data_management.generate_elec_configs
=====================================

.. py:module:: data_management.generate_elec_configs

.. autoapi-nested-parse::

   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 [-h] 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
----------

.. autoapisummary::

   data_management.generate_elec_configs.LMAX
   data_management.generate_elec_configs.NMAX
   data_management.generate_elec_configs.i_to_lchar
   data_management.generate_elec_configs.lchar_to_i


Classes
-------

.. autoapisummary::

   data_management.generate_elec_configs.AtomicData


Functions
---------

.. autoapisummary::

   data_management.generate_elec_configs.parse_symbols
   data_management.generate_elec_configs.parse_config_str
   data_management.generate_elec_configs.parse_nist_configs
   data_management.generate_elec_configs._write_configs
   data_management.generate_elec_configs.main
   data_management.generate_elec_configs.parse_args


Module Contents
---------------

.. py:data:: LMAX
   :value: 3


.. py:data:: NMAX
   :value: 7


.. py:data:: i_to_lchar

.. py:data:: lchar_to_i

.. py:class:: AtomicData

   .. py:attribute:: sym
      :value: ''



   .. py:attribute:: name
      :value: ''



   .. py:attribute:: Z
      :value: 0



   .. py:attribute:: confstr
      :value: ''



   .. py:attribute:: confdict


   .. py:property:: config_full

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

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




   .. py:property:: config

      return reduced config (number of electrons per l)

      :return: (Ns, Np, Nd, ...)
      :rtype: tuple[int]



   .. py:method:: __repr__()


.. py:function:: 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

   :param name_file: File with atomic numbers, symbols, and names for atoms.
   :type name_file: str

   :param atoms: Current collection of atoms. Loaded atoms will be added here.
   :type atoms: dict


.. py:function:: parse_config_str(sconf: str) -> dict

   parse an electronic configuration and return dict containing number
   of electrons in each shell, indexed by (n,l)

   :return: 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
   :rtype: dict[tuple[int,str],int]


.. py:function:: 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

   :param ip_file: path to file containing configs
   :type iso_file: str

   :param atoms: Collection of atoms. Loaded configs will be added here.
   :type atoms: dict of AtomicData


.. py:function:: _write_configs(out_dir: str, atoms: dict) -> None

   Generate the electronic_configurations.cpp source file.

   :param out_dir: Output directory for the generated header file.
   :type out_dir: str

   :param atoms: Collection of atoms.
   :type atoms: dict of AtomicData


.. py:function:: main(args: argparse.Namespace) -> None

   Entry point function to generate atomic info files.

   :param args: Command line argument namespace
   :type args: argparse.Namespace


.. py:function:: parse_args() -> argparse.Namespace

   Parse command line arguments.

   :return: Values of command line arguments.
   :rtype: argparse.Namespace