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 test_merge_tape9():
tape9_file = StringIO(sample_tape9)
tape9_file = origen22.parse_tape9(tape9_file)
tape9_dict = {1: {'_type': 'decay', 'half_life': {10010: 42.0}},
2: {'_type': 'decay', '_bad_key': None},
3: {'_type': 'decay', 'title': "Sweet Decay"},
382: {'_type': 'xsfpy', '_subtype': 'actinides', 'sigma_f': {922350: 16.0}},
}
# merge so that dict takes precedence
tape9 = origen22.merge_tape9([tape9_dict, tape9_file])
# run tests
assert_equal(tape9[1]['half_life'][10010], 42.0)
assert_true('_bad_key' in tape9[2])
assert_equal(tape9[3]['title'], "Sweet Decay")
assert_equal(tape9[382]['sigma_f'][922350], 16.0)
assert_true('_cards' not in tape9[1])
assert_true('_cards' not in tape9[2])
assert_true('_cards' not in tape9[3])
assert_true('_cards' in tape9[381])
assert_true('_cards' not in tape9[382])
assert_true('_cards' in tape9[383])
def test_merge_tape9():
tape9_file = StringIO(sample_tape9)
tape9_file = origen22.parse_tape9(tape9_file)
tape9_dict = {
1: {"_type": "decay", "half_life": {10010: 42.0}},
2: {"_type": "decay", "_bad_key": None},
3: {"_type": "decay", "title": "Sweet Decay"},
382: {"_type": "xsfpy", "_subtype": "actinides", "sigma_f": {922350: 16.0}},
}
# merge so that dict takes precedence
tape9 = origen22.merge_tape9([tape9_dict, tape9_file])
# run tests
assert_equal(tape9[1]["half_life"][10010], 42.0)
assert_true("_bad_key" in tape9[2])
assert_equal(tape9[3]["title"], "Sweet Decay")
assert_equal(tape9[382]["sigma_f"][922350], 16.0)
assert_true("_cards" not in tape9[1])
assert_true("_cards" not in tape9[2])
assert_true("_cards" not in tape9[3])
assert_true("_cards" in tape9[381])
assert_true("_cards" not in tape9[382])
assert_true("_cards" in tape9[383])
def __init__(self, *args, **kwargs):
tape9 = kwargs.pop('tape9', None)
super(OrigenReactorMG, self).__init__(*args, **kwargs)
self._nearest_neighbors = []
if tape9 is None:
raise ValueError("must supply a default TAPE9 file to OrigenReactorMG.")
elif isinstance(tape9, basestring):
self._tape9 = origen22.parse_tape9(tape9)
elif hasattr(tape9, 'keys'):
self._tape9 = tape9
else:
# assume sequence of tape9s
self._tape9 = origen22.merge_tape9(tape9)
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 main_gen(ns):
"""Generates an open TAPE9.INP file. by default this only uses completely open
data.
"""
files = glob(os.path.join(ns.build_dir, 'ENSDF', 'ensdf.*'))
if len(files) == 0:
grab_ensdf_decay(ns.build_dir)
files = glob(os.path.join(ns.build_dir, 'ENSDF', 'ensdf.*'))
print("parsing ENSDF decay data")
decays, branches = parse_ensdf(files)
print("creating ORIGEN decay libraries")
t9decay = gendecay(decays, branches, metastable_cutoff=ns.metastable_cutoff)
print("creating ORIGEN cross section libraries")
xsc = XSCache(data_source_classes=[EAFDataSource, SimpleDataSource,
NullDataSource])
xsc.load()
t9xsfpy = origen22.xslibs(xscache=xsc, verbose=True)
t9 = origen22.merge_tape9([t9decay, t9xsfpy])
origen22.write_tape9(t9, outfile=ns.filename)
def test_merge_tape9():
tape9_file = StringIO(sample_tape9)
tape9_file = origen22.parse_tape9(tape9_file)
tape9_dict = {
1: {
'_type': 'decay',
'half_life': {
10010: 42.0
}
},
2: {
'_type': 'decay',
'_bad_key': None
},
3: {
'_type': 'decay',
'title': "Sweet Decay"
},
382: {
'_type': 'xsfpy',
'_subtype': 'actinides',
'sigma_f': {
922350: 16.0
}
},
}
# merge so that dict takes precedence
tape9 = origen22.merge_tape9([tape9_dict, tape9_file])
# run tests
assert_equal(tape9[1]['half_life'][10010], 42.0)
assert_true('_bad_key' in tape9[2])
assert_equal(tape9[3]['title'], "Sweet Decay")
assert_equal(tape9[382]['sigma_f'][922350], 16.0)
assert_true('_cards' not in tape9[1])
assert_true('_cards' not in tape9[2])
assert_true('_cards' not in tape9[3])
assert_true('_cards' in tape9[381])
assert_true('_cards' not in tape9[382])
assert_true('_cards' in tape9[383])
def run_all_the_origens(self, state, transmute_time, phi_tot, results):
print("making tape9")
self.tape9 = origen22.make_tape9(self.rc.track_nucs, self.xscache, nlb=(219, 220, 221))
self.tape9 = origen22.merge_tape9((self.tape9,
origen22.loads_tape9(brightlitetape9)))
origen22.write_tape9(self.tape9)
for mat_id in results.keys():
pwd = self.pwd(state, "origen{}".format(mat_id))
mat = self.libs[mat_id]["material"][-1]
if not os.path.isdir(pwd):
os.makedirs(pwd)
with indir(pwd):
if not os.path.isfile("TAPE6.OUT"):
self._make_origen_input(transmute_time, phi_tot, mat)
origen_results = []
if self.rc.threads == 1:
for mat_id in results.keys():
pwd = self.pwd(state, "origen{}".format(mat_id))
origen_params = (state.burn_times,
transmute_time,
phi_tot,
mat_id,
self.libs[mat_id]["material"][-1],
pwd,
self.origen_call)
# self._make_origen_input)
origen_results.append(_origen(origen_params))
else:
origen_params_ls = [(state.burn_times,
transmute_time,
phi_tot,
mat_id,
self.libs[mat_id]["material"][-1],
self.pwd(state, "origen{}".format(mat_id)),
self.origen_call)
for mat_id in results]
pool = Pool(self.rc.threads)
origen_results = pool.map(_origen, origen_params_ls)
for result in origen_results:
result[1]["material"] = Material(dict(result[1]["material"]),
1000,
attrs={"units": "g"})
return dict(origen_results)
def main_gen(ns):
"""Generates an open TAPE9.INP file. by default this only uses completely open
data.
"""
files = glob(os.path.join(ns.build_dir, 'ENSDF', 'ensdf.*'))
if len(files) == 0:
grab_ensdf_decay(ns.build_dir)
files = glob(os.path.join(ns.build_dir, 'ENSDF', 'ensdf.*'))
print("parsing ENSDF decay data")
decays, branches = parse_ensdf(files)
print("creating ORIGEN decay libraries")
t9decay = gendecay(decays,
branches,
metastable_cutoff=ns.metastable_cutoff)
print("creating ORIGEN cross section libraries")
xsc = XSCache(
data_source_classes=[EAFDataSource, SimpleDataSource, NullDataSource])
xsc.load()
t9xsfpy = origen22.xslibs(xscache=xsc, verbose=True)
t9 = origen22.merge_tape9([t9decay, t9xsfpy])
origen22.write_tape9(t9, outfile=ns.filename)
def run_all_the_origens(self, state, transmute_time, phi_tot, results):
"""Call ORIGEN as much as necessary and unite the results.
Parameters
----------
state : namedtuple (State)
A namedtuple containing the state parameters.
transmute_time : float
The length of the transmutation timestep. Has units of [days].
phi_tot : float
The total neutron flux.
results : dict
A dict with material identifiers as keys, and dictionaries as
values. The basic data structure to fill.
Returns
-------
dict
A dict of all the ORIGEN results.
"""
if self.rc.verbose:
print("making tape9 for {0} with phi={1}".format(state, phi_tot))
self.tape9 = origen22.make_tape9(self.rc.track_nucs, self.xscache, nlb=(219, 220, 221))
self.tape9 = origen22.merge_tape9((self.tape9,
origen22.loads_tape9(brightlitetape9)))
origen22.write_tape9(self.tape9)
for mat_id in results.keys():
pwd = self.pwd(state, "origen{}".format(mat_id))
mat = self.libs[mat_id]["material"][-1]
if not os.path.isdir(pwd):
os.makedirs(pwd)
with indir(pwd):
if not os.path.isfile("TAPE6.OUT"):
self._make_origen_input(transmute_time, phi_tot, mat)
origen_results = []
if self.rc.threads == 1:
for mat_id in results.keys():
pwd = self.pwd(state, "origen{}".format(mat_id))
origen_params = (state.burn_times,
transmute_time,
phi_tot,
mat_id,
self.libs[mat_id]["material"][-1],
pwd,
self.origen_call)
origen_results.append(_origen(origen_params))
else:
origen_params_ls = [(state.burn_times,
transmute_time,
phi_tot,
mat_id,
self.libs[mat_id]["material"][-1],
self.pwd(state, "origen{}".format(mat_id)),
self.origen_call)
for mat_id in results]
pool = Pool(self.rc.threads)
origen_results = pool.map(_origen, origen_params_ls)
pool.close()
pool.join()
for result in origen_results:
result[1]["material"] = Material(dict(result[1]["material"]),
1000,
attrs={"units": "g"})
return dict(origen_results)
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
# Init a dumb overlay tape9
overlay_tape9 = {381: {'_type': 'xsfpy',
'_subtype': 'activation_products',
'sigma_gamma': {10010: base_h1_xs},
}
}
# Run origen, increasing the cross section each time.
h2_concentration = []
for i in range(11):
overlay_tape9[381]['sigma_gamma'][10010] = (1.0 + i*0.1) * base_h1_xs
# Merge the base and overlay, and write out
new_tape9 = origen22.merge_tape9([overlay_tape9, base_tape9])
origen22.write_tape9(new_tape9, 'TAPE9.INP')
# Run and parse origen output
rtn = check_call(['o2_therm_linux.exe'])
tape6 = origen22.parse_tape6('TAPE6.OUT')
h2_concentration.append(tape6['table_5']['summary']['activation_products']['H2'][-1])
print
print "H2 Concentration: ", h2_concentration
# Clean up
import os
for f in os.listdir('.'):
if (f.endswith('.INP') or f.endswith('.OUT')) and f != 'BASE_TAPE9.INP':
381: {
'_type': 'xsfpy',
'_subtype': 'activation_products',
'sigma_gamma': {
10010: base_h1_xs
},
}
}
# Run origen, increasing the cross section each time.
h2_concentration = []
for i in range(11):
overlay_tape9[381]['sigma_gamma'][10010] = (1.0 + i * 0.1) * base_h1_xs
# Merge the base and overlay, and write out
new_tape9 = origen22.merge_tape9([overlay_tape9, base_tape9])
origen22.write_tape9(new_tape9, 'TAPE9.INP')
# Run and parse origen output
rtn = check_call(['o2_therm_linux.exe'])
tape6 = origen22.parse_tape6('TAPE6.OUT')
h2_concentration.append(
tape6['table_5']['summary']['activation_products']['H2'][-1])
print
print "H2 Concentration: ", h2_concentration
# Clean up
import os
for f in os.listdir('.'):
if (f.endswith('.INP') or f.endswith('.OUT')) and f != 'BASE_TAPE9.INP':
