pyxray 1.0.2

Definitions and properties of X-ray transitions

pyxray is a Python library that defines basic object to specify atomic subshells and X-ray transitions. The objects also provide critical information as the energy, existence and different notations of the X-ray transitions.

pyxray supports 3.x (no Python 2.x support).

The library is provided under the MIT license.

pyxray was partially developed as part of the doctorate thesis project of Philippe T. Pinard at RWTH Aachen University (Aachen, Germany) under the supervision of Dr. Silvia Richter, in collaboration with Hendrix Demers (McGill University, Canada).

Installation

Easiest way to install using pip:

pip install pyxray

For development installation from the git repository:

git clone [e-mail]/openmicroanalysis/pyxray.git
cd pyxray
pip install -e .

See development section below

Methods

All methods below are accessed by importing pyxray:

import pyxray

Variables of the methods are defined as follows

• element:

  either

  • Element object

  • atomic number

  • symbol (case insensitive)

  • name (in any language, case insensitive)

  • object with attribute atomic_number or z

• atomic_shell:

  either

  • AtomicShell object

  • principal quantum number

  • any notation (case insensitive)

• atomic_subshell:

  either

  • AtomicSubshell object

  • a tuple of principal quantum number, azimuthal quantum number and total angular momentum nominator (e.g. (1, 0, 1) for the atomic subshell 1s^{0.5}

  • any notation (case insensitive)

• transition:

  either

  • Transition object

  • a tuple of source and destination subshells (or optionally secondary destination subshells)

  • any notation (case insensitive)

• transitionset:

  either

  • TransitionSet object

  • a tuple of transitions

  • any notation (case insensitive)

• language:

  language code (e.g. en, fr, de)

• notation:

  name of a notation (case insensitive), iupac, siegbahn and orbital are usually supported

• encoding:

  type of encoding, either ascii, utf16, html or latex

• reference:

  reference to use to retrieve this value, either

  • Reference object

  • BibTeX key of a reference

  • None, the default reference will be used or the first reference found

Element properties

Properties associated with an element, defined as the ground state of an atom where the number of protons equal the number of electrons.

• pyxray.element(element)

  Returns element descriptor.

• pyxray.element_atomic_number(element)

  Returns atomic number of an element.

  Examples:

  pyxray.element.atomic_number('fe') #=> 26
  pyxray.element.atomic_number('Fe') #=> 26
  pyxray.element.atomic_number('iron') #=> 26
  pyxray.element.atomic_number('eisen') #=> 26

• pyxray.element_symbol(element, reference=None)

  Returns symbol of an element.

• pyxray.element_name(element, language='en', reference=None)

  Returns full name of an element, in the language specified.

• pyxray.element_atomic_weight(element, reference=None)

  Returns atomic weight of an element. The atomic weight is defined by the CIAAW as it is the ratio of the average atomic mass of an element over 1/12 of the mass of the carbon-12 atom.

• pyxray.element_mass_density_kg_per_m3(element, reference=None)

  Returns mass density (in kg/m3) of an element.

• pyxray.element_mass_density_g_per_cm3(element, reference=None)

  Returns mass density (in g/cm3) of an element.

• pyxray.element_transitions(element, reference=None)

  Returns all transitions which have a probability greater than 0 for an element.

Atomic shell properties

Properties associated with an atomic shell, defined by its principal quantum number.

• pyxray.atomic_shell(atomic_shell)

  Returns atomic shell descriptor.

• pyxray.atomic_shell_notation(atomic_shell, notation, encoding='utf16', reference=None)

  Returns notation of an atomic shell.

Atomic subshell properties

Properties associated with an atomic subshell, a subdivision of atomic shells.

• pyxray.atomic_subshell(atomic_subshell)

  Returns atomic subshell descriptor.

• pyxray.atomic_subshell_notation(atomic_subshell, notation, encoding='utf16', reference=None)

  Returns notation of an atomic subshell.

  Examples:

  pyxray.atomic_subshell_notation('L3', 'iupac', 'latex') #=> 'L$_{3}$'
  pyxray.atomic_subshell_notation('L3', 'orbital') #-> '2p3/2'

• pyxray.atomic_subshell_binding_energy_eV(element, atomic_subshell, reference=None)

  Returns binding energy of an element and atomic subshell (in eV).

• pyxray.atomic_subshell_radiative_width_eV(element, atomic_subshell, reference=None)

  Returns radiative width of an element and atomic subshell (in eV).

• pyxray.atomic_subshell_nonradiative_width_eV(element, atomic_subshell, reference=None)

  Returns nonradiative width of an element and atomic subshell (in eV).

• pyxray.atomic_subshell_occupancy(element, atomic_subshell, reference=None)

  Returns occupancy of an element and atomic subshell.

Transition properties

Properties associated with an electron transition, relaxation process of an electron between quantum states leading to X-rays emission, Auger electrons or Coster-Kronig transitions.

• pyxray.transition(transition)

  Returns transition descriptor.

• pyxray.transition_notation(transition, notation, encoding='utf16', reference=None)

  Returns notation of a transition.

  Examples:

  pyxray.transition_notation('Ka1', 'iupac') #=> 'K-L3'
  pyxray.transition_notation('L3-M1', 'siegbahn', 'ascii') #=> 'Ll'

• pyxray.transition_energy_eV(element, transition, reference=None)

  Returns energy of an element and transition (in eV).

  Examples:

  pyxray.transition_energy_eV(14, 'Ka1') #=> 1740.0263764535946
  pyxray.transition_energy_eV(14, 'Ma1') #=> NotFound exception

• pyxray.transition_probability(element, transition, reference=None)

  Returns probability of an element and transition.

• pyxray.transition_relative_weight(element, transition, reference=None)

  Returns relative weight of an element and transition.

Transition set properties

Properties associated with a transition set, an indistinguishable transition (e.g. Ka from Ka1/Ka2).

• pyxray.transitionset(transitionset)

  Returns transition set descriptor.

• pyxray.transitionset_notation(transitionset, notation, encoding='utf16', reference=None)

  Returns notation of a transition set.

• pyxray.transitionset_energy_eV(element, transitionset, reference=None)

  Returns energy of an element and transition set (in eV).

• pyxray.transitionset_relative_weight(element, transitionset, reference=None)

  Returns relative weight of an element and transition set.

Development

pyxray stores all data for the above functions in a SQLite database. The database is constructed during the build process of the Python package (i.e. python setup.py build) using registered parsers. The provided parsers are located in the package pyxray.parser, but external parsers can be provided by registering to the entry point pyxray.parser. In short, the database is not provide in the source code, only in the distributed version. It is therefore necessary to build the SQLite database when running pyxray in development mode. Building the database will take several minutes.