def database_exists(sp):
if sp.get_system().material_class == 'bulk':
bdb = database.bulk_database()
bdb.download()
if bdb.exists(sp.get_system().name, sp.concentration, sp.temperature):
return True
else:
return False
elif sp.get_system().material_class == 'isolated':
idb = database.isolated_database()
idb.download()
if idb.exists(sp.get_system().name, sp.N, sp.concentration,
sp.temperature):
return True
else:
return False
else:
hdb = database.heterostructure_database()
hdb.download()
if hdb.exists(sp.get_system().name, sp.N, sp.N0, sp.concentration,
sp.n_cr, sp.Delta_W, sp.temperature):
return True
else:
return False
def main():
parser = argparse.ArgumentParser(description='Update database for heterostructure runs')
parser.add_argument('input', nargs=2, help='Two database files')
parser.add_argument('-d', '--database', default='hetero', help='Database type: bulk, isolated or hetero (default)')
parser.add_argument('-r', '--reverse', action='store_true', help='reverse input file order')
args = parser.parse_args()
#print args.overwrite
#print args.input
#print args.database
if args.reverse:
args.input.reverse()
# initialize databases
d1=None
d2=None
length=None
if args.database=='hetero':
d1=database.heterostructure_database()
d2=database.heterostructure_database()
length=6
elif args.database=='isolated':
d1=database.isolated_database()
d2=database.isolated_database()
length=3
elif args.database=='bulk':
d1=database.bulk_database()
d2=database.bulk_database()
length=2
else:
print "Database type must be 'bulk', 'isolated' or 'hetero' (default). Break"
exit(1)
d1.download("[email protected]:%s" % args.input[0])
d2.download("[email protected]:%s" % args.input[1])
print "Datasets present in %s but not in %s:" % (args.input[0], args.input[1])
reduced_data2=[dset2[:length] for dset2 in d2.data]
for dset1 in d1.data:
if not dset1[:length] in reduced_data2:
print dset1[:-1]
def main():
dataset_help="""Specify dataset
e.g. "Metal-Metal-Heterostructure 5 9 0.01 0.01 0.125"
(for material, N, M, ni, ncr and dW).
You may use "all" as a placeholder or do not specify
the last values e.g. "all 5 all 0.01
"""
parser = argparse.ArgumentParser(description='Update database for heterostructure runs')
parser.add_argument('input', nargs='*', help='Folders containing results of heterostructure material runs or folders containing subfolders with results')
parser.add_argument('-d', '--database', default='/users/stollenw/projects/euo/database/hetero.db', help='Database file name')
parser.add_argument('-s', '--dataset', nargs='*', help=dataset_help)
parser.add_argument('--overwrite', action='store_true', help='Overwrite database')
parser.add_argument('--archive', action='store_true', help='Archive all results')
parser.add_argument('--archive_destination', default='/users/stollenw/projects/euo/results/heterostructure/', help='Archive folder')
parser.add_argument('--dry', action='store_true', help='Simulate updating of database')
args = parser.parse_args()
#print args.overwrite
#print args.input
#print args.database
# initialize database
t=database.heterostructure_database()
# read in database if it already exists and overwrite flag is not given
if os.path.exists(args.database) and not args.overwrite:
t.read(args.database)
if args.dataset==None:
t.fill(args.input, args.overwrite)
if not args.dry:
t.write(args.database)
if args.archive:
t.archive(args.archive_destination)
else:
for iput in args.input:
t.archive(args.archive_destination, None, os.path.abspath(iput))
else:
print "Archive folder would be: ", args.archive_destination
else:
t.archive(args.archive_destination, args.dataset)
def database_exists(sp): if sp.get_system().material_class=='bulk': bdb=database.bulk_database() bdb.download() if bdb.exists(sp.get_system().name, sp.concentration, sp.temperature): return True else: return False elif sp.get_system().material_class=='isolated': idb=database.isolated_database() idb.download() if idb.exists(sp.get_system().name, sp.N, sp.concentration, sp.temperature): return True else: return False else: hdb=database.heterostructure_database() hdb.download() if hdb.exists(sp.get_system().name, sp.N, sp.N0, sp.concentration, sp.n_cr, sp.Delta_W, sp.temperature): return True else: return False
def main():
parser = argparse.ArgumentParser(
description='Analyse euo program results',
formatter_class=argparse.RawTextHelpFormatter)
keyword_help = """Calculate the temperature dependent
quantity specified by one of the following keywords
print
print full
tc
occNum_c (for bulk)
dopant_activation (for bulk)
totalmag (for bulk)
cond (for bulk)
resist (for bulk)
avmag (for isolated and heterostructures)
cond_para (for isolated and heterostructures)
resist_para (for isolated and heterostructures)
cond_perp (for isolated and heterostructures)
resist_perp (for isolated and heterostructures)
isodelta (energy shift (-mu) for isolated systems)
"""
dataset_help = """Specify dataset
e.g. "Metal-Metal-Heterostructure 5 9 0.01 0.01 0.125"
(for material, N, M, ni, ncr and dW).
You may use "all" as a placeholder or do not specify
the last values e.g. "all 5 all 0.01
"""
parser.add_argument('keyword', help=keyword_help)
parser.add_argument(
'-d',
'--database',
help='Type of database: "bulk", "isolated" or "hetero"')
parser.add_argument('-s', '--dataset', nargs='*', help=dataset_help)
parser.add_argument('-o',
'--output',
default='/users/stollenw/projects/euo/analysis/',
help='Output folder (optional)')
parser.add_argument('--dbpath', help='Path to database file (optional)')
parser.add_argument('--resultpath',
default='/users/stollenw/projects/euo/results/',
help='Path to results (optional)')
parser.add_argument(
'--temperatures',
nargs='*',
default=None,
help='Tempertures for tc search (optional, only for tc)',
type=float)
parser.add_argument(
'--tsteps',
nargs='*',
default=None,
help='Temperture steps for tc search (optional, only for tc)',
type=float)
parser.add_argument(
'--dM',
default=None,
help='Magnetisation resolution for tc search (optional, only for tc)',
type=float)
parser.add_argument(
'--layer',
default=0,
help='Layer to calculate parallel conductivity/resistivity in',
type=int)
parser.add_argument(
'--layerx',
help='First layer for perpendicular conductivity/resistivity',
type=int)
parser.add_argument(
'--layery',
help='First layer for perpendicular conductivity/resistivity',
type=int)
args = parser.parse_args()
if not args.database in ('bulk', 'isolated', 'hetero'):
parser.print_help()
exit(0)
# allowed keywords
print_keywords = ['print', 'printfull']
simple_result_keywords = None
sophisticated_result_keywords = None
if args.database == 'bulk':
simple_result_keywords = ['cond', 'resist', 'totalmag']
sophisticated_result_keywords = ['tc', 'dopant_activation', 'occNum_c']
elif args.database == 'isolated' or args.database == 'hetero':
simple_result_keywords = ['avmag']
sophisticated_result_keywords = [
'cond_para', 'resist_para', 'cond_perp', 'resist_perp', 'isodelta',
'tc'
]
# keywords that produce results
result_keywords = simple_result_keywords + sophisticated_result_keywords
# all keywords (including print keywords)
allowed_keywords = simple_result_keywords + sophisticated_result_keywords + print_keywords
# check if valid keyword was given
if not args.keyword in allowed_keywords:
parser.print_help()
print "Allowed keywords are:"
for ak in allowed_keywords:
print ak
exit(0)
# set output
output = args.output
db = None
corenames = None
special = None
subResultFolder = None
if args.database == 'bulk':
db = database.bulk_database()
output = output + 'bulk/'
subResultFolder = 'bulk/'
corenames = ('material', 'ni', 'T')
special = 'mag'
elif args.database == 'isolated':
db = database.isolated_database()
output = output + 'isolated/'
subResultFolder = 'isolated/'
corenames = ('material', 'N', 'ni', 'T')
special = 'isodelta'
else:
db = database.heterostructure_database()
output = output + 'hetero/'
subResultFolder = 'heterostructure/'
corenames = ('material', 'N', 'M', 'ni', 'ncr', 'dW', 'T')
special = 'avmag'
if args.dbpath == None:
db.download()
else:
db.download("[email protected]:%s" %
args.dbpath)
resultFolder = args.resultpath
# get filtered data, i.e. reduce to defining properties without temperature
filtered_data = database.filtrate(db.data, corenames, args.dataset,
len(corenames) - 1)
# lower threshold for displaying results
min_result_number = 1
# extract conductivity or other observables
if args.keyword in result_keywords:
# temperatrue sweep only makes sense if there are at least two temperatures
min_result_number = 2
# create folder if necessary
suboutput = output + "/data/%s/" % args.keyword
if not os.path.exists(suboutput):
os.makedirs(suboutput)
# in the Curie temperature case, create single file for all datasets
outfile = ''
tcd = ''
tci = 0
if args.keyword == 'tc' or args.keyword == 'dopant_activation' or args.keyword == 'occNum_c':
if args.dataset == None:
print "Dataset needed for Curie temperature / dopant activation at T=5K / occNum at T=5K"
exit(1)
# check if number single attribute is filterd out
if (args.dataset.count('all') +
(len(corenames) - 1 - len(args.dataset)) > 1):
print "Dataset has to many degrees of freedom."
exit(1)
tcc = []
i = 0
for d, n in zip(args.dataset, corenames):
if d != 'all':
if n == 'material':
tcc.append(d)
elif n == 'N' or n == 'M':
tcc.append(n + "%03i" % int(d))
else:
tcc.append(n + "%06.4f" % float(d))
else:
tcd = n
tci = i
i = i + 1
if (tcd == ''):
tcd = corenames[-2]
tci = len(corenames) - 2
tcname = '_'.join(tcc)
outfile = "%s/%s_%s.dat" % (suboutput, args.keyword, tcname)
#remove file if it already exists
f = open(outfile, 'w')
if args.keyword == 'tc':
f.write("# %s\tCurie temperature Tc\tAccuracy of Tc\n" % tcd)
elif args.keyword == 'dopant_activation':
f.write("# %s\tdopant activation (n_c/n_i)\n" % tcd)
elif args.keyword == 'occNum_c':
f.write("# %s\tConduction band occupation number (n_c)\n" % tcd)
f.close()
# iterate through database
for fd in filtered_data:
# defining name
material_folder = db.get_output(*fd)
namestr = material_folder.rstrip('/')
# get all datasets corresponding to fd (different temperatures)
temperature_datasets = database.filtrate(db.data, corenames, fd)
if args.keyword in simple_result_keywords:
# extract data from relevant folders
cmd = 'cat '
for td in temperature_datasets:
temperature_folder = db.get_temp_output(td[len(corenames) - 1])
#cmd=cmd + "%s/results/%s.dat " % (fd[-1], args.keyword)
cmd = cmd + "%s/%s/%s/%s/results/%s.dat " % (
resultFolder, subResultFolder, material_folder,
temperature_folder, args.keyword)
cmd = cmd + " > %s/%s_%s.dat" % (suboutput, args.keyword, namestr)
subprocess.call(cmd, shell=True)
elif args.keyword in sophisticated_result_keywords:
if args.keyword == 'cond_para':
key = args.keyword
if (args.layer != 0):
key = "%s_layer%03i" % (args.keyword, args.layer)
outfile = "%s/%s_%s.dat" % (suboutput, key, namestr)
f = open(outfile, 'w')
for td in temperature_datasets:
temperature_folder = db.get_temp_output(td[len(corenames) -
1])
filename = "%s/%s/%s/%s/results/%s.dat" % (
resultFolder, subResultFolder, material_folder,
temperature_folder, 'cond')
value = float(read(filename, line=args.layer)[1])
temp = td[len(corenames) - 1]
f.write("%0.17e\t%0.17e\n" % (temp, value))
f.close()
if args.keyword == 'resist_para':
key = args.keyword
if (args.layer != 0):
key = "%s_layer%03i" % (args.keyword, args.layer)
outfile = "%s/%s_%s.dat" % (suboutput, key, namestr)
f = open(outfile, 'w')
for td in temperature_datasets:
temperature_folder = db.get_temp_output(td[len(corenames) -
1])
filename = "%s/%s/%s/%s/results/%s.dat" % (
resultFolder, subResultFolder, material_folder,
temperature_folder, 'resist')
value = float(read(filename, line=args.layer)[1])
temp = td[len(corenames) - 1]
f.write("%0.17e\t%0.17e\n" % (temp, value))
f.close()
if args.keyword == 'cond_perp':
if args.layerx == None or args.layery == None:
outfile = "%s/%s_%s.dat" % (suboutput, args.keyword,
namestr)
f = open(outfile, 'w')
for td in temperature_datasets:
temperature_folder = db.get_temp_output(
td[len(corenames) - 1])
filename = "%s/%s/%s/%s/results/%s.dat" % (
resultFolder, subResultFolder, material_folder,
temperature_folder, 'cond_perp_matrix')
# read in conductivity matrix
cmat = np.loadtxt(filename)
# sum over all entries
cond_perp = np.sum(cmat)
temp = td[len(corenames) - 1]
f.write("%0.17e\t%0.17e\n" % (temp, cond_perp))
f.close()
else:
outfile = "%s/%s_%s_%03i_%03i.dat" % (
suboutput, args.keyword, namestr, args.layerx,
args.layery)
f = open(outfile, 'w')
for td in temperature_datasets:
temperature_folder = db.get_temp_output(
td[len(corenames) - 1])
filename = "%s/%s/%s/%s/results/%s.dat" % (
resultFolder, subResultFolder, material_folder,
temperature_folder, 'cond_perp_matrix')
value = float(
read(filename, line=args.layerx)[args.layery])
temp = td[len(corenames) - 1]
f.write("%0.17e\t%0.17e\n" % (temp, value))
f.close()
if args.keyword == 'resist_perp':
if args.layerx == None or args.layery == None:
outfile = "%s/%s_%s.dat" % (suboutput, args.keyword,
namestr)
f = open(outfile, 'w')
for td in temperature_datasets:
temperature_folder = db.get_temp_output(
td[len(corenames) - 1])
filename = "%s/%s/%s/%s/results/%s.dat" % (
resultFolder, subResultFolder, material_folder,
temperature_folder, 'cond_perp_matrix')
# read in conductivity matrix
cmat = np.loadtxt(filename)
# invert conductivity matrix
icmat = la.inv(cmat)
# sum over all entries
resist_perp = np.sum(icmat)
temp = td[len(corenames) - 1]
f.write("%0.17e\t%0.17e\n" % (temp, resist_perp))
f.close()
else:
outfile = "%s/%s_%s_%03i_%03i.dat" % (
suboutput, args.keyword, namestr, args.layerx,
args.layery)
print outfile
f = open(outfile, 'w')
for td in temperature_datasets:
temperature_folder = db.get_temp_output(
td[len(corenames) - 1])
filename = "%s/%s/%s/%s/results/%s.dat" % (
resultFolder, subResultFolder, material_folder,
temperature_folder, 'cond_perp_matrix')
value = float(
read(filename, line=args.layerx)[args.layery])
temp = td[len(corenames) - 1]
f.write("%0.17e\t%0.17e\n" % (temp, 1.0 / value))
f.close()
if args.keyword == 'isodelta':
outfile = "%s/%s_%s.dat" % (suboutput, args.keyword, namestr)
f = open(outfile, 'w')
for td in temperature_datasets:
temperature_folder = db.get_temp_output(td[len(corenames) -
1])
filename = "%s/%s/%s/%s/results/%s.dat" % (
resultFolder, subResultFolder, material_folder,
temperature_folder, 'mu')
mu = float(read(filename, line=0)[0])
isodelta = -mu
temp = td[len(corenames) - 1]
f.write("%0.17e\t%0.17e\n" % (temp, isodelta))
f.close()
if args.keyword == 'dopant_activation' or args.keyword == 'occNum_c':
folder = "%s/%s/%s/" % (resultFolder, subResultFolder,
material_folder)
filename = "%s/%s/results/%s.dat" % (
folder, db.get_temp_output(5.0), 'occNum_c')
if not os.path.exists(filename):
print "Warning: Dataset (T=5K) %s=%f is not present. %s does not exist." % (
tcd, fd[tci], filename)
else:
occNum_c = float(read(filename, line=0)[0])
f = open(outfile, 'a')
if args.keyword == 'dopant_activation':
f.write("%0.17e\t%0.17e\n" %
(fd[tci], occNum_c / fd[tci]))
else:
f.write("%0.17e\t%0.17e\n" % (fd[tci], occNum_c))
f.close()
if args.keyword == 'tc':
# get tc and error in tc
folder = "%s/%s/%s/" % (resultFolder, subResultFolder,
material_folder)
filename = "%s/tc.dat" % folder
success = True
if not os.path.exists(filename):
success = False
print "Warning: Dataset %s=%f is not present. %s does not exist." % (
tcd, fd[tci], filename)
answer = raw_input("Try to get? (Y/n)")
if answer != 'n':
success = gettc(args.database, db, folder,
args.temperatures, args.tsteps,
args.dM)
if not success:
print "Warning: Data for %s=%f is not present. -> Skip" % (
tcd, fd[tci])
if success:
print "Add dataset: %s=%f" % (tcd, fd[tci])
g = open(filename, 'r')
tc = 0.0
dtc = 0.0
for l in g.readlines():
if not l.startswith('#'):
tc = float(l.split()[0])
elif l.startswith('# Temperature accuracy'):
dtc = float(l.partition('=')[2])
g.close()
# write tc data row
f = open(outfile, 'a')
f.write("%f\t%f\t%f\n" % (fd[tci], tc, dtc))
f.close()
elif args.keyword == 'print':
print namestr
print 'Temperature\t%s' % special
for td in temperature_datasets:
print "%e\t%e" % (td[-3], td[-2])
print
elif args.keyword == 'printfull':
print namestr
print 'Temperature\t%s\tSource' % special
for td in temperature_datasets:
print "%e\t%e\t%s" % (td[-3], td[-2], td[-1])
print
parser.add_argument(
"-d", "--database", default="/users/stollenw/projects/euo/database/hetero.db", help="Database file name"
)
parser.add_argument(
"-p",
"--plotfolder",
default="/users/stollenw/projects/euo/database/analysis/hetero/avmag/",
help="Database file name",
)
parser.add_argument("-s", "--short", action="store_true", help="Less output")
args = parser.parse_args()
if not os.path.exists(args.plotfolder):
os.makedirs(args.plotfolder)
database = database.heterostructure_database()
if args.database != "/users/stollenw/projects/euo/database/hetero.db":
database.read(args.database)
else:
database.download()
# get columns of data and remove duplicates by converting to
# a set (no duplicates) and back to a list
material_list = list(set([row[0] for row in database.data]))
N_list = list(set([int(row[1]) for row in database.data]))
M_list = list(set([int(row[2]) for row in database.data]))
ni_list = list(set([float(row[3]) for row in database.data]))
ncr_list = list(set([float(row[4]) for row in database.data]))
dW_list = list(set([float(row[5]) for row in database.data]))
# sort data
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 __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='Analyse euo program results', formatter_class=argparse.RawTextHelpFormatter)
keyword_help="""Calculate the temperature dependent
quantity specified by one of the following keywords
print
print full
tc
occNum_c (for bulk)
dopant_activation (for bulk)
totalmag (for bulk)
cond (for bulk)
resist (for bulk)
avmag (for isolated and heterostructures)
cond_para (for isolated and heterostructures)
resist_para (for isolated and heterostructures)
cond_perp (for isolated and heterostructures)
resist_perp (for isolated and heterostructures)
isodelta (energy shift (-mu) for isolated systems)
"""
dataset_help="""Specify dataset
e.g. "Metal-Metal-Heterostructure 5 9 0.01 0.01 0.125"
(for material, N, M, ni, ncr and dW).
You may use "all" as a placeholder or do not specify
the last values e.g. "all 5 all 0.01
"""
parser.add_argument('keyword', help=keyword_help)
parser.add_argument('-d', '--database', help='Type of database: "bulk", "isolated" or "hetero"')
parser.add_argument('-s', '--dataset', nargs='*', help=dataset_help)
parser.add_argument('-o', '--output', default='/users/stollenw/projects/euo/analysis/', help='Output folder (optional)')
parser.add_argument('--dbpath', help='Path to database file (optional)')
parser.add_argument('--resultpath', default='/users/stollenw/projects/euo/results/', help='Path to results (optional)')
parser.add_argument('--temperatures', nargs='*', default=None, help='Tempertures for tc search (optional, only for tc)', type=float)
parser.add_argument('--tsteps', nargs='*', default=None, help='Temperture steps for tc search (optional, only for tc)', type=float)
parser.add_argument('--dM', default=None, help='Magnetisation resolution for tc search (optional, only for tc)', type=float)
parser.add_argument('--layer', default=0, help='Layer to calculate parallel conductivity/resistivity in', type=int)
parser.add_argument('--layerx', help='First layer for perpendicular conductivity/resistivity', type=int)
parser.add_argument('--layery', help='First layer for perpendicular conductivity/resistivity', type=int)
args = parser.parse_args()
if not args.database in ('bulk', 'isolated', 'hetero'):
parser.print_help()
exit(0)
# allowed keywords
print_keywords=['print', 'printfull']
simple_result_keywords=None
sophisticated_result_keywords=None
if args.database=='bulk':
simple_result_keywords=['cond', 'resist', 'totalmag']
sophisticated_result_keywords=['tc', 'dopant_activation', 'occNum_c']
elif args.database=='isolated' or args.database=='hetero':
simple_result_keywords=['avmag']
sophisticated_result_keywords=['cond_para', 'resist_para', 'cond_perp', 'resist_perp', 'isodelta', 'tc']
# keywords that produce results
result_keywords=simple_result_keywords + sophisticated_result_keywords
# all keywords (including print keywords)
allowed_keywords=simple_result_keywords + sophisticated_result_keywords + print_keywords
# check if valid keyword was given
if not args.keyword in allowed_keywords:
parser.print_help()
print "Allowed keywords are:"
for ak in allowed_keywords:
print ak
exit(0)
# set output
output=args.output
db=None
corenames=None
special=None
subResultFolder=None
if args.database=='bulk':
db=database.bulk_database()
output=output+'bulk/'
subResultFolder='bulk/'
corenames=('material', 'ni', 'T')
special='mag'
elif args.database=='isolated':
db=database.isolated_database()
output=output+'isolated/'
subResultFolder='isolated/'
corenames=('material', 'N', 'ni', 'T')
special='isodelta'
else:
db=database.heterostructure_database()
output=output+'hetero/'
subResultFolder='heterostructure/'
corenames=('material', 'N', 'M', 'ni', 'ncr', 'dW', 'T')
special='avmag'
if args.dbpath==None:
db.download()
else:
db.download("[email protected]:%s" % args.dbpath)
resultFolder=args.resultpath
# get filtered data, i.e. reduce to defining properties without temperature
filtered_data=database.filtrate(db.data, corenames, args.dataset, len(corenames)-1)
# lower threshold for displaying results
min_result_number=1
# extract conductivity or other observables
if args.keyword in result_keywords:
# temperatrue sweep only makes sense if there are at least two temperatures
min_result_number=2
# create folder if necessary
suboutput=output + "/data/%s/" % args.keyword
if not os.path.exists(suboutput):
os.makedirs(suboutput)
# in the Curie temperature case, create single file for all datasets
outfile=''
tcd=''
tci=0
if args.keyword=='tc' or args.keyword=='dopant_activation' or args.keyword=='occNum_c':
if args.dataset==None:
print "Dataset needed for Curie temperature / dopant activation at T=5K / occNum at T=5K"
exit(1)
# check if number single attribute is filterd out
if (args.dataset.count('all')+(len(corenames)-1-len(args.dataset))>1):
print "Dataset has to many degrees of freedom."
exit(1)
tcc=[]
i=0
for d,n in zip(args.dataset,corenames):
if d!='all':
if n=='material':
tcc.append(d)
elif n=='N' or n=='M':
tcc.append(n + "%03i" % int(d))
else:
tcc.append(n + "%06.4f" % float(d))
else:
tcd=n
tci=i
i=i+1
if (tcd==''):
tcd=corenames[-2]
tci=len(corenames)-2
tcname='_'.join(tcc)
outfile="%s/%s_%s.dat" % (suboutput, args.keyword, tcname)
#remove file if it already exists
f=open(outfile, 'w')
if args.keyword=='tc':
f.write("# %s\tCurie temperature Tc\tAccuracy of Tc\n" % tcd)
elif args.keyword=='dopant_activation':
f.write("# %s\tdopant activation (n_c/n_i)\n" % tcd)
elif args.keyword=='occNum_c':
f.write("# %s\tConduction band occupation number (n_c)\n" % tcd)
f.close()
# iterate through database
for fd in filtered_data:
# defining name
material_folder=db.get_output(*fd)
namestr=material_folder.rstrip('/')
# get all datasets corresponding to fd (different temperatures)
temperature_datasets=database.filtrate(db.data, corenames, fd)
if args.keyword in simple_result_keywords:
# extract data from relevant folders
cmd='cat '
for td in temperature_datasets:
temperature_folder=db.get_temp_output(td[len(corenames)-1])
#cmd=cmd + "%s/results/%s.dat " % (fd[-1], args.keyword)
cmd=cmd + "%s/%s/%s/%s/results/%s.dat " % (resultFolder, subResultFolder, material_folder, temperature_folder, args.keyword)
cmd=cmd + " > %s/%s_%s.dat" % (suboutput, args.keyword, namestr)
subprocess.call(cmd, shell=True)
elif args.keyword in sophisticated_result_keywords:
if args.keyword=='cond_para':
key=args.keyword
if (args.layer!=0):
key="%s_layer%03i" % (args.keyword, args.layer)
outfile="%s/%s_%s.dat" % (suboutput, key, namestr)
f=open(outfile, 'w')
for td in temperature_datasets:
temperature_folder=db.get_temp_output(td[len(corenames)-1])
filename="%s/%s/%s/%s/results/%s.dat" % (resultFolder, subResultFolder, material_folder, temperature_folder, 'cond')
value=float(read(filename, line=args.layer)[1])
temp=td[len(corenames)-1]
f.write("%0.17e\t%0.17e\n" % (temp, value))
f.close()
if args.keyword=='resist_para':
key=args.keyword
if (args.layer!=0):
key="%s_layer%03i" % (args.keyword, args.layer)
outfile="%s/%s_%s.dat" % (suboutput, key, namestr)
f=open(outfile, 'w')
for td in temperature_datasets:
temperature_folder=db.get_temp_output(td[len(corenames)-1])
filename="%s/%s/%s/%s/results/%s.dat" % (resultFolder, subResultFolder, material_folder, temperature_folder, 'resist')
value=float(read(filename, line=args.layer)[1])
temp=td[len(corenames)-1]
f.write("%0.17e\t%0.17e\n" % (temp, value))
f.close()
if args.keyword=='cond_perp':
if args.layerx==None or args.layery==None:
outfile="%s/%s_%s.dat" % (suboutput, args.keyword, namestr)
f=open(outfile, 'w')
for td in temperature_datasets:
temperature_folder=db.get_temp_output(td[len(corenames)-1])
filename="%s/%s/%s/%s/results/%s.dat" % (resultFolder, subResultFolder, material_folder, temperature_folder, 'cond_perp_matrix')
# read in conductivity matrix
cmat=np.loadtxt(filename)
# sum over all entries
cond_perp=np.sum(cmat)
temp=td[len(corenames)-1]
f.write("%0.17e\t%0.17e\n" % (temp, cond_perp))
f.close()
else:
outfile="%s/%s_%s_%03i_%03i.dat" % (suboutput, args.keyword, namestr, args.layerx, args.layery)
f=open(outfile, 'w')
for td in temperature_datasets:
temperature_folder=db.get_temp_output(td[len(corenames)-1])
filename="%s/%s/%s/%s/results/%s.dat" % (resultFolder, subResultFolder, material_folder, temperature_folder, 'cond_perp_matrix')
value=float(read(filename, line=args.layerx)[args.layery])
temp=td[len(corenames)-1]
f.write("%0.17e\t%0.17e\n" % (temp, value))
f.close()
if args.keyword=='resist_perp':
if args.layerx==None or args.layery==None:
outfile="%s/%s_%s.dat" % (suboutput, args.keyword, namestr)
f=open(outfile, 'w')
for td in temperature_datasets:
temperature_folder=db.get_temp_output(td[len(corenames)-1])
filename="%s/%s/%s/%s/results/%s.dat" % (resultFolder, subResultFolder, material_folder, temperature_folder, 'cond_perp_matrix')
# read in conductivity matrix
cmat=np.loadtxt(filename)
# invert conductivity matrix
icmat=la.inv(cmat)
# sum over all entries
resist_perp=np.sum(icmat)
temp=td[len(corenames)-1]
f.write("%0.17e\t%0.17e\n" % (temp, resist_perp))
f.close()
else:
outfile="%s/%s_%s_%03i_%03i.dat" % (suboutput, args.keyword, namestr, args.layerx, args.layery)
print outfile
f=open(outfile, 'w')
for td in temperature_datasets:
temperature_folder=db.get_temp_output(td[len(corenames)-1])
filename="%s/%s/%s/%s/results/%s.dat" % (resultFolder, subResultFolder, material_folder, temperature_folder, 'cond_perp_matrix')
value=float(read(filename, line=args.layerx)[args.layery])
temp=td[len(corenames)-1]
f.write("%0.17e\t%0.17e\n" % (temp, 1.0/value))
f.close()
if args.keyword=='isodelta':
outfile="%s/%s_%s.dat" % (suboutput, args.keyword, namestr)
f=open(outfile, 'w')
for td in temperature_datasets:
temperature_folder=db.get_temp_output(td[len(corenames)-1])
filename="%s/%s/%s/%s/results/%s.dat" % (resultFolder, subResultFolder, material_folder, temperature_folder, 'mu')
mu=float(read(filename, line=0)[0])
isodelta=-mu
temp=td[len(corenames)-1]
f.write("%0.17e\t%0.17e\n" % (temp, isodelta))
f.close()
if args.keyword=='dopant_activation' or args.keyword=='occNum_c':
folder="%s/%s/%s/" % (resultFolder, subResultFolder, material_folder)
filename="%s/%s/results/%s.dat" % (folder, db.get_temp_output(5.0), 'occNum_c')
if not os.path.exists(filename):
print "Warning: Dataset (T=5K) %s=%f is not present. %s does not exist." % (tcd, fd[tci], filename)
else:
occNum_c=float(read(filename, line=0)[0])
f=open(outfile, 'a')
if args.keyword=='dopant_activation':
f.write("%0.17e\t%0.17e\n" % (fd[tci], occNum_c/fd[tci]))
else:
f.write("%0.17e\t%0.17e\n" % (fd[tci], occNum_c))
f.close()
if args.keyword=='tc':
# get tc and error in tc
folder="%s/%s/%s/" % (resultFolder, subResultFolder, material_folder)
filename="%s/tc.dat" % folder
success=True
if not os.path.exists(filename):
success=False
print "Warning: Dataset %s=%f is not present. %s does not exist." % (tcd, fd[tci], filename)
answer=raw_input("Try to get? (Y/n)")
if answer!='n':
success=gettc(args.database, db, folder, args.temperatures, args.tsteps, args.dM)
if not success:
print "Warning: Data for %s=%f is not present. -> Skip" % (tcd, fd[tci])
if success:
print "Add dataset: %s=%f" % (tcd, fd[tci])
g=open(filename, 'r')
tc=0.0
dtc=0.0
for l in g.readlines():
if not l.startswith('#'):
tc=float(l.split()[0])
elif l.startswith('# Temperature accuracy'):
dtc=float(l.partition('=')[2])
g.close()
# write tc data row
f=open(outfile, 'a')
f.write("%f\t%f\t%f\n" % (fd[tci], tc, dtc))
f.close()
elif args.keyword=='print':
print namestr
print 'Temperature\t%s' % special
for td in temperature_datasets:
print "%e\t%e" % (td[-3], td[-2])
print
elif args.keyword=='printfull':
print namestr
print 'Temperature\t%s\tSource' % special
for td in temperature_datasets:
print "%e\t%e\t%s" % (td[-3], td[-2], td[-1])
print
def main():
parser = argparse.ArgumentParser(
description=
'Update database for heterostructure runs 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.heterostructure_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: Heterostructure 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: Heterostructure 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/heterostructure_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 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)
def main():
dataset_help = """Specify dataset
e.g. "Metal-Metal-Heterostructure 5 9 0.01 0.01 0.125"
(for material, N, M, ni, ncr and dW).
You may use "all" as a placeholder or do not specify
the last values e.g. "all 5 all 0.01
"""
parser = argparse.ArgumentParser(
description='Update database for heterostructure runs')
parser.add_argument(
'input',
nargs='*',
help=
'Folders containing results of heterostructure material runs or folders containing subfolders with results'
)
parser.add_argument(
'-d',
'--database',
default='/users/stollenw/projects/euo/database/hetero.db',
help='Database file name')
parser.add_argument('-s', '--dataset', nargs='*', help=dataset_help)
parser.add_argument('--overwrite',
action='store_true',
help='Overwrite database')
parser.add_argument('--archive',
action='store_true',
help='Archive all results')
parser.add_argument(
'--archive_destination',
default='/users/stollenw/projects/euo/results/heterostructure/',
help='Archive folder')
parser.add_argument('--dry',
action='store_true',
help='Simulate updating of database')
args = parser.parse_args()
#print args.overwrite
#print args.input
#print args.database
# initialize database
t = database.heterostructure_database()
# read in database if it already exists and overwrite flag is not given
if os.path.exists(args.database) and not args.overwrite:
t.read(args.database)
if args.dataset == None:
t.fill(args.input, args.overwrite)
if not args.dry:
t.write(args.database)
if args.archive:
t.archive(args.archive_destination)
else:
for iput in args.input:
t.archive(args.archive_destination, None,
os.path.abspath(iput))
else:
print "Archive folder would be: ", args.archive_destination
else:
t.archive(args.archive_destination, args.dataset)