"""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 pyne.utils import QA_warn
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
QA_warn(__name__)
# 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.mas16'
[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 2016 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)
