Unverified Commit 2fa6e913 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'master' into gran_mods

parents 3cc740b9 28a6dcd1

cmake/CMakeLists.txt

+59 −41
Original line number Diff line number Diff line
@@ -381,19 +381,10 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) 
endif()



if(PKG_PYTHON)

  find_package(PythonInterp REQUIRED)

  find_package(PythonLibs REQUIRED)

  add_definitions(-DLMP_PYTHON)

  include_directories(${PYTHON_INCLUDE_DIR})

  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})

  if(BUILD_LIB AND BUILD_SHARED_LIBS)

    if(NOT PYTHON_INSTDIR)

      execute_process(COMMAND ${PYTHON_EXECUTABLE}

        -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"

        OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)

    endif()

    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})

  endif()

endif()



find_package(JPEG QUIET)
@@ -613,8 +604,9 @@ if(PKG_USER-PLUMED) 
endif()



if(PKG_USER-MOLFILE)

  set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")

  add_library(molfile INTERFACE)

  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)

  target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})

  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})

  list(APPEND LAMMPS_LINK_LIBS molfile)

endif()
@@ -626,7 +618,6 @@ if(PKG_USER-NETCDF) 
  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)
@@ -670,6 +661,12 @@ if(PKG_USER-VTK) 
endif()



if(PKG_KIM)

  find_package(CURL)

  if(CURL_FOUND)

    include_directories(${CURL_INCLUDE_DIRS}) 

    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})

    add_definitions(-DLMP_KIM_CURL)

  endif()

  option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)

  if(DOWNLOAD_KIM)

    message(STATUS "KIM-API v2 download requested - we will build our own")
@@ -1331,36 +1328,14 @@ execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HE 
######################################

# 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 AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)

  set(temp_git_info "true")

  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse HEAD

    OUTPUT_VARIABLE temp_git_commit

    ERROR_QUIET

    OUTPUT_STRIP_TRAILING_WHITESPACE)

  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse --abbrev-ref HEAD

    OUTPUT_VARIABLE temp_git_branch

    ERROR_QUIET

    OUTPUT_STRIP_TRAILING_WHITESPACE)

  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git describe --dirty=-modified

    OUTPUT_VARIABLE temp_git_describe

    ERROR_QUIET

    OUTPUT_STRIP_TRAILING_WHITESPACE)

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")

add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}

  -DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"

  -DGIT_EXECUTABLE="${GIT_EXECUTABLE}"

  -DGIT_FOUND="${GIT_FOUND}"

  -DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"

  -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake)

set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h)

list(APPEND LAMMPS_DEPS gitversion)



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

# Actually add executable and lib to build
@@ -1483,6 +1458,49 @@ install( 
  DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d

)



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

# Install LAMMPS lib and python module into site-packages folder with

# "install-python" target.  Behaves exactly like "make install-python" for

# conventional build.  Only available, if a shared library is built.

# This is primarily for people that only want to use the Python wrapper.

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

if(BUILD_LIB AND BUILD_SHARED_LIBS)

  find_package(PythonInterp)

  if (PYTHONINTERP_FOUND)

    add_custom_target(

      install-python

      ${PYTHON_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h

      -m ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py

      -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}

      WORKING_DIRECTORY  ${CMAKE_CURRENT_SOURCE_DIR}/../python

      COMMENT "Installing LAMMPS Python module")

  else()

    add_custom_target(

      install-python

      ${CMAKE_COMMAND} -E echo "Must have Python installed to install the LAMMPS Python module")

  endif()

else()

  add_custom_target(

    install-python

    ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")

endif()



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

# Add LAMMPS python module to "install" target. This is taylored for building

# LAMMPS for package managers and with different prefix settings.

# This requires either a shared library or that the PYTHON package is included.

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

if((BUILD_LIB AND BUILD_SHARED_LIBS) OR (PKG_PYTHON))

  find_package(PythonInterp)

  if (PYTHONINTERP_FOUND)

    execute_process(COMMAND ${PYTHON_EXECUTABLE}

      -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"

      OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)

    set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")

    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})

  endif()

endif()



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

# Testing

#

cmake/Modules/generate_lmpgitversion.cmake

0 → 100644
+30 −0
Original line number Diff line number Diff line 
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 AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)

  set(temp_git_info "true")

  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD

    OUTPUT_VARIABLE temp_git_commit

    ERROR_QUIET

    OUTPUT_STRIP_TRAILING_WHITESPACE)

  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD

    OUTPUT_VARIABLE temp_git_branch

    ERROR_QUIET

    OUTPUT_STRIP_TRAILING_WHITESPACE)

  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified

    OUTPUT_VARIABLE temp_git_describe

    ERROR_QUIET

    OUTPUT_STRIP_TRAILING_WHITESPACE)

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")

doc/Makefile

+8 −8
Original line number Diff line number Diff line
@@ -116,6 +116,13 @@ mobi: epub 
	@echo "Conversion finished. The MOBI manual file is created."



pdf: $(OBJECTS) $(ANCHORCHECK)

	@(\

		cd src/Developer; \

		pdflatex developer; \

		pdflatex developer; \

		mv developer.pdf ../../Developer.pdf; \

		cd ../../; \

	)

	@(\

                . $(VENV)/bin/activate ;\

                cp -r src/* $(RSTDIR)/ ;\
@@ -136,13 +143,6 @@ pdf: $(OBJECTS) $(ANCHORCHECK) 
	  make && \

	  mv LAMMPS.pdf ../Manual.pdf && \

	  cd ../;

	@(\

		cd src/Developer; \

		pdflatex developer; \

		pdflatex developer; \

		mv developer.pdf ../../Developer.pdf; \

		cd ../../; \

	)

	@rm -rf latex/_sources

	@rm -rf latex/PDF

	@rm -rf latex/USER

doc/src/Build_extras.txt

+24 −8
Original line number Diff line number Diff line
@@ -169,16 +169,18 @@ used to build the GPU library. 


KIM package :h4,link(kim)



To build with this package, the KIM library must be downloaded and

built on your system.  It must include the KIM models that you want to

use with LAMMPS.

To build with this package, the KIM library with API v2 must be downloaded

and built on your system.  It must include the KIM models that you want to

use with LAMMPS. If you want to use the "kim_query"_kim_query.html

command, you also need to have libcurl installed with the matching

development headers and the curl-config tool.



Note that in LAMMPS lingo, a KIM model driver is a pair style

(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular

element or alloy and set of parameters, e.g. EAM for Cu with a

specific EAM potential file.  Also note that installing the KIM API

library with all its models, may take around 30 min to build.  Of

course you only need to do that once.

specific EAM potential file.  Also note that downloading and installing

the KIM API library with all its models, may take a long time (10s of

minutes to hours) to build.  Of course you only need to do that once.



See the list of KIM model drivers here:

https://openkim.org/browse/model-drivers/alphabetical
@@ -893,7 +895,17 @@ USER-MOLFILE package :h4,link(user-molfile) 


[CMake build]:



No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".

-D MOLFILE_INCLUDE_DIRS=path   # (optional) path where VMD molfile plugin headers are installed

-D PKG_USER-MOLFILE=yes     :pre





Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting

"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for

the molfile plugin header files. These should match the ABI of the

plugin files used, and thus one typically sets them to include

folder of the local VMD installation in use. LAMMPS ships with a

couple of default header files that correspond to a popular VMD

version, usually the latest release.



[Traditional make]:
@@ -902,7 +914,11 @@ loading library libdl.a that is typically present on all systems. It 
is required for LAMMPS to link with this package.  If the setting is

not valid for your system, you will need to edit the Makefile.lammps

file.  See lib/molfile/README and lib/molfile/Makefile.lammps for

details.

details. It is also possible to configure a different folder with

the VMD molfile plugin header files. LAMMPS ships with a couple of

default headers, but these are not compatible with all VMD versions,

so it is often best to change this setting to the location of the

same include files of the local VMD installation in use.



:line

doc/src/Commands_all.txt

+2 −0
Original line number Diff line number Diff line
@@ -68,6 +68,7 @@ An alphabetic list of all general LAMMPS commands. 
"improper_style"_improper_style.html,

"include"_include.html,

"jump"_jump.html,

"kim_query"_kim_query.html,

"kspace_modify"_kspace_modify.html,

"kspace_style"_kspace_style.html,

"label"_label.html,
@@ -78,6 +79,7 @@ An alphabetic list of all general LAMMPS commands. 
"minimize"_minimize.html,

"min_modify"_min_modify.html,

"min_style"_min_style.html,

"min_style spin"_min_spin.html,

"molecule"_molecule.html,

"ndx2group"_group2ndx.html,

"neb"_neb.html,

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