Merge pull request #2064 from akohlmey/next_lammps_version

Update version strings for the next patch release

.github/CODEOWNERS

@@ -22,7 +22,6 @@ src/SPIN/*            @julient31
 src/USER-CGDNA/*      @ohenrich
 src/USER-CGSDK/*      @akohlmey
 src/USER-COLVARS/*    @giacomofiorin
-src/USER-DPD/*        @timattox
 src/USER-INTEL/*      @wmbrownintel
 src/USER-MANIFOLD/*   @Pakketeretet2
 src/USER-MEAMC/*      @martok
@@ -46,7 +45,7 @@ src/GPU/pair_vashishta_gpu.*        @andeplane
 src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
-src/USER-MISC/fix_bond_react.*      @jrgissing
+src/USER-REACTION/fix_bond_react.*  @jrgissing
 src/USER-MISC/*_grem.*              @dstelter92
 src/USER-MISC/compute_stress_mop*.* @RomainVermorel
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -9,24 +9,24 @@ assignees: ''
 
 **Summary**
 
-_Please provide a clear and concise description of what the bug is._
+<!--Please provide a clear and concise description of what the bug is.-->
 
 **LAMMPS Version and Platform**
 
-_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
+<!--Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version-->
 
 **Expected Behavior**
 
-_Describe the expected behavior.  Quote from the LAMMPS manual where needed, or explain why the expected behavior is meaningful, especially when it differs from the manual_
+<!--Describe the expected behavior.  Quote from the LAMMPS manual where needed, or explain why the expected behavior is meaningful, especially when it differs from the manual-->
 
 **Actual Behavior**
 
-_Describe the actual behavior, how it differs from the expected behavior, and how this can be observed.  Try to be specific and do **not** use vague terms like "doesn't work" or "wrong result".  Do not assume that the person reading this has any experience with or knowledge of your specific area of research._
+<!--Describe the actual behavior, how it differs from the expected behavior, and how this can be observed.  Try to be specific and do **not** use vague terms like "doesn't work" or "wrong result".  Do not assume that the person reading this has any experience with or knowledge of your specific area of research.-->
 
 **Steps to Reproduce**
 
-_Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem._
+<!--Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem.-->
 
 **Further Information, Files, and Links**
 
-_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -9,12 +9,12 @@ assignees: ''
 
 **Summary**
 
-_Please provide a brief and concise description of the suggested feature or change_
+<!--Please provide a brief and concise description of the suggested feature or change-->
 
 **Detailed Description**
 
-_Please explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address._
+<!--Please explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address.-->
 
 **Further Information, Files, and Links**
 
-_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_
+<!--Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications-->

.github/ISSUE_TEMPLATE/generic.md

@@ -9,13 +9,13 @@ assignees: ''
 
 **Summary**
 
-_Please provide a clear and concise description of what this issue report is about._
+<!--Please provide a clear and concise description of what this issue report is about.-->
 
 **LAMMPS Version and Platform**
 
-_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
+<!--Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version-->
 
 **Details**
 
-_Please explain the issue in detail here_
+<!--Please explain the issue in detail here-->
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,14 +1,14 @@
 **Summary**
 
-_Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request._
+<!--Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request.-->
 
 **Related Issues**
 
-_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
+<!--If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged-->
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code._
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code.-->
 
 **Licensing**
 
@@ -16,15 +16,15 @@ By submitting this pull request, I agree, that my contribution will be included
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+<!--Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
 
 **Implementation Notes**
 
-_Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
+<!--Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
 
 **Post Submission Checklist**
 
-_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
+<!--Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply-->
 
 - [ ] The feature or features in this pull request is complete
 - [ ] Licensing information is complete
@@ -39,6 +39,6 @@ _Please check the fields below as they are completed **after** the pull request
 
 **Further Information, Files, and Links**
 
-_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->
 
 

.github/PULL_REQUEST_TEMPLATE/bug_fix.md

@@ -9,15 +9,15 @@ assignees: ''
 
 **Summary**
 
-_Briefly describe the bug or bugs, that are eliminated by this pull request._
+<!--Briefly describe the bug or bugs, that are eliminated by this pull request.-->
 
 **Related Issue(s)**
 
-_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`._
+<!--If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.-->
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
 
 **Licensing**
 
@@ -25,18 +25,18 @@ By submitting this pull request I implicitly accept, that my submission is subje
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+<!--Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
 
 **Detailed Description**
 
-_Provide any relevant details about how the fixed bug can be reproduced, how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
+<!--Provide any relevant details about how the fixed bug can be reproduced, how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
 
 ## Post Submission Checklist
 
-_Please check the fields below as they are completed *after* the pull request is submitted_
+<!--Please check the fields below as they are completed *after* the pull request is submitted-->
 - [ ] The code in this pull request is complete
 - [ ] The source code follows the LAMMPS formatting guidelines
 
 ## Further Information, Files, and Links
 
-_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. to download input decks for testing)_
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. to download input decks for testing)-->

.github/PULL_REQUEST_TEMPLATE/maintenance_refactoring.md

@@ -9,15 +9,15 @@ assignees: ''
 
 **Summary**
 
-_Briefly describe the included changes._
+<!--Briefly describe the included changes.-->
 
 **Related Issue(s)**
 
-_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.
+<!--If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
 
 **Licensing**
 
@@ -25,11 +25,11 @@ By submitting this pull request I implicitly accept, that my submission is subje
 
 **Detailed Description**
 
-_Provide any relevant details about the included changes._
+<!--Provide any relevant details about the included changes.-->
 
 ## Post Submission Checklist
 
-_Please check the fields below as they are completed *after* the pull request is submitted_
+<!--Please check the fields below as they are completed *after* the pull request is submitted-->
 - [ ] The pull request is complete
 - [ ] The source code follows the LAMMPS formatting guidelines
 

.github/PULL_REQUEST_TEMPLATE/new_feature.md

@@ -9,34 +9,34 @@ assignees: ''
 
 **Summary**
 
-_Briefly describe the new feature(s) included in this pull request._
+<!--Briefly describe the new feature(s) included in this pull request.-->
 
 **Related Issues**
 
-_If this addresses an existing (open) GitHub issue, e.g. a feature request, mention the issue number here following a pound sign (aka hashmark), e.g. `#331`._
+<!--If this addresses an existing (open) GitHub issue, e.g. a feature request, mention the issue number here following a pound sign (aka hashmark), e.g. `#331`.-->
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the features added in this pull request. Please provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future_
+<!--Please state name and affiliation of the author or authors that should be credited with the features added in this pull request. Please provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future-->
 
 **Licensing**
 
-_Please add *yes* or *no* to the following two statements (please contact @lammps/core if you have questions about this)_
+<!--Please add *yes* or *no* to the following two statements (please contact @lammps/core if you have questions about this)-->
 
 My contribution may be licensed as GPL v2 (default LAMMPS license):
 My contribution may be licensed as LGPL (for use as a library with proprietary software):
 
 **Backward Compatibility**
 
-_Please state if any of the changes in this pull request will affect backward compatibility for inputs, and - if yes - explain what has been changed and why_
+<!--Please state if any of the changes in this pull request will affect backward compatibility for inputs, and - if yes - explain what has been changed and why-->
 
 **Implementation Notes**
 
-_Provide any relevant details about how the new features are implemented, how correctness was verified, what platforms (OS, compiler, MPI, hardware, number of processors, accelerator(s)) it was tested on_
+<!--Provide any relevant details about how the new features are implemented, how correctness was verified, what platforms (OS, compiler, MPI, hardware, number of processors, accelerator(s)) it was tested on-->
 
 ## Post Submission Checklist
 
-_Please check the fields below as they are completed *after* the pull request has been submitted_
+<!--Please check the fields below as they are completed *after* the pull request has been submitted-->
 
 - [ ] The feature or features in this pull request is complete
 - [ ] Licensing information is complete
@@ -51,6 +51,6 @@ _Please check the fields below as they are completed *after* the pull request ha
 
 ## Further Information, Files, and Links
 
-_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->
 
 

.github/PULL_REQUEST_TEMPLATE/update_enhancement.md

@@ -9,11 +9,11 @@ assignees: ''
 
 **Summary**
 
-_Briefly describe what kind of updates or enhancements for a package or feature are included. If you are not the original author of the package or feature, please mention, whether your contribution was created independently or in collaboration/cooperation with the original author._
+<!--Briefly describe what kind of updates or enhancements for a package or feature are included. If you are not the original author of the package or feature, please mention, whether your contribution was created independently or in collaboration/cooperation with the original author.-->
 
 **Author(s)**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
+<!--Please state name and affiliation of the author or authors that should be credited with the changes in this pull request-->
 
 **Licensing**
 
@@ -21,15 +21,15 @@ By submitting this pull request I implicitly accept, that my submission is subje
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+<!--Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why-->
 
 **Implementation Notes**
 
-_Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_
+<!--Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected-->
 
 **Post Submission Checklist**
 
-_Please check the fields below as they are completed_
+<!--Please check the fields below as they are completed-->
 - [ ] The feature or features in this pull request is complete
 - [ ] Suitable updates to the existing docs are included
 - [ ] One or more example input decks are included
@@ -37,6 +37,6 @@ _Please check the fields below as they are completed_
 
 **Further Information, Files, and Links**
 
-_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_
+<!--Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)-->
 
 

cmake/CMakeLists.txt

@@ -135,23 +135,20 @@ if(PKG_USER-ADIOS)
   target_link_libraries(lammps PRIVATE adios2::adios2)
 endif()
 
-if (CMAKE_SYSTEM_NAME STREQUAL Windows)
-  option(BUILD_MPI "Build MPI version" OFF)
-else()
-  # do MPI detection after language activation,
-  # in case MPI for these languages is required
+if(NOT CMAKE_CROSSCOMPILING)
   set(MPI_CXX_SKIP_MPICXX TRUE)
   find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
+else()
+  option(BUILD_MPI "Build MPI version" OFF)
 endif()
 
 if(BUILD_MPI)
-  # We use a non-standard procedure to compile with MPI on windows
-  if (CMAKE_SYSTEM_NAME STREQUAL Windows)
+  # We use a non-standard procedure to cross-compile with MPI on Windows
+  if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
     include(MPI4WIN)
     target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
   else()
-    set(MPI_CXX_SKIP_MPICXX ON)
     find_package(MPI REQUIRED)
     target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
     option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
@@ -163,9 +160,6 @@ else()
   enable_language(C)
   file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
   add_library(mpi_stubs STATIC ${MPI_SOURCES})
-  if(NOT BUILD_SHARED_LIBS)
-    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  endif()
   set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
   target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS> $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi>)
   install(FILES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi)
@@ -252,9 +246,6 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
     enable_language(Fortran)
     file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
     add_library(linalg STATIC ${LAPACK_SOURCES})
-    if(NOT BUILD_SHARED_LIBS)
-      install(TARGETS linalg EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
     set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
     set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
     set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
@@ -332,8 +323,9 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific opt
 separate_arguments(CMAKE_TUNE_FLAGS)
 include(CheckCXXCompilerFlag)
 foreach(_FLAG ${CMAKE_TUNE_FLAGS})
-  check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
-  if(COMPILER_SUPPORTS${_FLAG})
+  string(REGEX REPLACE "[=\"]" "" _FLAGX ${_FLAG})
+  check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
+  if(COMPILER_SUPPORTS${_FLAGX})
     target_compile_options(lammps PRIVATE ${_FLAG})
   else()
     message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
@@ -413,9 +405,6 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
       ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
       ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
-    if(NOT BUILD_SHARED_LIBS)
-      install(TARGETS ${PKG_LIB} EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
     set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
     target_link_libraries(lammps PRIVATE ${PKG_LIB})
     if(PKG_LIB STREQUAL awpmd)
@@ -436,7 +425,12 @@ if(PKG_USER-ATC)
   if(LAMMPS_SIZES STREQUAL BIGBIG)
     message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
   endif()
-  target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} MPI::MPI_CXX)
+  target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
+  if(BUILD_MPI)
+    target_link_libraries(atc PRIVATE MPI::MPI_CXX)
+  else()
+    target_link_libraries(atc PRIVATE mpi_stubs)
+  endif()
   target_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR})
   target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 endif()
@@ -522,14 +516,15 @@ endif()
 
 set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
 set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
-install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
 target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
 file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
 foreach(_HEADER ${LAMMPS_CXX_HEADERS})
   add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
   add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
   add_dependencies(lammps ${_HEADER})
-  install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  if(BUILD_SHARED_LIBS)
+    install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  endif()
 endforeach()
 target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
 add_library(LAMMPS::lammps ALIAS lammps)
@@ -538,15 +533,18 @@ set(LAMMPS_API_DEFINES)
 foreach(_DEF ${LAMMPS_DEFINES})
   set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
 endforeach()
-configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
-file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
-install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
-include(CMakePackageConfigHelpers)
-configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
-write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
-install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
+if(BUILD_SHARED_LIBS)
+  install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+  install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
+  file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
+  install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
+  include(CMakePackageConfigHelpers)
+  configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
+  write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
+  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
+endif()
 install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
 
 if(BUILD_TOOLS)
@@ -555,7 +553,7 @@ if(BUILD_TOOLS)
   install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
 
   include(CheckGeneratorSupport)
-  if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
+  if(CMAKE_GENERATOR_SUPPORT_FORTRAN AND CMAKE_Fortran_COMPILER)
     enable_language(Fortran)
     add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
     target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
@@ -705,6 +703,7 @@ else()
 endif()
 if(BUILD_MPI)
   message(STATUS "<<< MPI flags >>>
+-- MPI_defines:      ${MPI_CXX_COMPILE_DEFINITIONS}
 -- MPI includes:     ${MPI_CXX_INCLUDE_PATH}
 -- MPI libraries:    ${MPI_CXX_LIBRARIES};${MPI_Fortran_LIBRARIES}")
 endif()

cmake/LAMMPSConfig.cmake.in

@@ -1,4 +1,4 @@
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
 include(CMakeFindDependencyMacro)
 if(@BUILD_MPI@)
   find_dependency(MPI REQUIRED CXX)
@@ -8,80 +8,4 @@ if(@PKG_KSPACE@)
     find_dependency(@FFTW@ REQUIRED MODULE)
   endif()
 endif()
-if(NOT @BUILD_SHARED_LIBS@)
-  if(@BUILD_OMP@)
-    find_dependency(OpenMP REQUIRED)
-  endif()
-  if(@WITH_JPEG@)
-    find_dependency(JPEG REQUIRED)
-  endif()
-  if(@WITH_PNG@)
-    find_dependency(PNG REQUIRED)
-    find_dependency(ZLIB REQUIRED)
-  endif()
-  if(@PKG_KIM@)
-    find_dependency(PkgConfig REQUIRED)
-    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=@KIM-API_MIN_VERSION@)
-    if(@CURL_FOUND@)
-      find_dependency(CURL REQUIRED)
-    endif()
-  endif()
-  if(@PKG_USER-SMD@)
-    find_dependency(Eigen3 NO_MODULE REQUIRED)
-  endif()
-  if(@PKG_USER-SCAFACOS@)
-    find_dependency(PkgConfig REQUIRED)
-    find_ependency(GSL REQUIRED)
-    find_dependency(MPI REQUIRED C Fortran)
-    pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)
-  endif()
-  if(@PKG_PYTHON@ AND NOT CMAKE_VERSION VERSION_LESS 3.12)
-    find_package(Python REQUIRED COMPONENTS Development)
-  endif()
-  if(@PKG_COMPRESS@)
-    find_dependency(ZLIB REQUIRED)
-  endif()
-  if(@PKG_KOKKOS@)
-    if(@EXTERNAL_KOKKOS@)
-      find_dependency(Kokkos 3 REQUIRED)
-    endif()
-  endif()
-  if(@PKG_VORONOI@)
-    find_dependency(VORO REQUIRED)
-  endif()
-  if(@PKG_USER-INTEL@)
-    if(@INTEL_LRT_MODE@ STREQUAL "THREADS")
-      find_dependency(Threads REQUIRED)
-    endif()
-    if(@TBB_MALLOC_FOUND@)
-      find_ependency(TBB_MALLOC REQUIRED)
-    endif()
-  endif()
-  if(@PKG_USER-ADIOS@)
-    find_ependency(ADIOS2 REQUIRED)
-  endif()
-  if(@PKG_LATTE@)
-    find_ependency(LATTE REQUIRED)
-  endif()
-  if(@PKG_MESSAGE@)
-    if(@MESSAGE_ZMQ@)
-      find_ependency(ZMQ REQUIRED)
-    endif()
-  endif()
-  if(@PKG_MSCG@)
-    find_ependency(GSL REQUIRED)
-    find_ependency(MSCG REQUIRED)
-  endif()
-  if(@USER-NETCDF@)
-    if(@NETCDF_FOUND@)
-      find_ependency(NetCDF REQUIRED)
-    endif()
-    if(@PNETCDF_FOUND@)
-      find_ependency(PNetCDF REQUIRED)
-    endif()
-  endif()
-  if(@PKG_QUIP@)
-    find_ependency(QUIP REQUIRED)
-  endif()
-endif()
 include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")

cmake/Modules/MPI4WIN.cmake

@@ -23,3 +23,8 @@ set_target_properties(MPI::MPI_CXX PROPERTIES
   INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
   INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
 add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+# set variables for status reporting at the end of CMake run
+set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")

cmake/Modules/Packages/GPU.cmake

@@ -330,7 +330,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   if(HIP_PLATFORM STREQUAL "nvcc")
     target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/include)
+    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
     target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
     target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
 
@@ -338,6 +338,12 @@ elseif(GPU_API STREQUAL "HIP")
     target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include)
     target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
     target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+  elseif(HIP_PLATFORM STREQUAL "hcc")
+    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__)
+    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+
+    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
+    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
   endif()
 
   target_link_libraries(lammps PRIVATE gpu)
@@ -353,9 +359,11 @@ RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
 
 get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
 
-target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
-if(NOT BUILD_SHARED_LIBS)
-  install(TARGETS gpu EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+if(NOT BUILD_MPI)
+  # mpistubs is aliased to MPI::MPI_CXX, but older versions of cmake won't work forward the include path
+  target_link_libraries(gpu PRIVATE mpi_stubs)
+else()
+  target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
 endif()
 target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})

cmake/Modules/Packages/KIM.cmake

@@ -1,7 +1,12 @@
 set(KIM-API_MIN_VERSION 2.1.3)
 find_package(CURL)
 if(CURL_FOUND)
-  target_link_libraries(lammps PRIVATE CURL::libcurl)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    target_include_directories(lammps PRIVATE ${CURL_INCLUDE_DIRS})
+    target_link_libraries(lammps PRIVATE ${CURL_LIBRARIES})
+  else()
+    target_link_libraries(lammps PRIVATE CURL::libcurl)
+  endif()
   target_compile_definitions(lammps PRIVATE -DLMP_KIM_CURL)
   set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
   mark_as_advanced(LMP_DEBUG_CURL)
@@ -51,9 +56,6 @@ if(DOWNLOAD_KIM)
     INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api")
   target_link_libraries(lammps PRIVATE LAMMPS::KIM)
   add_dependencies(LAMMPS::KIM kim_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(PkgConfig REQUIRED)
   pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})

cmake/Modules/Packages/KOKKOS.cmake

@@ -14,16 +14,30 @@ endif()
 option(EXTERNAL_KOKKOS "Build against external kokkos library" OFF)
 option(DOWNLOAD_KOKKOS "Download the KOKKOS library instead of using the bundled one" OFF)
 if(DOWNLOAD_KOKKOS)
+  # extract Kokkos-related variables and values so we can forward them to the Kokkos library build
+  get_cmake_property(_VARS VARIABLES)
+  list(FILTER _VARS INCLUDE REGEX ^Kokkos_)
+  foreach(_VAR IN LISTS _VARS)
+    list(APPEND KOKKOS_LIB_BUILD_ARGS "-D${_VAR}=${${_VAR}}")
+  endforeach()
   message(STATUS "KOKKOS download requested - we will build our own")
-  file(DOWNLOAD https://github.com/kokkos/kokkos/compare/3.0.00...stanmoore1:lammps.diff ${CMAKE_CURRENT_BINARY_DIR}/kokkos-lammps.patch)
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>")
+  if(CMAKE_REQUEST_PIC)
+    list(APPEND KOKKOS_LIB_BUILD_ARGS ${CMAKE_REQUEST_PIC})
+  endif()
+  # append other CMake variables that need to be forwarded to CMAKE_ARGS
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_INSTALL_LIBDIR=lib")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_STANDARD=${CMAKE_CXX_STANDARD}")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
+  list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
   ExternalProject_Add(kokkos_build
-    URL https://github.com/kokkos/kokkos/archive/3.0.00.tar.gz
-    URL_MD5 281c7093aa3a603276e93abdf4be23b9
-    PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/kokkos-lammps.patch
-    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
-    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_INSTALL_LIBDIR=lib
-    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+    URL https://github.com/kokkos/kokkos/archive/3.1.00.tar.gz
+    URL_MD5 f638a6c786f748a602b26faa0e96ebab
+    CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )
   ExternalProject_get_property(kokkos_build INSTALL_DIR)
@@ -35,13 +49,10 @@ if(DOWNLOAD_KOKKOS)
     INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
   add_dependencies(LAMMPS::KOKKOS kokkos_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3)
+  find_package(Kokkos 3.1)
   if(NOT Kokkos_FOUND)
-    message(FATAL_ERROR "KOKKOS library not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
+    message(FATAL_ERROR "KOKKOS library version 3.1 or later not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
   endif()
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()

cmake/Modules/Packages/LATTE.cmake

@@ -1,4 +1,11 @@
 enable_language(Fortran)
+
+# using lammps in a super-build setting
+if(TARGET LATTE::latte)
+  target_link_libraries(lammps PRIVATE LATTE::latte)
+  return()
+endif()
+
 find_package(LATTE)
 if(LATTE_FOUND)
   set(DOWNLOAD_LATTE_DEFAULT OFF)
@@ -27,13 +34,11 @@ if(DOWNLOAD_LATTE)
     INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
   target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
   add_dependencies(LAMMPS::LATTE latte_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(LATTE)
   if(NOT LATTE_FOUND)
     message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
   endif()
-  target_link_libraries(lammps PRIVATE LATTE::latte)
+  # latte needs lapack
+  target_link_libraries(lammps PRIVATE LATTE::latte ${LAPACK_LIBRARIES})
 endif()

cmake/Modules/Packages/MESSAGE.cmake

@@ -7,9 +7,6 @@ file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
     ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
 
 add_library(cslib STATIC ${cslib_SOURCES})
-if(NOT BUILD_SHARED_LIBS)
-  install(TARGETS cslib EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-endif()
 target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 set_target_properties(cslib PROPERTIES OUTPUT_NAME lammps_cslib${LAMMPS_MACHINE})
 if(BUILD_MPI)

cmake/Modules/Packages/MSCG.cmake

@@ -35,9 +35,6 @@ if(DOWNLOAD_MSCG)
     INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
   target_link_libraries(lammps PRIVATE LAMMPS::MSCG)
   add_dependencies(LAMMPS::MSCG mscg_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(MSCG)
   if(NOT MSCG_FOUND)

cmake/Modules/Packages/USER-COLVARS.cmake

@@ -9,9 +9,6 @@ if(COLVARS_LEPTON)
   set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
   file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
   add_library(lepton STATIC ${LEPTON_SOURCES})
-  if(NOT BUILD_SHARED_LIBS)
-    install(TARGETS lepton EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  endif()
   # Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
   target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
   set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
@@ -19,9 +16,6 @@ if(COLVARS_LEPTON)
 endif()
 
 add_library(colvars STATIC ${COLVARS_SOURCES})
-if(NOT BUILD_SHARED_LIBS)
-  install(TARGETS colvars EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-endif()
 target_compile_definitions(colvars PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
 target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)

cmake/Modules/Packages/USER-H5MD.cmake

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

cmake/Modules/Packages/USER-MOLFILE.cmake

@@ -1,8 +1,5 @@
 set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
 add_library(molfile INTERFACE)
-if(NOT BUILD_SHARED_LIBS)
-  install(TARGETS molfile EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-endif()
 target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
 # no need to link with -ldl on windows
 if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -1,11 +1,18 @@
 # USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
 # NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
-find_package(NetCDF)
-if(NETCDF_FOUND)
-  find_package(PNetCDF)
-else(NETCDF_FOUND)
-  find_package(PNetCDF REQUIRED)
-endif(NETCDF_FOUND)
+if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.12)
+  cmake_policy(SET CMP0074 NEW)
+endif()
+if(NOT BUILD_MPI)
+  find_package(NetCDF REQUIRED)
+else()
+  find_package(NetCDF)
+  if(NETCDF_FOUND)
+    find_package(PNetCDF)
+  else()
+    find_package(PNetCDF REQUIRED)
+  endif()
+endif()
 
 if(NETCDF_FOUND)
   target_link_libraries(lammps PRIVATE NetCDF::NetCDF)

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -70,16 +70,12 @@ if(DOWNLOAD_PLUMED)
   ExternalProject_get_property(plumed_build INSTALL_DIR)
   add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
   add_dependencies(LAMMPS::PLUMED plumed_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
   if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_WRAPPER_CXX=1")
     set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "SHARED")
     set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_HAS_DLOPEN=1;__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
     set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
   endif()
   set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
@@ -89,12 +85,11 @@ else()
   pkg_check_modules(PLUMED REQUIRED plumed)
   add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
   if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_WRAPPER_CXX=1")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
   elseif(PLUMED_MODE STREQUAL "SHARED")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_HAS_DLOPEN=1;__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
   endif()
   set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")

cmake/Modules/Packages/USER-QMMM.cmake

@@ -1,12 +1,6 @@
 enable_language(C)
 
-if(NOT BUILD_SHARED_LIBS)
-  message(WARNING "It is recommended to use BUILD_SHARED_LIBS=yes with USER-QMMM")
-endif()
 add_library(qmmm STATIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm/libqmmm.c)
-if(NOT BUILD_SHARED_LIBS)
-  install(TARGETS qmmm EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-endif()
 set_target_properties(qmmm PROPERTIES OUTPUT_NAME lammps_qmmm${LAMMPS_MACHINE})
 target_link_libraries(lammps PRIVATE qmmm)
 target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -52,9 +52,6 @@ if(DOWNLOAD_SCAFACOS)
     INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libfcs.a;${INSTALL_DIR}/lib/libfcs_direct.a;${INSTALL_DIR}/lib/libfcs_ewald.a;${INSTALL_DIR}/lib/libfcs_fmm.a;${INSTALL_DIR}/lib/libfcs_p2nfft.a;${INSTALL_DIR}/lib/libfcs_p3m.a;GSL::gsl;${INSTALL_DIR}/lib/libfcs_near.a;${INSTALL_DIR}/lib/libfcs_gridsort.a;${INSTALL_DIR}/lib/libfcs_resort.a;${INSTALL_DIR}/lib/libfcs_redist.a;${INSTALL_DIR}/lib/libfcs_common.a;${INSTALL_DIR}/lib/libfcs_pnfft.a;${INSTALL_DIR}/lib/libfcs_pfft.a;${INSTALL_DIR}/lib/libfcs_fftw3_mpi.a;${INSTALL_DIR}/lib/libfcs_fftw3.a;MPI::MPI_Fortran;MPI::MPI_C")
   target_link_libraries(lammps PRIVATE LAMMPS::SCAFACOS)
   add_dependencies(LAMMPS::SCAFACOS scafacos_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(PkgConfig REQUIRED)
   pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)

cmake/Modules/Packages/USER-SMD.cmake

@@ -18,9 +18,6 @@ if(DOWNLOAD_EIGEN3)
   set_target_properties(LAMMPS::EIGEN3 PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}")
   target_link_libraries(lammps PRIVATE LAMMPS::EIGEN3)
   add_dependencies(LAMMPS::EIGEN3 Eigen3_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(Eigen3 NO_MODULE)
   mark_as_advanced(Eigen3_DIR)

cmake/Modules/Packages/VORONOI.cmake

@@ -24,7 +24,11 @@ if(DOWNLOAD_VORO)
   ExternalProject_Add(voro_build
     URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
     URL_MD5 2338b824c3b7b25590e18e8df5d68af9
-    CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
+    PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND make ${VORO_BUILD_OPTIONS}
+    BUILD_IN_SOURCE 1
+    INSTALL_COMMAND ""
     BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
     )
   ExternalProject_get_property(voro_build SOURCE_DIR)
@@ -35,9 +39,6 @@ if(DOWNLOAD_VORO)
     INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src")
   target_link_libraries(lammps PRIVATE LAMMPS::VORO)
   add_dependencies(LAMMPS::VORO voro_build)
-  if(NOT BUILD_SHARED_LIBS)
-    install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
-  endif()
 else()
   find_package(VORO)
   if(NOT VORO_FOUND)

cmake/presets/clang.cmake

@@ -2,7 +2,7 @@
 
 set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
 set(MPI_CXX "clang++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)

cmake/presets/hip.cmake

@@ -0,0 +1,12 @@
+# preset that will enable hipcc plus gcc with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+
+set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)
+

cmake/presets/most.cmake

@@ -5,10 +5,10 @@
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL
         DIPOLE GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
         POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-        USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
-        USER-DPD USER-DRUDE USER-FEP USER-MEAMC USER-MESODPD
+        USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
+        USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
         USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
-        USER-REAXC USER-SPH USER-SMD USER-UEF USER-YAFF)
+        USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

doc/include-file-conventions.md

@@ -49,22 +49,15 @@ include files provided with LAMMPS are included with double quotes
 
 For headers declaring functions of the C-library, the corresponding
 C++ versions should be included (examples: `#include <cstdlib>` or
-`#include <cctypes>`).  However, these includes are limited to those defined
-in the C++98 standard.  Some files thus must use the older style until
-the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
-even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
-or `#include <inttypes.h>` versus `#include <cinttypes>`).
+`#include <cctypes>` instead of `#include <stdlib.h>` or
+`#include<ctypes.h>` ).
 
 ### C++ Standard Compliance
 
-LAMMPS core files currently correspond to the C++98 standard. Files
-requiring C++11 or later are only permitted in (optional) packages
-and particularly packages that are not part of the list of commonly
-used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
-
-Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.
-Since using both at the same time can cause problems, iostreams should
-be avoided where possible.
+LAMMPS core files use standard conforming C++ compatible with the
+C++11 standard, unless explicitly noted.  Also, LAMMPS uses the C-style
+stdio library for I/O instead of iostreams.  Since using both at the
+same time can cause problems, iostreams should be avoided where possible.
 
 ### Lean Header Files
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "15 April 2020" "2020-04-15"
+.TH LAMMPS "5 May 2020" "2020-05-5"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_extras.rst

@@ -320,11 +320,12 @@ to have an executable that will run on this and newer architectures.
 
 .. note::
 
-   NVIDIA GPUs with CC 5.0 (Maxwell) and newer are not compatible with
-   CC 3.x (Kepler).  If you run Kokkos on a newer architecture than what
-   LAMMPS was compiled with, there will be a significant delay during
-   device initialization since the just-in-time compiler has to
-   recompile the GPU kernel code for the new hardware.
+   If you run Kokkos on a newer GPU architecture than what LAMMPS was
+   compiled with, there will be a delay during device initialization
+   since the just-in-time compiler has to recompile all GPU kernels
+   for the new hardware.  This is, however, not possible when compiled
+   for NVIDIA GPUs with CC 3.x (Kepler) for GPUs with CC 5.0 (Maxwell)
+   and newer as they are not compatible.
 
 The settings discussed below have been tested with LAMMPS and are
 confirmed to work.  Kokkos is an active project with ongoing improvements
@@ -343,73 +344,109 @@ be specified in uppercase.
    :widths: auto
 
    *  - **Arch-ID**
+      - **HOST or GPU**
       - **Description**
    *  - AMDAVX
+      - HOST
       - AMD 64-bit x86 CPU (AVX 1)
    *  - EPYC
+      - HOST
       - AMD EPYC Zen class CPU (AVX 2)
    *  - ARMV80
+      - HOST
       - ARMv8.0 Compatible CPU
    *  - ARMV81
+      - HOST
       - ARMv8.1 Compatible CPU
    *  - ARMV8_THUNDERX
+      - HOST
       - ARMv8 Cavium ThunderX CPU
    *  - ARMV8_THUNDERX2
+      - HOST
       - ARMv8 Cavium ThunderX2 CPU
    *  - WSM
+      - HOST
       - Intel Westmere CPU (SSE 4.2)
    *  - SNB
+      - HOST
       - Intel Sandy/Ivy Bridge CPU (AVX 1)
    *  - HSW
+      - HOST
       - Intel Haswell CPU (AVX 2)
    *  - BDW
+      - HOST
       - Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
    *  - SKX
+      - HOST
       - Intel Sky Lake Xeon E-class HPC CPU (AVX512 + transactional mem)
    *  - KNC
+      - HOST
       - Intel Knights Corner Xeon Phi
    *  - KNL
+      - HOST
       - Intel Knights Landing Xeon Phi
    *  - BGQ
+      - HOST
       - IBM Blue Gene/Q CPU
    *  - POWER7
-      - IBM POWER8 CPU
+      - HOST
+      - IBM POWER7 CPU
    *  - POWER8
+      - HOST
       - IBM POWER8 CPU
    *  - POWER9
+      - HOST
       - IBM POWER9 CPU
    *  - KEPLER30
+      - GPU
       - NVIDIA Kepler generation CC 3.0 GPU
    *  - KEPLER32
+      - GPU
       - NVIDIA Kepler generation CC 3.2 GPU
    *  - KEPLER35
+      - GPU
       - NVIDIA Kepler generation CC 3.5 GPU
    *  - KEPLER37
+      - GPU
       - NVIDIA Kepler generation CC 3.7 GPU
    *  - MAXWELL50
+      - GPU
       - NVIDIA Maxwell generation CC 5.0 GPU
    *  - MAXWELL52
+      - GPU
       - NVIDIA Maxwell generation CC 5.2 GPU
    *  - MAXWELL53
+      - GPU
       - NVIDIA Maxwell generation CC 5.3 GPU
    *  - PASCAL60
+      - GPU
       - NVIDIA Pascal generation CC 6.0 GPU
    *  - PASCAL61
+      - GPU
       - NVIDIA Pascal generation CC 6.1 GPU
    *  - VOLTA70
+      - GPU
       - NVIDIA Volta generation CC 7.0 GPU
    *  - VOLTA72
+      - GPU
       - NVIDIA Volta generation CC 7.2 GPU
    *  - TURING75
+      - GPU
       - NVIDIA Turing generation CC 7.5 GPU
+   *  - VEGA900
+      - GPU
+      - AMD GPU MI25 GFX900
+   *  - VEGA906
+      - GPU
+      - AMD GPU MI50/MI60 GFX906
 
-CMake build settings:
-^^^^^^^^^^^^^^^^^^^^^
+Basic CMake build settings:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 For multicore CPUs using OpenMP, set these 2 variables.
 
 .. code-block:: bash
 
-   -D Kokkos_ARCH_CPUARCH=yes  # CPUARCH = CPU from list above
+   -D Kokkos_ARCH_HOSTARCH=yes  # HOSTARCH = HOST from list above
    -D Kokkos_ENABLE_OPENMP=yes
    -D BUILD_OMP=yes
 
@@ -427,15 +464,19 @@ For NVIDIA GPUs using CUDA, set these variables:
 
 .. code-block:: bash
 
-   -D Kokkos_ARCH_CPUARCH=yes    # CPUARCH = CPU from list above
+   -D Kokkos_ARCH_HOSTARCH=yes   # HOSTARCH = HOST from list above
    -D Kokkos_ARCH_GPUARCH=yes    # GPUARCH = GPU from list above
    -D Kokkos_ENABLE_CUDA=yes
    -D Kokkos_ENABLE_OPENMP=yes
    -D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper
 
-The wrapper value is the Cuda nvcc compiler wrapper provided in the
-Kokkos library: ``lib/kokkos/bin/nvcc_wrapper``\ .  The setting should
-include the full path name to the wrapper, e.g.
+This will also enable executing FFTs on the GPU, either via the internal
+KISSFFT library, or - by preference - with the cuFFT library bundled
+with the CUDA toolkit, depending on whether CMake can identify its
+location.  The *wrapper* value for ``CMAKE_CXX_COMPILER`` variable is
+the path to the CUDA nvcc compiler wrapper provided in the Kokkos
+library: ``lib/kokkos/bin/nvcc_wrapper``\ .  The setting should include
+the full path name to the wrapper, e.g.
 
 .. code-block:: bash
 
@@ -455,8 +496,8 @@ common packages enabled, you can do the following:
    cmake -C ../cmake/presets/minimal.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
    cmake --build .
 
-Traditional make settings:
-^^^^^^^^^^^^^^^^^^^^^^^^^^
+Basic traditional make settings:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Choose which hardware to support in ``Makefile.machine`` via
 ``KOKKOS_DEVICES`` and ``KOKKOS_ARCH`` settings.  See the
@@ -467,7 +508,7 @@ For multicore CPUs using OpenMP:
 .. code-block:: make
 
    KOKKOS_DEVICES = OpenMP
-   KOKKOS_ARCH = CPUARCH          # CPUARCH = CPU from list above
+   KOKKOS_ARCH = HOSTARCH          # HOSTARCH = HOST from list above
 
 For Intel KNLs using OpenMP:
 
@@ -481,7 +522,8 @@ For NVIDIA GPUs using CUDA:
 .. code-block:: make
 
    KOKKOS_DEVICES = Cuda
-   KOKKOS_ARCH = CPUARCH,GPUARCH  # CPUARCH = CPU from list above that is hosting the GPU
+   KOKKOS_ARCH = HOSTARCH,GPUARCH  # HOSTARCH = HOST from list above that is hosting the GPU
+   KOKKOS_CUDA_OPTIONS = "enable_lambda"
                                   # GPUARCH = GPU from list above
    FFT_INC = -DFFT_CUFFT          # enable use of cuFFT (optional)
    FFT_LIB = -lcufft              # link to cuFFT library
@@ -504,6 +546,44 @@ C++ compiler for non-Kokkos, non-CUDA files.
    KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
    CC = mpicxx -cxx=$(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
 
+
+Advanced KOKKOS compilation settings
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are other allowed options when building with the KOKKOS package
+that can improve performance or assist in debugging or profiling. Below
+are some examples that may be useful in combination with LAMMPS.  For
+the full list (which keeps changing as the Kokkos package itself evolves),
+please consult the Kokkos library documentation.
+
+As alternative to using multi-threading via OpenMP
+(``-DKokkos_ENABLE_OPENMP=on`` or ``KOKKOS_DEVICES=OpenMP``) it is also
+possible to use Posix threads directly (``-DKokkos_ENABLE_PTHREAD=on``
+or ``KOKKOS_DEVICES=Pthread``).  While binding of threads to individual
+or groups of CPU cores is managed in OpenMP with environment variables,
+you need assistance from either the "hwloc" or "libnuma" library for the
+Pthread thread parallelization option. To enable use with CMake:
+``-DKokkos_ENABLE_HWLOC=on`` or ``-DKokkos_ENABLE_LIBNUMA=on``; and with
+conventional make: ``KOKKOS_USE_TPLS=hwloc`` or
+``KOKKOS_USE_TPLS=libnuma``.
+
+The CMake option ``-DKokkos_ENABLE_LIBRT=on`` or the makefile setting
+``KOKKOS_USE_TPLS=librt`` enables the use of a more accurate timer
+mechanism on many Unix-like platforms for internal profiling.
+
+The CMake option ``-DKokkos_ENABLE_DEBUG=on`` or the makefile setting
+``KOKKOS_DEBUG=yes`` enables printing of run-time
+debugging information that can be useful. It also enables runtime
+bounds checking on Kokkos data structures.  As to be expected, enabling
+this option will negatively impact the performance and thus is only
+recommended when developing a Kokkos-enabled style in LAMMPS.
+
+The CMake option ``-DKokkos_ENABLE_CUDA_UVM=on`` or the makefile
+setting ``KOKKOS_CUDA_OPTIONS=enable_lambda,force_uvm`` enables the
+use of CUDA "Unified Virtual Memory" in Kokkos.  Please note, that
+the LAMMPS KOKKOS package must **always** be compiled with the
+*enable_lambda* option when using GPUs.
+
 ----------
 
 .. _latte:

doc/src/Commands_compute.rst

@@ -42,7 +42,7 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`com <compute_com>`
    * :doc:`com/chunk <compute_com_chunk>`
    * :doc:`contact/atom <compute_contact_atom>`
-   * :doc:`coord/atom <compute_coord_atom>`
+   * :doc:`coord/atom (k) <compute_coord_atom>`
    * :doc:`damage/atom <compute_damage_atom>`
    * :doc:`dihedral <compute_dihedral>`
    * :doc:`dihedral/local <compute_dihedral_local>`
@@ -87,7 +87,7 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`msd/chunk <compute_msd_chunk>`
    * :doc:`msd/nongauss <compute_msd_nongauss>`
    * :doc:`omega/chunk <compute_omega_chunk>`
-   * :doc:`orientorder/atom <compute_orientorder_atom>`
+   * :doc:`orientorder/atom (k) <compute_orientorder_atom>`
    * :doc:`pair <compute_pair>`
    * :doc:`pair/local <compute_pair_local>`
    * :doc:`pe <compute_pe>`
@@ -161,5 +161,6 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`torque/chunk <compute_torque_chunk>`
    * :doc:`vacf <compute_vacf>`
    * :doc:`vcm/chunk <compute_vcm_chunk>`
+   * :doc:`viscosity/cos <compute_viscosity_cos>`
    * :doc:`voronoi/atom <compute_voronoi_atom>`
    * :doc:`xrd <compute_xrd>`

doc/src/Commands_fix.rst

@@ -22,6 +22,7 @@ OPT.
 .. table_from_list::
    :columns: 5
 
+   * :doc:`accelerate/cos <fix_accelerate_cos>`
    * :doc:`adapt <fix_adapt>`
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`

doc/src/Howto_cmake.rst

@@ -378,9 +378,9 @@ change some variables later with additional *-D* flags.  A few examples:
 
 .. code-block:: bash
 
-   cmake -C ../cmake/preset/minimal.cmake -D PKG_MISC=on ../cmake
-   cmake -C ../cmake/preset/clang.cmake -C ../cmake/preset/most.cmake ../cmake
-   cmake -C ../cmake/preset/minimal.cmake -D BUILD_MPI=off ../cmake
+   cmake -C ../cmake/presets/minimal.cmake -D PKG_MISC=on ../cmake
+   cmake -C ../cmake/presets/clang.cmake -C ../cmake/presets/most.cmake ../cmake
+   cmake -C ../cmake/presets/minimal.cmake -D BUILD_MPI=off ../cmake
 
 The first command will install the packages ``KSPACE``, ``MANYBODY``,
 ``MOLECULE``, ``RIGID`` and ``MISC``; the first four from the preset
@@ -396,7 +396,7 @@ It is also possible to do this incrementally.
 
 .. code-block:: bash
 
-   cmake -C ../cmake/preset/minimal.cmake ../cmake
+   cmake -C ../cmake/presets/minimal.cmake ../cmake
    cmake -D PKG_MISC=on .
 
 will achieve the same configuration like in the first example above.  In

doc/src/Howto_viscosity.rst

@@ -1,10 +1,11 @@
 Calculate viscosity
 ===================
 
-The shear viscosity eta of a fluid can be measured in at least 5 ways
+The shear viscosity eta of a fluid can be measured in at least 6 ways
 using various options in LAMMPS.  See the examples/VISCOSITY directory
 for scripts that implement the 5 methods discussed here for a simple
-Lennard-Jones fluid model.  Also, see the :doc:`Howto kappa <Howto_kappa>` doc page for an analogous discussion for
+Lennard-Jones fluid model and 1 method for SPC/E water model.
+Also, see the :doc:`Howto kappa <Howto_kappa>` doc page for an analogous discussion for
 thermal conductivity.
 
 Eta is a measure of the propensity of a fluid to transmit momentum in
@@ -130,9 +131,25 @@ time-integrated momentum fluxes play the role of Cartesian
 coordinates, whose mean-square displacement increases linearly
 with time at sufficiently long times.
 
+The sixth is periodic perturbation method. It is also a non-equilibrium MD method.
+However, instead of measure the momentum flux in response of applied velocity gradient,
+it measures the velocity profile in response of applied stress.
+A cosine-shaped periodic acceleration is added to the system via the
+:doc:`fix accelerate/cos <fix_accelerate_cos>` command,
+and the :doc:`compute viscosity/cos<compute_viscosity_cos>` command is used to monitor the
+generated velocity profile and remove the velocity bias before thermostatting.
+
+.. note::
+
+    An article by :ref:`(Hess) <Hess3>` discussed the accuracy and efficiency of these methods.
+
 ----------
 
 .. _Daivis-viscosity:
 
 **(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
 Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
+
+.. _Hess3:
+
+**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.

doc/src/Install_linux.rst

@@ -24,12 +24,13 @@ allows you to install LAMMPS with a single command, and stay
 up-to-date with the current version of LAMMPS by simply updating your
 operating system.
 
-To install the appropriate personal-package archive (PPA), do the
+To install the appropriate personal-package archives (PPAs), do the
 following once:
 
 .. code-block:: bash
 
    $ sudo add-apt-repository ppa:gladky-anton/lammps
+   $ sudo add-apt-repository ppa:openkim/latest
    $ sudo apt-get update
 
 To install LAMMPS do the following once:
@@ -38,7 +39,7 @@ To install LAMMPS do the following once:
 
    $ sudo apt-get install lammps-daily
 
-This downloads an executable named "lmp_daily" to your box, which
+This downloads an executable named ``lmp_daily`` to your box, which
 can then be used in the usual way to run input scripts:
 
 .. code-block:: bash
@@ -60,11 +61,29 @@ To get a copy of the current documentation and examples:
    $ sudo apt-get install lammps-daily-doc
 
 which will download the doc files in
-/usr/share/doc/lammps-daily-doc/doc and example problems in
-/usr/share/doc/lammps-doc/examples.
+``/usr/share/doc/lammps-daily-doc/doc`` and example problems in
+``/usr/share/doc/lammps-doc/examples``.
 
-Note that you may still wish to download the tarball to get potential
-files and auxiliary tools.
+To get a copy of the current potentials files:
+
+.. code-block:: bash
+
+   $ sudo apt-get install lammps-daily-data
+
+which will download the potentials files to
+``/usr/share/lammps-daily/potentials``.  The ``lmp_daily`` binary is
+hard-coded to look for potential files in this directory (it does not
+use the `LAMMPS_POTENTIALS` environment variable, as described
+in :doc:`pair_coeff <pair_coeff>` command).
+
+The ``lmp_daily`` binary is built with the :ref:`KIM package <kim>` which
+results in the above command also installing the `kim-api` binaries when LAMMPS
+is installed.  In order to use potentials from `openkim.org <openkim_>`_, you
+can install the `openkim-models` package
+
+.. code-block:: bash
+
+   $ sudo apt-get install openkim-models
 
 To un-install LAMMPS, do the following:
 
@@ -72,17 +91,8 @@ To un-install LAMMPS, do the following:
 
    $ sudo apt-get remove lammps-daily
 
-Note that the lammps-daily executable is built with the following
-sequence of make commands, as if you had done the same with the
-unpacked tarball files in the src directory:
-
-.. code-block:: bash
-
-    $ make yes-all
-    $ make no-lib
-    $ make mpi
-
-Thus it builds with FFTW3 and OpenMPI.
+Please use ``lmp_daily -help`` to see which compilation options, packages,
+and styles are included in the binary.
 
 Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this
 Ubuntu package capability.
@@ -103,14 +113,14 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel,
 lammps-openmpi-devel), the header for compiling programs using
 the C library interface (lammps-headers), and the LAMMPS python
 module for Python 3. All packages can be installed at the same
-time and the name of the LAMMPS executable is *lmp* and *lmp_openmpi*
-or *lmp_mpich* respectively.  By default, *lmp* will refer to the
+time and the name of the LAMMPS executable is ``lmp`` and ``lmp_openmpi``
+or ``lmp_mpich`` respectively.  By default, ``lmp`` will refer to the
 serial executable, unless one of the MPI environment modules is loaded
-("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
+(``module load mpi/mpich-x86_64`` or ``module load mpi/openmpi-x86_64``).
 Then the corresponding parallel LAMMPS executable can be used.
 The same mechanism applies when loading the LAMMPS python module.
 
-To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
+To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do:
 
 .. code-block:: bash
 
@@ -118,10 +128,10 @@ To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
    $ module load mpi/openmpi-x86_64
    $ mpirun -np 2 lmp -in in.lj
 
-The "dnf install" command is needed only once. In case of a new LAMMPS
-stable release, "dnf update" will automatically update to the newer
+The ``dnf install`` command is needed only once. In case of a new LAMMPS
+stable release, ``dnf update`` will automatically update to the newer
 version as soon at the RPM files are built and uploaded to the download
-mirrors. The "module load" command is needed once per (shell) session
+mirrors. The ``module load`` command is needed once per (shell) session
 or shell terminal instance, unless it is automatically loaded from the
 shell profile.
 
@@ -134,7 +144,7 @@ can install the `openkim-models` package
 
    $ dnf install openkim-models
 
-Please use "lmp -help" to see which compilation options, packages,
+Please use ``lmp -help`` to see which compilation options, packages,
 and styles are included in the binary.
 
 Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
@@ -153,10 +163,10 @@ in the `Extra Packages for Enterprise Linux (EPEL) repository <https://fedorapro
 for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
 and compatible Linux distributions. Names of packages, executable,
 and content are the same as described above for Fedora Linux.
-But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf"
+But RHEL/CentOS 7.x uses the ``yum`` package manager instead of ``dnf``
 in Fedora 28.
 
-Please use "lmp -help" to see which compilation options, packages,
+Please use ``lmp -help`` to see which compilation options, packages,
 and styles are included in the binary.
 
 Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
@@ -176,13 +186,13 @@ in OpenSuse as of Leap 15.0. You can install the package with:
    $ zypper install lammps
 
 This includes support for OpenMPI. The name of the LAMMPS executable
-is *lmp*\ . Thus to run an input in parallel on 2 CPUs you would do:
+is ``lmp``. Thus to run an input in parallel on 2 CPUs you would do:
 
 .. code-block:: bash
 
    $ mpirun -np 2 lmp -in in.lj
 
-Please use "lmp -help" to see which compilation options, packages,
+Please use ``lmp -help`` to see which compilation options, packages,
 and styles are included in the binary.
 
 The LAMMPS binary is built with the :ref:`KIM package <kim>` which

doc/src/Speed_kokkos.rst

@@ -9,10 +9,7 @@ different back end languages such as CUDA, OpenMP, or Pthreads.  The
 Kokkos library also provides data abstractions to adjust (at compile
 time) the memory layout of data structures like 2d and 3d arrays to
 optimize performance on different hardware. For more information on
-Kokkos, see `GitHub <https://github.com/kokkos/kokkos>`_. Kokkos is
-part of `Trilinos <https://www.trilinos.org/>`_. The Kokkos
-library was written primarily by Carter Edwards, Christian Trott, and
-Dan Sunderland (all Sandia).
+Kokkos, see `GitHub <https://github.com/kokkos/kokkos>`_.
 
 The LAMMPS KOKKOS package contains versions of pair, fix, and atom
 styles that use data structures and macros provided by the Kokkos
@@ -21,7 +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 programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf.
+see the Kokkos `Wiki <https://github.com/kokkos/kokkos/wiki>`_.
 
 Kokkos currently provides support for 3 modes of execution (per MPI
 task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
@@ -31,33 +28,30 @@ compatible with specific hardware.
 
 .. note::
 
-   Kokkos support within LAMMPS must be built with a C++11 compatible
-   compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
-   Clang 3.5.2 or later is required.
-
-.. note::
-
-   To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA
+   To build with Kokkos support for NVIDIA GPUs, the NVIDIA CUDA toolkit
    software version 9.0 or later must be installed on your system. See
-   the discussion for the :doc:`GPU package <Speed_gpu>` for details of how
-   to check and do this.
+   the discussion for the :doc:`GPU package <Speed_gpu>` for details of
+   how to check and do this.
 
 .. note::
 
-   Kokkos with CUDA currently implicitly assumes that the MPI library
-   is CUDA-aware. This is not always the case, especially when using
-   pre-compiled MPI libraries provided by a Linux distribution. This is not
-   a problem when using only a single GPU with a single MPI rank. When
-   running with multiple MPI ranks, you may see segmentation faults without
-   CUDA-aware MPI support. These can be avoided by adding the flags :doc:`-pk kokkos cuda/aware off <Run_options>` to the LAMMPS command line or by
-   using the command :doc:`package kokkos cuda/aware off <package>` in the
-   input file.
+   Kokkos with CUDA currently implicitly assumes that the MPI library is
+   CUDA-aware. This is not always the case, especially when using
+   pre-compiled MPI libraries provided by a Linux distribution. This is
+   not a problem when using only a single GPU with a single MPI
+   rank. When running with multiple MPI ranks, you may see segmentation
+   faults without CUDA-aware MPI support. These can be avoided by adding
+   the flags :doc:`-pk kokkos cuda/aware off <Run_options>` to the
+   LAMMPS command line or by using the command :doc:`package kokkos
+   cuda/aware off <package>` in the input file.
 
-**Building LAMMPS with the KOKKOS package:**
+Building LAMMPS with the KOKKOS package
+"""""""""""""""""""""""""""""""""""""""
 
 See the :ref:`Build extras <kokkos>` doc page for instructions.
 
-**Running LAMMPS with the KOKKOS package:**
+Running LAMMPS with the KOKKOS package
+""""""""""""""""""""""""""""""""""""""
 
 All Kokkos operations occur within the context of an individual MPI
 task running on a single node of the machine. The total number of MPI
@@ -66,7 +60,8 @@ usual manner via the mpirun or mpiexec commands, and is independent of
 Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
 -npernode switches. Ditto for MPICH via -np and -ppn.
 
-**Running on a multi-core CPU:**
+Running on a multi-core CPU
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Here is a quick overview of how to use the KOKKOS package
 for CPU acceleration, assuming one or more 16-core nodes.
@@ -142,7 +137,8 @@ atom.  When using the Kokkos Serial back end or the OpenMP back end with
 a single thread, no duplication or atomic operations are used. For CUDA
 and half neighbor lists, the KOKKOS package always uses atomic operations.
 
-**Core and Thread Affinity:**
+CPU Cores, Sockets and Thread Affinity
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 When using multi-threading, it is important for performance to bind
 both MPI tasks to physical cores, and threads to physical cores, so
@@ -156,15 +152,16 @@ for your MPI installation), binding can be forced with these flags:
    OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
    Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ...
 
-For binding threads with KOKKOS OpenMP, use thread affinity
-environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
-later, intel 12 or later) setting the environment variable
-OMP_PROC_BIND=true should be sufficient. In general, for best
-performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and
-OMP_PLACES=threads.  For binding threads with the KOKKOS pthreads
-option, compile LAMMPS the KOKKOS HWLOC=yes option as described below.
+For binding threads with KOKKOS OpenMP, use thread affinity environment
+variables to force binding. With OpenMP 3.1 (gcc 4.7 or later, intel 12
+or later) setting the environment variable ``OMP_PROC_BIND=true`` should
+be sufficient. In general, for best performance with OpenMP 4.0 or later
+set ``OMP_PROC_BIND=spread`` and ``OMP_PLACES=threads``.  For binding
+threads with the KOKKOS pthreads option, compile LAMMPS with the hwloc
+or libnuma support enabled as described in the :ref:`extra build options page <kokkos>`.
 
-**Running on Knight's Landing (KNL) Intel Xeon Phi:**
+Running on Knight's Landing (KNL) Intel Xeon Phi
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Here is a quick overview of how to use the KOKKOS package for the
 Intel Knight's Landing (KNL) Xeon Phi:
@@ -222,7 +219,8 @@ threads/task as Nt. The product of these two values should be N, i.e.
    them in "native" mode, not "offload" mode like the USER-INTEL package
    supports.
 
-**Running on GPUs:**
+Running on GPUs
+^^^^^^^^^^^^^^^
 
 Use the "-k" :doc:`command-line switch <Run_options>` to specify the
 number of GPUs per node. Typically the -np setting of the mpirun command
@@ -257,7 +255,7 @@ one or more nodes, each with two GPUs:
    running on GPUs is to use "full" neighbor lists and set the Newton flag
    to "off" for both pairwise and bonded interactions, along with threaded
    communication. When running on Maxwell or Kepler GPUs, this will
-   typically be best. For Pascal GPUs, using "half" neighbor lists and
+   typically be best. For Pascal GPUs and beyond, using "half" neighbor lists and
    setting the Newton flag to "on" may be faster. For many pair styles,
    setting the neighbor binsize equal to twice the CPU default value will
    give speedup, which is the default when running on GPUs. Use the "-pk
@@ -270,13 +268,6 @@ one or more nodes, each with two GPUs:
 
    mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff
 
-.. note::
-
-   For good performance of the KOKKOS package on GPUs, you must
-   have Kepler generation GPUs (or later). The Kokkos library exploits
-   texture cache options not supported by Telsa generation GPUs (or
-   older).
-
 .. note::
 
    When using a GPU, you will achieve the best performance if your
@@ -293,7 +284,8 @@ one or more nodes, each with two GPUs:
    kspace, etc., you must set the environment variable CUDA_LAUNCH_BLOCKING=1.
    However, this will reduce performance and is not recommended for production runs.
 
-**Run with the KOKKOS package by editing an input script:**
+Run with the KOKKOS package by editing an input script
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Alternatively the effect of the "-sf" or "-pk" switches can be
 duplicated by adding the :doc:`package kokkos <package>` or :doc:`suffix kk <suffix>` commands to your input script.
@@ -316,17 +308,24 @@ You only need to use the :doc:`package kokkos <package>` command if you
 wish to change any of its option defaults, as set by the "-k on"
 :doc:`command-line switch <Run_options>`.
 
-**Using OpenMP threading and CUDA together (experimental):**
+**Using OpenMP threading and CUDA together:**
 
 With the KOKKOS package, both OpenMP multi-threading and GPUs can be
-used together in a few special cases. In the Makefile, the
-KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is
-the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
+compiled and used together in a few special cases. In the makefile for
+the conventional build, the KOKKOS_DEVICES variable must include both,
+"Cuda" and "OpenMP", as is the case for ``/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi``.
 
 .. code-block:: bash
 
    KOKKOS_DEVICES=Cuda,OpenMP
 
+When building with CMake you need to enable both features as it is done
+in the ``kokkos-cuda.cmake`` CMake preset file.
+
+.. code-block:: bash
+
+   cmake ../cmake -DKokkos_ENABLE_CUDA=yes -DKokkos_ENABLE_OPENMP=yes
+
 The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
 using the "-sf kk" in the command line gives the default CUDA version
 everywhere.  However, if the "/kk/host" suffix is added to a specific
@@ -360,7 +359,8 @@ suffix for kspace and bonds, angles, etc.  in the input file and the
 sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
 so CPU/GPU overlap can occur.
 
-**Speed-ups to expect:**
+Performance to expect
+"""""""""""""""""""""
 
 The performance of KOKKOS running in different modes is a function of
 your hardware, which KOKKOS-enable styles are used, and the problem
@@ -377,52 +377,26 @@ Generally speaking, the following rules of thumb apply:
   performance of a KOKKOS style is a bit slower than the USER-OMP
   package.
 * When running large number of atoms per GPU, KOKKOS is typically faster
-  than the GPU package.
+  than the GPU package when compiled for double precision. The benefit
+  of using single or mixed precision with the GPU package depends
+  significantly on the hardware in use and the simulated system and pair
+  style.
 * When running on Intel hardware, KOKKOS is not as fast as
-  the USER-INTEL package, which is optimized for that hardware.
+  the USER-INTEL package, which is optimized for x86 hardware (not just
+  from Intel) and compilation with the Intel compilers.  The USER-INTEL
+  package also can increase the vector length of vector instructions
+  by switching to single or mixed precision mode.
 
 See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the
 LAMMPS web site for performance of the KOKKOS package on different
 hardware.
 
-**Advanced Kokkos options:**
+Advanced Kokkos options
+"""""""""""""""""""""""
 
-There are other allowed options when building with the KOKKOS package.
-As explained on the :ref:`Build extras <kokkos>` doc page,
-they can be set either as variables on the make command line or in
-Makefile.machine, or they can be specified as CMake variables.  Each
-takes a value shown below.  The default value is listed, which is set
-in the lib/kokkos/Makefile.kokkos file.
-
-* KOKKOS_DEBUG, values = *yes*\ , *no*\ , default = *no*
-* KOKKOS_USE_TPLS, values = *hwloc*\ , *librt*\ , *experimental_memkind*, default = *none*
-* KOKKOS_CXX_STANDARD, values = *c++11*\ , *c++1z*\ , default = *c++11*
-* KOKKOS_OPTIONS, values = *aggressive_vectorization*, *disable_profiling*, default = *none*
-* KOKKOS_CUDA_OPTIONS, values = *force_uvm*, *use_ldg*, *rdc*\ , *enable_lambda*, default = *enable_lambda*
-
-KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
-migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
-used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
-necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
-provides alternative methods via environment variables for binding
-threads to hardware cores.  More info on binding threads to cores is
-given on the :doc:`Speed omp <Speed_omp>` doc page.
-
-KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
-on most Unix platforms. This library is not available on all
-platforms.
-
-KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
-within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
-debugging information that can be useful. It also enables runtime
-bounds checking on Kokkos data structures.
-
-KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when
-building LAMMPS.
-
-KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS
-package must be compiled with the *enable_lambda* option when using
-GPUs.
+There are other allowed options when building with the KOKKOS package
+that can improve performance or assist in debugging or profiling.
+They are explained on the :ref:`KOKKOS section of the build extras <kokkos>` doc page,
 
 Restrictions
 """"""""""""

doc/src/change_box.rst

@@ -299,6 +299,12 @@ match what is stored in the restart file.  So if you wish to change
 them, you should use the change_box command after the read_restart
 command.
 
+.. note::
+
+   Changing a periodic boundary to a non-periodic one will also
+   cause the image flag for that dimension to be reset to 0 for
+   all atoms.  LAMMPS will print a warning message, if that happens.
+
 ----------
 
 The *ortho* and *triclinic* keywords convert the simulation box to be

doc/src/compute.rst

@@ -307,6 +307,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
 * :doc:`torque/chunk <compute_torque_chunk>` - torque applied on each chunk
 * :doc:`vacf <compute_vacf>` - velocity auto-correlation function of group of atoms
 * :doc:`vcm/chunk <compute_vcm_chunk>` - velocity of center-of-mass for each chunk
+* :doc:`viscosity/cos <compute_viscosity_cos>` - velocity profile under cosine-shaped acceleration
 * :doc:`voronoi/atom <compute_voronoi_atom>` - Voronoi volume and neighbors for each atom
 * :doc:`xrd <compute_xrd>` - x-ray diffraction intensity on a mesh of reciprocal lattice nodes
 

doc/src/compute_coord_atom.rst

@@ -3,6 +3,9 @@
 compute coord/atom command
 ==========================
 
+compute coord/atom/kk command
+===================================
+
 Syntax
 """"""
 
@@ -109,6 +112,30 @@ too frequently.
    :doc:`special_bonds <special_bonds>` command that includes all pairs in
    the neighbor list.
 
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
 **Output info:**
 
 For *cstyle* cutoff, this compute can calculate a per-atom vector or

doc/src/compute_orientorder_atom.rst

@@ -3,6 +3,9 @@
 compute orientorder/atom command
 ================================
 
+compute orientorder/atom/kk command
+===================================
+
 Syntax
 """"""
 
@@ -16,13 +19,14 @@ Syntax
 
   .. parsed-literal::
 
-     keyword = *cutoff* or *nnn* or *degrees* or *components*
+     keyword = *cutoff* or *nnn* or *degrees* or *components* or *chunksize*
        *cutoff* value = distance cutoff
        *nnn* value = number of nearest neighbors
        *degrees* values = nlvalues, l1, l2,...
        *wl* value = yes or no
        *wl/hat* value = yes or no
        *components* value = ldegree
+       *chunksize* value = number of atoms in each pass 
 
 Examples
 """"""""
@@ -104,6 +108,14 @@ in conjunction with :doc:`compute coord_atom <compute_coord_atom>` to
 calculate the ten Wolde's criterion to identify crystal-like
 particles, as discussed in :ref:`ten Wolde <tenWolde2>`.
 
+The optional keyword *chunksize* is only applicable when using the
+the KOKKOS package and is ignored otherwise. This keyword controls
+the number of atoms in each pass used to compute the bond-orientational
+order parameters and is used to avoid running out of memory. For example
+if there are 4000 atoms in the simulation and the *chunksize*
+is set to 2000, the parameter calculation will be broken up
+into two passes.
+
 The value of :math:`Q_l` is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
 *nnn* neighbors within the distance cutoff, unless *nnn* is NULL.
@@ -128,6 +140,30 @@ too frequently.
    :doc:`special_bonds <special_bonds>` command that includes all pairs in
    the neighbor list.
 
+----------
+
+
+Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` doc page for more
+instructions on how to use the accelerated styles effectively.
+
+
+----------
+
 **Output info:**
 
 This compute calculates a per-atom array with *nlvalues* columns,
@@ -165,7 +201,7 @@ Default
 
 The option defaults are *cutoff* = pair style cutoff, *nnn* = 12,
 *degrees* = 5 4 6 8 10 12 i.e. :math:`Q_4`, :math:`Q_6`, :math:`Q_8`, :math:`Q_{10}`, and :math:`Q_{12}`,
-*wl* = no, *wl/hat* = no, and *components* off
+*wl* = no, *wl/hat* = no, *components* off, and *chunksize* = 2000
 
 ----------
 

doc/src/compute_stress_atom.rst

@@ -2,6 +2,7 @@
 
 compute stress/atom command
 ===========================
+
 compute centroid/stress/atom command
 ====================================
 
@@ -223,15 +224,14 @@ The per-atom array values will be in pressure\*volume
 
 Restrictions
 """"""""""""
-Currently, compute *centroid/stress/atom* does not support
-pair styles with many-body interactions,
-such as :doc:`Tersoff <pair_tersoff>`,
-and LAMMPS will generate an error in such cases.
-In principal, equivalent formulation
-to that of angle, dihedral and improper contributions
-in the virial :math:`W_{ab}` formula
-can also be applied to the many-body pair styles,
-and is planned in the future.
+
+Currently (Spring 2020), compute *centroid/stress/atom* does not support
+pair styles with many-body interactions, such as :doc:`Tersoff
+<pair_tersoff>`, or pair styles with long-range Coulomb interactions.
+LAMMPS will generate an error in such cases.  In principal, equivalent
+formulation to that of angle, dihedral and improper contributions in the
+virial :math:`W_{ab}` formula can also be applied to the many-body pair
+styles, and is planned in the future.
 
 Related commands
 """"""""""""""""

doc/src/compute_viscosity_cos.rst

@@ -0,0 +1,156 @@
+.. index:: compute viscosity/cos
+
+compute viscosity/cos command
+=============================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   compute ID group-ID viscosity/cos
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* viscosity/cos = style name of this compute command
+
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   compute  cos all viscosity/cos
+   variable V equal c_cos[7]
+   variable A equal 0.02E-5
+   variable density equal density
+   variable lz equal lz
+   variable reciprocalViscosity equal v_V/${A}/v_density*39.4784/v_lz/v_lz*100
+
+Description
+"""""""""""
+
+Define a computation that calculates the velocity amplitude of a group of atoms
+with an cosine-shaped velocity profile and the temperature of them
+after subtracting out the velocity profile before computing the kinetic energy.
+A compute of this style can be used by any command that computes a temperature,
+e.g. :doc:`thermo_modify <thermo_modify>`, :doc:`fix npt <fix_nh>`, etc.
+
+This command together with :doc:`fix_accelerate/cos<fix_accelerate_cos>`
+enables viscosity calculation with periodic perturbation method,
+as described by :ref:`Hess<Hess1>`.
+An acceleration along the x-direction is applied to the simulation system
+by using :doc:`fix_accelerate/cos<fix_accelerate_cos>` command.
+The acceleration is a periodic function along the z-direction:
+
+.. math::
+
+   a_{x}(z) = A \cos \left(\frac{2 \pi z}{l_{z}}\right)
+
+where :math:`A` is the acceleration amplitude, :math:`l_z` is the z-length
+of the simulation box. At steady state, the acceleration generates
+a velocity profile:
+
+.. math::
+
+   v_{x}(z) = V \cos \left(\frac{2 \pi z}{l_{z}}\right)
+
+The generated velocity amplitude :math:`V` is related to the
+shear viscosity :math:`\eta` by:
+
+.. math::
+
+   V = \frac{A \rho}{\eta}\left(\frac{l_{z}}{2 \pi}\right)^{2}
+
+
+and it can be obtained from ensemble average of the velocity profile:
+
+.. math::
+
+   V = \frac{\sum_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum_i m_{i}}
+
+
+where :math:`m_i`, :math:`v_{i,x}` and :math:`z_i` are the mass,
+x-component velocity and z coordinate of a particle.
+
+After the cosine-shaped collective velocity in :math:`x` direction
+has been subtracted for each atom, the temperature is calculated by the formula
+KE = dim/2 N k T, where KE = total kinetic energy of the group of
+atoms (sum of 1/2 m v\^2), dim = 2 or 3 = dimensionality of the
+simulation, N = number of atoms in the group, k = Boltzmann constant,
+and T = temperature.
+
+A kinetic energy tensor, stored as a 6-element vector, is also
+calculated by this compute for use in the computation of a pressure
+tensor. The formula for the components of the tensor is the same as
+the above formula, except that v\^2 is replaced by vx\*vy for the xy
+component, etc. The 6 components of the vector are ordered xx, yy,
+zz, xy, xz, yz.
+
+The number of atoms contributing to the temperature is assumed to be
+constant for the duration of the run; use the *dynamic* option of the
+:doc:`compute_modify <compute_modify>` command if this is not the case.
+However, in order to get meaningful result, the group ID of this compute should be all.
+
+The removal of the cosine-shaped velocity component by this command is
+essentially computing the temperature after a "bias" has been removed
+from the velocity of the atoms.  If this compute is used with a fix
+command that performs thermostatting then this bias will be subtracted
+from each atom, thermostatting of the remaining thermal velocity will
+be performed, and the bias will be added back in.  Thermostatting
+fixes that work in this way include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin <fix_langevin>`.
+
+This compute subtracts out degrees-of-freedom due to fixes that
+constrain molecular motion, such as :doc:`fix shake <fix_shake>` and
+:doc:`fix rigid <fix_rigid>`.  This means the temperature of groups of
+atoms that include these constraints will be computed correctly.  If
+needed, the subtracted degrees-of-freedom can be altered using the
+*extra* option of the :doc:`compute_modify <compute_modify>` command.
+
+See the :doc:`Howto thermostat <Howto_thermostat>` doc page for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
+----------
+
+**Output info:**
+
+This compute calculates a global scalar (the temperature) and a global
+vector of length 7, which can be accessed by indices 1-7.
+The first 6 elements of the vector are the KE tensor,
+and the 7-th is the cosine-shaped velocity amplitude :math:`V`,
+which can be used to calculate the reciprocal viscosity, as shown in the example.
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.
+See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output options.
+
+The scalar value calculated by this compute is "intensive".  The
+first 6 elements of vector values are "extensive",
+and the 7-th element of vector values is "intensive".
+
+The scalar value will be in temperature :doc:`units <units>`.  The
+first 6 elements of vector values will be in energy :doc:`units <units>`.
+The 7-th element of vector value will be in velocity :doc:`units <units>`.
+
+Restrictions
+""""""""""""
+
+This command is only available when LAMMPS was built with the USER-MISC package.
+Since this compute depends on :doc:`fix accelerate/cos <fix_accelerate_cos>` which can
+only work for 3d systems, it cannot be used for 2d systems.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix accelerate/cos <fix_accelerate_cos>`
+
+Default
+"""""""
+ none
+
+----------
+
+.. _Hess1:
+
+**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.

doc/src/fix.rst

@@ -165,6 +165,7 @@ The individual style names on the :doc:`Commands fix <Commands_fix>` doc
 page are followed by one or more of (g,i,k,o,t) to indicate which
 accelerated styles exist.
 
+* :doc:`accelerate/cos <fix_accelerate_cos>` - apply cosine-shaped acceleration to atoms
 * :doc:`adapt <fix_adapt>` - change a simulation parameter over time
 * :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
 * :doc:`addforce <fix_addforce>` - add a force to each atom

doc/src/fix_accelerate_cos.rst

@@ -0,0 +1,104 @@
+.. index:: fix accelerate/cos
+
+fix accelerate/cos command
+==========================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID accelerate value
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* accelerate/cos = style name of this fix command
+* value = amplitude of acceleration (in unit of force/mass)
+
+
+Examples
+""""""""
+
+
+.. code-block:: LAMMPS
+
+   fix 1 all accelerate/cos 0.02e-5
+
+Description
+"""""""""""
+
+Give each atom a acceleration in x-direction based on its z coordinate.
+The acceleration is a periodic function along the z-direction:
+
+.. math::
+
+   a_{x}(z) = A \cos \left(\frac{2 \pi z}{l_{z}}\right)
+
+where :math:`A` is the acceleration amplitude, :math:`l_z` is the z-length
+of the simulation box.
+At steady state, the acceleration generates a velocity profile:
+
+.. math::
+
+   v_{x}(z) = V \cos \left(\frac{2 \pi z}{l_{z}}\right)
+
+The generated velocity amplitude :math:`V` is related to the
+shear viscosity :math:`\eta` by:
+
+.. math::
+
+   V = \frac{A \rho}{\eta}\left(\frac{l_{z}}{2 \pi}\right)^{2}
+
+
+and it can be obtained from ensemble average of the velocity profile:
+
+.. math::
+
+   V = \frac{\sum_i 2 m_{i} v_{i, x} \cos \left(\frac{2 \pi z_i}{l_{z}}\right)}{\sum_i m_{i}}
+
+where :math:`m_i`, :math:`v_{i,x}` and :math:`z_i` are the mass,
+x-component velocity and z coordinate of a particle.
+
+The velocity amplitude :math:`V` can be calculated with :doc:`compute viscosity/cos <compute_viscosity_cos>`,
+which enables viscosity calculation with periodic perturbation method,
+as described by :ref:`Hess<Hess2>`.
+Because the applied acceleration drives the system away from equilibration,
+the calculated shear viscosity is lower than the intrinsic viscosity
+due to the shear-thinning effect.
+Extrapolation to zero acceleration should generally be performed to
+predict the zero-shear viscosity.
+As the shear stress decreases, the signal-noise ratio decreases rapidly,
+the simulation time must be extended accordingly to get converged result.
+
+In order to get meaningful result, the group ID of this fix should be all.
+
+----------
+
+**Restart, fix_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to binary restart files.
+None of the fix_modify options are relevant to this fix.
+No global or per-atom quantities are stored by this fix for access by various output commands.
+No parameter of this fix can be used with the start/stop keywords of the run command.
+This fix is not invoked during energy minimization.
+
+Restrictions
+""""""""""""
+
+This command is only available when LAMMPS was built with the USER-MISC package.
+Since this fix depends on the z-coordinate of atoms, it cannot be used in 2d simulations.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute viscosity/cos <compute_viscosity_cos>`
+
+Default
+"""""""
+ none
+
+----------
+
+.. _Hess2:
+
+**(Hess)** Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.

doc/src/fix_ave_correlate_long.rst

@@ -26,7 +26,7 @@ Syntax
        v_name = global value calculated by an equal-style variable with name
 
 * zero or more keyword/arg pairs may be appended
-* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *p* or *m*
+* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount*
 
   .. parsed-literal::
 

doc/src/fix_bond_react.rst

@@ -158,7 +158,9 @@ The following comments pertain to each *react* argument (in other
 words, can be customized for each reaction, or reaction step):
 
 A check for possible new reaction sites is performed every *Nevery*
-timesteps.
+timesteps. *Nevery* can be specified with an equal-style
+:doc:`variable <variable>`, whose value is rounded up to the nearest
+integer.
 
 Three physical conditions must be met for a reaction to occur. First,
 a bonding atom pair must be identified within the reaction distance
@@ -171,19 +173,29 @@ modified to match the post-reaction template.
 A bonding atom pair will be identified if several conditions are met.
 First, a pair of atoms I,J within the specified react-group-ID of type
 itype and jtype must be separated by a distance between *Rmin* and
-*Rmax*\ . It is possible that multiple bonding atom pairs are
-identified: if the bonding atoms in the pre-reacted template are  1-2
-neighbors, i.e. directly bonded, the farthest bonding atom partner is
-set as its bonding partner; otherwise, the closest potential partner
-is chosen. Then, if both an atom I and atom J have each other as their
-bonding partners, these two atoms are identified as the bonding atom
-pair of the reaction site. Once this unique bonding atom pair is
-identified for each reaction, there could two or more reactions that
-involve a given atom on the same timestep. If this is the case, only
-one such reaction is permitted to occur. This reaction is chosen
-randomly from all potential reactions. This capability allows e.g. for
-different reaction pathways to proceed from identical reaction sites
-with user-specified probabilities.
+*Rmax*\ . *Rmin* and *Rmax* can be specified with equal-style
+:doc:`variables <variable>`. For example, these reaction cutoffs can
+be a function of the reaction conversion using the following commands:
+
+.. code-block:: LAMMPS
+
+   variable rmax equal 0 # initialize variable before bond/react
+   fix myrxn all bond/react react myrxn1 all 1 0 v_rmax mol1 mol2 map_file.txt
+   variable rmax equal 3+f_myrxn[1]/100 # arbitrary function of reaction count
+
+It is possible that multiple bonding atom pairs are identified: if the
+bonding atoms in the pre-reacted template are  1-2 neighbors, i.e.
+directly bonded, the farthest bonding atom partner is set as its
+bonding partner; otherwise, the closest potential partner is chosen.
+Then, if both an atom I and atom J have each other as their bonding
+partners, these two atoms are identified as the bonding atom pair of
+the reaction site. Once this unique bonding atom pair is identified
+for each reaction, there could two or more reactions that involve a
+given atom on the same timestep. If this is the case, only one such
+reaction is permitted to occur. This reaction is chosen randomly from
+all potential reactions. This capability allows e.g. for different
+reaction pathways to proceed from identical reaction sites with
+user-specified probabilities.
 
 The pre-reacted molecule template is specified by a molecule command.
 This molecule template file contains a sample reaction site and its
@@ -419,7 +431,8 @@ it occurs:
 
 The *prob* keyword can affect whether or not an eligible reaction
 actually occurs. The fraction setting must be a value between 0.0 and
-1.0. A uniform random number between 0.0 and 1.0 is generated and the
+1.0, and can be specified with an equal-style :doc:`variable <variable>`.
+A uniform random number between 0.0 and 1.0 is generated and the
 eligible reaction only occurs if the random number is less than the
 fraction. Up to N reactions are permitted to occur, as optionally
 specified by the *max_rxn* keyword.
@@ -489,10 +502,11 @@ local command.
 
 **Restart, fix_modify, output, run start/stop, minimize info:**
 
-Cumulative reaction counts for each reaction are written to :doc:`binary restart files <restart>`. These values are associated with the
-reaction name (react-ID). Additionally, internally-created per-atom
-properties are stored to allow for smooth restarts. None of the
-:doc:`fix_modify <fix_modify>` options are relevant to this fix.
+Cumulative reaction counts for each reaction are written to :doc:`binary restart files <restart>`.
+These values are associated with the reaction name (react-ID).
+Additionally, internally-created per-atom properties are stored to
+allow for smooth restarts. None of the :doc:`fix_modify <fix_modify>`
+options are relevant to this fix.
 
 This fix computes one statistic for each *react* argument that it
 stores in a global vector, of length 'number of react arguments', that

doc/src/fix_halt.rst

@@ -160,7 +160,7 @@ the :doc:`run <run>` command.
 
 Restrictions
 """"""""""""
-The *diskfree* attribute is currently only supported on Linux and MacOS.
+The *diskfree* attribute is currently only supported on Linux, MacOSX, and BSD.
 
 Related commands
 """"""""""""""""

doc/src/fix_heat.rst

@@ -47,16 +47,22 @@ and the specified geometric :doc:`region <region>` in order to have
 energy added or subtracted to it.  If not specified, then the atoms in
 the group are affected wherever they may move to.
 
-Heat addition/subtraction is performed every N timesteps.  The *eflux*
-parameter can be specified as a numeric constant or as a variable (see
-below).  If it is a numeric constant or equal-style variable which
-evaluates to a scalar value, then the *eflux* determines the change in
-aggregate energy of the entire group of atoms per unit time, e.g. in
-eV/psec for :doc:`metal units <units>`.  In this case it is an
-"extensive" quantity, meaning its magnitude should be scaled with the
-number of atoms in the group.  Note that since *eflux* has per-time
-units (i.e. it is a flux), this means that a larger value of N will
-add/subtract a larger amount of energy each time the fix is invoked.
+Heat addition/subtraction is performed every N timesteps.
+
+The *eflux* parameter can be specified as a numeric constant or as an
+equal- or atom-style :doc:`variable <variable>`.  If the value is a
+variable, it should be specified as v_name, where *name* is the variable
+name.  In this case, the variable will be evaluated each timestep, and
+its current value(s) used to determine the flux.
+
+If *eflux* is a numeric constant or equal-style variable which evaluates
+to a scalar value, then *eflux* determines the change in aggregate energy
+of the entire group of atoms per unit time, e.g. in eV/psec for
+:doc:`metal units <units>`.  In this case it is an "extensive" quantity,
+meaning its magnitude should be scaled with the number of atoms in the
+group.  Note that since *eflux* also has per-time units (i.e. it is a
+flux), this means that a larger value of N will add/subtract a larger
+amount of energy each time the fix is invoked.
 
 .. note::
 
@@ -71,12 +77,6 @@ the energy flux for a single atom, again in units of energy per unit
 time.  In this case, each value is an "intensive" quantity, which need
 not be scaled with the number of atoms in the group.
 
-As mentioned above, the *eflux* parameter can be specified as an
-equal-style or atom_style :doc:`variable <variable>`.  If the value is a
-variable, it should be specified as v_name, where name is the variable
-name.  In this case, the variable will be evaluated each timestep, and
-its value(s) used to determine the flux.
-
 Equal-style variables can specify formulas with various mathematical
 functions, and include :doc:`thermo_style <thermo_style>` command
 keywords for the simulation box parameters and timestep and elapsed

doc/src/fix_wall_body_polyhedron.rst

@@ -15,15 +15,14 @@ Syntax
 * k_n = normal repulsion strength (force/distance units or pressure units - see discussion below)
 * c_n = normal damping coefficient (force/distance units or pressure units - see discussion below)
 * c_t = tangential damping coefficient (force/distance units or pressure units - see discussion below)
-* wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder*
+* wallstyle = *xplane* or *yplane* or *zplane*
 * args = list of arguments for a particular style
 
   .. parsed-literal::
 
-       *xplane* or *yplane* args = lo hi
+       *xplane* or *yplane* or *zplane* args = lo hi
          lo,hi = position of lower and upper plane (distance units), either can be NULL)
-       *zcylinder* args = radius
-         radius = cylinder radius (distance units)
+
 
 * zero or more keyword/value pairs may be appended to args
 * keyword = *wiggle*
@@ -60,8 +59,7 @@ those specified with the :doc:`pair_style body/rounded/polyhedron <pair_body_rou
 The *wallstyle* can be planar or cylindrical.  The 3 planar options
 specify a pair of walls in a dimension.  Wall positions are given by
 *lo* and *hi*\ .  Either of the values can be specified as NULL if a
-single wall is desired.  For a *zcylinder* wallstyle, the cylinder's
-axis is at x = y = 0.0, and the radius of the cylinder is specified.
+single wall is desired.
 
 Optionally, the wall can be moving, if the *wiggle* keyword is appended.
 
@@ -71,8 +69,7 @@ particles.  The arguments to the *wiggle* keyword specify a dimension
 for the motion, as well as it's *amplitude* and *period*\ .  Note that
 if the dimension is in the plane of the wall, this is effectively a
 shearing motion.  If the dimension is perpendicular to the wall, it is
-more of a shaking motion.  A *zcylinder* wall can only be wiggled in
-the z dimension.
+more of a shaking motion.
 
 Each timestep, the position of a wiggled wall in the appropriate *dim*
 is set according to this equation:

doc/src/hyper.rst

@@ -51,19 +51,17 @@ each timestep.  In the bond-boost hyperdynamics context, a "bond" is
 not a covalent bond between a pair of atoms in a molecule.  Rather it
 is simply a pair of nearby atoms as discussed below.
 
-Both global and local HD are described in :ref:`(Voter2013) <Voter2013>` by
-Art Voter and collaborators.  Similar to parallel replica dynamics
-(PRD), global and local HD are methods for performing accelerated
-dynamics that are suitable for infrequent-event systems that obey
-first-order kinetics.  A good overview of accelerated dynamics methods
-for such systems in given in :ref:`(Voter2002) <Voter2002hd>` from the same
-group.  To quote from the review paper: "The dynamical evolution is
-characterized by vibrational excursions within a potential basin,
-punctuated by occasional transitions between basins."  The transition
-probability is characterized by p(t) = k\*exp(-kt) where k is the rate
-constant.  Running multiple replicas gives an effective enhancement in
-the timescale spanned by the multiple simulations, while waiting for
-an event to occur.
+Both global and local HD are described in :ref:`(Voter2013)
+<Voter2013>` by Art Voter and collaborators.  Similar to parallel
+replica dynamics (PRD), global and local HD are methods for performing
+accelerated dynamics that are suitable for infrequent-event systems
+that obey first-order kinetics.  A good overview of accelerated
+dynamics methods (AMD) for such systems in given in :ref:`(Voter2002)
+<Voter2002hd>` from the same group.  To quote from the review paper:
+"The dynamical evolution is characterized by vibrational excursions
+within a potential basin, punctuated by occasional transitions between
+basins.  The transition probability is characterized by p(t) =
+k\*exp(-kt) where k is the rate constant."
 
 Both HD and PRD produce a time-accurate trajectory that effectively
 extends the timescale over which a system can be simulated, but they

doc/src/pair_momb.rst

@@ -31,7 +31,7 @@ Style *momb* computes pairwise van der Waals (vdW) and short-range
 interactions using the Morse potential and :ref:`(Grimme) <Grimme>` method
 implemented in the Many-Body Metal-Organic (MOMB) force field
 described comprehensively in :ref:`(Fichthorn) <Fichthorn>` and
-:ref:`(Zhou) <Zhou4>`. Grimme's method is widely used to correct for
+:ref:`(Zhou) <Zhou5>`. Grimme's method is widely used to correct for
 dispersion in density functional theory calculations.
 
 .. math::
@@ -76,6 +76,6 @@ Related commands
 
 **(Fichthorn)** Fichthorn, Balankura, Qi, CrystEngComm, 18(29), 5410-5417 (2016).
 
-.. _Zhou4:
+.. _Zhou5:
 
 **(Zhou)** Zhou, Saidi, Fichthorn, J Phys Chem C, 118(6), 3366-3374 (2014).

doc/src/pair_polymorphic.rst

@@ -18,21 +18,22 @@ Examples
 .. code-block:: LAMMPS
 
    pair_style polymorphic
-   pair_coeff * * TlBr_msw.polymorphic Tl Br
-   pair_coeff * * AlCu_eam.polymorphic Al Cu
-   pair_coeff * * GaN_tersoff.polymorphic Ga N
-   pair_coeff * * GaN_sw.polymorphic GaN
+   pair_coeff * * FeCH_BOP_I.poly Fe C H
+   pair_coeff * * TlBr_msw.poly Tl Br
+   pair_coeff * * CuTa_eam.poly Cu Ta
+   pair_coeff * * GaN_tersoff.poly Ga N
+   pair_coeff * * GaN_sw.poly Ga N
 
 Description
 """""""""""
 
 The *polymorphic* pair style computes a 3-body free-form potential
-(:ref:`Zhou <Zhou3>`) for the energy E of a system of atoms as
+(:ref:`Zhou3 <Zhou3>`) for the energy E of a system of atoms as
 
 .. math::
 
-   E & = \frac{1}{2}\sum_{i=1}^{i=N}\sum_{j=1}^{j=N}\left[\left(1-\delta_{ij}\right)\cdot U_{IJ}\left(r_{ij}\right)-\left(1-\eta_{ij}\right)\cdot F_{IJ}\left(r_{ij}\right)\cdot V_{IJ}\left(r_{ij}\right)\right] \\
-   X_{ij} & = \sum_{k=i_1,k\neq i,j}^{i_N}W_{IK}\left(r_{ik}\right)\cdot G_{JIK}\left(\theta_{jik}\right)\cdot P_{IK}\left(\Delta r_{jik}\right) \\
+   E & = \frac{1}{2}\sum_{i=1}^{i=N}\sum_{j=1}^{j=N}\left[\left(1-\delta_{ij}\right)\cdot U_{IJ}\left(r_{ij}\right)-\left(1-\eta_{ij}\right)\cdot F_{IJ}\left(X_{ij}\right)\cdot V_{IJ}\left(r_{ij}\right)\right] \\
+   X_{ij} & = \sum_{k=i_1,k\neq j}^{i_N}W_{IK}\left(r_{ik}\right)\cdot G_{JIK}\left(\cos\theta_{jik}\right)\cdot P_{JIK}\left(\Delta r_{jik}\right) \\
    \Delta r_{jik} & = r_{ij}-\xi_{IJ}\cdot r_{ik}
 
 where I, J, K represent species of atoms i, j, and k, :math:`i_1, ...,
@@ -42,230 +43,267 @@ Dirac constant (i.e., :math:`\delta_{ij} = 1` when :math:`i = j`, and
 constant that can be set either to :math:`\eta_{ij} = \delta_{ij}` or
 :math:`\eta_{ij} = 1 - \delta_{ij}` depending on the potential type,
 :math:`U_{IJ}(r_{ij})`, :math:`V_{IJ}(r_{ij})`, :math:`W_{IK}(r_{ik})`
-are pair functions, :math:`G_{JIK}(\cos(\theta))` is an angular
-function, :math:`P_{IK}(\Delta r_{jik})` is a function of atomic spacing
-differential :math:`\Delta r_{jik} = r_{ij} - \xi_{IJ} \cdot r_{ik}`
-with :math:`\xi_{IJ}` being a pair-dependent parameter, and
+are pair functions, :math:`G_{JIK}(\cos\theta_{jik})` is an angular
+function, :math:`P_{JIK}(\Delta r_{jik})` is a function of atomic
+spacing differential :math:`\Delta r_{jik} = r_{ij} - \xi_{IJ} \cdot
+r_{ik}` with :math:`\xi_{IJ}` being a pair-dependent parameter, and
 :math:`F_{IJ}(X_{ij})` is a function of the local environment variable
 :math:`X_{ij}`. This generic potential is fully defined once the
 constants :math:`\eta_{ij}` and :math:`\xi_{IJ}`, and the six functions
 :math:`U_{IJ}(r_{ij})`, :math:`V_{IJ}(r_{ij})`, :math:`W_{IK}(r_{ik})`,
-:math:`G_{JIK}(\cos(\theta))`, :math:`P_{IK}(\Delta r_{jik})`, and
-:math:`F_{IJ}(X_{ij})` are given. Note that these six functions are all
-one dimensional, and hence can be provided in an analytic or tabular
-form. This allows users to design different potentials solely based on a
-manipulation of these functions. For instance, the potential reduces to
-Stillinger-Weber potential (:ref:`SW <SW>`) if we set
+:math:`G_{JIK}(\cos\theta_{jik})`, :math:`P_{JIK}(\Delta r_{jik})`, and
+:math:`F_{IJ}(X_{ij})` are given. Here LAMMPS uses a global parameter
+:math:`\eta` to represent :math:`\eta_{ij}`. When :math:`\eta = 1`,
+:math:`\eta_{ij} = 1 - \delta_{ij}`, otherwise :math:`\eta_{ij} =
+\delta_{ij}`. Additionally, :math:`\eta = 3` indicates that the function
+:math:`P_{JIK}(\Delta r)` depends on species I, J and K, otherwise
+:math:`P_{JIK}(\Delta r) = P_{IK}(\Delta r)` only depends on species I
+and K. Note that these six functions are all one dimensional, and hence
+can be provided in a tabular form. This allows users to design different
+potentials solely based on a manipulation of these functions. For
+instance, the potential reduces to a Stillinger-Weber potential
+(:ref:`SW <SW>`) if we set
 
 .. math::
 
-   \left\{\begin{array}{l}
-   \eta_{ij} = \delta_{ij},\xi_{IJ}=0 \\
-   U_{IJ}\left(r\right)=A_{IJ}\cdot\epsilon_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^q\cdot \left[B_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^{p-q}-1\right]\cdot exp\left(\frac{\sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
-   V_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
-   F_{IJ}\left(X\right)=-X \\
-   P_{IJ}\left(\Delta r\right)=1 \\
-   W_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
-   G_{JIK}\left(\theta\right)=\left(cos\theta+\frac{1}{3}\right)^2
-   \end{array}\right.
+   \eta_{ij} & = \delta_{ij} (\eta = 2~or~\eta = 0),\xi_{IJ}=0 \\
+   U_{IJ}\left(r\right) & = A_{IJ}\cdot\epsilon_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^q\cdot \left[B_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^{p-q}-1\right]\cdot exp\left(\frac{\sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
+   V_{IJ}\left(r\right) & = \sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
+   F_{IJ}\left(X\right) & = -X \\
+   P_{JIK}\left(\Delta r\right) & = P_{IK}\left(\Delta r\right) = 1 \\
+   W_{IJ}\left(r\right) & = \sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
+   G_{JIK}\left(\cos\theta\right) & = \left(\cos\theta+\frac{1}{3}\right)^2
 
-The potential reduces to Tersoff types of potential
-(:ref:`Tersoff <Tersoff>` or :ref:`Albe <poly-Albe>`) if we set
+The potential reduces to a Tersoff potential (:ref:`Tersoff <Tersoff>`
+or :ref:`Albe <poly-Albe>`) if we set
 
 .. math::
 
-   \left\{\begin{array}{l}
-   \eta_{ij}=\delta_{ij},\xi_{IJ}=1 \\
-   U_{IJ}\left(r\right)=\frac{D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{2S_{IJ}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\
-   V_{IJ}\left(r\right)=\frac{S_{IJ}\cdot D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{\frac{2}{S_{IJ}}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\
-   F_{IJ}\left(X\right)=\left(1+X\right)^{-\frac{1}{2}} \\
-   P_{IJ}\left(\Delta r\right)=exp\left(2\mu_{IK}\cdot \Delta r\right) \\
-   W_{IJ}\left(r\right)=f_{c,IK}\left(r\right) \\
-   G_{JIK}\left(\theta\right)=\gamma_{IK}\left[1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2}\right]
-   \end{array}\right.
+   \eta_{ij} & = \delta_{ij} (\eta = 2~or~\eta = 0),\xi_{IJ}=1 \\
+   U_{IJ}\left(r\right) & = \frac{D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{2S_{IJ}}\left(r-r_{e,IJ}\right)\right]\cdot f_{c,IJ}\left(r\right) \\
+   V_{IJ}\left(r\right) & = \frac{S_{IJ}\cdot D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{\frac{2}{S_{IJ}}}\left(r-r_{e,IJ}\right)\right]\cdot f_{c,IJ}\left(r\right) \\
+   F_{IJ}\left(X\right) & = \left(1+X\right)^{-\frac{1}{2}} \\
+   P_{JIK}\left(\Delta r\right) & = P_{IK}\left(\Delta r\right) = exp\left(2\mu_{IK}\cdot \Delta r\right) \\
+   W_{IJ}\left(r\right) & = f_{c,IJ}\left(r\right) \\
+   G_{JIK}\left(\cos\theta\right) & = \gamma_{IK}\left[1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+\cos\theta\right)^2}\right]
+
+where
 
 .. math::
 
-   f_{c,IJ}=\left\{\begin{array}{lr}
-   1, & r\leq r_{s,IJ} \\
-   \frac{1}{2}+\frac{1}{2} cos \left[\frac{\pi \left(r-r_{s,IJ}\right)}{r_{c,IJ}-r_{s,IJ}}\right], & r_{s,IJ}<r<r_{c,IJ} \\
-   0, & r \geq r_{c,IJ} \\
+   f_{c,IJ}\left(r\right)=\left\{\begin{array}{l}
+   1, r\leq R_{IJ}-D_{IJ} \\
+   \frac{1}{2}+\frac{1}{2}cos\left[\frac{\pi\left(r+D_{IJ}-R_{IJ}\right)}{2D_{IJ}}\right], R_{IJ}-D_{IJ} < r < R_{IJ}+D_{IJ} \\
+   0, r \geq R_{IJ}+D_{IJ}
    \end{array}\right.
 
-The potential reduces to Rockett-Tersoff (:ref:`Wang <Wang3>`) type if we set
+The potential reduces to a modified Stillinger-Weber potential
+(:ref:`Zhou3 <Zhou3>`) if we set
 
 .. math::
 
-   \left\{\begin{array}{l}
-   \eta_{ij}=\delta_{ij},\xi_{IJ}=1 \\
-   U_{IJ}\left(r\right)=\left\{\begin{array}{lr}
-   A_{IJ}\cdot exp\left(-\lambda_{1,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right), & r\leq r_{s,1,IJ} \\
-   A_{IJ}\cdot exp\left(-\lambda_{1,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right)\cdot f_{c,1,IJ}\left(r\right), & r_{s,1,IJ}<r<r_{c,1,IJ} \\
-   0, & r\ge r_{c,1,IJ}
-   \end{array}\right. \\
-   V_{IJ}\left(r\right)=\left\{\begin{array}{lr}
-   B_{IJ} \cdot exp\left(-\lambda_{2,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right), & r\le r_{s,1,IJ} \\
-   B_{IJ} \cdot exp\left(-\lambda_{2,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right)+A_{IJ}\cdot exp\left(-\lambda_{1,IJ}\cdot r\right)\cdot & \\ ~~~~~~ f_{c,IJ}\left(r\right)\cdot \left[1-f_{c,1,IJ}\left(r\right)\right], & r_{s,1,IJ}<r<r_{c,1,IJ} \\
-   B_{IJ} \cdot exp\left(-\lambda_{2,IJ}\cdot r\right)\cdot f_{c,IJ}\left(r\right)+A_{IJ}\cdot exp\left(-\lambda_{1,IJ}\cdot r\right)\cdot & \\ ~~~~~~ f_{c,IJ}\left(r\right) & r \ge r_{c,1,IJ}
-   \end{array}\right. \\
-   F_{IJ}\left(X\right)=\left[1+\left(\beta_{IJ}\cdot X\right)^{n_{IJ}}\right]^{-\frac{1}{2n_{IJ}}} \\
-   P_{IJ}\left(\Delta r\right)=exp\left(\lambda_{3,IK}\cdot \Delta r^3\right) \\
-   W_{IJ}\left(r\right)=f_{c,IK}\left(r\right) \\
-   G_{JIK}\left(\theta\right)=1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2}
-   \end{array}\right.
+   \eta_{ij} & = \delta_{ij} (\eta = 2~or~\eta = 0),\xi_{IJ}=0 \\
+   U_{IJ}\left(r\right) & = \varphi_{R,IJ}\left(r\right)-\varphi_{A,IJ}\left(r\right) \\
+   V_{IJ}\left(r\right) & = u_{IJ}\left(r\right) \\
+   F_{IJ}\left(X\right) & = -X \\
+   P_{JIK}\left(\Delta r\right) & = P_{IK}\left(\Delta r\right) = 1 \\
+   W_{IJ}\left(r\right) & = u_{IJ}\left(r\right) \\
+   G_{JIK}\left(\cos\theta\right) & = g_{JIK}\left(\cos\theta\right)
+
+The potential reduces to a Rockett-Tersoff potential (:ref:`Wang3
+<Wang3>`) if we set
 
 .. math::
 
-   f_{c,IJ}=\left\{\begin{array}{lr}
-   1, & r\leq r_{s,IJ} \\
-   \frac{1}{2}+\frac{1}{2} cos \left[\frac{\pi \left(r-r_{s,IJ}\right)}{r_{c,IJ}-r_{s,IJ}}\right], & r_{s,IJ}<r<r_{c,IJ} \\
-   0, & r \geq r_{c,IJ} \\
-   \end{array}\right.
+   \eta_{ij} & = \delta_{ij} (\eta = 2~or~\eta = 0),\xi_{IJ}=1 \\
+   U_{IJ}\left(r\right) & = A_{IJ}exp\left(-\lambda_{1,IJ}\cdot r\right)f_{c,IJ}\left(r\right)f_{ca,IJ}\left(r\right) \\
+   V_{IJ}\left(r\right) & = \left\{\begin{array}{l}B_{IJ}exp\left(-\lambda_{2,IJ}\cdot r\right)f_{c,IJ}\left(r\right)+ \\ A_{IJ}exp\left(-\lambda_{1,IJ}\cdot r\right)f_{c,IJ}\left(r\right) \left[1-f_{ca,IJ}\left(r\right)\right]\end{array} \right\} \\
+   F_{IJ}\left(X\right) & = \left[1+\left(\beta_{IJ}X\right)^{n_{IJ}}\right]^{-\frac{1}{2n_{IJ}}} \\
+   P_{JIK}\left(\Delta r\right) & = P_{IK}\left(\Delta r\right) = exp\left(\lambda_{3,IK}\cdot \Delta r^3\right) \\
+   W_{IJ}\left(r\right) & = f_{c,IJ}\left(r\right) \\
+   G_{JIK}\left(\cos\theta\right) & = 1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+\cos\theta\right)^2}
+
+where :math:`f_{ca,IJ}(r)` is similar to the :math:`f_{c,IJ}(r)` defined
+above:
 
 .. math::
 
-   f_{c,1,IJ}=\left\{\begin{array}{lr}
-   1, & r\leq r_{s,1,IJ} \\
-   \frac{1}{2}+\frac{1}{2} cos \left[\frac{\pi \left(r-r_{s,1,IJ}\right)}{r_{c,1,IJ}-r_{s,1,IJ}}\right], & r_{s,1,IJ}<r<r_{c,1,IJ} \\
-   0, & r \geq r_{c,1,IJ} \\
+   f_{ca,IJ}\left(r\right)=\left\{\begin{array}{l}
+   1, r\leq R_{a,IJ}-D_{a,IJ} \\
+   \frac{1}{2}+\frac{1}{2}cos\left[\frac{\pi\left(r+D_{a,IJ}-R_{a,IJ}\right)}{2D_{a,IJ}}\right], R_{a,IJ}-D_{a,IJ} < r < R_{a,IJ}+D_{a,IJ} \\
+   0, r \geq R_{a,IJ}+D_{a,IJ}
    \end{array}\right.
 
-The potential becomes embedded atom method (:ref:`Daw <poly-Daw>`) if we set
+The potential becomes the embedded atom method (:ref:`Daw <poly-Daw>`)
+if we set
 
 .. math::
 
-   \left\{\begin{array}{l}
-   \eta_{ij}=1-\delta_{ij},\xi_{IJ}=0 \\
-   U_{IJ}\left(r\right)=\phi_{IJ}\left(r\right) \\
-   V_{IJ}\left(r\right)=1 \\
-   F_{II}\left(X\right)=-2F_I\left(X\right) \\
-   P_{IJ}\left(\Delta r\right)=1 \\
-   W_{IJ}\left(r\right)=f_{K}\left(r\right) \\
-   G_{JIK}\left(\theta\right)=1
-   \end{array}\right.
+   \eta_{ij} & = 1-\delta_{ij} (\eta = 1),\xi_{IJ}=0 \\
+   U_{IJ}\left(r\right) & = \phi_{IJ}\left(r\right) \\
+   V_{IJ}\left(r\right) & = 1 \\
+   F_{II}\left(X\right) & = -2F_I\left(X\right) \\
+   P_{JIK}\left(\Delta r\right) & = P_{IK}\left(\Delta r\right) = 1 \\
+   W_{IJ}\left(r\right) & = f_{J}\left(r\right) \\
+   G_{JIK}\left(\cos\theta\right) & = 1
 
-In the embedded atom method case, :math:`\phi_{IJ}(r_{ij})` is the pair
+In the embedded atom method case, :math:`\phi_{IJ}(r)` is the pair
 energy, :math:`F_I(X)` is the embedding energy, *X* is the local
-electron density, and :math:`f_K(r)` is the atomic electron density function.
+electron density, and :math:`f_J(r)` is the atomic electron density
+function.
 
-If the tabulated functions are created using the parameters of sw,
-tersoff, and eam potentials, the polymorphic pair style will produce
-the same global properties (energies and stresses) and the same forces
-as the sw, tersoff, and eam pair styles. The polymorphic pair style
-also produces the same atom properties (energies and stresses) as the
-corresponding tersoff and eam pair styles. However, due to a different
-partition of global properties to atom properties, the polymorphic
-pair style will produce different atom properties (energies and
-stresses) as the sw pair style. This does not mean that polymorphic
-pair style is different from the sw pair style in this case. It just
-means that the definitions of the atom energies and atom stresses are
-different.
+The potential reduces to another type of Tersoff potential (:ref:`Zhou4
+<Zhou4>`) if we set
 
-Only a single pair_coeff command is used with the polymorphic style
-which specifies an potential file for all needed elements. These are
+.. math::
+
+   \eta_{ij} & = \delta_{ij} (\eta = 3),\xi_{IJ}=1 \\
+   U_{IJ}\left(r\right) & = \frac{D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{2S_{IJ}}\left(r-r_{e,IJ}\right)\right]\cdot f_{c,IJ}\left(r\right) \cdot T_{IJ}\left(r\right)+V_{ZBL,IJ}\left(r\right)\left[1-T_{IJ}\left(r\right)\right] \\
+   V_{IJ}\left(r\right) & = \frac{S_{IJ}\cdot D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{\frac{2}{S_{IJ}}}\left(r-r_{e,IJ}\right)\right]\cdot f_{c,IJ}\left(r\right) \cdot T_{IJ}\left(r\right) \\
+   F_{IJ}\left(X\right) & = \left(1+X\right)^{-\frac{1}{2}} \\
+   P_{JIK}\left(\Delta r\right) & = \omega_{JIK} \cdot exp\left(\alpha_{JIK}\cdot \Delta r\right) \\
+   W_{IJ}\left(r\right) & = f_{c,IJ}\left(r\right) \\
+   G_{JIK}\left(\cos\theta\right) & = \gamma_{JIK}\left[1+\frac{c_{JIK}^2}{d_{JIK}^2}-\frac{c_{JIK}^2}{d_{JIK}^2+\left(h_{JIK}+\cos\theta\right)^2}\right] \\
+   T_{IJ}\left(r\right) & = \frac{1}{1+exp\left[-b_{f,IJ}\left(r-r_{f,IJ}\right)\right]} \\
+   V_{ZBL,IJ}\left(r\right) & = 14.4 \cdot \frac{Z_I \cdot Z_J}{r}\sum_{k=1}^{4}\mu_k \cdot exp\left[-\nu_k \left(Z_I^{0.23}+Z_J^{0.23}\right) r\right]
+
+where :math:`f_{c,IJ}(r)` is the same as defined above. This Tersoff
+potential differs from the one above because the :math:`P_{JIK}(\Delta
+r)` function is now dependent on all three species I, J, and K.
+
+If the tabulated functions are created using the parameters of
+Stillinger-Weber, Tersoff, and EAM potentials, the polymorphic pair
+style will produce the same global properties (energies and stresses)
+and the same forces as the :doc:`sw <pair_sw>`, :doc:`tersoff
+<pair_tersoff>`, and :doc:`eam <pair_eam>` pair styles. The polymorphic
+pair style also produces the same per-atom properties (energies and
+stresses) as the corresponding :doc:`tersoff <pair_tersoff>` and
+:doc:`eam <pair_eam>` pair styles. However, due to a different
+partitioning of global properties to per-atom properties, the
+polymorphic pair style will produce different per-atom properties
+(energies and stresses) as the :doc:`sw <pair_sw>` pair style. This does
+not mean that polymorphic pair style is different from the sw pair
+style. It just means that the definitions of the atom energies and atom
+stresses are different.
+
+Only a single pair_coeff command is used with the polymorphic pair style
+which specifies a potential file for all needed elements.  These are
 mapped to LAMMPS atom types by specifying N additional arguments after
-the filename in the pair_coeff command, where N is the number of
-LAMMPS atom types:
+the filename in the pair_coeff command, where N is the number of LAMMPS
+atom types:
 
 * filename
-* N element names = mapping of Tersoff elements to atom types
+* N element names = mapping of polymorphic potential elements to atom types
 
 See the pair_coeff doc page for alternate ways to specify the path for
-the potential file.  Several files for polymorphic potentials are
-included in the potentials directory of the LAMMPS distribution.  They
+the potential file. Several files for polymorphic potentials are
+included in the potentials directory of the LAMMPS distribution. They
 have a "poly" suffix.
 
-As an example, imagine the SiC_tersoff.poly file has tabulated
-functions for Si-C tersoff potential. If your LAMMPS simulation has 4
-atoms types and you want the 1st 3 to be Si, and the 4th to be C, you
-would use the following pair_coeff command:
+As an example, imagine the GaN_tersoff.poly file has tabulated functions
+for Ga-N tersoff potential. If your LAMMPS simulation has 4 atoms types
+and you want the 1st 3 to be Ga, and the 4th to be N, you would use the
+following pair_coeff command:
 
 .. code-block:: LAMMPS
 
-   pair_coeff * * SiC_tersoff.poly Si Si Si C
+   pair_coeff * * GaN_tersoff.poly Ga Ga Ga N
 
-The 1st 2 arguments must be \* \* so as to span all LAMMPS atom
-types. The first three Si arguments map LAMMPS atom types 1,2,3 to the
-Si element in the polymorphic file. The final C argument maps LAMMPS
-atom type 4 to the C element in the polymorphic file. If a mapping
-value is specified as NULL, the mapping is not performed. This can be
-used when an polymorphic potential is used as part of the hybrid pair
-style. The NULL values are placeholders for atom types that will be
-used with other potentials.
+The first two arguments must be \* \* to span all pairs of LAMMPS atom
+types. The first three Ga arguments map LAMMPS atom types 1,2,3 to the
+Ga element in the polymorphic file. The final N argument maps LAMMPS
+atom type 4 to the N element in the polymorphic file. If a mapping value
+is specified as NULL, the mapping is not performed. This can be used
+when an polymorphic potential is used as part of the hybrid pair
+style. The NULL values are placeholders for atom types that will be used
+with other potentials.
 
 Potential files in the potentials directory of the LAMMPS distribution
 have a ".poly" suffix. At the beginning of the files, an unlimited
-number of lines starting with '#' are used to describe the potential
-and are ignored by LAMMPS. The next line lists two numbers:
+number of lines starting with '#' are used to describe the potential and
+are ignored by LAMMPS. The next line lists two numbers:
 
 .. parsed-literal::
 
-   ntypes :math:`\eta`
+   ntypes eta
 
-Here ntypes represent total number of species defined in the potential
-file, and :math:`\eta = 0` or 1. The number ntypes must equal the total
-number of different species defined in the pair_coeff command. When
-:math:`\eta = 1`, :math:\eta_{ij}` defined in the potential functions
-above is set to :math:`1 - \delta_{ij}`, otherwise :math:`\eta_{ij}` is
-set to :math:`\delta_{ij}`. The next ntypes lines each lists two numbers
-and a character string representing atomic number, atomic mass, and name
-of the species of the ntypes elements:
+Here *ntypes* represent total number of species defined in the potential
+file, :math:`\eta = 1` reduces to embedded atom method, :math:`\eta = 3`
+assumes a three species dependent :math:`P_{JIK}(\Delta r)` function,
+and all other values of :math:`\eta` assume a two species dependent
+:math:`P_{JK}(\Delta r)` function. The value of *ntypes* must equal the
+total number of different species defined in the pair_coeff command. The
+next *ntypes* lines each lists two numbers and a character string
+representing atomic number, atomic mass, and name of the species of the
+ntypes elements:
 
 .. parsed-literal::
 
-   atomic_number atomic-mass element (1)
-   atomic_number atomic-mass element (2)
+   atomic-number atomic-mass element-name(1)
+   atomic-number atomic-mass element-name(2)
    ...
-   atomic_number atomic-mass element (ntypes)
+   atomic-number atomic-mass element-name(ntypes)
+
+The next line contains four numbers:
+
+.. parsed-literal::
+
+   nr ntheta nx xmax
+
+Here nr is total number of tabular points for radial functions U, V, W,
+P, ntheta is total number of tabular points for the angular function G,
+nx is total number of tabular points for the function F, xmax is a
+maximum value of the argument of function F. Note that the pair
+functions :math:`U_{IJ}(r)`, :math:`V_{IJ}(r)`, :math:`W_{IJ}(r)` are
+uniformly tabulated between 0 and cutoff distance of the IJ pair,
+:math:`G_{JIK}(\cos\theta)` is uniformly tabulated between -1 and 1,
+:math:`P_{JIK}(\Delta r)` is uniformly tabulated between -rcmax and
+rcmax where rcmax is the maximum cutoff distance of all pairs, and
+:math:`F_{IJ}(X)` is uniformly tabulated between 0 and xmax. Linear
+extrapolation is assumed if actual simulations exceed these ranges.
 
 The next ntypes\*(ntypes+1)/2 lines contain two numbers:
 
 .. parsed-literal::
 
-   cut :math:`xi` (1)
-   cut :math:`xi` (2)
+   cut xi(1)
+   cut xi(2)
    ...
-   cut :math:`xi` (ntypes\*(ntypes+1)/2)
+   cut xi(ntypes\*(ntypes+1)/2)
 
-Here cut means the cutoff distance of the pair functions, :math:`\xi` is
-the same as defined in the potential functions above. The
+Here cut means the cutoff distance of the pair functions, "xi" is
+:math:`\xi` as defined in the potential functions above. The
 ntypes\*(ntypes+1)/2 lines are related to the pairs according to the
-sequence of first ii (self) pairs, i = 1, 2, ..., ntypes, and then then
-ij (cross) pairs, i = 1, 2, ..., ntypes-1, and j = i+1, i+2, ..., ntypes
+sequence of first ii (self) pairs, i = 1, 2, ..., ntypes, and then ij
+(cross) pairs, i = 1, 2, ..., ntypes-1, and j = i+1, i+2, ..., ntypes
 (i.e., the sequence of the ij pairs follows 11, 22, ..., 12, 13, 14,
 ..., 23, 24, ...).
 
-The final blocks of the potential file are the U, V, W, P, G, and F
-functions are listed sequentially. First, U functions are given for
-each of the ntypes\*(ntypes+1)/2 pairs according to the sequence
-described above. For each of the pairs, nr values are listed. Next,
-similar arrays are given for V, W, and P functions. Then G functions
-are given for all the ntypes\*ntypes\*ntypes ijk triplets in a natural
-sequence i from 1 to ntypes, j from 1 to ntypes, and k from 1 to
-ntypes (i.e., ijk = 111, 112, 113, ..., 121, 122, 123 ..., 211, 212,
-...). Each of the ijk functions contains ng values. Finally, the F
-functions are listed for all ntypes\*(ntypes+1)/2 pairs, each
-containing nx values. Either analytic or tabulated functions can be
-specified. Currently, constant, exponential, sine and cosine analytic
-functions are available which are specified with: constant c1 , where
-f(x) = c1 exponential c1 c2 , where f(x) = c1 exp(c2\*x) sine c1 c2 ,
-where f(x) = c1 sin(c2\*x) cos c1 c2 , where f(x) = c1 cos(c2\*x)
-Tabulated functions are specified by spline n x1 x2, where n=number of
-point, (x1,x2)=range and then followed by n values evaluated uniformly
-over these argument ranges.  The valid argument ranges of the
-functions are between 0 <= r <= cut for the U(r), V(r), W(r)
-functions, -cutmax <= delta_r <= cutmax for the P(delta_r) functions,
--1 <= :math:`\cos\theta` <= 1 for the G(:math:`\cos\theta`) functions,
-and 0 <= X <= maxX for the F(X) functions.
+In the final blocks of the potential file, U, V, W, P, G, and F
+functions are listed sequentially. First, U functions are given for each
+of the ntypes\*(ntypes+1)/2 pairs according to the sequence described
+above. For each of the pairs, nr values are listed. Next, similar arrays
+are given for V and W functions. If P functions depend only on pair
+species, i.e., :math:`\eta \neq 3`, then P functions are also listed the
+same way the next. If P functions depend on three species, i.e.,
+:math:`\eta = 3`, then P functions are listed for all the
+ntypes*ntypes*ntypes IJK triplets in a natural sequence I from 1 to
+ntypes, J from 1 to ntypes, and K from 1 to ntypes (i.e., IJK = 111,
+112, 113, ..., 121, 122, 123 ..., 211, 212, ...). Next, G functions are
+listed for all the ntypes*ntypes*ntypes IJK triplets similarly. For each
+of the G functions, ntheta values are listed. Finally, F functions are
+listed for all the ntypes*(ntypes+1)/2 pairs in the same sequence as
+described above.  For each of the F functions, nx values are listed.
 
 **Mixing, shift, table tail correction, restart**\ :
 
 This pair styles does not support the :doc:`pair_modify <pair_modify>`
 shift, table, and tail options.
 
-This pair style does not write their information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
-need to re-specify the pair_style and pair_coeff commands in an input
-script that reads a restart file.
+This pair style does not write their information to :doc:`binary restart
+files <restart>`, since it is stored in potential files. Thus, you need
+to re-specify the pair_style and pair_coeff commands in an input script
+that reads a restart file.
 
 ----------
 
@@ -277,15 +315,15 @@ input script. If using read_data, atomic masses must be defined in the
 atomic structure data file.
 
 This pair style is part of the MANYBODY package. It is only enabled if
-LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 This pair potential requires the :doc:`newtion <newton>` setting to be
 "on" for pair interactions.
 
-The potential files provided with LAMMPS (see the potentials
-directory) are parameterized for metal :doc:`units <units>`. You can use
-any LAMMPS units, but you would need to create your own potential
-files.
+The potential files provided with LAMMPS (see the potentials directory)
+are parameterized for metal :doc:`units <units>`. You can use any LAMMPS
+units, but you would need to create your own potential files.
 
 Related commands
 """"""""""""""""
@@ -296,12 +334,15 @@ Related commands
 
 .. _Zhou3:
 
-**(Zhou)** X. W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and
-F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015).
+**(Zhou3)** X. W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015).
+
+.. _Zhou4:
+
+**(Zhou4)** X. W. Zhou, M. E. Foster, J. A. Ronevich, and C. W. San Marchi, J. Comp. Chem., 41, 1299 (2020).
 
 .. _SW:
 
-**(SW)** F. H. Stillinger-Weber, and T. A. Weber, Phys. Rev. B, 31, 5262 (1985).
+**(SW)** F. H. Stillinger, and T. A. Weber, Phys. Rev. B, 31, 5262 (1985).
 
 .. _Tersoff:
 
@@ -309,8 +350,7 @@ F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015).
 
 .. _poly-Albe:
 
-**(Albe)** K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B,
-66, 035205 (2002).
+**(Albe)** K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002).
 
 .. _Wang3:
 

doc/src/pair_reaxc.rst

@@ -21,12 +21,13 @@ Syntax
 
   .. parsed-literal::
 
-     keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap*
+     keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds*
        *checkqeq* value = *yes* or *no* = whether or not to require qeq/reax fix
        *enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
        *lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
        *safezone* = factor used for array allocation
        *mincap* = minimum size for array allocation
+       *minhbonds* = minimum size use for storing hydrogen bonds
 
 Examples
 """"""""
@@ -146,11 +147,11 @@ zero.  The latter behavior is usual not desired, as it causes
 discontinuities in the potential energy when the bonding of an atom
 drops to zero.
 
-Optional keywords *safezone* and *mincap* are used for allocating
-reax/c arrays.  Increasing these values can avoid memory problems,
-such as segmentation faults and bondchk failed errors, that could
-occur under certain conditions. These keywords are not used by the
-Kokkos version, which instead uses a more robust memory allocation
+Optional keywords *safezone*\ , *mincap*\ , and *minhbonds* are used
+for allocating reax/c arrays.  Increasing these values can avoid memory
+problems, such as segmentation faults and bondchk failed errors, that
+could occur under certain conditions. These keywords are not used by
+the Kokkos version, which instead uses a more robust memory allocation
 scheme that checks if the sizes of the arrays have been exceeded and
 automatically allocates more memory.
 
@@ -352,7 +353,7 @@ Default
 """""""
 
 The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no,
-safezone = 1.2, mincap = 50.
+safezone = 1.2, mincap = 50, minhbonds = 25.
 
 ----------
 

doc/src/prd.rst

@@ -52,19 +52,16 @@ replicas of a system.  One or more replicas can be used.  The total
 number of steps *N* to run can be interpreted in one of two ways; see
 discussion of the *time* keyword below.
 
-PRD is described in :ref:`(Voter1998) <Voter1998>` by Art Voter.  Similar to
-global or local hyperdynamics (HD), PRD is a method for performing
-accelerated dynamics that is suitable for infrequent-event systems
-that obey first-order kinetics.  A good overview of accelerated
-dynamics methods for such systems in given in this review paper
-:ref:`(Voter2002) <Voter2002prd>` from Art's group.  To quote from the
-paper: "The dynamical evolution is characterized by vibrational
-excursions within a potential basin, punctuated by occasional
-transitions between basins."  The transition probability is
-characterized by p(t) = k\*exp(-kt) where k is the rate constant.
-Running multiple replicas gives an effective enhancement in the
-timescale spanned by the multiple simulations, while waiting for an
-event to occur.
+PRD is described in :ref:`(Voter1998) <Voter1998>` by Art Voter.
+Similar to global or local hyperdynamics (HD), PRD is a method for
+performing accelerated dynamics that is suitable for infrequent-event
+systems that obey first-order kinetics.  A good overview of
+accelerated dynamics methods (AMD) for such systems in given in this
+review paper :ref:`(Voter2002) <Voter2002prd>` from Art's group.  To
+quote from the paper: "The dynamical evolution is characterized by
+vibrational excursions within a potential basin, punctuated by
+occasional transitions between basins.  The transition probability is
+characterized by p(t) = k\*exp(-kt) where k is the rate constant."
 
 Both PRD and HD produce a time-accurate trajectory that effectively
 extends the timescale over which a system can be simulated, but they

doc/src/tad.rst

@@ -58,18 +58,21 @@ Run a temperature accelerated dynamics (TAD) simulation. This method
 requires two or more partitions to perform NEB transition state
 searches.
 
-TAD is described in :ref:`this paper <Voter2000>` by Art Voter.  It is a method
-that uses accelerated dynamics at an elevated temperature to generate
-results at a specified lower temperature.  A good overview of
-accelerated dynamics methods for such systems is given in :ref:`this review paper <Voter2002>` from the same group. In general, these methods assume
-that the long-time dynamics is dominated by infrequent events i.e. the
-system is confined to low energy basins for long periods,
-punctuated by brief, randomly-occurring transitions to adjacent
-basins.  TAD is suitable for infrequent-event systems, where in
+TAD is described in :ref:`this paper <Voter2000>` by Art Voter.  It is
+a method that uses accelerated dynamics at an elevated temperature to
+generate results at a specified lower temperature.  A good overview of
+accelerated dynamics methods (AMD) for such systems is given in
+:ref:`this review paper <Voter2002>` from the same group.  To quote
+from the review paper: "The dynamical evolution is characterized by
+vibrational excursions within a potential basin, punctuated by
+occasional transitions between basins.  The transition probability is
+characterized by p(t) = k\*exp(-kt) where k is the rate constant."
+
+TAD is a suitable AMD method for infrequent-event systems, where in
 addition, the transition kinetics are well-approximated by harmonic
-transition state theory (hTST). In hTST, the temperature dependence of
-transition rates follows the Arrhenius relation.  As a consequence a
-set of event times generated in a high-temperature simulation can be
+transition state theory (hTST).  In hTST, the temperature dependence
+of transition rates follows the Arrhenius relation.  As a consequence
+a set of event times generated in a high-temperature simulation can be
 mapped to a set of much longer estimated times in the low-temperature
 system. However, because this mapping involves the energy barrier of
 the transition event, which is different for each event, the first
@@ -79,8 +82,8 @@ events from the current basin. After each event, the simulation is
 reflected backwards into the current basin.  This is repeated until
 the stopping criterion is satisfied, at which point the event with the
 earliest low-temperature occurrence time is selected.  The stopping
-criterion is that the confidence measure be greater than
-1-\ *delta*\ . The confidence measure is the probability that no earlier
+criterion is that the confidence measure be greater than 1-\ *delta*\
+. The confidence measure is the probability that no earlier
 low-temperature event will occur at some later time in the
 high-temperature simulation.  hTST provides an lower bound for this
 probability, based on the user-specified minimum pre-exponential

doc/utils/sphinx-config/false_positives.txt

@@ -499,6 +499,7 @@ cuda
 Cuda
 CUDA
 CuH
+cuFFT
 Cummins
 Curk
 customIDs
@@ -1544,6 +1545,7 @@ libmeam
 libmessage
 libmpi
 libmpich
+libnuma
 libplumed
 libplumedKernel
 libpng
@@ -1663,6 +1665,7 @@ manybody
 MANYBODY
 Maras
 Marchetti
+Marchi
 Mariella
 Marrink
 Marroquin
@@ -1783,6 +1786,7 @@ Militzer
 Minary
 mincap
 Mindlin
+minhbonds
 mingw
 minima
 minimizations
@@ -2442,6 +2446,7 @@ Ravelo
 rc
 Rc
 Rcm
+rcmax
 Rcmx
 Rcmy
 Rcut
@@ -2560,6 +2565,7 @@ Rockett
 Rodrigues
 Rohart
 Ronchetti
+Ronevich
 Rosati
 Rosenberger
 Rossky

examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability

@@ -0,0 +1,56 @@
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+
+variable runsteps equal 1000
+variable prob1 equal step/v_runsteps*2
+variable prob2 equal (step/v_runsteps)>0.5
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+molecule mol2 rxn1_stp1_reacted.data_template
+molecule mol3 rxn1_stp2_unreacted.data_template
+molecule mol4 rxn1_stp2_reacted.data_template
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 &
+  react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 &
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
+
+fix 1 statted_grp_REACT nvt temp 300 300 100
+
+# optionally, you can customize behavior of reacting atoms,
+# by using the internally-created 'bond_react_MASTER_group', like so:
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run ${runsteps}
+
+# write_restart restart_longrun
+# write_data restart_longrun.data

examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1

@@ -0,0 +1,201 @@
+LAMMPS (15 Apr 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000385045 secs
+  read_data CPU = 0.013443 secs
+
+variable runsteps equal 1000
+variable prob1 equal step/v_runsteps*2
+variable prob2 equal (step/v_runsteps)>0.5
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule template mol1:
+  1 molecules
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule template mol2:
+  1 molecules
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule template mol3:
+  1 molecules
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule template mol4:
+  1 molecules
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+
+fix 1 statted_grp_REACT nvt temp 300 300 100
+
+# optionally, you can customize behavior of reacting atoms,
+# by using the internally-created 'bond_react_MASTER_group', like so:
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run ${runsteps}
+run 1000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTW3
+  3d grid and FFT values/proc = 343 8
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+WARNING: Inconsistent image flags (src/domain.cpp:812)
+Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes
+Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0            0            0 
+      50    262.63913   -492.10749 0.0034851739          0.1            0            1            0 
+     100    766.52962   -29.714349 0.0034851739          0.2            0            1            0 
+     150    503.86837    50.220304 0.0034851739          0.3            0            1            0 
+     200    456.51295    12.312892 0.0034851739          0.4            0            1            0 
+     250    391.54928    9.2335844 0.0034851739          0.5            0            1            0 
+     300     336.6988   -47.193937 0.0034851739          0.6            0            1            0 
+     350    254.06985   -9.2867898 0.0034851739          0.7            0            1            0 
+     400    259.41098   -25.657321 0.0034851739          0.8            0            1            0 
+     450    258.10364      22.5086 0.0034851739          0.9            0            1            0 
+     500    272.13412   -6.5391448 0.0034851739            1            0            1            0 
+     550    202.75504    54.658731 0.0034851739          1.1            1            1            1 
+     600    344.79887    23.798478 0.0034851739          1.2            1            1            1 
+     650    328.44488   -29.908484 0.0034851739          1.3            1            1            1 
+     700    280.13593   -8.3223255 0.0034851739          1.4            1            1            1 
+     750    300.67624    1.0632669 0.0034851739          1.5            1            1            1 
+     800    376.64234    12.488392 0.0034851739          1.6            1            1            1 
+     850    321.07642    19.814074 0.0034851739          1.7            1            1            1 
+     900    332.23751    30.814079 0.0034851739          1.8            1            1            1 
+     950    311.14029    5.7853136 0.0034851739          1.9            1            1            1 
+    1000    253.14634   -37.560642 0.0034851739            2            1            1            1 
+Loop time of 0.379454 on 1 procs for 1000 steps with 44 atoms
+
+Performance: 227.696 ns/day, 0.105 hours/ns, 2635.368 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.069723   | 0.069723   | 0.069723   |   0.0 | 18.37
+Bond    | 0.14802    | 0.14802    | 0.14802    |   0.0 | 39.01
+Kspace  | 0.044252   | 0.044252   | 0.044252   |   0.0 | 11.66
+Neigh   | 0.072359   | 0.072359   | 0.072359   |   0.0 | 19.07
+Comm    | 0.0044748  | 0.0044748  | 0.0044748  |   0.0 |  1.18
+Output  | 0.0022775  | 0.0022775  | 0.0022775  |   0.0 |  0.60
+Modify  | 0.036509   | 0.036509   | 0.036509   |   0.0 |  9.62
+Other   |            | 0.00184    |            |       |  0.48
+
+Nlocal:    44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    3 ave 3 max 3 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    722 ave 722 max 722 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 722
+Ave neighs/atom = 16.4091
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4

@@ -0,0 +1,201 @@
+LAMMPS (15 Apr 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000431282 secs
+  read_data CPU = 0.0129571 secs
+
+variable runsteps equal 1000
+variable prob1 equal step/v_runsteps*2
+variable prob2 equal (step/v_runsteps)>0.5
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule template mol1:
+  1 molecules
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule template mol2:
+  1 molecules
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule template mol3:
+  1 molecules
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule template mol4:
+  1 molecules
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+
+fix 1 statted_grp_REACT nvt temp 300 300 100
+
+# optionally, you can customize behavior of reacting atoms,
+# by using the internally-created 'bond_react_MASTER_group', like so:
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run ${runsteps}
+run 1000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTW3
+  3d grid and FFT values/proc = 252 2
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+WARNING: Inconsistent image flags (src/domain.cpp:812)
+Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes
+Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0            0            0 
+      50     266.5092   -90.813802 0.0034851739          0.1            0            1            0 
+     100    559.41271    -53.23688 0.0034851739          0.2            0            1            0 
+     150    489.90516    31.555817 0.0034851739          0.3            0            1            0 
+     200    326.18391    7.7889992 0.0034851739          0.4            0            1            0 
+     250    339.78203    2.3919541 0.0034851739          0.5            0            1            0 
+     300    370.90263    -32.01673 0.0034851739          0.6            0            1            0 
+     350    294.07547   -5.4019813 0.0034851739          0.7            0            1            0 
+     400    287.76477    12.254133 0.0034851739          0.8            0            1            0 
+     450    293.36482    66.372956 0.0034851739          0.9            0            1            0 
+     500    246.84496    26.132317 0.0034851739            1            0            1            0 
+     550    253.08778   -15.350262 0.0034851739          1.1            1            1            1 
+     600    358.83641    25.007371 0.0034851739          1.2            1            1            1 
+     650    320.51492    -32.34823 0.0034851739          1.3            1            1            1 
+     700    310.87976   -8.2306669 0.0034851739          1.4            1            1            1 
+     750    307.54142    12.025818 0.0034851739          1.5            1            1            1 
+     800    272.51724    -22.92823 0.0034851739          1.6            1            1            1 
+     850    268.66181    10.069534 0.0034851739          1.7            1            1            1 
+     900     265.5531   -10.471377 0.0034851739          1.8            1            1            1 
+     950    259.43086    9.4546712 0.0034851739          1.9            1            1            1 
+    1000    247.14622    20.250308 0.0034851739            2            1            1            1 
+Loop time of 0.357762 on 4 procs for 1000 steps with 44 atoms
+
+Performance: 241.502 ns/day, 0.099 hours/ns, 2795.157 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0003917  | 0.015545   | 0.033317   |  11.9 |  4.35
+Bond    | 0.0010131  | 0.030153   | 0.076975   |  18.2 |  8.43
+Kspace  | 0.092857   | 0.1462     | 0.18688    |  10.7 | 40.87
+Neigh   | 0.043786   | 0.044014   | 0.044189   |   0.1 | 12.30
+Comm    | 0.03636    | 0.038345   | 0.040538   |   0.8 | 10.72
+Output  | 0.00091578 | 0.0012541  | 0.0020923  |   1.4 |  0.35
+Modify  | 0.075379   | 0.080791   | 0.086052   |   1.8 | 22.58
+Other   |            | 0.00146    |            |       |  0.41
+
+Nlocal:    11 ave 32 max 0 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+Nghost:    40 ave 51 max 19 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+Neighs:    191 ave 529 max 0 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 764
+Ave neighs/atom = 17.3636
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/VISCOSITY/README

@@ -1,5 +1,6 @@
-This directory has 5 scripts that compute the viscosity (eta) of a
-Lennard-Jones fluid using 5 different methods.  See the discussion in
+This directory has 6 scripts that compute the viscosity (eta) of fluid
+using 6 different methods. 5 of them are for a Lennard-Jones fluid
+and the last one is for SPC/E water model. See the discussion in
 Section 6.21 of the manual for an overview of the methods and pointers
 to doc pages for the commands which implement them.  Citations for the
 various methods can also be found in the manual.
@@ -10,7 +11,7 @@ enough to generate good statistics and highly accurate results.
 
 -------------
 
-These are the 5 methods for computing viscosity.  The first 3 are
+These are the 5 methods for computing viscosity of a LJ fluid.  The first 3 are
 non-equilibrium methods; the last 2 are equilibrium methods.
 
 in.wall = move a wall to shear the fluid between two walls
@@ -89,3 +90,18 @@ heat/flux doc page - the resulting value prints at the end of the run
 and is in the log file
 
 eta = 1.07
+
+-------------
+
+in.cos.1000SPCE is an example script of using cosine periodic perturbation method
+to calculate the viscosity of SPC/E water model.
+
+The reciprocal of eta is computed within the script, and printed out as v_invVis
+in thermo_style command. The result will converge after hundreds of picoseconds.
+Then eta is obtained from the reciprocal of time average of v_invVis.
+
+eta = 0.75 mPa*s
+
+Note that the calculated viscosity by this method decreases with increased acceleration.
+It is therefore generally necessary to perform calculation at different accelerations
+and extrapolate the viscosity to zero shear.

examples/VISCOSITY/in.cos.1000SPCE

@@ -0,0 +1,53 @@
+# DFF generated Lammps input file
+
+units          real
+atom_style     full
+boundary       p p p
+
+pair_style     lj/cut/coul/long     10.0
+pair_modify    mix arithmetic
+pair_modify    tail yes
+kspace_style   pppm 1.0e-4
+dielectric     1.0
+special_bonds  amber
+bond_style     harmonic
+angle_style    harmonic
+dihedral_style none
+improper_style none
+
+read_data      data.cos.1000SPCE
+
+variable T equal 300
+variable P equal 1.0
+
+velocity       all create ${T} 12345 mom yes rot yes dist gaussian
+
+timestep       1.0
+
+# Constraint ##################################
+fix com        all momentum 100 linear 1 1 1
+fix rigid      all shake 1e-4 20 0 b 1 a 1
+
+# Viscosity  ##################################
+variable       A equal 0.05e-5 # angstrom/fs^2
+
+fix            cos all accelerate/cos ${A}
+compute        cos all viscosity/cos
+
+variable       density equal density
+variable       lz equal lz
+variable       vMax equal c_cos[7] # velocity of atoms at z=0
+variable       invVis equal v_vMax/${A}/v_density*39.4784/v_lz/v_lz*100 # reciprocal of viscosity 1/Pa/s
+
+fix            npt all npt temp ${T} ${T} 100 iso ${P} ${P} 1000
+fix_modify     npt temp cos
+
+thermo_style   custom step cpu temp press pe density v_vMax v_invVis
+thermo_modify  temp cos
+thermo         100
+################################################
+
+dump           1 all custom 10000 dump.lammpstrj id mol type element q xu yu zu
+dump_modify    1 sort id element O H
+
+run            2000

examples/VISCOSITY/log.30Apr20.cos.1000SPCE.g++.1

@@ -0,0 +1,160 @@
+LAMMPS (3 Mar 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# DFF generated Lammps input file
+
+units          real
+atom_style     full
+boundary       p p p
+
+pair_style     lj/cut/coul/long     10.0
+pair_modify    mix arithmetic
+pair_modify    tail yes
+kspace_style   pppm 1.0e-4
+dielectric     1.0
+special_bonds  amber
+bond_style     harmonic
+angle_style    harmonic
+dihedral_style none
+improper_style none
+
+read_data      data.1000SPCE.lmp
+  orthogonal box = (0 0 0) to (31.043 31.043 31.043)
+  2 by 2 by 2 MPI processor grid
+  reading atoms ...
+  3000 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  2000 bonds
+  reading angles ...
+  1000 angles
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.00114917 secs
+  read_data CPU = 0.00953543 secs
+
+variable T equal 300
+variable P equal 1.0
+
+velocity       all create ${T} 12345 mom yes rot yes dist gaussian
+velocity       all create 300 12345 mom yes rot yes dist gaussian
+
+timestep       1.0
+
+# Constraint ##################################
+fix com        all momentum 100 linear 1 1 1
+fix rigid      all shake 1e-4 20 0 b 1 a 1
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  1000 = # of frozen angles
+  find clusters CPU = 0.000442737 secs
+
+# Viscosity  ##################################
+variable       A equal 0.02e-5 # angstrom/fs^2
+
+fix            cos all accelerate/cos ${A}
+fix            cos all accelerate/cos 2e-07
+compute        cos all viscosity/cos
+
+variable       density equal density
+variable       lz equal lz
+variable       vMax equal c_cos[7] # velocity of atoms at z=0
+variable       invVis equal v_vMax/${A}/v_density*39.4784/v_lz/v_lz*100 # reciprocal of viscosity 1/Pa/s
+variable       invVis equal v_vMax/2e-07/v_density*39.4784/v_lz/v_lz*100 
+
+fix            npt all npt temp ${T} ${T} 100 iso ${P} ${P} 1000
+fix            npt all npt temp 300 ${T} 100 iso ${P} ${P} 1000
+fix            npt all npt temp 300 300 100 iso ${P} ${P} 1000
+fix            npt all npt temp 300 300 100 iso 1 ${P} 1000
+fix            npt all npt temp 300 300 100 iso 1 1 1000
+fix_modify     npt temp cos
+
+thermo_style   custom step cpu temp press pe density v_vMax v_invVis
+thermo_modify  temp cos
+thermo         100
+################################################
+
+dump           1 all custom 10000 dump.lammpstrj id mol type element q xu yu zu
+dump_modify    1 sort id element O H
+
+run            2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
+  G vector (1/distance) = 0.263539
+  grid = 16 16 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325342
+  estimated relative force accuracy = 9.79757e-05
+  using double precision MKL FFT
+  3d grid and FFT values/proc = 3375 512
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 10.14 | 10.14 | 10.14 Mbytes
+Step CPU Temp Press PotEng Density v_vMax v_invVis 
+       0            0    450.04468    9838.6886    -7651.736   0.99999331 0.0001293705    2649.9663 
+     100   0.33736925    497.65155    2024.4827   -8342.2499   0.98595028 0.00019602427    4034.2452 
+     200   0.67116638    446.48518    27.075082   -8908.9684    0.9652009 0.00027615455    5723.7907 
+     300   0.99760895    401.79875   -776.99871   -9381.8986   0.95205822 0.00019626685    4086.6103 
+     400    1.3239019    369.65373    -510.5336   -9803.6463   0.94817309 0.00022998514    4795.2142 
+     500    1.6488092    343.35807   -936.31982   -10146.023   0.94840581 0.0001434423    2990.5423 
+     600    1.9826063    319.86131   -1381.3302   -10405.812   0.95459202 6.6411532e-05    1381.5767 
+     700    2.3172637    307.74606   -98.775733     -10643.5   0.96669652 0.00010446317    2164.0664 
+     800    2.6562841    305.14214   -540.57804   -10865.742   0.97808367 5.4381233e-05    1122.1765 
+     900    2.9938415    288.01316    639.00486    -10925.39   0.98686357 0.00010878474    2238.1355 
+    1000     3.327893    295.07773   -226.06503   -11033.826   0.99128496 0.00011935058    2451.8608 
+    1100    3.6618862    299.21578    306.34231   -11049.152   0.99552203 8.9538943e-05    1836.8166 
+    1200    3.9984287    301.82462    85.804646   -11013.564   0.99713434 0.00015912276      3262.51 
+    1300    4.3320735     308.6009    268.08897   -11009.836   0.99695358 0.00026212596      5374.72 
+    1400     4.668875    298.36903   -258.75495   -10962.299   0.99503447 0.00033087355    6788.7027 
+    1500    5.0003694    299.96073    99.512082   -10980.551   0.99315631 0.00033996557    6979.6425 
+    1600    5.3367337    304.18018   -500.65441   -11002.054    0.9914558 0.00039075642    8026.9849 
+    1700    5.6780828    301.63978   -499.07458    -10992.88   0.99234354 0.00038101175    7824.4738 
+    1800    6.0140638    303.25858    640.03432   -11053.335   0.99553958 0.00041336203    8479.7267 
+    1900    6.3532521    301.40882    208.28331   -11119.481   0.99534534 0.00032474734    6662.3144 
+    2000    6.6938104     298.0462   -236.47954   -11162.212   0.99421846 0.00023869721    4898.8129 
+Loop time of 6.69387 on 8 procs for 2000 steps with 3000 atoms
+
+Performance: 25.815 ns/day, 0.930 hours/ns, 298.781 timesteps/s
+99.7% CPU use with 8 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.36       | 4.4981     | 4.6781     |   5.1 | 67.20
+Bond    | 0.00074545 | 0.00088463 | 0.0012464  |   0.0 |  0.01
+Kspace  | 0.86696    | 1.0476     | 1.1863     |  10.5 | 15.65
+Neigh   | 0.37733    | 0.37785    | 0.3784     |   0.1 |  5.64
+Comm    | 0.19874    | 0.20168    | 0.20729    |   0.6 |  3.01
+Output  | 0.0015529  | 0.0015803  | 0.0017546  |   0.2 |  0.02
+Modify  | 0.54083    | 0.55143    | 0.55445    |   0.6 |  8.24
+Other   |            | 0.01483    |            |       |  0.22
+
+Nlocal:    375 ave 385 max 361 min
+Histogram: 1 1 0 0 1 0 2 0 1 2
+Nghost:    5772.25 ave 5789 max 5757 min
+Histogram: 1 1 2 0 0 0 2 0 0 2
+Neighs:    135285 ave 144189 max 127550 min
+Histogram: 1 2 1 1 0 0 0 0 1 2
+
+Total # of neighbors = 1082280
+Ave neighs/atom = 360.76
+Ave special neighs/atom = 2
+Neighbor list builds = 101
+Dangerous builds = 1
+Total wall time: 0:00:06

lib/atc/Function.cpp

@@ -1,5 +1,11 @@
-#ifndef _WIN32
+#if !defined(_WIN32)
+
+#if defined(__FreeBSD__) || defined(__DragonFly__) || defined(__OpenBSD__) || defined(__NetBSD__)
+#include <cstdlib>
+#else
 #include <alloca.h>
+#endif
+
 #endif
 #include "Function.h"
 #include "ATC_Error.h"

lib/gpu/lal_atom.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : brownw@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_preprocessor.h"

lib/gpu/lal_beck.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_born.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_born_coul_long.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_born_coul_long_cs.cu

@@ -11,7 +11,7 @@
 //
 //    begin                : June 2018
 //    email                : ndactrung@gmail.com
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 
@@ -109,7 +109,7 @@ __kernel void k_born_coul_long_cs(const __global numtyp4 *restrict x_,
       numtyp rsq = delx*delx+dely*dely+delz*delz;
 
       int mtype=itype*lj_types+jtype;
-      if (rsq<cutsq_sigma[mtype].x) { // cutsq 
+      if (rsq<cutsq_sigma[mtype].x) { // cutsq
         numtyp forcecoul,forceborn,force,r6inv,prefactor,_erfc,rexp;
 
         rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
@@ -250,7 +250,7 @@ __kernel void k_born_coul_long_cs_fast(const __global numtyp4 *restrict x_,
       numtyp delz = ix.z-jx.z;
       numtyp rsq = delx*delx+dely*dely+delz*delz;
 
-      if (rsq<cutsq_sigma[mtype].x) { // cutsq 
+      if (rsq<cutsq_sigma[mtype].x) { // cutsq
         numtyp forcecoul,forceborn,force,r6inv,prefactor,_erfc,rexp;
 
         rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;

lib/gpu/lal_born_coul_wolf.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_born_coul_wolf_cs.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : ndactrung@gmail.com
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_buck.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_buck_coul.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_buck_coul_long.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_charmm_long.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : brownw@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_colloid.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_coul.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : ndtrung@umich.edu
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_coul_debye.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : ndtrung@umich.edu
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_coul_dsf.cu

@@ -11,7 +11,7 @@
 //
 //    begin                : 8/15/2012
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_coul_long.cu

@@ -11,7 +11,7 @@
 //
 //    begin                : July 2011
 //    email                : a.kohlmeyer@temple.edu
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_coul_long_cs.cu

@@ -11,7 +11,7 @@
 //
 //    begin                : June 2018
 //    email                : ndactrung@gmail.com
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_dipole_lj.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_dipole_lj_sf.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_dipole_long_lj.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_dpd.cu

@@ -11,7 +11,7 @@
 //
 //    begin                : Jan 15, 2014
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_eam.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : brownw@ornl.gov nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_ellipsoid_nbor.cu

@@ -9,9 +9,8 @@
 //    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
 // __________________________________________________________________________
 //
-//    begin                :
 //    email                : brownw@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_preprocessor.h"
@@ -53,8 +52,8 @@ __kernel void kernel_nbor(const __global numtyp4 *restrict x_,
     int itype=fast_mul(iw,ntypes);
     int newj=0;
     for ( ; nbor<nbor_end; nbor+=nbor_pitch) {
-      int j=dev_ij[nbor];
-      j &= NEIGHMASK;
+      int sj=dev_ij[nbor];
+      int j = sj & NEIGHMASK;
       numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
       int jtype=jx.w;
       int mtype=itype+jtype;
@@ -69,7 +68,7 @@ __kernel void kernel_nbor(const __global numtyp4 *restrict x_,
         rsq+=t*t;
 
         if (rsq<cf.x) {
-          dev_nbor[packed]=j;
+          dev_nbor[packed]=sj;
           packed+=nbor_pitch;
           newj++;
         }
@@ -117,8 +116,8 @@ __kernel void kernel_nbor_fast(const __global numtyp4 *restrict x_,
 
     int newj=0;
     for ( ; nbor<nbor_end; nbor+=nbor_pitch) {
-      int j=dev_ij[nbor];
-      j &= NEIGHMASK;
+      int sj=dev_ij[nbor];
+      int j = sj & NEIGHMASK;
       numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
       int jtype=jx.w;
       int mtype=itype+jtype;
@@ -133,7 +132,7 @@ __kernel void kernel_nbor_fast(const __global numtyp4 *restrict x_,
         rsq+=t*t;
 
         if (rsq<cutsq[mtype]) {
-          dev_nbor[packed]=j;
+          dev_nbor[packed]=sj;
           packed+=nbor_pitch;
           newj++;
         }

lib/gpu/lal_gauss.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_gayberne.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : brownw@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_ellipsoid_extra.h"

lib/gpu/lal_gayberne_lj.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : brownw@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_ellipsoid_extra.h"

lib/gpu/lal_lj.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : brownw@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_lj96.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : brownw@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 #include "lal_aux_fun1.h"

lib/gpu/lal_lj_class2_long.cu

@@ -11,7 +11,7 @@
 //
 //    begin                : Mon May 16 2011
 //    email                : brownw@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_lj_coul.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : brownw@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_lj_coul_debye.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : nguyentd@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)
 

lib/gpu/lal_lj_coul_long.cu

@@ -11,7 +11,7 @@
 //
 //    begin                :
 //    email                : brownw@ornl.gov
-// ***************************************************************************/
+// ***************************************************************************
 
 #if defined(NV_KERNEL) || defined(USE_HIP)