Merge branch 'master' into team

---

name: Generic Issue

about: For issues that do not fit any of the other categories

title: "_Replace With a Descriptive Title_"

labels: 

assignees: ''

---

**Summary**

_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_

**Details**

_Please explain the issue in detail here_

---

name: Request for Help

about: "Don't post help requests here, email the lammps-users mailing list"

title: ""

labels: invalid

assignees: ''

---

Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.

Instead send an e-mail to the lammps-users mailing list.

This issue tracker is for tracking LAMMPS development related issues only.

Thanks for your cooperation.

**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 (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 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**

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under the GNU General Public License version 2.

_Please complete the following statement by adding "yes" or "no":_

My contribution may be re-licensed as LGPL (for use of LAMMPS as a library linked to proprietary software):

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

**Backward Compatibility**

get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)

get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)

find_package(Git)

# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed

if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)

  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )

# this is fast, so check for it all the time

message(STATUS "Running check for auto-generated files from make-based build system")

file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)

list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h)

list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h ${LAMMPS_SOURCE_DIR}/lmpgitversion.h)

foreach(_SRC ${SRC_AUTOGEN_FILES})

  get_filename_component(FILENAME "${_SRC}" NAME)

  if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})

  USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF

  USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS

  USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK

  USER-QUIP USER-QMMM USER-YAFF)

  USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)

set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)

set(OTHER_PACKAGES CORESHELL QEQ)

foreach(PKG ${DEFAULT_PACKAGES})

include_directories(${LAMMPS_SOURCE_DIR})

if(PKG_USER-ADIOS)

  # The search for ADIOS2 must come before MPI because

  # it includes its own MPI search with the latest FindMPI.cmake

  # script that defines the MPI::MPI_C target 

  enable_language(C)

  find_package(ADIOS2 REQUIRED)

  list(APPEND LAMMPS_LINK_LIBS adios2::adios2)

endif()

# do MPI detection after language activation, if MPI for these language is required

find_package(MPI QUIET)

option(BUILD_MPI "Build MPI version" ${MPI_FOUND})

  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)

endif()

if(PKG_USER-SMD)

  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)

  if(DOWNLOAD_EIGEN3)

    enable_language(Fortran)

    include(ExternalProject)

    ExternalProject_Add(kim_build

      URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.0.txz

      URL_MD5 1ff8f563ad5991f7a2a25b35a13d7308

      URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.1.txz

      URL_MD5 289c57f0c3bc2a549662283cac1c4ef1

      BINARY_DIR build

      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}

file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" )

execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h")

######################################

# Generate lmpgitversion.h

######################################

set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")

set(temp_git_commit "(unknown)")

set(temp_git_branch "(unknown)")

set(temp_git_describe "(unknown)")

set(temp_git_info "false")

if(GIT_FOUND)

  execute_process(COMMAND ${GIT_EXECUTABLE} describe HEAD

    RESULT_VARIABLE temp_in_git_checkout

    ERROR_QUIET

    OUTPUT_STRIP_TRAILING_WHITESPACE)

  if(temp_in_git_checkout EQUAL 0)

    set(temp_git_info "true")

    execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD

      OUTPUT_VARIABLE temp_git_commit

      ERROR_QUIET

      OUTPUT_STRIP_TRAILING_WHITESPACE)

    execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD

      OUTPUT_VARIABLE temp_git_branch

      ERROR_QUIET

      OUTPUT_STRIP_TRAILING_WHITESPACE)

    execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified

      OUTPUT_VARIABLE temp_git_describe

      ERROR_QUIET

      OUTPUT_STRIP_TRAILING_WHITESPACE)

  endif()

endif()

set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")

set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")

set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")

set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")

set(temp "${temp}#endif\n\n")

message(STATUS "Generating lmpgitversion.h...")

file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )

execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")

###########################################

# Actually add executable and lib to build

############################################

  endif()

endif()

###############################################################################

# Build documentation

###############################################################################

"POEMS"_#poems,

"PYTHON"_#python,

"VORONOI"_#voronoi,

"USER-ADIOS"_#user-adios,

"USER-ATC"_#user-atc,

"USER-AWPMD"_#user-awpmd,

"USER-COLVARS"_#user-colvars,

course you only need to do that once.

See the list of KIM model drivers here:

https://openkim.org/kim-items/model-drivers/alphabetical

https://openkim.org/browse/model-drivers/alphabetical

See the list of all KIM models here:

https://openkim.org/kim-items/models/by-model-drivers

See the list of example KIM models included by default here:

https://openkim.org/kim-api on the "What is in the KIM API source

package?" page.

https://openkim.org/browse/models/by-model-drivers

[CMake build]:

:line

USER-ADIOS package :h4,link(user-adios)

The USER-ADIOS package requires the "ADIOS I/O library"_https://github.com/ornladios/ADIOS2,

version 2.3.1 or newer. Make sure that you have ADIOS built either with or

without MPI to match if you build LAMMPS with or without MPI.

ADIOS compilation settings for LAMMPS are automatically detected, if the PATH

and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS

installation and the instructions below are followed for the respective build systems.

[CMake build]:

-D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed

-D PKG_USER-ADIOS=yes     :pre

[Traditional make]:

Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:

make yes-user-adios                       :pre

otherwise, set ADIOS2_DIR environment variable when turning on the package:

ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed :pre

:line

USER-ATC package :h4,link(user-atc)

The USER-ATC package requires the MANYBODY package also be installed.