data_management.generate_atomicinfo

This script is used to create the experimental data look up tables for the atom class.

Original author: Ben Pritchard

Modified by: Zachery Crandall

In order to run, this script needs to know the location of the data directory to read from and the src code directory to output the result into. One can also optionally provide a nondefault value for the electron mass to Dalton ratio.

For readability and convenience we use a few abbreviations throughout this script:

Z: the atomic number of an atom
Sym: the atomic symbol of an atom (e.g. H for hydrogen, He for helium)

Usage

usage: generate_atomicinfo.py [-h] [--amu2me AMU2ME] data_dir src_dir

positional arguments:
  data_dir         Data directory for atomic information files.
  src_dir          Destination directory for generated source files.

optional arguments:
  -h, --help       show this help message and exit
  --amu2me AMU2ME  Ratio of mass of electron to one Dalton. (Default: 1822.888486192)

This script looks for the following file(s):

+---data_dir
|       ElementNames.txt
|       CIAAW-ISOTOPEMASSES.txt
|       CIAAW-MASSES.txt

This script creates the following file(s):

+---src_dir
|       load_elements.hpp

Classes

AtomicData

Functions

`parse_symbols`(→ None)	Parse the given symbols file and add them to the existing atom
`_parse_ciaaw_isotopes`(→ None)	Parses an isotope mass file from the Commission on Isotopic Abundances
`_parse_ciaww_mass`(→ None)	Parses a mass file from the Commission on Isotopic Abundances
`_write_z_from_sym`(→ None)	Generate the Z_from_sym.cpp source file.
`_write_sym_from_z`(→ None)	Generate the sym_from_Z.cpp source file.
`_write_atoms_average`(→ None)	Generate the atoms_average.cpp source file.
`_write_atoms_isotope`(→ None)	Generate the atoms_isotopes.cpp source file.
`main`(→ None)	Entry point function to generate atomic info files.
`parse_args`(→ argparse.Namespace)	Parse command line arguments.

Module Contents

class data_management.generate_atomicinfo.AtomicData

sym = ''

name = ''

Z = 0

mass = 0.0

isotopes = []

isotope_masses

add_isotope(num: int, mass: float) → None

Add a new isotope mass to the list of isotopes for this element.

Parameters:

num (int) – Isotope mass number (Z + number of neutrons, N)
mass (float) – Isotope mass value

__repr__()

Return a formatted text representation of the atomic data.

Returns:: Formatted representation of the atomic data
Return type:: str

data_management.generate_atomicinfo.parse_symbols(name_file: str, atoms: dict) → None

Parse the given symbols file and add them to the existing atom collection.

Parameters:

name_file (str) – File with atomic numbers, symbols, and names for atoms.
atoms (dict) – Current collection of atoms. Loaded atoms will be added here.

data_management.generate_atomicinfo._parse_ciaaw_isotopes(iso_file: str, atoms: dict) → None

Parses an isotope mass file from the Commission on Isotopic Abundances and Atomic Weights (CIAAW) and adds it to a given atomic collection.

Parameters:

iso_file (str) – CIAAW isotope mass file
atoms (dict of AtomicData) – Collection of atoms. Loaded isotopes will be added here.

data_management.generate_atomicinfo._parse_ciaww_mass(mass_file: str, atoms: dict) → None

Parses a mass file from the Commission on Isotopic Abundances and Atomic Weights (CIAAW) and adds it to a given atomic collection.

Parameters:

iso_file (str) – CIAAW mass file
atoms (dict of AtomicData) – Collection of atoms. Loaded masses will be added here.

data_management.generate_atomicinfo._write_z_from_sym(out_dir: str, amu2me: float, atoms: dict) → None

Generate the Z_from_sym.cpp source file.

Parameters:

out_dir (str) – Output directory for the generated header file.
amu2me (float) – Ratio of mass of electron to a Dalton.
atoms (dict of AtomicData) – Collection of atoms.

data_management.generate_atomicinfo._write_sym_from_z(out_dir: str, amu2me: float, atoms: dict) → None

Generate the sym_from_Z.cpp source file.

Parameters:

out_dir (str) – Output directory for the generated header file.
amu2me (float) – Ratio of mass of electron to a Dalton.
atoms (dict of AtomicData) – Collection of atoms.

data_management.generate_atomicinfo._write_atoms_average(out_dir: str, amu2me: float, atoms: dict) → None

Generate the atoms_average.cpp source file.

Parameters:

out_dir (str) – Output directory for the generated header file.
amu2me (float) – Ratio of mass of electron to a Dalton.
atoms (dict of AtomicData) – Collection of atoms.

data_management.generate_atomicinfo._write_atoms_isotope(out_dir: str, amu2me: float, atoms: dict) → None

Generate the atoms_isotopes.cpp source file.

Parameters:

out_dir (str) – Output directory for the generated header file.
amu2me (float) – Ratio of mass of electron to a Dalton.
atoms (dict of AtomicData) – Collection of atoms.

data_management.generate_atomicinfo.main(args: argparse.Namespace) → None

Entry point function to generate atomic info files.

Parameters:: args (argparse.Namespace) – Command line argument namespace

data_management.generate_atomicinfo.parse_args() → argparse.Namespace

Parse command line arguments.

Returns:: Values of command line arguments.
Return type:: argparse.Namespace