def __init__(self,
atomicAbundance: AtomicAbundance = None,
kuruczPfPath: str = None):
if atomicAbundance is None:
atomicAbundance = DefaultAtomicAbundance
self.atomicAbundance = atomicAbundance
kuruczPfPath = get_data_path(
) + 'pf_Kurucz.input' if kuruczPfPath is None else kuruczPfPath
with open(kuruczPfPath, 'rb') as f:
s = f.read()
u = Unpacker(s)
# NOTE(cmo): Each of these terms is simply in flat lists indexed by Atomic Number Z-1
self.Tpf = np.array(u.unpack_array(u.unpack_double))
stages = []
pf = []
ionpot = []
for i in range(99):
z = u.unpack_int()
stages.append(u.unpack_int())
pf.append(
np.array(
u.unpack_farray(stages[-1] * self.Tpf.shape[0],
u.unpack_double)).reshape(
stages[-1], self.Tpf.shape[0]))
ionpot.append(
np.array(u.unpack_farray(stages[-1], u.unpack_double)))
ionpot = [i * Const.HC / Const.CM_TO_M for i in ionpot]
pf = [np.log(p) for p in pf]
self.pf = pf
self.ionpot = ionpot
def getvalue(self):
if isinstance(self.var, SequenceType):
out = []
mark = self._unpack_uint()
while mark == 1509949440:
var = self.var
# Create a structure with the sequence vars:
self.var = StructureType(name=self.var.name)
self.var.update(var)
out.append(self.getvalue())
self.var = var
mark = self._unpack_uint()
elif isinstance(self.var, StructureType):
out = []
for child in self.var.walk():
var = self.var
self.var = child
out.append(self.getvalue())
self.var = var
out = tuple(out)
else:
# Get data length.
n = 1
if getattr(self.var, 'shape', False):
n = self._unpack_uint()
if self.var.type not in [Url, String]:
self._unpack_uint()
# Bytes are treated differently.
if self.var.type == Byte:
out = self._unpack_bytes(n)
out = numpy.array(out, self.var.type.typecode)
# As are strings...
elif self.var.type in [Url, String]:
out = self._unpack_string(n)
out = numpy.array(out, self.var.type.typecode)
else:
i = self._pos
self._pos = j = i + (n*self.var.type.size)
#dtype = ">%s%s" % (self.var.type.typecode, self.var.type.size)
#out = numpy.fromstring(self._buf[i:j], dtype=dtype)
if self.var.type.typecode == 'i':
un = Unpacker(self._buf[i:j])
out = un.unpack_farray( n, un.unpack_int )
elif (self.var.type.typecode == 'f') and (self.var.type.size == 8):
un = Unpacker(self._buf[i:j])
out = un.unpack_farray( n, un.unpack_double )
elif (self.var.type.typecode == 'f') and (self.var.type.size == 4):
un = Unpacker(self._buf[i:j])
out = un.unpack_farray( n, un.unpack_float )
else:
print "type", self.var.type.typecode
pass
#print out
return out
def __init__(self, kuruczPfPath: Optional[str]=None, metallicity: float=0.0,
abundances: Dict=None, abundDex: bool=True):
if set(AtomicWeights.keys()) != set(AtomicAbundances.keys()):
raise ValueError('AtomicWeights and AtomicAbundances keys differ (Problem keys: %s)' % repr(set(AtomicWeights.keys()) - set(AtomicAbundances.keys())))
self.indices = OrderedDict(zip(AtomicWeights.keys(), range(len(AtomicWeights))))
# Convert abundances and overwrite any provided secondary abundances
self.abund = deepcopy(AtomicAbundances)
if self.abund['H '] == 12.0:
for k, v in self.abund.items():
self.abund[k] = 10**(v - 12.0)
if abundances is not None:
if abundDex:
for k, v in abundances.items():
abundances[k] = 10**(v - 12.0)
for k, v in abundances.items():
self.abund[k] = v
metallicity = 10**metallicity
for k, v in self.abund.items():
if k != 'H ':
self.abund[k] = v*metallicity
kuruczPfPath = get_data_path() + 'pf_Kurucz.input' if kuruczPfPath is None else kuruczPfPath
with open(kuruczPfPath, 'rb') as f:
s = f.read()
u = Unpacker(s)
self.Tpf = np.array(u.unpack_array(u.unpack_double))
ptIndex = [] # Index in the periodic table (fortran based, so +1) -- could be used for validation
stages = []
pf = []
ionpot = []
for i in range(len(AtomicWeights)):
ptIndex.append(u.unpack_int())
stages.append(u.unpack_int())
pf.append(np.array(u.unpack_farray(stages[-1] * self.Tpf.shape[0], u.unpack_double)).reshape(stages[-1], self.Tpf.shape[0]))
ionpot.append(np.array(u.unpack_farray(stages[-1], u.unpack_double)))
ionpot = [i * Const.HC / Const.CM_TO_M for i in ionpot]
pf = [np.log(p) for p in pf]
totalAbund = 0.0
avgWeight = 0.0
self.elements: List[Element] = []
for k, v in AtomicWeights.items():
i = self.indices[k]
ele = Element(k, v, self.abund[k], ionpot[i], self.Tpf, pf[i])
self.elements.append(ele)
totalAbund += ele.abundance
avgWeight += ele.abundance * ele.weight
self.totalAbundance = totalAbund
self.weightPerH = avgWeight
self.avgMolWeight = avgWeight / totalAbund
def read_pf(path):
with open(path, 'rb') as f:
s = f.read()
u = Unpacker(s)
Tpf = u.unpack_array(u.unpack_double)
ptis = []
stages = []
pf = []
ionpot = []
for i in range(len(AtomicWeights)):
ptis.append(u.unpack_int())
stages.append(u.unpack_int())
pf.append(u.unpack_farray(stages[-1] * len(Tpf), u.unpack_double))
ionpot.append(u.unpack_farray(stages[-1], u.unpack_double))
return {'Tpf': Tpf, 'stages': stages, 'pf': pf, 'ionpot': ionpot}