def convert_to_serpent_tra(isoname, lib_temp):
metastable_flag = 0
if isoname[-2] == 'm':
new_isoname = isoname[:-1]
if int(isoname[-1]) == 1:
serpent_name = nucname.serpent(new_isoname) + lib_temp
metastable_flag = 1
else:
metastable_flag = int(isoname[-1])
else:
serpent_name = nucname.serpent(isoname) + lib_temp
return serpent_name, metastable_flag
def _mat_to_nucs(mat):
nucs = []
template = '<nuclide name="{nuc}" wo="{mass}" />'
for nuc, mass in mat.comp.items():
nucs.append(template.format(nuc=nucname.serpent(nuc), mass=mass*100))
nucs = "\n ".join(nucs)
return nucs
def test_serpent():
assert_equal(nucname.serpent(942390), "Pu-239")
assert_equal(nucname.serpent(952421), "Am-242m")
assert_equal(nucname.serpent("Pu-239"), "Pu-239")
assert_equal(nucname.serpent(94239), "Pu-239")
assert_equal(nucname.serpent(95642), "Am-242")
assert_equal(nucname.serpent(95242), "Am-242m")
assert_equal(nucname.serpent(92636), "U-236m")
assert_equal(nucname.serpent(2390940), "Pu-239")
assert_equal(nucname.serpent(2420951), "Am-242m")
def test_serpent():
assert_equal(nucname.serpent(942390), "Pu-239")
assert_equal(nucname.serpent(952421), "Am-242m")
assert_equal(nucname.serpent("Pu-239"), "Pu-239")
assert_equal(nucname.serpent(94239), "Pu-239")
assert_equal(nucname.serpent(95642), "Am-242")
assert_equal(nucname.serpent(95242), "Am-242m")
assert_equal(nucname.serpent(92636), "U-236m")
assert_equal(nucname.serpent(2390940), "Pu-239")
assert_equal(nucname.serpent(2420951), "Am-242m")
def photon_source_hdf5_to_mesh(mesh, filename, tags):
"""This function reads in an hdf5 file produced by photon_source_to_hdf5
and tags the requested data to the mesh of a PyNE Mesh object. Any
combinations of nuclides and decay times are allowed. The photon source
file is assumed to be in mesh.__iter__() order
Parameters
----------
mesh : PyNE Mesh
The object containing the imesh instance to be tagged.
filename : str
The path of the hdf5 version of the photon source file.
tags: dict
A dictionary were the keys are tuples with two values. The first is a
string denoting an nuclide in any form that is understood by
pyne.nucname (e.g. '1001', 'U-235', '242Am') or 'TOTAL' for all
nuclides. The second is a string denoting the decay time as it appears
in the file (e.g. 'shutdown', '1 h' '3 d'). The values of the
dictionary are the requested tag names for the combination of nuclide
and decay time. For example if one wanted tags for the photon source
densities from U235 at shutdown and from all nuclides at 1 hour, the
dictionary could be:
tags = {('U-235', 'shutdown') : 'tag1', ('TOTAL', '1 h') : 'tag2'}
"""
# find number of energy groups
with tb.openFile(filename) as h5f:
num_e_groups = len(h5f.root.data[0][3])
# create a dict of tag handles for all keys of the tags dict
tag_handles = {}
for tag_name in tags.values():
tag_handles[tag_name] = \
mesh.mesh.createTag(tag_name, num_e_groups, float)
# iterate through each requested nuclide/dectay time
for cond in tags.keys():
with tb.openFile(filename) as h5f:
# Convert nuclide to the form found in the ALARA phtn_src
# file, which is similar to the Serpent form. Note this form is
# different from the ALARA input nuclide form found in nucname.
if cond[0] != "TOTAL":
nuc = serpent(cond[0]).lower()
else:
nuc = "TOTAL"
# create of array of rows that match the nuclide/decay criteria
matched_data = h5f.root.data.readWhere(
"(nuc == '{0}') & (time == '{1}')".format(nuc, cond[1]))
idx = 0
for i, _, ve in mesh:
if matched_data[idx][0] == i:
tag_handles[tags[cond]][ve] = matched_data[idx][3]
idx += 1
else:
tag_handles[tags[cond]][ve] = [0] * num_e_groups
def photon_source_hdf5_to_mesh(mesh, filename, tags):
"""This function reads in an hdf5 file produced by photon_source_to_hdf5
and tags the requested data to the mesh of a PyNE Mesh object. Any
combinations of nuclides and decay times are allowed. The photon source
file is assumed to be in mesh.__iter__() order
Parameters
----------
mesh : PyNE Mesh
The object containing the imesh instance to be tagged.
filename : str
The path of the hdf5 version of the photon source file.
tags: dict
A dictionary were the keys are tuples with two values. The first is a
string denoting an nuclide in any form that is understood by
pyne.nucname (e.g. '1001', 'U-235', '242Am') or 'TOTAL' for all
nuclides. The second is a string denoting the decay time as it appears
in the file (e.g. 'shutdown', '1 h' '3 d'). The values of the
dictionary are the requested tag names for the combination of nuclide
and decay time. For example if one wanted tags for the photon source
densities from U235 at shutdown and from all nuclides at 1 hour, the
dictionary could be:
tags = {('U-235', 'shutdown') : 'tag1', ('TOTAL', '1 h') : 'tag2'}
"""
# find number of energy groups
with tb.openFile(filename) as h5f:
num_e_groups = len(h5f.root.data[0][3])
# create a dict of tag handles for all keys of the tags dict
tag_handles = {}
for tag_name in tags.values():
tag_handles[tag_name] = \
mesh.mesh.createTag(tag_name, num_e_groups, float)
# iterate through each requested nuclide/dectay time
for cond in tags.keys():
with tb.openFile(filename) as h5f:
# Convert nuclide to the form found in the ALARA phtn_src
# file, which is similar to the Serpent form. Note this form is
# different from the ALARA input nuclide form found in nucname.
if cond[0] != "TOTAL":
nuc = serpent(cond[0]).lower()
else:
nuc = "TOTAL"
# create of array of rows that match the nuclide/decay criteria
matched_data = h5f.root.data.readWhere(
"(nuc == '{0}') & (time == '{1}')".format(nuc, cond[1]))
idx = 0
for i, _, ve in mesh:
if matched_data[idx][0] == i:
tag_handles[tags[cond]][ve] = matched_data[idx][3]
idx += 1
else:
tag_handles[tags[cond]][ve] = [0] * num_e_groups
def _mat_to_nucs(mat):
"""Convert a ``pyne.material.Material`` into OpenMC ``materials.xml`` format.
Parameters
----------
mat : ``pyne.material.Material``
Material to convert.
Returns
-------
nucs : string
OpenMC-friendly XML tag with material composition.
"""
nucs = []
template = '<nuclide name="{nuc}" wo="{mass}" />'
for nuc, mass in mat.comp.items():
nucs.append(template.format(nuc=nucname.serpent(nuc), mass=mass*100))
nucs = "\n ".join(nucs)
return nucs
def _make_omc_input(self, state):
pwd = self.pwd(state)
ctx = self.context(state)
rc = self.rc
# settings
settings = SETTINGS_TEMPLATE.format(**ctx)
with open(os.path.join(pwd, 'settings.xml'), 'w') as f:
f.write(settings)
# materials
valid_nucs = self.nucs_in_cross_sections()
core_nucs = set(ctx['core_transmute'])
ctx['_fuel_nucs'] = _mat_to_nucs(rc.fuel_material[valid_nucs])
ctx['_clad_nucs'] = _mat_to_nucs(rc.clad_material[valid_nucs])
ctx['_cool_nucs'] = _mat_to_nucs(rc.cool_material[valid_nucs])
materials = MATERIALS_TEMPLATE.format(**ctx)
with open(os.path.join(pwd, 'materials.xml'), 'w') as f:
f.write(materials)
# geometry
ctx['lattice'] = ctx['lattice'].strip().replace('\n', '\n ')
ctx['_latt_shape0'] = ctx['lattice_shape'][0]
ctx['_latt_shape1'] = ctx['lattice_shape'][1]
ctx['_latt_x_pitch'] = ctx['unit_cell_pitch'] * ctx['lattice_shape'][0]
ctx['_latt_y_pitch'] = ctx['unit_cell_pitch'] * ctx['lattice_shape'][1]
ctx['_latt_x_half_pitch'] = ctx['_latt_x_pitch'] / 2.0
ctx['_latt_y_half_pitch'] = ctx['_latt_y_pitch'] / 2.0
geometry = GEOMETRY_TEMPLATE.format(**ctx)
with open(os.path.join(pwd, 'geometry.xml'), 'w') as f:
f.write(geometry)
# tallies
ctx['_egrid'] = " ".join(map(str, sorted(ctx['group_structure'])))
ctx['_cds_egrid'] = " ".join(map(str, sorted(self.cinderds.src_group_struct)))
ctx['_eafds_egrid'] = " ".join(map(str, sorted(self.eafds.src_group_struct)))
ctx['_omcds_egrid'] = " ".join(map(str, sorted(self.omcds.src_group_struct)))
nucs = core_nucs & valid_nucs
ctx['_nucs'] = " ".join([nucname.serpent(nuc) for nuc in sorted(nucs)])
tallies = TALLIES_TEMPLATE.format(**ctx)
with open(os.path.join(pwd, 'tallies.xml'), 'w') as f:
f.write(tallies)
# plots
plots = PLOTS_TEMPLATE.format(**ctx)
with open(os.path.join(pwd, 'plots.xml'), 'w') as f:
f.write(plots)
def rem_elements(self, inflow):
"""Updates Materialflow object `inflow` after removal target isotopes
with specific efficiency in single component of fuel reprocessing
system and returns waste stream Materialflow object.
Parameters
----------
inflow : Materialflow obj
Target material stream to remove poisons from.
Returns
-------
Materialflow object
Waste stream from the reprocessing system component.
"""
waste_nucvec = {}
out_nucvec = {}
# print("Xe concentration in inflow before % f g" % inflow['Xe136'])
# print("Current time %f" % (t))
for iso in inflow.comp.keys():
el_name = pyname.serpent(iso).split('-')[0]
if el_name in self.efficiency:
# Evaluate removal efficiency for el_name (float)
self.efficiency[el_name] = self.calc_rem_efficiency(el_name)
out_nucvec[iso] = \
float(inflow.comp[iso]) * \
float(1.0 - self.efficiency[el_name])
waste_nucvec[iso] = \
float(inflow[iso]) * self.efficiency[el_name]
else:
out_nucvec[iso] = float(inflow.comp[iso])
waste_nucvec[iso] = 0.0 # zeroes everywhere else
waste = Materialflow(waste_nucvec)
inflow.mass = float(inflow.mass - waste.mass)
inflow.comp = out_nucvec
inflow.norm_comp()
print("Xe concentration in inflow after %f g" % inflow['Xe136'])
print("Waste mass %f g\n" % waste.mass)
del out_nucvec, waste_nucvec, el_name
return waste
burnup_plot = False
calculate_post_burnup = False
find_mix = True
isotopes = [
'922330', '922340', '922350', '922360', '922370', '922380', '922390',
'932340', '932350', '932360', '932370', '932380', '932390', '932400',
'942350', '942360', '942370', '942380', '942390', '942400', '942410',
'942420', '942430', '952400', '952410', '952420', '952421', '952430',
'952440', '962420', '962430', '962440', '962450'
]
# 92 U, 93 Np, 94 Pu, 95 Am, 96 Cm
iso_names = []
for i, iso in enumerate(isotopes):
try:
iso_names.append(nucname.serpent(iso))
except:
iso_names.append(iso)
iso_names.append('Lumped-Act.')
iso_names.append('FPs')
conc = np.zeros(len(isotopes) + 2)
conc[2] = 0.05
conc[5] = 0.95
nat_conc = copy.deepcopy(conc)
nat_conc[2] = 0.00711 # Weight percent
nat_conc[5] = (1 - 0.00711)
years = 50 / (35 * 1e-6 *
1e3) / 365.25 # MWd/kg / W/g * MW/W * g/kg / days/year
def response_hdf5_to_mesh(mesh, filename, tags, response):
"""This function reads in an hdf5 file produced by response_to_hdf5
and tags the requested data to the mesh of a PyNE Mesh object. Any
combinations of nuclides and decay times are allowed. The photon source
file is assumed to be in mesh.__iter__() order
Parameters
----------
mesh : PyNE Mesh
The object containing the PyMOAB instance to be tagged.
filename : str
The path of the hdf5 version of the response file.
tags: dict
A dictionary were the keys are tuples with two values. The first is a
string denoting an nuclide in any form that is understood by
pyne.nucname (e.g. '1001', 'U-235', '242Am') or 'TOTAL' for all
nuclides. The second is a string denoting the decay time as it appears
in the file (e.g. 'shutdown', '1 h' '3 d'). The values of the
dictionary are the requested tag names for the combination of nuclide
and decay time. For example if one wanted tags for the photon source
densities from U235 at shutdown and from all nuclides at 1 hour, the
dictionary could be:
tags = {('U-235', 'shutdown') : 'tag1', ('TOTAL', '1 h') : 'tag2'}
response : str
The keyword of the response. Supported responses:
- decay_heat
- specific_activity
- alpha_heat
- beta_heat
- gamma_heat
- wdr
- photon_source
"""
# create a dict of tag handles for all keys of the tags dict
tag_handles = {}
for tag_name in tags.values():
mesh.tag(tag_name,
np.zeros(1, dtype=float),
"nat_mesh",
size=1,
dtype=float)
tag_handles[tag_name] = mesh.get_tag(tag_name)
decay_times = _read_h5_dt(filename)
# iterate through each requested nuclide/dectay time
for cond in tags.keys():
with tb.open_file(filename) as h5f:
# Convert nuclide to the form found in the ALARA response file
# file, which is similar to the Serpent form. Note this form is
# different from the ALARA input nuclide form found in nucname.
if cond[0] != "TOTAL":
nuc = serpent(cond[0]).lower()
else:
nuc = "TOTAL"
# time match, convert string mathch to float mathch
dt = _find_dt(cond[1], decay_times)
# create of array of rows that match the nuclide/decay criteria
matched_data = h5f.root.data.read_where(
"(nuc == '{0}') & (time == '{1}')".format(nuc, dt))
idx = 0
# index, mat, volume element
for i, _, ve in mesh:
if matched_data[idx][0] == i:
tag_handles[tags[cond]][ve] = matched_data[idx][3]
idx += 1
else:
tag_handles[tags[cond]][ve] = [0]
def photon_source_hdf5_to_mesh(mesh,
filename,
tags,
sub_voxel=False,
cell_mats=None):
"""This function reads in an hdf5 file produced by photon_source_to_hdf5
and tags the requested data to the mesh of a PyNE Mesh object. Any
combinations of nuclides and decay times are allowed. The photon source
file is assumed to be in mesh.__iter__() order
Parameters
----------
mesh : PyNE Mesh
The object containing the PyMOAB instance to be tagged.
filename : str
The path of the hdf5 version of the photon source file.
tags: dict
A dictionary were the keys are tuples with two values. The first is a
string denoting an nuclide in any form that is understood by
pyne.nucname (e.g. '1001', 'U-235', '242Am') or 'TOTAL' for all
nuclides. The second is a string denoting the decay time as it appears
in the file (e.g. 'shutdown', '1 h' '3 d'). The values of the
dictionary are the requested tag names for the combination of nuclide
and decay time. For example if one wanted tags for the photon source
densities from U235 at shutdown and from all nuclides at 1 hour, the
dictionary could be:
tags = {('U-235', 'shutdown') : 'tag1', ('TOTAL', '1 h') : 'tag2'}
sub_voxel: bool, optional
If the sub_voxel is True, then the sub-voxel r2s will be used.
Then the photon_source will be interpreted as sub-voxel photon source.
cell_mats : dict, optional
cell_mats is required when sub_voxel is True.
Maps geometry cell numbers to PyNE Material objects.
"""
# find number of energy groups
with tb.open_file(filename) as h5f:
num_e_groups = len(h5f.root.data[0][3])
max_num_cells = 1
ve0 = next(mesh.iter_ve())
if sub_voxel:
num_vol_elements = len(mesh)
subvoxel_array = _get_subvoxel_array(mesh, cell_mats)
# get max_num_cells
max_num_cells = len(np.atleast_1d(mesh.cell_number[ve0]))
# create a dict of tag handles for all keys of the tags dict
tag_handles = {}
tag_size = num_e_groups * max_num_cells
for tag_name in tags.values():
mesh.tag(
tag_name,
np.zeros(tag_size, dtype=float),
"nat_mesh",
size=tag_size,
dtype=float,
)
tag_handles[tag_name] = mesh.get_tag(tag_name)
decay_times = _read_h5_dt(filename)
# iterate through each requested nuclide/dectay time
for cond in tags.keys():
with tb.open_file(filename) as h5f:
# Convert nuclide to the form found in the ALARA phtn_src
# file, which is similar to the Serpent form. Note this form is
# different from the ALARA input nuclide form found in nucname.
if cond[0] != "TOTAL":
nuc = serpent(cond[0]).lower()
else:
nuc = "TOTAL"
# time match, convert string mathch to float mathch
dt = _find_dt(cond[1], decay_times)
# create of array of rows that match the nuclide/decay criteria
matched_data = h5f.root.data.read_where(
"(nuc == '{0}') & (time == '{1}')".format(nuc, dt))
if not sub_voxel:
idx = 0
for i, _, ve in mesh:
if matched_data[idx][0] == i:
tag_handles[tags[cond]][ve] = matched_data[idx][3]
idx += 1
else:
tag_handles[tags[cond]][ve] = [0] * num_e_groups
else:
temp_mesh_data = np.empty(shape=(num_vol_elements, max_num_cells,
num_e_groups),
dtype=float)
temp_mesh_data.fill(0.0)
for sve, subvoxel in enumerate(subvoxel_array):
temp_mesh_data[subvoxel["idx"],
subvoxel["scid"], :] = matched_data[sve][3][:]
for i, _, ve in mesh:
tag_handles[tags[cond]][ve] = temp_mesh_data[i, :].reshape(
max_num_cells * num_e_groups)
print(np.log(2)/data.decay_const('922340000')/3.15e7)
print('-------Np-239 to Pu-239 test--------')
print(data.decay_const('932390'))
print(data.decay_children('932390'))
print(data.decay_const('932390'))
print(data.decay_children('932390'))
print(data.branch_ratio(932390,942390))
print('-------U-240 decay test--------')
print(np.log(2)/data.decay_const('922400')/3600)
print(data.branch_ratio('922400','932400', use_metastable=False))
print('-----U234 Capture Test-----')
print(float('922350')-float('922340') == 10)
print('-----Mass Test-----')
print(nucname.anum('922350'))
print('-----Name Test-----')
print(nucname.serpent('922350'))
print('-------U-236 test--------')
print(data.decay_const('922360'))
print(data.half_life('922360')/(3.15e7))
print('-------Np-234 to U-234 test--------')
print(data.decay_const('932340'))
print(data.decay_children('932340'))
print(data.branch_ratio(932340,922340))
