Merge branch 'fetch-potentials' into feature-cnt

This commit is contained in:
Axel Kohlmeyer 2020-06-12 05:54:45 -04:00
commit d61d8899ff
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18 changed files with 78 additions and 2006018 deletions

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@ -126,7 +126,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB 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-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY 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-ADIOS USER-MESONT) USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS USER-MESONT)
@ -365,6 +365,15 @@ target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
include(StyleHeaderUtils) include(StyleHeaderUtils)
RegisterStyles(${LAMMPS_SOURCE_DIR}) RegisterStyles(${LAMMPS_SOURCE_DIR})
########################################################
# Fetch missing external files and archives for packages
########################################################
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
if(PKG_${PKG})
FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
endif()
endforeach()
############################################## ##############################################
# add sources of enabled packages # add sources of enabled packages
############################################ ############################################

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@ -85,3 +85,20 @@ function(GenerateBinaryHeader varname outfile files)
file(APPEND ${outfile} "const unsigned int ${varname}_size = sizeof(${varname});\n") file(APPEND ${outfile} "const unsigned int ${varname}_size = sizeof(${varname});\n")
endforeach() endforeach()
endfunction(GenerateBinaryHeader) endfunction(GenerateBinaryHeader)
# fetch missing potential files
function(FetchPotentials pkgfolder potfolder)
if (EXISTS "${pkgfolder}/potentials.txt")
set(LAMMPS_POTENTIALS_URL "https://download.lammps.org/potentials")
file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
foreach(line ${linelist})
string(FIND ${line} " " blank)
math(EXPR plusone "${blank}+1")
string(SUBSTRING ${line} 0 ${blank} pot)
string(SUBSTRING ${line} ${plusone} -1 sum)
message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${LAMMPS_POTENTIALS_DIR}/${pot}"
EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
endforeach()
endif()
endfunction(FetchPotentials)

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@ -126,7 +126,7 @@ if(GPU_API STREQUAL "CUDA")
elseif(GPU_API STREQUAL "OPENCL") elseif(GPU_API STREQUAL "OPENCL")
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
# download and unpack support binaries for compilation of windows binaries. # download and unpack support binaries for compilation of windows binaries.
set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty") set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz" file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d) EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})

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@ -9,7 +9,7 @@ if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own") message(STATUS "Eigen3 download requested - we will build our own")
include(ExternalProject) include(ExternalProject)
ExternalProject_Add(Eigen3_build ExternalProject_Add(Eigen3_build
URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz URL https://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07 URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
) )

0
doc/src/99/crib.html Executable file → Normal file
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0
doc/src/fix_nh.rst Executable file → Normal file
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@ -118,7 +118,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions Restrictions
"""""""""""" """"""""""""
This style is part of the USER-MISC package. It is only This style is part of the USER-MESONT package. It is only
enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info. enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
This pair potential requires the :doc:`newton <newton>` setting to be This pair potential requires the :doc:`newton <newton>` setting to be

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@ -78,7 +78,7 @@ if pathflag:
if buildflag: if buildflag:
print("Downloading Eigen ...") print("Downloading Eigen ...")
eigentar = os.path.join(homepath, tarball) eigentar = os.path.join(homepath, tarball)
url = "http://bitbucket.org/eigen/eigen/get/%s.tar.gz" % version url = "https://bitbucket.org/eigen/eigen/get/%s.tar.gz" % version
geturl(url, eigentar) geturl(url, eigentar)
# verify downloaded archive integrity via md5 checksum, if known. # verify downloaded archive integrity via md5 checksum, if known.

1
potentials/.gitignore vendored Normal file
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@ -0,0 +1 @@
C_10_10.mesocnt

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40
src/Fetch.sh Executable file
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@ -0,0 +1,40 @@
# transparently fetch external files for a given package
fetch_potentials() {
pdir="$1"
shift
type curl > /dev/null 2>&1 && have_curl=1 || have_curl=0
type wget > /dev/null 2>&1 && have_wget=1 || have_wget=0
if [ $have_curl -ne 1 ] && [ $have_wget -ne 1 ]
then \
echo "Need 'curl' or 'wget' to fetch external potential files"
return
fi
while [ $# -gt 1 ]
do \
file=$1; sum=$2
shift; shift
echo ${sum} ${pdir}/${file} | md5sum -c - > /dev/null 2>&1 \
&& need_fetch=0 || need_fetch=1
if [ ${need_fetch} -eq 1 ]
then \
url="https://download.lammps.org/potentials/${file}.${sum}"
echo "Fetching external potential file ${file} from ${url}"
if [ ${have_curl} ]
then \
curl -L -o ${pdir}/${file} ${url}
elif [ ${have_wget} ]
then \
wget -O ${pdir}/${file} ${url}
fi
fi
done
}
if [ -f "$1/potentials.txt" ]
then
fetch_potentials "$1/../../potentials" `sed -e 's/#.*$//' "$1/potentials.txt"`
fi

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@ -280,7 +280,7 @@ install-python:
tar: tar:
@cd STUBS; $(MAKE) clean @cd STUBS; $(MAKE) clean
@cd ..; tar cvzf src/$(ROOT)_src.tar.gz \ @cd ..; tar cvzf src/$(ROOT)_src.tar.gz \
src/Make* src/Package.sh src/Depend.sh src/Install.sh \ src/Make* src/Package.sh src/Depend.sh src/Install.sh src/Fetch.sh \
src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \ src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \
$(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \ $(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \
--exclude=*/.svn --exclude=*/.svn
@ -369,6 +369,7 @@ yes-%:
cd $(YESDIR); $(SHELL) ../Install.sh 1; cd ..; \ cd $(YESDIR); $(SHELL) ../Install.sh 1; cd ..; \
$(SHELL) Depend.sh $(YESDIR) 1; \ $(SHELL) Depend.sh $(YESDIR) 1; \
fi; fi;
@$(SHELL) Fetch.sh $(YESDIR)
no-%: no-%:
@if [ ! -e $(NODIR) ]; then \ @if [ ! -e $(NODIR) ]; then \

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@ -0,0 +1,3 @@
# list of potential files to be fetched when this package is installed
# potential file md5sum
C_10_10.mesocnt 028de73ec828b7830d762702eda571c1

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src/fix_nh.cpp Executable file → Normal file
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src/fix_nh.h Executable file → Normal file
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@ -76,7 +76,7 @@
#if __cplusplus == 201103L || __cplusplus == 201402L #if __cplusplus == 201103L || __cplusplus == 201402L
# if defined(__clang__) # if defined(__clang__)
# define FMT_FALLTHROUGH [[clang::fallthrough]] # define FMT_FALLTHROUGH [[clang::fallthrough]]
# elif FMT_GCC_VERSION >= 700 && !defined(__PGI) # elif FMT_GCC_VERSION >= 700 && !defined(__PGI) && !defined(__INTEL_COMPILER)
# define FMT_FALLTHROUGH [[gnu::fallthrough]] # define FMT_FALLTHROUGH [[gnu::fallthrough]]
# else # else
# define FMT_FALLTHROUGH # define FMT_FALLTHROUGH