geom.classes.parameters
=======================

.. py:module:: geom.classes.parameters


Classes
-------

.. autoapisummary::

   geom.classes.parameters.parameters


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

.. py:class:: parameters

   Parameters Class for Metal and Graphene Structures.

   This class provides essential lattice parameters, minimum interatomic distances,
   and atomic arrangements for various elements, including FCC, BCC, HCP metals,
   and graphene.

   .. attribute:: convergence

      Convergence threshold for numerical operations.

      :type: float

   .. attribute:: convergence_step

      Step size for convergence calculations.

      :type: float

   .. attribute:: min_dist_translate

      Minimum allowable distance for translation operations.

      :type: float

   .. attribute:: lattice_constant

      Lattice constants (in Ångströms) for various elements.
      - Keys: Atomic symbols (e.g., "Ag", "Au", "C").
      - Values: Single float (for cubic structures) or tuple (for HCP structures).

      :type: dict

   .. attribute:: min_dist

      Minimum interatomic distances (in Ångströms).
      - Keys: Atomic symbols.
      - Values: Distance thresholds based on lattice parameters.

      :type: dict

   .. attribute:: atomic_arrangement

      Crystallographic structure of elements.
      - Keys: Atomic symbols.
      - Values: String representation of atomic packing ("FCC", "BCC", "HCP").

      :type: dict

   .. attribute:: metal_atomtypes

      List of valid atomic types for metal nanoparticles.

      :type: list

   Sources:
       - Chemistry LibreTexts - Crystal Structures of Metals
         https://chem.libretexts.org/Bookshelves/Inorganic_Chemistry/Introduction_to_Inorganic_Chemistry_(Wikibook)/06%3A_Metals_and_Alloys-_Structure_Bonding_Electronic_and_Magnetic_Properties/6.04%3A_Crystal_Structures_of_Metals
       - Wikipedia - Graphene
         https://en.wikipedia.org/wiki/Graphene

         (Both accessed on 21st February 2025.)

   .. rubric:: Notes

   - All values are in Ångströms.
   - The `lattice_constant` dictionary includes FCC, BCC, HCP metals and graphene.
   - The `min_dist` dictionary ensures reasonable atomic separations for simulations.
   - The class is mainly used for molecular structure generation and validation.


   .. py:attribute:: convergence
      :value: 0.01



   .. py:attribute:: convergence_step
      :value: 0.001



   .. py:attribute:: min_dist_translate
      :value: 1.0



   .. py:attribute:: lattice_constant


   .. py:attribute:: min_dist


   .. py:attribute:: atomic_arrangement


   .. py:attribute:: metal_atomtypes
      :value: ['ag', 'au', 'al', 'ni', 'cu', 'pd', 'pt', 'pb', 'th', 'ce', 'yb', 'na', 'fe', 'mo', 'w', 'v',...



   .. py:attribute:: rdkit_file_extensions
      :value: ['.smi', '.sdf', '.mol', '.pdb', '.xyz']



   .. py:attribute:: rdkit_file_extensions_opt
      :value: ['.pdb', '.xyz', '.sdf']



   .. py:attribute:: rdkit_file_extensions_confs
      :value: ['.pdb', '.xyz', '.sdf']



   .. py:attribute:: rdkit_force_fields
      :value: ['mmff94', 'mmff94s', 'uff']