Unverified Commit 5412204f authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge branch 'master' into granular-kokkos

parents 56c21271 ad88ecd3

.github/CODEOWNERS

+2 −0
Original line number Diff line number Diff line
@@ -17,6 +17,7 @@ src/GPU/* @ndtrung81 
src/KOKKOS/*          @stanmoore1

src/KIM/*             @ellio167

src/LATTE/*           @cnegre

src/SPIN/*            @julient31

src/USER-CGDNA/*      @ohenrich

src/USER-CGSDK/*      @akohlmey

src/USER-COLVARS/*    @giacomofiorin
@@ -44,6 +45,7 @@ src/USER-MISC/*_grem.* @dstelter92 


# tools

tools/msi2lmp/*       @akohlmey

tools/emacs/*         @HaoZeke



# cmake

cmake/*               @junghans @rbberger

cmake/CMakeLists.txt

+135 −6
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ set(SOVERSION 0) 
get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE)

get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE)

get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)

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





# To avoid conflicts with the conventional Makefile build system, we build everything here
@@ -153,14 +154,15 @@ if(ENABLE_TESTING) 
  enable_testing()

endif(ENABLE_TESTING)



set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR

  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SPIN SNAP

set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR

  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP

  SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS

  USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE

  USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC

  USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD

  USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)

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

set(OTHER_PACKAGES CORESHELL QEQ)

foreach(PKG ${DEFAULT_PACKAGES})

  option(PKG_${PKG} "Build ${PKG} Package" OFF)

endforeach()
@@ -174,13 +176,12 @@ macro(pkg_depends PKG1 PKG2) 
  endif()

endmacro()



# "hard" dependencies between packages resulting

# in an error instead of skipping over files

pkg_depends(MPIIO MPI)

pkg_depends(QEQ MANYBODY)

pkg_depends(USER-ATC MANYBODY)

pkg_depends(USER-LB MPI)

pkg_depends(USER-MISC MANYBODY)

pkg_depends(USER-PHONON KSPACE)

pkg_depends(CORESHELL KSPACE)



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

# packages with special compiler needs or external libs
@@ -332,7 +333,7 @@ if(PKG_LATTE) 
    include(ExternalProject)

    ExternalProject_Add(latte_build

      URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz

      URL_MD5 bed76e7e76c545c36dd848a8f1fd35eb

      URL_MD5 85ac414fdada2d04619c8f936344df14

      SOURCE_SUBDIR cmake

      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}

      )
@@ -574,6 +575,41 @@ endif() 
# packages which selectively include variants based on enabled styles

# e.g. accelerator packages

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

if(PKG_CORESHELL)

    set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)

    set(CORESHELL_SOURCES)

    set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")



    # detects styles which have a CORESHELL version

    RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)



    get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)



    list(APPEND LIB_SOURCES ${CORESHELL_SOURCES})

    include_directories(${CORESHELL_SOURCES_DIR})

endif()



# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed

if(PKG_QEQ)

  set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)

  file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)

  file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)



  if(NOT PKG_MANYBODY)

    list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)

    list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)

  endif()

  set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")



  foreach(MY_HEADER ${QEQ_HEADERS})

    AddStyleHeader(${MY_HEADER} FIX)

  endforeach()



  get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)

  list(APPEND LIB_SOURCES ${QEQ_SOURCES})

  include_directories(${QEQ_SOURCES_DIR})

endif()



if(PKG_USER-OMP)

    set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)

    set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
@@ -585,8 +621,27 @@ if(PKG_USER-OMP) 
    # detects styles which have USER-OMP version

    RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)





    get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)



    # manually add package dependent source files from USER-OMP that do not provide styles



    if(PKG_RIGID)

      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)

    endif()



    if(PKG_USER-REAXC)

      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp

                                   ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp

                                   ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp

                                   ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp

                                   ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp

                                   ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp

                                   ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp

                                   ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp

                                   ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)

    endif()



    list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})

    include_directories(${USER-OMP_SOURCES_DIR})

endif()
@@ -900,6 +955,80 @@ if(BUILD_EXE) 
  endif()

endif()



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

# Build documentation

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

option(BUILD_DOC "Build LAMMPS documentation" OFF)

if(BUILD_DOC)

  include(ProcessorCount)

  ProcessorCount(NPROCS)

  find_package(PythonInterp 3 REQUIRED)



  set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)



  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt)

  file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)

  list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})



  add_custom_command(

    OUTPUT docenv

    COMMAND ${VIRTUALENV} docenv

  )



  set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)



  add_custom_command(

    OUTPUT requirements.txt

    DEPENDS docenv

    COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt

    COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade

    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters

  )



  set(RST_FILES "")

  set(RST_DIR ${CMAKE_BINARY_DIR}/rst)

  file(MAKE_DIRECTORY ${RST_DIR})

  foreach(TXT_FILE ${DOC_SOURCES})

    get_filename_component(FILENAME ${TXT_FILE} NAME_WE)

    set(RST_FILE ${RST_DIR}/${FILENAME}.rst)

    list(APPEND RST_FILES ${RST_FILE})

    add_custom_command(

      OUTPUT ${RST_FILE}

      DEPENDS requirements.txt docenv ${TXT_FILE}

      COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}

    )

  endforeach()



  add_custom_command(

    OUTPUT html

    DEPENDS ${RST_FILES}

    COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}

    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html

  )



  add_custom_target(

    doc ALL

    DEPENDS html

    SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}

  )



  install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})

endif()



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

# Install potential files in data directory

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

set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)

install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials DESTINATION ${CMAKE_INSTALL_DATADIR}/lammps/potentials)



configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)

configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)

install(

  FILES ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh

        ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh

  DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d

)



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

# Testing

#

cmake/README.md

+15 −5
Original line number Diff line number Diff line
@@ -275,6 +275,16 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on 
  </dl>

  </td>

</tr>

<tr>

  <td><code>BUILD_DOC</code></td>

  <td>control whether to build LAMMPS documentation</td>

  <td>

  <dl>

    <dt><code>off</code> (default)</dt>

    <dt><code>on</code></dt>

  </dl>

  </td>

</tr>

<tr>

  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>

  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
@@ -1421,11 +1431,11 @@ target API. 
  <td>CUDA SM architecture targeted by GPU package</td>

  <td>

  <dl>

    <dt><code>sm20</code> (Fermi)</dt>

    <dt><code>sm30</code> (Kepler)</dt>

    <dt><code>sm50</code> (Maxwell)</dt>

    <dt><code>sm60</code> (Pascal)</dt>

    <dt><code>sm70</code> (Volta)</dt>

    <dt><code>sm_20</code> (Fermi)</dt>

    <dt><code>sm_30</code> (Kepler)</dt>

    <dt><code>sm_50</code> (Maxwell)</dt>

    <dt><code>sm_60</code> (Pascal)</dt>

    <dt><code>sm_70</code> (Volta)</dt>

  </dl>

  </td>

</tr>

cmake/etc/profile.d/lammps.csh.in

0 → 100644
+2 −0
Original line number Diff line number Diff line 
# set environment for LAMMPS executables to find potential files

if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@

cmake/etc/profile.d/lammps.sh.in

0 → 100644
+2 −0
Original line number Diff line number Diff line 
# set environment for LAMMPS executables to find potential files

export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}

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