def _make_origen_input(self, transmute_time, phi_tot, mat):
"""Make ORIGEN input files for a given state.
Parameters
----------
transmute_time : float
The time, in days, to run the transmutation for.
phi_tot: float
Total neutron flux.
mat : pyne.material.Material
The fuel material to transmute.
Returns
-------
None
"""
# may need to filter tape4 for Bad Nuclides
# if sum(mat.comp.values()) > 1:
for nuc in mat.comp:
if mat.comp[nuc] < self.rc.track_nuc_threshold:
del mat.comp[nuc]
origen22.write_tape4(mat)
origen22.write_tape5_irradiation("IRF",
transmute_time,
phi_tot,
xsfpy_nlb=(219, 220, 221),
cut_off=self.rc.track_nuc_threshold)
origen22.write_tape9(self.tape9)
def execute_origen(xs_tape9, time, nuclide, phi, origen, decay_tape9):
xs_tape9 = xs_tape9
if not os.path.isabs(xs_tape9):
xs_tape9 = os.path.join(LIBS_DIR, xs_tape9)
parsed_xs_tape9 = parse_tape9(xs_tape9)
parsed_decay_tape9 = parse_tape9(decay_tape9)
merged_tape9 = merge_tape9([parsed_decay_tape9, parsed_xs_tape9])
# Can set outfile to change directory, but the file name needs to be
# TAPE9.INP.
write_tape9(merged_tape9)
decay_nlb, xsfpy_nlb = nlbs(parsed_xs_tape9)
# Can set outfile, but the file name should be called TAPE5.INP.
write_tape5_irradiation("IRF", time/(60*60*24), phi,
xsfpy_nlb=xsfpy_nlb, cut_off=0, out_table_num=[4, 5],
out_table_nes=[True, False, False])
M = from_atom_frac({nuclide: 1}, mass=1, atoms_per_molecule=1)
write_tape4(M)
# Make pyne use naive atomic mass numbers to match ORIGEN
for i in pyne.data.atomic_mass_map:
pyne.data.atomic_mass_map[i] = float(pyne.nucname.anum(i))
origen_time, data = time_func(run_origen, origen)
logger.info("ORIGEN runtime: %s", origen_time)
return origen_time, data
def _make_origen_input(self, transmute_time, phi_tot, mat):
"""Make ORIGEN input files for a given state.
Parameters
----------
state : namedtuple (State)
A namedtuple containing the state parameters.
transmute_time : float
The time, in days, to run the transmutation for.
phi_tot: float
Total neutron flux.
mat : pyne.material.Material
The fuel material to transmute.
Returns
-------
None
"""
# may need to filter tape4 for Bad Nuclides
# if sum(mat.comp.values()) > 1:
origen22.write_tape4(mat)
origen22.write_tape5_irradiation("IRF",
transmute_time,
phi_tot,
xsfpy_nlb=(219, 220, 221),
cut_off=1e-300)
origen22.write_tape9(self.tape9)
def test_write_tape4():
mat = Material({"U235": 0.95, 80160000: 0.05})
tape4 = StringIO()
origen22.write_tape4(mat, tape4)
tape4.seek(0)
observed = tape4.read()
expected = ("1 80160 5.0000000000E-02 0 0 0 0 0 0\n"
"2 922350 9.5000000000E-01 0 0 0 0 0 0\n"
"0 0 0 0\n")
assert_equal(observed, expected)
def test_write_tape4():
mat = Material({"U235": 0.95, 80160000: 0.05})
tape4 = StringIO()
origen22.write_tape4(mat, tape4)
tape4.seek(0)
observed = tape4.read()
expected = ("1 80160 5.0000000000E-02 0 0 0 0 0 0\n"
"2 922350 9.5000000000E-01 0 0 0 0 0 0\n"
"0 0 0 0\n")
assert_equal(observed, expected)
def calc_transmutation(self):
"""Use ORIGEN as a backend to perform the transmutation calculation."""
K = self.K
s = self.bt_s
T_it = self.T_it
# Make origen cross section library
t9 = origen22.merge_tape9([self._xs, self._tape9])
origen22.write_tape9(t9)
# Make input mass stream
mat = Material({iso: 1E3 * T_it[iso][s] for iso in K})
origen22.write_tape4(mat)
# Make origen input file
irr_type = 'IRP'
irr_time = self.burn_times[s+1] - self.burn_times[s]
irr_value = self.specific_power
t5kw = {
'decay_nlb': sorted(nlb for nlb in t9.keys() if t9[nlb]['_type'] == 'decay')[:3],
'xsfpy_nlb': sorted(nlb for nlb in t9.keys() if t9[nlb]['_type'] == 'xsfpy')[:3],
'out_table_nes': (True, False, False),
'cut_off': 1E-300,
'out_table_num': [5],
}
origen22.write_tape5_irradiation(irr_type, irr_time, irr_value, **t5kw)
# Run origen
rtn = subprocess.check_call("o2_therm_linux.exe", shell=True)
# Parse origen output
res = origen22.parse_tape6()
#outvec = {key: sum([v[-1] for v in value]) * 1E-3 for key, value in res['table_5']['nuclide']['data'].items() if (key in K) and not np.isnan(value).any()}
outvec = res['materials'][-1].comp
nullvec = {k: 0.0 for k in K if k not in outvec}
outvec.update(nullvec)
# update the transmutation matrix
sp1 = s + 1
for nuc in K:
T_it[nuc][sp1] = outvec[nuc]
self.T_it = T_it
# update the burnup
BU_t = self.BU_t
deltaBU = irr_time * irr_value
BU_t[sp1] = BU_t[s] + deltaBU
self.BU_t = BU_t
print " BU_t = {0}".format(BU_t[sp1])
def transmute(self, x, t=None, phi=None, tol=None, cwd=None, xscache=None,
o2exe=None, *args, **kwargs):
"""Transmutes a material into its daughters.
Parameters
----------
x : Material or similar
Input material for transmutation.
t : float
Transmutations time [sec].
phi : float or array of floats
Neutron flux vector [n/cm^2/sec]. Currently this must either be
a scalar or match the group structure of EAF.
tol : float
Tolerance level for chain truncation.
cwd : str, optional
Current working directory for origen runs. Defaults to this dir.
xscache : XSCache, optional
A cross section cache to generate cross sections with.
o2exe : str, optional
Name or path to ORIGEN 2.2 executable.
Returns
-------
y : Material
The output material post-transmutation.
"""
if not isinstance(x, Material):
x = Material(x)
if t is not None:
self.t = t
if phi is not None:
self.phi = phi
if tol is not None:
self.tol = tol
if cwd is not None:
self.cwd = os.path.abspath(cwd)
if xscache is not None:
self.xscache = xscache
if o2exe is not None:
self.o2exe = o2exe
# prepare new tape9
nucs = set(x.comp.keys())
base_tape9 = self.base_tape9
decay_nlb, xsfpy_nlb = origen22.nlbs(base_tape9)
new_tape9 = origen22.xslibs(nucs=nucs, xscache=self.xscache, nlb=xsfpy_nlb)
t9 = origen22.merge_tape9([new_tape9, base_tape9])
# write out files
origen22.write_tape4(x, outfile=os.path.join(self.cwd, 'TAPE4.INP'))
origen22.write_tape5_irradiation('IRF', self.t/86400.0, self.xscache['phi_g'][0],
outfile=os.path.join(self.cwd, 'TAPE5.INP'), decay_nlb=decay_nlb,
xsfpy_nlb=xsfpy_nlb, cut_off=self.tol)
origen22.write_tape9(t9, outfile=os.path.join(self.cwd, 'TAPE9.INP'))
# run origen & get results
f = tempfile.NamedTemporaryFile()
try:
subprocess.check_call([self.o2exe], cwd=self.cwd, stdout=f, stderr=f)
except subprocess.CalledProcessError:
f.seek(0)
print("ORIGEN output:\n\n{0}".format(f.read()))
raise
finally:
f.close()
t6 = origen22.parse_tape6(tape6=os.path.join(self.cwd, 'TAPE6.OUT'))
y = t6['materials'][-1]
return y
def transmute(self,
x,
t=None,
phi=None,
tol=None,
cwd=None,
xscache=None,
o2exe=None,
*args,
**kwargs):
"""Transmutes a material into its daughters.
Parameters
----------
x : Material or similar
Input material for transmutation.
t : float
Transmutations time [sec].
phi : float or array of floats
Neutron flux vector [n/cm^2/sec]. Currently this must either be
a scalar or match the group structure of EAF.
tol : float
Tolerance level for chain truncation.
cwd : str, optional
Current working directory for origen runs. Defaults to this dir.
xscache : XSCache, optional
A cross section cache to generate cross sections with.
o2exe : str, optional
Name or path to ORIGEN 2.2 executable.
Returns
-------
y : Material
The output material post-transmutation.
"""
if not isinstance(x, Material):
x = Material(x)
if t is not None:
self.t = t
if phi is not None:
self.phi = phi
if tol is not None:
self.tol = tol
if cwd is not None:
self.cwd = os.path.abspath(cwd)
if xscache is not None:
self.xscache = xscache
if o2exe is not None:
self.o2exe = o2exe
# prepare new tape9
nucs = set(x.comp.keys())
base_tape9 = self.base_tape9
decay_nlb, xsfpy_nlb = origen22.nlbs(base_tape9)
new_tape9 = origen22.xslibs(nucs=nucs,
xscache=self.xscache,
nlb=xsfpy_nlb)
t9 = origen22.merge_tape9([new_tape9, base_tape9])
# write out files
origen22.write_tape4(x, outfile=os.path.join(self.cwd, 'TAPE4.INP'))
origen22.write_tape5_irradiation('IRF',
self.t / 86400.0,
self.xscache['phi_g'][0],
outfile=os.path.join(
self.cwd, 'TAPE5.INP'),
decay_nlb=decay_nlb,
xsfpy_nlb=xsfpy_nlb,
cut_off=self.tol)
origen22.write_tape9(t9, outfile=os.path.join(self.cwd, 'TAPE9.INP'))
# run origen & get results
f = tempfile.NamedTemporaryFile()
try:
subprocess.check_call([self.o2exe],
cwd=self.cwd,
stdout=f,
stderr=f)
except subprocess.CalledProcessError:
f.seek(0)
print("ORIGEN output:\n\n{0}".format(f.read()))
raise
finally:
f.close()
t6 = origen22.parse_tape6(tape6=os.path.join(self.cwd, 'TAPE6.OUT'))
y = t6['materials'][-1]
return y
capture cross section of Hydrogen-1 by 10% each time. The Hydrogen-2 concentration
is then gathered and displayed.
"""
from subprocess import check_call
from pyne import origen22
from pyne.api import Material
# 1 kg of water
water = Material()
water.from_atom_frac({'H1': 2.0, 'O16': 1.0})
water.mass = 1E3
# Make a tape4 file for water
origen22.write_tape4(water)
# Make a tape 5 for this calculation
# * Just output the concentration tables
# * The cross-section library numbers must
# the library / deck numbers in tape9
origen22.write_tape5_irradiation("IRF", 1000.0, 4E14,
xsfpy_nlb=(381, 382, 383),
out_table_num=[5])
# Grab a base tape9 from which we will overlay new values
# This must be supplied by the user
base_tape9 = origen22.parse_tape9("BASE_TAPE9.INP")
base_h1_xs = base_tape9[381]['sigma_gamma'][10010]
"""This example irradiates 1 kg of water for 100 days in ORIGEN 2.2, increasing the
capture cross section of Hydrogen-1 by 10% each time. The Hydrogen-2 concentration
is then gathered and displayed.
"""
from subprocess import check_call
from pyne import origen22
from pyne.api import Material
# 1 kg of water
water = Material()
water.from_atom_frac({'H1': 2.0, 'O16': 1.0})
water.mass = 1E3
# Make a tape4 file for water
origen22.write_tape4(water)
# Make a tape 5 for this calculation
# * Just output the concentration tables
# * The cross-section library numbers must
# the library / deck numbers in tape9
origen22.write_tape5_irradiation("IRF",
1000.0,
4E14,
xsfpy_nlb=(381, 382, 383),
out_table_num=[5])
# Grab a base tape9 from which we will overlay new values
# This must be supplied by the user
base_tape9 = origen22.parse_tape9("BASE_TAPE9.INP")