def main():
# get list of nuclides
data.atomic_mass('U235')
nucs = set(data.atomic_mass_map.keys())
for nuc in data.atomic_mass_map:
nucm = nuc + 1
if nucname.anum(nuc) == 0 or data.decay_const(nucm) < 1e-16 or \
data.decay_const(nuc) == data.decay_const(nucm):
continue
nucs.add(nucm)
nucs = [nuc for nuc in nucs if nucname.anum(nuc) > 0]
#and
# not np.isnan(data.decay_const(nuc)) and
# nuc < 200000000]
nucs.sort()
# get symbols
symbols = {}
channels = {}
for nuc in nucs:
add_child_decays(nuc, symbols)
add_child_xss(nuc, channels, nucs)
# print symbols
ns = []
for nuc in nucs:
try:
nname = nucname.name(nuc)
except RuntimeError:
continue
ns.append(nname)
nucs = ns
d = {'symbols': symbols, 'nucs': nucs, 'channels': channels}
s = json.dumps(d, indent=4, sort_keys=True)
print(s)
def _build_matrix(N):
"""This function builds burnup matrix, A. Decay only."""
A = np.zeros((len(N), len(N)))
# convert N to id form
N_id = []
for i in range(len(N)):
if isinstance(N[i], str):
ID = nucname.id(N[i])
else:
ID = N[i]
N_id.append(ID)
sds = SimpleDataSource()
# Decay
for i in range(len(N)):
A[i, i] -= decay_const(N_id[i])
# Find decay parents
for k in range(len(N)):
if N_id[i] in decay_children(N_id[k]):
A[i,
k] += branch_ratio(N_id[k], N_id[i]) * decay_const(N_id[k])
return A
def decayheat(c):
"""Lists decay heats at 0, 10, 100, 1000, 10000 years summed over all
nuclides and facilities.
Args:
c: connection cursor to sqlite database.
"""
# Conversion of time from months to seconds
MCONV = 3.16e7 / 12
# Conversion of years to seconds
YCONV = 3.16e7
# Retrieve list of decay heats of each nuclide
alldecayheats = query(c)
dict_decayheat = {}
sim_time = alldecayheats[-1][0]
# Get only one nuclide per entry by adding decay heats
for time_step, nuc, dh in alldecayheats:
sec = (sim_time - time_step) * MCONV
q_i = dh * 0.5**(sec * data.decay_const(nuc))
if nuc in dict_decayheat.keys():
dict_decayheat[nuc] += q_i
else:
dict_decayheat[nuc] = q_i
# Put back into list of tuples & sort by time-step
decayheat = dict_decayheat.items()
decayheat.sort()
# calculate decay heats of each nuc 0, 10, 100, 1000, 10000 yrs after sim
decayheats = []
for nuc, dh0 in decayheat:
t = 10
dhs = (dh0,)
while t <= 10000:
sec = t * YCONV
dh = dh0 * 0.5**(sec * data.decay_const(nuc))
dhs += (dh,)
t = 10 * t
row = (nuc,) + tuple(dhs)
decayheats.append(row)
# Write to csv file
fname = 'decayheat.csv'
with open(fname,'w') as out:
csv_out=csv.writer(out)
csv_out.writerow(['nuclide',
'decay heat at 0 yrs [MW]',
'decay heat at 10 yrs [MW]',
'decay heat at 100 yrs [MW]',
'decay heat at 1000 yrs [MW]',
'decay heat at 10000 yrs [MW]'])
for row in decayheats:
csv_out.writerow(row)
print('file saved as ' + fname + '!')
def decayheat(c):
"""Lists decay heats at 0, 10, 100, 1000, 10000 years summed over all
nuclides and facilities.
Args:
c: connection cursor to sqlite database.
"""
# Conversion of time from months to seconds
MCONV = 3.16e7 / 12
# Conversion of years to seconds
YCONV = 3.16e7
# Retrieve list of decay heats of each nuclide
alldecayheats = query(c)
dict_decayheat = {}
sim_time = alldecayheats[-1][0]
# Get only one nuclide per entry by adding decay heats
for time_step, nuc, dh in alldecayheats:
sec = (sim_time - time_step) * MCONV
q_i = dh * 0.5**(sec * data.decay_const(nuc))
if nuc in dict_decayheat.keys():
dict_decayheat[nuc] += q_i
else:
dict_decayheat[nuc] = q_i
# Put back into list of tuples & sort by time-step
decayheat = dict_decayheat.items()
decayheat.sort()
# calculate decay heats of each nuc 0, 10, 100, 1000, 10000 yrs after sim
decayheats = []
for nuc, dh0 in decayheat:
t = 10
dhs = (dh0, )
while t <= 10000:
sec = t * YCONV
dh = dh0 * 0.5**(sec * data.decay_const(nuc))
dhs += (dh, )
t = 10 * t
row = (nuc, ) + tuple(dhs)
decayheats.append(row)
# Write to csv file
fname = 'decayheat.csv'
with open(fname, 'w') as out:
csv_out = csv.writer(out)
csv_out.writerow([
'nuclide', 'decay heat at 0 yrs [MW]', 'decay heat at 10 yrs [MW]',
'decay heat at 100 yrs [MW]', 'decay heat at 1000 yrs [MW]',
'decay heat at 10000 yrs [MW]'
])
for row in decayheats:
csv_out.writerow(row)
print('file saved as ' + fname + '!')
def activity(c):
"""Lists activities of all nuclides at 10, 100, 1000, 10000 yrs from the end of the sim.
Args:
c: connection cursor to sqlite database.
"""
activities = query(c)
# Conversion of time from months to seconds
MCONV = 3.16e7 / 12
# Conversion of years to seconds
YCONV = 3.16e7
dict_acts = {}
sim_time = activities[-1][0]
# Get only one nuclide per entry, add activities @ end of sim
for time_step, nuc, mass, act in activities:
sec = (sim_time - time_step) * MCONV
acts = act * math.exp(-sec * data.decay_const(nuc))
if nuc in dict_acts.keys():
dict_acts[nuc] += acts
else:
dict_acts[nuc] = acts
# Put back into list of tuples & sort by nuclide
act_endsim = dict_acts.items()
act_endsim.sort()
# calculate activities 10, 100, 1000, 10000 yrs later
acts = []
for nuc, act0 in act_endsim:
t = 10
nuc_acts = (act0,)
while t <= 10000:
sec = t * YCONV
nuc_act = act0 * math.exp(-sec * data.decay_const(nuc))
nuc_acts += (nuc_act,)
t = 10 * t
row = (nuc,) + tuple(nuc_acts)
acts.append(row)
# Write to csv file
fname = 'activity.csv'
with open(fname,'w') as out:
csv_out=csv.writer(out)
csv_out.writerow(['nuclide',
'act at 0 yrs [Bq]',
'act at 10 yrs [Bq]',
'act at 100 yrs [Bq]',
'act at 1000 yrs [Bq]',
'act at 10000 yrs [Bq]'])
for row in acts:
csv_out.writerow(row)
print('file saved as ' + fname + '!')
def activity(c):
"""Lists activities of all nuclides at 10, 100, 1000, 10000 yrs from the end of the sim.
Args:
c: connection cursor to sqlite database.
"""
activities = query(c)
# Conversion of time from months to seconds
MCONV = 3.16e7 / 12
# Conversion of years to seconds
YCONV = 3.16e7
dict_acts = {}
sim_time = activities[-1][0]
# Get only one nuclide per entry, add activities @ end of sim
for time_step, nuc, mass, act in activities:
sec = (sim_time - time_step) * MCONV
acts = act * math.exp(-sec * data.decay_const(nuc))
if nuc in dict_acts.keys():
dict_acts[nuc] += acts
else:
dict_acts[nuc] = acts
# Put back into list of tuples & sort by nuclide
act_endsim = dict_acts.items()
act_endsim.sort()
# calculate activities 10, 100, 1000, 10000 yrs later
acts = []
for nuc, act0 in act_endsim:
t = 10
nuc_acts = (act0, )
while t <= 10000:
sec = t * YCONV
nuc_act = act0 * math.exp(-sec * data.decay_const(nuc))
nuc_acts += (nuc_act, )
t = 10 * t
row = (nuc, ) + tuple(nuc_acts)
acts.append(row)
# Write to csv file
fname = 'activity.csv'
with open(fname, 'w') as out:
csv_out = csv.writer(out)
csv_out.writerow([
'nuclide', 'act at 0 yrs [Bq]', 'act at 10 yrs [Bq]',
'act at 100 yrs [Bq]', 'act at 1000 yrs [Bq]',
'act at 10000 yrs [Bq]'
])
for row in acts:
csv_out.writerow(row)
print('file saved as ' + fname + '!')
def get_activity_Ci(isodict=moldict, valtype="mol"):
activity_Ci={}
ci_dec_per_sec = 3.7E10 # conversion factor 1 curie = 3.7E10 decays/sec
if valtype=="mol":
for iso, mols in isodict.iteritems():
dec_per_sec = mols*constants.N_A*data.decay_const(nucname.id(iso))
activity_Ci[nucname.name(iso)]= dec_per_sec/ci_dec_per_sec
elif valtype=="mass":
for iso, mass in isodict.iteritems():
dec_per_sec = mass*data.atomic_mass(nucname.id(iso))*constants.N_A*data.decay_const(nucname.id(iso))
activity_Ci[nucname.name(iso)]= dec_per_sec/ci_dec_per_sec
sorted_a = sorted(activity_Ci.iteritems(), key=operator.itemgetter(0))
print sorted_a
return activity_Ci
def query(c):
"""Lists activities of all nuclides with respect to time for all facilities.
Args:
c: connection cursor to sqlite database.
"""
# SQL query returns a table with the nuclides and their masses at each timestep
sql = ("SELECT resources.TimeCreated, compositions.NucID,"
"compositions.MassFrac*resources.Quantity ")
sql += (
"FROM resources "
"INNER JOIN compositions ON resources.QualId = compositions.QualId "
"GROUP BY resources.TimeCreated, compositions.NucId "
"ORDER BY resources.TimeCreated;")
cur = c.execute(sql)
results = cur.fetchall()
# Gives avogadro's number with a kg to g conversion
CONV = 1000 * 6.022e23
activities = []
# Calculates activities (/s) of each nuclide at each timestep
for time_step, nuc, mass in results:
act = CONV * mass * data.decay_const(nuc) / data.atomic_mass(nuc)
row = (time_step, nuc, mass, act)
activities.append(row)
return activities
def query(c):
"""Lists decay heats of all nuclides with respect to time for all facilities.
Args:
c: connection cursor to sqlite database.
"""
# gives avogadro's number with a kg to g conversion
ACT_CONV = 1000 * 6.022e23
# converts from MeV/s to MW
Q_CONV = 1.602e-19
# SQL query returns a table with the nuclides (and their masses) transacted from reactor
sql = ("SELECT resources.TimeCreated, compositions.NucId,"
"compositions.MassFrac*resources.Quantity ")
sql += (
"FROM resources "
"INNER JOIN compositions ON resources.QualId = compositions.QualId "
"INNER JOIN transactions ON resources.TimeCreated = transactions.Time "
"WHERE transactions.SenderId=13 "
"GROUP BY resources.TimeCreated, compositions.NucId "
"ORDER BY resources.TimeCreated;")
cur = c.execute(sql)
results = cur.fetchall()
alldecayheats = []
# Calculates decay heat (MW) at each timestep
for time_step, nuc, mass in results:
act = ACT_CONV * mass * data.decay_const(nuc) / data.atomic_mass(nuc)
dh = Q_CONV * act * data.q_val(nuc)
row = (time_step, nuc, dh)
alldecayheats.append(row)
return alldecayheats
def query(c):
"""Lists activities of all nuclides with respect to time for all facilities.
Args:
c: connection cursor to sqlite database.
"""
# SQL query returns a table with the nuclides and their masses at each timestep
sql = ("SELECT Resources.TimeCreated, Compositions.NucID,"
"Compositions.MassFrac*Resources.Quantity ")
sql += ("FROM Resources "
"INNER JOIN Compositions ON Resources.StateID = Compositions.StateID "
"GROUP BY Resources.TimeCreated, Compositions.NucID "
"ORDER BY Resources.TimeCreated;")
cur = c.execute(sql)
results = cur.fetchall()
# Gives avogadro's number with a kg to g conversion
CONV = 1000*6.022e23
activities = []
# Calculates activities (/s) of each nuclide at each timestep
for time_step, nuc, mass in results:
act = CONV * mass * data.decay_const(nuc) / data.atomic_mass(nuc)
row = (time_step, nuc, act)
activities.append(row)
return activities
def query(c):
"""Lists decay heats of all nuclides with respect to time for all facilities.
Args:
c: connection cursor to sqlite database.
"""
# gives avogadro's number with a kg to g conversion
ACT_CONV = 1000*6.022e23
# converts from MeV/s to MW
Q_CONV = 1.602e-19
# SQL query returns a table with the nuclides (and their masses) transacted from reactor
sql = ("SELECT resources.TimeCreated, compositions.NucId,"
"compositions.MassFrac*resources.Quantity ")
sql += ("FROM resources "
"INNER JOIN compositions ON resources.QualId = compositions.QualId "
"INNER JOIN transactions ON resources.TimeCreated = transactions.Time "
"WHERE transactions.SenderId=13 "
"GROUP BY resources.TimeCreated, compositions.NucId "
"ORDER BY resources.TimeCreated;")
cur = c.execute(sql)
results = cur.fetchall()
alldecayheats = []
# Calculates decay heat (MW) at each timestep
for time_step, nuc, mass in results:
act = ACT_CONV * mass * data.decay_const(nuc) / data.atomic_mass(nuc)
dh = Q_CONV * act * data.q_val(nuc)
row = (time_step, nuc, dh)
alldecayheats.append(row)
return alldecayheats
def test_tm171_decay():
"Tests if decay is properly implemented"
t_sim = 1.2119E+8 # Run for 3.843 years (approx 2 half lives)
lamb = data.decay_const('TM171')
exp = np.exp(-1*lamb*t_sim)
inp = Material({'TM171': 1.0}, mass=1.0)
obs = tm.transmute(inp, t=t_sim, phi=0.0, tol=1e-7)
assert_equal(exp, obs['TM171'])
def test_tm171_decay():
"Tests if decay is properly implemented"
t_sim = 1.2119E+8 # Run for 3.843 years (approx 2 half lives)
lamb = data.decay_const('TM171')
exp = np.exp(-1 * lamb * t_sim)
inp = Material({'TM171': 1.0}, mass=1.0)
obs = tm.transmute(inp, t=t_sim, phi=0.0, tol=1e-7)
assert_equal(exp, obs['TM171'])
def load_default_nucs():
with tb.open_file(nuc_data) as f:
ll = f.root.decay.level_list
stable = ll.read_where('(nuc_id%10000 == 0) & (nuc_id != 0)')
metastable = ll.read_where('metastable > 0')
nucs = set(int(nuc) for nuc in stable['nuc_id'])
nucs |= set(int(nuc) for nuc in metastable['nuc_id'])
nucs = sorted(nuc for nuc in nucs if not np.isnan(decay_const(nuc, False)))
return nucs
def load_default_nucs():
with tb.open_file(nuc_data) as f:
ll = f.root.decay.level_list
stable = ll.read_where("(nuc_id%10000 == 0) & (nuc_id != 0)")
metastable = ll.read_where("metastable > 0")
nucs = set(int(nuc) for nuc in stable["nuc_id"])
nucs |= set(int(nuc) for nuc in metastable["nuc_id"])
nucs = sorted(nuc for nuc in nucs if not np.isnan(decay_const(nuc, False)))
return nucs
def genchains(chains, sf=False):
chain = chains[-1]
children = all_children(chain[-1])
# filters spontaneous fission
if not sf:
children = {c for c in children if (0.0 == fpyield(chain[-1], c)) and (c not in chain) }
if decay_const(chain[-1]) != 0:
for child in children:
if child not in chain:
chains.append(chain + (child,))
chains = genchains(chains, sf=sf)
return chains
def genchains(chains, sf=False):
chain = chains[-1]
children = decay_children(chain[-1])
# filters spontaneous fission
if not sf:
children = {
c for c in children if (0.0 == fpyield(chain[-1], c)) and (c not in chain)
}
if decay_const(chain[-1]) != 0:
for child in children:
if child not in chain:
chains.append(chain + (child,))
chains = genchains(chains, sf=sf)
return chains
def _get_destruction(self, nuc, decay=True):
"""Computes the destruction rate of the nuclide.
Parameters
----------
nuc : int
Name of the nuclide in question
decay : bool
True if the decay constant should be added to the returned value.
False if only destruction from neutron reactions should be considered.
Returns
-------
d : float
Destruction rate of the nuclide.
"""
xscache = self.xscache
sig_a = sigma_a(nuc, xs_cache=xscache)
d = utils.from_barns(sig_a[0], 'cm2') * xscache['phi_g'][0]
if decay and not np.isnan(data.decay_const(nuc)):
d += data.decay_const(nuc)
return d
def _get_destruction(self, nuc, decay=True):
"""Computes the destruction rate of the nuclide.
Parameters
----------
nuc : int
Name of the nuclide in question
decay : bool
True if the decay constant should be added to the returned value.
False if only destruction from neutron reactions should be considered.
Returns
-------
d : float
Destruction rate of the nuclide.
"""
xscache = self.xscache
sig_a = sigma_a(nuc, xs_cache=xscache)
d = utils.from_barns(sig_a[0], 'cm2') * xscache['phi_g'][0]
if decay and not np.isnan(data.decay_const(nuc)):
d += data.decay_const(nuc)
return d
def calc_decay_depletion(isotopes, DATA):
# Create dictionary to keep track of daughters
daughter_flags = dict()
for iso in isotopes:
daughter_flags[iso] = False
dec_depletion = np.zeros([len(isotopes) + 2, len(isotopes) + 2])
# Decay from j to i
for i, iso_i in enumerate(isotopes):
for j, iso_j in enumerate(isotopes):
# Off-diagonal terms
if j < i or j > i:
# if j < i:
ratio = data.branch_ratio(iso_j, iso_i)
# print('print(iso_j, iso_i, ratio)')
# print(iso_j, iso_i, ratio)
# print(iso_j, iso_i, ratio)
if ratio > 0:
decay_const = data.decay_const(iso_j)
dec_depletion[i, j] -= ratio * decay_const
daughter_flags[iso_j] = True
# if iso_j=='932340':
# print(iso_j, iso_i, data.branch_ratio(iso_j,iso_i))
# Diagonal terms
elif i == j:
# Add decay constant here
# print(iso_j, data.half_life(iso_j))
dec_depletion[i, j] += data.decay_const(iso_j)
for i, iso in enumerate(isotopes):
if not daughter_flags[iso] and dec_depletion[i, i] != 0:
print("Warning: no decay daughter for ", iso)
dec_depletion[-2, i] += -dec_depletion[i, i]
return dec_depletion
def _build_matrix(N):
""" This function builds burnup matrix, A. Decay only.
"""
A = np.zeros((len(N), len(N)))
# convert N to id form
N_id = []
for i in xrange(len(N)):
ID = id(N[i])
N_id.append(ID)
sds = SimpleDataSource()
# Decay
for i in xrange(len(N)):
A[i, i] -= decay_const(N_id[i])
# Find decay parents
for k in xrange(len(N)):
if N_id[i] in decay_children(N_id[k]):
A[k, i] += decay_const(N_id[k])
return A
def activity(series):
"""Activity metric returns the instantaneous activity of a nuclide
in a material (material mass * decay constant / atomic mass)
indexed by the SimId, QualId, ResourceId, ObjId, TimeCreated, and NucId.
"""
tools.raise_no_pyne('Activity could not be computed', HAVE_PYNE)
mass = series[0]
act = []
for (simid, qual, res, obj, time, nuc), m in mass.iteritems():
val = (1000 * data.N_A * m * data.decay_const(nuc) \
/ data.atomic_mass(nuc))
act.append(val)
act = pd.Series(act, index=mass.index)
act.name = 'Activity'
rtn = act.reset_index()
return rtn
def activity(series):
"""Activity metric returns the instantaneous activity of a nuclide
in a material (material mass * decay constant / atomic mass)
indexed by the SimId, QualId, ResourceId, ObjId, TimeCreated, and NucId.
"""
tools.raise_no_pyne('Activity could not be computed', HAVE_PYNE)
mass = series[0]
act = []
for (simid, qual, res, obj, time, nuc), m in mass.iteritems():
val = (1000 * data.N_A * m * data.decay_const(nuc) \
/ data.atomic_mass(nuc))
act.append(val)
act = pd.Series(act, index=mass.index)
act.name = 'Activity'
rtn = act.reset_index()
return rtn
def add_child_decays(nuc, symbols):
try:
childname = nucname.name(nuc)
except RuntimeError:
return
for rx in DECAY_RXS:
try:
parent = rxname.parent(nuc, rx, b'decay')
except RuntimeError:
continue
if data.branch_ratio(parent, nuc) < 1e-16:
continue
parname = nucname.name(parent)
symbols['lambda_' + parname] = data.decay_const(parent)
gamma = 'gamma_{0}_{1}_{2}'.format(parname, childname, rx)
symbols[gamma] = data.branch_ratio(parent, nuc)
def k_a(chain, short=1e-8):
# gather data
hl = np.array([half_life(n, False) for n in chain])
a = -1.0 / hl
dc = np.array(list(map(lambda nuc: decay_const(nuc, False), chain)))
if np.isnan(dc).any():
# NaNs are bad, mmmkay. Nones mean we should skip
return None, None
ends_stable = (dc[-1] < 1e-16) # check if last nuclide is a stable species
# compute cij -> ci in prep for k
cij = dc[:, np.newaxis] / (dc[:, np.newaxis] - dc)
if ends_stable:
cij[-1] = -1.0 / dc # adjustment for stable end nuclide
mask = np.ones(len(chain), dtype=bool)
cij[mask, mask] = 1.0 # identity is ignored, set to unity
ci = cij.prod(axis=0)
# compute k
if ends_stable:
k = dc * ci
k[-1] = 1.0
else:
k = (dc / dc[-1]) * ci
if np.isinf(k).any():
# if this happens then something wen very wrong, skip
return None, None
# compute and apply branch ratios
gamma = np.prod(
[all_branch_ratio(p, c) for p, c in zip(chain[:-1], chain[1:])])
if gamma == 0.0 or np.isnan(gamma):
return None, None
k *= gamma
# half-life filter, makes compiling faster by pre-ignoring negligible species
# in this chain. They'll still be picked up in their own chains.
if ends_stable:
mask = (hl[:-1] / hl[:-1].sum()) > short
mask = np.append(mask, True)
else:
mask = (hl / hl.sum()) > short
if mask.sum() < 2:
mask = np.ones(len(chain), dtype=bool)
return k[mask], a[mask]
def k_a(chain, short=1e-8):
# gather data
hl = np.array([half_life(n, False) for n in chain])
a = -1.0 / hl
dc = np.array(list(map(lambda nuc: decay_const(nuc, False), chain)))
if np.isnan(dc).any():
# NaNs are bad, mmmkay. Nones mean we should skip
return None, None
ends_stable = (dc[-1] < 1e-16) # check if last nuclide is a stable species
# compute cij -> ci in prep for k
cij = dc[:, np.newaxis] / (dc[:, np.newaxis] - dc)
if ends_stable:
cij[-1] = -1.0 / dc # adjustment for stable end nuclide
mask = np.ones(len(chain), dtype=bool)
cij[mask, mask] = 1.0 # identity is ignored, set to unity
ci = cij.prod(axis=0)
# compute k
if ends_stable:
k = dc * ci
k[-1] = 1.0
else:
k = (dc / dc[-1]) * ci
if np.isinf(k).any():
# if this happens then something wen very wrong, skip
return None, None
# compute and apply branch ratios
gamma = np.prod([all_branch_ratio(p, c) for p, c in zip(chain[:-1], chain[1:])])
if gamma == 0.0 or np.isnan(gamma):
return None, None
k *= gamma
# half-life filter, makes compiling faster by pre-ignoring negligible species
# in this chain. They'll still be picked up in their own chains.
if ends_stable:
mask = (hl[:-1] / hl[:-1].sum()) > short
mask = np.append(mask, True)
else:
mask = (hl / hl.sum()) > short
if mask.sum() < 2:
mask = np.ones(len(chain), dtype=bool)
return k[mask], a[mask]
def enddecayheat(c):
"""Lists decay heat at end of simulation.
Args:
c: connection cursor to sqlite database.
"""
# Conversion of time from months to seconds
CONV = 3.16e7 / 12
# Retrieve list of decay heats of each nuclide
alldecayheats = query(c)
end_heat = 0
sim_time = alldecayheats[-1][0]
# Sum decayed heats for each time-step/nuclide
for time_step, nuc, dh in alldecayheats:
t = (sim_time - time_step) * CONV
exp = t * data.decay_const(nuc)
q_i = dh * 0.5**exp
end_heat += q_i
return end_heat
def enddecayheat(c):
"""Lists decay heat at end of simulation.
Args:
c: connection cursor to sqlite database.
"""
# Conversion of time from months to seconds
CONV = 3.16e7 / 12
# Retrieve list of decay heats of each nuclide
alldecayheats = query(c)
end_heat = 0
sim_time = alldecayheats[-1][0]
# Sum decayed heats for each time-step/nuclide
for time_step, nuc, dh in alldecayheats:
t = (sim_time - time_step) * CONV
exp = t * data.decay_const(nuc)
q_i = dh * 0.5**exp
end_heat += q_i
return end_heat
def inventories_activity(evaler, facilities=(), nucs=()):
"""
Get a simple time series of the activity of the inventory in the selcted
facilities. Applying nuclides selection when required.
Parameters
----------
evaler : evaler
facilities : of the facility
nucs : of nuclide to select.
"""
if len(nucs) != 0:
nucs = format_nucs(nucs)
df = inventories(evaler, facilities, nucs)
for i, row in df.iterrows():
val = 1000 * data.N_A * row['Quantity'] * \
data.decay_const(int(row['NucId']))
df.set_value(i, 'Activity', val)
return df
def inventories_activity(evaler, facilities=(), nucs=()):
"""
Get a simple time series of the activity of the inventory in the selcted
facilities. Applying nuclides selection when required.
Parameters
----------
evaler : evaler
facilities : of the facility
nucs : of nuclide to select.
"""
if len(nucs) != 0:
nucs = format_nucs(nucs)
df = inventories(evaler, facilities, nucs)
for i, row in df.iterrows():
val = 1000 * data.N_A * row['Quantity'] * \
data.decay_const(int(row['NucId']))
df.set_value(i, 'Activity', val)
return df
def gencase(nuc, idx, b, short=1e-8, sf=False):
case = ['}} case {0}: {{'.format(nuc)]
dc = decay_const(nuc, False)
if dc == 0.0:
# stable nuclide
case.append(CHAIN_STMT.format(idx[nuc], 'it->second'))
else:
chains = genchains([(nuc,)], sf=sf)
print(len(chains), len(set(chains)), nuc)
cse = {} # common sub-expression exponents to elimnate
bt = 0
for c in chains:
if c[-1] not in idx:
continue
cexpr, b, bt = chainexpr(c, cse, b, bt, short=short)
if cexpr is None:
continue
case.append(CHAIN_STMT.format(idx[c[-1]], cexpr))
bstmts = [' ' + B_STMT.format(exp=exp, b=bval) for exp, bval in \
sorted(cse.items(), key=lambda x: x[1])]
case = case[:1] + bstmts + case[1:]
case.append(BREAK)
return case, b
def activity(c):
"""Lists activities of all nuclides at a given time (in years) from the end of the sim.
Args:
c: connection cursor to sqlite database.
"""
activities = query(c)
# Conversion of time from months to seconds
MCONV = 3.16e7 / 12
# Conversion of years to seconds
YCONV = 3.16e7
dict_acts = {}
t = input("Enter a time in years: ")
sim_time = activities[-1][0]
time = sim_time * MCONV + t * YCONV
# Get only one nuclide per entry, add activities
for time_step, nuc, act in activities:
sec = time - time_step * MCONV
act = act * math.exp(-sec * data.decay_const(nuc))
if nuc in dict_acts.keys():
dict_acts[nuc] += act
else:
dict_acts[nuc] = act
# Put back into list of tuples & sort by nuclide
acts = dict_acts.items()
acts.sort()
return acts
from pyne import data, nucname
import numpy as np
print(data.decay_const('U-235'))
print(data.decay_const('922350'))
print(data.decay_const('922350000'))
print(data.branch_ratio('932390000','942390000', use_metastable=False))
print(data.decay_children('932390000'))
print(data.decay_const('942420000'))
print(data.decay_children('942420000'))
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-----')
def get_decay_constant(self):
return OrderedDict(
(nuc_name, data.decay_const(nuc_id)) for nuc_id, nuc_name in zip(
self.get_all_children(), self.get_all_children_nuc_name()))
def test_decay_const():
assert_equal(data.decay_const('H1'), 0.0)
assert_equal(data.decay_const(922351), np.log(2.0) / 1560.0)
def test_decay_const():
assert_equal(data.decay_const("H1"), 0.0)
assert_equal(data.decay_const(922351), np.log(2.0) / 1560.0)
def test_decay_const():
assert_equal(data.decay_const('H1'), 0.0)
assert_equal(data.decay_const(922350001), np.log(2.0) / 1560.0)
else:
term = "0"
else:
b = ensure_cse(a_i, b, cse)
term = kbexpr(k_i, b_from_a(cse, a_i))
# multiply by t if needed
if t_term_i:
term += "*t"
terms.append(term)
terms = " + ".join(terms)
return CHAIN_EXPR.format(terms), b, bt
def gencase(nuc, idx, b, short=1e-16, small=1e-16, sf=False, debug=False):
case = ["}} case {0}: {{".format(nuc)]
dc = decay_const(nuc, False)
if dc == 0.0:
# stable nuclide
case.append(CHAIN_STMT.format(idx[nuc], "it->second"))
else:
chains = genchains([(nuc,)], sf=sf)
print("{} has {} chains".format(nucname.name(nuc), len(set(chains))))
cse = {} # common sub-expression exponents to elimnate
bt = 0
for c in chains:
if c[-1] not in idx:
continue
cexpr, b, bt = chainexpr(c, cse, b, bt, short=short, small=small)
if cexpr is None:
continue
if debug:
def rel_activity(c):
"""Lists activity of spent fuel from all facilities relative to natural U
0, 10, 100, 1000, 10000 years after the end of the simulation.
Args:
c: connection cursor to sqlite database.
"""
activities = activity.query(c)
dict_acts = {}
sim_time = activities[-1][0]
# Conversion of time from months to seconds
MCONV = 3.16e7 / 12
# Conversion of years to seconds
YCONV = 3.16e7
dict_acts = {}
tot_mass = 0.0
sim_time = activities[-1][0]
# Get list of one activity per nuclide wrt end of sim & sum total mass
for time_step, nuc, mass, act in activities:
tot_mass += mass
sec = (sim_time - time_step) * MCONV
acts = act * math.exp(-sec * data.decay_const(nuc))
if nuc in dict_acts.keys():
dict_acts[nuc] += acts
else:
dict_acts[nuc] = acts
# Put back into list of tuples & sort by nuclide
act_endsim = dict_acts.items()
act_endsim.sort()
# calculate natural uranium activity
CONV_235 = 0.007*1000*6.022e23
CONV_238 = 0.993*1000*6.022e23
actU235 = CONV_235 * tot_mass * data.decay_const('U235') / data.atomic_mass('U235')
actU238 = CONV_238 * tot_mass * data.decay_const('U235') / data.atomic_mass('U235')
act_U = actU235 + actU238
# calculate relative activities to nat U after 0, 10, 100, 1000, 10000 yrs
rel_acts = []
for nuc, act0 in act_endsim:
t = 10
nuc_acts = (act0,)
while t <= 10000:
sec = t * YCONV
nuc_act = act0 * math.exp(-sec * data.decay_const(nuc))
nuc_acts += (nuc_act,)
t = 10 * t
rel = []
for i in nuc_acts:
frac = i / act_U
rel.append(frac)
row = (nuc,) + tuple(rel)
rel_acts.append(row)
# Write to csv file
fname = 'relative_activity.csv'
with open(fname,'w') as out:
csv_out=csv.writer(out)
csv_out.writerow(['nuclide',
'rel_act at 0 yrs',
'rel_act at 10 yrs',
'rel_act at 100 yrs',
'rel_act at 1000 yrs',
'rel_act at 10000 yrs'])
for row in rel_acts:
csv_out.writerow(row)
print('file saved as ' + fname + '!')
def _traversal(self, nuc, A, out, depth=0):
"""Nuclide transmutation traversal method.
This method will traverse the reaction tree recursively, using a DFS
algorithm. On termination, the method will return all number densities
after a given time that are a result of the starting nuclide.
Parameters
----------
nuc : int
ID of the active nuclide for the traversal.
A : NumPy 2-dimensional array
Current state of the coupled equation matrix.
out : dict
A dictionary containing the final recorded number densities for each
nuclide. Keys are nuclide names in integer id form. Values are
number densities for the coupled nuclide in float format. This is
modified in place.
depth : int
Current depth of traversal (root at 0). Should never be provided by user.
"""
t = self.t
tol = self.tol
phi = self.xscache['phi_g'][0]
temp = self.temp
xscache = self.xscache
if self.log is not None:
self._log_tree(depth, nuc, 1.0)
prod = {}
# decay info
lam = data.decay_const(nuc)
decay_branches = {} if lam == 0 else self._decay_branches(nuc)
for decay_child, branch_ratio in decay_branches.items():
prod[decay_child] = lam * branch_ratio
# reaction daughters
for rx in self.rxs:
try:
child = rxname.child(nuc, rx)
except RuntimeError:
continue
child_xs = xscache[nuc, rx, temp][0]
rr = utils.from_barns(child_xs, 'cm2') * phi # reaction rate
prod[child] = rr + prod.get(child, 0.0)
# Cycle production dictionary
for child in prod:
# Grow matrix
d = self._get_destruction(child)
B = self._grow_matrix(A, prod[child], d)
# Create initial density vector
n = B.shape[0]
N0 = np.zeros((n, 1), dtype=float)
N0[0] = 1.0
# Compute matrix exponential and dot with density vector
eB = linalg.expm(B * t)
N_final = np.dot(eB, N0) # <-- DENSE
#N_final = eB.dot(N0) # <-- SPARSE
if self.log is not None:
self._log_tree(depth + 1, child, N_final[-1])
# Check against tolerance and continue traversal
if N_final[-1] > tol:
self._traversal(child, B, out, depth=depth + 1)
# On recursion exit or truncation, write data from this nuclide
outval = N_final[-1, 0] + out.get(child, 0.0)
if 0.0 < outval:
out[child] = outval
def test_decay_const():
assert_equal(data.decay_const("H1"), 0.0)
assert_equal(data.decay_const(922350001), np.log(2.0) / 1560.0)
def _create_decay_matrix(nucs):
nnucs = len(nucs)
nucsrange = np.arange(nnucs)
A = np.zeros((nnucs, nnucs), dtype=float)
A[nucsrange, nucsrange] = [-data.decay_const(nuc) for nuc in nucs]
return A
def _traversal(self, nuc, A, out, depth=0):
"""Nuclide transmutation traversal method.
This method will traverse the reaction tree recursively, using a DFS
algorithm. On termination, the method will return all number densities
after a given time that are a result of the starting nuclide.
Parameters
----------
nuc : int
ID of the active nuclide for the traversal.
A : NumPy 2-dimensional array
Current state of the coupled equation matrix.
out : dict
A dictionary containing the final recorded number densities for each
nuclide. Keys are nuclide names in integer id form. Values are
number densities for the coupled nuclide in float format. This is
modified in place.
depth : int
Current depth of traversal (root at 0). Should never be provided by user.
"""
t = self.t
tol = self.tol
phi = self.xscache['phi_g'][0]
temp = self.temp
xscache = self.xscache
if self.log is not None:
self._log_tree(depth, nuc, 1.0)
prod = {}
# decay info
lam = data.decay_const(nuc)
decay_branches = {} if lam == 0 else self._decay_branches(nuc)
for decay_child, branch_ratio in decay_branches.items():
prod[decay_child] = lam * branch_ratio
# reaction daughters
for rx in self.rxs:
try:
child = rxname.child(nuc, rx)
except RuntimeError:
continue
child_xs = xscache[nuc, rx, temp][0]
rr = utils.from_barns(child_xs, 'cm2') * phi # reaction rate
prod[child] = rr + prod.get(child, 0.0)
# Cycle production dictionary
for child in prod:
# Grow matrix
d = self._get_destruction(child)
B = self._grow_matrix(A, prod[child], d)
# Create initial density vector
n = B.shape[0]
N0 = np.zeros((n, 1), dtype=float)
N0[0] = 1.0
# Compute matrix exponential and dot with density vector
eB = linalg.expm(B * t)
N_final = np.dot(eB, N0) # <-- DENSE
#N_final = eB.dot(N0) # <-- SPARSE
if self.log is not None:
self._log_tree(depth+1, child, N_final[-1])
# Check against tolerance and continue traversal
if N_final[-1] > tol:
self._traversal(child, B, out, depth=depth+1)
# On recursion exit or truncation, write data from this nuclide
outval = N_final[-1,0] + out.get(child, 0.0)
if 0.0 < outval:
out[child] = outval