data_management.generate_elec_configs

This script parses a file containing ground state atomic electronic configurations and generates a function to load that data into a PeriodicTable object.

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_ptable_configs.py [OPTIONS]... 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

This script looks for the following file(s):

<data_dir>
├── ElementNames.txt
└── NIST-ATOMICION.txt

This script creates the following file(s):

<src_dir>
└── atomic_configurations
    └── atomconfigs.cpp

Attributes

`LMAX`
`NMAX`
`i_to_lchar`
`lchar_to_i`

Classes

AtomicData

Functions

`parse_symbols`(→ None)	Parse the given symbols file and add them to the existing atom
`parse_config_str`(→ dict)	Parse an electronic configuration.
`parse_nist_configs`(→ None)	Parses file containing ionization energy data from the NIST Atomic
`_write_configs`(→ None)	Generate the electronic_configurations.cpp source file.
`main`(→ None)	Entry point function to generate atomic info files.
`parse_args`(→ argparse.Namespace)	Parse command line arguments.

Module Contents

data_management.generate_elec_configs.LMAX = 3

data_management.generate_elec_configs.NMAX = 7

data_management.generate_elec_configs.i_to_lchar = 'spdf'

data_management.generate_elec_configs.lchar_to_i

class data_management.generate_elec_configs.AtomicData

sym = ''

name = ''

Z = 0

confstr = ''

confdict

property config_full

Full electronic configuration (number of electrons for each (l, n))

Returns:: number of electrons for each (l, n); indexed by [l][n-(l+1)]
Return type:: list[list[int]]

property config

Reduced config (number of electrons per l)

Returns:: (Ns, Np, Nd, …)
Return type:: tuple[int]

__repr__()

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

Parse the given symbols file and add them to the existing atom collection. Atoms will be added twice (same data with two keys) to allow access via either Z or Sym

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.

Raises:

RuntimeError – Z value was not able to be parsed properly.

data_management.generate_elec_configs.parse_config_str(sconf: str) → dict

Parse an electronic configuration.

Parameters:: sconf (str) – Electronic configuration string (TODO: specify exact format further)
Raises:: RuntimeError – Shell was unable to be parsed properly.
Returns:: dictionary with number of electrons in each shell, indexed by (n, l) where n is an int and l is a str with length 1
Return type:: dict[tuple[int,str],int]

data_management.generate_elec_configs.parse_nist_configs(ip_file: str, atoms: dict) → None

Parses file containing ionization energy data from the NIST Atomic Spectra Database or other file with similar format each line should contain “Z element_name atomic_config […]”

If an element symbol is used to represent a closed-shell core in a config, the config for that element must be parsed and added to atoms before it is used to represent a core configuration. e.g. Ne config must be added before [Ne]3s2

Parameters:

ip_file – path to file containing configs
atoms (dict of AtomicData) – Collection of atoms. Loaded configs will be added here.

data_management.generate_elec_configs._write_configs(out_dir: str, atoms: dict) → None

Generate the electronic_configurations.cpp source file.

Parameters:

out_dir (str) – Output directory for the generated header file.
atoms (dict of AtomicData) – Collection of atoms.

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

Entry point function to generate atomic info files.

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

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

Parse command line arguments.

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