jarvis.core.specie
==================

.. py:module:: jarvis.core.specie

.. autoapi-nested-parse::

   Modules related to chemistry of periodic-table elements.



Attributes
----------

.. autoapisummary::

   jarvis.core.specie.el_chem_json_file
   jarvis.core.specie.el_chem_json
   jarvis.core.specie.chem_data
   jarvis.core.specie.chem_data_magpie
   jarvis.core.specie.el_chrg_json_file
   jarvis.core.specie.el_chrg_json
   jarvis.core.specie.chrg_data
   jarvis.core.specie.cgcnn_feature_json
   jarvis.core.specie.element_full_name
   jarvis.core.specie.BASIC_FEATURES
   jarvis.core.specie.keys
   jarvis.core.specie.info_z


Classes
-------

.. autoapisummary::

   jarvis.core.specie.Specie


Functions
---------

.. autoapisummary::

   jarvis.core.specie.get_element_full_names
   jarvis.core.specie.get_descrp_arr_name
   jarvis.core.specie.get_node_attributes
   jarvis.core.specie.get_specie_data
   jarvis.core.specie.get_digitized_feats_hot_encoded
   jarvis.core.specie.get_feats_hot_encoded
   jarvis.core.specie.atomic_numbers_to_symbols


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

.. py:data:: el_chem_json_file
   :value: ''


.. py:data:: el_chem_json

.. py:data:: chem_data

.. py:data:: chem_data_magpie

.. py:data:: el_chrg_json_file
   :value: ''


.. py:data:: el_chrg_json

.. py:data:: chrg_data

.. py:data:: cgcnn_feature_json

.. py:data:: element_full_name

.. py:function:: get_element_full_names()

.. py:function:: get_descrp_arr_name(elm='Al')

   Get chemical descriptors for an element.

   Can be used in JARVIS-ML.

   Args:

          elm: element name

   Returns:
            arr: array value


.. py:class:: Specie(symbol='', source='cfid')

   Bases: :py:obj:`object`


   Specie object for chemistry information.

   Used in defining chemistry of a material.

   >>> el = Specie('Al')
   >>> el.Z
   13
   >>> round(el.atomic_mass,2)
   26.98
   >>> el.symbol
   'Al'
   >>> round(el.get_chgdescrp_arr[1],2)
   12.17
   >>> round(el.get_descrp_arr[1],2)
   2792.11
   >>> el = Specie('asdfg')
   >>> el.element_property("asdfg")
   nan



   .. py:attribute:: symbol
      :value: ''



   .. py:property:: Z

      Get atomic number.



   .. py:property:: atomic_mass

      Get atomic mass.



   .. py:property:: get_chgdescrp_arr

      Get charge descriptors for an element.

      Gives 378 array data.

      Args:

         elm: element name

      Returns:
           arr: array value



   .. py:property:: get_descrp_arr

      Get chemical descriptors for an element.

      Gives 438 array data.

      Args:

         elm: element name

      Returns:
           arr: array value



   .. py:property:: atomic_rad

      Get atomic radii.



   .. py:property:: X

      Get electronegativity.



   .. py:method:: element_property(key='')

      Get element property from the list of keys.

      These 84 keys are:
      keys = [
              "is_halogen",
              "row",
              "GV",
              "nfunfill",
              "C-9",
              "C-8",
              "C-7",
              "C-6",
              "C-5",
              "C-4",
              "C-3",
              "C-2",
              "C-1",
              "C-0",
              "me1",
              "me3",
              "me2",
              "max_oxid_s",
              "npvalence",
              "mp",
              "first_ion_en",
              "ndunfill",
              "op_eg",
              "jv_enp",
              "nfvalence",
              "polzbl",
              "oq_bg",
              "atom_rad",
              "atom_mass",
              "is_alkali",
              "C-13",
              "C-12",
              "C-11",
              "C-10",
              "C-17",
              "C-16",
              "C-15",
              "C-14",
              "C-19",
              "C-18",
              "voro_coord",
              "is_noble_gas",
              "e1",
              "e3",
              "e2",
              "is_lanthanoid",
              "ndvalence",
              "KV",
              "min_oxid_s",
              "nsunfill",
              "C-26",
              "X",
              "is_actinoid",
              "C-28",
              "C-29",
              "C-27",
              "C-24",
              "C-25",
              "C-22",
              "C-23",
              "C-20",
              "C-21",
              "avg_ion_rad",
              "nsvalence",
              "is_metalloid",
              "elec_aff",
              "coulmn",
              "mol_vol",
              "bp",
              "C-31",
              "C-30",
              "C-33",
              "C-32",
              "C-35",
              "C-34",
              "is_transition_metal",
              "block",
              "therm_cond",
              "Z",
              "is_alkaline",
              "npunfill",
              "oq_enp",
              "mop_eg",
              "hfus",
          ]



.. py:data:: BASIC_FEATURES
   :value: ['Z', 'coulmn', 'row', 'X', 'atom_rad', 'nsvalence', 'npvalence', 'ndvalence', 'nfvalence',...


.. py:function:: get_node_attributes(species, atom_features='atomic_number')

   Get specific node features for an element.


.. py:data:: keys
   :value: ['is_halogen', 'row', 'GV', 'nfunfill', 'C-9', 'C-8', 'C-7', 'C-6', 'C-5', 'C-4', 'C-3', 'C-2',...


.. py:function:: get_specie_data()

   Get the json and key data from Specie.


.. py:function:: get_digitized_feats_hot_encoded(feature_names=keys, filename='feats_encoded.json')

   Get OneHotEncoded features with digitized features.


.. py:function:: get_feats_hot_encoded(feature_names=keys, filename='feats_encoded.json')

   Get OneHotEncoded features.


.. py:data:: info_z

.. py:function:: atomic_numbers_to_symbols(numbers=[1, 2, 3, 4])

   Convert atomic number array to atomic symbols.