def test_half_life():
f = StringIO(ensdf3_sample)
f.seek(0)
hl = ensdf.half_life(f)
assert_equal(hl, [(10030, 0.0, 20030, to_sec(12.32, 'Y'), 1.0),
(20030, 0.0, 20030, np.inf, 1.0),
(20030, 0.0, 20030, np.inf, 1.0),
])
def test_half_life():
f = StringIO(ensdf3_sample)
f.seek(0)
hl = ensdf.half_life(f)
assert_equal(hl, [
(10030, 0.0, 20030, to_sec(12.32, 'Y'), 1.0),
(20030, 0.0, 20030, np.inf, 1.0),
(20030, 0.0, 20030, np.inf, 1.0),
])
def _to_time(tstr, errstr):
t = tstr.strip()
# This accepts questionable levels
t = t.replace('?', '')
tobj = [s.strip(' ()') for s in t.split()]
if len(tobj) == 2:
t, t_unit = tobj
t, terr = _get_val_err(t, errstr)
tfinal = to_sec(t, t_unit)
tfinalerr = None
if type(terr) == float:
tfinalerr = to_sec(terr, t_unit)
elif terr is not None:
tfinalerr = to_sec(terr[0], t_unit), to_sec(terr[1], t_unit)
elif 'STABLE' in t:
tfinal = np.inf
tfinalerr = None
else:
tfinal = None
tfinalerr = None
return tfinal, tfinalerr
def _to_time(tstr, errstr):
t = tstr.strip()
# This accepts questionable levels
t = t.replace('?', '')
tobj = [s.strip(' ()') for s in t.split()]
if len(tobj) == 2:
t, t_unit = tobj
t, terr = _get_val_err(t, errstr)
tfinal = to_sec(t, t_unit)
tfinalerr = None
if type(terr) == float:
tfinalerr = to_sec(terr, t_unit)
elif terr is not None:
tfinalerr = to_sec(terr[0], t_unit), to_sec(terr[1], t_unit)
elif 'STABLE' in t:
tfinal = np.inf
tfinalerr = None
else:
tfinal = None
tfinalerr = None
return tfinal, tfinalerr
def step2():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean("general", "structured")
sub_voxel = config.getboolean("general", "sub_voxel")
decay_times = config.get("step2", "decay_times").split(",")
output = config.get("step2", "output")
tot_phtn_src_intensities = config.get("step2", "tot_phtn_src_intensities")
tag_name = "source_density"
if sub_voxel:
geom = config.get("step1", "geom")
load(geom)
cell_mats = cell_materials(geom)
else:
cell_mats = None
h5_file = "phtn_src.h5"
if not isfile(h5_file):
photon_source_to_hdf5(filename="phtn_src", nucs="total")
intensities = "Total photon source intensities (p/s)\n"
e_bounds = phtn_src_energy_bounds("alara_inp")
for i in range(len(e_bounds)):
e_bounds[i] /= 1.0e6 # convert unit from eV to MeV
for i, dt in enumerate(decay_times):
print("Writing source for decay time: {0} to mesh".format(dt))
mesh = Mesh(structured=structured, mesh="blank_mesh.h5m")
tags = {("TOTAL", dt): tag_name}
photon_source_hdf5_to_mesh(mesh,
h5_file,
tags,
sub_voxel=sub_voxel,
cell_mats=cell_mats)
p_src_filename = "{0}_{1}.h5m".format(output, i + 1)
intensity = total_photon_source_intensity(mesh,
tag_name,
sub_voxel=sub_voxel)
mesh = tag_e_bounds(mesh, e_bounds)
mesh = tag_source_intensity(mesh, intensity)
# get and tag decay time
decay_time = to_sec(float(dt.split()[0]), dt.split()[1])
mesh = tag_decay_time(mesh, decay_time)
# set version manually when changing the information of source.h5m
mesh = tag_version(mesh)
mesh.write_hdf5("{0}_{1}.h5m".format(output, i + 1))
intensities += "{0}: {1}\n".format(dt, intensity)
with open(tot_phtn_src_intensities, "w") as f:
f.write(intensities)
print("R2S step2 complete.")
def _convert_unit_to_s(dc):
"""
This function return a float number represent a time in unit of s.
Parameters
----------
dc : string. Contain a num and an unit.
Returns
-------
a float number
"""
# get num and unit
num, unit = dc.split()
return to_sec(float(num), unit)
def step2():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean('general', 'structured')
sub_voxel = config.getboolean('general', 'sub_voxel')
decay_times = config.get('step2', 'decay_times').split(',')
output = config.get('step2', 'output')
tot_phtn_src_intensities = config.get('step2', 'tot_phtn_src_intensities')
tag_name = "source_density"
if sub_voxel:
geom = config.get('step1', 'geom')
load(geom)
cell_mats = cell_materials(geom)
else:
cell_mats = None
h5_file = 'phtn_src.h5'
if not isfile(h5_file):
photon_source_to_hdf5(filename='phtn_src', nucs='total')
intensities = "Total photon source intensities (p/s)\n"
e_bounds = phtn_src_energy_bounds("alara_inp")
for i in range(len(e_bounds)):
e_bounds[i] /= 1.0e6 # convert unit from eV to MeV
for i, dt in enumerate(decay_times):
print('Writing source for decay time: {0} to mesh'.format(dt))
mesh = Mesh(structured=structured, mesh='blank_mesh.h5m')
tags = {('TOTAL', dt): tag_name}
photon_source_hdf5_to_mesh(mesh, h5_file, tags, sub_voxel=sub_voxel,
cell_mats=cell_mats)
intensity = total_photon_source_intensity(mesh, tag_name,
sub_voxel=sub_voxel)
mesh = tag_e_bounds(mesh, e_bounds)
mesh = tag_source_intensity(mesh, intensity)
# get and tag decay time
decay_time = to_sec(float(dt.split()[0]), dt.split()[1])
mesh = tag_decay_time(mesh, decay_time)
# set version manually when changing the information of source.h5m
mesh = tag_version(mesh)
mesh.write_hdf5('{0}_{1}.h5m'.format(output, i+1))
intensities += "{0}: {1}\n".format(dt, intensity)
with open(tot_phtn_src_intensities, 'w') as f:
f.write(intensities)
print('R2S step2 complete.')
def _convert_unit_to_s(dt):
"""
This function return a float number represent a time in unit of s.
Parameters
----------
dt : string.
Decay time. Contain a num and an unit.
Returns
-------
a float number
"""
dt = str_to_unicode(dt)
# get num and unit
if dt == "shutdown":
num, unit = "0.0", "s"
else:
num, unit = dt.split()
return to_sec(float(num), unit)
def half_life(ensdf):
"""Grabs the half-lives from an ENSDF file.
Parameters
----------
ensdf : str or file-like object
ENSDF file to inspect for half-life data
Returns
-------
data : list of 5-tuples
List of tuples where the indices match
1. from_nuclide, int (zzaaam)
2. level, float (MeV) - from_nuc's energy level
3. to_nuclide, int (zzaaam)
4. half_life, float (seconds)
5. branch_ratio, float (frac)
"""
opened_here = False
if isinstance(ensdf, basestring):
ensdf = open(ensdf, 'r')
opened_here = True
data = []
from_nuc = 0
half_life = 0.0
level = 0.0
valid_from_nuc = False
# Run through the file
lines = ensdf.readlines()
for i, line in enumerate(lines):
# See if the line matches
m = _level_regex.match(line)
if m is not None:
g = m.groups()
# grab the from nuclide
try:
from_nuc = _to_zzaaam(g[0], g[-2], g[-1])
valid_from_nuc = True
except:
valid_from_nuc = False
continue
# parse energy level
try:
level = float(g[1]) * 1E-3
except ValueError:
pass
# Grab the half-lives
time_info = g[2].replace('?', '').strip()
if 0 == len(time_info):
valid_from_nuc = False
elif time_info == 'STABLE':
half_life = np.inf
data += [(from_nuc, 0.0, from_nuc, half_life, 1.0)]
else:
time_unit = [s.strip() for s in time_info.split()]
if 2 == len(time_unit):
hl, unit = time_unit
half_life = to_sec(float(hl), unit)
continue
m = _level_cont_regex.match(line)
if m is not None and valid_from_nuc:
g = m.groups()
dat = dict([d.split('=')[:2] for d in g[-1].replace('$', ' ').split() if '=' in d])
dat = dict([(_decay_to[key](from_nuc), _to_float(val)*0.01)
for key, val in dat.items() if key in _decay_to.keys()])
data += [(from_nuc, level, to_nuc, half_life, br) for to_nuc, br in dat.items() if 0.0 < br]
continue
if opened_here:
ensdf.close()
return data
def test_to_sec():
assert_equal(120.0, utils.to_sec(2, 'M'))
def test_to_sec():
# as
assert_equal(2e-18, utils.to_sec(2, 'AS'))
assert_equal(2e-18, utils.to_sec(2, 'attosec'))
assert_equal(2e-18, utils.to_sec(2, 'attosecond'))
assert_equal(2e-18, utils.to_sec(2, 'attoseconds'))
# fs
assert_equal(2e-15, utils.to_sec(2, 'FS'))
assert_equal(2e-15, utils.to_sec(2, 'femtosec'))
assert_equal(2e-15, utils.to_sec(2, 'femtosecond'))
assert_equal(2e-15, utils.to_sec(2, 'femtoseconds'))
# ps
assert_equal(2e-12, utils.to_sec(2, 'PS'))
assert_equal(2e-12, utils.to_sec(2, 'picosec'))
assert_equal(2e-12, utils.to_sec(2, 'picosecond'))
assert_equal(2e-12, utils.to_sec(2, 'picoseconds'))
# ns
assert_equal(2e-9, utils.to_sec(2, 'NS'))
assert_equal(2e-9, utils.to_sec(2, 'nanosec'))
assert_equal(2e-9, utils.to_sec(2, 'nanosecond'))
assert_equal(2e-9, utils.to_sec(2, 'nanoseconds'))
# us
assert_equal(2e-6, utils.to_sec(2, 'US'))
assert_equal(2e-6, utils.to_sec(2, 'microsec'))
assert_equal(2e-6, utils.to_sec(2, 'microsecond'))
assert_equal(2e-6, utils.to_sec(2, 'microseconds'))
# ms
assert_equal(2e-3, utils.to_sec(2, 'MS'))
assert_equal(2e-3, utils.to_sec(2, 'millisec'))
assert_equal(2e-3, utils.to_sec(2, 'millisecond'))
assert_equal(2e-3, utils.to_sec(2, 'milliseconds'))
# s
assert_equal(2.0, utils.to_sec(2, 'S'))
assert_equal(2.0, utils.to_sec(2, 'sec'))
assert_equal(2.0, utils.to_sec(2, 'second'))
assert_equal(2.0, utils.to_sec(2, 'seconds'))
# m
assert_equal(120.0, utils.to_sec(2, 'M'))
assert_equal(120.0, utils.to_sec(2, 'min'))
assert_equal(120.0, utils.to_sec(2, 'minute'))
assert_equal(120.0, utils.to_sec(2, 'minutes'))
# h
assert_equal(7200.0, utils.to_sec(2, 'H'))
assert_equal(7200.0, utils.to_sec(2, 'hour'))
assert_equal(7200.0, utils.to_sec(2, 'hours'))
# d
assert_equal(172800.0, utils.to_sec(2, 'D'))
assert_equal(172800.0, utils.to_sec(2, 'day'))
assert_equal(172800.0, utils.to_sec(2, 'days'))
# w
assert_equal(1209600.0, utils.to_sec(2, 'W'))
assert_equal(1209600.0, utils.to_sec(2, 'week'))
assert_equal(1209600.0, utils.to_sec(2, 'weeks'))
# y
assert_equal(63115200.0, utils.to_sec(2, 'Y'))
assert_equal(63115200.0, utils.to_sec(2, 'year'))
assert_equal(63115200.0, utils.to_sec(2, 'years'))
# c
assert_equal(6311520000.0, utils.to_sec(2, 'C'))
assert_equal(6311520000.0, utils.to_sec(2, 'century'))
assert_equal(6311520000.0, utils.to_sec(2, 'centuries'))
# undifined unit trigs ValueError
assert_raises(ValueError, utils.to_sec, 2, 'month')
def test_to_sec():
assert_equal(120.0, utils.to_sec(2, 'M'))
def half_life(ensdf):
"""Grabs the half-lives from an ENSDF file.
Parameters
----------
ensdf : str or file-like object
ENSDF file to inspect for half-life data
Returns
-------
data : list of 5-tuples
List of tuples where the indices match
1. from_nuclide, int (zzaaam)
2. level, float (MeV) - from_nuc's energy level
3. to_nuclide, int (zzaaam)
4. half_life, float (seconds)
5. branch_ratio, float (frac)
"""
opened_here = False
if isinstance(ensdf, basestring):
ensdf = open(ensdf, 'r')
opened_here = True
data = []
from_nuc = 0
half_life = 0.0
level = 0.0
valid_from_nuc = False
# Run through the file
lines = ensdf.readlines()
for i, line in enumerate(lines):
# See if the line matches
m = _level_regex.match(line)
if m is not None:
g = m.groups()
# grab the from nuclide
try:
from_nuc = _to_zzaaam(g[0], g[-2], g[-1])
valid_from_nuc = True
except:
valid_from_nuc = False
continue
# parse energy level
try:
level = float(g[1]) * 1E-3
except ValueError:
pass
# Grab the half-lives
time_info = g[2].replace('?', '').strip()
if 0 == len(time_info):
valid_from_nuc = False
elif time_info == 'STABLE':
half_life = np.inf
data += [(from_nuc, 0.0, from_nuc, half_life, 1.0)]
else:
time_unit = [s.strip() for s in time_info.split()]
if 2 == len(time_unit):
hl, unit = time_unit
half_life = to_sec(float(hl), unit)
continue
m = _level_cont_regex.match(line)
if m is not None and valid_from_nuc:
g = m.groups()
dat = dict([
d.split('=')[:2] for d in g[-1].replace('$', ' ').split()
if '=' in d
])
dat = dict([(_decay_to[key](from_nuc), _to_float(val) * 0.01)
for key, val in dat.items()
if key in _decay_to.keys()])
data += [(from_nuc, level, to_nuc, half_life, br)
for to_nuc, br in dat.items() if 0.0 < br]
continue
if opened_here:
ensdf.close()
return data
def test_to_sec():
# as
assert_equal(2e-18, utils.to_sec(2, "AS"))
assert_equal(2e-18, utils.to_sec(2, "attosec"))
assert_equal(2e-18, utils.to_sec(2, "attosecond"))
assert_equal(2e-18, utils.to_sec(2, "attoseconds"))
# fs
assert_equal(2e-15, utils.to_sec(2, "FS"))
assert_equal(2e-15, utils.to_sec(2, "femtosec"))
assert_equal(2e-15, utils.to_sec(2, "femtosecond"))
assert_equal(2e-15, utils.to_sec(2, "femtoseconds"))
# ps
assert_equal(2e-12, utils.to_sec(2, "PS"))
assert_equal(2e-12, utils.to_sec(2, "picosec"))
assert_equal(2e-12, utils.to_sec(2, "picosecond"))
assert_equal(2e-12, utils.to_sec(2, "picoseconds"))
# ns
assert_equal(2e-9, utils.to_sec(2, "NS"))
assert_equal(2e-9, utils.to_sec(2, "nanosec"))
assert_equal(2e-9, utils.to_sec(2, "nanosecond"))
assert_equal(2e-9, utils.to_sec(2, "nanoseconds"))
# us
assert_equal(2e-6, utils.to_sec(2, "US"))
assert_equal(2e-6, utils.to_sec(2, "microsec"))
assert_equal(2e-6, utils.to_sec(2, "microsecond"))
assert_equal(2e-6, utils.to_sec(2, "microseconds"))
# ms
assert_equal(2e-3, utils.to_sec(2, "MS"))
assert_equal(2e-3, utils.to_sec(2, "millisec"))
assert_equal(2e-3, utils.to_sec(2, "millisecond"))
assert_equal(2e-3, utils.to_sec(2, "milliseconds"))
# s
assert_equal(2.0, utils.to_sec(2, "S"))
assert_equal(2.0, utils.to_sec(2, "sec"))
assert_equal(2.0, utils.to_sec(2, "second"))
assert_equal(2.0, utils.to_sec(2, "seconds"))
# m
assert_equal(120.0, utils.to_sec(2, "M"))
assert_equal(120.0, utils.to_sec(2, "min"))
assert_equal(120.0, utils.to_sec(2, "minute"))
assert_equal(120.0, utils.to_sec(2, "minutes"))
# h
assert_equal(7200.0, utils.to_sec(2, "H"))
assert_equal(7200.0, utils.to_sec(2, "hour"))
assert_equal(7200.0, utils.to_sec(2, "hours"))
# d
assert_equal(172800.0, utils.to_sec(2, "D"))
assert_equal(172800.0, utils.to_sec(2, "day"))
assert_equal(172800.0, utils.to_sec(2, "days"))
# w
assert_equal(1209600.0, utils.to_sec(2, "W"))
assert_equal(1209600.0, utils.to_sec(2, "week"))
assert_equal(1209600.0, utils.to_sec(2, "weeks"))
# y
assert_equal(63115200.0, utils.to_sec(2, "Y"))
assert_equal(63115200.0, utils.to_sec(2, "year"))
assert_equal(63115200.0, utils.to_sec(2, "years"))
# c
assert_equal(6311520000.0, utils.to_sec(2, "C"))
assert_equal(6311520000.0, utils.to_sec(2, "century"))
assert_equal(6311520000.0, utils.to_sec(2, "centuries"))
# undifined unit trigs ValueError
assert_raises(ValueError, utils.to_sec, 2, "month")
