Merge branch 'master' into progguide (9dc9cdf5) · Commits · 郑智淋 / lammps

cmake/Modules/Testing.cmake

+9 −6

Original line number	Original line	Diff line number	Diff line
	@@ -23,14 +23,17 @@ if(ENABLE_TESTING)
	OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))		OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
	include(CheckCXXCompilerFlag)		include(CheckCXXCompilerFlag)
	set(CMAKE_CUSTOM_LINKER_DEFAULT default)		set(CMAKE_CUSTOM_LINKER_DEFAULT default)
	check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER)		check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
	check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER)		check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
	check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER)		check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER_FLAG)
	if(HAVE_LLD_LINKER)		find_program(HAVE_LLD_LINKER_BIN lld ld.lld)
			find_program(HAVE_GOLD_LINKER_BIN ld.gold)
			find_program(HAVE_BFD_LINKER_BIN ld.bfd)
			if(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
	set(CMAKE_CUSTOM_LINKER_DEFAULT lld)		set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
	elseif(HAVE_GOLD_LINKER)		elseif(HAVE_GOLD_LINKER_FLAG AND HAVE_GOLD_LINKER_BIN)
	set(CMAKE_CUSTOM_LINKER_DEFAULT gold)		set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
	elseif(HAVE_BFD_LINKER)		elseif(HAVE_BFD_LINKER_FLAG AND HAVE_BFD_LINKER_BIN)
	set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)		set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
	endif()		endif()
	set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)		set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)

doc/src/pair_ufm.rst

+2 −4

Original line number	Original line	Diff line number	Diff line
	@@ -94,10 +94,8 @@ of a run:

	Mixing, shift, table, tail correction, restart, rRESPA info\ :		Mixing, shift, table, tail correction, restart, rRESPA info\ :

	For atom type pairs I,J and I != J, the A coefficient and cutoff		For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff
	distance for this pair style can be mixed. A is always mixed via a		distance for this pair style can be mixed. The default mix value is geometric\ . See the
	geometric rule. The cutoff is mixed according to the pair_modify
	mix value. The default mix value is geometric\ . See the
	"pair_modify" command for details.		"pair_modify" command for details.

	This pair style support the :doc:`pair_modify <pair_modify>` shift option for the energy of the pair interaction.		This pair style support the :doc:`pair_modify <pair_modify>` shift option for the energy of the pair interaction.

doc/utils/check-packages.py

+59 −51

Original line number	Original line	Diff line number	Diff line
	#!/usr/bin/env python3		#!/usr/bin/env python3

	from __future__ import print_function		import os, re, sys
	from glob import glob		from glob import glob
	from argparse import ArgumentParser		from argparse import ArgumentParser
	import os, re, sys

	parser = ArgumentParser(prog='check-packages.py',		parser = ArgumentParser(prog='check-packages.py',
	description="Check package table completeness")		description="Check package table completeness")

	parser.add_argument("-v", "--verbose",		parser.add_argument("-v", "--verbose",
	action='store_const',		action='store_true',
	const=True, default=False,
	help="Enable verbose output")		help="Enable verbose output")

	parser.add_argument("-d", "--doc",		parser.add_argument("-d", "--doc",
	@@ -20,20 +18,28 @@ parser.add_argument("-s", "--src",

	args = parser.parse_args()		args = parser.parse_args()
	verbose = args.verbose		verbose = args.verbose
	src = args.src		src_dir = args.src
	doc = args.doc		doc_dir = args.doc

			LAMMPS_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), '..', '..'))

			if not src_dir:
			src_dir = os.path.join(LAMMPS_DIR , 'src')

			if not doc_dir:
			doc_dir = os.path.join(LAMMPS_DIR, 'doc', 'src')

	if not args.src or not args.doc:		if not src_dir or not doc_dir:
	parser.print_help()		parser.print_help()
	sys.exit(1)		sys.exit(1)

	if not os.path.isdir(src):		if not os.path.isdir(src_dir):
	sys.exit("LAMMPS source path %s does not exist" % src)		sys.exit(f"LAMMPS source path {src_dir} does not exist")

	if not os.path.isdir(doc):		if not os.path.isdir(doc_dir):
	sys.exit("LAMMPS documentation source path %s does not exist" % doc)		sys.exit(f"LAMMPS documentation source path {doc_dir} does not exist")

	pkgdirs = glob(os.path.join(src, '[A-Z][A-Z]*'))		pkgdirs = glob(os.path.join(src_dir, '[A-Z][A-Z]*'))
	dirs = re.compile(".*/([0-9A-Z-]+)$")		dirs = re.compile(".*/([0-9A-Z-]+)$")
	user = re.compile("USER-.*")		user = re.compile("USER-.*")

	@@ -46,52 +52,54 @@ usrpkg = []

	for d in pkgdirs:		for d in pkgdirs:
	pkg = dirs.match(d).group(1)		pkg = dirs.match(d).group(1)
	if not os.path.isdir(os.path.join(src,pkg)): continue		if not os.path.isdir(os.path.join(src_dir, pkg)): continue
	files = glob(os.path.join(src,pkg,"*.cpp"))		# skip over folders without C++ source files
			files = glob(os.path.join(src_dir, pkg, "*.cpp"))
	if len(files) == 0: continue		if len(files) == 0: continue
			# skip over known non-package folders
	if pkg in ['DEPEND','MAKE','STUBS']: continue		if pkg in ['DEPEND','MAKE','STUBS']: continue
	if user.match(pkg):		if user.match(pkg):
	usrpkg.append(pkg)		usrpkg.append(pkg)
	else:		else:
	stdpkg.append(pkg)		stdpkg.append(pkg)

	print("Found %d standard and %d user packages" % (len(stdpkg),len(usrpkg)))		print(f"Found {len(stdpkg)} standard and {len(usrpkg)} user packages")

	counter = 0		counter = 0
	fp = open(os.path.join(doc,'Packages_standard.rst'))
			with open(os.path.join(doc_dir, 'Packages_standard.rst')) as fp:
	text = fp.read()		text = fp.read()
	fp.close()
	matches = re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`',text,re.MULTILINE)		matches = set(re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`', text, re.MULTILINE))
	for p in stdpkg:		for p in stdpkg:
	if not p in matches:		if not p in matches:
	++counter		counter += 1
	print("Standard package %s missing in Packages_standard.rst" % p)		print(f"Standard package {p} missing in Packages_standard.rst")

	fp = open(os.path.join(doc,'Packages_user.rst'))		with open(os.path.join(doc_dir, 'Packages_user.rst')) as fp:
	text = fp.read()		text = fp.read()
	fp.close()
	matches = re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`',text,re.MULTILINE)		matches = set(re.findall(':ref:`([A-Z0-9-]+) <[A-Z0-9-]+>`', text, re.MULTILINE))
	for p in usrpkg:		for p in usrpkg:
	if not p in matches:		if not p in matches:
	++counter		counter += 1
	print("User package %s missing in Packages_user.rst" % p)		print(f"User package {p} missing in Packages_user.rst")

	fp = open(os.path.join(doc,'Packages_details.rst'))		with open(os.path.join(doc_dir, 'Packages_details.rst')) as fp:
	text = fp.read()		text = fp.read()
	fp.close()
	matches = re.findall(':ref:`([A-Z0-9]+) <PKG-\\1>`',text,re.MULTILINE)		matches = set(re.findall(':ref:`([A-Z0-9]+) <PKG-\\1>`', text, re.MULTILINE))
	for p in stdpkg:		for p in stdpkg:
	if not p in matches:		if not p in matches:
	++counter		counter += 1
	print("Standard package %s missing in Packages_details.rst"		print(f"Standard package {p} missing in Packages_details.rst")
	% p)
	matches = re.findall(':ref:`(USER-[A-Z0-9]+) <PKG-\\1>`',text,re.MULTILINE)		matches = set(re.findall(':ref:`(USER-[A-Z0-9]+) <PKG-\\1>`', text, re.MULTILINE))
	for p in usrpkg:		for p in usrpkg:
	if not p in matches:		if not p in matches:
	++counter		counter +=1
	print("User package %s missing in Packages_details.rst"		print(f"User package {p} missing in Packages_details.rst")
	% p)

	if counter:		if counter:
	print("Found %d issue(s) with package lists" % counter)		print(f"Found {counter} issue(s) with package lists")

doc/utils/check-styles.py

+141 −140

Original line number	Original line	Diff line number	Diff line
	#!/usr/bin/env python3		#!/usr/bin/env python3

	from __future__ import print_function		import os, re, sys
	from glob import glob		from glob import glob
	from argparse import ArgumentParser		from argparse import ArgumentParser
	import os, re, sys

	parser = ArgumentParser(prog='check-styles.py',		parser = ArgumentParser(prog='check-styles.py',
	description="Check style table completeness")		description="Check style table completeness")

	parser.add_argument("-v", "--verbose",		parser.add_argument("-v", "--verbose",
	action='store_const',		action='store_true',
	const=True, default=False,
	help="Enable verbose output")		help="Enable verbose output")

	parser.add_argument("-d", "--doc",		parser.add_argument("-d", "--doc",
	@@ -20,21 +18,29 @@ parser.add_argument("-s", "--src",

	args = parser.parse_args()		args = parser.parse_args()
	verbose = args.verbose		verbose = args.verbose
	src = args.src		src_dir = args.src
	doc = args.doc		doc_dir = args.doc

			LAMMPS_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), '..', '..'))

			if not src_dir:
			src_dir = os.path.join(LAMMPS_DIR , 'src')

			if not doc_dir:
			doc_dir = os.path.join(LAMMPS_DIR, 'doc', 'src')

	if not args.src or not args.doc:		if not src_dir or not doc_dir:
	parser.print_help()		parser.print_help()
	sys.exit(1)		sys.exit(1)

	if not os.path.isdir(src):		if not os.path.isdir(src_dir):
	sys.exit("LAMMPS source path %s does not exist" % src)		sys.exit(f"LAMMPS source path {src_dir} does not exist")

	if not os.path.isdir(doc):		if not os.path.isdir(doc_dir):
	sys.exit("LAMMPS documentation source path %s does not exist" % doc)		sys.exit(f"LAMMPS documentation source path {doc_dir} does not exist")

	headers = glob(os.path.join(src, '', '.h'))		headers = glob(os.path.join(src_dir, '', '.h'))
	headers += glob(os.path.join(src, '*.h'))		headers += glob(os.path.join(src_dir, '*.h'))

	angle = {}		angle = {}
	atom = {}		atom = {}
	@@ -54,6 +60,7 @@ reader = {}
	region = {}		region = {}
	total = 0		total = 0

			style_pattern = re.compile(r"(.+)Style$(.+),(.+)$")
	upper = re.compile("[A-Z]+")		upper = re.compile("[A-Z]+")
	gpu = re.compile("(.+)/gpu$")		gpu = re.compile("(.+)/gpu$")
	intel = re.compile("(.+)/intel$")		intel = re.compile("(.+)/intel$")
	@@ -63,61 +70,54 @@ omp = re.compile("(.+)/omp$")
	opt = re.compile("(.+)/opt$")		opt = re.compile("(.+)/opt$")
	removed = re.compile("(.*)Deprecated$")		removed = re.compile("(.*)Deprecated$")

	def register_style(list,style,info):		def register_style(styles, name, info):
	if style in list.keys():		if name in styles:
	list[style]['gpu'] += info['gpu']		for key, value in info.items():
	list[style]['intel'] += info['intel']		styles[name][key] += value
	list[style]['kokkos'] += info['kokkos']
	list[style]['omp'] += info['omp']
	list[style]['opt'] += info['opt']
	list[style]['removed'] += info['removed']
	else:		else:
	list[style] = info		styles[name] = info

	def add_suffix(list,style):		def add_suffix(styles, name):
	suffix = ""		suffix = ""
	if list[style]['gpu']:		if styles[name]['gpu']:
	suffix += 'g'		suffix += 'g'
	if list[style]['intel']:		if styles[name]['intel']:
	suffix += 'i'		suffix += 'i'
	if list[style]['kokkos']:		if styles[name]['kokkos']:
	suffix += 'k'		suffix += 'k'
	if list[style]['omp']:		if styles[name]['omp']:
	suffix += 'o'		suffix += 'o'
	if list[style]['opt']:		if styles[name]['opt']:
	suffix += 't'		suffix += 't'
	if suffix:		if suffix:
	return style + ' (' + suffix + ')'		return f"{name} ({suffix})"
	else:		else:
	return style		return name

			def check_style(filename, dirname, pattern, styles, name, suffix=False, skip=set()):
			with open(os.path.join(dirname, filename)) as f:
			text = f.read()

	def check_style(file,dir,pattern,list,name,suffix=False,skip=()):
	f = os.path.join(dir, file)
	fp = open(f)
	text = fp.read()
	fp.close()
	matches = re.findall(pattern, text, re.MULTILINE)		matches = re.findall(pattern, text, re.MULTILINE)

	counter = 0		counter = 0
	for c in list.keys():		for c in styles:
	# known undocumented aliases we need to skip		# known undocumented aliases we need to skip
	if c in skip: continue		if c in skip: continue
	s = c		s = c
	if suffix: s = add_suffix(list,c)		if suffix: s = add_suffix(styles, c)
	if not s in matches:		if not s in matches:
	if not list[c]['removed']:		if not styles[c]['removed']:
	print("%s style entry %s" % (name,s),		print(f"{name} style entry {s} is missing or incomplete in {filename}")
	"is missing or incomplete in %s" % file)
	counter += 1		counter += 1
	return counter		return counter

	for h in headers:		for header in headers:
	if verbose: print("Checking ", h)		if verbose: print("Checking ", header)
	fp = open(h)		with open(header) as f:
	text = fp.read()		for line in f:
	fp.close()		matches = style_pattern.findall(line)
	matches = re.findall("(.+)Style$(.+),(.+)$",text,re.MULTILINE)
	for m in matches:		for m in matches:

	# skip over internal styles w/o explicit documentation		# skip over internal styles w/o explicit documentation
	style = m[1]		style = m[1]
	total += 1		total += 1
	@@ -202,44 +202,45 @@ print("""Parsed style names w/o suffixes from C++ tree in %s:
	Reader styles: %3d Region styles: %3d		Reader styles: %3d Region styles: %3d
	----------------------------------------------------		----------------------------------------------------
	Total number of styles (including suffixes): %d""" \		Total number of styles (including suffixes): %d""" \
	% (src, len(angle), len(atom), len(body), len(bond), \		% (src_dir, len(angle), len(atom), len(body), len(bond), \
	len(command), len(compute), len(dihedral), len(dump), \		len(command), len(compute), len(dihedral), len(dump), \
	len(fix), len(improper), len(integrate), len(kspace), \		len(fix), len(improper), len(integrate), len(kspace), \
	len(minimize), len(pair), len(reader), len(region), total))		len(minimize), len(pair), len(reader), len(region), total))


	counter = 0		counter = 0

	counter += check_style('Commands_all.rst',doc,":doc:`(.+) <.+>`",		counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",
	command,'Command',suffix=False)		command,'Command',suffix=False)
	counter += check_style('Commands_compute.rst',doc,":doc:`(.+) <compute.+>`",		counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",
	compute,'Compute',suffix=True)		compute,'Compute',suffix=True)
	counter += check_style('compute.rst',doc,":doc:`(.+) <compute.+>` -",		counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",
	compute,'Compute',suffix=False)		compute,'Compute',suffix=False)
	counter += check_style('Commands_fix.rst',doc,":doc:`(.+) <fix.+>`",		counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",
	fix,'Fix',skip=('python'),suffix=True)		fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=True)
	counter += check_style('fix.rst',doc,":doc:`(.+) <fix.+>` -",		counter += check_style('fix.rst', doc_dir, ":doc:`(.+) <fix.+>` -",
	fix,'Fix',skip=('python'),suffix=False)		fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=False)
	counter += check_style('Commands_pair.rst',doc,":doc:`(.+) <pair.+>`",		counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",
	pair,'Pair',skip=('meam','lj/sf'),suffix=True)		pair,'Pair',skip=('meam','lj/sf'),suffix=True)
	counter += check_style('pair_style.rst',doc,":doc:`(.+) <pair.+>` -",		counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",
	pair,'Pair',skip=('meam','lj/sf'),suffix=False)		pair,'Pair',skip=('meam','lj/sf'),suffix=False)
	counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <bond.+>`",		counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",
	bond,'Bond',suffix=True)		bond,'Bond',suffix=True)
	counter += check_style('bond_style.rst',doc,":doc:`(.+) <bond.+>` -",		counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",
	bond,'Bond',suffix=False)		bond,'Bond',suffix=False)
	counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <angle.+>`",		counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",
	angle,'Angle',suffix=True)		angle,'Angle',suffix=True)
	counter += check_style('angle_style.rst',doc,":doc:`(.+) <angle.+>` -",		counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",
	angle,'Angle',suffix=False)		angle,'Angle',suffix=False)
	counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <dihedral.+>`",		counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",
	dihedral,'Dihedral',suffix=True)		dihedral,'Dihedral',suffix=True)
	counter += check_style('dihedral_style.rst',doc,":doc:`(.+) <dihedral.+>` -",		counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",
	dihedral,'Dihedral',suffix=False)		dihedral,'Dihedral',suffix=False)
	counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <improper.+>`",		counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",
	improper,'Improper',suffix=True)		improper,'Improper',suffix=True)
	counter += check_style('improper_style.rst',doc,":doc:`(.+) <improper.+>` -",		counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",
	improper,'Improper',suffix=False)		improper,'Improper',suffix=False)
	counter += check_style('Commands_kspace.rst',doc,":doc:`(.+) <kspace_style>`",		counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",
	kspace,'KSpace',suffix=True)		kspace,'KSpace',suffix=True)

	if counter:		if counter:

lib/gpu/lal_ufm.cpp

+15 −16

Original line number	Original line	Diff line number	Diff line
	@@ -48,7 +48,7 @@ template <class numtyp, class acctyp>
	int UFMT::init(const int ntypes,		int UFMT::init(const int ntypes,
	double host_cutsq, double host_uf1,		double host_cutsq, double host_uf1,
	double host_uf2, double host_uf3,		double host_uf2, double host_uf3,
	double host_uf4, double host_offset,		double **host_offset,
	double *host_special_lj, const int nlocal,		double *host_special_lj, const int nlocal,
	const int nall, const int max_nbors,		const int nall, const int max_nbors,
	const int maxspecial, const double cell_size,		const int maxspecial, const double cell_size,
	@@ -81,7 +81,7 @@ int UFMT::init(const int ntypes,
	host_cutsq);		host_cutsq);

	uf3.alloc(lj_typeslj_types,(this->ucl_device),UCL_READ_ONLY);		uf3.alloc(lj_typeslj_types,(this->ucl_device),UCL_READ_ONLY);
	this->atom->type_pack4(ntypes,lj_types,uf3,host_write,host_uf3,host_uf4,		this->atom->type_pack4(ntypes,lj_types,uf3,host_write,host_uf3,host_uf2,
	host_offset);		host_offset);

	UCL_H_Vec<double> dview;		UCL_H_Vec<double> dview;
	@@ -96,8 +96,7 @@ int UFMT::init(const int ntypes,

	template <class numtyp, class acctyp>		template <class numtyp, class acctyp>
	void UFMT::reinit(const int ntypes, double host_cutsq, double host_uf1,		void UFMT::reinit(const int ntypes, double host_cutsq, double host_uf1,
	double host_uf2, double host_uf3,		double host_uf2, double host_uf3, double **host_offset) {
	double host_uf4, double host_offset) {
	// Allocate a host write buffer for data initialization		// Allocate a host write buffer for data initialization
	UCL_H_Vec<numtyp> host_write(_lj_types_lj_types32,*(this->ucl_device),		UCL_H_Vec<numtyp> host_write(_lj_types_lj_types32,*(this->ucl_device),
	UCL_WRITE_ONLY);		UCL_WRITE_ONLY);
	@@ -107,7 +106,7 @@ void UFMT::reinit(const int ntypes, double host_cutsq, double host_uf1,

	this->atom->type_pack4(ntypes,_lj_types,uf1,host_write,host_uf1,host_uf2,		this->atom->type_pack4(ntypes,_lj_types,uf1,host_write,host_uf1,host_uf2,
	host_cutsq);		host_cutsq);
	this->atom->type_pack4(ntypes,_lj_types,uf3,host_write,host_uf3,host_uf4,		this->atom->type_pack4(ntypes,_lj_types,uf3,host_write,host_uf3,host_uf2,
	host_offset);		host_offset);
	}		}

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