def test_parsers(self):
# populate a property tree from an input file
ptree = PropertyTree()
# INFO parser
info_file = 'input.info'
today = 'april 8th, 2016'
with open(info_file, 'w') as fout:
fout.write('date "' + today + '"')
ptree.parse_info(info_file)
self.assertEqual(ptree.get_string('date'), today)
remove(info_file)
# XML parser
xml_file = 'input.xml'
pi = 3.14
with open(xml_file, 'w') as fout:
fout.write('<pi>' + str(pi) + '</pi>')
ptree.parse_xml(xml_file)
self.assertEqual(ptree.get_double('pi'), pi)
remove(xml_file)
# JSON parser
json_file = 'input.json'
with open(json_file, 'w') as fout:
fout.write('{')
fout.write(' "foo":')
fout.write(' {')
fout.write(' "bar": false')
fout.write(' }')
fout.write('}')
ptree.parse_json(json_file)
self.assertFalse(ptree.get_bool('foo.bar'))
remove(json_file)
def run():
# parse uq database
input_database=PropertyTree()
input_database.parse_xml('uq.xml')
uq_database=input_database.get_child('uq')
# declare parameters
params=uq_database.get_int('params')
parameter_list=[]
for p in range(params):
parameter_database=uq_database.get_child('param_'+str(p))
distribution_type=parameter_database.get_string('distribution_type')
parameter_name=parameter_database.get_string('name')
if distribution_type=='uniform':
parameter_range=parameter_database.get_array_double('range')
parameter_list.append(UniformParameter('param_'+str(p),
parameter_name,
min=parameter_range[0],
max=parameter_range[1]))
elif distribution_type=='normal':
parameter_mean=parameter_database.get_double('mean')
parameter_standard_deviation=parameter_database.get_double('standard_deviation')
parameter_list.append(NormalParameter('param_'+str(p),
parameter_name,
mean=parameter_mean,
dev=parameter_standard_deviation))
else:
raise RuntimeError('invalid distribution type '+distribution_type+' for param_'+str(p))
# create a host
host_database=uq_database.get_child('host')
host_type=host_database.get_string('type')
if host_type=="Interactive":
host=InteractiveHost(cpus=host_database.get_int_with_default_value('cpus',1),
cpus_per_node=host_database.get_int_with_default_value('cpus_per_node',0))
elif host_type=="PBS":
host=PBSHost(host_database.get_string('env'),
cpus=host_database.get_int_with_default_value('cpus',0),
cpus_per_node=host_database.get_int_with_default_value('cpus_per_node',0),
qname=host_database.get_string_with_default_value('qname','standby'),
walltime=host_database.get_string_with_default_value('walltime','1:00:00'),
modules=host_database.get_string_with_default_value('modules',''),
pack=host_database.get_int_with_default_value('pack',1),
qlimit=host_database.get_int_with_default_value('qlimit',200))
else:
raise RuntimeError('invalid host type '+host_type)
# pick UQ method
method=uq_database.get_string('method')
if method=='SmolyakSparseGrid':
level=uq_database.get_int('level')
uq=Smolyak(parameter_list,level=level)
elif method=='MonteCarlo':
samples=uq_database.get_int('samples')
uq=MonteCarlo(parameter_list,num=samples)
elif method=='LatinHypercubeSampling':
samples=uq_database.get_int('samples')
uq=LHS(parameter_list,num=samples)
else:
raise RuntimeError('invalid UQ method '+method)
# make a test program
test_program_database=uq_database.get_child('test_program')
description=test_program_database.get_string('description')
executable_name=test_program_database.get_string('executable')
for p in range(params):
executable_name+=' --param_'+str(p)+' $param_'+str(p)
prog=TestProgram(exe=executable_name,
desc=description)
# run
return Sweep(uq,host,prog)
def run():
# parse uq database
input_database = PropertyTree()
input_database.parse_xml('uq.xml')
uq_database = input_database.get_child('uq')
# declare parameters
params = uq_database.get_int('params')
parameter_list = []
for p in range(params):
parameter_database = uq_database.get_child('param_' + str(p))
distribution_type = parameter_database.get_string('distribution_type')
parameter_name = parameter_database.get_string('name')
if distribution_type == 'uniform':
parameter_range = parameter_database.get_array_double('range')
parameter_list.append(
UniformParameter('param_' + str(p),
parameter_name,
min=parameter_range[0],
max=parameter_range[1]))
elif distribution_type == 'normal':
parameter_mean = parameter_database.get_double('mean')
parameter_standard_deviation = parameter_database.get_double(
'standard_deviation')
parameter_list.append(
NormalParameter('param_' + str(p),
parameter_name,
mean=parameter_mean,
dev=parameter_standard_deviation))
else:
raise RuntimeError('invalid distribution type ' +
distribution_type + ' for param_' + str(p))
# create a host
host_database = uq_database.get_child('host')
host_type = host_database.get_string('type')
if host_type == "Interactive":
host = InteractiveHost(
cpus=host_database.get_int_with_default_value('cpus', 1),
cpus_per_node=host_database.get_int_with_default_value(
'cpus_per_node', 0))
elif host_type == "PBS":
host = PBSHost(
host_database.get_string('env'),
cpus=host_database.get_int_with_default_value('cpus', 0),
cpus_per_node=host_database.get_int_with_default_value(
'cpus_per_node', 0),
qname=host_database.get_string_with_default_value(
'qname', 'standby'),
walltime=host_database.get_string_with_default_value(
'walltime', '1:00:00'),
modules=host_database.get_string_with_default_value('modules', ''),
pack=host_database.get_int_with_default_value('pack', 1),
qlimit=host_database.get_int_with_default_value('qlimit', 200))
else:
raise RuntimeError('invalid host type ' + host_type)
# pick UQ method
method = uq_database.get_string('method')
if method == 'SmolyakSparseGrid':
level = uq_database.get_int('level')
uq = Smolyak(parameter_list, level=level)
elif method == 'MonteCarlo':
samples = uq_database.get_int('samples')
uq = MonteCarlo(parameter_list, num=samples)
elif method == 'LatinHypercubeSampling':
samples = uq_database.get_int('samples')
uq = LHS(parameter_list, num=samples)
else:
raise RuntimeError('invalid UQ method ' + method)
# make a test program
test_program_database = uq_database.get_child('test_program')
description = test_program_database.get_string('description')
executable_name = test_program_database.get_string('executable')
for p in range(params):
executable_name += ' --param_' + str(p) + ' $param_' + str(p)
prog = TestProgram(exe=executable_name, desc=description)
# run
return Sweep(uq, host, prog)
#!/usr/bin/env python
from puq import dump_hdf5
from optparse import OptionParser
from pycap import PropertyTree,EnergyStorageDevice
from pycap import measure_impedance_spectrum
from numpy import real,imag,log10,absolute,angle
# read uq database
uq_database=PropertyTree()
uq_database.parse_xml('uq.xml')
# get number of parameters
params=uq_database.get_int('uq.params')
# usage
usage='usage: %prog'
for p in range(params):
usage+=' --param_'+str(p)+' val_'+str(p)
parser=OptionParser(usage)
# register options
for p in range(params):
parser.add_option('--param_'+str(p),type=float)
# parse the command line arguments
(options,args)=parser.parse_args()
# make device database
device_database=PropertyTree()
device_database.parse_xml('super_capacitor.xml')
# adjust the parameters in the database
options_dict=vars(options)
for var in options_dict:
#!/usr/bin/env python
from puq import dump_hdf5
from optparse import OptionParser
from pycap import PropertyTree, EnergyStorageDevice
from pycap import measure_impedance_spectrum
from numpy import real, imag, log10, absolute, angle
# read uq database
uq_database = PropertyTree()
uq_database.parse_xml('uq.xml')
# get number of parameters
params = uq_database.get_int('uq.params')
# usage
usage = 'usage: %prog'
for p in range(params):
usage += ' --param_' + str(p) + ' val_' + str(p)
parser = OptionParser(usage)
# register options
for p in range(params):
parser.add_option('--param_' + str(p), type=float)
# parse the command line arguments
(options, args) = parser.parse_args()
# make device database
device_database = PropertyTree()
device_database.parse_xml('super_capacitor.xml')
# adjust the parameters in the database
options_dict = vars(options)
for var in options_dict:
