` on macOS), or
+clicking on the red button in the status bar.  This will cause that the
+running LAMMPS process will complete the current iteration and then
+stop.  This is equivalent to the command :doc:`timer timeout 0 <timer>`
+and implemented by calling the :cpp:func:`lammps_force_timeout()` function
+of the LAMMPS C-library interface.
+
+
+Viewing Snapshot Images
+^^^^^^^^^^^^^^^^^^^^^^^
+
+By selecting the ``View Image`` entry in the ``Run`` menu, by hitting
+the `Ctrl-I` (`Command-I` on macOS) hotkey or by clicking on the
+"palette" button in the status bar, LAMMPS GUI will issue a
+:doc:`write_dump image <dump_image>` command and read the resulting
+snapshot image into an image viewer window.  When possible, LAMMPS
+GUI will try to detect which elements the atoms correspond to (via
+their mass) and then colorize them accordingly. Otherwise just some
+predefined sequence of colors are assigned to different atom types.
+
+.. image:: JPG/lammps-gui-image.png
+   :align: center
+   :scale: 50%
+
+The default image size, some default image quality settings, the view
+style and some colors can be changed in the ``Preferences`` dialog
+window.  From the image viewer window further adjustments can be made:
+actual image size, high-quality rendering, anti-aliasing, view style,
+display of box or axes, zoom factor. The the image can be rotated
+horizontally and vertically and it is possible to only display the atoms
+within a predefined group (default is "all").  After each change, the
+image is rendered again and the display updated.  The small palette icon
+on the top left will be colored while LAMMPS is running to render the
+image and it will be grayed out again, when it is done.  When there are
+many items to show and high quality images with anti-aliasing are
+requested, re-rendering can take several seconds.  From the ``File``
+menu, the shown image can be saved to a file permanently or copied into
+the cut-n-paste buffer for pasting into another application.
+
+
+Editor Functions
+^^^^^^^^^^^^^^^^
+
+The editor has most the usual functionality that similar programs have:
+text selection via mouse or with cursor moves while holding the Shift
+key, Cut, Copy, Paste, Undo, Redo.  All of these editing functions are
+available via hotkeys.  When trying to exit the editor with a modified
+buffer, a dialog will pop up asking whether to cancel the quit, or don't
+save or save the buffer's contents to a file.
+
+Context Specific Help
+^^^^^^^^^^^^^^^^^^^^^
+
+.. image:: JPG/lammps-gui-popup-help.png
+   :align: center
+   :scale: 50%
+
+A unique feature of the LAMMPS GUI is the option to look up the
+documentation for the command in the current line.  This can be achieved
+by either clicking the right mouse button or by using the `Ctrl-?`
+hotkey.  When clicking the mouse there are additional entries in the
+context menu that will open the corresponding documentation page in the
+online LAMMPS documentation.  When using the hotkey, the first of those
+entries will be chosen directly.
+
+Menu
+----
+
+The menu bar the entries ``File``, ``Edit``, ``Run``, ``View``, and ``About``.
+Instead of using the mouse to click on them, the individual menus can also
+be activated by hitting the `Alt` key together with the corresponding underlined
+letter, that is `Alt-f` will activate the ``File`` menu.  For the corresponding
+activated sub-menus, also the underlined letter, together with the `Alt` key can
+be used to select instead of the mouse.
+
+File
+^^^^
+
+The ``File`` menu offers the usual options:
+
+- ``New`` will clear the current buffer and reset the file name to ``*unknown*``
+- ``Open`` will open a dialog to select a new file
+- ``Save`` will save the current file; if the file name is ``*unknown*``
+  a dialog will open to select a new file name
+- ``Save As`` will open a dialog to select and new file name and save
+  the buffer to it
+- ``Quit`` will exit LAMMPS GUI. If there are unsaved changes, a dialog
+  will appear to either cancel the quit, save or don't save the file.
+
+In addition, up to 5 recent file names will be listed after the ``Open``
+entry that allows to re-open recent files. This list is stored when
+quitting and recovered when starting again.
+
+Edit
+^^^^
+
+The ``Edit`` menu offers the usual editor functions like ``Undo``,
+``Redo``, ``Cut``, ``Copy``, ``Paste``, but also offers to open the
+``Preferences`` dialog and to delete all stored preferences so they
+will be reset to their defaults.
+
+Run
+^^^
+
+The ``Run`` menu allows to start and stop a LAMMPS process.  Rather than
+calling the LAMMPS executable as a separate executable, the LAMMPS GUI
+is linked to the LAMMPS library and thus can run LAMMPS internally
+through the :ref:`LAMMPS C-library interface <lammps_c_api>`.
+Specifically, a LAMMPS instance will be created by calling
+:cpp:func:`lammps_open_no_mpi` and then the buffer contents run by
+calling :cpp:func:`lammps_commands_string`.  Certain commands and
+features are only available, after a LAMMPS instance is created.  Its
+presence is indicated by a small LAMMPS ``L`` logo in the status bar at
+the bottom left of the main window.
+
+The LAMMPS calculation will be run in a concurrent thread so that the
+GUI will stay responsive and will be updated during the run.  This can
+be used to tell the running LAMMPS instance to stop at the next
+timestep.  The ``Stop LAMMPS`` entry will do this by calling
+:cpp:func:`lammps_force_timeout`, which is equivalent to a :doc:`timer
+timeout 0 <timer>` command.
+
+The ``Set Variables`` entry will open a dialog box where :doc:`index style variables <variable>`
+can be set. Those variables will be passed to the LAMMPS instance when
+it is created and are thus set *before* a run is started.
+
+.. image:: JPG/lammps-gui-variables.png
+   :align: center
+   :scale: 75%
+
+The ``Set Variables`` dialog will be pre-populated with entries that are
+set as index variables in the input and any variables that are used but
+not defined as far as the built-in parser can detect them.  New rows for
+additional variables can be added through the ``Add Row`` button and
+existing rows deleted by clicking on the ``X`` icons on the right.
+
+The ``View Image`` entry will send a :doc:`dump image <dump_image>`
+command to the LAMMPS instance, read the resulting file, and show it in
+an ``Image Viewer`` window.
+
+The ``View in OVITO`` entry will launch `OVITO <https://ovito.org>`_
+with a :doc:`data file <write_data>` of the current state of the system.
+This option is only available, if the LAMMPS GUI can find the OVITO
+executable in the system path.
+
+The ``View in VMD`` entry will instead launch VMD, also to load a
+:doc:`data file <write_data>` of the current state of the system.  This
+option is only available, if the LAMMPS GUI can find the VMD executable
+in the system path.
+
+View
+^^^^
+
+The ``View`` menu offers to show or hide the three optional windows
+with log output, graphs, or images.  The default settings for those
+can be changed in the ``Preferences dialog``.
+
+About
+^^^^^
+
+The ``About`` menu finally offers a couple of dialog windows and an
+option to launch the LAMMPS online documentation in a web browser.  The
+``About LAMMPS GUI`` entry displays a dialog with a summary of the
+configuration settings of the LAMMPS library in use and the version
+number of LAMMPS GUI itself.  The ``Quick Help`` displays a dialog with
+a minimal description of LAMMPS GUI.  And ``LAMMPS Manual`` will open
+the main page of this LAMMPS documentation at https://docs.lammps.org/.
+
+Preferences
+-----------
+
+The ``Preferences`` dialog allows to customize some of the behavior
+and looks of the LAMMPS GUI application.  The settings are grouped
+and each group is displayed within a tab.
+
+.. |guiprefs1| image:: JPG/lammps-gui-prefs-general.png
+   :width: 25%
+
+.. |guiprefs2| image:: JPG/lammps-gui-prefs-accel.png
+   :width: 25%
+
+.. |guiprefs3| image:: JPG/lammps-gui-prefs-image.png
+   :width: 25%
+
+|guiprefs1|  |guiprefs2|  |guiprefs3|
+
+General Settings:
+^^^^^^^^^^^^^^^^^
+
+- *Echo input to log:* when checked, all input commands, including
+  variable expansions, will be echoed to the log window. This is
+  equivalent to using `-echo screen` at the command line.  There is no
+  log *file* produced since it always uses `-log none`.
+- *Include citation details:* when checked full citation info will be
+  included to the log window.  This is equivalent to using `-cite
+  screen` on the command line.
+- *Show log window by default:* when checked, the screen output of a
+  LAMMPS run will be collected in a log window during the run
+- *Show chart window by default:* when checked, the thermodynamic
+  output of a LAMMPS run will be collected and displayed in a chart
+  window as line graphs.
+- *Replace log window on new run:* when checked, an existing log
+  window will be replaced on a new LAMMPS run, otherwise each run will
+  create a new log window.
+- *Replace chart window on new run:* when checked, an existing chart
+  window will be replaced on a new LAMMPS run, otherwise each run will
+  create a new chart window.
+- *Replace image window on new render:* when checked, an existing
+  chart window will be replaced when a new snapshot image is requested,
+  otherwise each command will create a new image window.
+- *Path to LAMMPS Shared Library File:* this options is only available
+  when LAMMPS GUI was compiled to load the LAMMPS library at run time
+  instead of being linked to it directly.  With the ``Browse..`` button
+  or by changing the text, a different shared library file with a
+  different compilation of LAMMPS with different settings or from a
+  different version can be loaded.  After this setting was changed,
+  LAMMPS GUI needs to be re-launched.
+- *Select Default Font:* Opens a font selection dialog where the type
+  and size for the default font (used for everything but the editor and
+  log) of the application can be set.
+- *Select Text Font:* Opens a font selection dialog where the type and
+  size for the text editor and log font of the application can be set.
+
+Accelerators:
+^^^^^^^^^^^^^
+
+This tab enables to select which accelerator package is used and is
+equivalent to using the `-suffix` and `-package` flags on the command
+line.  Only settings supported by the LAMMPS library and local hardware
+are available.  The `Number of threads` field allows to set the maximum
+number of threads for the accelerator packages that use threads.
+
+Snapshot Image:
+^^^^^^^^^^^^^^^
+
+This tab allows to set some defaults for the snapshot images displayed
+in the ``Image Viewer`` window, like its dimensions and the zoom factor
+applied.  The *Antialias* switch requests to render images with twice
+the number of pixels for width and height and then smoothly scales the
+image back to the requested size.  This produces higher quality images
+with smoother edges at the expense of requiring more CPU time to render
+the image.  The *HQ Image mode* option turns on using a screen space
+ambient occlusion mode (SSAO) when rendering images.  This is also more
+time consuming, but produces a more 'spatial' representation of the
+system.  The *VDW Style* checkbox selects whether atoms are represented
+by space filling spheres when checked or by smaller spheres and stick.
+Finally there are a couple of drop down lists to select the background
+and box color.
+
+
+Hotkeys
+-------
+
+Almost all functionality is accessible from the menu or via hotkeys.
+The following hotkeys are available (On macOS use the Command key
+instead of Ctrl/Control).
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Hotkey
+     - Function
+     - Hotkey
+     - Function
+     - Hotkey
+     - Function
+     - Hotkey
+     - Function
+   * - Ctrl+N
+     - New File
+     - Ctrl+Z
+     - Undo edit
+     - Ctrl+Enter
+     - Run LAMMPS
+     - Ctrl+Shift+A
+     - About LAMMPS GUI
+   * - Ctrl+O
+     - Open File
+     - Ctrl+Shift+Z
+     - Redo edit
+     - Ctrl+/
+     - Stop Active Run
+     - Ctrl+Shift+H
+     - Quick Help
+   * - CTRL+S
+     - Save File
+     - Ctrl+C
+     - Copy text
+     - Ctrl+Shift+V
+     - Set Variables
+     - Ctrl+Shift+G
+     - LAMMPS GUI Howto
+   * - Ctrl+Shift+S
+     - Save File As
+     - Ctrl+X
+     - Cut text
+     - Ctrl+I
+     - Create Snapshot Image
+     - Ctrl+Shift+M
+     - LAMMPS Manual
+   * - Ctrl+Q
+     - Quit
+     - Ctrl+V
+     - Paste text
+     - Ctrl+P
+     - Preferences
+     - Ctrl+?
+     - Context Help
+
+Further editing keybindings `are documented with the Qt documentation
+<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_.  In
+case of conflicts the list above takes precedence.

doc/src/Manual.rst

@@ -23,10 +23,23 @@ coordinated.
 
 ----------
 
-The content for this manual is part of the LAMMPS distribution.  The
-online version always corresponds to the latest feature release version.
-If needed, you can build a local copy of the manual as HTML pages or a
-PDF file by following the steps on the :doc:`Build_manual` page.  If you
+The content for this manual is part of the LAMMPS distribution in its
+doc directory.
+
+* The version of the manual on the LAMMPS website corresponds to the
+  latest LAMMPS feature release.  It is available at:
+  `https://docs.lammps.org/ <https://docs.lammps.org/>`_.
+* A version of the manual corresponding to the latest LAMMPS stable
+  release (state of the *stable* branch on GitHub) is available online
+  at: `https://docs.lammps.org/stable/
+  <https://docs.lammps.org/stable/>`_
+* A version of the manual with the features most recently added to
+  LAMMPS (state of the *develop* branch on GitHub) is available at:
+  `https://docs.lammps.org/latest/ <https://docs.lammps.org/latest/>`_
+
+If needed, you can build a copy on your local machine of the manual
+(HTML pages or PDF file) for the version of LAMMPS you have
+downloaded.  Follow the steps on the :doc:`Build_manual` page.  If you
 have difficulties viewing the pages, please :ref:`see this note
 <webbrowser>`.
 

doc/src/Speed_kokkos.rst

@@ -18,7 +18,7 @@ package was developed primarily by Christian Trott (Sandia) and Stan
 Moore (Sandia) with contributions of various styles by others,
 including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez
 (Sandia). For more information on developing using Kokkos abstractions
-see the Kokkos `Wiki <https://github.com/kokkos/kokkos/wiki>`_.
+see the `Kokkos Wiki <https://github.com/kokkos/kokkos/wiki>`_.
 
 Kokkos currently provides support for 4 modes of execution (per MPI
 task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
@@ -29,11 +29,12 @@ produce an executable compatible with a specific hardware.
 .. admonition:: C++14 support
    :class: note
 
-   Kokkos requires using a compiler that supports the c++14 standard. For
-   some compilers, it may be necessary to add a flag to enable c++14 support.
+   Kokkos version 3.x requires using a compiler that supports the c++14 standard.
+   For some compilers, it may be necessary to add a flag to enable c++14 support.
    For example, the GNU compiler uses the -std=c++14 flag. For a list of
-   compilers that have been tested with the Kokkos library, see the Kokkos
-   `README <https://github.com/kokkos/kokkos/blob/master/README.md>`_.
+   compilers that have been tested with the Kokkos library, see the
+   `requirements document of the Kokkos Wiki
+   <https://kokkos.github.io/kokkos-core-wiki/requirements.html>`_.
 
 .. admonition:: NVIDIA CUDA support
    :class: note

doc/src/Tools.rst

@@ -645,106 +645,49 @@ LAMMPS GUI
 Overview
 ^^^^^^^^
 
-LAMMPS GUI is essentially a small graphical text editor that is linked
-to the :ref:`LAMMPS C-library interface <lammps_c_api>` and thus can run
-LAMMPS directly using the contents of the editor's text buffer as input.
-This is similar to what people usually would do using a text editor to
-edit the input and then a command line terminal window to run the input
-commands.  The main benefit is that this integrates very well with
-graphical desktop environments and that it is easier to use for
-beginners in running computations and thus very suitable for tutorials
-on LAMMPS.  A small difference is that for the LAMMPS GUI it is not
-require to first commit its buffer of the text editor to a file.
+LAMMPS GUI is a simple graphical text editor that is linked to the
+:ref:`LAMMPS C-library interface <lammps_c_api>` and thus can run LAMMPS
+directly using the contents of the editor's text buffer as input.
+
+This is similar to what people traditionally would do to run LAMMPS:
+using a regular text editor to edit the input and run the necessary
+commands, possibly including the text editor, too, from a command line
+terminal window.  This similarity is a design goal. While making it easy
+for beginners to start with LAMMPS, it is also the intention to simplify
+the transition to workflows like most experienced LAMMPS users do.
+
+All features have been extensively exposed to hotkeys, so that there is
+also appeal for experienced LAMMPS users, too, especially for
+prototyping and testing simulations setups.
 
 Features
 ^^^^^^^^
 
-The main window of the LAMMPS GUI is a generic text editor window with
-line numbers and syntax highlighting set up for LAMMPS input files.  It
-can be used to edit any kind of text file, though.  The output of a run
-is captured and displayed in a separate dialog window and *not* sent to
-the console or a log file (unless the :doc:`log command <log>` is used
-in the input.  The log window is regularly updated during the run and a
-progress bar for the run command shown at the bottom of the main window.
-Starting a new run will open another log windows.  The state of LAMMPS
-will be reset between two runs.  After the simulation is finished, an
-image of the simulated system can be created and shown in an image
-viewer window.  Ongoing runs can be stopped at the next iteration via
-triggering a timeout.
+A detailed discussion and explanation of all features and functionality
+are in the :doc:`Howto_lammps_gui` tutorial Howto page.
 
-When opening a file, the editor will determine the directory where the
-file resides and switch its current working directory to the folder of
-that file.  Many LAMMPS inputs contain commands that read other files,
-typically from the folder of the input file.  The GUI will always show
-the current working directory in the bottom.  The editor window can also
-receive (entire) files via drag-n-drop from a file manager GUI or a
-desktop environment.  When exiting the GUI with a modified buffer, a
-dialog asking to either cancel, ignore the modifications, or save the
-file with show up. Same when attempting to load a new file into a
-modified buffer.
+Here are a few highlights of LAMMPS GUI
 
-Hotkeys
-^^^^^^^
-
-Almost all functionality is accessible from the menu or via hotkeys.
-The following hotkeys are available (On macOS use the Command key
-instead of Ctrl (aka Control)).
-
-.. list-table::
-   :header-rows: 1
-   :widths: auto
-
-   * - Hotkey
-     - Function
-     - Hotkey
-     - Function
-     - Hotkey
-     - Function
-     - Hotkey
-     - Function
-   * - Ctrl+N
-     - New File
-     - Ctrl+Z
-     - Undo edit
-     - Ctrl+V
-     - Paste text
-     - Ctrl+Q
-     - Quit (Main Window only)
-   * - Ctrl+O
-     - Open File
-     - Ctrl+Shift+Z
-     - Redo edit
-     - Ctrl+Enter
-     - Run LAMMPS
-     - Ctrl+W
-     - Close (Log and Image Window only)
-   * - CTRL+S
-     - Save File
-     - Ctrl+C
-     - Copy text
-     - Ctrl+/
-     - Stop Active Run
-     - Ctrl+P
-     - Preferences
-   * - Ctrl+Shift+S
-     - Save File As
-     - Ctrl+X
-     - Cut text
-     - Ctrl+I
-     - Create Snapshot Image
-     - Ctrl+Shift+/
-     - Quick Help
-
-Further editing keybindings `are documented with the Qt documentation
-<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_.  In
-case of conflicts the list above takes precedence.
+- Text editor with syntax highlighting customized for LAMMPS
+- Text editor will switch working directory to folder of file in buffer
+- Text editor will remember up to 5 recent files
+- Context specific LAMMPS command help via online documentation
+- LAMMPS is running in a concurrent thread, so the GUI remains responsive
+- Support for accelerator packages
+- Progress bar indicates that LAMMPS is running
+- LAMMPS can be started and stopped with a hotkey
+- Screen output is captured in a Log Window
+- Thermodynamic output is captured and displayed as line graph in a Chart Window
+- Visualization of current state in Image Viewer (via :doc:`dump image <dump_image>`)
+- Many adjustable settings and preferences that are persistent
+- Dialog to set variables from the LAMMPS command line
 
 Parallelization
 ^^^^^^^^^^^^^^^
 
 Due to its nature as a graphical application, it is not possible to use
-the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading is
-available and enabled by default.
+the LAMMPS GUI in parallel with MPI, but OpenMP multi-threading and GPU
+acceleration is available and enabled by default.
 
 Prerequisites and portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -752,63 +695,65 @@ Prerequisites and portability
 LAMMPS GUI is programmed in C++ based on the C++11 standard and using
 the `Qt GUI framework <https://www.qt.io/product/framework>`_.
 Currently, Qt version 5.12 or later is required; Qt 5.15LTS is
-recommended Qt 6.x not (yet) supported. Furthermore, CMake version 3.16
-is required and LAMMPS must be configured with ``-D
-LAMMPS_EXCETIONS=on`` and ``-D BUILD_MPI=off``. It has been successfully
-compiled and tested on:
+recommended; Qt 6.x not (yet) supported.  Building LAMMPS with CMake 3.16
+or later is required.  The LAMMPS GUI has been successfully compiled and tested on:
 
 - Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
 - Fedora Linux 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS
 - Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
+- Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
 
 Pre-compiled executables
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 Pre-compiled LAMMPS executables including the GUI are currently
-available from https://download.lammps.org/static. You can unpack the
-archive (or mount the macOS disk image) and run the GUI directly in
-place. The folder may also be moved around and added to the ``PATH``
-environment variable so the executables will be found automatically. The
-LAMMPS GUI executable is called ``lammps-gui`` and takes no arguments or
-will interpret the first argument as filename to load.
+available from https://download.lammps.org/static or
+https://github.com/lammps/lammps/releases.  You can unpack the archives
+(or mount the macOS disk image) and run the GUI directly in place. The
+folder may also be moved around and added to the ``PATH`` environment
+variable so the executables will be found automatically.  The LAMMPS GUI
+executable is called ``lammps-gui`` and either takes no arguments or
+attempts to load the first argument as LAMMPS input file.
 
 Compilation
 ^^^^^^^^^^^
 
 The source for the LAMMPS GUI is included with the LAMMPS source code
-distribution in the folder `tools/lammps-gui` and thus it can be can be
-built as part of a regular LAMMPS compilation.
-:doc:`Using CMake <Howto_cmake>` is required.
-To enable its compilation the CMake variable ``-D BUILD_LAMMPS_GUI=on``
-must be set when creating the CMake configuration.  All other settings
-(compiler, flags, compile type) for LAMMPS GUI are then inherited from
-the regular LAMMPS build.  If the Qt library is packaged for Linux
-distributions, then its location is typically auto-detected since the
-required CMake configuration files are stored in a location where CMake
-can find them without additional help.  Otherwise, the location of the
-Qt library installation must be indicated by setting
-``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to a folder inside
-the Qt installation that contains the file ``Qt5Config.cmake``.
+distribution in the folder ``tools/lammps-gui`` and thus it can be can
+be built as part of a regular LAMMPS compilation.  :doc:`Using CMake
+<Howto_cmake>` is required.  To enable its compilation, the CMake
+variable ``-D BUILD_LAMMPS_GUI=on`` must be set when creating the CMake
+configuration.  All other settings (compiler, flags, compile type) for
+LAMMPS GUI are then inherited from the regular LAMMPS build.  If the Qt
+library is packaged for Linux distributions, then its location is
+typically auto-detected since the required CMake configuration files are
+stored in a location where CMake can find them without additional help.
+Otherwise, the location of the Qt library installation must be indicated
+by setting ``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to
+a folder inside the Qt installation that contains the file
+``Qt5Config.cmake``.
 
-It is also possible to build the LAMMPS GUI as a standalone executable
-(e.g. when LAMMPS has been compiled with traditional make), then the
-CMake configuration needs to be told where to find the LAMMPS headers
-and the LAMMPS library, via `-D LAMMPS_SOURCE_DIR=/path/to/lammps/src`.
-CMake will try to guess a build folder with the LAMMPS library from that
-path, but it can also be set with `-D LAMMPS_LIB_DIR=/path/to/lammps/lib`.
+It should be possible to build the LAMMPS GUI as a standalone
+compilation (e.g. when LAMMPS has been compiled with traditional make),
+then the CMake configuration needs to be told where to find the LAMMPS
+headers and the LAMMPS library, via ``-D
+LAMMPS_SOURCE_DIR=/path/to/lammps/src``.  CMake will try to guess a
+build folder with the LAMMPS library from that path, but it can also be
+set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
 
 Rather than linking to the LAMMPS library during compilation, it is also
 possible to compile the GUI with a plugin loader library that will load
 the LAMMPS library dynamically at runtime during the start of the GUI
-from a shared library; e.g. `liblammps.so` or `liblammps.dylib` or
-`liblammps.dll` (depending on the operating system).  This has the
+from a shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
+``liblammps.dll`` (depending on the operating system).  This has the
 advantage that the LAMMPS library can be updated LAMMPS without having
 to recompile the GUI.  The ABI of the LAMMPS C-library interface is very
 stable and generally backward compatible.  This feature is enabled by
-setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then
-``-D LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
-would be the ``examples/COUPLE/plugin`` folder of the LAMMPS distribution.
+setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
+LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
+would be the ``examples/COUPLE/plugin`` folder of the LAMMPS
+distribution.
 
 Platform notes
 ^^^^^^^^^^^^^^
@@ -818,7 +763,7 @@ macOS
 
 When building on macOS, the build procedure will try to manufacture a
 drag-n-drop installer, LAMMPS-macOS-multiarch.dmg, when using the 'dmg'
-target (i.e. `cmake --build <build dir> --target dmg` or `make dmg`.
+target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
 
 To build multi-arch executables that will run on both, arm64 and x86_64
 architectures natively, it is necessary to set the CMake variable ``-D
@@ -831,29 +776,50 @@ version.
 Windows
 """""""
 
-On Windows currently only compilation from within Visual Studio 2022 is
-supported and tested. Using CMake and Ninja as build system is
-required. Qt needs to be installed, tested was a package downloaded from
-https://www.qt.io, into the ``C:\\Qt`` folder.  There is a custom
-`x64-GUI-MSVC` build configuration provided that will activate building
-the `lammps-gui.exe` executable in addition to LAMMPS.  When requesting
-an installation from the `Build` menu, it will create a compressed zip
-file with the executables and required dependent .dll files.  This zip
-file can be uncompressed and ``lammps-gui.exe`` run directly from there.
-The uncompressed folder can be added to the ``PATH`` environment and
-LAMMPS and LAMMPS GUI can be launched from anywhere from the command
-line.
+On Windows either native compilation from within Visual Studio 2022 with
+Visual C++ is supported and tested, or compilation with the MinGW / GCC
+cross-compiler environment on Fedora Linux.
+
+**Visual Studio**
+
+Using CMake and Ninja as build system are required.  Qt needs to be
+installed, tested was a binary package downloaded from
+https://www.qt.io, which installs into the ``C:\\Qt`` folder by default.
+There is a custom `x64-GUI-MSVC` build configuration provided in the
+``CMakeSettings.json`` file that Visual Studio uses to store different
+compilation settings for project.  Choosing this configuration will
+activate building the `lammps-gui.exe` executable in addition to LAMMPS
+through importing package selection from the ``windows.cmake`` preset
+file and enabling building the LAMMPS GUI and disabling building with MPI.
+When requesting an installation from the `Build` menu in Visual Studio,
+it will create a compressed ``LAMMPS-Win10-amd64.zip`` zip file with the
+executables and required dependent .dll files.  This zip file can be
+uncompressed and ``lammps-gui.exe`` run directly from there.  The
+uncompressed folder can be added to the ``PATH`` environment and LAMMPS
+and LAMMPS GUI can be launched from anywhere from the command line.
+
+**MinGW64 Cross-compiler**
+
+The standard CMake build procedure can be applied and the
+``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
+command will automatically include a suitable CMake toolchain file (the
+regular cmake command can be used after that).  After building the
+libraries and executables, you can build the target 'zip'
+(i.e. ``cmake --build <build dir> --target zip`` or ``make zip``
+to stage all installed files into a LAMMPS_GUI folder and then
+run a script to copy all required dependencies, some other files,
+and create a zip file from it.
 
 Linux
 """""
 
-Version 5.12 or later of the Qt library and CMake version 3.16 are
-required and those are provided by, e.g., Ubuntu 20.04LTS.  Thus older
-Linux distributions are not likely to be supported, while more recent
-ones will work, even for pre-compiled executables (see above).  After
-compiling with ``cmake --build <build folder>``, use
-``cmake --build <build folder> --target tgz`` or ``make tgz`` to build
-a ``LAMMPS-Linux-amd64.tar.gz`` file with the executables and their
+Version 5.12 or later of the Qt library is required. Those are provided
+by, e.g., Ubuntu 20.04LTS.  Thus older Linux distributions are not
+likely to be supported, while more recent ones will work, even for
+pre-compiled executables (see above).  After compiling with
+``cmake --build <build folder>``, use ``cmake --build <build
+folder> --target tgz`` or ``make tgz`` to build a
+``LAMMPS-Linux-amd64.tar.gz`` file with the executables and their
 support libraries.
 
 ----------

doc/src/compute_saed.rst

@@ -68,7 +68,7 @@ reciprocal lattice nodes. The mesh spacing is defined either (a)  by
 the entire simulation domain or (b) manually using selected values as
 shown in the 2D diagram below.
 
-.. image:: img/saed_mesh.jpg
+.. image:: img/saed_mesh.png
    :scale: 75%
    :align: center
 

doc/src/compute_stress_atom.rst

@@ -223,7 +223,7 @@ result. I.e. the last 2 columns of thermo output will be the same:
    system pressure.
 
 The compute stress/atom can be used in a number of ways.  Here is an
-example to compute a 1-d pressure profile in z-direction across the
+example to compute a 1-d pressure profile in x-direction across the
 complete simulation box. You will need to adjust the number of bins and the
 selections for time averaging to your specific simulation.  This assumes
 that the dimensions of the simulation cell does not change.

doc/src/compute_xrd.rst

@@ -72,7 +72,7 @@ reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire
 simulation domain or (b) manually using selected values as
 shown in the 2D diagram below.
 
-.. image:: img/xrd_mesh.jpg
+.. image:: img/xrd_mesh.png
    :scale: 75%
    :align: center
 

doc/src/fix_adapt_fep.rst

@@ -307,7 +307,9 @@ the :doc:`run <run>` command.  This fix is not invoked during
 
 Restrictions
 """"""""""""
- none
+
+The keyword "scale yes" is not supported for scaling per-atom parameters
+diameter and change. You can use :doc:`fix adapt <fix_adapt>` for those.
 
 Related commands
 """"""""""""""""

doc/src/fix_atom_swap.rst

@@ -181,6 +181,12 @@ This fix is part of the MC package.  It is only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
+This fix cannot be used with systems that do not have per-type masses
+(e.g. atom style sphere) since the implemented algorithm pre-computes
+velocity rescaling factors from per-type masses and ignores any per-atom
+masses, if present.  In case both, per-type and per-atom masses are
+present, a warning is printed.
+
 Related commands
 """"""""""""""""
 

doc/src/fix_ave_chunk.rst

@@ -541,10 +541,10 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`, `fix
-:doc:ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
-:doc:`variable <variable>`, :doc:`fix ave/correlate
-:doc:<fix_ave_correlate>`, `fix ave/atogrid <fix_ave_grid>`
+:doc:`compute <compute>`, :doc:`fix ave/atom <fix_ave_atom>`,
+:doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`variable <variable>`, :doc:`fix ave/correlate <fix_ave_correlate>`,
+:doc:`fix ave/grid <fix_ave_grid>`
 
 
 Default

doc/src/fix_ave_correlate.rst

@@ -65,7 +65,6 @@ Examples
    fix 1 all ave/correlate 1 50 10000 &
              c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
              type upper ave running title1 "My correlation data"
-
    fix 1 all ave/correlate 1 50 10000 c_thermo_press[*]
 
 Description

doc/src/fix_ave_correlate_long.rst

@@ -20,11 +20,11 @@ Syntax
   .. parsed-literal::
 
        c_ID = global scalar calculated by a compute with ID
-       c_ID[I] = Ith component of global vector calculated by a compute with ID
+       c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
        f_ID = global scalar calculated by a fix with ID
-       f_ID[I] = Ith component of global vector calculated by a fix with ID
+       f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
        v_name = global value calculated by an equal-style variable with name
-       v_name[I] = Ith component of global vector calculated by a vector-style variable with name
+       v_name[I] = Ith component of a vector-style variable with name, I can include wildcard (see below)
 
 * zero or more keyword/arg pairs may be appended
 * keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount*
@@ -63,6 +63,7 @@ Examples
    fix 1 all ave/correlate/long 1 10000 &
              c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
              type upper title1 "My correlation data" nlen 15 ncount 3
+   fix 1 all ave/correlate/long 1 10000 c_thermo_press[*]
 
 Description
 """""""""""
@@ -80,8 +81,10 @@ specified values may represent calculations performed by computes and
 fixes which store their own "group" definitions.
 
 Each listed value can be the result of a compute or fix or the
-evaluation of an equal-style variable. See the
-:doc:`fix ave/correlate <fix_ave_correlate>` page for details.
+evaluation of an equal-style or vector-style variable.  For
+vector-style variables, the specified indices can include a wildcard
+character.  See the :doc:`fix ave/correlate <fix_ave_correlate>` page
+for details.
 
 The *Nevery* and *Nfreq* arguments specify on what time steps the input
 values will be used to calculate correlation data and the frequency

doc/src/fix_charge_regulation.rst

@@ -253,11 +253,11 @@ built with that package.  See the :doc:`Build package <Build_package>`
 page for more info.
 
 The :doc:`atom_style <atom_style>`, used must contain the charge
-property, for example, the style could be *charge* or *full*. Only
-usable for 3D simulations. Atoms specified as free ions cannot be part
-of rigid bodies or molecules and cannot have bonding interactions. The
-scheme is limited to integer charges, any atoms with non-integer charges
-will not be considered by the fix.
+property and have per atom type masses, for example, the style could be
+*charge* or *full*. Only usable for 3D simulations.  Atoms specified as
+free ions cannot be part of rigid bodies or molecules and cannot have
+bonding interactions.  The scheme is limited to integer charges, any
+atoms with non-integer charges will not be considered by the fix.
 
 All interaction potentials used must be continuous, otherwise the MD
 integration and the particle exchange MC moves do not correspond to the

doc/src/fix_gcmc.rst

@@ -440,8 +440,11 @@ This fix is part of the MC package.  It is only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
+This fix style requires an :doc:`atom style <atom_style>` with per atom
+type masses.
+
 Do not set "neigh_modify once yes" or else this fix will never be
-called.  Reneighboring is required.
+called.  Reneighboring is **required**.
 
 Only usable for 3D simulations.
 

doc/src/fix_nh_uef.rst

@@ -62,7 +62,7 @@ performed using the :doc:`fix deform <fix_deform>`, :doc:`fix nvt/sllod
 <fix_nvt_sllod>`, and :doc:`compute temp/deform <compute_temp_deform>`
 commands.
 
-The applied flow field is set by the *eps* keyword. The values
+The applied flow field is set by the *erate* keyword. The values
 *edot_x* and *edot_y* correspond to the strain rates in the xx and yy
 directions.  It is implicitly assumed that the flow field is
 traceless, and therefore the strain rate in the zz direction is eqal

doc/src/fix_plumed.rst

@@ -24,7 +24,7 @@ Examples
 
 .. code-block:: LAMMPS
 
-   fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
+   fix pl all plumed plumedfile plumed.dat outfile p.log
 
 Description
 """""""""""

doc/src/fix_qeq.rst

@@ -232,8 +232,6 @@ These fixes are part of the QEQ package.  They are only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-These qeq fixes are not compatible with the GPU and USER-INTEL packages.
-
 These qeq fixes will ignore electric field contributions from
 :doc:`fix efield <fix_efield>`.
 

doc/src/fix_sgcmc.rst

@@ -155,6 +155,9 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 page for more info.
 
+This fix style requires an :doc:`atom style <atom_style>` with per atom
+type masses.
+
 At present the fix provides optimized subroutines for EAM type
 potentials (see above) that calculate potential energy changes due to
 *local* atom type swaps very efficiently.  Other potentials are

doc/src/fix_widom.rst

@@ -195,8 +195,11 @@ doc page for more info.
 Do not set "neigh_modify once yes" or else this fix will never be
 called.  Reneighboring is **required**.
 
-Can be run in parallel, but aspects of the GCMC part will not scale well
-in parallel. Only usable for 3D simulations.
+This fix style requires an :doc:`atom style <atom_style>` with per atom
+type masses.
+
+Can be run in parallel, but some aspects of the insertion procedure
+will not scale well in parallel. Only usable for 3D simulations.
 
 
 Related commands

doc/src/improper_amoeba.rst

@@ -68,8 +68,8 @@ for more info.
 Related commands
 """"""""""""""""
 
-:doc:`improper_coeff <improper_coeff>`, `improper_harmonic
-:doc:<improper_harmonic>`
+:doc:`improper_coeff <improper_coeff>`,
+:doc:`improper_harmonic <improper_harmonic>`
 
 Default
 """""""

doc/src/pair_beck.rst

@@ -30,11 +30,11 @@ Description
 
 Style *beck* computes interactions based on the potential by
 :ref:`(Beck) <Beck>`, originally designed for simulation of Helium.  It
-includes truncation at a cutoff distance Rc.
+includes truncation at a cutoff distance :math:`r_c`.
 
 .. math::
 
-   E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < R_c \\
+   E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < r_c \\
 
 The following coefficients must be defined for each pair of atoms
 types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@@ -50,7 +50,7 @@ commands.
 * cutoff (distance units)
 
 The last coefficient is optional.  If not specified, the global cutoff
-:math:`R_c` is used.
+:math:`r_c` is used.
 
 ----------
 

doc/src/pair_dsmc.rst

@@ -138,8 +138,12 @@ This pair style can only be used via the *pair* keyword of the
 Restrictions
 """"""""""""
 
-This style is part of the MC package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+This pair style is part of the MC package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style requires an :doc:`atom style <atom_style>` with per
+atom type masses.
 
 Related commands
 """"""""""""""""

doc/src/pair_lj_smooth_linear.rst

@@ -31,13 +31,13 @@ Style *lj/smooth/linear* computes a truncated and force-shifted LJ
 interaction (aka Shifted Force Lennard-Jones) that combines the
 standard 12/6 Lennard-Jones function and subtracts a linear term based
 on the cutoff distance, so that both, the potential and the force, go
-continuously to zero at the cutoff Rc :ref:`(Toxvaerd) <Toxvaerd>`:
+continuously to zero at the cutoff :math:`r_c` :ref:`(Toxvaerd) <Toxvaerd>`:
 
 .. math::
 
    \phi\left(r\right) & =  4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
                        \left(\frac{\sigma}{r}\right)^6 \right] \\
-   E\left(r\right) & =  \phi\left(r\right)  - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c}       \qquad r < R_c
+   E\left(r\right) & =  \phi\left(r\right)  - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c}       \qquad r < r_c
 
 The following coefficients must be defined for each pair of atoms
 types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@@ -77,8 +77,9 @@ tail option for adding long-range tail corrections to energy and
 pressure, since the energy of the pair interaction is smoothed to 0.0
 at the cutoff.
 
-This pair style writes its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
-to be specified in an input script that reads a restart file.
+This pair style writes its information to :doc:`binary restart files <restart>`,
+so pair_style and pair_coeff commands do not need to be specified
+in an input script that reads a restart file.
 
 This pair style can only be used via the *pair* keyword of the
 :doc:`run_style respa <run_style>` command.  It does not support the

doc/src/pair_mie.rst

@@ -35,7 +35,7 @@ The *mie/cut* style computes the Mie potential, given by
    E =  C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right]
                          \qquad r < r_c
 
-Rc is the cutoff and C is a function that depends on the repulsive and
+:math:`r_c` is the cutoff and C is a function that depends on the repulsive and
 attractive exponents, given by:
 
 .. math::

doc/src/pair_morse.rst

@@ -53,7 +53,7 @@ Style *morse* computes pairwise interactions with the formula
    E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
        \qquad r < r_c
 
-Rc is the cutoff.
+:math:`r_c` is the cutoff.
 
 The following coefficients must be defined for each pair of atoms
 types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@@ -78,7 +78,7 @@ so that both, potential energy and force, go to zero at the cut-off:
 .. math::
 
    \phi\left(r\right) & =  D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c \\
-   E\left(r\right) & =  \phi\left(r\right)  - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c}       \qquad r < R_c
+   E\left(r\right) & =  \phi\left(r\right)  - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c}       \qquad r < r_c
 
 The syntax of the pair_style and pair_coeff commands are the same for
 the *morse* and *morse/smooth/linear* styles.

doc/src/pair_soft.rst

@@ -44,8 +44,9 @@ It is useful for pushing apart overlapping atoms, since it does not
 blow up as r goes to 0.  A is a prefactor that can be made to vary in
 time from the start to the end of the run (see discussion below),
 e.g. to start with a very soft potential and slowly harden the
-interactions over time.  Rc is the cutoff.  See the :doc:`fix nve/limit <fix_nve_limit>` command for another way to push apart
-overlapping atoms.
+interactions over time.  :math:`r_c` is the cutoff.
+See the :doc:`fix nve/limit <fix_nve_limit>` command for another way
+to push apart overlapping atoms.
 
 The following coefficients must be defined for each pair of atom types
 via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,

doc/src/pair_spica.rst

@@ -81,7 +81,7 @@ given by
 
 as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
 :ref:`(Shinoda) <Shinoda3>`, :ref:`(DeVane) <DeVane>`, :ref:`(Seo) <Seo>`, and :ref:`(Miyazaki) <Miyazaki>`.
-Rc is the cutoff.
+:math:`r_c` is the cutoff.
 Summary information on these force fields can be found at https://www.spica-ff.org
 
 Style *lj/spica/coul/long* computes the adds Coulombic interactions

doc/utils/requirements.txt

@@ -1,4 +1,4 @@
-Sphinx >= 5.3.0, <7.2.0
+Sphinx >= 5.3.0, <7.5
 sphinxcontrib-spelling
 sphinxcontrib-jquery
 git+https://github.com/akohlmey/sphinx-fortran@parallel-read

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -76,12 +76,12 @@ class LAMMPSLexer(RegexLexer):
             include('conditionals'),
             include('keywords'),
             (r'#.*?\n', Comment),
-            ('"', String, 'string'),
-            ('\'', String, 'single_quote_string'),
+            (r'"', String, 'string'),
+            (r'\'', String, 'single_quote_string'),
             (r'[0-9]+:[0-9]+(:[0-9]+)?', Number),
             (r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number),
-            ('\$?\(', Name.Variable, 'expression'),
-            ('\$\{', Name.Variable, 'variable'),
+            (r'\$?\(', Name.Variable, 'expression'),
+            (r'\$\{', Name.Variable, 'variable'),
             (r'[\w_\.\[\]]+', Name),
             (r'\$[\w_]+', Name.Variable),
             (r'\s+', Whitespace),
@@ -97,21 +97,21 @@ class LAMMPSLexer(RegexLexer):
         ]
         ,
         'variable' : [
-            ('[^\}]+', Name.Variable),
-            ('\}', Name.Variable, '#pop'),
+            (r'[^\}]+', Name.Variable),
+            (r'\}', Name.Variable, '#pop'),
         ],
         'string' : [
-            ('[^"]+', String),
-            ('"', String, '#pop'),
+            (r'[^"]+', String),
+            (r'"', String, '#pop'),
         ],
         'single_quote_string' : [
-            ('[^\']+', String),
-            ('\'', String, '#pop'),
+            (r'[^\']+', String),
+            (r'\'', String, '#pop'),
         ],
         'expression' : [
-            ('[^\(\)]+', Name.Variable),
-            ('\(', Name.Variable, 'expression'),
-            ('\)', Name.Variable, '#pop'),
+            (r'[^\(\)]+', Name.Variable),
+            (r'\(', Name.Variable, 'expression'),
+            (r'\)', Name.Variable, '#pop'),
         ],
         'modify_cmd' : [
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),

examples/ASPHERE/tri/in.tri.srd

@@ -2,7 +2,7 @@
 
 units		lj
 atom_style	tri
-atom_modify	first big
+atom_modify	first big map yes
 
 read_data	data.tri.srd
 
@@ -52,12 +52,12 @@ pair_coeff	1 2 0.0 1.0 0.0
 
 timestep	0.001
 
-fix		1 big rigid molecule #langevin 1.0 1.0 0.1 12398 
-fix	        2 small srd 20 big 1.0 0.25 49894 &
+fix		1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398 
+fix	        2 small srd 20 big 1.0 1.0 49894 &
 		search 0.2 cubic warn 0.0001 shift yes 49829 &
-		overlap yes collision noslip
+		overlap yes collision noslip inside ignore
 
-fix		3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
+fix		3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
 
 # diagnostics
 
@@ -73,8 +73,8 @@ compute		2 all ke
 compute		3 all pe
 variable	toteng equal (c_1+c_2+c_3)/atoms
 
-thermo		1000
-thermo_style	custom step f_1 c_tsmall f_2[9] temp press
+thermo		100
+thermo_style	custom step f_1 c_tsmall temp press f_2[9] f_2[4] 
 thermo_modify	temp tbig
 
 compute		10 all property/atom corner1x corner1y corner1z &
@@ -93,9 +93,9 @@ unfix		3
 
 change_box      all triclinic
 
-fix	        2 small srd 20 big 1.0 0.25 49894 &
+fix	        2 small srd 20 big 1.0 1.0 49894 &
 		search 0.2 cubic warn 0.0001 shift yes 49829 &
-		overlap yes collision noslip tstat yes
+		overlap yes collision noslip tstat yes inside ignore
 
 #dump		1 all custom 500 dump2.atom.srd id type x y z ix iy iz
 #dump		2 all custom 500 dump2.tri.srd id type &

examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8

@@ -0,0 +1,812 @@
+LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-114-gdad8081d55-modified)
+WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:537)
+# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
+
+units		lj
+atom_style	tri
+atom_modify	first big map yes
+
+read_data	data.tri.srd
+Reading data file ...
+  orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
+  2 by 2 by 2 MPI processor grid
+  reading atoms ...
+  1500 atoms
+  1500 triangles
+  read_data CPU = 0.007 seconds
+
+# add small particles as hi density lattice
+
+lattice		sc 0.4
+Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
+region		box block INF INF INF INF INF INF
+lattice		sc 20.0
+Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315
+create_atoms	2 region box
+Created 91125 atoms
+  using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405)
+  create_atoms CPU = 0.002 seconds
+
+group		big type 1
+1500 atoms in group big
+group		small type 2
+91125 atoms in group small
+set		group small mass 0.01
+Setting atom values ...
+  91125 settings made for mass
+
+# delete overlaps
+# must set 1-2 cutoff to non-zero value
+
+pair_style	lj/cut 1.5
+pair_coeff	1 1 1.0 1.0
+pair_coeff	2 2 0.0 1.0 0.0
+pair_coeff	1 2 0.0 1.0
+
+delete_atoms	overlap 1.5 small big
+System init for delete_atoms ...
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.8
+  ghost atom cutoff = 1.8
+  binsize = 0.9, bins = 19 19 19
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) command delete_atoms, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:312)
+Deleted 76354 atoms, new total = 16271
+
+# SRD run
+
+reset_timestep	0
+
+velocity	small create 1.44 87287 loop geom
+
+neighbor	0.3 multi
+neigh_modify	delay 0 every 1 check yes
+neigh_modify	exclude molecule/intra big include big
+
+comm_modify	mode multi group big vel yes
+neigh_modify	include big
+
+# no pairwise interactions with small particles
+
+pair_style	tri/lj 3.5
+pair_coeff	1 1 0.1 1.0
+pair_coeff	2 2 0.0 1.0 0.0
+pair_coeff	1 2 0.0 1.0 0.0
+
+# use fix SRD to push small particles out from inside big ones
+# if comment out, big particles won't see SRD particles
+
+timestep	0.001
+
+fix		1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398
+  create bodies CPU = 0.000 seconds
+  125 rigid bodies with 1500 atoms
+  1.8601881 = max distance from body owner to body atom
+fix	        2 small srd 20 big 1.0 1.0 49894 		search 0.2 cubic warn 0.0001 shift yes 49829 		overlap yes collision noslip inside ignore
+
+fix		3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8
+
+# diagnostics
+
+compute		tsmall small temp/deform
+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
+variable	toteng equal (c_1+c_2+c_3)/atoms
+
+thermo		100
+thermo_style	custom step f_1 c_tsmall temp press f_2[9] f_2[4]
+thermo_modify	temp tbig
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:527)
+
+compute		10 all property/atom corner1x corner1y corner1z 		corner2x corner2y corner2z corner3x corner3y corner3z
+
+#dump		1 all custom 500 dump1.atom.srd id type x y z ix iy iz
+#dump		2 all custom 500 dump1.tri.srd id type #		c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #		c_10[7] c_10[8] c_10[9]
+
+run		10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2
+
+@Article{Intveld08,
+ author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
+ title =   {Accurate and Efficient Methods for Modeling Colloidal
+            Mixtures in an Explicit Solvent using Molecular Dynamics},
+ journal = {Comput.\ Phys.\ Commut.},
+ year =    2008,
+ volume =  179,
+ pages =   {320--329}
+}
+
+@article{Shire2020,
+ author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
+ title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
+          Detection Applied to Investigate the Quasi-Static Limit},
+ journal = {Computational Particle Mechanics},
+ year = {2020}
+@article{Monti2022,
+ author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
+           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
+           and Lechman, Jeremy B.},
+ title = {Large-scale frictionless jamming with power-law particle 
+          size distributions},
+ journal = {Phys. Rev. E},
+ volume = {106}
+ issue = {3}
+ year = {2022}
+}
+
+- fix srd command: doi:10.1063/1.3419070
+
+@Article{Petersen10,
+ author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and
+ G. S. Grest and in 't Veld, P. J. and P. R. Schunk},
+ title =   {Mesoscale Hydrodynamics via Stochastic Rotation
+    Dynamics: Comparison with {L}ennard-{J}ones Fluid},
+ journal = {J.~Chem.\ Phys.},
+ year =    2010,
+ volume =  132,
+ pages =   174106
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:71)
+WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:405)
+SRD info:
+  SRD/big particles = 14771 1500
+  big particle diameter max/min = 2.9202881 0.87320391
+  SRD temperature & lamda = 1 0.2
+  SRD max distance & max velocity = 0.8 40
+  SRD grid counts: 17 17 17
+  SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829
+  SRD per actual grid cell = -3.9971745
+  SRD viscosity = -34.162587
+  big/SRD mass density ratio = -3.3753691
+WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
+WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
+WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
+  # of rescaled SRD velocities = 0
+  ave/max small velocity = 19.970837 35.150443
+  ave/max big velocity = 0 0
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.8
+  ghost atom cutoff = 3.8
+  binsize = 16.874681, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair tri/lj, perpetual
+      attributes: half, newton on
+      pair build: half/multi/newton
+      stencil: half/multi/3d
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 125.9 | 126.4 | 126.7 Mbytes
+   Step          f_1          c_tsmall         Temp          Press          f_2[9]         f_2[4]    
+         0   0              1.4401779      0             -0.15917996     0              0            
+       100   0.36662911     1.1475389      0.24585067     1.0290503      1.1382325      18           
+       200   0.73133134     1.0558153      0.49986673     0.73932383     1.049638       34           
+       300   1.1229361      1.0218621      0.82641583     0.7589689      1.0205369      40           
+       400   1.5826262      0.99541508     1.2201293      0.69171726     0.99190857     52           
+       500   1.8834563      0.99351667     1.4778822      1.0147794      1.0005581      63           
+       600   2.4225372      0.98954834     1.8740966      1.1362893      0.99760042     61           
+       700   3.0172772      0.99153625     2.3351502      1.3284877      0.98731355     39           
+       800   3.5307913      1.0012521      2.6477224      1.1404922      0.9846605      52           
+       900   3.757064       0.99743944     2.7220653      1.4078087      0.97538456     55           
+      1000   4.3165268      1.002214       3.055501       1.2252972      0.99123745     63           
+      1100   4.2796945      1.0075233      3.1022956      1.1893685      1.0139864      69           
+      1200   4.3719315      1.0037271      3.0054509      1.3886162      1.002661       64           
+      1300   4.5628012      0.99368316     3.2690604      1.3621012      0.9810568      56           
+      1400   4.6954389      0.99365088     3.1940001      1.8485712      0.99571089     71           
+      1500   5.0270163      0.99455258     3.4120396      1.5992539      0.98294263     77           
+      1600   5.5897797      1.0021621      3.647347       1.7796904      0.98967622     66           
+      1700   5.5330194      1.0130853      3.6407996      1.8005429      1.0068955      62           
+      1800   5.3606928      1.0090284      3.5863618      1.3308757      1.0214092      59           
+      1900   5.6086195      1.0071865      3.7427101      1.5296314      0.99886937     55           
+      2000   5.3726474      1.0064207      3.603621       1.9473142      0.99999816     54           
+      2100   5.836183       1.0124553      3.7321841      1.7889397      1.0188986      59           
+      2200   5.5090061      1.0113832      3.5884963      1.6617781      1.0071583      59           
+      2300   5.4011211      1.0095947      3.520406       1.8937582      0.99689983     61           
+      2400   5.2219281      1.0053246      3.3699458      1.7231672      0.99899754     59           
+      2500   5.7695275      1.0141459      3.6211469      1.7767598      1.0143133      65           
+      2600   5.4206253      1.0182828      3.521774       2.0800518      1.0081603      70           
+      2700   5.1401099      1.0085209      3.4200563      2.4019836      1.0107652      59           
+      2800   6.5420721      1.0159876      4.1996904      1.863842       1.0160738      61           
+      2900   5.9082962      1.0106921      3.7223419      2.0586998      1.0073885      67           
+      3000   5.6556123      1.0099021      3.6768976      1.921987       1.0068962      76           
+      3100   5.2913762      1.0008567      3.4103831      1.9831969      0.99187526     80           
+      3200   5.1032361      0.99756662     3.1967156      2.2448433      0.99743574     93           
+      3300   5.2622386      1.0024934      3.3325614      2.0078097      1.0047789      86           
+      3400   5.1247527      0.99810102     3.1363556      1.8907269      0.98936508     82           
+      3500   4.9424333      1.0009344      3.2153968      1.9002728      0.99161849     71           
+      3600   5.1243735      1.0037377      3.3117313      2.1267438      1.0078943      65           
+      3700   5.5045819      1.0006119      3.5686193      2.3466538      0.99876164     68           
+      3800   5.5355384      1.0022639      3.6701457      2.0383269      1.0008683      76           
+      3900   6.4915796      1.0137733      4.3225864      2.6996933      1.0064787      79           
+      4000   6.6631737      1.0236248      4.3057163      2.6352666      1.0255232      75           
+      4100   6.2999507      1.0263876      4.0101385      2.5479077      1.0168303      79           
+      4200   6.7902489      1.0247392      4.4616158      2.4926177      1.0191403      91           
+      4300   6.505908       1.0182073      4.0675428      2.168754       1.0177101      74           
+      4400   5.9554283      1.0115938      3.5787297      2.9258144      1.0133896      72           
+      4500   6.2276609      1.0202416      3.8211204      2.5308249      1.0174385      74           
+      4600   6.0485727      1.0195757      3.8217434      2.6421797      1.0201441      78           
+      4700   6.511063       1.0220764      3.933486       2.8591093      1.0147269      83           
+      4800   6.9478172      1.0106414      4.345402       3.3257663      1.00469        85           
+      4900   6.7547045      1.0211842      4.1874576      3.6503845      1.022873       94           
+      5000   7.2603949      1.0234313      4.5393985      3.4667806      1.0222306      105          
+      5100   7.1899652      1.0256566      4.5421834      3.8137207      1.0317242      99           
+      5200   7.1960739      1.026746       4.4288606      3.5523675      1.0242269      97           
+      5300   7.1294458      1.017883       4.5799808      3.3917274      1.0145317      99           
+      5400   6.2810892      1.0291953      4.0109229      2.8604571      1.0289438      97           
+      5500   6.15246        1.0288734      3.8714587      3.2760394      1.0210757      89           
+      5600   6.5860526      1.0192882      4.0272883      3.3124298      1.0096258      93           
+      5700   7.0296116      1.0097293      4.2652722      3.6049788      1.012463       82           
+      5800   6.8372302      1.0140065      4.2205065      4.3686183      1.0088542      93           
+      5900   7.8887098      1.0090612      4.9724078      4.457317       1.0045137      92           
+      6000   10.120663      1.0312443      6.3025192      4.72018        1.0374722      91           
+      6100   9.1318265      1.0304199      5.7084296      4.244548       1.0259056      97           
+      6200   8.9758903      1.0295285      5.1842704      4.870955       1.0178851      95           
+      6300   9.0088218      1.022484       5.3742805      5.1554352      1.0138365      101          
+      6400   10.470322      1.0287848      6.4602103      4.5461489      1.0335978      105          
+      6500   11.100779      1.0347405      6.9630121      4.9840664      1.0339044      99           
+      6600   10.139333      1.0476079      6.4284839      4.5523893      1.0433517      104          
+      6700   8.9706766      1.0386262      5.8387485      4.247024       1.0408151      101          
+      6800   7.7799532      1.0362651      4.9946283      4.6093924      1.0274763      102          
+      6900   8.0866551      1.0337743      4.9942769      4.1679939      1.0454805      102          
+      7000   8.0224277      1.0193598      4.9380527      3.9173115      1.0185001      109          
+      7100   7.8361001      1.0211143      4.872673       5.3471479      1.024779       110          
+      7200   7.8542147      1.0057183      4.8666653      4.668317       0.99980296     122          
+      7300   7.9313852      1.0159181      5.0062527      4.1410294      1.0195705      114          
+      7400   7.2769846      1.0155245      4.6349779      4.9138895      1.0005886      119          
+      7500   7.5974523      1.0196295      4.7918247      4.2525935      1.0211412      124          
+      7600   6.7835063      1.0203187      4.2674694      4.9251624      1.0218296      113          
+      7700   6.4039017      1.0119494      4.1086667      5.5240525      1.0078246      118          
+      7800   7.0715134      1.0149015      4.2450776      4.8796778      1.0164737      125          
+      7900   6.3626535      1.02294        4.202778       4.482164       1.0235878      136          
+      8000   6.2423869      1.0212553      4.0460303      5.2753307      1.0124884      132          
+      8100   6.550891       1.0223318      4.2993545      5.2634985      1.0163244      143          
+      8200   6.9122202      1.008347       4.3551124      5.4108909      1.0084913      142          
+      8300   6.9104634      1.0103936      4.4622206      5.6762373      0.99559355     143          
+      8400   6.4918879      1.0084381      4.1050732      5.8389788      1.0036021      135          
+      8500   7.4377218      1.0216662      4.5229841      5.5431311      1.0260799      123          
+      8600   7.572198       1.0228381      4.9058913      7.1028185      1.0015164      116          
+      8700   8.204675       1.03457        5.2231696      6.4790244      1.0214635      132          
+      8800   8.3118914      1.0381333      5.1795799      6.7437722      1.0290086      132          
+      8900   8.2559198      1.0268665      5.218352       7.2191395      1.019804       138          
+      9000   8.0403128      1.0339414      4.9310394      6.4942331      1.041527       156          
+      9100   7.1773079      1.0397062      4.4993688      7.0272109      1.0388012      167          
+      9200   7.1793935      1.0373589      4.3481663      7.4894459      1.0078785      157          
+      9300   8.3705146      1.0248112      5.1036971      8.2173072      1.010168       156          
+      9400   9.4935002      1.0252907      5.7846951      9.7466018      1.028941       170          
+      9500   9.5208037      1.0371093      5.9635099      7.6444933      1.022673       165          
+      9600   8.9992217      1.0292895      5.6224192      8.8071452      1.0101362      169          
+      9700   8.682661       1.0422224      5.3997636      8.6827834      1.0337928      149          
+      9800   7.6191562      1.0350948      4.7198842      8.6125595      1.0300395      151          
+      9900   8.0910913      1.0319432      4.8843183      7.9013334      1.0272495      167          
+     10000   7.4438347      1.0186098      4.7184985      8.999795       0.99762661     177          
+Loop time of 162.325 on 8 procs for 10000 steps with 16271 atoms
+
+Performance: 5322.658 tau/day, 61.605 timesteps/s, 1.002 Matom-step/s
+99.3% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 33.647     | 64.106     | 79.639     | 169.5 | 39.49
+Neigh   | 0.30808    | 0.44033    | 0.50863    |   9.8 |  0.27
+Comm    | 26.611     | 43.438     | 74.998     | 215.7 | 26.76
+Output  | 0.0072573  | 0.0087791  | 0.0097993  |   0.9 |  0.01
+Modify  | 53.171     | 54.121     | 55.362     |  12.3 | 33.34
+Other   |            | 0.2104     |            |       |  0.13
+
+Nlocal:        2033.88 ave        2601 max        1413 min
+Histogram: 1 2 0 0 0 0 2 1 1 1
+Nghost:        1647.25 ave        1714 max        1617 min
+Histogram: 4 0 1 0 0 1 1 0 0 1
+Neighs:        12482.8 ave       17009 max        8679 min
+Histogram: 1 1 1 0 1 1 2 0 0 1
+
+Total # of neighbors = 99862
+Ave neighs/atom = 6.1374224
+Neighbor list builds = 562
+Dangerous builds = 0
+
+#undump          1
+#undump          2
+unfix		3
+
+change_box      all triclinic
+Changing box ...
+  triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0)
+
+fix	        2 small srd 20 big 1.0 1.0 49894 		search 0.2 cubic warn 0.0001 shift yes 49829 		overlap yes collision noslip tstat yes inside ignore
+
+#dump		1 all custom 500 dump2.atom.srd id type x y z ix iy iz
+#dump		2 all custom 500 dump2.tri.srd id type #		c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #		c_10[7] c_10[8] c_10[9]
+
+fix		3 all deform 1 xy erate 0.05 units box remap v
+
+run		40000
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+SRD info:
+  SRD/big particles = 14771 1500
+  big particle diameter max/min = 2.9202881 0.87320391
+  SRD temperature & lamda = 1 0.2
+  SRD max distance & max velocity = 0.8 40
+  SRD grid counts: 13 13 13
+  SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419
+  SRD per actual grid cell = -2.775698
+  SRD viscosity = -12.180602
+  big/SRD mass density ratio = -5.5653033
+WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2805)
+WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826)
+WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828)
+  # of rescaled SRD velocities = 1
+  ave/max small velocity = 16.14994 40
+  ave/max big velocity = 1.6952661 5.2200074
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.8
+  ghost atom cutoff = 3.8
+  binsize = 13.499745, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair tri/lj, perpetual
+      attributes: half, newton on
+      pair build: half/multi/newton/tri
+      stencil: half/multi/3d/tri
+      bin: multi
+Per MPI rank memory allocation (min/avg/max) = 106.9 | 107.5 | 107.7 Mbytes
+   Step          f_1          c_tsmall         Temp          Press          f_2[9]         f_2[4]    
+     10000   7.4438347      1.0189789      4.7184481      7.9505614      0              0            
+     10100   7.0770142      1.0021471      4.4491455      6.606701       1              141          
+     10200   6.7628072      1.002308       4.152988       8.5190386      1              125          
+     10300   6.5333319      1.0007472      4.1295404      8.2341747      1              109          
+     10400   6.3237519      1.0024029      3.8636034      9.4058128      1              95           
+     10500   6.6411054      1.0026261      4.2975997      7.6122304      1              82           
+     10600   5.7470775      1.0004827      3.7959947      7.3091777      1              67           
+     10700   5.9744919      1.0014977      3.6885649      7.5517197      1              59           
+     10800   5.8028731      1.0029627      3.7553961      6.2787087      1              49           
+     10900   5.3755286      1.0019318      3.5334739      7.1318348      1              41           
+     11000   5.3915962      1.001463       3.483172       7.6362496      1              40           
+     11100   5.8683672      1.0022459      3.6697589      6.9711866      1              33           
+     11200   5.4351801      0.99956703     3.4548447      7.0745257      1              29           
+     11300   4.9397513      1.0008287      3.1990325      6.0917337      1              27           
+     11400   4.9159845      1.0017862      3.0005677      7.653817       1              26           
+     11500   4.9243103      1.0013135      3.1799841      7.744414       1              23           
+     11600   5.2036357      1.0017984      3.2963749      7.540477       1              22           
+     11700   4.8991892      1.0020757      3.1773032      8.7218471      1              27           
+     11800   4.9489399      1.003438       3.1679764      7.1605486      1              26           
+     11900   4.82398        1.0019946      3.1939566      7.1397869      1              21           
+     12000   4.3531411      1.000532       2.8321416      7.6672501      1              23           
+     12100   4.8226081      1.0018898      3.0382137      6.8343432      1              25           
+     12200   4.7456418      1.0032116      2.9186038      7.3067818      1              20           
+     12300   4.4280468      1.0005857      2.734593       8.0365684      1              22           
+     12400   4.7311239      1.0000982      2.8898839      7.9231831      1              22           
+     12500   4.7261054      1.0016127      2.9090517      7.6085854      1              24           
+     12600   4.7719025      1.0016702      2.9736761      7.6101796      1              26           
+     12700   4.386248       1.001394       2.8508378      6.4765102      1              28           
+     12800   4.3313538      1.0019737      2.6258221      6.3164681      1              19           
+     12900   4.2219861      1.0007469      2.5345699      7.0901077      1              22           
+     13000   4.1775643      1.0011891      2.5807017      7.3579938      1              25           
+     13100   4.3060837      1.0008671      2.5974066      6.9301328      1              22           
+     13200   4.3529062      0.99996469     2.7571632      6.7806287      1              21           
+     13300   4.2178709      1.000673       2.7819091      7.6449064      1              18           
+     13400   4.2714169      1.0021294      2.7280794      8.0986691      1              18           
+     13500   4.3430969      1.0037732      2.6768429      8.1267941      1              18           
+     13600   4.3664374      1.0016083      2.6470186      6.2797727      1              20           
+     13700   4.4904769      1.0008993      2.7885718      7.7410193      1              22           
+     13800   4.2966193      1.001532       2.73862        7.9651302      1              21           
+     13900   4.4003185      1.0009984      2.7484129      8.7160439      1              24           
+     14000   4.5948292      1.0011748      2.9051777      7.842121       1              22           
+     14100   4.6901122      1.0001265      2.9404111      8.9953816      1              20           
+     14200   4.8517518      0.99998743     2.9647625      6.6450509      1              22           
+     14300   4.889628       1.0018051      3.0891097      7.2671824      1              20           
+     14400   4.578862       1.0010629      2.8239776      6.1317183      1              23           
+     14500   4.0865406      1.0013917      2.5119661      6.864665       1              19           
+     14600   4.30688        1.0009041      2.6817814      6.9007433      1              18           
+     14700   4.1295726      1.002342       2.6032093      7.1441648      1              15           
+     14800   4.2176021      1.0015157      2.7332903      6.8394683      1              16           
+     14900   4.2012664      0.99986345     2.6498409      7.4568241      1              15           
+     15000   4.6124269      1.0014751      2.9584178      7.9341875      1              16           
+     15100   4.947327       1.0010615      3.0784409      7.6241305      1              21           
+     15200   5.253281       1.002095       3.3093754      8.1872718      1              25           
+     15300   5.2642369      1.0017799      3.1511136      7.4668389      1              25           
+     15400   5.1967916      1.0029407      3.247548       8.0840111      1              23           
+     15500   5.7465412      1.001896       3.468834       9.5990471      1              15           
+     15600   6.2245772      1.0021086      3.6127689      7.8242016      1              19           
+     15700   5.5626191      0.99984979     3.3893723      7.8124588      1              20           
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+     39200   8.2406701      1.002062       5.0117425      8.778159       1              24           
+     39300   8.3134114      1.0008218      5.0067136      7.9871787      1              22           
+     39400   7.4307571      1.0014205      4.5858283      8.8596594      1              25           
+     39500   7.1146821      1.0016367      4.5021057      7.4890018      1              22           
+     39600   8.0048978      0.99992107     4.9235747      7.8770845      1              24           
+     39700   8.070853       1.0029024      5.0842957      9.020664       1              21           
+     39800   7.6939108      1.0012543      4.8986595      8.3306129      1              20           
+     39900   7.2915444      1.00267        4.5038291      8.3844384      1              20           
+     40000   7.3023994      1.0020441      4.4960911      8.1023709      1              18           
+     40100   7.0221648      1.0033695      4.6374149      8.3756822      1              24           
+     40200   7.4114756      1.0019246      4.6733475      7.6547258      1              23           
+     40300   7.5323108      1.0005472      4.8284493      8.2820085      1              26           
+     40400   7.3890772      1.0010491      4.6599273      8.9203575      1              19           
+     40500   7.5786764      1.0016114      4.8166885      8.6760107      1              25           
+     40600   8.165763       1.0006961      5.1488995      7.9321524      1              22           
+     40700   8.1277597      0.99933464     5.0441567      10.069551      1              16           
+     40800   8.1050904      1.0024705      5.4408599      8.3244459      1              21           
+     40900   7.805318       1.0022992      4.9965408      9.7193723      1              21           
+     41000   9.0130932      1.0006842      5.7931112      6.1646073      1              20           
+     41100   8.0387975      1.0017359      5.3355655      9.6123191      1              21           
+     41200   8.4484723      1.0014151      5.4461007      8.5146504      1              27           
+     41300   8.6181909      1.0007562      5.2963876      9.1122306      1              30           
+     41400   9.6762899      1.0010931      5.950456       9.2851025      1              25           
+     41500   9.9414226      1.0016186      6.1433384      10.741453      1              24           
+     41600   9.3348435      1.0003483      5.9291766      11.460717      1              20           
+     41700   9.6125587      1.0013661      5.8530052      9.2105722      1              19           
+     41800   11.383056      1.0032034      7.1988684      10.312945      1              22           
+     41900   10.884524      1.0034888      6.9126707      10.775457      1              20           
+     42000   11.071218      1.0026753      7.0004189      10.740627      1              20           
+     42100   11.054304      1.0008347      6.9602414      8.9885498      1              22           
+     42200   22.478691      1.0020466      14.997099      12.72513       1              19           
+     42300   18.303508      1.0027626      11.336523      12.638769      1              18           
+     42400   15.998712      1.0030312      9.4092725      11.070501      1              24           
+     42500   15.034488      1.0024472      9.3543751      11.48052       1              28           
+     42600   14.538257      1.0033153      9.2523745      10.909576      1              27           
+     42700   13.986613      1.001458       8.5544184      10.765136      1              29           
+     42800   13.240256      1.0027899      8.2014429      10.506497      1              32           
+     42900   12.784336      1.0001406      8.0823431      12.258209      1              33           
+     43000   13.374145      1.0012996      8.4207155      10.32817       1              31           
+     43100   13.142334      1.0022503      8.5908808      10.152205      1              32           
+     43200   12.669284      1.0018944      7.8511966      10.580104      1              32           
+     43300   13.155032      1.001144       8.0337768      10.6652        1              39           
+     43400   12.155928      1.0019472      7.5886584      11.234772      1              35           
+     43500   12.385603      1.0007639      7.8865245      9.3868914      1              32           
+     43600   12.236179      1.0027456      7.7521353      10.456701      1              42           
+     43700   11.49535       1.0008758      7.3633144      8.8490079      1              40           
+     43800   11.469157      1.0015845      7.0035577      10.594522      1              41           
+     43900   11.228266      1.0013014      7.0137223      8.0653711      1              38           
+     44000   10.56742       1.0016631      6.6908938      8.1094154      1              35           
+     44100   9.8964699      1.0008351      6.3550438      8.6578181      1              36           
+     44200   9.041539       1.0019541      5.6721401      8.6518043      1              38           
+     44300   9.0767434      1.0034191      5.7446596      8.3838528      1              38           
+     44400   9.2299608      1.0019526      5.7117964      8.3106491      1              37           
+     44500   9.458981       1.0030409      5.7612138      7.7679755      1              37           
+     44600   8.9611997      1.0014848      5.6490756      6.9224078      1              37           
+     44700   8.0853184      1.0018894      5.2288749      8.0910912      1              32           
+     44800   7.9999755      1.0015853      4.8088312      7.1854304      1              30           
+     44900   7.6598023      1.0009751      4.6690664      7.1999858      1              28           
+     45000   7.4939315      1.0010307      4.8119666      7.9615769      1              26           
+     45100   7.4690079      0.99913423     4.9704428      7.6026835      1              32           
+     45200   7.7001199      1.001626       4.9315953      7.4926686      1              25           
+     45300   7.8794405      1.0011648      4.8624857      8.0804457      1              26           
+     45400   7.493909       1.0016257      4.7631808      8.0330626      1              26           
+     45500   7.5963141      1.0005825      4.7220659      7.0971298      1              23           
+     45600   7.9028612      1.0017008      4.9561022      8.440428       1              23           
+     45700   7.2285584      1.0006033      4.5521456      9.385579       1              23           
+     45800   7.5687284      1.0024318      4.8557498      8.3052658      1              23           
+     45900   7.8938604      1.0013937      5.1393944      5.5323667      1              26           
+     46000   8.318466       1.0020803      5.4761811      8.2227801      1              25           
+     46100   7.9169512      1.0024598      5.0406355      8.64365        1              27           
+     46200   7.5535458      1.0016318      4.8010133      9.370726       1              26           
+     46300   7.8926896      1.0001525      5.18463        7.9830196      1              27           
+     46400   7.487145       1.002671       4.7718312      8.300134       1              29           
+     46500   7.3564658      1.0006114      4.6762189      7.34947        1              26           
+     46600   7.2261291      1.0005569      4.4751221      6.5847138      1              27           
+     46700   7.2943203      1.0020164      4.3335327      7.7296507      1              25           
+     46800   8.5849411      1.0014634      5.4501531      9.0933014      1              25           
+     46900   10.176752      1.0023799      6.0456779      9.4050423      1              16           
+     47000   9.1913098      1.0029076      5.7577256      9.1826215      1              22           
+     47100   9.5479771      1.0022102      6.1100973      8.9440056      1              28           
+     47200   9.9944172      1.0004924      6.3649417      9.1507264      1              25           
+     47300   9.3543283      1.0013246      6.0873147      10.41657       1              24           
+     47400   8.594101       1.0020068      5.6864295      9.2388304      1              24           
+     47500   9.3191964      1.002411       6.0537511      9.3506828      1              23           
+     47600   8.1615734      1.001364       5.3757905      10.303962      1              30           
+     47700   8.3615046      1.0003075      5.2727936      9.3162209      1              32           
+     47800   8.3566467      1.0026031      5.4379524      7.7644422      1              33           
+     47900   8.4062556      1.0006471      5.3098736      8.0181121      1              33           
+     48000   8.2233307      1.0012304      4.9650027      9.2644288      1              34           
+     48100   8.4495256      1.000088       4.9940422      10.01023       1              27           
+     48200   8.8068097      1.0014275      5.4732649      8.410093       1              31           
+     48300   8.0008187      1.0017459      4.7732764      9.25726        1              27           
+     48400   7.7242529      1.0026909      4.9084505      8.7147295      1              30           
+     48500   8.3752816      1.001333       5.1071228      8.2267308      1              32           
+     48600   9.0777805      1.0019328      5.7331841      9.6679383      1              29           
+     48700   9.3623061      1.0001767      5.7117062      8.396895       1              25           
+     48800   8.1186637      1.0013185      5.2697427      8.6058372      1              27           
+     48900   7.3685497      1.0007173      4.6097553      7.8047228      1              24           
+     49000   7.1661421      1.0023152      4.5389038      8.8759552      1              22           
+     49100   6.9857144      1.0016394      4.6489319      8.2022359      1              24           
+     49200   6.7160336      1.0018413      4.2488082      8.3393245      1              25           
+     49300   7.9703755      1.0010628      5.2328567      7.968278       1              28           
+     49400   8.2628465      1.0010877      5.2292977      8.0196533      1              27           
+     49500   8.1436558      1.0015175      5.0344712      8.0712037      1              30           
+     49600   8.5182498      1.0021589      5.1029028      8.6869789      1              28           
+     49700   8.3604444      1.0015016      5.0333696      9.4861656      1              25           
+     49800   7.336335       1.0020055      4.6365173      8.7210022      1              30           
+     49900   7.432996       1.0016415      4.7090587      8.7033033      1              29           
+     50000   7.4937053      1.001014       4.7212573      9.0890363      1              29           
+Loop time of 999.576 on 8 procs for 40000 steps with 16271 atoms
+
+Performance: 3457.466 tau/day, 40.017 timesteps/s, 651.116 katom-step/s
+99.3% CPU use with 8 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 293.48     | 403.7      | 545.29     | 357.5 | 40.39
+Neigh   | 2.4176     | 3.2721     | 3.8303     |  25.2 |  0.33
+Comm    | 163.58     | 305.88     | 419.83     | 416.7 | 30.60
+Output  | 0.032483   | 0.034794   | 0.040514   |   1.2 |  0.00
+Modify  | 281.15     | 285.67     | 293.8      |  24.3 | 28.58
+Other   |            | 1.023      |            |       |  0.10
+
+Nlocal:        2033.88 ave        2657 max        1198 min
+Histogram: 2 0 0 0 0 2 1 0 1 2
+Nghost:        1628.12 ave        1719 max        1569 min
+Histogram: 2 0 1 1 2 1 0 0 0 1
+Neighs:          13566 ave       18212 max        8488 min
+Histogram: 1 0 0 1 2 1 2 0 0 1
+
+Total # of neighbors = 108528
+Ave neighs/atom = 6.6700264
+Neighbor list builds = 2447
+Dangerous builds = 2
+Total wall time: 0:19:22

examples/ASPHERE/tri/log.1Feb14.tri.srd.g++.8

@@ -1,243 +0,0 @@
-LAMMPS (1 Feb 2014)
-# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
-
-units		lj
-atom_style	tri
-atom_modify	first big
-
-read_data	data.tri.srd
-  orthogonal box = (-8.43734 -8.43734 -8.43734) to (8.43734 8.43734 8.43734)
-  2 by 2 by 2 MPI processor grid
-  reading atoms ...
-  1500 atoms
-  1500 triangles
-
-# add small particles as hi density lattice
-
-lattice		sc 0.4
-Lattice spacing in x,y,z = 1.35721 1.35721 1.35721
-region		box block INF INF INF INF INF INF
-lattice		sc 20.0
-Lattice spacing in x,y,z = 0.368403 0.368403 0.368403
-create_atoms	2 region box
-Created 91125 atoms
-
-group		big type 1
-1500 atoms in group big
-group		small type 2
-91125 atoms in group small
-set		group small mass 0.01
-  91125 settings made for mass
-
-# delete overlaps
-# must set 1-2 cutoff to non-zero value
-
-pair_style	lj/cut 1.5
-pair_coeff	1 1 1.0 1.0
-pair_coeff	2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0
-
-delete_atoms	overlap 1.5 small big
-Deleted 76354 atoms, new total = 16271
-
-# SRD run
-
-reset_timestep	0
-
-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
-
-communicate	multi group big vel yes
-neigh_modify	include big
-
-# no pairwise interactions with small particles
-
-pair_style	tri/lj 3.5
-pair_coeff	1 1 0.1 1.0
-pair_coeff	2 2 0.0 1.0 0.0
-pair_coeff	1 2 0.0 1.0 0.0
-
-# use fix SRD to push small particles out from inside big ones
-# if comment out, big particles won't see SRD particles
-
-timestep	0.001
-
-fix		1 big rigid molecule #langevin 1.0 1.0 0.1 12398
-125 rigid bodies with 1500 atoms
-fix	        2 small srd 20 big 1.0 0.25 49894 		search 0.2 cubic warn 0.0001 shift yes 49829 		overlap yes collision noslip
-
-fix		3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
-
-# diagnostics
-
-compute		tsmall small temp/deform
-compute		tbig big temp
-variable	pebig equal pe*atoms/count(big)
-variable	ebig equal etotal*atoms/count(big)
-
-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 f_1 c_tsmall f_2[9] temp press
-thermo_modify	temp tbig
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
-
-compute		10 all property/atom corner1x corner1y corner1z 		corner2x corner2y corner2z corner3x corner3y corner3z
-
-#dump		1 all custom 500 dump1.atom.srd id type x y z ix iy iz
-#dump		2 all custom 500 dump1.tri.srd id type #		c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #		c_10[7] c_10[8] c_10[9]
-
-run		10000
-WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
-SRD info:
-  SRD/big particles = 14771 1500
-  big particle diameter max/min = 1.46014 0.436602
-  SRD temperature & lamda = 1 0.2
-  SRD max distance & max velocity = 0.8 40
-  SRD grid counts: 67 67 67
-  SRD grid size: request, actual (xyz) = 0.25, 0.251861 0.251861 0.251861
-  SRD per actual grid cell = 0.0647662
-  SRD viscosity = -1.09837
-  big/SRD mass density ratio = 24.668
-WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
-WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
-WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
-  # of rescaled SRD velocities = 0
-  ave/max small velocity = 19.9708 35.1504
-  ave/max big velocity = 0 0
-WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
-Memory usage per processor = 116.135 Mbytes
-Step 1 tsmall 2[9] Temp Press 
-       0            0    1.4405441            0            0  -0.15917996 
-    1000    1.0535509    1.1241378    1.1224038            0   0.15526438 
-    2000    2.4635987    1.0240667   0.94231519            0  0.011069846 
-    3000    3.1093028    1.0070585    1.0176028            0   0.34124888 
-    4000    2.9524179    1.0101774    1.0311733            0  -0.22118101 
-    5000    2.9175438    1.0109144    1.0284445            0    0.1839507 
-    6000    3.3200928   0.99108983   0.95968219            0    1.0229339 
-    7000    3.3020156   0.99661428   0.98000621            0    2.3333851 
-    8000    4.1500999   0.99129645   0.99723707            0    4.3054414 
-    9000     6.537028    1.0074533    1.0251098            0    18.782913 
-   10000    16.233245    1.0145766    1.0219787            0    147.83787 
-Loop time of 228.558 on 8 procs for 10000 steps with 16271 atoms
-
-Pair  time (%) = 145.018 (63.4492)
-Neigh time (%) = 32.6283 (14.2757)
-Comm  time (%) = 43.3283 (18.9572)
-Outpt time (%) = 0.000848889 (0.00037141)
-Other time (%) = 7.58254 (3.31755)
-
-Nlocal:    2033.88 ave 2092 max 1902 min
-Histogram: 1 0 0 0 1 1 0 1 1 3
-Nghost:    2805 ave 2855 max 2751 min
-Histogram: 1 0 2 1 0 0 0 2 1 1
-Neighs:    30026.5 ave 38700 max 24367 min
-Histogram: 1 0 2 1 3 0 0 0 0 1
-
-Total # of neighbors = 240212
-Ave neighs/atom = 14.7632
-Neighbor list builds = 501
-Dangerous builds = 0
-
-#undump          1
-#undump          2
-unfix		3
-
-change_box      all triclinic
-  triclinic box = (-5.0624 -5.0624 -5.0624) to (5.0624 5.0624 5.0624) with tilt (0 0 0)
-
-fix	        2 small srd 20 big 1.0 0.25 49894 		search 0.2 cubic warn 0.0001 shift yes 49829 		overlap yes collision noslip tstat yes
-
-#dump		1 all custom 500 dump2.atom.srd id type x y z ix iy iz
-#dump		2 all custom 500 dump2.tri.srd id type #		c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] #		c_10[7] c_10[8] c_10[9]
-
-fix		3 all deform 1 xy erate 0.05 units box remap v
-
-run		40000
-SRD info:
-  SRD/big particles = 14771 1500
-  big particle diameter max/min = 1.46014 0.436602
-  SRD temperature & lamda = 1 0.2
-  SRD max distance & max velocity = 0.8 40
-  SRD grid counts: 40 40 40
-  SRD grid size: request, actual (xyz) = 0.25, 0.25312 0.25312 0.25312
-  SRD per actual grid cell = -1.93929
-  SRD viscosity = -0.36972
-  big/SRD mass density ratio = -0.836253
-WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
-WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
-WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
-  # of rescaled SRD velocities = 1
-  ave/max small velocity = 16.0639 40
-  ave/max big velocity = 2.05735 6.73052
-Memory usage per processor = 65.2471 Mbytes
-Step 1 tsmall 2[9] Temp Press 
-   10000    16.233245    1.0144194            0            0    146.27032 
-   11000    17.301043    1.0619209            1            0    84.226323 
-   12000    13.481177     1.063945            1            0     80.42834 
-   13000    12.616615    1.0536125            1            0    68.365053 
-   14000     12.16592    1.0581344            1            0    59.709941 
-   15000    10.811557    1.0650453            1            0    59.869798 
-   16000    9.9303081    1.0641012            1            0    59.289126 
-   17000    10.452639    1.0589904            1            0    52.680235 
-   18000    9.2488947    1.0556713            1            0    51.044123 
-   19000    8.7179788    1.0566791            1            0    50.927924 
-   20000    7.8641299    1.0668891            1            0    53.961014 
-   21000    8.4333975    1.0628003            1            0    54.677068 
-   22000     8.554623    1.0591872            1            0    51.784737 
-   23000     7.895462    1.0598512            1            0     53.26885 
-   24000    7.7014869     1.055569            1            0    54.236941 
-   25000     7.508138    1.0581539            1            0    53.297709 
-   26000    8.0707381    1.0586451            1            0    51.411341 
-   27000     8.224223    1.0585509            1            0    52.775784 
-   28000    8.8720461    1.0648837            1            0    49.681447 
-   29000     8.503895    1.0538278            1            0    52.478556 
-   30000    8.2272425    1.0625583            1            0    52.795709 
-   31000    8.4626161    1.0599557            1            0    52.905343 
-   32000    7.7410527    1.0587681            1            0    57.464472 
-   33000    7.2765481    1.0677531            1            0     59.46728 
-   34000     7.036016    1.0640728            1            0    60.636828 
-   35000     8.497203    1.0577458            1            0    55.257312 
-   36000    8.9218761    1.0585038            1            0    55.668201 
-   37000    8.0469115    1.0561193            1            0    58.711565 
-   38000    8.6456966    1.0663818            1            0    53.691658 
-   39000     8.566667    1.0616928            1            0    52.866468 
-   40000    7.7081259    1.0577046            1            0    54.105829 
-   41000    7.4051952    1.0570277            1            0    56.094997 
-   42000     7.331432    1.0632261            1            0    55.661067 
-   43000    7.5587053    1.0602077            1            0     54.30762 
-   44000    7.4521497    1.0594391            1            0    52.993548 
-   45000    7.6234559    1.0641992            1            0    53.352202 
-   46000    8.0659693    1.0609367            1            0    50.302682 
-   47000    7.5227882    1.0563543            1            0     50.43551 
-   48000    8.0798684    1.0628968            1            0    48.419201 
-   49000     7.130784    1.0594143            1            0    50.656081 
-   50000    7.3219268    1.0608236            1            0    54.808358 
-Loop time of 1651.84 on 8 procs for 40000 steps with 16271 atoms
-
-Pair  time (%) = 1232.76 (74.6296)
-Neigh time (%) = 171.893 (10.4061)
-Comm  time (%) = 193.625 (11.7218)
-Outpt time (%) = 0.00338289 (0.000204795)
-Other time (%) = 53.5578 (3.24231)
-
-Nlocal:    2033.88 ave 2229 max 1953 min
-Histogram: 2 1 2 2 0 0 0 0 0 1
-Nghost:    2757.88 ave 2810 max 2692 min
-Histogram: 1 1 1 0 1 0 0 1 1 2
-Neighs:    30098.6 ave 37369 max 25592 min
-Histogram: 1 3 0 1 0 1 1 0 0 1
-
-Total # of neighbors = 240789
-Ave neighs/atom = 14.7987
-Neighbor list builds = 2007
-Dangerous builds = 0
-
-Please see the log.cite file for references relevant to this simulation
-

examples/PACKAGES/cgdna/util/generate.py

@@ -22,22 +22,26 @@
 """
 Import basic modules
 """
+
+# for python2/3 compatibility
+from __future__ import print_function
+
 import sys, os, timeit
 
 from timeit import default_timer as timer
 start_time = timer()
 """
-Try to import numpy; if failed, import a local version mynumpy 
+Try to import numpy; if failed, import a local version mynumpy
 which needs to be provided
 """
 try:
     import numpy as np
 except:
-    print >> sys.stderr, "numpy not found. Exiting."
+    print("numpy not found. Exiting.", file=sys.stderr)
     sys.exit(1)
 
 """
-Check that the required arguments (box offset and size in simulation units 
+Check that the required arguments (box offset and size in simulation units
 and the sequence file were provided
 """
 try:
@@ -45,8 +49,8 @@ try:
     box_length = float(sys.argv[2])
     infile = sys.argv[3]
 except:
-    print >> sys.stderr, "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
-	"box offset", "box length", "file with sequences")
+    print( "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
+	"box offset", "box length", "file with sequences"), file=sys.stderr)
     sys.exit(1)
 box = np.array ([box_length, box_length, box_length])
 
@@ -57,8 +61,7 @@ try:
     inp = open (infile, 'r')
     inp.close()
 except:
-    print >> sys.stderr, "Could not open file '%s' for reading. \
-					      Aborting." % infile
+    print( "Could not open file '%s' for reading. Aborting." % infile, file=sys.stderr)
     sys.exit(2)
 
 # return parts of a string
@@ -86,7 +89,7 @@ Define auxiliary variables for the construction of a helix
 # center of the double strand
 CM_CENTER_DS = POS_BASE + 0.2
 
-# ideal distance between base sites of two nucleotides 
+# ideal distance between base sites of two nucleotides
 # which are to be base paired in a duplex
 BASE_BASE = 0.3897628551303122
 
@@ -118,7 +121,7 @@ strandnum = []
 
 bonds = []
 
-""" 
+"""
 Convert local body frame to quaternion DOF
 """
 def exyz_to_quat (mya1, mya3):
@@ -135,25 +138,25 @@ def exyz_to_quat (mya1, mya3):
     # compute other components from it
 
     if q0sq >= 0.25:
-	myquat[0] = np.sqrt(q0sq)
-	myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
-	myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
-	myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
+        myquat[0] = np.sqrt(q0sq)
+        myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
+        myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
+        myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
     elif q1sq >= 0.25:
-	myquat[1] = np.sqrt(q1sq)
-	myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
-	myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
-	myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
+        myquat[1] = np.sqrt(q1sq)
+        myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
+        myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
+        myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
     elif q2sq >= 0.25:
-	myquat[2] = np.sqrt(q2sq)
-	myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
-	myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
-	myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
+        myquat[2] = np.sqrt(q2sq)
+        myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
+        myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
+        myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
     elif q3sq >= 0.25:
-	myquat[3] = np.sqrt(q3sq)
-	myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
-	myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
-	myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
+        myquat[3] = np.sqrt(q3sq)
+        myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
+        myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
+        myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
 
     norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \
 			  myquat[2]*myquat[2] + myquat[3]*myquat[3])
@@ -169,62 +172,62 @@ Adds a strand to the system by appending it to the array of previous strands
 """
 def add_strands (mynewpositions, mynewa1s, mynewa3s):
     overlap = False
-	
-    # This is a simple check for each of the particles where for previously 
-    # placed particles i we check whether it overlaps with any of the 
+
+    # This is a simple check for each of the particles where for previously
+    # placed particles i we check whether it overlaps with any of the
     # newly created particles j
 
-    print >> sys.stdout, "## Checking for overlaps"
+    print( "## Checking for overlaps", file=sys.stdout)
 
-    for i in xrange(len(positions)):
+    for i in range(len(positions)):
 
-	p = positions[i]
-	pa1 = a1s[i]
+        p = positions[i]
+        pa1 = a1s[i]
 
-	for j in xrange (len(mynewpositions)):
+        for j in range (len(mynewpositions)):
 
-	    q = mynewpositions[j]
-	    qa1 = mynewa1s[j]
+            q = mynewpositions[j]
+            qa1 = mynewa1s[j]
 
-	    # skip particles that are anyway too far away
-	    dr = p - q
-	    dr -= box * np.rint (dr / box)
-	    if np.dot(dr, dr) > RC2:
-		continue
+            # skip particles that are anyway too far away
+            dr = p - q
+            dr -= box * np.rint(dr / box)
+            if np.dot(dr, dr) > RC2:
+                continue
 
-	    # base site and backbone site of the two particles
+            # base site and backbone site of the two particles
             p_pos_back = p + pa1 * POS_BACK
             p_pos_base = p + pa1 * POS_BASE
             q_pos_back = q + qa1 * POS_BACK
             q_pos_base = q + qa1 * POS_BASE
 
-	    # check for no overlap between the two backbone sites
+            # check for no overlap between the two backbone sites
             dr = p_pos_back - q_pos_back
-            dr -= box * np.rint (dr / box)
+            dr -= box * np.rint(dr / box)
             if np.dot(dr, dr) < RC2_BACK:
                 overlap = True
 
-	    # check for no overlap between the two base sites
+            # check for no overlap between the two base sites
             dr = p_pos_base -  q_pos_base
-            dr -= box * np.rint (dr / box)
+            dr -= box * np.rint(dr / box)
             if np.dot(dr, dr) < RC2_BASE:
                 overlap = True
 
-	    # check for no overlap between backbone site of particle p 
-	    # with base site of particle q
+            # check for no overlap between backbone site of particle p
+            # with base site of particle q
             dr = p_pos_back - q_pos_base
             dr -= box * np.rint (dr / box)
             if np.dot(dr, dr) < RC2_BACK_BASE:
                 overlap = True
 
-	    # check for no overlap between base site of particle p and 
-	    # backbone site of particle q
+            # check for no overlap between base site of particle p and
+            # backbone site of particle q
             dr = p_pos_base - q_pos_back
             dr -= box * np.rint (dr / box)
             if np.dot(dr, dr) < RC2_BACK_BASE:
                 overlap = True
 
-	    # exit if there is an overlap
+            # exit if there is an overlap
             if overlap:
                 return False
 
@@ -237,10 +240,10 @@ def add_strands (mynewpositions, mynewa1s, mynewa3s):
             a1s.append (p)
         for p in mynewa3s:
             a3s.append (p)
-	# calculate quaternion from local body frame and append
-	for ia in xrange(len(mynewpositions)):
-	    mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
-	    quaternions.append(mynewquaternions)
+        # calculate quaternion from local body frame and append
+        for ia in range(len(mynewpositions)):
+            mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
+            quaternions.append(mynewquaternions)
 
     return True
 
@@ -281,7 +284,7 @@ def get_rotation_matrix(axis, anglest):
                     [olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]])
 
 """
-Generates the position and orientation vectors of a 
+Generates the position and orientation vectors of a
 (single or double) strand from a sequence string
 """
 def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
@@ -295,76 +298,75 @@ def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
     # overall direction of the helix
     dir = np.array(dir, dtype=float)
     if sequence == None:
-	sequence = np.random.randint(1, 5, bp)
+        sequence = np.random.randint(1, 5, bp)
 
-    # the elseif here is most likely redundant 
+    # the elseif here is most likely redundant
     elif len(sequence) != bp:
-	n = bp - len(sequence)
-	sequence += np.random.randint(1, 5, n)
-	print >> sys.stderr, "sequence is too short, adding %d random bases" % n
+        n = bp - len(sequence)
+        sequence += np.random.randint(1, 5, n)
+        print( "sequence is too short, adding %d random bases" % n, file=sys.stderr)
 
     # normalize direction
     dir_norm = np.sqrt(np.dot(dir,dir))
     if dir_norm < 1e-10:
-	print >> sys.stderr, "direction must be a valid vector, \
-			      defaulting to (0, 0, 1)"
-	dir = np.array([0, 0, 1])
+        print( "direction must be a valid vector, defaulting to (0, 0, 1)", file=sys.stderr)
+        dir = np.array([0, 0, 1])
     else: dir /= dir_norm
 
     # find a vector orthogonal to dir to act as helix direction,
     # if not provided switch off random orientation
     if perp is None or perp is False:
-	v1 = np.random.random_sample(3)
-	v1 -= dir * (np.dot(dir, v1))
-	v1 /= np.sqrt(sum(v1*v1))
+        v1 = np.random.random_sample(3)
+        v1 -= dir * (np.dot(dir, v1))
+        v1 /= np.sqrt(sum(v1*v1))
     else:
-	v1 = perp;
+        v1 = perp;
 
     # generate rotational matrix representing the overall rotation of the helix
     R0 = get_rotation_matrix(dir, rot)
-	    
+
     # rotation matrix corresponding to one step along the helix
     R = get_rotation_matrix(dir, [1, "bp"])
 
-    # set the vector a1 (backbone to base) to v1 
+    # set the vector a1 (backbone to base) to v1
     a1 = v1
-    
-    # apply the global rotation to a1 
+
+    # apply the global rotation to a1
     a1 = np.dot(R0, a1)
-    
+
     # set the position of the fist backbone site to start_pos
     rb = np.array(start_pos)
-	    
+
     # set a3 to the direction of the helix
     a3 = dir
     for i in range(bp):
     # work out the position of the centre of mass of the nucleotide
-	rcdm = rb - CM_CENTER_DS * a1
-	
-	# append to newpositions
-	mynewpositions.append(rcdm)
-	mynewa1s.append(a1)
-	mynewa3s.append(a3)
-	
-	# if we are not at the end of the helix, we work out a1 and rb for the 
-	# next nucleotide along the helix
-	if i != bp - 1:
-	    a1 = np.dot(R, a1)
-	    rb += a3 * BASE_BASE
+        rcdm = rb - CM_CENTER_DS * a1
 
-    # if we are working on a double strand, we do a cycle similar 
+        # append to newpositions
+        mynewpositions.append(rcdm)
+        mynewa1s.append(a1)
+        mynewa3s.append(a3)
+
+        # if we are not at the end of the helix, we work out a1 and rb for the
+        # next nucleotide along the helix
+        if i != bp - 1:
+            a1 = np.dot(R, a1)
+            rb += a3 * BASE_BASE
+
+    # if we are working on a double strand, we do a cycle similar
     # to the previous one but backwards
     if double == True:
-	a1 = -a1
-	a3 = -dir
-	R = R.transpose()
-	for i in range(bp):
-	    rcdm = rb - CM_CENTER_DS * a1
-	    mynewpositions.append (rcdm)
-	    mynewa1s.append (a1)
-	    mynewa3s.append (a3)
-	    a1 = np.dot(R, a1)
-	    rb += a3 * BASE_BASE
+        a1 = -a1
+        a3 = -dir
+        R = R.transpose()
+        for i in range(bp):
+            rcdm = rb - CM_CENTER_DS * a1
+            mynewpositions.append (rcdm)
+            mynewa1s.append (a1)
+            mynewa3s.append (a3)
+            a1 = np.dot(R, a1)
+            rb += a3 * BASE_BASE
 
     assert (len (mynewpositions) > 0)
 
@@ -391,10 +393,10 @@ def read_strands(filename):
     try:
         infile = open (filename)
     except:
-        print >> sys.stderr, "Could not open file '%s'. Aborting." % filename
+        print( "Could not open file '%s'. Aborting." % filename, file=sys.stderr )
         sys.exit(2)
 
-    # This block works out the number of nucleotides and strands by reading 
+    # This block works out the number of nucleotides and strands by reading
     # the number of non-empty lines in the input file and the number of letters,
     # taking the possible DOUBLE keyword into account.
     nstrands, nnucl, nbonds = 0, 0, 0
@@ -406,30 +408,29 @@ def read_strands(filename):
         if line[:6] == 'DOUBLE':
             line = line.split()[1]
             length = len(line)
-            print >> sys.stdout, "## Found duplex of %i base pairs" % length
+            print( "## Found duplex of %i base pairs" % length, file=sys.stdout)
             nnucl += 2*length
             nstrands += 2
-	    nbonds += (2*length-2)
+            nbonds += (2*length-2)
         else:
             line = line.split()[0]
             length = len(line)
-            print >> sys.stdout, \
-		    "## Found single strand of %i bases" % length
+            print( "## Found single strand of %i bases" % length, file=sys.stdout)
             nnucl += length
             nstrands += 1
-	    nbonds += length-1
+            nbonds += length-1
     # rewind the sequence input file
     infile.seek(0)
 
-    print >> sys.stdout, "## nstrands, nnucl = ", nstrands, nnucl
+    print( "## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
 
     # generate the data file in LAMMPS format
     try:
         out = open ("data.oxdna", "w")
     except:
-        print >> sys.stderr, "Could not open data file for writing. Aborting."
+        print( "Could not open data file for writing. Aborting.", file=sys.stderr)
         sys.exit(2)
-	
+
     lines = infile.readlines()
     nlines = len(lines)
     i = 1
@@ -440,115 +441,114 @@ def read_strands(filename):
         line = line.upper().strip()
 
         # skip empty lines
-        if len(line) == 0: 
-	    i += 1
-	    continue
+        if len(line) == 0:
+            i += 1
+            continue
 
-	# block for duplexes: last argument of the generate function 
-	# is set to 'True'
+        # block for duplexes: last argument of the generate function
+        # is set to 'True'
         if line[:6] == 'DOUBLE':
             line = line.split()[1]
             length = len(line)
             seq = [(base_to_number[x]) for x in line]
 
-	    myns += 1
-	    for b in xrange(length):
-		basetype.append(seq[b])
-		strandnum.append(myns)
+            myns += 1
+            for b in range(length):
+                basetype.append(seq[b])
+                strandnum.append(myns)
 
-	    for b in xrange(length-1):
-		bondpair = [noffset + b, noffset + b + 1]
-		bonds.append(bondpair)
-	    noffset += length
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+            noffset += length
 
-	    # create the sequence of the second strand as made of 
-	    # complementary bases
-	    seq2 = [5-s for s in seq]
-	    seq2.reverse()
+            # create the sequence of the second strand as made of
+            # complementary bases
+            seq2 = [5-s for s in seq]
+            seq2.reverse()
 
-	    myns += 1
-	    for b in xrange(length):
-		basetype.append(seq2[b])
-		strandnum.append(myns)
+            myns += 1
+            for b in range(length):
+                basetype.append(seq2[b])
+                strandnum.append(myns)
 
-	    for b in xrange(length-1):
-		bondpair = [noffset + b, noffset + b + 1]
-		bonds.append(bondpair)
-	    noffset += length
- 
-            print >> sys.stdout, "## Created duplex of %i bases" % (2*length)
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+            noffset += length
 
-	    # generate random position of the first nucleotide
+            print( "## Created duplex of %i bases" % (2*length), file=sys.stdout)
+
+            # generate random position of the first nucleotide
             cdm = box_offset + np.random.random_sample(3) * box
 
-            # generate the random direction of the helix 
+            # generate the random direction of the helix
             axis = np.random.random_sample(3)
             axis /= np.sqrt(np.dot(axis, axis))
 
-            # use the generate function defined above to create 
-	    # the position and orientation vector of the strand 
+            # use the generate function defined above to create
+            # the position and orientation vector of the strand
             newpositions, newa1s, newa3s = generate_strand(len(line), \
-		    sequence=seq, dir=axis, start_pos=cdm, double=True)
+                sequence=seq, dir=axis, start_pos=cdm, double=True)
 
             # generate a new position for the strand until it does not overlap
-	    # with anything already present
-	    start = timer()
+            # with anything already present
+            start = timer()
             while not add_strands(newpositions, newa1s, newa3s):
                 cdm = box_offset + np.random.random_sample(3) * box
                 axis = np.random.random_sample(3)
                 axis /= np.sqrt(np.dot(axis, axis))
                 newpositions, newa1s, newa3s = generate_strand(len(line), \
-		      sequence=seq, dir=axis, start_pos=cdm, double=True)
-                print >> sys.stdout, "## Trying %i" % i
-	    end = timer()
-            print >> sys.stdout, "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
-				      (2*length, i, nlines, end-start, len(positions), nnucl)
+                    sequence=seq, dir=axis, start_pos=cdm, double=True)
+                print( "## Trying %i" % i, file=sys.stdout)
+            end = timer()
+            print( "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
+				      (2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
 
-	# block for single strands: last argument of the generate function 
-	# is set to 'False'
+        # block for single strands: last argument of the generate function
+        # is set to 'False'
         else:
             length = len(line)
             seq = [(base_to_number[x]) for x in line]
 
-	    myns += 1
-	    for b in xrange(length):
-		basetype.append(seq[b])
-		strandnum.append(myns)
+            myns += 1
+            for b in range(length):
+                basetype.append(seq[b])
+                strandnum.append(myns)
 
-	    for b in xrange(length-1):
-		bondpair = [noffset + b, noffset + b + 1]
-		bonds.append(bondpair)
-	    noffset += length
+            for b in range(length-1):
+                bondpair = [noffset + b, noffset + b + 1]
+                bonds.append(bondpair)
+            noffset += length
 
-	    # generate random position of the first nucleotide
+            # generate random position of the first nucleotide
             cdm = box_offset + np.random.random_sample(3) * box
 
-            # generate the random direction of the helix 
+            # generate the random direction of the helix
             axis = np.random.random_sample(3)
             axis /= np.sqrt(np.dot(axis, axis))
 
-            print >> sys.stdout, \
-		      "## Created single strand of %i bases" % length
+            print("## Created single strand of %i bases" % length, file=sys.stdout)
 
             newpositions, newa1s, newa3s = generate_strand(length, \
 		      sequence=seq, dir=axis, start_pos=cdm, double=False)
-	    start = timer()
+            start = timer()
             while not add_strands(newpositions, newa1s, newa3s):
                 cdm = box_offset + np.random.random_sample(3) * box
                 axis = np.random.random_sample(3)
-		axis /= np.sqrt(np.dot(axis, axis))
+                axis /= np.sqrt(np.dot(axis, axis))
                 newpositions, newa1s, newa3s = generate_strand(length, \
-			  sequence=seq, dir=axis, start_pos=cdm, double=False)
+                    sequence=seq, dir=axis, start_pos=cdm, double=False)
                 print >> sys.stdout, "## Trying  %i" % (i)
-	    end = timer()
-            print >> sys.stdout, "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
-				      (length, i, nlines, end-start,len(positions), nnucl)
+            end = timer()
+            print( "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
+				      (length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
 
         i += 1
 
     # sanity check
     if not len(positions) == nnucl:
-        print len(positions), nnucl
+        print( len(positions), nnucl )
         raise AssertionError
 
     out.write('# LAMMPS data file\n')
@@ -580,44 +580,41 @@ def read_strands(filename):
     out.write('Atoms\n')
     out.write('\n')
 
-    for i in xrange(nnucl):
-	out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
-		  % (i+1, basetype[i], \
-		     positions[i][0], positions[i][1], positions[i][2], \
-		     strandnum[i]))
+    for i in range(nnucl):
+        out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
+            % (i+1, basetype[i], positions[i][0], positions[i][1], positions[i][2], strandnum[i]))
 
     out.write('\n')
     out.write('# Atom-ID, translational, rotational velocity\n')
     out.write('Velocities\n')
     out.write('\n')
 
-    for i in xrange(nnucl):
-	out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
-		  % (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
+    for i in range(nnucl):
+        out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
+            % (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
 
     out.write('\n')
     out.write('# Atom-ID, shape, quaternion\n')
     out.write('Ellipsoids\n')
     out.write('\n')
 
-    for i in xrange(nnucl):
-	out.write(\
-    "%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n"  \
-      % (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
-	quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
- 
+    for i in range(nnucl):
+        out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n"  \
+            % (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
+            quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
+
     out.write('\n')
     out.write('# Bond topology\n')
     out.write('Bonds\n')
     out.write('\n')
 
-    for i in xrange(nbonds):
-	out.write("%d  %d  %d  %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
+    for i in range(nbonds):
+        out.write("%d  %d  %d  %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
 
     out.close()
 
-    print >> sys.stdout, "## Wrote data to 'data.oxdna'"
-    print >> sys.stdout, "## DONE"
+    print("## Wrote data to 'data.oxdna'", file=sys.stdout)
+    print("## DONE", file=sys.stdout)
 
 # call the above main() function, which executes the program
 read_strands (infile)
@@ -627,4 +624,6 @@ runtime = end_time-start_time
 hours = runtime/3600
 minutes = (runtime-np.rint(hours)*3600)/60
 seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
-print >> sys.stdout, "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds)
+print( "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)
+
+

examples/PACKAGES/cgdna/util/generate_simple.py

@@ -1,5 +1,8 @@
 # Setup tool for oxDNA input in LAMMPS format.
 
+# for python2/3 compatibility
+from __future__ import print_function
+
 import math,numpy as np,sys,os
 
 # system size
@@ -250,59 +253,59 @@ def duplex_array():
       qrot3=math.sin(0.5*twist)
 
       for letter in strand[2]:
-	temp1=[]
-	temp2=[]
+        temp1=[]
+        temp2=[]
 
-	temp1.append(nt2num[letter])
-	temp2.append(compnt2num[letter])
+        temp1.append(nt2num[letter])
+        temp2.append(compnt2num[letter])
 
-	temp1.append([posx1,posy1,posz1])
-	temp2.append([posx2,posy2,posz2])
+        temp1.append([posx1,posy1,posz1])
+        temp2.append([posx2,posy2,posz2])
 
-	vel=[0,0,0,0,0,0]
-	temp1.append(vel)
-	temp2.append(vel)
+        vel=[0,0,0,0,0,0]
+        temp1.append(vel)
+        temp2.append(vel)
 
-	temp1.append(shape)
-	temp2.append(shape)
+        temp1.append(shape)
+        temp2.append(shape)
 
-	temp1.append(quat1)
-	temp2.append(quat2)
+        temp1.append(quat1)
+        temp2.append(quat2)
 
-	quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3 
-	quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2 
-	quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3 
-	quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1 
+        quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
+        quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
+        quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
+        quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
 
-	quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
+        quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
 
-	posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
-	posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
-	posz1=posz1+risez
+        posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
+        posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
+        posz1=posz1+risez
 
-	quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3 
-	quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2 
-	quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3 
-	quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1 
+        quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
+        quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
+        quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
+        quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
 
-	quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
+        quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
 
-	posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
-	posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
-	posz2=posz1
+        posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
+        posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
+        posz2=posz1
 
-	if (len(nucleotide)+1 > strandstart):
-	  topology.append([1,len(nucleotide),len(nucleotide)+1])
-	  comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
+        if (len(nucleotide)+1 > strandstart):
+          topology.append([1,len(nucleotide),len(nucleotide)+1])
+          comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
 
-	nucleotide.append(temp1)
-	compstrand.append(temp2)
+        nucleotide.append(temp1)
+        compstrand.append(temp2)
 
       for ib in range(len(compstrand)):
-	nucleotide.append(compstrand[len(compstrand)-1-ib])
+        nucleotide.append(compstrand[len(compstrand)-1-ib])
 
       for ib in range(len(comptopo)):
-	topology.append(comptopo[ib])
+        topology.append(comptopo[ib])
 
   return
 

examples/meam/msmeam/HGa.meam

@@ -1,30 +0,0 @@
-bkgd_dyn        =       1
-emb_lin_neg = 1
-augt1=0 
-ialloy=1 
-rc	=	 5.9 
-#H
-attrac(1,1)=0.460 
-repuls(1,1)=0.460 
-Cmin(1,1,1)=1.3 # PuMS
-Cmax(1,1,1)= 2.80 
-nn2(1,1)=1
-#Ga
-rho0(2)         =       0.6
-attrac(2,2)=0.097 
-repuls(2,2)=0.097 
-nn2(2,2)=1
-#HGa
-attrac(1,2)=0.300 
-repuls(1,2)=0.300 
-lattce(1,2)=l12 
-re(1,2)=3.19 
-delta(1,2)=-0.48  
-alpha(1,2)=6.6 
-Cmin(1,1,2)=2.0 
-Cmin(2,1,2)= 2.0 
-Cmin(1,2,1)=2.0 
-Cmin(2,2,1)     =       1.4
-Cmin(1,2,2)     =       1.4
-Cmin(1,1,2)     =       1.4
-nn2(1,2)=1

examples/meam/msmeam/HGa.msmeam

@@ -0,0 +1 @@
+../../../potentials/HGa.msmeam

examples/meam/msmeam/data.msmeam.bu

@@ -1,25 +0,0 @@
-LAMMPS data file via write_data, version 16 Feb 2016, timestep = 1
-
-3 atoms
-2 atom types
-
--4.0000000000000000e+00 4.0000000000000000e+00 xlo xhi
--4.0000000000000000e+00 4.0000000000000000e+00 ylo yhi
--4.0000000000000000e+00 4.0000000000000000e+00 zlo zhi
-
-Masses
-
-1 1.0079
-2 69.723
-
-Atoms # atomic
-
-1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
-2 2 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
-3 2 2.9999999999999999e-01 2.2999999999999998e+00 0.0000000000000000e+00 0 0 0
-
-Velocities
-
-1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
-2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
-3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00

examples/meam/msmeam/in.msmeam

@@ -1,5 +1,3 @@
-echo	both
-log	log.msmeam
 # Test of MEAM potential for HGa
 
 # ------------------------ INITIALIZATION ----------------------------
@@ -21,11 +19,11 @@ create_atoms    1 single 0 0 0  units box
 create_atoms    2 single 2.2 0 0  units box
 create_atoms    2 single 0.3 2.3 0  units box
 # ---------- Define Settings ---------------------
-variable	teng equal "c_eatoms"
+variable        teng equal "c_eatoms"
 compute pot_energy all pe/atom
 compute stress all stress/atom NULL
 dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
-run	1
-write_data	data.msmeam
+run     1
+#write_data      data.msmeam
 
 print "All done!"

examples/meam/msmeam/library.msmeam

@@ -1,14 +0,0 @@
-# DATE: 2018-09-22 UNITS: metal CONTRIBUTOR: Steve Valone, smv@lanl.gov CITATION: Baskes, PRB 1992; smv, sr, mib, JNM 2010
-# ms-meam data format May 2010
-#  elt   lat    z     ielement      atwt
-#  alpha b0     b1    b2     b3     b1m     b2m   b3m      alat   esub   asub
-#    -   t0     t1    t2     t3     t1m     t2m   t3m      rozero ibar
-#  NOTE:  leading character cannot be a space
-
-'H'    'dim'  1.0   1      1.0079
-2.960  2.960  3.0   1.0    1.0    1.0    3.0  1.0       0.741  2.235  2.50
-1.0    0.44721 0.0  0.00   0.0    0.31623 0  6.70 0
-
-'Ga4'  'fcc'  12.0  31     69.723
-4.42   4.80   3.10  6.00   0.00   0.0    0.0  0.5       4.247  2.897  0.97
-1.0    1.649 1.435  0.00   0.0    0.0  2.0       0.70   0

examples/meam/msmeam/library.msmeam

@@ -0,0 +1 @@
+../../../potentials/library.msmeam

examples/meam/msmeam/log.1Mar2024.msmeam.g++.1

@@ -0,0 +1,126 @@
+LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-182-g93942f2013-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Test of MEAM potential for HGa
+
+# ------------------------ INITIALIZATION ----------------------------
+units           metal
+dimension       3
+boundary        p       p       p
+atom_style      atomic
+variable latparam equal 4.646
+variable ncell equal 3
+
+# ----------------------- ATOM DEFINITION ----------------------------
+region          box block -4 4 -4 4 -4 4
+create_box      2 box
+Created orthogonal box = (-4 -4 -4) to (4 4 4)
+  1 by 1 by 1 MPI processor grid
+
+#
+
+include potential.mod
+# NOTE: This script can be modified for different pair styles
+# See in.elastic for more info.
+
+variable Pu string H
+print "potential chosen ${Pu}"
+potential chosen H
+# Choose potential
+pair_style meam/ms
+print		"we just executed"
+we just executed
+
+pair_coeff      * * library.msmeam ${Pu} Ga4  HGa.msmeam ${Pu} Ga4
+pair_coeff      * * library.msmeam H Ga4  HGa.msmeam ${Pu} Ga4
+pair_coeff      * * library.msmeam H Ga4  HGa.msmeam H Ga4
+Reading MEAM library file library.msmeam with DATE: 2018-09-22
+# Setup neighbor style
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Setup minimization style
+variable dmax equal 1.0e-2
+min_style	     cg
+min_modify	     dmax ${dmax} line quadratic
+min_modify	     dmax 0.01 line quadratic
+compute eng all pe/atom
+compute eatoms all reduce sum c_eng
+
+# Setup output
+thermo		100
+thermo_style custom step temp etotal  press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
+thermo_modify norm yes
+create_atoms    1 single 0 0 0  units box
+Created 1 atoms
+  using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
+  create_atoms CPU = 0.000 seconds
+create_atoms    2 single 2.2 0 0  units box
+Created 1 atoms
+  using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
+  create_atoms CPU = 0.000 seconds
+create_atoms    2 single 0.3 2.3 0  units box
+Created 1 atoms
+  using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
+  create_atoms CPU = 0.000 seconds
+# ---------- Define Settings ---------------------
+variable        teng equal "c_eatoms"
+compute pot_energy all pe/atom
+compute stress all stress/atom NULL
+# dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
+run     1
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.9
+  ghost atom cutoff = 6.9
+  binsize = 3.45, bins = 3 3 3
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/ms, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/ms, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.587 | 8.587 | 8.587 Mbytes
+   Step          Temp          TotEng         Press           Pxx            Pyy            Pzz            Pxy            Pxz            Pyz             Lx             Ly             Lz           Volume        c_eatoms   
+         0   0              15.433079      491354.7       838670.96      635393.15      0              80195.797      0              0              8              8              8              512            15.433079    
+         1   0              15.433079      491354.7       838670.96      635393.15      0              80195.797      0              0              8              8              8              512            15.433079    
+Loop time of 4.4446e-05 on 1 procs for 1 steps with 3 atoms
+
+Performance: 1943.932 ns/day, 0.012 hours/ns, 22499.213 timesteps/s, 67.498 katom-step/s
+31.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.9908e-05 | 2.9908e-05 | 2.9908e-05 |   0.0 | 67.29
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.033e-06  | 1.033e-06  | 1.033e-06  |   0.0 |  2.32
+Output  | 9.347e-06  | 9.347e-06  | 9.347e-06  |   0.0 | 21.03
+Modify  | 2.02e-07   | 2.02e-07   | 2.02e-07   |   0.0 |  0.45
+Other   |            | 3.956e-06  |            |       |  8.90
+
+Nlocal:              3 ave           3 max           3 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             78 ave          78 max          78 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              7 ave           7 max           7 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:           14 ave          14 max          14 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 14
+Ave neighs/atom = 4.6666667
+Neighbor list builds = 0
+Dangerous builds = 0
+#write_data      data.msmeam
+
+print "All done!"
+All done!
+Total wall time: 0:00:00

examples/meam/msmeam/log.1Mar2024.msmeam.g++.4

@@ -0,0 +1,126 @@
+LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-182-g93942f2013-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Test of MEAM potential for HGa
+
+# ------------------------ INITIALIZATION ----------------------------
+units           metal
+dimension       3
+boundary        p       p       p
+atom_style      atomic
+variable latparam equal 4.646
+variable ncell equal 3
+
+# ----------------------- ATOM DEFINITION ----------------------------
+region          box block -4 4 -4 4 -4 4
+create_box      2 box
+Created orthogonal box = (-4 -4 -4) to (4 4 4)
+  1 by 2 by 2 MPI processor grid
+
+#
+
+include potential.mod
+# NOTE: This script can be modified for different pair styles
+# See in.elastic for more info.
+
+variable Pu string H
+print "potential chosen ${Pu}"
+potential chosen H
+# Choose potential
+pair_style meam/ms
+print		"we just executed"
+we just executed
+
+pair_coeff      * * library.msmeam ${Pu} Ga4  HGa.msmeam ${Pu} Ga4
+pair_coeff      * * library.msmeam H Ga4  HGa.msmeam ${Pu} Ga4
+pair_coeff      * * library.msmeam H Ga4  HGa.msmeam H Ga4
+Reading MEAM library file library.msmeam with DATE: 2018-09-22
+# Setup neighbor style
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Setup minimization style
+variable dmax equal 1.0e-2
+min_style	     cg
+min_modify	     dmax ${dmax} line quadratic
+min_modify	     dmax 0.01 line quadratic
+compute eng all pe/atom
+compute eatoms all reduce sum c_eng
+
+# Setup output
+thermo		100
+thermo_style custom step temp etotal  press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
+thermo_modify norm yes
+create_atoms    1 single 0 0 0  units box
+Created 1 atoms
+  using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
+  create_atoms CPU = 0.000 seconds
+create_atoms    2 single 2.2 0 0  units box
+Created 1 atoms
+  using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
+  create_atoms CPU = 0.000 seconds
+create_atoms    2 single 0.3 2.3 0  units box
+Created 1 atoms
+  using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
+  create_atoms CPU = 0.000 seconds
+# ---------- Define Settings ---------------------
+variable        teng equal "c_eatoms"
+compute pot_energy all pe/atom
+compute stress all stress/atom NULL
+# dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
+run     1
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.9
+  ghost atom cutoff = 6.9
+  binsize = 3.45, bins = 3 3 3
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair meam/ms, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair meam/ms, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.965 | 8.123 | 8.594 Mbytes
+   Step          Temp          TotEng         Press           Pxx            Pyy            Pzz            Pxy            Pxz            Pyz             Lx             Ly             Lz           Volume        c_eatoms   
+         0   0              15.433079      491354.7       838670.96      635393.15      0              80195.797      0              0              8              8              8              512            15.433079    
+         1   0              15.433079      491354.7       838670.96      635393.15      0              80195.797      0              0              8              8              8              512            15.433079    
+Loop time of 8.70645e-05 on 4 procs for 1 steps with 3 atoms
+
+Performance: 992.368 ns/day, 0.024 hours/ns, 11485.738 timesteps/s, 34.457 katom-step/s
+29.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.3957e-05 | 4.67e-05   | 5.1056e-05 |   0.0 | 53.64
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.105e-05  | 1.3822e-05 | 1.7033e-05 |   0.0 | 15.88
+Output  | 1.5765e-05 | 1.9045e-05 | 2.5216e-05 |   0.0 | 21.87
+Modify  | 2.58e-07   | 3.465e-07  | 3.81e-07   |   0.0 |  0.40
+Other   |            | 7.151e-06  |            |       |  8.21
+
+Nlocal:           0.75 ave           3 max           0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost:          38.25 ave          42 max          36 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Neighs:           1.75 ave           7 max           0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+FullNghs:          3.5 ave          14 max           0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 14
+Ave neighs/atom = 4.6666667
+Neighbor list builds = 0
+Dangerous builds = 0
+#write_data      data.msmeam
+
+print "All done!"
+All done!
+Total wall time: 0:00:00

examples/meam/msmeam/log.msmeam.bu

@@ -1,107 +0,0 @@
-# Test of MEAM potential for HGa
-
-# ------------------------ INITIALIZATION ----------------------------
-units           metal
-dimension       3
-boundary        p       p       p
-atom_style      atomic
-variable latparam equal 4.646
-variable ncell equal 3
-
-# ----------------------- ATOM DEFINITION ----------------------------
-region          box block -4 4 -4 4 -4 4
-create_box      2 box
-Created orthogonal box = (-4 -4 -4) to (4 4 4)
-  1 by 1 by 1 MPI processor grid
-
-#
-
-include potential.mod
-# NOTE: This script can be modified for different pair styles
-# See in.elastic for more info.
-
-variable Pu string H
-print "potential chosen ${Pu}"
-potential chosen H
-# Choose potential
-pair_style      MSmeam
-print		"we just executed"
-we just executed
-
-pair_coeff      * * library.MSmeam ${Pu} Ga4  HGaMS.meam ${Pu} Ga4
-pair_coeff      * * library.MSmeam H Ga4  HGaMS.meam ${Pu} Ga4
-pair_coeff      * * library.MSmeam H Ga4  HGaMS.meam H Ga4
-Reading potential file library.MSmeam with DATE: 2018-09-22
-# Setup neighbor style
-neighbor 1.0 nsq
-neigh_modify once no every 1 delay 0 check yes
-
-# Setup minimization style
-variable dmax equal 1.0e-2
-min_style	     cg
-min_modify	     dmax ${dmax} line quadratic
-min_modify	     dmax 0.01 line quadratic
-compute eng all pe/atom
-compute eatoms all reduce sum c_eng
-
-# Setup output
-thermo		100
-thermo_style custom step temp etotal  press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
-thermo_modify norm yes
-create_atoms    1 single 0 0 0  units box
-Created 1 atoms
-create_atoms    2 single 2.2 0 0  units box
-Created 1 atoms
-create_atoms    2 single 0.3 2.3 0  units box
-Created 1 atoms
-# ---------- Define Settings ---------------------
-variable	teng equal "c_eatoms"
-compute pot_energy all pe/atom
-compute stress all stress/atom NULL
-dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
-run	1
-WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
-Neighbor list info ...
-  2 neighbor list requests
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.9
-  ghost atom cutoff = 6.9
-Memory usage per processor = 12.9295 Mbytes
-Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume eatoms 
-       0            0    15.433079    491354.68    838670.91    635393.13            0    80195.793            0            0            8            8            8          512    15.433079 
-       1            0    15.433079    491354.68    838670.91    635393.13            0    80195.793            0            0            8            8            8          512    15.433079 
-Loop time of 0.000172138 on 1 procs for 1 steps with 3 atoms
-
-Performance: 501.922 ns/day, 0.048 hours/ns, 5809.285 timesteps/s
-81.3% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 6.6996e-05 | 6.6996e-05 | 6.6996e-05 |   0.0 | 38.92
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 |   0.0 |  1.11
-Output  | 9.7036e-05 | 9.7036e-05 | 9.7036e-05 |   0.0 | 56.37
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 6.199e-06  |            |       |  3.60
-
-Nlocal:    3 ave 3 max 3 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    78 ave 78 max 78 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    7 ave 7 max 7 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  14 ave 14 max 14 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 14
-Ave neighs/atom = 4.66667
-Neighbor list builds = 0
-Dangerous builds = 0
-write_data	data.msmeam
-
-print "All done!"
-All done!
-Total wall time: 0:00:00
-

examples/meam/msmeam/msmeam.dump.bu

@@ -1,24 +0,0 @@
-ITEM: TIMESTEP
-0
-ITEM: NUMBER OF ATOMS
-3
-ITEM: BOX BOUNDS pp pp pp
--4 4
--4 4
--4 4
-ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] 
-1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0 
-2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0 
-3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0 
-ITEM: TIMESTEP
-1
-ITEM: NUMBER OF ATOMS
-3
-ITEM: BOX BOUNDS pp pp pp
--4 4
--4 4
--4 4
-ITEM: ATOMS id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6] 
-1 0 0 0 -131.925 -88.3005 0 22.9153 -2.147e+08 -1.62661e+08 -0 -2.05301e+07 -0 -0 
-2 2.2 0 0 120.809 -0.482171 0 14.7692 -2.12028e+08 -0 -0 403352 -0 -0 
-3 0.3 2.3 0 11.1159 88.7827 0 8.61478 -2.67145e+06 -1.62661e+08 -0 -2.09335e+07 -0 -0 

examples/meam/msmeam/potential.mod

@@ -7,7 +7,7 @@ print "potential chosen ${Pu}"
 pair_style meam/ms
 print		"we just executed"
 
-pair_coeff      * * library.msmeam ${Pu} Ga4  HGa.meam ${Pu} Ga4
+pair_coeff      * * library.msmeam ${Pu} Ga4  HGa.msmeam ${Pu} Ga4
 # Setup neighbor style
 neighbor 1.0 bin
 neigh_modify once no every 1 delay 0 check yes

fortran/lammps.f90

@@ -3633,7 +3633,7 @@ CONTAINS
 
     n = LEN_TRIM(f_string)
     ptr = lammps_malloc(n+1)
-    CALL C_F_POINTER(ptr, c_string, [1])
+    CALL C_F_POINTER(ptr, c_string, [n+1])
     DO i=1, n
         c_string(i) = f_string(i:i)
     END DO

lib/awpmd/ivutils/include/wavepacket.h

@@ -23,7 +23,7 @@ class WavePacket;
 
 ///\en Template for v=der operation in \ref Wavepacket::int2phys_der()
 template<class Type>
-struct eq_second : public binary_function <Type, Type, Type> {
+struct eq_second {
   Type operator()(const Type& /* _Left */, const Type& _Right) const{
     return _Right;
   }
@@ -31,7 +31,7 @@ struct eq_second : public binary_function <Type, Type, Type> {
 
 ///\en Template for v=-der operation in \ref Wavepacket::int2phys_der()
 template<class Type>
-struct eq_minus_second : public binary_function <Type, Type, Type> {
+struct eq_minus_second {
   Type operator()(const Type& /* _Left */, const Type& _Right) const{
     return -_Right;
   }

lib/colvars/colvar.cpp

@@ -30,6 +30,7 @@ colvar::colvar()
   after_restart = false;
   kinetic_energy = 0.0;
   potential_energy = 0.0;
+  period = 0.0;
 
 #ifdef LEPTON
   dev_null = 0.0;

lib/gpu/geryon/nvd_device.h

@@ -138,7 +138,7 @@ class UCL_Device {
   /** \note You cannot delete the default stream **/
   inline void pop_command_queue() {
     if (_cq.size()<2) return;
-    CU_SAFE_CALL_NS(cuStreamDestroy(_cq.back()));
+    cuStreamDestroy(_cq.back());
     _cq.pop_back();
   }
 
@@ -426,8 +426,8 @@ void UCL_Device::clear() {
   if (_device>-1) {
     for (int i=1; i<num_queues(); i++) pop_command_queue();
 #if GERYON_NVD_PRIMARY_CONTEXT
-    CU_SAFE_CALL_NS(cuCtxSetCurrent(_old_context));
-    CU_SAFE_CALL_NS(cuDevicePrimaryCtxRelease(_cu_device));
+    cuCtxSetCurrent(_old_context);
+    cuDevicePrimaryCtxRelease(_cu_device);
 #else
     cuCtxDestroy(_context);
 #endif

lib/gpu/lal_base_amoeba.h

@@ -33,6 +33,7 @@
 
 //#define ASYNC_DEVICE_COPY
 
+#if 0
 #if !defined(USE_OPENCL) && !defined(USE_HIP)
 // temporary workaround for int2 also defined in cufft
 #ifdef int2
@@ -40,6 +41,7 @@
 #endif
 #include "cufft.h"
 #endif
+#endif
 
 namespace LAMMPS_AL {
 
@@ -313,10 +315,11 @@ class BaseAmoeba {
   virtual int fphi_mpole();
   virtual int polar_real(const int eflag, const int vflag) = 0;
 
-
+#if 0
   #if !defined(USE_OPENCL) && !defined(USE_HIP)
   cufftHandle plan;
   #endif
+#endif
   bool fft_plan_created;
 };
 

lib/gpu/lal_dpd.cu

@@ -301,9 +301,10 @@ __kernel void k_dpd_fast(const __global numtyp4 *restrict x_,
   __local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
   __local numtyp sp_lj[4];
   __local numtyp sp_sqrt[4];
-  if (tid<4)
+  if (tid<4) {
     sp_lj[tid]=sp_lj_in[tid];
     sp_sqrt[tid]=sp_sqrt_in[tid];
+  }
   if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
     coeff[tid]=coeff_in[tid];
   }

lib/machdyn/Install.py

@@ -31,8 +31,8 @@ checksums = { \
 # help message
 
 HELP = """
-Syntax from src dir: make lib-smd args="-b"
-                 or: make lib-smd args="-p /usr/include/eigen3"
+Syntax from src dir: make lib-machdyn args="-b"
+                 or: make lib-machdyn args="-p /usr/include/eigen3"
 
 Syntax from lib dir: python Install.py -b
                  or: python Install.py -p /usr/include/eigen3"
@@ -40,8 +40,8 @@ Syntax from lib dir: python Install.py -b
 
 Example:
 
-make lib-smd args="-b"   # download/build in default lib/smd/eigen-eigen-*
-make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
+make lib-machdyn args="-b"   # download/build in default lib/machdyn/eigen-eigen-*
+make lib-machdyn args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
 """
 
 pgroup = parser.add_mutually_exclusive_group()
@@ -105,7 +105,7 @@ if buildflag:
   edir = os.path.join(homepath, "eigen-%s" % version)
   os.rename(edir, eigenpath)
 
-# create link in lib/smd to Eigen src dir
+# create link in lib/machdyn to Eigen src dir
 
 print("Creating link to Eigen include folder")
 if os.path.isfile("includelink") or os.path.islink("includelink"):

lib/machdyn/README

@@ -4,7 +4,7 @@ to use the MACHDYN package in a LAMMPS input script.
 The Eigen library is available at http://eigen.tuxfamily.org.  It's
 a general C++ template library for linear algebra.
 
-You can type "make lib-smd" from the src directory to see help on how
+You can type "make lib-machdyn" from the src directory to see help on how
 to download build this library via make commands, or you can do the
 same thing by typing "python Install.py" from within this directory,
 or you can do it manually by following the instructions below.
@@ -12,13 +12,13 @@ or you can do it manually by following the instructions below.
 Instructions:
 
 1.  Download the Eigen tarball at http://eigen.tuxfamily.org and
-    unpack the tarball either in this /lib/smd directory or somewhere
+    unpack the tarball either in this lib/machdyn directory or somewhere
     else on your system.  It should unpack with into a directory with
     a name similar to eigen-eigen-bdd17ee3b1b3.  You can rename
     the directory to just "eigen" if you wish.  Note that Eigen is a
     template library, so you do not have to build it.
 
-2.  Create a soft link in this dir (lib/smd)
+2.  Create a soft link in this dir (lib/machdyn)
     to the eigen directory.  E.g if you unpacked Eigen in this dir:
       % ln -s eigen-eigen-bdd17ee3b1b3 includelink
     If you unpacked Eigen somewhere else and renamed

lib/mdi/Install.py

@@ -32,7 +32,7 @@ make lib-mdi args="-m mpi" # build MDI lib with same settings as in the mpi Make
 
 # settings
 
-version = "1.4.16"
+version = "1.4.26"
 url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version
 
 # known checksums for different MDI versions. used to validate the download.
@@ -41,6 +41,7 @@ checksums = { \
               '1.4.12' : '7a222353ae8e03961d5365e6cd48baee', \
               '1.4.14' : '7a059bb12535360fdcb7de8402f9a0fc', \
               '1.4.16' : '407db44e2d79447ab5c1233af1965f65', \
+              '1.4.26' : '3124bb85259471e2a53a891f04bf697a', \
               }
 
 # print error message or help

lib/pace/Install.py

@@ -18,11 +18,11 @@ from install_helpers import fullpath, geturl, checkmd5sum, getfallback
 # settings
 
 thisdir = fullpath('.')
-version ='v.2023.01.3.fix'
+version ='v.2023.10.04'
 
 # known checksums for different PACE versions. used to validate the download.
 checksums = { \
-    'v.2023.01.3.fix': '4f0b3b5b14456fe9a73b447de3765caa'
+    'v.2023.10.04': '70ff79f4e59af175e55d24f3243ad1ff'
 }
 
 parser = ArgumentParser(prog='Install.py', description="LAMMPS library build wrapper script")

lib/plumed/Install.py

@@ -16,8 +16,10 @@ parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
 # settings
+# Note: must also adjust check for supported API versions in
+# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
 
-version = "2.8.2"
+version = "2.9.1"
 mode = "static"
 
 # help message
@@ -45,6 +47,10 @@ checksums = { \
         '2.7.6' : 'fb8c0ec10f97a9353eb123a5c4c35aa6', \
         '2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \
         '2.8.2' : '599092b6a0aa6fff992612537ad98994', \
+        '2.8.3' : '76d23cd394eba9e6530316ed1184e219', \
+        '2.8.4' : '9f59c4f9bda86fe5bef19543c295a981', \
+        '2.9.0' : '661eabeebee05cf84bbf9dc23d7d5f46', \
+        '2.9.1' : 'c3b2d31479c1e9ce211719d40e9efbd7', \
         }
 
 # parse and process arguments

lib/python/Makefile.lammps

@@ -1,7 +1,14 @@
 # Settings that the LAMMPS build will import when this package library is used
 # See the README file for more explanation
-
-python_SYSINC = $(shell which python-config > /dev/null 2>&1 && python-config --includes || :)
-python_SYSLIB = $(shell which python-config > /dev/null 2>&1 && python-config --ldflags --embed > /dev/null 2>&1 && python-config --ldflags --embed || (which python-config > /dev/null 2>&1 && python-config --ldflags || :) )
-python_SYSPATH =
+ifeq ($(shell type python3 >/dev/null 2>&1; echo $$?), 0)
+PYTHON=python3
+PYTHONCONFIG = python3-config
+else
+PYTHONCONFIG = python-config
 PYTHON=python
+endif
+
+
+python_SYSINC = $(shell which $(PYTHONCONFIG) > /dev/null 2>&1 && $(PYTHONCONFIG) --includes || :)
+python_SYSLIB = $(shell which $(PYTHONCONFIG) > /dev/null 2>&1 && $(PYTHONCONFIG) --ldflags --embed > /dev/null 2>&1 && $(PYTHONCONFIG) --ldflags --embed || (which $(PYTHONCONFIG) > /dev/null 2>&1 && $(PYTHONCONFIG) --ldflags || :) )
+python_SYSPATH =

potentials/HGa.msmeam

@@ -1,29 +1,29 @@
 bkgd_dyn        =       1
 emb_lin_neg = 1
-augt1=0 
-ialloy=1 
-rc	=	 5.9 
+augt1=0
+ialloy=1
+rc      =        5.9
 #H
-attrac(1,1)=0.460 
-repuls(1,1)=0.460 
+attrac(1,1)=0.460
+repuls(1,1)=0.460
 Cmin(1,1,1)=1.3 # PuMS
-Cmax(1,1,1)= 2.80 
+Cmax(1,1,1)= 2.80
 nn2(1,1)=1
 #Ga
 rho0(2)         =       0.6
-attrac(2,2)=0.097 
-repuls(2,2)=0.097 
+attrac(2,2)=0.097
+repuls(2,2)=0.097
 nn2(2,2)=1
 #HGa
-attrac(1,2)=0.300 
-repuls(1,2)=0.300 
-lattce(1,2)=l12 
-re(1,2)=3.19 
-delta(1,2)=-0.48  
-alpha(1,2)=6.6 
-Cmin(1,1,2)=2.0 
-Cmin(2,1,2)= 2.0 
-Cmin(1,2,1)=2.0 
+attrac(1,2)=0.300
+repuls(1,2)=0.300
+lattce(1,2)=l12
+re(1,2)=3.19
+delta(1,2)=-0.48
+alpha(1,2)=6.6
+Cmin(1,1,2)=2.0
+Cmin(2,1,2)= 2.0
+Cmin(1,2,1)=2.0
 Cmin(2,2,1)     =       1.4
 Cmin(1,2,2)     =       1.4
 Cmin(1,1,2)     =       1.4

python/install.py

@@ -18,7 +18,7 @@ parser = ArgumentParser(prog='install.py',
                         description='LAMMPS python package installer script')
 
 parser.add_argument("-p", "--package", required=True,
-                    help="path to the LAMMPS Python package")
+                    help="path to the LAMMPS Python package folder")
 parser.add_argument("-l", "--lib", required=True,
                     help="path to the compiled LAMMPS shared library")
 parser.add_argument("-n", "--noinstall", action="store_true", default=False,
@@ -34,15 +34,21 @@ args = parser.parse_args()
 
 if args.package:
   if not os.path.exists(args.package):
-    print("ERROR: LAMMPS package folder %s does not exist" % args.package)
+    print("\nERROR: LAMMPS package folder %s does not exist\n" % args.package)
     parser.print_help()
     sys.exit(1)
   else:
     args.package = os.path.abspath(args.package)
+    if ((os.path.basename(args.package) != "lammps")
+        and ((os.path.basename(os.path.dirname(args.package)) != "python"))):
+             print("\nERROR: LAMMPS package folder path %s does not end in %s\n"
+                   % (args.package, os.path.join("python", "lammps")))
+             parser.print_help()
+             sys.exit(1)
 
 if args.lib:
   if not os.path.exists(args.lib):
-    print("ERROR: LAMMPS shared library %s does not exist" % args.lib)
+    print("\nERROR: LAMMPS shared library %s does not exist\n" % args.lib)
     parser.print_help()
     sys.exit(1)
   else:
@@ -50,7 +56,7 @@ if args.lib:
 
 if args.wheeldir:
   if not os.path.exists(args.wheeldir):
-    print("ERROR: directory %s to store the wheel does not exist" % args.wheeldir)
+    print("\nERROR: directory %s to store the wheel does not exist\n" % args.wheeldir)
     parser.print_help()
     sys.exit(1)
   else:
@@ -58,7 +64,7 @@ if args.wheeldir:
 
 if args.versionfile:
   if not os.path.exists(args.versionfile):
-    print("ERROR: LAMMPS version file at %s does not exist" % args.versionfile)
+    print("\nERROR: LAMMPS version file at %s does not exist\n" % args.versionfile)
     parser.print_help()
     sys.exit(1)
   else:

python/lammps/core.py

@@ -334,8 +334,8 @@ class lammps(object):
     if self.has_mpi_support:
       try:
         from mpi4py import __version__ as mpi4py_version
-        # tested to work with mpi4py versions 2 and 3
-        self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
+        # tested to work with mpi4py versions 2, 3, and 4
+        self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3','4']
       except ImportError:
         # ignore failing import
         pass
@@ -361,7 +361,7 @@ class lammps(object):
         if not self.has_mpi_support:
           raise Exception('LAMMPS not compiled with real MPI library')
         if not self.has_mpi4py:
-          raise Exception('Python mpi4py version is not 2 or 3')
+          raise Exception('Python mpi4py version is not 2, 3, or 4')
         if self.MPI._sizeof(self.MPI.Comm) == sizeof(c_int):
           MPI_Comm = c_int
         else:
@@ -374,13 +374,18 @@ class lammps(object):
         narg = 0
         cargs = None
         if cmdargs is not None:
-          cmdargs.insert(0,"lammps")
-          narg = len(cmdargs)
-          for i in range(narg):
-            if type(cmdargs[i]) is str:
-              cmdargs[i] = cmdargs[i].encode()
-          cargs = (c_char_p*narg)(*cmdargs)
-          self.lib.lammps_open.argtypes = [c_int, c_char_p*narg, MPI_Comm, c_void_p]
+          myargs = ["lammps".encode()]
+          narg = len(cmdargs) + 1
+          for arg in cmdargs:
+            if type(arg) is str:
+              myargs.append(arg.encode())
+            elif type(arg) is bytes:
+              myargs.append(arg)
+            else:
+              raise TypeError('Unsupported cmdargs type ', type(arg))
+          cargs = (c_char_p*(narg+1))(*myargs)
+          cargs[narg] = None
+          self.lib.lammps_open.argtypes = [c_int, c_char_p*(narg+1), MPI_Comm, c_void_p]
         else:
           self.lib.lammps_open.argtypes = [c_int, c_char_p, MPI_Comm, c_void_p]
 
@@ -394,13 +399,18 @@ class lammps(object):
           self.comm = self.MPI.COMM_WORLD
         self.opened = 1
         if cmdargs is not None:
-          cmdargs.insert(0,"lammps")
-          narg = len(cmdargs)
-          for i in range(narg):
-            if type(cmdargs[i]) is str:
-              cmdargs[i] = cmdargs[i].encode()
-          cargs = (c_char_p*narg)(*cmdargs)
-          self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*narg, c_void_p]
+          myargs = ["lammps".encode()]
+          narg = len(cmdargs) + 1
+          for arg in cmdargs:
+            if type(arg) is str:
+              myargs.append(arg.encode())
+            elif type(arg) is bytes:
+              myargs.append(arg)
+            else:
+              raise TypeError('Unsupported cmdargs type ', type(arg))
+          cargs = (c_char_p*(narg+1))(*myargs)
+          cargs[narg] = None
+          self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*(narg+1), c_void_p]
           self.lmp = c_void_p(self.lib.lammps_open_no_mpi(narg,cargs,None))
         else:
           self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p, c_void_p]

python/lammps/numpy_wrapper.py

@@ -63,12 +63,16 @@ class numpy_wrapper:
 
     .. note::
 
-       While the returned arrays of per-atom data are dimensioned
-       for the range [0:nmax] - as is the underlying storage -
-       the data is usually only valid for the range of [0:nlocal],
-       unless the property of interest is also updated for ghost
-       atoms.  In some cases, this depends on a LAMMPS setting, see
-       for example :doc:`comm_modify vel yes <comm_modify>`.
+       The returned arrays of per-atom data are by default dimensioned
+       for the range [0:nlocal] since that data is *always* valid.  The
+       underlying storage for the data, however, is typically allocated
+       for the range of [0:nmax]. Whether there is valid data in the range
+       [nlocal:nlocal+nghost] depends on whether the property of interest
+       is also updated for ghost atoms.  This is not often the case.  In
+       some cases, it depends on a LAMMPS setting, see for example
+       :doc:`comm_modify vel yes <comm_modify>`.  By using the optional
+       *nelem* parameter the size of the returned NumPy can be overridden.
+       There is no check whether the number of elements chosen is valid.
 
     :param name: name of the property
     :type name:  string

python/lammps/pylammps.py

@@ -192,11 +192,23 @@ class Atom(object):
   @property
   def mass(self):
     """
-    Return the atom mass
+    Return the atom mass as a per-atom property.
+    This returns either the per-type mass or the per-atom
+    mass (AKA 'rmass') depending on what is available with
+    preference for the per-atom mass.
+
+    .. versionchanged:: 2Aug2023_update_4
+
+       Support both per-type and per-atom masses. With
+       per-type return "mass[type[i]]" else return "rmass[i]".
+       Per-atom mass is preferred if available.
 
     :type: float
     """
-    return self.get("mass", self.index)
+    if self._pylmp.lmp.extract_setting('rmass_flag'):
+      return self.get("rmass", self.index)
+    else:
+      return self.get("mass", self.type)
 
   @property
   def radius(self):

src/ADIOS/dump_atom_adios.cpp

@@ -281,8 +281,8 @@ void DumpAtomADIOS::init_style()
       auto nstreams = std::to_string(num_aggregators);
       internal->io.SetParameters({{"substreams", nstreams}});
       if (me == 0)
-        utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename,
-                       nstreams);
+        utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n",
+                       filename, nstreams);
     }
 
     internal->io.DefineVariable<uint64_t>("ntimestep");
@@ -325,6 +325,6 @@ void DumpAtomADIOS::init_style()
     // it will be correctly defined at the moment of write
     size_t UnknownSizeYet = 1;
     internal->varAtoms = internal->io.DefineVariable<double>(
-      "atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns});
+        "atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns});
   }
 }

src/ADIOS/dump_custom_adios.cpp

@@ -290,58 +290,60 @@ void DumpCustomADIOS::init_style()
 
   /* Define the group of variables for the atom style here since it's a fixed
    * set */
-  internal->io = internal->ad->DeclareIO(internal->ioName);
-  if (!internal->io.InConfigFile()) {
-    // if not defined by user, we can change the default settings
-    // BPFile is the default writer
-    internal->io.SetEngine("BPFile");
-    int num_aggregators = multiproc;
-    if (num_aggregators == 0) num_aggregators = 1;
-    auto nstreams = std::to_string(num_aggregators);
-    internal->io.SetParameters({{"substreams", nstreams}});
-    if (me == 0)
-      utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename,
-                     nstreams);
+  if (!internal->io) {
+    internal->io = internal->ad->DeclareIO(internal->ioName);
+    if (!internal->io.InConfigFile()) {
+      // if not defined by user, we can change the default settings
+      // BPFile is the default writer
+      internal->io.SetEngine("BPFile");
+      int num_aggregators = multiproc;
+      if (num_aggregators == 0) num_aggregators = 1;
+      auto nstreams = std::to_string(num_aggregators);
+      internal->io.SetParameters({{"substreams", nstreams}});
+      if (me == 0)
+        utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n",
+                       filename, nstreams);
+    }
+
+    internal->io.DefineVariable<uint64_t>("ntimestep");
+    internal->io.DefineVariable<uint64_t>("natoms");
+
+    internal->io.DefineVariable<int>("nprocs");
+    internal->io.DefineVariable<int>("ncolumns");
+
+    internal->io.DefineVariable<double>("boxxlo");
+    internal->io.DefineVariable<double>("boxxhi");
+    internal->io.DefineVariable<double>("boxylo");
+    internal->io.DefineVariable<double>("boxyhi");
+    internal->io.DefineVariable<double>("boxzlo");
+    internal->io.DefineVariable<double>("boxzhi");
+
+    internal->io.DefineVariable<double>("boxxy");
+    internal->io.DefineVariable<double>("boxxz");
+    internal->io.DefineVariable<double>("boxyz");
+
+    internal->io.DefineAttribute<int>("triclinic", domain->triclinic);
+
+    int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
+    internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
+
+    auto nColumns = static_cast<size_t>(size_one);
+    internal->io.DefineAttribute<std::string>("columns", internal->columnNames.data(), nColumns);
+    internal->io.DefineAttribute<std::string>("columnstr", columns);
+    internal->io.DefineAttribute<std::string>("boundarystr", boundstr);
+    internal->io.DefineAttribute<std::string>("LAMMPS/dump_style", "custom");
+    internal->io.DefineAttribute<std::string>("LAMMPS/version", lmp->version);
+    internal->io.DefineAttribute<std::string>("LAMMPS/num_ver", std::to_string(lmp->num_ver));
+
+    internal->io.DefineVariable<uint64_t>("nme",
+                                          {adios2::LocalValueDim});    // local dimension variable
+    internal->io.DefineVariable<uint64_t>("offset",
+                                          {adios2::LocalValueDim});    // local dimension variable
+
+    // atom table size is not known at the moment
+    // it will be correctly defined at the moment of write
+    size_t UnknownSizeYet = 1;
+    internal->varAtoms = internal->io.DefineVariable<double>(
+        "atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns});
   }
-
-  internal->io.DefineVariable<uint64_t>("ntimestep");
-  internal->io.DefineVariable<uint64_t>("natoms");
-
-  internal->io.DefineVariable<int>("nprocs");
-  internal->io.DefineVariable<int>("ncolumns");
-
-  internal->io.DefineVariable<double>("boxxlo");
-  internal->io.DefineVariable<double>("boxxhi");
-  internal->io.DefineVariable<double>("boxylo");
-  internal->io.DefineVariable<double>("boxyhi");
-  internal->io.DefineVariable<double>("boxzlo");
-  internal->io.DefineVariable<double>("boxzhi");
-
-  internal->io.DefineVariable<double>("boxxy");
-  internal->io.DefineVariable<double>("boxxz");
-  internal->io.DefineVariable<double>("boxyz");
-
-  internal->io.DefineAttribute<int>("triclinic", domain->triclinic);
-
-  int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
-  internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
-
-  auto nColumns = static_cast<size_t>(size_one);
-  internal->io.DefineAttribute<std::string>("columns", internal->columnNames.data(), nColumns);
-  internal->io.DefineAttribute<std::string>("columnstr", columns);
-  internal->io.DefineAttribute<std::string>("boundarystr", boundstr);
-  internal->io.DefineAttribute<std::string>("LAMMPS/dump_style", "custom");
-  internal->io.DefineAttribute<std::string>("LAMMPS/version", lmp->version);
-  internal->io.DefineAttribute<std::string>("LAMMPS/num_ver", std::to_string(lmp->num_ver));
-
-  internal->io.DefineVariable<uint64_t>("nme",
-                                        {adios2::LocalValueDim});    // local dimension variable
-  internal->io.DefineVariable<uint64_t>("offset",
-                                        {adios2::LocalValueDim});    // local dimension variable
-
-  // atom table size is not known at the moment
-  // it will be correctly defined at the moment of write
-  size_t UnknownSizeYet = 1;
-  internal->varAtoms = internal->io.DefineVariable<double>(
-      "atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns});
 }

src/ASPHERE/pair_ylz.cpp

@@ -300,6 +300,7 @@ double PairYLZ::init_one(int i, int j)
   zeta[j][i] = zeta[i][j];
   mu[j][i] = mu[i][j];
   beta[j][i] = beta[i][j];
+  cut[j][i] = cut[i][j];
 
   return cut[i][j];
 }
@@ -409,7 +410,7 @@ void PairYLZ::write_data_all(FILE *fp)
 {
   for (int i = 1; i <= atom->ntypes; i++)
     for (int j = i; j <= atom->ntypes; j++)
-      fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][i], sigma[i][i], cut[i][j],
+      fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][j], sigma[i][j], cut[i][j],
               zeta[i][j], mu[i][j], beta[i][j]);
 }