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Merge branch 'develop' of https://github.com/lammps/lammps into kokkos-dipole-lj-expand

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This commit is contained in:
Stan Moore
2023-02-02 11:10:56 -07:00
parent 9c46f4dd39 b8b5e385b6
commit ffdca466e9
42 changed files with 483 additions and 401 deletions
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18
cmake/Modules/ExternalCMakeProject.cmake
View File

@ -9,8 +9,22 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
get_filename_component(archive ${url} NAME)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
message(STATUS "Downloading ${url}")
file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
if(EXISTS ${CMAKE_BINARY_DIR}/_deps/${archive})
file(MD5 ${CMAKE_BINARY_DIR}/_deps/${archive} DL_MD5)
endif()
if(NOT "${DL_MD5}" STREQUAL "${hash}")
message(STATUS "Downloading ${url}")
file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} STATUS DL_STATUS SHOW_PROGRESS)
file(MD5 ${CMAKE_BINARY_DIR}/_deps/${archive} DL_MD5)
if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${hash}"))
set(${target}_URL ${url})
GetFallbackURL(${target}_URL fallback)
message(WARNING "Download from primary URL ${url} failed\nTrying fallback URL ${fallback}")
file(DOWNLOAD ${fallback} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
endif()
else()
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/_deps/${archive}")
endif()
message(STATUS "Unpacking and configuring ${archive}")
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ${CMAKE_BINARY_DIR}/_deps/${archive}
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)

11
cmake/Modules/LAMMPSUtils.cmake
View File

@ -158,3 +158,14 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
set(CMAKE_LINUX_DISTRO ${distro})
set(CMAKE_DISTRO_VERSION ${disversion})
endif()
function(GetFallbackURL input output)
string(REPLACE "_URL" "" _tmp ${input})
string(TOLOWER ${_tmp} libname)
string(REGEX REPLACE "^https://.*/([^/]+gz)" "${LAMMPS_THIRDPARTY_URL}/${libname}-\\1" newurl "${${input}}")
if ("${newurl}" STREQUAL "${${input}}")
set(${output} "" PARENT_SCOPE)
else()
set(${output} ${newurl} PARENT_SCOPE)
endif()
endfunction(GetFallbackURL)

6
cmake/Modules/Packages/GPU.cmake
View File

@ -428,15 +428,17 @@ elseif(GPU_API STREQUAL "HIP")
if(DOWNLOAD_CUB)
message(STATUS "CUB download requested")
set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
# TODO: test update to current version 1.17.2
set(CUB_URL "https://github.com/nvidia/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball")
mark_as_advanced(CUB_URL)
mark_as_advanced(CUB_MD5)
GetFallbackURL(CUB_URL CUB_FALLBACK)
include(ExternalProject)
ExternalProject_Add(CUB
URL ${CUB_URL}
URL ${CUB_URL} ${CUB_FALLBACK}
URL_MD5 ${CUB_MD5}
PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
CONFIGURE_COMMAND ""

4
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -53,8 +53,10 @@ if(DOWNLOAD_KOKKOS)
set(KOKKOS_MD5 "f140e02b826223b1045207d9bc10d404" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
ExternalProject_Add(kokkos_build
URL ${KOKKOS_URL}
URL ${KOKKOS_URL} ${KOKKOS_FALLBACK}
URL_MD5 ${KOKKOS_MD5}
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a <INSTALL_DIR>/lib/libkokkoscontainers.a

3
cmake/Modules/Packages/LATTE.cmake
View File

@ -19,6 +19,7 @@ if(DOWNLOAD_LATTE)
set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
mark_as_advanced(LATTE_URL)
mark_as_advanced(LATTE_MD5)
GetFallbackURL(LATTE_URL LATTE_FALLBACK)
# CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
@ -30,7 +31,7 @@ if(DOWNLOAD_LATTE)
include(ExternalProject)
ExternalProject_Add(latte_build
URL ${LATTE_URL}
URL ${LATTE_URL} ${LATTE_FALLBACK}
URL_MD5 ${LATTE_MD5}
SOURCE_SUBDIR cmake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib

3
cmake/Modules/Packages/MDI.cmake
View File

@ -12,6 +12,7 @@ if(DOWNLOAD_MDI)
set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
GetFallbackURL(MDI_URL MDI_FALLBACK)
enable_language(C)
# only ON/OFF are allowed for "mpi" flag when building MDI library
@ -63,7 +64,7 @@ if(DOWNLOAD_MDI)
# support cross-compilation and ninja-build
include(ExternalProject)
ExternalProject_Add(mdi_build
URL ${MDI_URL}
URL ${MDI_URL} ${MDI_FALLBACK}
URL_MD5 ${MDI_MD5}
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
CMAKE_ARGS

3
cmake/Modules/Packages/ML-HDNNP.cmake
View File

@ -10,6 +10,7 @@ if(DOWNLOAD_N2P2)
set(N2P2_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of N2P2 tarball")
mark_as_advanced(N2P2_URL)
mark_as_advanced(N2P2_MD5)
GetFallbackURL(N2P2_URL N2P2_FALLBACK)
# adjust settings from detected compiler to compiler platform in n2p2 library
# set compiler specific flag to turn on C++11 syntax (required on macOS and CentOS 7)
@ -72,7 +73,7 @@ if(DOWNLOAD_N2P2)
# download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling)
include(ExternalProject)
ExternalProject_Add(n2p2_build
URL ${N2P2_URL}
URL ${N2P2_URL} ${N2P2_FALLBACK}
URL_MD5 ${N2P2_MD5}
UPDATE_COMMAND ""
CONFIGURE_COMMAND ""

20
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -1,11 +1,25 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "f418d32b60e531063ac4285bf702b468" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
# download library sources to build folder
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5}) #SHOW_PROGRESS
if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
endif()
if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
message(STATUS "Downloading ${PACELIB_URL}")
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
else()
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
endif()
endif()
# uncompress downloaded sources
execute_process(

3
cmake/Modules/Packages/PLUMED.cmake
View File

@ -59,10 +59,11 @@ if(DOWNLOAD_PLUMED)
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
include(ExternalProject)
ExternalProject_Add(plumed_build
URL ${PLUMED_URL}
URL ${PLUMED_URL} ${PLUMED_FALLBACK}
URL_MD5 ${PLUMED_MD5}
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>

4
cmake/Modules/Packages/SCAFACOS.cmake
View File

@ -18,6 +18,8 @@ if(DOWNLOAD_SCAFACOS)
set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
mark_as_advanced(SCAFACOS_URL)
mark_as_advanced(SCAFACOS_MD5)
GetFallbackURL(SCAFACOS_URL SCAFACOS_FALLBACK)
# version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
@ -30,7 +32,7 @@ if(DOWNLOAD_SCAFACOS)
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL ${SCAFACOS_URL}
URL ${SCAFACOS_URL} ${SCAFACOS_FALLBACK}
URL_MD5 ${SCAFACOS_MD5}
PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc

2
doc/src/pair_pace.rst
View File

@ -6,7 +6,7 @@
pair_style pace command
=======================
Accelerator Variants: *pace/kk*
Accelerator Variants: *pace/kk*, *pace/extrapolation/kk*
pair_style pace/extrapolation command
=====================================

3
lib/hdnnp/.gitignore vendored Normal file
View File

@ -0,0 +1,3 @@
/includelink
/liblink
/n2p2-*

17
lib/hdnnp/Install.py
View File

@ -10,7 +10,7 @@ import sys, os, platform, subprocess, shutil
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import get_cpus, fullpath, geturl, checkmd5sum
from install_helpers import get_cpus, fullpath, geturl, checkmd5sum, getfallback
parser = ArgumentParser(prog='Install.py',
description="LAMMPS library build wrapper script")
@ -76,14 +76,21 @@ if pathflag:
if buildflag:
url = "https://github.com/CompPhysVienna/n2p2/archive/v%s.tar.gz" % (version)
filename = "n2p2-%s.tar.gz" %version
print("Downloading n2p2 ...")
geturl(url, filename)
filename = "n2p2-%s.tar.gz" % version
fallback = getfallback('n2p2', url)
print("Downloading n2p2 from", url)
try:
geturl(url, filename)
except:
geturl(fallback, filename)
# verify downloaded archive integrity via md5 checksum, if known.
if version in checksums:
if not checkmd5sum(checksums[version], filename):
sys.exit("Checksum for n2p2 library does not match")
print("Checksum did not match. Trying fallback URL", fallback)
geturl(fallback, filename)
if not checkmd5sum(checksums[version], filename):
sys.exit("Checksum for n2p2 library does not match for fallback, too.")
print("Unpacking n2p2 source tarball ...")
if os.path.exists("%s/n2p2-%s" % (homepath, version)):

24
lib/install_helpers.py
View File

@ -1,4 +1,7 @@
import hashlib,os,subprocess
import hashlib
import os
import re
import subprocess
# try to auto-detect the maximum number of available CPUs
def get_cpus():
@ -32,31 +35,31 @@ def which(program):
return None
def geturl(url,fname):
def geturl(url, fname):
success = False
if which('curl') != None:
cmd = 'curl -L -o "%s" %s' % (fname,url)
cmd = 'curl -L -o "%s" %s' % (fname, url)
try:
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
success = True
except subprocess.CalledProcessError as e:
print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
if not success and which('wget') != None:
cmd = 'wget -O "%s" %s' % (fname,url)
cmd = 'wget -O "%s" %s' % (fname, url)
try:
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
success = True
except subprocess.CalledProcessError as e:
print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
if not success:
error("Failed to download source code with 'curl' or 'wget'")
raise Exception("Failed to download source code with 'curl' or 'wget' from " + url)
return
def checkmd5sum(md5sum,fname):
with open(fname,'rb') as fh:
def checkmd5sum(md5sum, fname):
with open(fname, 'rb') as fh:
m = hashlib.md5()
while True:
data = fh.read(81920)
@ -66,3 +69,6 @@ def checkmd5sum(md5sum,fname):
fh.close()
return m.hexdigest() == md5sum
def getfallback(lib, url):
archive = re.sub(r'^https://.*/([^/]+gz)', r'-\1', url)
return 'https://download.lammps.org/thirdparty/' + lib + archive

16
lib/latte/Install.py
View File

@ -10,7 +10,7 @@ import sys, os, subprocess, shutil, tarfile
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import fullpath, geturl, checkmd5sum
from install_helpers import fullpath, geturl, checkmd5sum, getfallback
parser = ArgumentParser(prog='Install.py',
description="LAMMPS library build wrapper script")
@ -86,17 +86,25 @@ if buildflag:
url = "https://github.com/lanl/LATTE/archive/v%s.tar.gz" % version
lattepath = fullpath(homepath)
lattedir = os.path.join(lattepath, homedir)
fallback = getfallback('latte', url)
filename = 'LATTE.tar.gz'
# download and unpack LATTE tarball
if buildflag:
print("Downloading LATTE ...")
geturl(url, "LATTE.tar.gz")
try:
geturl(url, filename)
except:
geturl(fallback, filename)
# verify downloaded archive integrity via md5 checksum, if known.
if version in checksums:
if not checkmd5sum(checksums[version], 'LATTE.tar.gz'):
sys.exit("Checksum for LATTE library does not match")
if not checkmd5sum(checksums[version], filename):
print("Checksum did not match. Trying fallback URL", fallback)
geturl(fallback, filename)
if not checkmd5sum(checksums[version], filename):
sys.exit("Checksum for LATTE library does not match for fallback, too.")
print("Unpacking LATTE ...")
if os.path.exists(lattedir):

61
lib/mdi/Install.py
View File

@ -9,7 +9,7 @@ import sys,os,subprocess
import glob
sys.path.append('..')
from install_helpers import checkmd5sum
from install_helpers import fullpath, geturl, checkmd5sum, getfallback
# help message
@ -51,49 +51,6 @@ def error(str=None):
# expand to full path name
# process leading '~' or relative path
def fullpath(path):
return os.path.abspath(os.path.expanduser(path))
def which(program):
def is_exe(fpath):
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
fpath, fname = os.path.split(program)
if fpath:
if is_exe(program):
return program
else:
for path in os.environ["PATH"].split(os.pathsep):
path = path.strip('"')
exe_file = os.path.join(path, program)
if is_exe(exe_file):
return exe_file
return None
def geturl(url,fname):
success = False
if which('curl') != None:
cmd = 'curl -L -o "%s" %s' % (fname,url)
try:
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
success = True
except subprocess.CalledProcessError as e:
print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
if not success and which('wget') != None:
cmd = 'wget -O "%s" %s' % (fname,url)
try:
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
success = True
except subprocess.CalledProcessError as e:
print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
if not success:
error("Failed to download source code with 'curl' or 'wget'")
return
# parse args
args = sys.argv[1:]
@ -123,17 +80,24 @@ lib = os.path.basename(cwd)
# download and unpack MDI_Library tarball
homepath = "."
homepath = fullpath('.')
homedir = "%s/MDI_Library" % homepath
print("Downloading MDI_Library ...")
mditar = "%s/v%s.tar.gz" % (homepath,version)
geturl(url, mditar)
mditar = "%s/v%s.tar.gz" % (homepath, version)
fallback = getfallback('mdi', url)
try:
geturl(url, mditar)
except:
geturl(fallback, mditar)
# verify downloaded archive integrity via md5 checksum, if known.
if version in checksums:
if not checkmd5sum(checksums[version], mditar):
sys.exit("Checksum for MDI library does not match")
print("Checksum did not match. Trying fallback URL", fallback)
geturl(fallback, mditar)
if not checkmd5sum(checksums[version], mditar):
sys.exit("Checksum for MDI library does not match")
print("Unpacking MDI_Library tarball ...")
if os.path.exists("%s/v%s" % (homepath,version)):
@ -199,7 +163,6 @@ makefile_lammps = open(str(dir_path) + "/Makefile.lammps", "a")
makefile_lammps.write(str(rpath_option) + "\n")
makefile_lammps.close()
shared_files = glob.glob( os.path.join( homepath, "liblink", "lib%s.a" % lib) )
if len(shared_files) > 0:
print("Build was successful")

16
lib/mscg/Install.py
View File

@ -10,7 +10,7 @@ import sys, os, subprocess, shutil, tarfile
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import fullpath, geturl
from install_helpers import fullpath, geturl, checkmd5sum, getfallback
parser = ArgumentParser(prog='Install.py',
description="LAMMPS library build wrapper script")
@ -84,7 +84,19 @@ if pathflag:
if buildflag:
print("Downloading MS-CG ...")
tarname = os.path.join(homepath, tarname)
geturl(url, tarname)
fallback = getfallback('mscg', url)
try:
geturl(url, tarname)
except:
geturl(fallback, tarname)
# verify downloaded archive integrity via md5 checksum, if known.
if mscgver in checksums:
if not checkmd5sum(checksums[mscgver], tarname):
print("Checksum did not match. Trying fallback URL", fallback)
geturl(fallback, tarname)
if not checkmd5sum(checksums[mscgver], tarname):
sys.exit("Checksum for LATTE library does not match for fallback, too.")
print("Unpacking MS-CG tarfile ...")

19
lib/pace/Install.py
View File

@ -13,16 +13,16 @@ import sys
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import fullpath, geturl, checkmd5sum
from install_helpers import fullpath, geturl, checkmd5sum, getfallback
# settings
thisdir = fullpath('.')
version ='v.2023.01.3'
version ='v.2023.01.3.fix'
# known checksums for different PACE versions. used to validate the download.
checksums = { \
'v.2023.01.3': 'f418d32b60e531063ac4285bf702b468'
'v.2023.01.3.fix': '4f0b3b5b14456fe9a73b447de3765caa'
}
parser = ArgumentParser(prog='Install.py', description="LAMMPS library build wrapper script")
@ -77,14 +77,21 @@ if buildflag:
print("Downloading pace tarball ...")
archive_filename = "%s.%s" % (version, archive_extension)
download_filename = "%s/%s" % (thisdir, archive_filename)
fallback = getfallback('pacelib', url)
print("Downloading from ", url, " to ", download_filename, end=" ")
geturl(url, download_filename)
try:
geturl(url, download_filename)
except:
geturl(fallback, download_filename)
print(" done")
# verify downloaded archive integrity via md5 checksum, if known.
if version in checksums:
if not checkmd5sum(checksums[version], archive_filename):
sys.exit("Checksum for pace library does not match")
if not checkmd5sum(checksums[version], download_filename):
print("Checksum did not match. Trying fallback URL", fallback)
geturl(fallback, download_filename)
if not checkmd5sum(checksums[version], download_filename):
sys.exit("Checksum for pace library does not match for fallback, too.")
print("Unpacking pace tarball ...")
src_folder = thisdir + "/src"

16
lib/plumed/Install.py
View File

@ -10,7 +10,7 @@ import sys, os, platform, subprocess, shutil
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import get_cpus, fullpath, geturl, checkmd5sum
from install_helpers import get_cpus, fullpath, geturl, checkmd5sum, getfallback
parser = ArgumentParser(prog='Install.py',
description="LAMMPS library build wrapper script")
@ -86,6 +86,7 @@ buildflag = args.build
pathflag = args.path is not None
plumedpath = args.path
mode = args.mode
version = args.version
homepath = fullpath('.')
homedir = "%s/plumed2" % (homepath)
@ -101,14 +102,21 @@ if pathflag:
if buildflag:
url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version, version)
filename = "plumed-src-%s.tar.gz" %version
filename = "plumed-src-%s.tar.gz" % version
fallback = getfallback('plumed', url)
print("Downloading plumed ...")
geturl(url, filename)
try:
geturl(url, filename)
except:
geturl(fallback, filename)
# verify downloaded archive integrity via md5 checksum, if known.
if version in checksums:
if not checkmd5sum(checksums[version], filename):
sys.exit("Checksum for plumed2 library does not match")
print("Checksum did not match. Trying fallback URL", fallback)
geturl(fallback, filename)
if not checkmd5sum(checksums[version], filename):
sys.exit("Checksum for plumed2 library does not match for fallback, too.")
print("Unpacking plumed2 source tarball ...")
if os.path.exists("%s/plumed-%s" % (homepath, version)):

21
lib/scafacos/Install.py
View File

@ -10,15 +10,13 @@ import sys, os, subprocess, shutil, tarfile
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import fullpath, geturl, get_cpus, checkmd5sum
from install_helpers import fullpath, geturl, get_cpus, checkmd5sum, getfallback
parser = ArgumentParser(prog='Install.py',
description="LAMMPS library build wrapper script")
parser = ArgumentParser(prog='Install.py', description="LAMMPS library build wrapper script")
# settings
version = "1.0.1"
url = "https://github.com/scafacos/scafacos/releases/download/v%s/scafacos-%s.tar.gz" % (version, version)
# known checksums for different ScaFaCoS versions. used to validate the download.
checksums = { \
@ -59,6 +57,7 @@ if not args.build and not args.path:
buildflag = args.build
pathflag = args.path is not None
version = args.version
url = "https://github.com/scafacos/scafacos/releases/download/v%s/scafacos-%s.tar.gz" % (version, version)
homepath = fullpath(".")
scafacospath = os.path.join(homepath, "scafacos-%s" % version)
@ -76,12 +75,20 @@ if pathflag:
if buildflag:
print("Downloading ScaFaCoS ...")
geturl(url, "%s/scafacos-%s.tar.gz" % (homepath, version))
filename = "%s/scafacos-%s.tar.gz" % (homepath, version)
fallback = getfallback('scafacos', url)
try:
geturl(url, filename)
except:
geturl(fallback, filename)
# verify downloaded archive integrity via md5 checksum, if known.
if version in checksums:
if not checkmd5sum(checksums[version], '%s/scafacos-%s.tar.gz' % (homepath, version)):
sys.exit("Checksum for ScaFaCoS library does not match")
if not checkmd5sum(checksums[version], filename):
print("Checksum did not match. Trying fallback URL", fallback)
geturl(fallback, filename)
if not checkmd5sum(checksums[version], filename):
sys.exit("Checksum for ScaFaCoS library does not match for fallback, too.")
print("Unpacking ScaFaCoS tarball ...")
if os.path.exists(scafacospath):

2
src/KOKKOS/fix_qeq_reaxff_kokkos.cpp
View File

@ -175,8 +175,6 @@ void FixQEqReaxFFKokkos<DeviceType>::init_hist()
template<class DeviceType>
void FixQEqReaxFFKokkos<DeviceType>::setup_pre_force(int vflag)
{
//neighbor->build_one(list);
pre_force(vflag);
}

151
src/KOKKOS/npair_kokkos.cpp
View File

@ -28,8 +28,8 @@ namespace LAMMPS_NS {
/* ---------------------------------------------------------------------- */
template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI, int SIZE>
NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::NPairKokkos(LAMMPS *lmp) : NPair(lmp) {
template<class DeviceType, int HALF, int NEWTON, int GHOST, int TRI, int SIZE>
NPairKokkos<DeviceType,HALF,NEWTON,GHOST,TRI,SIZE>::NPairKokkos(LAMMPS *lmp) : NPair(lmp) {
last_stencil_old = -1;
@ -49,8 +49,8 @@ NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::NPairKokkos(LAMMPS *lmp) : NP
copy needed info from Neighbor class to this build class
------------------------------------------------------------------------- */
template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI, int SIZE>
void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::copy_neighbor_info()
template<class DeviceType, int HALF, int NEWTON, int GHOST, int TRI, int SIZE>
void NPairKokkos<DeviceType,HALF,NEWTON,GHOST,TRI,SIZE>::copy_neighbor_info()
{
NPair::copy_neighbor_info();
@ -58,7 +58,6 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::copy_neighbor_info()
// general params
newton_pair = force->newton_pair;
k_cutneighsq = neighborKK->k_cutneighsq;
// overwrite per-type Neighbor cutoffs with custom value set by requestor
@ -93,8 +92,8 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::copy_neighbor_info()
copy per-atom and per-bin vectors from NBin class to this build class
------------------------------------------------------------------------- */
template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI, int SIZE>
void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::copy_bin_info()
template<class DeviceType, int HALF, int NEWTON, int GHOST, int TRI, int SIZE>
void NPairKokkos<DeviceType,HALF,NEWTON,GHOST,TRI,SIZE>::copy_bin_info()
{
NPair::copy_bin_info();
@ -110,8 +109,8 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::copy_bin_info()
copy needed info from NStencil class to this build class
------------------------------------------------------------------------- */
template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI, int SIZE>
void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::copy_stencil_info()
template<class DeviceType, int HALF, int NEWTON, int GHOST, int TRI, int SIZE>
void NPairKokkos<DeviceType,HALF,NEWTON,GHOST,TRI,SIZE>::copy_stencil_info()
{
NPair::copy_stencil_info();
nstencil = ns->nstencil;
@ -145,8 +144,8 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::copy_stencil_info()
/* ---------------------------------------------------------------------- */
template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI, int SIZE>
void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::build(NeighList *list_)
template<class DeviceType, int HALF, int NEWTON, int GHOST, int TRI, int SIZE>
void NPairKokkos<DeviceType,HALF,NEWTON,GHOST,TRI,SIZE>::build(NeighList *list_)
{
NeighListKokkos<DeviceType>* list = (NeighListKokkos<DeviceType>*) list_;
const int nlocal = includegroup?atom->nfirst:atom->nlocal;
@ -244,7 +243,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::build(NeighList *list_)
#endif
if (GHOST) {
NPairKokkosBuildFunctorGhost<DeviceType,HALF_NEIGH> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
NPairKokkosBuildFunctorGhost<DeviceType,HALF> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
#ifdef LMP_KOKKOS_GPU
if (ExecutionSpaceFromDevice<DeviceType>::space == Device) {
int team_size = atoms_per_bin*factor;
@ -262,82 +261,42 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::build(NeighList *list_)
Kokkos::parallel_for(nall, f);
#endif
} else {
if (newton_pair) {
if (SIZE) {
NPairKokkosBuildFunctorSize<DeviceType,TRI?0:HALF_NEIGH,1,TRI> f(data,atoms_per_bin * 6 * sizeof(X_FLOAT) * factor);
if (SIZE) {
NPairKokkosBuildFunctorSize<DeviceType,TRI?0:HALF,NEWTON,TRI> f(data,atoms_per_bin * 6 * sizeof(X_FLOAT) * factor);
#ifdef LMP_KOKKOS_GPU
if (ExecutionSpaceFromDevice<DeviceType>::space == Device) {
int team_size = atoms_per_bin*factor;
int team_size_max = Kokkos::TeamPolicy<DeviceType>(team_size,Kokkos::AUTO).team_size_max(f,Kokkos::ParallelForTag());
if (team_size <= team_size_max) {
Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,team_size);
Kokkos::parallel_for(config, f);
} else { // fall back to flat method
f.sharedsize = 0;
Kokkos::parallel_for(nall, f);
}
} else
if (ExecutionSpaceFromDevice<DeviceType>::space == Device) {
int team_size = atoms_per_bin*factor;
int team_size_max = Kokkos::TeamPolicy<DeviceType>(team_size,Kokkos::AUTO).team_size_max(f,Kokkos::ParallelForTag());
if (team_size <= team_size_max) {
Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,team_size);
Kokkos::parallel_for(config, f);
} else { // fall back to flat method
f.sharedsize = 0;
Kokkos::parallel_for(nall, f);
#else
}
} else
Kokkos::parallel_for(nall, f);
#endif
} else {
NPairKokkosBuildFunctor<DeviceType,TRI?0:HALF_NEIGH,1,TRI> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
#ifdef LMP_KOKKOS_GPU
if (ExecutionSpaceFromDevice<DeviceType>::space == Device) {
int team_size = atoms_per_bin*factor;
int team_size_max = Kokkos::TeamPolicy<DeviceType>(team_size,Kokkos::AUTO).team_size_max(f,Kokkos::ParallelForTag());
if (team_size <= team_size_max) {
Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,team_size);
Kokkos::parallel_for(config, f);
} else { // fall back to flat method
f.sharedsize = 0;
Kokkos::parallel_for(nall, f);
}
} else
Kokkos::parallel_for(nall, f);
#else
Kokkos::parallel_for(nall, f);
Kokkos::parallel_for(nall, f);
#endif
}
} else {
if (SIZE) {
NPairKokkosBuildFunctorSize<DeviceType,HALF_NEIGH,0,0> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
NPairKokkosBuildFunctor<DeviceType,TRI?0:HALF,NEWTON,TRI> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
#ifdef LMP_KOKKOS_GPU
if (ExecutionSpaceFromDevice<DeviceType>::space == Device) {
int team_size = atoms_per_bin*factor;
int team_size_max = Kokkos::TeamPolicy<DeviceType>(team_size,Kokkos::AUTO).team_size_max(f,Kokkos::ParallelForTag());
if (team_size <= team_size_max) {
Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,team_size);
Kokkos::parallel_for(config, f);
} else { // fall back to flat method
f.sharedsize = 0;
Kokkos::parallel_for(nall, f);
}
} else
if (ExecutionSpaceFromDevice<DeviceType>::space == Device) {
int team_size = atoms_per_bin*factor;
int team_size_max = Kokkos::TeamPolicy<DeviceType>(team_size,Kokkos::AUTO).team_size_max(f,Kokkos::ParallelForTag());
if (team_size <= team_size_max) {
Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,team_size);
Kokkos::parallel_for(config, f);
} else { // fall back to flat method
f.sharedsize = 0;
Kokkos::parallel_for(nall, f);
#else
}
} else
Kokkos::parallel_for(nall, f);
#endif
} else {
NPairKokkosBuildFunctor<DeviceType,HALF_NEIGH,0,0> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
#ifdef LMP_KOKKOS_GPU
if (ExecutionSpaceFromDevice<DeviceType>::space == Device) {
int team_size = atoms_per_bin*factor;
int team_size_max = Kokkos::TeamPolicy<DeviceType>(team_size,Kokkos::AUTO).team_size_max(f,Kokkos::ParallelForTag());
if (team_size <= team_size_max) {
Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,team_size);
Kokkos::parallel_for(config, f);
} else { // fall back to flat method
f.sharedsize = 0;
Kokkos::parallel_for(nall, f);
}
} else
Kokkos::parallel_for(nall, f);
#else
Kokkos::parallel_for(nall, f);
Kokkos::parallel_for(nall, f);
#endif
}
}
}
Kokkos::deep_copy(h_scalars, d_scalars);
@ -1402,20 +1361,30 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeGPU(typename Kokkos::TeamP
}
namespace LAMMPS_NS {
template class NPairKokkos<LMPDeviceType,0,0,0,0>;
template class NPairKokkos<LMPDeviceType,0,1,0,0>;
template class NPairKokkos<LMPDeviceType,1,0,0,0>;
template class NPairKokkos<LMPDeviceType,1,1,0,0>;
template class NPairKokkos<LMPDeviceType,1,0,1,0>;
template class NPairKokkos<LMPDeviceType,1,0,0,1>;
template class NPairKokkos<LMPDeviceType,1,0,1,1>;
template class NPairKokkos<LMPDeviceType,0,0,0,0,0>;
template class NPairKokkos<LMPDeviceType,0,0,1,0,0>;
template class NPairKokkos<LMPDeviceType,1,1,0,0,0>;
template class NPairKokkos<LMPDeviceType,1,0,0,0,0>;
template class NPairKokkos<LMPDeviceType,1,1,1,0,0>;
template class NPairKokkos<LMPDeviceType,1,0,1,0,0>;
template class NPairKokkos<LMPDeviceType,1,1,0,1,0>;
template class NPairKokkos<LMPDeviceType,1,0,0,1,0>;
template class NPairKokkos<LMPDeviceType,1,1,0,0,1>;
template class NPairKokkos<LMPDeviceType,1,0,0,0,1>;
template class NPairKokkos<LMPDeviceType,1,1,0,1,1>;
template class NPairKokkos<LMPDeviceType,1,0,0,1,1>;
#ifdef LMP_KOKKOS_GPU
template class NPairKokkos<LMPHostType,0,0,0,0>;
template class NPairKokkos<LMPHostType,0,1,0,0>;
template class NPairKokkos<LMPHostType,1,0,0,0>;
template class NPairKokkos<LMPHostType,1,1,0,0>;
template class NPairKokkos<LMPHostType,1,0,1,0>;
template class NPairKokkos<LMPHostType,1,0,0,1>;
template class NPairKokkos<LMPHostType,1,0,1,1>;
template class NPairKokkos<LMPHostType,0,0,0,0,0>;
template class NPairKokkos<LMPHostType,0,0,1,0,0>;
template class NPairKokkos<LMPHostType,1,1,0,0,0>;
template class NPairKokkos<LMPHostType,1,0,0,0,0>;
template class NPairKokkos<LMPHostType,1,1,1,0,0>;
template class NPairKokkos<LMPHostType,1,0,1,0,0>;
template class NPairKokkos<LMPHostType,1,1,0,1,0>;
template class NPairKokkos<LMPHostType,1,0,0,1,0>;
template class NPairKokkos<LMPHostType,1,1,0,0,1>;
template class NPairKokkos<LMPHostType,1,0,0,0,1>;
template class NPairKokkos<LMPHostType,1,1,0,1,1>;
template class NPairKokkos<LMPHostType,1,0,0,1,1>;
#endif
}

172
src/KOKKOS/npair_kokkos.h
View File

@ -13,75 +13,125 @@
#ifdef NPAIR_CLASS
// clang-format off
typedef NPairKokkos<LMPHostType,0,0,0,0> NPairKokkosFullBinHost;
typedef NPairKokkos<LMPHostType,0,0,0,0,0> NPairKokkosFullBinHost;
NPairStyle(full/bin/kk/host,
NPairKokkosFullBinHost,
NP_FULL | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI);
NP_BIN | NP_KOKKOS_HOST | NP_FULL | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI);
typedef NPairKokkos<LMPDeviceType,0,0,0,0> NPairKokkosFullBinDevice;
typedef NPairKokkos<LMPDeviceType,0,0,0,0,0> NPairKokkosFullBinDevice;
NPairStyle(full/bin/kk/device,
NPairKokkosFullBinDevice,
NP_FULL | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI);
NP_BIN | NP_KOKKOS_DEVICE | NP_FULL | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI);
typedef NPairKokkos<LMPHostType,0,1,0,0> NPairKokkosFullBinGhostHost;
typedef NPairKokkos<LMPHostType,0,0,1,0,0> NPairKokkosFullBinGhostHost;
NPairStyle(full/bin/ghost/kk/host,
NPairKokkosFullBinGhostHost,
NP_FULL | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI);
NP_BIN | NP_KOKKOS_HOST | NP_FULL | NP_NEWTON | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI);
typedef NPairKokkos<LMPDeviceType,0,1,0,0> NPairKokkosFullBinGhostDevice;
typedef NPairKokkos<LMPDeviceType,0,0,1,0,0> NPairKokkosFullBinGhostDevice;
NPairStyle(full/bin/ghost/kk/device,
NPairKokkosFullBinGhostDevice,
NP_FULL | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI);
NP_BIN | NP_KOKKOS_DEVICE | NP_FULL | NP_NEWTON | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI);
typedef NPairKokkos<LMPHostType,1,0,0,0> NPairKokkosHalfBinHost;
NPairStyle(half/bin/kk/host,
NPairKokkosHalfBinHost,
NP_HALF | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_ORTHO);
typedef NPairKokkos<LMPHostType,1,1,0,0,0> NPairKokkosHalfBinNewtonHost;
NPairStyle(half/bin/newton/kk/host,
NPairKokkosHalfBinNewtonHost,
NP_BIN | NP_KOKKOS_HOST | NP_HALF | NP_NEWTON | NP_ORTHO);
typedef NPairKokkos<LMPDeviceType,1,0,0,0> NPairKokkosHalfBinDevice;
NPairStyle(half/bin/kk/device,
NPairKokkosHalfBinDevice,
NP_HALF | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_ORTHO);
typedef NPairKokkos<LMPHostType,1,0,0,0,0> NPairKokkosHalfBinNewtoffHost;
NPairStyle(half/bin/newtoff/kk/host,
NPairKokkosHalfBinNewtoffHost,
NP_BIN | NP_KOKKOS_HOST | NP_HALF | NP_NEWTOFF | NP_ORTHO);
typedef NPairKokkos<LMPHostType,1,0,1,0> NPairKokkosHalfBinHostTri;
NPairStyle(half/bin/kk/host,
NPairKokkosHalfBinHostTri,
NP_HALF | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_TRI);
typedef NPairKokkos<LMPDeviceType,1,1,0,0,0> NPairKokkosHalfBinNewtonDevice;
NPairStyle(half/bin/newton/kk/device,
NPairKokkosHalfBinNewtonDevice,
NP_KOKKOS_DEVICE | NP_HALF | NP_BIN | NP_NEWTON | NP_ORTHO);
typedef NPairKokkos<LMPDeviceType,1,0,1,0> NPairKokkosHalfBinDeviceTri;
NPairStyle(half/bin/kk/device,
NPairKokkosHalfBinDeviceTri,
NP_HALF | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_TRI);
typedef NPairKokkos<LMPDeviceType,1,0,0,0,0> NPairKokkosHalfBinNewtoffDevice;
NPairStyle(half/bin/newtoff/kk/device,
NPairKokkosHalfBinNewtoffDevice,
NP_KOKKOS_DEVICE | NP_HALF | NP_BIN | NP_NEWTOFF | NP_ORTHO);
typedef NPairKokkos<LMPHostType,1,1,0,0> NPairKokkosHalfBinGhostHost;
NPairStyle(half/bin/ghost/kk/host,
NPairKokkosHalfBinGhostHost,
NP_HALF | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI);
typedef NPairKokkos<LMPHostType,1,1,0,1,0> NPairKokkosHalfBinNewtonTriHost;
NPairStyle(half/bin/newton/kk/host,
NPairKokkosHalfBinNewtonTriHost,
NP_BIN | NP_KOKKOS_HOST | NP_HALF | NP_NEWTON | NP_TRI);
typedef NPairKokkos<LMPDeviceType,1,1,0,0> NPairKokkosHalfBinGhostDevice;
NPairStyle(half/bin/ghost/kk/device,
NPairKokkosHalfBinGhostDevice,
NP_HALF | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI);
typedef NPairKokkos<LMPHostType,1,0,0,1,0> NPairKokkosHalfBinNewtoffTriHost;
NPairStyle(half/bin/newtoff/kk/host,
NPairKokkosHalfBinNewtoffTriHost,
NP_BIN | NP_KOKKOS_HOST | NP_HALF | NP_NEWTOFF | NP_TRI);
typedef NPairKokkos<LMPHostType,1,0,0,1> NPairKokkosHalfSizeBinHost;
NPairStyle(half/size/bin/kk/host,
NPairKokkosHalfSizeBinHost,
NP_HALF | NP_SIZE | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_ORTHO);
typedef NPairKokkos<LMPDeviceType,1,1,0,1,0> NPairKokkosHalfBinNewtonTriDevice;
NPairStyle(half/bin/newton/kk/device,
NPairKokkosHalfBinNewtonTriDevice,
NP_KOKKOS_DEVICE | NP_HALF | NP_BIN | NP_NEWTON | NP_TRI);
typedef NPairKokkos<LMPDeviceType,1,0,0,1> NPairKokkosHalfSizeBinDevice;
NPairStyle(half/size/bin/kk/device,
NPairKokkosHalfSizeBinDevice,
NP_HALF | NP_SIZE | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_ORTHO);
typedef NPairKokkos<LMPDeviceType,1,0,0,1,0> NPairKokkosHalfBinNewtoffTriDevice;
NPairStyle(half/bin/newtoff/kk/device,
NPairKokkosHalfBinNewtoffTriDevice,
NP_KOKKOS_DEVICE | NP_HALF | NP_BIN | NP_NEWTOFF | NP_TRI);
typedef NPairKokkos<LMPHostType,1,0,1,1> NPairKokkosHalfSizeBinHostTri;
NPairStyle(half/size/bin/kk/host,
NPairKokkosHalfSizeBinHostTri,
NP_HALF | NP_SIZE | NP_BIN | NP_KOKKOS_HOST | NP_NEWTON | NP_NEWTOFF | NP_TRI);
typedef NPairKokkos<LMPHostType,1,1,1,0,0> NPairKokkosHalfBinNewtonGhostHost;
NPairStyle(half/bin/newton/ghost/kk/host,
NPairKokkosHalfBinNewtonGhostHost,
NP_BIN | NP_KOKKOS_HOST | NP_HALF | NP_NEWTON | NP_GHOST | NP_ORTHO | NP_TRI);
typedef NPairKokkos<LMPDeviceType,1,0,1,1> NPairKokkosHalfSizeBinDeviceTri;
NPairStyle(half/size/bin/kk/device,
NPairKokkosHalfSizeBinDeviceTri,
NP_HALF | NP_SIZE | NP_BIN | NP_KOKKOS_DEVICE | NP_NEWTON | NP_NEWTOFF | NP_TRI);
typedef NPairKokkos<LMPHostType,1,0,1,0,0> NPairKokkosHalfBinNewtoffGhostHost;
NPairStyle(half/bin/newtoff/ghost/kk/host,
NPairKokkosHalfBinNewtoffGhostHost,
NP_BIN | NP_KOKKOS_HOST | NP_HALF | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI);
typedef NPairKokkos<LMPDeviceType,1,1,1,0,0> NPairKokkosHalfBinNewtonGhostDevice;
NPairStyle(half/bin/newton/ghost/kk/device,
NPairKokkosHalfBinNewtonGhostDevice,
NP_KOKKOS_DEVICE | NP_HALF | NP_BIN | NP_NEWTON | NP_GHOST | NP_ORTHO | NP_TRI);
typedef NPairKokkos<LMPDeviceType,1,0,1,0,0> NPairKokkosHalfBinNewtoffGhostDevice;
NPairStyle(half/bin/newtoff/ghost/kk/device,
NPairKokkosHalfBinNewtoffGhostDevice,
NP_KOKKOS_DEVICE | NP_HALF | NP_BIN | NP_NEWTOFF | NP_GHOST | NP_ORTHO | NP_TRI);
typedef NPairKokkos<LMPHostType,1,1,0,0,1> NPairKokkosHalfBinNewtonSizeHost;
NPairStyle(half/bin/newton/size/kk/host,
NPairKokkosHalfBinNewtonSizeHost,
NP_BIN | NP_KOKKOS_HOST | NP_HALF | NP_NEWTON | NP_SIZE | NP_ORTHO);
typedef NPairKokkos<LMPHostType,1,0,0,0,1> NPairKokkosHalfBinNewtoffSizeHost;
NPairStyle(half/bin/newtoff/size/kk/host,
NPairKokkosHalfBinNewtoffSizeHost,
NP_BIN | NP_KOKKOS_HOST | NP_HALF | NP_NEWTOFF | NP_SIZE | NP_ORTHO);
typedef NPairKokkos<LMPDeviceType,1,1,0,0,1> NPairKokkosHalfBinNewtonSizeDevice;
NPairStyle(half/bin/newton/size/kk/device,
NPairKokkosHalfBinNewtonSizeDevice,
NP_KOKKOS_DEVICE | NP_HALF | NP_BIN | NP_NEWTON | NP_SIZE | NP_ORTHO);
typedef NPairKokkos<LMPDeviceType,1,0,0,0,1> NPairKokkosHalfBinNewtoffSizeDevice;
NPairStyle(half/bin/newtoff/size/kk/device,
NPairKokkosHalfBinNewtoffSizeDevice,
NP_KOKKOS_DEVICE | NP_HALF | NP_BIN | NP_NEWTOFF | NP_SIZE | NP_ORTHO);
typedef NPairKokkos<LMPHostType,1,1,0,1,1> NPairKokkosHalfBinNewtonSizeTriHost;
NPairStyle(half/bin/newton/size/kk/host,
NPairKokkosHalfBinNewtonSizeTriHost,
NP_BIN | NP_KOKKOS_HOST | NP_HALF | NP_NEWTON | NP_SIZE | NP_TRI);
typedef NPairKokkos<LMPHostType,1,0,0,1,1> NPairKokkosHalfBinNewtoffSizeTriHost;
NPairStyle(half/bin/newtoff/size/kk/host,
NPairKokkosHalfBinNewtoffSizeTriHost,
NP_BIN | NP_KOKKOS_HOST | NP_HALF | NP_NEWTOFF | NP_SIZE | NP_TRI);
typedef NPairKokkos<LMPDeviceType,1,1,0,1,1> NPairKokkosHalfBinNewtonSizeTriDevice;
NPairStyle(half/bin/newton/size/kk/device,
NPairKokkosHalfBinNewtonSizeTriDevice,
NP_KOKKOS_DEVICE | NP_HALF | NP_BIN | NP_NEWTON | NP_SIZE | NP_TRI);
typedef NPairKokkos<LMPDeviceType,1,0,0,1,1> NPairKokkosHalfBinNewtoffSizeTriDevice;
NPairStyle(half/bin/newtoff/size/kk/device,
NPairKokkosHalfBinNewtoffSizeTriDevice,
NP_KOKKOS_DEVICE | NP_HALF | NP_BIN | NP_NEWTOFF | NP_SIZE | NP_TRI);
// clang-format on
#else
@ -94,7 +144,7 @@ NPairStyle(half/size/bin/kk/device,
namespace LAMMPS_NS {
template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI, int SIZE>
template<class DeviceType, int HALF_NEIGH, int NEWTON, int GHOST, int TRI, int SIZE>
class NPairKokkos : public NPair {
typedef ArrayTypes<DeviceType> AT;
@ -379,7 +429,7 @@ class NeighborKokkosExecute
};
template<class DeviceType, int HALF_NEIGH, int GHOST_NEWTON, int TRI>
template<class DeviceType, int HALF_NEIGH, int NEWTON, int TRI>
struct NPairKokkosBuildFunctor {
typedef DeviceType device_type;
@ -392,19 +442,19 @@ struct NPairKokkosBuildFunctor {
KOKKOS_INLINE_FUNCTION
void operator() (const int & i) const {
c.template build_Item<HALF_NEIGH,GHOST_NEWTON,TRI>(i);
c.template build_Item<HALF_NEIGH,NEWTON,TRI>(i);
}
#ifdef LMP_KOKKOS_GPU
LAMMPS_DEVICE_FUNCTION inline
void operator() (typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const {
c.template build_ItemGPU<HALF_NEIGH,GHOST_NEWTON,TRI>(dev, sharedsize);
c.template build_ItemGPU<HALF_NEIGH,NEWTON,TRI>(dev, sharedsize);
}
size_t team_shmem_size(const int team_size) const { (void) team_size; return sharedsize; }
#endif
};
template<int HALF_NEIGH, int GHOST_NEWTON, int TRI>
struct NPairKokkosBuildFunctor<LMPHostType,HALF_NEIGH,GHOST_NEWTON,TRI> {
template<int HALF_NEIGH, int NEWTON, int TRI>
struct NPairKokkosBuildFunctor<LMPHostType,HALF_NEIGH,NEWTON,TRI> {
typedef LMPHostType device_type;
const NeighborKokkosExecute<LMPHostType> c;
@ -416,7 +466,7 @@ struct NPairKokkosBuildFunctor<LMPHostType,HALF_NEIGH,GHOST_NEWTON,TRI> {
KOKKOS_INLINE_FUNCTION
void operator() (const int & i) const {
c.template build_Item<HALF_NEIGH,GHOST_NEWTON,TRI>(i);
c.template build_Item<HALF_NEIGH,NEWTON,TRI>(i);
}
void operator() (typename Kokkos::TeamPolicy<LMPHostType>::member_type /*dev*/) const {} // Should error out
@ -466,7 +516,7 @@ struct NPairKokkosBuildFunctorGhost<LMPHostType,HALF_NEIGH> {
void operator() (typename Kokkos::TeamPolicy<LMPHostType>::member_type /*dev*/) const {} // Should error out
};
template <class DeviceType, int HALF_NEIGH, int GHOST_NEWTON, int TRI>
template <class DeviceType, int HALF_NEIGH, int NEWTON, int TRI>
struct NPairKokkosBuildFunctorSize {
typedef DeviceType device_type;
@ -478,20 +528,20 @@ struct NPairKokkosBuildFunctorSize {
KOKKOS_INLINE_FUNCTION
void operator() (const int & i) const {
c.template build_ItemSize<HALF_NEIGH,GHOST_NEWTON,TRI>(i);
c.template build_ItemSize<HALF_NEIGH,NEWTON,TRI>(i);
}
#ifdef LMP_KOKKOS_GPU
LAMMPS_DEVICE_FUNCTION inline
void operator() (typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const {
c.template build_ItemSizeGPU<HALF_NEIGH,GHOST_NEWTON,TRI>(dev, sharedsize);
c.template build_ItemSizeGPU<HALF_NEIGH,NEWTON,TRI>(dev, sharedsize);
}
size_t team_shmem_size(const int team_size) const { (void) team_size; return sharedsize; }
#endif
};
template <int HALF_NEIGH, int GHOST_NEWTON, int TRI>
struct NPairKokkosBuildFunctorSize<LMPHostType,HALF_NEIGH,GHOST_NEWTON,TRI> {
template <int HALF_NEIGH, int NEWTON, int TRI>
struct NPairKokkosBuildFunctorSize<LMPHostType,HALF_NEIGH,NEWTON,TRI> {
typedef LMPHostType device_type;
const NeighborKokkosExecute<LMPHostType> c;
@ -502,7 +552,7 @@ struct NPairKokkosBuildFunctorSize<LMPHostType,HALF_NEIGH,GHOST_NEWTON,TRI> {
KOKKOS_INLINE_FUNCTION
void operator() (const int & i) const {
c.template build_ItemSize<HALF_NEIGH,GHOST_NEWTON,TRI>(i);
c.template build_ItemSize<HALF_NEIGH,NEWTON,TRI>(i);
}
void operator() (typename Kokkos::TeamPolicy<LMPHostType>::member_type /*dev*/) const {} // Should error out

1
src/KOKKOS/pair_lj_cut_kokkos.cpp
View File

@ -130,6 +130,7 @@ void PairLJCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
copymode = 0;
}
template<class DeviceType>

22
src/KOKKOS/pair_reaxff_kokkos.cpp
View File

@ -95,6 +95,8 @@ PairReaxFFKokkos<DeviceType>::~PairReaxFFKokkos()
{
if (copymode) return;
DeAllocate_System(api->system);
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->destroy_kokkos(k_vatom,vatom);
@ -184,6 +186,8 @@ void PairReaxFFKokkos<DeviceType>::init_style()
if (neighflag == FULL)
error->all(FLERR,"Must use half neighbor list with pair style reaxff/kk");
need_dup = lmp->kokkos->need_dup<DeviceType>();
allocate();
setup();
init_md();
@ -577,17 +581,17 @@ void PairReaxFFKokkos<DeviceType>::Deallocate_Lookup_Tables()
for (j = i; j <= ntypes; ++j) {
if (map[i] == -1) continue;
if (LR[i][j].n) {
sfree(api->control->error_ptr, LR[i][j].y, "LR[i,j].y");
sfree(api->control->error_ptr, LR[i][j].H, "LR[i,j].H");
sfree(api->control->error_ptr, LR[i][j].vdW, "LR[i,j].vdW");
sfree(api->control->error_ptr, LR[i][j].CEvd, "LR[i,j].CEvd");
sfree(api->control->error_ptr, LR[i][j].ele, "LR[i,j].ele");
sfree(api->control->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb");
sfree(LR[i][j].y);
sfree(LR[i][j].H);
sfree(LR[i][j].vdW);
sfree(LR[i][j].CEvd);
sfree(LR[i][j].ele);
sfree(LR[i][j].CEclmb);
}
}
sfree(api->control->error_ptr, LR[i], "LR[i]");
sfree(LR[i]);
}
sfree(api->control->error_ptr, LR, "LR");
sfree(LR);
}
/* ---------------------------------------------------------------------- */
@ -738,8 +742,6 @@ void PairReaxFFKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
}
need_dup = lmp->kokkos->need_dup<DeviceType>();
// allocate duplicated memory
if (need_dup) {
dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, Kokkos::Experimental::ScatterDuplicated>(f);

2
src/KOKKOS/pair_sw_kokkos.cpp
View File

@ -47,7 +47,6 @@ PairSWKokkos<DeviceType>::PairSWKokkos(LAMMPS *lmp) : PairSW(lmp)
{
respa_enable = 0;
kokkosable = 1;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
@ -138,6 +137,7 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
}
if ((int)d_numneigh_short.extent(0) < ignum)
d_numneigh_short = Kokkos::View<int*,DeviceType>("SW::numneighs_short",ignum*1.2);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairSWComputeShortNeigh>(0,inum), *this);
// loop over neighbor list of my atoms

61
src/KOKKOS/pair_vashishta_kokkos.cpp
View File

@ -117,24 +117,23 @@ void PairVashishtaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
EV_FLOAT ev;
EV_FLOAT ev_all;
// build short neighbor list
int max_neighs = d_neighbors.extent(1);
if (((int)d_neighbors_short_2body.extent(1) != max_neighs) ||
((int)d_neighbors_short_2body.extent(0) != ignum)) {
d_neighbors_short_2body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_2body",ignum,max_neighs);
}
if ((int)d_numneigh_short_2body.extent(0)!=ignum) {
d_numneigh_short_2body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_2body",ignum);
if (((int)d_neighbors_short_2body.extent(1) < max_neighs) ||
((int)d_neighbors_short_2body.extent(0) < ignum)) {
d_neighbors_short_2body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_2body",ignum*1.2,max_neighs);
}
if ((int)d_numneigh_short_2body.extent(0) < ignum)
d_numneigh_short_2body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_2body",ignum*1.2);
if (((int)d_neighbors_short_3body.extent(1) != max_neighs) ||
((int)d_neighbors_short_3body.extent(0) != ignum)) {
d_neighbors_short_3body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_3body",ignum,max_neighs);
}
if ((int)d_numneigh_short_3body.extent(0)!=ignum) {
d_numneigh_short_3body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_3body",ignum);
if (((int)d_neighbors_short_3body.extent(1) < max_neighs) ||
((int)d_neighbors_short_3body.extent(0) < ignum)) {
d_neighbors_short_3body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_3body",ignum*1.2,max_neighs);
}
if ((int)d_numneigh_short_3body.extent(0) < ignum)
d_numneigh_short_3body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_3body",ignum*1.2);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairVashishtaComputeShortNeigh>(0,neighflag==FULL?ignum:inum), *this);
@ -217,17 +216,17 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeShortNei
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < d_params[ijparam].cutsq) {
d_neighbors_short_2body(i,inside_2body) = j;
d_neighbors_short_2body(ii,inside_2body) = j;
inside_2body++;
}
if (rsq < d_params[ijparam].cutsq2) {
d_neighbors_short_3body(i,inside_3body) = j;
d_neighbors_short_3body(ii,inside_3body) = j;
inside_3body++;
}
}
d_numneigh_short_2body(i) = inside_2body;
d_numneigh_short_3body(i) = inside_3body;
d_numneigh_short_2body(ii) = inside_2body;
d_numneigh_short_3body(ii) = inside_3body;
}
template<class DeviceType>
@ -252,14 +251,14 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeHalf<NEI
// two-body interactions, skip half of them
const int jnum = d_numneigh_short_2body[i];
const int jnum = d_numneigh_short_2body[ii];
F_FLOAT fxtmpi = 0.0;
F_FLOAT fytmpi = 0.0;
F_FLOAT fztmpi = 0.0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors_short_2body(i,jj);
int j = d_neighbors_short_2body(ii,jj);
j &= NEIGHMASK;
const tagint jtag = tag[j];
@ -297,10 +296,10 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeHalf<NEI
}
}
const int jnumm1 = d_numneigh_short_3body[i];
const int jnumm1 = d_numneigh_short_3body[ii];
for (int jj = 0; jj < jnumm1-1; jj++) {
int j = d_neighbors_short_3body(i,jj);
int j = d_neighbors_short_3body(ii,jj);
j &= NEIGHMASK;
const int jtype = d_map[type[j]];
const int ijparam = d_elem3param(itype,jtype,jtype);
@ -314,7 +313,7 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeHalf<NEI
F_FLOAT fztmpj = 0.0;
for (int kk = jj+1; kk < jnumm1; kk++) {
int k = d_neighbors_short_3body(i,kk);
int k = d_neighbors_short_3body(ii,kk);
k &= NEIGHMASK;
const int ktype = d_map[type[k]];
const int ikparam = d_elem3param(itype,ktype,ktype);
@ -382,14 +381,14 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeFullA<NE
// two-body interactions
const int jnum = d_numneigh_short_2body[i];
const int jnum = d_numneigh_short_2body[ii];
F_FLOAT fxtmpi = 0.0;
F_FLOAT fytmpi = 0.0;
F_FLOAT fztmpi = 0.0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors_short_2body(i,jj);
int j = d_neighbors_short_2body(ii,jj);
j &= NEIGHMASK;
const int jtype = d_map[type[j]];
@ -413,10 +412,10 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeFullA<NE
}
}
const int jnumm1 = d_numneigh_short_3body[i];
const int jnumm1 = d_numneigh_short_3body[ii];
for (int jj = 0; jj < jnumm1-1; jj++) {
int j = d_neighbors_short_3body(i,jj);
int j = d_neighbors_short_3body(ii,jj);
j &= NEIGHMASK;
const int jtype = d_map[type[j]];
const int ijparam = d_elem3param(itype,jtype,jtype);
@ -426,7 +425,7 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeFullA<NE
const F_FLOAT rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
for (int kk = jj+1; kk < jnumm1; kk++) {
int k = d_neighbors_short_3body(i,kk);
int k = d_neighbors_short_3body(ii,kk);
k &= NEIGHMASK;
const int ktype = d_map[type[k]];
const int ikparam = d_elem3param(itype,ktype,ktype);
@ -481,14 +480,14 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeFullB<NE
const X_FLOAT ytmpi = x(i,1);
const X_FLOAT ztmpi = x(i,2);
const int jnum = d_numneigh_short_3body[i];
const int jnum = d_numneigh_short_3body[ii];
F_FLOAT fxtmpi = 0.0;
F_FLOAT fytmpi = 0.0;
F_FLOAT fztmpi = 0.0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors_short_3body(i,jj);
int j = d_neighbors_short_3body(ii,jj);
j &= NEIGHMASK;
if (j >= nlocal) continue;
const int jtype = d_map[type[j]];
@ -502,10 +501,10 @@ void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeFullB<NE
delr1[2] = ztmpi - ztmpj;
const F_FLOAT rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
const int j_jnum = d_numneigh_short_3body[j];
const int j_jnum = d_numneigh_short_3body[jj];
for (int kk = 0; kk < j_jnum; kk++) {
int k = d_neighbors_short_3body(j,kk);
int k = d_neighbors_short_3body(jj,kk);
k &= NEIGHMASK;
if (k == i) continue;
const int ktype = d_map[type[k]];

2
src/OPENMP/pair_reaxff_omp.cpp
View File

@ -93,7 +93,7 @@ PairReaxFFOMP::~PairReaxFFOMP()
if (setup_flag) {
reax_list * bonds = api->lists+BONDS;
for (int i=0; i<bonds->num_intrs; ++i)
sfree(error, bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction");
sfree(bonds->select.bond_list[i].bo_data.CdboReduction);
}
memory->destroy(num_nbrs_offset);
}

1
src/OPENMP/reaxff_bonds_omp.cpp
View File

@ -99,6 +99,7 @@ namespace ReaxFF {
/* set the pointers */
type_i = system->my_atoms[i].type;
type_j = system->my_atoms[j].type;
if ((type_i < 0) || (type_j < 0)) continue;
sbp_i = &(system->reax_param.sbp[type_i]);
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);

3
src/OPENMP/reaxff_forces_omp.cpp
View File

@ -265,6 +265,7 @@ namespace ReaxFF {
for (int i = 0; i < system->N; ++i) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
if (type_i < 0) continue;
sbp_i = &(system->reax_param.sbp[type_i]);
start_i = Start_Index(i, far_nbrs);
@ -276,6 +277,7 @@ namespace ReaxFF {
int j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
type_j = atom_j->type;
if (type_j < 0) continue;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
@ -376,6 +378,7 @@ namespace ReaxFF {
for (int i = 0; i < system->n; ++i) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
if (type_i < 0) continue;
sbp_i = &(system->reax_param.sbp[type_i]);
ihb = sbp_i->p_hbond;

6
src/OPENMP/reaxff_hydrogen_bonds_omp.cpp
View File

@ -98,14 +98,14 @@ namespace ReaxFF {
// for (j = 0; j < system->n; ++j)
for (j = ifrom; j < ito; ++j) {
/* j has to be of type H */
if (system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1) {
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
if (system->reax_param.sbp[type_j].p_hbond == 1) {
/*set j's variables */
type_j = system->my_atoms[j].type;
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
hb_start_j = Start_Index(system->my_atoms[j].Hindex, hbonds);
hb_end_j = End_Index(system->my_atoms[j].Hindex, hbonds);
if (type_j < 0) continue;
top = 0;
for (pi = start_j; pi < end_j; ++pi) {

25
src/REAXFF/pair_reaxff.cpp
View File

@ -110,9 +110,7 @@ PairReaxFF::PairReaxFF(LAMMPS *lmp) : Pair(lmp)
setup_flag = 0;
fixspecies_flag = 0;
nmax = 0;
list_blocking_flag = 0;
}
@ -130,13 +128,13 @@ PairReaxFF::~PairReaxFF()
// deallocate reax data-structures
if (api->control->tabulate) Deallocate_Lookup_Tables(api->system);
if (api->control->hbond_cut > 0) Delete_List(api->lists+HBONDS);
Delete_List(api->lists+BONDS);
Delete_List(api->lists+THREE_BODIES);
Delete_List(api->lists+FAR_NBRS);
DeAllocate_Workspace(api->control, api->workspace);
DeAllocate_Workspace(api->workspace);
DeAllocate_System(api->system);
}
@ -153,17 +151,16 @@ PairReaxFF::~PairReaxFF()
memory->destroy(cutsq);
memory->destroy(cutghost);
delete [] chi;
delete [] eta;
delete [] gamma;
delete [] bcut_acks2;
delete[] chi;
delete[] eta;
delete[] gamma;
delete[] bcut_acks2;
}
memory->destroy(tmpid);
memory->destroy(tmpbo);
delete [] pvector;
delete[] pvector;
}
/* ---------------------------------------------------------------------- */
@ -282,11 +279,6 @@ void PairReaxFF::coeff(int nargs, char **args)
if (nargs != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// ensure I,J args are * *
if (strcmp(args[0],"*") != 0 || strcmp(args[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read ffield file
Read_Force_Field(args[2], &(api->system->reax_param), api->control, world);
@ -536,7 +528,6 @@ void PairReaxFF::compute(int eflag, int vflag)
}
FindBond();
}
}
/* ---------------------------------------------------------------------- */
@ -654,7 +645,7 @@ int PairReaxFF::write_reax_lists()
jlist = firstneigh[i];
Set_Start_Index(i, num_nbrs, far_nbrs);
if (i < inum)
if (itr_i < inum)
cutoff_sqr = SQR(api->control->nonb_cut);
else
cutoff_sqr = SQR(api->control->bond_cut);

57
src/REAXFF/reaxff_allocate.cpp
View File

@ -62,11 +62,10 @@ namespace ReaxFF {
void DeAllocate_System(reax_system *system)
{
auto error = system->error_ptr;
auto memory = system->mem_ptr;
// deallocate the atom list
sfree(error, system->my_atoms, "system->my_atoms");
sfree(system->my_atoms);
// deallocate the ffield parameters storage
memory->destroy(system->reax_param.gp.l);
@ -78,45 +77,44 @@ namespace ReaxFF {
}
/************* workspace *************/
void DeAllocate_Workspace(control_params *control, storage *workspace)
void DeAllocate_Workspace(storage *workspace)
{
if (!workspace->allocated)
return;
workspace->allocated = 0;
auto error = control->error_ptr;
/* bond order storage */
sfree(error, workspace->total_bond_order, "total_bo");
sfree(error, workspace->Deltap, "Deltap");
sfree(error, workspace->Deltap_boc, "Deltap_boc");
sfree(error, workspace->dDeltap_self, "dDeltap_self");
sfree(error, workspace->Delta, "Delta");
sfree(error, workspace->Delta_lp, "Delta_lp");
sfree(error, workspace->Delta_lp_temp, "Delta_lp_temp");
sfree(error, workspace->dDelta_lp, "dDelta_lp");
sfree(error, workspace->dDelta_lp_temp, "dDelta_lp_temp");
sfree(error, workspace->Delta_e, "Delta_e");
sfree(error, workspace->Delta_boc, "Delta_boc");
sfree(error, workspace->Delta_val, "Delta_val");
sfree(error, workspace->nlp, "nlp");
sfree(error, workspace->nlp_temp, "nlp_temp");
sfree(error, workspace->Clp, "Clp");
sfree(error, workspace->vlpex, "vlpex");
sfree(error, workspace->bond_mark, "bond_mark");
sfree(workspace->total_bond_order);
sfree(workspace->Deltap);
sfree(workspace->Deltap_boc);
sfree(workspace->dDeltap_self);
sfree(workspace->Delta);
sfree(workspace->Delta_lp);
sfree(workspace->Delta_lp_temp);
sfree(workspace->dDelta_lp);
sfree(workspace->dDelta_lp_temp);
sfree(workspace->Delta_e);
sfree(workspace->Delta_boc);
sfree(workspace->Delta_val);
sfree(workspace->nlp);
sfree(workspace->nlp_temp);
sfree(workspace->Clp);
sfree(workspace->vlpex);
sfree(workspace->bond_mark);
/* force related storage */
sfree(error, workspace->f, "f");
sfree(error, workspace->CdDelta, "CdDelta");
sfree(workspace->f);
sfree(workspace->CdDelta);
/* reductions */
if (workspace->CdDeltaReduction)
sfree(error, workspace->CdDeltaReduction, "cddelta_reduce");
sfree(workspace->CdDeltaReduction);
if (workspace->forceReduction)
sfree(error, workspace->forceReduction, "f_reduce");
sfree(workspace->forceReduction);
if (workspace->valence_angle_atom_myoffset)
sfree(error, workspace->valence_angle_atom_myoffset, "valence_angle_atom_myoffset");
sfree(workspace->valence_angle_atom_myoffset);
}
void Allocate_Workspace(control_params *control, storage *workspace, int total_cap)
@ -206,7 +204,7 @@ namespace ReaxFF {
if (system->omp_active)
for (i = 0; i < bonds->num_intrs; ++i)
sfree(system->error_ptr, bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction");
sfree(bonds->select.bond_list[i].bo_data.CdboReduction);
Delete_List(bonds);
Make_List(system->total_cap, *total_bonds, TYP_BOND, bonds);
@ -245,7 +243,7 @@ namespace ReaxFF {
system->my_atoms = (reax_atom *)::realloc(system->my_atoms,
system->total_cap*sizeof(reax_atom));
/* workspace */
DeAllocate_Workspace(control, workspace);
DeAllocate_Workspace(workspace);
Allocate_Workspace(control, workspace, system->total_cap);
}
@ -292,8 +290,7 @@ namespace ReaxFF {
reax_list *bonds = (*lists)+BONDS;
for (int i = 0; i < bonds->num_intrs; ++i) {
sfree(error, bonds->select.bond_list[i].bo_data.CdboReduction,
"CdboReduction");
sfree(bonds->select.bond_list[i].bo_data.CdboReduction);
bonds->select.bond_list[i].bo_data.CdboReduction =
(double*) smalloc(error, sizeof(double)*nthreads, "CdboReduction");

4
src/REAXFF/reaxff_api.h
View File

@ -41,7 +41,7 @@ struct API {
extern void Allocate_Workspace(control_params *, storage *, int);
extern void DeAllocate_System(reax_system *);
extern void DeAllocate_Workspace(control_params *, storage *);
extern void DeAllocate_Workspace(storage *);
extern void PreAllocate_Space(reax_system *, storage *);
extern void ReAllocate(reax_system *, control_params *, simulation_data *, storage *, reax_list **);
@ -142,7 +142,7 @@ extern void Reset_Workspace(reax_system *, storage *);
extern void *scalloc(LAMMPS_NS::Error *, rc_bigint, rc_bigint, const std::string &);
extern void *smalloc(LAMMPS_NS::Error *, rc_bigint, const std::string &);
extern void sfree(LAMMPS_NS::Error *, void *, const std::string &);
extern void sfree(void *);
// torsion angles

1
src/REAXFF/reaxff_bonds.cpp
View File

@ -75,6 +75,7 @@ namespace ReaxFF {
/* set the pointers */
type_i = system->my_atoms[i].type;
type_j = system->my_atoms[j].type;
if ((type_i < 0) || (type_j < 0)) continue;
sbp_i = &(system->reax_param.sbp[type_i]);
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);

9
src/REAXFF/reaxff_hydrogen_bonds.cpp
View File

@ -59,14 +59,14 @@ namespace ReaxFF {
hbonds = (*lists) + HBONDS;
hbond_list = hbonds->select.hbond_list;
for (j = 0; j < system->n; ++j)
if (system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1) {
type_j = system->my_atoms[j].type;
for (j = 0; j < system->n; ++j) {
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
if (system->reax_param.sbp[type_j].p_hbond == 1) {
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
hb_start_j = Start_Index(system->my_atoms[j].Hindex, hbonds);
hb_end_j = End_Index(system->my_atoms[j].Hindex, hbonds);
if (type_j < 0) continue;
top = 0;
for (pi = start_j; pi < end_j; ++pi) {
@ -154,5 +154,6 @@ namespace ReaxFF {
}
}
}
}
}
}

3
src/REAXFF/reaxff_init_md.cpp
View File

@ -56,7 +56,8 @@ namespace ReaxFF {
if (control->hbond_cut > 0)
for (i = 0; i < system->n; ++i) {
atom = &(system->my_atoms[i]);
if (system->reax_param.sbp[atom->type].p_hbond == 1 && atom->type >= 0)
if ((atom->type >= 0)
&& (system->reax_param.sbp[atom->type].p_hbond == 1 && atom->type >= 0))
atom->Hindex = system->numH++;
else atom->Hindex = -1;
}

24
src/REAXFF/reaxff_list.cpp
View File

@ -39,8 +39,8 @@ namespace ReaxFF {
l->n = n;
l->num_intrs = num_intrs;
if (l->index) sfree(l->error_ptr, l->index, "list:index");
if (l->end_index) sfree(l->error_ptr, l->end_index, "list:end_index");
if (l->index) sfree(l->index);
if (l->end_index) sfree(l->end_index);
l->index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:index");
l->end_index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:end_index");
@ -48,26 +48,26 @@ namespace ReaxFF {
switch(l->type) {
case TYP_THREE_BODY:
if (l->select.three_body_list) sfree(l->error_ptr, l->select.three_body_list,"list:three_bodies");
if (l->select.three_body_list) sfree(l->select.three_body_list);
l->select.three_body_list = (three_body_interaction_data*)
smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(three_body_interaction_data),
"list:three_bodies");
break;
case TYP_BOND:
if (l->select.bond_list) sfree(l->error_ptr, l->select.bond_list,"list:bonds");
if (l->select.bond_list) sfree(l->select.bond_list);
l->select.bond_list = (bond_data*)
smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(bond_data), "list:bonds");
break;
case TYP_FAR_NEIGHBOR:
if (l->select.far_nbr_list) sfree(l->error_ptr, l->select.far_nbr_list,"list:far_nbrs");
if (l->select.far_nbr_list) sfree(l->select.far_nbr_list);
l->select.far_nbr_list = (far_neighbor_data*)
smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(far_neighbor_data), "list:far_nbrs");
break;
case TYP_HBOND:
if (l->select.hbond_list) sfree(l->error_ptr, l->select.hbond_list,"list:hbonds");
if (l->select.hbond_list) sfree(l->select.hbond_list);
l->select.hbond_list = (hbond_data*)
smalloc(l->error_ptr, (rc_bigint) num_intrs * sizeof(hbond_data), "list:hbonds");
break;
@ -83,26 +83,26 @@ namespace ReaxFF {
return;
l->allocated = 0;
sfree(l->error_ptr, l->index, "list:index");
sfree(l->error_ptr, l->end_index, "list:end_index");
sfree(l->index);
sfree(l->end_index);
l->index = nullptr;
l->end_index = nullptr;
switch(l->type) {
case TYP_HBOND:
sfree(l->error_ptr, l->select.hbond_list, "list:hbonds");
sfree(l->select.hbond_list);
l->select.hbond_list = nullptr;
break;
case TYP_FAR_NEIGHBOR:
sfree(l->error_ptr, l->select.far_nbr_list, "list:far_nbrs");
sfree(l->select.far_nbr_list);
l->select.far_nbr_list = nullptr;
break;
case TYP_BOND:
sfree(l->error_ptr, l->select.bond_list, "list:bonds");
sfree(l->select.bond_list);
l->select.bond_list = nullptr;
break;
case TYP_THREE_BODY:
sfree(l->error_ptr, l->select.three_body_list, "list:three_bodies");
sfree(l->select.three_body_list);
l->select.three_body_list = nullptr;
break;

36
src/REAXFF/reaxff_lookup.cpp
View File

@ -90,11 +90,11 @@ namespace ReaxFF {
coef[i-1].a = f[i];
}
sfree(error_ptr, a, "cubic_spline:a");
sfree(error_ptr, b, "cubic_spline:b");
sfree(error_ptr, c, "cubic_spline:c");
sfree(error_ptr, d, "cubic_spline:d");
sfree(error_ptr, v, "cubic_spline:v");
sfree(a);
sfree(b);
sfree(c);
sfree(d);
sfree(v);
}
void Complete_Cubic_Spline(LAMMPS_NS::Error* error_ptr, const double *h,
@ -138,11 +138,11 @@ namespace ReaxFF {
coef[i-1].a = f[i];
}
sfree(error_ptr, a, "cubic_spline:a");
sfree(error_ptr, b, "cubic_spline:b");
sfree(error_ptr, c, "cubic_spline:c");
sfree(error_ptr, d, "cubic_spline:d");
sfree(error_ptr, v, "cubic_spline:v");
sfree(a);
sfree(b);
sfree(c);
sfree(d);
sfree(v);
}
void Init_Lookup_Tables(reax_system *system, control_params *control,
@ -276,16 +276,16 @@ namespace ReaxFF {
for (i = 0; i < ntypes; ++i) {
for (j = i; j < ntypes; ++j)
if (LR[i][j].n) {
sfree(system->error_ptr, LR[i][j].y, "LR[i,j].y");
sfree(system->error_ptr, LR[i][j].H, "LR[i,j].H");
sfree(system->error_ptr, LR[i][j].vdW, "LR[i,j].vdW");
sfree(system->error_ptr, LR[i][j].CEvd, "LR[i,j].CEvd");
sfree(system->error_ptr, LR[i][j].ele, "LR[i,j].ele");
sfree(system->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb");
sfree(LR[i][j].y);
sfree(LR[i][j].H);
sfree(LR[i][j].vdW);
sfree(LR[i][j].CEvd);
sfree(LR[i][j].ele);
sfree(LR[i][j].CEclmb);
}
sfree(system->error_ptr, LR[i], "LR[i]");
sfree(LR[i]);
}
sfree(system->error_ptr, LR, "LR");
sfree(LR);
}
}

8
src/REAXFF/reaxff_nonbonded.cpp
View File

@ -233,8 +233,8 @@ namespace ReaxFF {
flag = 0;
/* kinetic energy terms */
double xcut = 0.5 * ( system->reax_param.sbp[ system->my_atoms[i].type ].bcut_acks2
+ system->reax_param.sbp[ system->my_atoms[j].type ].bcut_acks2 );
double xcut = 0.5 * (system->reax_param.sbp[system->my_atoms[i].type].bcut_acks2
+ system->reax_param.sbp[system->my_atoms[j].type].bcut_acks2);
if(nbr_pj->d <= xcut) {
if (j < natoms) flag = 1;
@ -409,8 +409,8 @@ namespace ReaxFF {
flag = 0;
/* kinetic energy terms */
double xcut = 0.5 * ( system->reax_param.sbp[ system->my_atoms[i].type ].bcut_acks2
+ system->reax_param.sbp[ system->my_atoms[j].type ].bcut_acks2 );
double xcut = 0.5 * (system->reax_param.sbp[ system->my_atoms[i].type ].bcut_acks2
+ system->reax_param.sbp[ system->my_atoms[j].type ].bcut_acks2);
if(nbr_pj->d <= xcut) {
if (j < natoms) flag = 1;

11
src/REAXFF/reaxff_tool_box.cpp
View File

@ -96,16 +96,9 @@ void *scalloc(LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const st
}
/* safe free */
void sfree(LAMMPS_NS::Error *error_ptr, void *ptr, const std::string &name)
void sfree(void *ptr)
{
if (ptr == nullptr) {
auto errmsg = std::string("Trying to free the already free()'d pointer: ") + name;
if (error_ptr)
error_ptr->one(FLERR, errmsg);
else
fputs(errmsg.c_str(), stderr);
return;
}
if (ptr == nullptr) return;
free(ptr);
ptr = nullptr;

13
src/pair_hybrid.cpp
View File

@ -304,8 +304,6 @@ void PairHybrid::settings(int narg, char **arg)
// allocate list of sub-styles as big as possibly needed if no extra args
styles = new Pair *[narg];
cutmax_style = new double[narg];
memset(cutmax_style, 0.0, narg*sizeof(double));
keywords = new char *[narg];
multiple = new int[narg];
@ -347,6 +345,10 @@ void PairHybrid::settings(int narg, char **arg)
nstyles++;
}
delete[] cutmax_style;
cutmax_style = new double[nstyles];
memset(cutmax_style, 0, nstyles*sizeof(double));
// multiple[i] = 1 to M if sub-style used multiple times, else 0
int num_tip4p = 0, num_coul = 0; // count sub-styles with tip4p and coulomb
@ -582,6 +584,8 @@ void PairHybrid::init_style()
{
int i,m,itype,jtype,used,istyle,skip;
memset(cutmax_style, 0, nstyles*sizeof(double));
// error if a sub-style is not used
int ntypes = atom->ntypes;
@ -750,7 +754,7 @@ double PairHybrid::init_one(int i, int j)
cutmax_style[istyle] = cut;
for (auto &request : neighbor->get_pair_requests()) {
if (styles[istyle] == request->get_requestor() && styles[istyle]->trim_flag) {
if (styles[istyle] == request->get_requestor()) {
request->set_cutoff(cutmax_style[istyle]);
break;
}
@ -819,8 +823,9 @@ void PairHybrid::read_restart(FILE *fp)
delete[] compute_tally;
styles = new Pair*[nstyles];
delete[] cutmax_style;
cutmax_style = new double[nstyles];
memset(cutmax_style, 0.0, nstyles*sizeof(double));
memset(cutmax_style, 0, nstyles*sizeof(double));
keywords = new char*[nstyles];
multiple = new int[nstyles];