"""This module provides a way to grab and store raw data for atomic mass."""
from __future__ import print_function
import os
import re
import pkgutil
from warnings import warn
from pyne.utils import QAWarning
import numpy as np
import tables as tb
from pyne import nucname
from pyne.dbgen.api import BASIC_FILTERS
from pyne.dbgen.isotopic_abundance import get_isotopic_abundances
warn(__name__ + " is not yet QA compliant.", QAWarning)
# Note that since ground state and meta-stable isotopes are of the same atomic mass,
# the meta-stables have been discluded from the following data sets.
MASS_FILE = 'mass.mas12'
[docs]def copy_atomic_mass_adjustment(build_dir=""):
"""Copies the atomic mass evaluation originally from the Atomic Mass Data
Center. These are courtesy of Georges Audi and Wang Meng via a private
communication, November 2012."""
if os.path.exists(os.path.join(build_dir, MASS_FILE)):
return
mass = pkgutil.get_data('pyne.dbgen', MASS_FILE)
with open(os.path.join(build_dir, MASS_FILE), 'wb') as f:
f.write(mass)
# Note, this regex specifically leaves our free neutrons
# amdc_regex = re.compile('[ \d-]*? (\d{1,3})[ ]{1,4}(\d{1,3}) [A-Z][a-z]? .*? (\d{1,3}) ([ #.\d]{10,11}) ([ #.\d]{1,10})[ ]*?$')
amdc_regex = re.compile('[ \d-]*? (\d{1,3})[ ]{1,4}(\d{1,3}) [A-Z][a-z]? .*? (\d{1,3}) ([ #.\d]{5,12}) ([ #.\d]+)[ ]*?$')
[docs]def parse_atomic_mass_adjustment(build_dir=""):
"""Parses the atomic mass adjustment data into a list of tuples of
the nuclide, atomic mass, and error."""
f = open(os.path.join(build_dir, MASS_FILE), 'r')
atomic_masses = []
for line in f:
m = amdc_regex.search(line)
if m is None:
continue
nuc = (10000000 * int(m.group(1))) + (10000 * int(m.group(2)))
mass = float(m.group(3)) + 1E-6 * float(m.group(4).strip().replace('#', ''))
error = 1E-6 * float(m.group(5).strip().replace('#', ''))
atomic_masses.append((nuc, mass, error))
f.close()
return atomic_masses
atomic_mass_desc = {
'nuc': tb.IntCol(pos=1),
'mass': tb.FloatCol(pos=2),
'error': tb.FloatCol(pos=3),
'abund': tb.FloatCol(pos=4),
}
atomic_mass_dtype = np.dtype([
('nuc', int),
('mass', float),
('error', float),
('abund', float),
])
[docs]def make_atomic_mass_table(nuc_data, build_dir=""):
"""Makes an atomic mass table in the nuc_data library.
Parameters
----------
nuc_data : str
Path to nuclide data file.
build_dir : str
Directory to place html files in.
"""
# Grab raw data
atomic_abund = get_isotopic_abundances()
atomic_masses = parse_atomic_mass_adjustment(build_dir)
A = {}
# Add normal isotopes to A
for nuc, mass, error in atomic_masses:
if nuc in atomic_abund:
A[nuc] = nuc, mass, error, atomic_abund[nuc]
else:
A[nuc] = nuc, mass, error, 0.0
# Add naturally occuring elements
for element in nucname.name_zz:
nuc = nucname.id(element)
A[nuc] = nuc, 0.0, 0.0, 0.0
for nuc, abund in atomic_abund.items():
zz = nucname.znum(nuc)
element_zz = nucname.id(zz)
element = nucname.zz_name[zz]
_nuc, nuc_mass, _error, _abund = A[nuc]
elem_zz, elem_mass, _error, _abund = A[element_zz]
new_elem_mass = elem_mass + (nuc_mass * abund)
A[element_zz] = element_zz, new_elem_mass, 0.0, float(0.0 < new_elem_mass)
A = sorted(A.values(), key=lambda x: x[0])
# Open the HDF5 File
kdb = tb.open_file(nuc_data, 'a', filters=BASIC_FILTERS)
# Make a new the table
Atable = kdb.create_table("/", "atomic_mass", atomic_mass_desc,
"Atomic Mass Data [amu]", expectedrows=len(A))
Atable.append(A)
# Ensure that data was written to table
Atable.flush()
# Close the hdf5 file
kdb.close()
[docs]def make_atomic_mass(args):
"""Controller function for adding atomic_mass."""
nuc_data, build_dir = args.nuc_data, args.build_dir
if os.path.exists(nuc_data):
with tb.open_file(nuc_data, 'r') as f:
if hasattr(f.root, 'atomic_mass'):
print("skipping atomic mass data table creation; already exists.")
return
# Then grab mass data
print("Copying AME 2012 atomic mass data.")
copy_atomic_mass_adjustment(build_dir)
# Make atomic mass table once we have the array
print("Making atomic mass data table.")
make_atomic_mass_table(nuc_data, build_dir)
