"""Module handles parsing EAF formatted cross section files and adding
the data to PyNE's HDF5 storage. The data here is autonatically grabbed from
the IAEA.
"""
from __future__ import print_function
import re
import os
from pyne.utils import QA_warn
try:
import urllib.request as urllib
except ImportError:
import urllib
from gzip import GzipFile
import numpy as np
import tables as tb
from .. import nucname
from .api import BASIC_FILTERS
QA_warn(__name__)
[docs]def grab_eaf_data(build_dir=""):
"""Grabs the EAF activation data files
if not already present.
Parameters
----------
build_dir : str
Major directory to place EAF data file(s) in. 'EAF/' will be appended.
"""
# Add EAF to build_dir
build_dir = os.path.join(build_dir, 'EAF')
try:
os.makedirs(build_dir)
print("{0} created".format(build_dir))
except OSError:
pass
# Grab ENSDF files and unzip them.
# This link was taken from 'http://www-nds.iaea.org/fendl/fen-activation.htm'
iaea_url = 'http://www-nds.iaea.org/fendl2/activation/processed/vitj_e/libout/fendlg-2.0_175-gz'
cf_base_url = 'https://github.com/pyne/data/raw/master/'
eaf_gzip = 'fendlg-2.0_175-gz'
fpath = os.path.join(build_dir, eaf_gzip)
if eaf_gzip not in os.listdir(build_dir):
print(" grabbing {0} and placing it in {1}".format(eaf_gzip, fpath))
try:
urllib.urlretrieve(iaea_url, fpath)
except (OSError, IOError):
open(fpath, 'a').close() # touch the file
if os.path.getsize(fpath) < 3215713:
print(" could not get {0} from IAEA; trying S3 mirror".format(eaf_gzip))
os.remove(fpath)
try:
urllib.urlretrieve(cf_base_url + eaf_gzip, fpath)
except (OSError, IOError):
open(fpath, 'a').close() # touch the file
if os.path.getsize(fpath) < 3215713:
print(" could not get {0} from S3 mirror".format(eaf_gzip))
return False
# Write contents of single-file gzip archive to a new file
try:
gf = GzipFile(fpath)
ofile = os.path.join(build_dir, 'fendlg-2.0_175')
with open(ofile, 'w') as fw:
for line in gf:
fw.write(line.decode("us-ascii"))
finally:
gf.close()
return True
# numpy array row storage information for EAF data
eaf_dtype = np.dtype([
('nuc_zz', int ),
('rxnum', 'S7' ),
('rxstr', 'S7' ),
('daughter', 'S7' ),
('xs', float, (175,))
])
# Regular expression for parsing an individual set of EAF data.
# Includes some groupnames that are currently unused.
eaf_info_pattern = \
"(?P<iso>\d{5,7})\s*" + \
"(?P<rxnum>\d{2,4})\s*" + \
"(?P<ngrps>\d{1,3})\s*" + \
"(?P<parent>[a-zA-Z]{1,2}\s{0,3}\d{1,3}[M ][12 ])" + \
"(?P<rxstr>\(N,[\w\s]{3}\))" + \
"(?P<daugh>[a-zA-Z.]{1,2}\s{0,3}\d{1,3}[MG]{0,1}\d{0,1})" + \
"(.*?)"
eaf_bin_pattern = "(?P<xs>(\d\.\d{5}E[-+]\d{2}\s*){1,175})"
[docs]def parse_eaf_xs(build_file):
"""Create numpy array by parsing EAF data
using regular expressions
Parameters
----------
build_file : str
Path where EAF data is stored.
Returns
-------
eaf_array : numpy array
Numpy array with a row for each isotope+reaction combination
found in the EAF data.
"""
with open(build_file, 'r') as f:
raw_data = f.read()
eaf_data = list()
eaf_pattern = eaf_info_pattern + eaf_bin_pattern
# Iterate over all iso/rx combinations in file
for m in re.finditer(eaf_pattern, raw_data, re.DOTALL):
md = m.groupdict()
xs_list = [float(x) for x in md['xs'].split()]
xs_list += (175-len(xs_list))*[0.0]
# Store information in new row of array.
eafrow = (
nucname.id(md['iso']),
md['rxnum'],
md['rxstr'],
md['daugh'],
xs_list
)
eaf_data.append(eafrow)
eaf_array = np.array(eaf_data, dtype=eaf_dtype)
print("Read in {0} sets of EAF data.".format(len(eaf_array)))
return eaf_array
[docs]def make_eaf_table(nuc_data, build_path=""):
"""Function for adding EAF group and table to HDF5 storage.
Parameters
----------
nuc_data : str
Path to nuclide data file.
build_path : str
Directory where EAF data is located.
"""
print("Grabbing the EAF activation data.")
eaf_array = parse_eaf_xs(build_path)
# Open the HDF5 file
db = tb.open_file(nuc_data, 'a', filters=BASIC_FILTERS)
# Ensure that the appropriate file structure is present
if not hasattr(db.root, 'neutron'):
neutron_group = db.create_group('/', 'neutron', \
'Neutron Interaction Data')
# Create eaf_xs group
if not hasattr(db.root.neutron, 'eaf_xs'):
eaf_group = db.create_group("/neutron", "eaf_xs", \
"EAF 175-Group Neutron Activation Cross Section Data")
eaf_table = db.create_table("/neutron/eaf_xs", "eaf_xs", \
np.empty(0, dtype=eaf_dtype), \
"EAF Activation Cross Section Data [barns]", \
expectedrows=len(eaf_array))
# Put eaf_array in the table
eaf_table.append(eaf_array)
# Write the table
eaf_table.flush()
# Add group structure by calling placeholder function to get boundaries
db.create_array('/neutron/eaf_xs', 'E_g', _get_eaf_groups(), \
'Neutron energy group bounds [MeV]')
# Close the HDF5 file
db.close()
def _get_eaf_groups():
"""Function for retrieving EAF group structure.
Note, energies are entered high to low in the HDF5 storage.
This is used as a placeholder for a future PyNE implementation of a database
storing group structures. This hypothetical database would return the
group structure like this method does.
Returns
----------
eaf_E_g_array : 1D list
List of energy group boundaries from high to low.
"""
eaf_E_g_array = [0.0,
1.0000E-07, 4.1399E-07, 5.3158E-07, 6.8256E-07, 8.7643E-07,
1.1254E-06, 1.4450E-06, 1.8554E-06, 2.3824E-06, 3.0590E-06,
3.9279E-06, 5.0435E-06, 6.4760E-06, 8.3153E-06, 1.0677E-05,
1.3710E-05, 1.7604E-05, 2.2603E-05, 2.9023E-05, 3.7267E-05,
4.7851E-05, 6.1442E-05, 7.8893E-05, 1.0130E-04, 1.3007E-04,
1.6702E-04, 2.1445E-04, 2.7536E-04, 3.5358E-04, 4.5400E-04,
5.8295E-04, 7.4852E-04, 9.6112E-04, 1.2341E-03, 1.5846E-03,
2.0347E-03, 2.2487E-03, 2.4852E-03, 2.6126E-03, 2.7465E-03,
3.0354E-03, 3.3546E-03, 3.7074E-03, 4.3074E-03, 5.5308E-03,
7.1017E-03, 9.1188E-03, 1.0595E-02, 1.1709E-02, 1.5034E-02,
1.9305E-02, 2.1875E-02, 2.3579E-02, 2.4176E-02, 2.4788E-02,
2.6058E-02, 2.7000E-02, 2.8501E-02, 3.1828E-02, 3.4307E-02,
4.0868E-02, 4.6309E-02, 5.2475E-02, 5.6562E-02, 6.7380E-02,
7.2025E-02, 7.9499E-02, 8.2503E-02, 8.6517E-02, 9.8037E-02,
1.1109E-01, 1.1679E-01, 1.2277E-01, 1.2907E-01, 1.3569E-01,
1.4264E-01, 1.4996E-01, 1.5764E-01, 1.6573E-01, 1.7422E-01,
1.8316E-01, 1.9255E-01, 2.0242E-01, 2.1280E-01, 2.2371E-01,
2.3518E-01, 2.4724E-01, 2.7324E-01, 2.8725E-01, 2.9452E-01,
2.9721E-01, 2.9849E-01, 3.0197E-01, 3.3373E-01, 3.6883E-01,
3.8774E-01, 4.0762E-01, 4.5049E-01, 4.9787E-01, 5.2340E-01,
5.5023E-01, 5.7844E-01, 6.0810E-01, 6.3928E-01, 6.7206E-01,
7.0651E-01, 7.4274E-01, 7.8082E-01, 8.2085E-01, 8.6294E-01,
9.0718E-01, 9.6167E-01, 1.0026E+00, 1.1080E+00, 1.1648E+00,
1.2246E+00, 1.2874E+00, 1.3534E+00, 1.4227E+00, 1.4957E+00,
1.5724E+00, 1.6530E+00, 1.7377E+00, 1.8268E+00, 1.9205E+00,
2.0190E+00, 2.1225E+00, 2.2313E+00, 2.3069E+00, 2.3457E+00,
2.3653E+00, 2.3851E+00, 2.4660E+00, 2.5924E+00, 2.7253E+00,
2.8651E+00, 3.0119E+00, 3.1664E+00, 3.3287E+00, 3.6788E+00,
4.0657E+00, 4.4933E+00, 4.7237E+00, 4.9659E+00, 5.2205E+00,
5.4881E+00, 5.7695E+00, 6.0653E+00, 6.3763E+00, 6.5924E+00,
6.7032E+00, 7.0469E+00, 7.4082E+00, 7.7880E+00, 8.1873E+00,
8.6071E+00, 9.0484E+00, 9.5123E+00, 1.0000E+01, 1.0513E+01,
1.1052E+01, 1.1618E+01, 1.2214E+01, 1.2523E+01, 1.2840E+01,
1.3499E+01, 1.3840E+01, 1.4191E+01, 1.4550E+01, 1.4918E+01,
1.5683E+01, 1.6487E+01, 1.6905E+01, 1.7333E+01, 1.9640E+01]
eaf_E_g_array.reverse()
return eaf_E_g_array
[docs]def make_eaf(args):
"""Controller function for adding cross section data from EAF format file.
"""
nuc_data, build_dir, datapath = args.nuc_data, args.build_dir, args.datapath
# Check if the table already exists
with tb.open_file(nuc_data, 'a', filters=BASIC_FILTERS) as f:
if hasattr(f.root, 'neutron') and hasattr(f.root.neutron, 'eaf_xs'):
print("skipping EAF activation data table creation; already exists.")
return
# grab the EAF data
print("Grabbing the EAF activation data from IAEA")
grabbed = grab_eaf_data(build_dir)
if not grabbed:
return
build_filename = os.path.join(build_dir, 'EAF/fendlg-2.0_175')
if os.path.exists(build_filename):
build_path = build_filename
else:
return
#
print("Making EAF activation data table.")
make_eaf_table(nuc_data, build_path)
