def get_worker():
host = database.get_host()
idb = database.isolated_database()
idb.download()
for worker in idb.workers:
if worker.host == host:
return worker
print "Error: get_worker: %s is an unknown working host. Break." % host
exit(1)
def get_worker(): host=database.get_host() idb=database.isolated_database() idb.download() for worker in idb.workers: if worker.host==host: return worker print "Error: get_worker: %s is an unknown working host. Break." % host exit(1)
def main():
parser = argparse.ArgumentParser(description='Update database for energy shifts in EuO and substrate on remote database')
parser.add_argument('input', nargs='+', help='Folders containing results of isolated material runs or folders containing subfolders with results')
parser.add_argument('--dry', action='store_true', help='Simulate updating of database')
parser.add_argument('--archive', action='store_true', help='Archive all results')
args = parser.parse_args()
# get host
host=database.get_host()
idb=database.isolated_database()
idb.download()
found=False
serverdir=''
clientdir=''
for worker in idb.workers:
if host==worker.host:
serverdir=worker.serverdir
clientdir=worker.clientdir
found=True
if not found:
print "Error: Isolated database remote: Unknow host: %s" % host
print "Break."
exit(1)
# get path on steinschal-tradigist
inputs=[]
for ipath in args.input:
# get absolute path
apath=os.path.abspath(ipath)
if not apath.startswith(clientdir):
print "Error: Isolated database remote: %s is an unknown run path. Break." % apath
exit(1)
inputs.append(apath.replace(clientdir, serverdir, 1))
cmd='/users/stollenw/projects/euo/tools/euoscripts/isolated_update.py'
for inp in inputs:
cmd+=" %s" % inp
if args.dry:
cmd+=" --dry"
if args.archive:
cmd+=" --archive"
try:
rcmd=['ssh', 'steinschal-tradigist.th.physik.uni-bonn.de', '%s' % cmd]
subprocess.call(rcmd)
except:
print "Unable to update remote database. Break."
exit(1)
def __init__(self,
np,
material,
N=5,
M=None,
ni=0.01,
ncr=None,
dW=None,
output=None,
input=None,
initial_input=None,
inputFlag=True,
isoDeltaFlag=True,
updatedbFlag=True,
iteration_parameter=None,
get_default_iteration_parameter=None,
check_database=False,
source=None,
input_system_name=None,
log='run',
verbose=True,
email='*****@*****.**',
mailcmd='mailx -s'):
# number of nodes
self.np = np
# material name
self.material = material
# number of left layers
self.N = N
# number of right layers
self.M = M
# number of charge carriers in the left system
self.ni = ni
# number of charge carriers in the right system
self.ncr = ncr
# workfunction difference between left and right system
self.dW = dW
# initial input folder
self.initial_input = initial_input
# search automatically for suitable input
self.inputFlag = inputFlag
# add isolated delta values automatically
self.isoDeltaFlag = isoDeltaFlag
# update databases after succesfful runs automatically
self.updatedbFlag = updatedbFlag
# additional parameter (like max2, wr1, etc.)
# user defined parameter (if not defined add nothing)
if iteration_parameter != None:
self.iteration_parameter = iteration_parameter
else:
self.iteration_parameter = ''
# function which gives the default iteration parameter depending on the material
# (only relevant for automatic isodelta runs)
if get_default_iteration_parameter != None:
self.get_default_iteration_parameter = get_default_iteration_parameter
else:
self.get_default_iteration_parameter = database.get_iteration_parameter
# check database before a run, if it exists don't run again
self.check_database = check_database
# source for searching suitable input ('local', 'remote' or None(=both))
self.source = source
# alternative system name which can serve as an input (only if source!=local)
self.input_system_name = input_system_name
# logfile name
self.log = log
# email address
self.email = email
# send intermediate notifications
self.verbose = verbose
# email command
self.mailcmd = mailcmd
# keep an instance of the system parameter class for later use
self.sp = system_parameter.system_parameter()
# keep an instance of bulk database for later use
self.bdb = database.bulk_database()
self.bdb.download()
# keep an instance of isolated database for later use
self.idb = database.isolated_database()
self.idb.download()
# keep an instance of heterostructure database for later use
self.hdb = database.heterostructure_database()
self.hdb.download()
# get material class
self.material_class = self.sp.get_system_by_name(
self.material).material_class
# get mpicmd
self.mpicmd = get_worker().mpicmd
# get name which defines the system
self.name = None
if self.material_class == 'bulk':
self.name = self.bdb.get_output(self.material, self.ni)
elif self.material_class == 'isolated':
self.name = self.idb.get_output(self.material, self.N, self.ni)
else:
self.name = self.hdb.get_output(self.material, self.N, self.M,
self.ni, self.ncr, self.dW)
# set top output folder to current working directory by default
if output == None:
if self.material_class == 'bulk':
self.output = self.bdb.get_output(self.material, self.ni)
elif self.material_class == 'isolated':
self.output = self.idb.get_output(self.material, self.N,
self.ni)
else:
self.output = self.hdb.get_output(self.material, self.N,
self.M, self.ni, self.ncr,
self.dW)
else:
self.output = output
# set top input search folder to output folder by default
if input == None:
self.input = self.output
else:
self.input = input
# host
self.host = database.get_host()
def main():
parser = argparse.ArgumentParser(
description='Update database for bulk results')
parser.add_argument(
'input',
nargs='*',
help=
'Folders containing results of bulk runs or folders containing subfolders with results'
)
parser.add_argument('--dry',
action='store_true',
help='Simulate updating of database')
parser.add_argument('--archive',
action='store_true',
help='Archive all results')
args = parser.parse_args()
# get host
host = database.get_host()
bdb = database.bulk_database()
bdb.download()
found = False
serverdir = ''
clientdir = ''
for worker in bdb.workers:
if host == worker.host:
serverdir = worker.serverdir
clientdir = worker.clientdir
found = True
if not found:
print "Error: Bulk database remote: Unknow host: %s" % host
print "Break."
exit(1)
# get path on steinschal-tradigist
inputs = []
for ipath in args.input:
# get absolute path
apath = os.path.abspath(ipath)
if not apath.startswith(clientdir):
print "Error: Bulk database remote: %s is an unknown run path. Break." % apath
exit(1)
inputs.append(apath.replace(clientdir, serverdir, 1))
cmd = '/users/stollenw/projects/euo/tools/euoscripts/bulk_update.py'
for inp in inputs:
cmd += " %s" % inp
if args.dry:
cmd += " --dry"
if args.archive:
cmd += " --archive"
try:
rcmd = [
'ssh', 'steinschal-tradigist.th.physik.uni-bonn.de',
'%s' % cmd
]
subprocess.call(rcmd)
except:
print "Unable to update remote database. Break."
exit(1)
def __init__(self, np, material, N=5, M=None, ni=0.01, ncr=None, dW=None, output=None, input=None, initial_input=None, inputFlag=True, isoDeltaFlag=True, updatedbFlag=True, iteration_parameter=None, get_default_iteration_parameter=None, check_database=False, source=None, input_system_name=None, log='run', verbose=True, email='*****@*****.**', mailcmd='mailx -s'):
# number of nodes
self.np=np
# material name
self.material=material
# number of left layers
self.N=N
# number of right layers
self.M=M
# number of charge carriers in the left system
self.ni=ni
# number of charge carriers in the right system
self.ncr=ncr
# workfunction difference between left and right system
self.dW=dW
# initial input folder
self.initial_input=initial_input
# search automatically for suitable input
self.inputFlag=inputFlag
# add isolated delta values automatically
self.isoDeltaFlag=isoDeltaFlag
# update databases after succesfful runs automatically
self.updatedbFlag=updatedbFlag
# additional parameter (like max2, wr1, etc.)
# user defined parameter (if not defined add nothing)
if iteration_parameter!=None:
self.iteration_parameter=iteration_parameter
else:
self.iteration_parameter=''
# function which gives the default iteration parameter depending on the material
# (only relevant for automatic isodelta runs)
if get_default_iteration_parameter!=None:
self.get_default_iteration_parameter=get_default_iteration_parameter
else:
self.get_default_iteration_parameter=database.get_iteration_parameter
# check database before a run, if it exists don't run again
self.check_database=check_database
# source for searching suitable input ('local', 'remote' or None(=both))
self.source=source
# alternative system name which can serve as an input (only if source!=local)
self.input_system_name=input_system_name
# logfile name
self.log=log
# email address
self.email=email
# send intermediate notifications
self.verbose=verbose
# email command
self.mailcmd=mailcmd
# keep an instance of the system parameter class for later use
self.sp=system_parameter.system_parameter()
# keep an instance of bulk database for later use
self.bdb=database.bulk_database()
self.bdb.download()
# keep an instance of isolated database for later use
self.idb=database.isolated_database()
self.idb.download()
# keep an instance of heterostructure database for later use
self.hdb=database.heterostructure_database()
self.hdb.download()
# get material class
self.material_class=self.sp.get_system_by_name(self.material).material_class
# get mpicmd
self.mpicmd=get_worker().mpicmd
# get name which defines the system
self.name=None
if self.material_class=='bulk':
self.name=self.bdb.get_output(self.material, self.ni)
elif self.material_class=='isolated':
self.name=self.idb.get_output(self.material, self.N, self.ni)
else:
self.name=self.hdb.get_output(self.material, self.N, self.M, self.ni, self.ncr, self.dW)
# set top output folder to current working directory by default
if output==None:
if self.material_class=='bulk':
self.output=self.bdb.get_output(self.material, self.ni)
elif self.material_class=='isolated':
self.output=self.idb.get_output(self.material, self.N, self.ni)
else:
self.output=self.hdb.get_output(self.material, self.N, self.M, self.ni, self.ncr, self.dW)
else:
self.output=output
# set top input search folder to output folder by default
if input==None:
self.input=self.output
else:
self.input=input
# host
self.host=database.get_host()
def main():
parser = argparse.ArgumentParser(description='Calculate conductivity out of euo program results')
parser.add_argument('-d', '--database', help='specify database')
parser.add_argument('-s', '--dataset', nargs='+', help='specify dataset without temperature')
parser.add_argument('-n', '--np', default=1, help='Number of processes for parallel use', type=int)
parser.add_argument('-i', '--input', help='Input folder containing result of a single run.')
parser.add_argument('-o', '--output', default=None, help='Output Folder for the single run results (optional, default=input)')
parser.add_argument('--no_isodelta_db', action='store_false', help='No fetching of more accurate isodeltas in the case of heterostructures')
parser.add_argument('--no_overwrite', action="store_true", help='recalculate conductivity, even if it is present in the database')
#parser.add_argument('--force_download', action="store_true", help='Download *all* results from database, even if they exist in the current folder')
args = parser.parse_args()
# remote or steinschal-tradigist
host=database.get_host()
# get mpi run command depening on host
mpicmd=get_worker().mpicmd
# add current working directory to system path
sys.path.append(os.getcwd())
if not args.input==None:
getcond(args.input, np=args.np, isodeltadb=args.no_isodelta_db, outputFolder=args.output)
else:
if not args.database in ('bulk', 'isolated', 'hetero'):
print "Database must be 'bulk', 'isolated' or 'hetero'"
exit(1)
db=None
corenames=None
isodeltadb=False
if args.database=='bulk':
db=database.bulk_database()
corenames=('material', 'ni', 'T')
filenames=("cond.dat", "resist.dat")
top_result_folder = "/users/stollenw/projects/euo/results/bulk/"
elif args.database=='isolated':
db=database.isolated_database()
corenames=('material', 'N', 'ni', 'T')
top_result_folder = "/users/stollenw/projects/euo/results/isolated/"
filenames=("cond.dat", "resist.dat", "cond_perp.dat", "resist_perp.dat", "cond_perp_matrix.dat", "resist_perp_matrix.dat")
else:
db=database.heterostructure_database()
corenames=('material', 'N', 'M', 'ni', 'ncr', 'dW', 'T')
top_result_folder = "/users/stollenw/projects/euo/results/heterostructure/"
filenames=("cond.dat", "resist.dat", "cond_perp.dat", "resist_perp.dat", "cond_perp_matrix.dat", "resist_perp_matrix.dat")
isodeltadb=args.no_isodelta_db
db.download()
# get filtered data, i.e. reduce according to args.dataset (if not given, only sort)
filtered_data=database.filtrate(db.data, corenames, args.dataset)
for fd in filtered_data:
print fd
result_folder = fd[-1] + "/"
# check if conductivity calculation was already performed
print "check existence ..."
exists=check_file_exists(host, '%s/results/%s' % (result_folder, filenames[0]))
# calculate conductivity if necessary or forced
if not exists or not args.no_overwrite:
print "calculate conductivity ..."
getcondremote(host, db, filenames, result_folder, mpicmd, args.np, isodeltadb)