156 lines
4.2 KiB
Python
156 lines
4.2 KiB
Python
"""
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@package pmsco.elements.bindingenergy
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electron binding energies of the elements
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extends the element table of the `periodictable` package
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(https://periodictable.readthedocs.io/en/latest/index.html)
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by the electron binding energies.
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the binding energies are compiled from Gwyn Williams' web page
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(https://userweb.jlab.org/~gwyn/ebindene.html).
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please refer to the original web page or the x-ray data booklet
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for original sources, definitions and remarks.
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usage
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-----
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this module requires the periodictable package (https://pypi.python.org/pypi/periodictable).
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~~~~~~{.py}
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import periodictable as pt
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import pmsco.elements.bindingenergy
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# read any periodictable's element interfaces, e.g.
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print(pt.gold.binding_energy['4f7/2'])
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print(pt.elements.symbol('Au').binding_energy['4f7/2'])
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print(pt.elements.name('gold').binding_energy['4f7/2'])
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print(pt.elements[79].binding_energy['4f7/2'])
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~~~~~~
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note that attributes are writable.
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you may assign refined values in your instance of the database.
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the query_binding_energy() function queries all terms with a particular binding energy.
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@author Matthias Muntwiler
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@copyright (c) 2020 by Paul Scherrer Institut @n
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Licensed under the Apache License, Version 2.0 (the "License"); @n
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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"""
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import json
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import numpy as np
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import os
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import periodictable as pt
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from pmsco.compat import open
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index_energy = np.zeros(0)
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index_number = np.zeros(0)
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index_term = []
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def load_data():
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data_path = os.path.join(os.path.dirname(__file__), "bindingenergy.json")
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with open(data_path) as fp:
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data = json.load(fp)
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return data
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def init(table, reload=False):
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if 'binding_energy' in table.properties and not reload:
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return
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table.properties.append('binding_energy')
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pt.core.Element.binding_energy = {}
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pt.core.Element.binding_energy_units = "eV"
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data = load_data()
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for el_key, el_data in data.items():
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try:
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el = table[int(el_key)]
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except ValueError:
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el = table.symbol(el_key)
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el.binding_energy = el_data
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def build_index():
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"""
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build an index for query_binding_energy().
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the index is kept in global variables of the module.
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@return None
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"""
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global index_energy
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global index_number
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global index_term
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n = 0
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for element in pt.elements:
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n += len(element.binding_energy)
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index_energy = np.zeros(n)
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index_number = np.zeros(n)
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index_term = []
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for element in pt.elements:
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for term, energy in element.binding_energy.items():
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index_term.append(term)
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i = len(index_term) - 1
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index_energy[i] = energy
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index_number[i] = element.number
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def query_binding_energy(energy, tol=1.0):
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"""
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search the periodic table for a specific binding energy and return all matching terms.
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@param energy: binding energy in eV.
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@param tol: tolerance in eV.
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@return: list of dictionaries containing element and term specification.
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the list is ordered arbitrarily.
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each dictionary contains the following keys:
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@arg 'number': element number
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@arg 'symbol': element symbol
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@arg 'term': spectroscopic term
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@arg 'energy': actual binding energy
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"""
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if len(index_energy) == 0:
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build_index()
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sel = np.abs(index_energy - energy) < tol
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idx = np.where(sel)
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result = []
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for i in idx[0]:
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el_num = int(index_number[i])
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d = {'number': el_num,
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'symbol': pt.elements[el_num].symbol,
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'term': index_term[i],
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'energy': index_energy[i]}
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result.append(d)
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return result
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def export_flat_text(f):
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"""
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export the binding energies to a flat general text file.
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@param f: file path or open file object
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@return: None
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"""
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if hasattr(f, "write") and callable(f.write):
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f.write("number symbol term energy\n")
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for element in pt.elements:
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for term, energy in element.binding_energy.items():
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f.write(f"{element.number} {element.symbol} {term} {energy}\n")
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else:
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with open(f, "w") as fi:
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export_flat_text(fi)
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