Merge branch 'kim-install' into install-and-docs-reviewed (e7d9aabc) · Commits · 郑智淋 / lammps

doc/src/pair_kim.txt

+27 −6

Original line number	Diff line number	Diff line
		@@ -27,13 +27,34 @@ pair_coeff * * Ar Ar :pre
		[Description:]

		This pair style is a wrapper on the "Knowledge Base for Interatomic
		Models (KIM)"_https://openkim.org repository of interatomic potentials,
		so that they can be used by LAMMPS scripts.
		Models (OpenKIM)"_https://openkim.org repository of interatomic
		potentials, so that they can be used by LAMMPS scripts.

		In KIM lingo, a potential is a "model" and a model contains both the
		analytic formulas that define the potential as well as the parameters
		needed to run it for one or more materials, including coefficients and
		cutoffs.
		Note that in LAMMPS lingo, a KIM model driver is a pair style
		(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
		element or alloy and set of parameters, e.g. EAM for Cu with a
		specific EAM potential file.

		See the current list of "KIM model
		drivers"_https://openkim.org/kim-items/model-drivers/alphabetical.

		See the current list of all "KIM
		models"_https://openkim.org/kim-items/models/by-model-drivers

		See the list of "example KIM models"_https://openkim.org/kim-api which
		are included in the KIM library by default, in the "What is in the KIM
		API source package?" section.

		To use this pair style, you must first download and install the KIM
		API library from the "OpenKIM website"_https://openkim.org. The "KIM
		section of Section packages"_Section_packages.html#kim-package has
		instructions on how to do this with a simple make command, when
		building LAMMPS.

		See the examples/kim dir for an input script that uses a KIM model
		(potential) for Lennard-Jones.

		:line

		The argument {virialmode} determines how the global virial is
		calculated. If {KIMvirial} is specified, the KIM model performs the

lib/kim/Install.py

+54 −46

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

		# install.pa tool to setup the kim-api library
		# install.py tool to setup the kim-api library
		# used to automate the steps described in the README file in this dir
		from __future__ import print_function
		import sys,os,re,subprocess
		@@ -8,28 +8,25 @@ try: from urllib.request import urlretrieve as geturl
		except: from urllib import urlretrieve as geturl

		help = """
		Syntax from src dir: make lib-kim args="-v version -b kim-install-dir kim-name -a kim-name"
		Syntax from lib dir: python Install.py -v version -b kim-install-dir kim-name -a kim-name
		Syntax from src dir: make lib-kim args="-v version -b -a kim-name"
		Syntax from lib dir: python Install.py -v version -b -a kim-name

		specify one or more options, order does not matter

		-v = version of KIM API library to use
		default = kim-api-v1.8.2 (current as of June 2017)
		-b = download and build KIM API library with KIM models
		kim-dir = where to install/build the KIM API library
		use "." to install in lib/kim
		kim-name = none to install only the example KIM models
		kim-name = KIM model name (see example below) + examples
		kim-name = OpenKIM to install all models
		from the openkim.org site (this can take 30 minutes or more)
		-b = download and build KIM API library with example Models
		-a = add single KIM model or model driver with kim-name
		to existing KIM API lib (see example below)
		to existing KIM API lib (see example below).
		If kim-name = everything, then rebuild KIM API library with
		all available OpenKIM Models (this implies -b).
		-vv = be more verbose about what is happening while the script runs

		Examples:

		make lib-kim args="-b . none" # install KIM API lib with only example models
		make lib-kim args="-b . Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
		make lib-kim args="-b . OpenKIM" # install KIM API lib with all models
		make lib-kim args="-b" # install KIM API lib with only example models
		make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # Ditto plus one model
		make lib-kim args="-b -a everything" # install KIM API lib with all models
		make lib-kim args="-a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver

		See the list of KIM model drivers here:
		@@ -57,7 +54,9 @@ thisdir = os.environ['PWD']
		version = "kim-api-v1.8.2"

		buildflag = False
		everythingflag = False
		addflag = False
		verboseflag = False

		iarg = 0
		while iarg < len(args):
		@@ -67,15 +66,19 @@ while iarg < len(args):
		iarg += 2
		elif args[iarg] == "-b":
		buildflag = True
		if iarg+3 > len(args): error()
		dir = args[iarg+1]
		modelname = args[iarg+2]
		iarg += 3
		iarg += 1
		elif args[iarg] == "-a":
		addflag = True
		if iarg+2 > len(args): error()
		addmodelname = args[iarg+1]
		if addmodelname == "everything":
		buildflag = True
		everythingflag = True
		addflag = False
		iarg += 2
		elif args[iarg] == "-vv":
		verboseflag = True
		iarg += 1
		else: error()

		thisdir = os.path.abspath(thisdir)
		@@ -88,14 +91,14 @@ if buildflag:

		# set install directory

		dir = os.path.join(os.path.abspath(dir), "installed-" + version)
		dir = os.path.join(os.path.abspath(thisdir), "installed-" + version)

		# check to see if an installed kim-api already exists and wipe it out.

		if os.path.isdir(dir):
		print("kim-api is already installed at %s.\nRemoving it for re-install" % dir)
		cmd = "rm -rf %s" % dir
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

		# configure LAMMPS to use kim-api to be installed

		@@ -116,44 +119,48 @@ if buildflag:
		geturl(url,"%s/%s.tgz" % (thisdir,version))
		print("Unpacking kim-api tarball ...")
		cmd = "cd %s; rm -rf %s; tar zxvf %s.tgz" % (thisdir,version,version)
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

		# configure kim-api

		print("Configuring kim-api ...")
		cmd = "cd %s/%s; ./configure --prefix='%s'" % (thisdir,version,dir)
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

		# build kim-api

		print("Configuring model : %s" % modelname)
		if modelname == "none":
		print("Configuring example Models")
		cmd = "cd %s/%s; make add-examples" % (thisdir,version)
		else:
		if modelname == "OpenKIM":
		print("configuring all OpenKIM models, this will take a while ...")
		cmd = "cd %s/%s; make add-examples; make add-%s" % \
		(thisdir,version,modelname)
		subprocess.check_output(cmd,shell=True)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if verboseflag: print (txt.decode("UTF-8"))

		if everythingflag:
		print("Configuring all OpenKIM models, this will take a while ...")
		cmd = "cd %s/%s; make add-OpenKIM" % (thisdir,version)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if verboseflag: print(txt.decode("UTF-8"))

		print("Building kim-api ...")
		cmd = "cd %s/%s; make" % (thisdir,version)
		subprocess.check_output(cmd,shell=True)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if verboseflag: print(txt.decode("UTF-8"))

		# install kim-api

		print("Installing kim-api ...")
		cmd = "cd %s/%s; make install" % (thisdir,version)
		subprocess.check_output(cmd,shell=True)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if verboseflag: print(txt.decode("UTF-8"))

		cmd = "cd %s/%s; make install-set-default-to-v1" %(thisdir,version)
		subprocess.check_output(cmd,shell=True)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if verboseflag: print(txt.decode("UTF-8"))

		# remove source files

		print("Removing kim-api source and build files ...")
		cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" % (thisdir,version,version)
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

		# add a single model (and possibly its driver) to existing KIM installation

		@@ -166,19 +173,18 @@ if addflag:
		error()
		else:
		cmd = "cd %s; make -f Makefile.KIM_DIR print_dir" % thisdir
		dir = subprocess.check_output(cmd,shell=True)[1]
		dir = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)[1]

		# download single model
		# try first via urllib
		# if fails (probably due to no SSL support), use wget

		print("Downloading item tarball ...")
		print("Downloading tarball for %s..." % addmodelname)
		url = "https://openkim.org/download/%s.tgz" % addmodelname
		geturl(url,"%s/%s.tgz" % (thisdir,addmodelname))

		print("Unpacking item tarball ...")
		cmd = "cd %s; tar zxvf %s.tgz" % (thisdir,addmodelname)
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

		print("Building item ...")
		cmd = "cd %s/%s; make; make install" %(thisdir,addmodelname)
		@@ -187,19 +193,19 @@ if addflag:
		except subprocess.CalledProcessError as e:

		# Error: but first, check to see if it needs a driver
		firstRunOutput = e.output.decode()
		firstRunOutput = e.output.decode("UTF-8")

		cmd = "cd %s/%s; make kim-item-type" % (thisdir,addmodelname)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		txt = txt.decode().strip()
		txt = txt.decode("UTF-8")
		if txt == "ParameterizedModel":

		# Get and install driver

		cmd = "cd %s/%s; make model-driver-name" % (thisdir,addmodelname)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		adddrivername = txt.decode().strip()
		print("First installing model driver: %s" % adddrivername)
		adddrivername = txt.decode("UTF-8").strip()
		print("First installing model driver: %s..." % adddrivername)
		cmd = "cd %s; python Install.py -a %s" % (thisdir,adddrivername)
		try:
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		@@ -207,6 +213,8 @@ if addflag:
		print(e.output)
		sys.exit()

		if verboseflag: print(txt.decode("UTF-8"))

		# now install the model that needed the driver

		print("Now installing model : %s" % addmodelname)
		@@ -216,7 +224,7 @@ if addflag:
		except subprocess.CalledProcessError as e:
		print(e.output)
		sys.exit()
		print(txt.decode())
		print(txt.decode("UTF-8"))
		sys.exit()
		else:
		print(firstRunOutput)
		@@ -226,7 +234,7 @@ if addflag:

		# success the first time

		print(txt)
		if verboseflag: print(txt.decode("UTF-8"))
		print("Removing kim item source and build files ...")
		cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" %(thisdir,addmodelname,addmodelname)
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

lib/voronoi/.gitignore

0 → 100644

+4 −0

Original line number	Diff line number	Diff line
		# files to ignore
		/liblink
		/includelink
		/voro++-*

lib/voronoi/Install.py

+37 −39

Original line number	Diff line number	Diff line
		@@ -10,27 +10,23 @@ except: from urllib import urlretrieve as geturl
		# help message

		help = """
		Syntax from src dir: make lib-voronoi args="-v version -h hpath hdir -g -b -l"
		Syntax from lib dir: python Install.py -v version -h hpath hdir -g -b -l
		Syntax from src dir: make lib-voronoi
		or: make lib-voronoi args="-p /usr/local/voro++-0.4.6"
		or: make lib-voronoi args="-v voro++-0.4.6 -b"
		Syntax from lib dir: python Install.py -v voro++-0.4.6 -b
		or: python Install.py
		or: python Install.py -p /usr/local/voro++-0.4.6

		specify one or more options, order does not matter

		-b = download and build the Voro++ library (default)
		-p = specify folder of existing Voro++ installation
		-v = version of Voro++ to download and build
		default version = voro++-0.4.6 (current as of Jan 2015)
		-h = set home dir of Voro++ to be hpath/hdir
		hpath can be full path, contain '~' or '.' chars
		default hpath = . = lib/voronoi
		default hdir = voro++-0.4.6 = what tarball unpacks to
		-g = grab (download) tarball from math.lbl.gov/voro++ website
		unpack it to hpath/hdir
		hpath must already exist
		if hdir already exists, it will be deleted before unpack
		-b = build Voro++ library in its src dir
		-l = create 2 softlinks (includelink,liblink) in lib/voronoi to Voro++ src dir

		Example:

		make lib-voronoi args="-g -b -l" # download/build in lib/voronoi/voro++-0.4.6
		make lib-voronoi args="-b" # download/build in lib/voronoi/voro++-0.4.6
		"""

		# settings
		@@ -60,9 +56,10 @@ if nargs == 0: error()
		homepath = "."
		homedir = version

		grabflag = False
		buildflag = False
		linkflag = False
		grabflag = True
		buildflag = True
		pathflag = False
		linkflag = True

		iarg = 0
		while iarg < nargs:
		@@ -70,25 +67,26 @@ while iarg < nargs:
		if iarg+2 > nargs: error()
		version = args[iarg+1]
		iarg += 2
		elif args[iarg] == "-h":
		if iarg+3 > nargs: error()
		homepath = args[iarg+1]
		homedir = args[iarg+2]
		iarg += 3
		elif args[iarg] == "-g":
		grabflag = True
		iarg += 1
		elif args[iarg] == "-p":
		if iarg+2 > nargs: error()
		voropath = fullpath(args[iarg+1])
		pathflag = True
		buildflag = False
		iarg += 2
		elif args[iarg] == "-b":
		buildflag = True
		iarg += 1
		elif args[iarg] == "-l":
		linkflag = True
		iarg += 1
		else: error()

		homepath = fullpath(homepath)
		if not os.path.isdir(homepath): error("Voro++ path does not exist")
		homedir = "%s/%s" % (homepath,homedir)
		homedir = "%s/%s" % (homepath,version)

		if (pathflag):
		if not os.path.isdir(voropath): error("Voro++ path does not exist")
		homedir = voropath

		if (buildflag and pathflag):
		error("Cannot use -b and -p flag at the same time")

		# download and unpack Voro++ tarball

		@@ -99,13 +97,13 @@ if grabflag:
		print("Unpacking Voro++ tarball ...")
		if os.path.exists("%s/%s" % (homepath,version)):
		cmd = 'rm -rf "%s/%s"' % (homepath,version)
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version)
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		if os.path.basename(homedir) != version:
		if os.path.exists(homedir):
		cmd = 'rm -rf "%s"' % homedir
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		os.rename("%s/%s" % (homepath,version),homedir)

		# build Voro++
		@@ -113,8 +111,8 @@ if grabflag:
		if buildflag:
		print("Building Voro++ ...")
		cmd = 'cd "%s"; make' % homedir
		txt = subprocess.check_output(cmd,shell=True)
		print(txt)
		txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		print(txt.decode('UTF-8'))

		# create 2 links in lib/voronoi to Voro++ src dir

		@@ -125,6 +123,6 @@ if linkflag:
		if os.path.isfile("liblink") or os.path.islink("liblink"):
		os.remove("liblink")
		cmd = ['ln -s "%s/src" includelink' % homedir, 'includelink']
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
		cmd = ['ln -s "%s/src" liblink' % homedir]
		subprocess.check_output(cmd,shell=True)
		subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

lib/voronoi/README

+1 −1

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