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"""This module provides a way to grab and store simple cross sections from KAERI."""
import os
import re
import urllib2
import numpy as np
import tables as tb
from pyne import nucname
from pyne.utils import to_barns
from pyne.dbgen.api import BASIC_FILTERS
from pyne.dbgen.kaeri import grab_kaeri_nuclide, parse_for_all_isotopes
def grab_kaeri_simple_xs(build_dir=""):
"""Grabs the KAERI files needed for the simple cross sections table,
if not already present.
build_dir : str
Major directory to place html files in. 'KAERI/' will be appended.
# Add kaeri to build_dir
build_dir = os.path.join(build_dir, 'KAERI')
except OSError:
already_grabbed = set(os.listdir(build_dir))
# Grab and parse elemental summary files.
all_nuclides = set()
for element in nucname.name_zz.keys():
htmlfile = element + '.html'
if htmlfile not in already_grabbed:
grab_kaeri_nuclide(element, build_dir)
all_nuclides = all_nuclides | parse_for_all_isotopes(os.path.join(build_dir, htmlfile))
# Grab nuclide XS summary files
for nuc in sorted(all_nuclides):
nuc =
htmlfile = nuc + '_2.html'
if htmlfile not in already_grabbed:
grab_kaeri_nuclide(nuc, build_dir, 2)
simple_xs_channels = {
"sigma_t": "Total Cross Section",
"sigma_e": "Elastic Scattering Cross Section",
"sigma_i": "Total Inelastic Cross Section",
"sigma_2n": "(n,2n) Cross Section",
"sigma_3n": "(n,3n) Cross Section",
"sigma_4n": "(n,4n) Cross Section",
"sigma_f": "Total Fission Cross Section",
"sigma_gamma": "Radiative Capture Cross Section",
"sigma_alpha": "(n,alpha) Cross Section",
"sigma_proton": "(n,p) Cross Section",
"sigma_deut": "(n,d) Cross Section",
"sigma_trit": "(n,t) Cross Section",
simple_xs_energy = {
"thermal": "at 0.0253 eV",
"thermal_maxwell_ave": "Maxwell avg. at 0.0253 eV",
"resonance_integral": "Resonance integral",
"fourteen_MeV": "at 14 MeV",
"fission_spectrum_ave": "Fission spectrum avg.",
simple_xs_dtype = np.dtype([
('nuc_name', 'S6'),
('nuc_zz', int),
('sigma_t', float),
('sigma_s', float),
('sigma_e', float),
('sigma_i', float),
('sigma_a', float),
('sigma_gamma', float),
('sigma_f', float),
('sigma_alpha', float),
('sigma_proton', float),
('sigma_deut', float),
('sigma_trit', float),
('sigma_2n', float),
('sigma_3n', float),
('sigma_4n', float),
def get_xs_from_file(filename, eng, chan):
"""Parses out a cross section from a KAERI file.
filename : str
Local path to a KAERI neutron cross section summary html file.
eng : str
Energy flag to find this cross section for. (Must be key
of simple_xs_energy dictionary).
chan : str
Cross section (interaction channel) to find. (Must be key
of simple_xs_channels dict).
data : float
Microscopic cross section in [barns].
with open(filename, 'r') as f:
in_channel = False
for line in f:
if simple_xs_channels[chan] in line:
in_channel = True
if in_channel and ("<li>"+simple_xs_energy[eng] in line):
du = line.partition("=")[2].split()
data = float(du.pop(0))
unit = ""
for u in du:
unit = unit + u
unit = unit.partition("\\")[0]
data = to_barns(data, unit)
return data
elif in_channel and ("</ul>" in line):
# XS not defined for this energy, returning zero
return 0.0
# If the specific XS was not found in this file, return zero
return 0.0
def parse_simple_xs(build_dir=""):
"""Builds and returns a dictionary from cross-section types to nuclides."""
build_dir = os.path.join(build_dir, 'KAERI')
# Grab and parse elemental summary files.
all_nuclides = set()
for element in nucname.name_zz.keys():
htmlfile = element + '.html'
all_nuclides = all_nuclides | parse_for_all_isotopes(os.path.join(build_dir, htmlfile))
all_nuclides = sorted([nucname.zzaaam(nuc) for nuc in all_nuclides])
energy_tables = {eng: np.zeros(len(all_nuclides), dtype=simple_xs_dtype) for eng in simple_xs_energy.keys()}
# Loop through species
for i, nuc_zz in enumerate(all_nuclides):
nuc_name =
filename = os.path.join(build_dir, nuc_name + '_2.html')
# Loop through all energy types
for eng in simple_xs_energy:
energy_tables[eng]['nuc_name'][i] = nuc_name
energy_tables[eng]['nuc_zz'][i] = nuc_zz
# Loop trhough reactions
for chan in simple_xs_channels:
energy_tables[eng][chan][i] = get_xs_from_file(filename, eng, chan)
for eng in simple_xs_energy:
# Store only non-trivial entries
mask = (energy_tables[eng][simple_xs_channels.keys()] != np.zeros(1, dtype=simple_xs_dtype)[simple_xs_channels.keys()])
energy_tables[eng] = energy_tables[eng][mask]
# Calculate some xs
energy_tables[eng]['sigma_s'] = energy_tables[eng]['sigma_e'] + energy_tables[eng]['sigma_i']
energy_tables[eng]['sigma_a'] = energy_tables[eng]['sigma_gamma'] + \
energy_tables[eng]['sigma_f'] + \
energy_tables[eng]['sigma_alpha'] + \
energy_tables[eng]['sigma_proton'] + \
energy_tables[eng]['sigma_deut'] + \
energy_tables[eng]['sigma_trit'] + \
energy_tables[eng]['sigma_2n'] + \
energy_tables[eng]['sigma_3n'] + \
return energy_tables
def make_simple_xs_tables(nuc_data, build_dir=""):
"""Make the simple cross section tables.
nuc_data : str
Path to nuclide data file.
build_dir : str
Directory to place html files in.
# Grab raw data
simple_xs_tables = parse_simple_xs(build_dir)
# Open the HDF5 File
db = tb.openFile(nuc_data, 'a', filters=BASIC_FILTERS)
# Create neutron group
if not hasattr(db.root, 'neutron'):
neutron_group = db.createGroup('/', 'neutron', 'Neutron Interaction Data')
# Create simple_xs Group
if not hasattr(db.root.neutron, 'simple_xs'):
simple_xs_group = db.createGroup("/neutron", "simple_xs", "Simple Neutron Cross Section Data")
# Create tables for every energy
for eng, eng_flag in simple_xs_energy.items():
simple_xs_table = db.createTable(simple_xs_group, eng,
np.empty(0, dtype=simple_xs_dtype),
"{0} [barns]".format(eng_flag.capitalize()),
# Close the hdf5 file
def make_simple_xs(args):
"""Controller function for adding basic cross section data."""
nuc_data, build_dir = args.nuc_data, args.build_dir
with tb.openFile(nuc_data, 'a', filters=BASIC_FILTERS) as f:
if hasattr(f.root, 'neutron') and hasattr(f.root.neutron, 'simple_xs'):
# First grab the atomic abundance data
print "Grabing neutron summary files from KAERI"
# Make simple table once we have the array
print "Making simple cross section data tables"
make_simple_xs_tables(nuc_data, build_dir)
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