diff --git a/lib/kim/Install.py b/lib/kim/Install.py index aa244ee6e..0e8738895 100644 --- a/lib/kim/Install.py +++ b/lib/kim/Install.py @@ -1,317 +1,257 @@ #!/usr/bin/env python # install.py tool to download, compile, and 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 # help message help = """ Syntax from src dir: make lib-kim args="-b -v version -a kim-name" or: make lib-kim args="-b -a everything" or: make lib-kim args="-n -a kim-name" or: make lib-kim args="-p /usr/local/open-kim -a kim-name" Syntax from lib dir: python Install.py -b -v version -a kim-name or: python Install.py -b -a everything or: python Install.py -n -a kim-name or: python Install.py -p /usr/local/open-kim -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) + default = kim-api-v1.9.2 (current as of Oct 2017) -b = download and build base KIM API library with example Models this will delete any previous installation in the current folder -n = do NOT download and build base KIM API library. Use an existing installation -p = specify location of KIM API installation (implies -n) -a = add single KIM model or model driver with kim-name to existing KIM API lib (see example below). If kim-name = everything, then rebuild KIM API library with *all* available OpenKIM Models (make take a long time). -vv = be more verbose about what is happening while the script runs Examples: make lib-kim args="-b" # install KIM API lib with only example models make lib-kim args="-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="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # only add one model or model driver See the list of KIM model drivers here: https://openkim.org/kim-items/model-drivers/alphabetical See the list of all KIM models here: https://openkim.org/kim-items/models/by-model-drivers See the list of example KIM models included by default here: https://openkim.org/kim-api in the "What is in the KIM API source package?" section """ def error(str=None): if not str: print(help) else: print("ERROR",str) sys.exit() # 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:] nargs = len(args) if nargs == 0: error() thisdir = os.environ['PWD'] -version = "kim-api-v1.8.2" +version = "kim-api-v1.9.2" buildflag = False everythingflag = False addflag = False verboseflag = False pathflag = False iarg = 0 while iarg < len(args): if args[iarg] == "-v": if iarg+2 > len(args): error() version = args[iarg+1] iarg += 2 elif args[iarg] == "-b": buildflag = True iarg += 1 elif args[iarg] == "-n": buildflag = False iarg += 1 elif args[iarg] == "-p": if iarg+2 > len(args): error() kimdir = fullpath(args[iarg+1]) pathflag = True buildflag = False iarg += 2 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) -url = "https://s3.openkim.org/kim-api/%s.tgz" % version +url = "https://s3.openkim.org/kim-api/%s.txz" % version # set KIM API directory if pathflag: if not os.path.isdir(kimdir): print("\nkim-api is not installed at %s" % kimdir) error() # configure LAMMPS to use existing kim-api installation with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile: mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir) mkfile.write(".DUMMY: print_dir\n\n") mkfile.write("print_dir:\n") mkfile.write(" @printf $(KIM_INSTALL_DIR)\n") with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile: cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir) print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir)) else: kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version) # download KIM tarball, unpack, build KIM if buildflag: # check to see if an installed kim-api already exists and wipe it out. if os.path.isdir(kimdir): print("kim-api is already installed at %s.\nRemoving it for re-install" % kimdir) cmd = 'rm -rf "%s"' % kimdir subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) # configure LAMMPS to use kim-api to be installed with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile: mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir) mkfile.write(".DUMMY: print_dir\n\n") mkfile.write("print_dir:\n") mkfile.write(" @printf $(KIM_INSTALL_DIR)\n") with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile: cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir) print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir)) # download entire kim-api tarball print("Downloading kim-api tarball ...") - geturl(url,"%s/%s.tgz" % (thisdir,version)) + geturl(url,"%s/%s.txz" % (thisdir,version)) print("Unpacking kim-api tarball ...") - cmd = 'cd "%s"; rm -rf "%s"; tar -xzvf %s.tgz' % (thisdir,version,version) + cmd = 'cd "%s"; rm -rf "%s"; tar -xJvf %s.txz' % (thisdir,version,version) 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,kimdir) subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) # build kim-api - - print("Configuring example Models") - cmd = 'cd "%s/%s"; make add-examples' % (thisdir,version) - 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) 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) 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) - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - if verboseflag: print(txt.decode("UTF-8")) - # remove source files + print("Building and installing example Models") + cmd = 'cd "%s/%s/examples"; make model-drivers-all-system' % (thisdir,version) + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + if verboseflag: print (txt.decode("UTF-8")) + cmd = 'cd "%s/%s/examples"; make models-all-system' % (thisdir,version) + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + if verboseflag: print (txt.decode("UTF-8")) + print("Removing kim-api source and build files ...") - cmd = 'cd "%s"; rm -rf %s; rm -rf %s.tgz' % (thisdir,version,version) + cmd = 'cd "%s"; rm -rf %s; rm -rf %s.txz' % (thisdir,version,version) subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) -# add a single model (and possibly its driver) to existing KIM installation + # add all OpenKIM models, if desired + if everythingflag: + print("Adding all OpenKIM models, this will take a while ...") + cmd = '%s/bin/kim-api-v1-collections-management install system OpenKIM' % (kimdir) + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + if verboseflag: print(txt.decode("UTF-8")) +# add single OpenKIM model if addflag: if not os.path.isdir(kimdir): print("\nkim-api is not installed") error() # download single model - - 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 -xzvf %s.tgz' % (thisdir,addmodelname) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - - print("Building item ...") - cmd = 'cd "%s/%s"; make; make install' %(thisdir,addmodelname) - try: - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - except subprocess.CalledProcessError as e: - - # Error: but first, check to see if it needs a driver - 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("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("UTF-8").strip() - print("First installing model driver: %s..." % adddrivername) - cmd = 'cd "%s"; python Install.py -n -a %s' % (thisdir,adddrivername) - try: - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - except subprocess.CalledProcessError as e: - 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) - cmd = 'cd "%s"; python Install.py -n -a %s' % (thisdir,addmodelname) - try: - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - except subprocess.CalledProcessError as e: - print(e.output) - sys.exit() - print(txt.decode("UTF-8")) - sys.exit() - else: - print(firstRunOutput) - print("Error, unable to build and install OpenKIM item: %s" \ - % addmodelname) - sys.exit() - - # success the first time - - 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,stderr=subprocess.STDOUT,shell=True) + cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir, addmodelname) + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + if verboseflag: print (txt.decode("UTF-8")) diff --git a/lib/kim/Makefile.lammps b/lib/kim/Makefile.lammps index b66d7005a..d73891d1e 100644 --- a/lib/kim/Makefile.lammps +++ b/lib/kim/Makefile.lammps @@ -1,32 +1,32 @@ # This file contains the hooks to build and link LAMMPS with the OpenKIM # library so that a LAMMPS input script can use a KIM potential, via the # pair_style kim command. # # The KIM API package can be downloaded from https://openkim.org/kim-api # Follow the instructions in the INSTALL file to build and install the # KIM API. Add the openkim.org Models you are interested in using. # Make sure the directory where the "kim-api-build-conifg" utility is # located is on the PATH. # # As long as you have followed the KIM API build and install instructions, # there should not be any reason to change this file. # ----------------------------------------------------------- # Settings that the LAMMPS build will import when this package is installed include ../../lib/kim/Makefile.KIM_DIR -ifeq ($(wildcard $(KIM_INSTALL_DIR)/bin/kim-api-build-config),) - KIM_CONFIG_HELPER = kim-api-build-config +ifeq ($(wildcard $(KIM_INSTALL_DIR)/bin/kim-api-v1-build-config),) + KIM_CONFIG_HELPER = kim-api-v1-build-config else - KIM_CONFIG_HELPER = $(KIM_INSTALL_DIR)/bin/kim-api-build-config + KIM_CONFIG_HELPER = $(KIM_INSTALL_DIR)/bin/kim-api-v1-build-config endif ifeq ($(shell $(KIM_CONFIG_HELPER) --version 2> /dev/null),) $(error $(KIM_CONFIG_HELPER) utility is not available. Something is wrong with your KIM API package setup) endif kim_SYSINC = $(shell $(KIM_CONFIG_HELPER) --includes) kim_SYSLIB = $(shell $(KIM_CONFIG_HELPER) --ldlibs) kim_SYSPATH = $(shell $(KIM_CONFIG_HELPER) --ldflags)