Merge branch 'master' into multi-comm-tiled (f4aede49) · Commits · 郑智淋 / lammps

.github/codecov.yml

0 → 100644

+29 −0

Original line number	Diff line number	Diff line
		comment: false
		coverage:
		notify:
		slack:
		default:
		url: "secret:HWZbvgtc6OD7F3v3PfrK3/rzCJvScbh69Fi1CkLwuHK0+wIBIHVR+Q5i7q6F9Ln4OChbiRGtYAEUUsT8/jmBu4qDpIi8mx746codc0z/Z3aafLd24pBrCEPLvdCfIZxqPnw3TuUgGhwmMDZf0+thg8YNUr/MbOZ7Li2L6+ZbYuA="
		threshold: 10%
		only_pulls: false
		branches:
		- "master"
		flags:
		- "unit"
		paths:
		- "src"
		status:
		project:
		default:
		branches:
		- "master"
		paths:
		- "src"
		informational: true
		patch:
		default:
		branches:
		- "master"
		paths:
		- "src"
		informational: true

cmake/Modules/Testing.cmake

+9 −6

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

doc/src/Errors_warnings.rst

+18 −0

Original line number	Diff line number	Diff line
		@@ -118,6 +118,24 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
		incorrect periodic images of atoms in interaction lists. To avoid, either use
		:doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.

		Communication cutoff is shorter than a bond length based estimate. This may lead to errors.

		Since LAMMPS stores topology data with individual atoms, all atoms
		comprising a bond, angle, dihedral or improper must be present on any
		sub-domain that "owns" the atom with the information, either as a
		local or a ghost atom. The communication cutoff is what determines up
		to what distance from a sub-domain boundary ghost atoms are created.
		The communication cutoff is by default the largest non-bonded cutoff
		plus the neighbor skin distance, but for short or non-bonded cutoffs
		and/or long bonds, this may not be sufficient. This warning indicates
		that there is an increased risk of a simulation stopping unexpectedly
		because of Bond/Angle/Dihedral/Improper atoms missing. It can be
		silenced by manually setting the communication cutoff via
		:doc:`comm_modify cutoff <comm_modify>`. However, since the
		heuristic used to determine the estimate is not always accurate, it
		is not changed automatically and the warning may be ignored depending
		on the specific system being simulated.

		Communication cutoff is too small for SNAP micro load balancing, increased to %lf
		Self-explanatory.

doc/src/pair_ufm.rst

+2 −4

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

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

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

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

doc/utils/check-packages.py

+56 −52

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

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

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

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

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

		args = parser.parse_args()
		verbose = args.verbose
		src = args.src
		doc = args.doc
		src_dir = args.src
		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()
		sys.exit(1)

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

		if not os.path.isdir(doc):
		sys.exit("LAMMPS documentation source path %s does not exist" % doc)
		if not os.path.isdir(doc_dir):
		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-]+)$")
		user = re.compile("USER-.*")

		@@ -46,52 +52,50 @@ usrpkg = []

		for d in pkgdirs:
		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
		if pkg in ['DEPEND','MAKE','STUBS']: continue
		if user.match(pkg):
		usrpkg.append(pkg)
		else:
		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
		fp = open(os.path.join(doc,'Packages_standard.rst'))

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

		matches = set(re.findall(':ref:`(USER-[A-Z0-9]+) <PKG-\\1>`', text, re.MULTILINE))
		for p in usrpkg:
		if not p in matches:
		++counter
		print("User package %s missing in Packages_details.rst"
		% p)
		counter +=1
		print(f"User package {p} missing in Packages_details.rst")

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

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