diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index 5a623e5ece39d4b482b9fa11a40921639df4b938..5ee607c2b090decb758af797419290a4a68444c3 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -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 diff --git a/lib/kim/Install.py b/lib/kim/Install.py index 1405cc5fade86aa78695f6447378a4a5f3abd8b7..1d022a58755c0f791aa99adf7acb54f967bc3a3b 100644 --- a/lib/kim/Install.py +++ b/lib/kim/Install.py @@ -1,6 +1,6 @@ #!/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": - 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) + 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) - 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) diff --git a/lib/voronoi/.gitignore b/lib/voronoi/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..6ca01c094f57a17dd29df3d78128897b4fcf9854 --- /dev/null +++ b/lib/voronoi/.gitignore @@ -0,0 +1,4 @@ +# files to ignore +/liblink +/includelink +/voro++-* diff --git a/lib/voronoi/Install.py b/lib/voronoi/Install.py index 1c4bc5cb6d8fbc33404269dc45d32d721ea047c1..285e11fb9ab8fc5fcbe410f36123921c52c91412 100644 --- a/lib/voronoi/Install.py +++ b/lib/voronoi/Install.py @@ -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 @@ -47,10 +43,10 @@ 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)) - + # parse args args = sys.argv[1:] @@ -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: @@ -70,42 +67,43 @@ 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 if grabflag: print("Downloading Voro++ ...") geturl(url,"%s/%s.tar.gz" % (homepath,version)) - + 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) diff --git a/lib/voronoi/README b/lib/voronoi/README index 9863632be0d1ea7e3f5c4158197291a5cd43ab30..2ca11c9221a9f4751b739b9a71f484ba9b88bf1a 100644 --- a/lib/voronoi/README +++ b/lib/voronoi/README @@ -22,7 +22,7 @@ Instructions: or somewhere else on your system. 2. compile Voro++ from within its home directory - % make + % make 3. There is no need to install Voro++ if you only wish to use it from LAMMPS. You can install it if you