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OpenMC/openmc/data/multipole.py
Sterling Harper efade329a8 Address #983 comments
2018-03-19 12:55:46 -04:00

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from numbers import Integral, Real
from math import exp, erf, pi, sqrt
import h5py
import numpy as np
from . import WMP_VERSION
from .data import K_BOLTZMANN
import openmc.checkvalue as cv
from openmc.mixin import EqualityMixin
# Formalisms
_FORM_MLBW = 2
_FORM_RM = 3
# Constants that determine which value to access
_MP_EA = 0 # Pole
# Reich-Moore indices
_RM_RT = 1 # Residue total
_RM_RA = 2 # Residue absorption
_RM_RF = 3 # Residue fission
# Multi-level Breit Wigner indices
_MLBW_RT = 1 # Residue total
_MLBW_RX = 2 # Residue competitive
_MLBW_RA = 3 # Residue absorption
_MLBW_RF = 4 # Residue fission
# Polynomial fit indices
_FIT_T = 0 # Total
_FIT_A = 1 # Absorption
_FIT_F = 2 # Fission
def _faddeeva(z):
r"""Evaluate the complex Faddeeva function.
Technically, the value we want is given by the equation:
.. math::
w(z) = \frac{i}{\pi} \int_{-\infty}^{\infty} \frac{1}{z - t}
\exp(-t^2) \text{d}t
as shown in Equation 63 from Hwang, R. N. "A rigorous pole
representation of multilevel cross sections and its practical
applications." Nuclear Science and Engineering 96.3 (1987): 192-209.
The :func:`scipy.special.wofz` function evaluates
:math:`w(z) = \exp(-z^2) \text{erfc}(-iz)`. These two forms of the Faddeeva
function are related by a transformation.
If we call the integral form :math:`w_\text{int}`, and the function form
:math:`w_\text{fun}`:
.. math::
w_\text{int}(z) =
\begin{cases}
w_\text{fun}(z) & \text{for } \text{Im}(z) > 0\\
-w_\text{fun}(z^*)^* & \text{for } \text{Im}(z) < 0
\end{cases}
Parameters
----------
z : complex
Argument to the Faddeeva function.
Returns
-------
complex
:math:`\frac{i}{\pi} \int_{-\infty}^{\infty} \frac{1}{z - t} \exp(-t^2)
\text{d}t`
"""
from scipy.special import wofz
if np.angle(z) > 0:
return wofz(z)
else:
return -np.conj(wofz(z.conjugate()))
def _broaden_wmp_polynomials(E, dopp, n):
r"""Evaluate Doppler-broadened windowed multipole curvefit.
The curvefit is a polynomial of the form :math:`\frac{a}{E}
+ \frac{b}{\sqrt{E}} + c + d \sqrt{E} + \ldots`
Parameters
----------
E : Real
Energy to evaluate at.
dopp : Real
sqrt(atomic weight ratio / kT) in units of eV.
n : Integral
Number of components to the polynomial.
Returns
-------
numpy.ndarray
The value of each Doppler-broadened curvefit polynomial term.
"""
sqrtE = sqrt(E)
beta = sqrtE * dopp
half_inv_dopp2 = 0.5 / dopp**2
quarter_inv_dopp4 = half_inv_dopp2**2
if beta > 6.0:
# Save time, ERF(6) is 1 to machine precision.
# beta/sqrtpi*exp(-beta**2) is also approximately 1 machine epsilon.
erf_beta = 1.0
exp_m_beta2 = 0.0
else:
erf_beta = erf(beta)
exp_m_beta2 = exp(-beta**2)
# Assume that, for sure, we'll use a second order (1/E, 1/V, const)
# fit, and no less.
factors = np.zeros(n)
factors[0] = erf_beta / E
factors[1] = 1.0 / sqrtE
factors[2] = (factors[0] * (half_inv_dopp2 + E)
+ exp_m_beta2 / (beta * sqrt(pi)))
# Perform recursive broadening of high order components. range(1, n-2)
# replaces a do i = 1, n-3. All indices are reduced by one due to the
# 1-based vs. 0-based indexing.
for i in range(1, n-2):
if i != 1:
factors[i+2] = (-factors[i-2] * (i - 1.0) * i * quarter_inv_dopp4
+ factors[i] * (E + (1.0 + 2.0 * i) * half_inv_dopp2))
else:
factors[i+2] = factors[i]*(E + (1.0 + 2.0 * i) * half_inv_dopp2)
return factors
class WindowedMultipole(EqualityMixin):
"""Resonant cross sections represented in the windowed multipole format.
Parameters
----------
formalism : {'MLBW', 'RM'}
The R-matrix formalism used to reconstruct resonances. Either 'MLBW'
for multi-level Breit Wigner or 'RM' for Reich-Moore.
Attributes
----------
num_l : Integral
Number of possible l quantum states for this nuclide.
fit_order : Integral
Order of the windowed curvefit.
fissionable : bool
Whether or not the target nuclide has fission data.
formalism : {'MLBW', 'RM'}
The R-matrix formalism used to reconstruct resonances. Either 'MLBW'
for multi-level Breit Wigner or 'RM' for Reich-Moore.
spacing : Real
The width of each window in sqrt(E)-space. For example, the frst window
will end at (sqrt(start_E) + spacing)**2 and the second window at
(sqrt(start_E) + 2*spacing)**2.
sqrtAWR : Real
Square root of the atomic weight ratio of the target nuclide.
start_E : Real
Lowest energy in eV the library is valid for.
end_E : Real
Highest energy in eV the library is valid for.
data : np.ndarray
A 2D array of complex poles and residues. data[i, 0] gives the energy
at which pole i is located. data[i, 1:] gives the residues associated
with the i-th pole. There are 3 residues for Reich-Moore data, one each
for the total, absorption, and fission channels. Multi-level
Breit Wigner data has an additional residue for the competitive channel.
pseudo_k0RS : np.ndarray
A 1D array of Real values. There is one value for each valid l
quantum number. The values are equal to
sqrt(2 m / hbar) * AWR / (AWR + 1) * r
where m is the neutron mass, AWR is the atomic weight ratio, and r
is the l-dependent scattering radius.
l_value : np.ndarray
A 1D array of Integral values equal to the l quantum number for each
pole + 1.
w_start : np.ndarray
A 1D array of Integral values. w_start[i] - 1 is the index of the first
pole in window i.
w_end : np.ndarray
A 1D array of Integral values. w_end[i] - 1 is the index of the last
pole in window i.
broaden_poly : np.ndarray
A 1D array of boolean values indicating whether or not the polynomial
curvefit in that window should be Doppler broadened.
curvefit : np.ndarray
A 3D array of Real curvefit polynomial coefficients. curvefit[i, 0, :]
gives coefficients for the total cross section in window i.
curvefit[i, 1, :] gives absorption coefficients and curvefit[i, 2, :]
gives fission coefficients. The polynomial terms are increasing powers
of sqrt(E) starting with 1/E e.g:
a/E + b/sqrt(E) + c + d sqrt(E) + ...
"""
def __init__(self, formalism):
self._num_l = None
self.formalism = formalism
self.spacing = None
self.sqrtAWR = None
self.start_E = None
self.end_E = None
self.data = None
self.pseudo_k0RS = None
self.l_value = None
self.w_start = None
self.w_end = None
self.broaden_poly = None
self.curvefit = None
@property
def num_l(self):
return self._num_l
@property
def fit_order(self):
return self.curvefit.shape[1] - 1
@property
def fissionable(self):
if self.formalism == 'RM':
return self.data.shape[1] == 4
else:
# Assume self.formalism == 'MLBW'
return self.data.shape[1] == 5
@property
def formalism(self):
return self._formalism
@property
def spacing(self):
return self._spacing
@property
def sqrtAWR(self):
return self._sqrtAWR
@property
def start_E(self):
return self._start_E
@property
def end_E(self):
return self._end_E
@property
def data(self):
return self._data
@property
def pseudo_k0RS(self):
return self._pseudo_k0RS
@property
def l_value(self):
return self._l_value
@property
def w_start(self):
return self._w_start
@property
def w_end(self):
return self._w_end
@property
def broaden_poly(self):
return self._broaden_poly
@property
def curvefit(self):
return self._curvefit
@formalism.setter
def formalism(self, formalism):
cv.check_type('formalism', formalism, str)
cv.check_value('formalism', formalism, ('MLBW', 'RM'))
self._formalism = formalism
@spacing.setter
def spacing(self, spacing):
if spacing is not None:
cv.check_type('spacing', spacing, Real)
cv.check_greater_than('spacing', spacing, 0.0, equality=False)
self._spacing = spacing
@sqrtAWR.setter
def sqrtAWR(self, sqrtAWR):
if sqrtAWR is not None:
cv.check_type('sqrtAWR', sqrtAWR, Real)
cv.check_greater_than('sqrtAWR', sqrtAWR, 0.0, equality=False)
self._sqrtAWR = sqrtAWR
@start_E.setter
def start_E(self, start_E):
if start_E is not None:
cv.check_type('start_E', start_E, Real)
cv.check_greater_than('start_E', start_E, 0.0, equality=True)
self._start_E = start_E
@end_E.setter
def end_E(self, end_E):
if end_E is not None:
cv.check_type('end_E', end_E, Real)
cv.check_greater_than('end_E', end_E, 0.0, equality=False)
self._end_E = end_E
@data.setter
def data(self, data):
if data is not None:
cv.check_type('data', data, np.ndarray)
if len(data.shape) != 2:
raise ValueError('Multipole data arrays must be 2D')
if self.formalism == 'RM':
if data.shape[1] not in (3, 4):
raise ValueError('For the Reich-Moore formalism, '
'data.shape[1] must be 3 or 4. One value for the pole.'
' One each for the total and absorption residues. '
'Possibly one more for a fission residue.')
else:
# Assume self.formalism == 'MLBW'
if data.shape[1] not in (4, 5):
raise ValueError('For the Multi-level Breit-Wigner '
'formalism, data.shape[1] must be 4 or 5. One value '
'for the pole. One each for the total, competitive, '
'and absorption residues. Possibly one more for a '
'fission residue.')
if not np.issubdtype(data.dtype, complex):
raise TypeError('Multipole data arrays must be complex dtype')
self._data = data
@pseudo_k0RS.setter
def pseudo_k0RS(self, pseudo_k0RS):
if pseudo_k0RS is not None:
cv.check_type('pseudo_k0RS', pseudo_k0RS, np.ndarray)
if len(pseudo_k0RS.shape) != 1:
raise ValueError('Multipole pseudo_k0RS arrays must be 1D')
if not np.issubdtype(pseudo_k0RS.dtype, float):
raise TypeError('Multipole data arrays must be float dtype')
self._pseudo_k0RS = pseudo_k0RS
@l_value.setter
def l_value(self, l_value):
if l_value is not None:
cv.check_type('l_value', l_value, np.ndarray)
if len(l_value.shape) != 1:
raise ValueError('Multipole l_value arrays must be 1D')
if not np.issubdtype(l_value.dtype, int):
raise TypeError('Multipole l_value arrays must be integer'
' dtype')
self._num_l = len(np.unique(l_value))
else:
self._num_l = None
self._l_value = l_value
@w_start.setter
def w_start(self, w_start):
if w_start is not None:
cv.check_type('w_start', w_start, np.ndarray)
if len(w_start.shape) != 1:
raise ValueError('Multipole w_start arrays must be 1D')
if not np.issubdtype(w_start.dtype, int):
raise TypeError('Multipole w_start arrays must be integer'
' dtype')
self._w_start = w_start
@w_end.setter
def w_end(self, w_end):
if w_end is not None:
cv.check_type('w_end', w_end, np.ndarray)
if len(w_end.shape) != 1:
raise ValueError('Multipole w_end arrays must be 1D')
if not np.issubdtype(w_end.dtype, int):
raise TypeError('Multipole w_end arrays must be integer dtype')
self._w_end = w_end
@broaden_poly.setter
def broaden_poly(self, broaden_poly):
if broaden_poly is not None:
cv.check_type('broaden_poly', broaden_poly, np.ndarray)
if len(broaden_poly.shape) != 1:
raise ValueError('Multipole broaden_poly arrays must be 1D')
if not np.issubdtype(broaden_poly.dtype, bool):
raise TypeError('Multipole broaden_poly arrays must be boolean'
' dtype')
self._broaden_poly = broaden_poly
@curvefit.setter
def curvefit(self, curvefit):
if curvefit is not None:
cv.check_type('curvefit', curvefit, np.ndarray)
if len(curvefit.shape) != 3:
raise ValueError('Multipole curvefit arrays must be 3D')
if curvefit.shape[2] not in (2, 3): # sig_t, sig_a (maybe sig_f)
raise ValueError('The third dimension of multipole curvefit'
' arrays must have a length of 2 or 3')
if not np.issubdtype(curvefit.dtype, float):
raise TypeError('Multipole curvefit arrays must be float dtype')
self._curvefit = curvefit
@classmethod
def from_hdf5(cls, group_or_filename):
"""Construct a WindowedMultipole object from an HDF5 group or file.
Parameters
----------
group_or_filename : h5py.Group or str
HDF5 group containing multipole data. If given as a string, it is
assumed to be the filename for the HDF5 file, and the first group is
used to read from.
Returns
-------
openmc.data.WindowedMultipole
Resonant cross sections represented in the windowed multipole
format.
"""
if isinstance(group_or_filename, h5py.Group):
group = group_or_filename
else:
h5file = h5py.File(group_or_filename, 'r')
try:
version = h5file['version'].value.decode()
except AttributeError:
version = h5file['version'].value[0].decode()
if version != WMP_VERSION:
raise ValueError('The given WMP data uses version '
+ version + ' whereas your installation of the OpenMC '
'Python API expects version ' + WMP_VERSION)
group = h5file['nuclide']
# Read scalars.
if group['formalism'].value == _FORM_MLBW:
out = cls('MLBW')
elif group['formalism'].value == _FORM_RM:
out = cls('RM')
else:
raise ValueError('Unrecognized/Unsupported R-matrix formalism')
out.spacing = group['spacing'].value
out.sqrtAWR = group['sqrtAWR'].value
out.start_E = group['start_E'].value
out.end_E = group['end_E'].value
# Read arrays.
err = "WMP '{}' array shape is not consistent with the '{}' array shape"
out.data = group['data'].value
out.l_value = group['l_value'].value
if out.l_value.shape[0] != out.data.shape[0]:
raise ValueError(err.format('l_value', 'data'))
out.pseudo_k0RS = group['pseudo_K0RS'].value
if out.pseudo_k0RS.shape[0] != out.num_l:
raise ValueError(err.format('pseudo_k0RS', 'l_value'))
out.w_start = group['w_start'].value
out.w_end = group['w_end'].value
if out.w_end.shape[0] != out.w_start.shape[0]:
raise ValueError(err.format('w_end', 'w_start'))
out.broaden_poly = group['broaden_poly'].value.astype(np.bool)
if out.broaden_poly.shape[0] != out.w_start.shape[0]:
raise ValueError(err.format('broaden_poly', 'w_start'))
out.curvefit = group['curvefit'].value
if out.curvefit.shape[0] != out.w_start.shape[0]:
raise ValueError(err.format('curvefit', 'w_start'))
# _broaden_wmp_polynomials assumes the curve fit has at least 3 terms.
if out.fit_order < 2:
raise ValueError("Windowed multipole is only supported for "
"curvefits with 3 or more terms.")
return out
def _evaluate(self, E, T):
"""Compute total, absorption, and fission cross sections.
Parameters
----------
E : Real
Energy of the incident neutron in eV.
T : Real
Temperature of the target in K.
Returns
-------
3-tuple of Real
Total, absorption, and fission microscopic cross sections at the
given energy and temperature.
"""
if E < self.start_E: return (0, 0, 0)
if E > self.end_E: return (0, 0, 0)
# ======================================================================
# Bookkeeping
# Define some frequently used variables.
sqrtkT = sqrt(K_BOLTZMANN * T)
sqrtE = sqrt(E)
invE = 1.0 / E
# Locate us. The i_window calc omits a + 1 present in F90 because of
# the 1-based vs. 0-based indexing. Similarly startw needs to be
# decreased by 1. endw does not need to be decreased because
# range(startw, endw) does not include endw.
i_window = int(np.floor((sqrtE - sqrt(self.start_E)) / self.spacing))
startw = self.w_start[i_window] - 1
endw = self.w_end[i_window]
# Fill in factors. Because of the unique interference dips in scatering
# resonances, the total cross section has a special "factor" that does
# not appear in the absorption and fission equations.
if startw <= endw:
twophi = np.zeros(self.num_l, dtype=np.float)
sig_t_factor = np.zeros(self.num_l, dtype=np.cfloat)
for iL in range(self.num_l):
twophi[iL] = self.pseudo_k0RS[iL] * sqrtE
if iL == 1:
twophi[iL] = twophi[iL] - np.arctan(twophi[iL])
elif iL == 2:
arg = 3.0 * twophi[iL] / (3.0 - twophi[iL]**2)
twophi[iL] = twophi[iL] - np.arctan(arg)
elif iL == 3:
arg = (twophi[iL] * (15.0 - twophi[iL]**2)
/ (15.0 - 6.0 * twophi[iL]**2))
twophi[iL] = twophi[iL] - np.arctan(arg)
twophi = 2.0 * twophi
sig_t_factor = np.cos(twophi) - 1j*np.sin(twophi)
# Initialize the ouptut cross sections.
sig_t = 0.0
sig_a = 0.0
sig_f = 0.0
# ======================================================================
# Add the contribution from the curvefit polynomial.
if sqrtkT != 0 and self.broaden_poly[i_window]:
# Broaden the curvefit.
dopp = self.sqrtAWR / sqrtkT
broadened_polynomials = _broaden_wmp_polynomials(E, dopp,
self.fit_order + 1)
for i_poly in range(self.fit_order+1):
sig_t += (self.curvefit[i_window, i_poly, _FIT_T]
* broadened_polynomials[i_poly])
sig_a += (self.curvefit[i_window, i_poly, _FIT_A]
* broadened_polynomials[i_poly])
if self.fissionable:
sig_f += (self.curvefit[i_window, i_poly, _FIT_F]
* broadened_polynomials[i_poly])
else:
temp = invE
for i_poly in range(self.fit_order+1):
sig_t += self.curvefit[i_window, i_poly, _FIT_T] * temp
sig_a += self.curvefit[i_window, i_poly, _FIT_A] * temp
if self.fissionable:
sig_f += self.curvefit[i_window, i_poly, _FIT_F] * temp
temp *= sqrtE
# ======================================================================
# Add the contribution from the poles in this window.
if sqrtkT == 0.0:
# If at 0K, use asymptotic form.
for i_pole in range(startw, endw):
psi_chi = -1j / (self.data[i_pole, _MP_EA] - sqrtE)
c_temp = psi_chi / E
if self.formalism == 'MLBW':
sig_t += ((self.data[i_pole, _MLBW_RT] * c_temp *
sig_t_factor[self.l_value[i_pole]-1]).real
+ (self.data[i_pole, _MLBW_RX] * c_temp).real)
sig_a += (self.data[i_pole, _MLBW_RA] * c_temp).real
if self.fissionable:
sig_f += (self.data[i_pole, _MLBW_RF] * c_temp).real
elif self.formalism == 'RM':
sig_t += (self.data[i_pole, _RM_RT] * c_temp *
sig_t_factor[self.l_value[i_pole]-1]).real
sig_a += (self.data[i_pole, _RM_RA] * c_temp).real
if self.fissionable:
sig_f += (self.data[i_pole, _RM_RF] * c_temp).real
else:
raise ValueError('Unrecognized/Unsupported R-matrix'
' formalism')
else:
# At temperature, use Faddeeva function-based form.
dopp = self.sqrtAWR / sqrtkT
for i_pole in range(startw, endw):
Z = (sqrtE - self.data[i_pole, _MP_EA]) * dopp
w_val = _faddeeva(Z) * dopp * invE * sqrt(pi)
if self.formalism == 'MLBW':
sig_t += ((self.data[i_pole, _MLBW_RT] *
sig_t_factor[self.l_value[i_pole]-1] +
self.data[i_pole, _MLBW_RX]) * w_val).real
sig_a += (self.data[i_pole, _MLBW_RA] * w_val).real
if self.fissionable:
sig_f += (self.data[i_pole, _MLBW_RF] * w_val).real
elif self.formalism == 'RM':
sig_t += (self.data[i_pole, _RM_RT] * w_val *
sig_t_factor[self.l_value[i_pole]-1]).real
sig_a += (self.data[i_pole, _RM_RA] * w_val).real
if self.fissionable:
sig_f += (self.data[i_pole, _RM_RF] * w_val).real
else:
raise ValueError('Unrecognized/Unsupported R-matrix'
' formalism')
return sig_t, sig_a, sig_f
def __call__(self, E, T):
"""Compute total, absorption, and fission cross sections.
Parameters
----------
E : Real or Iterable of Real
Energy of the incident neutron in eV.
T : Real
Temperature of the target in K.
Returns
-------
3-tuple of Real or 3-tuple of numpy.ndarray
Total, absorption, and fission microscopic cross sections at the
given energy and temperature.
"""
fun = np.vectorize(lambda x: self._evaluate(x, T))
return fun(E)
def export_to_hdf5(self, path, libver='earliest'):
"""Export windowed multipole data to an HDF5 file.
Parameters
----------
path : str
Path to write HDF5 file to
libver : {'earliest', 'latest'}
Compatibility mode for the HDF5 file. 'latest' will produce files
that are less backwards compatible but have performance benefits.
"""
# Open file and write version.
with h5py.File(path, 'w', libver=libver) as f:
f.create_dataset('version', (1, ), dtype='S10')
f['version'][:] = WMP_VERSION.encode('ASCII')
# Make a nuclide group.
g = f.create_group('nuclide')
# Write scalars.
if self.formalism == 'MLBW':
g.create_dataset('formalism',
data=np.array(_FORM_MLBW, dtype=np.int32))
else:
# Assume RM.
g.create_dataset('formalism',
data=np.array(_FORM_RM, dtype=np.int32))
g.create_dataset('spacing', data=np.array(self.spacing))
g.create_dataset('sqrtAWR', data=np.array(self.sqrtAWR))
g.create_dataset('start_E', data=np.array(self.start_E))
g.create_dataset('end_E', data=np.array(self.end_E))
# Write arrays.
g.create_dataset('data', data=self.data)
g.create_dataset('l_value', data=self.l_value)
g.create_dataset('pseudo_K0RS', data=self.pseudo_k0RS)
g.create_dataset('w_start', data=self.w_start)
g.create_dataset('w_end', data=self.w_end)
g.create_dataset('broaden_poly',
data=self.broaden_poly.astype(np.int8))
g.create_dataset('curvefit', data=self.curvefit)
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