geom.classes.parameters

Classes

parameters

Parameters Class for Metal and Graphene Structures.

Module Contents

class geom.classes.parameters.parameters[source]

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.

convergence[source]

Convergence threshold for numerical operations.

Type:: float

convergence_step[source]

Step size for convergence calculations.

Type:: float

min_dist_translate[source]

Minimum allowable distance for translation operations.

Type:: float

lattice_constant[source]

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

min_dist[source]

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

Type:: dict

atomic_arrangement[source]

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

Type:: dict

metal_atomtypes[source]

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.)

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.

convergence = 0.01[source]

convergence_step = 0.001[source]

min_dist_translate = 1.0[source]

lattice_constant[source]

min_dist[source]

atomic_arrangement[source]

metal_atomtypes = ['ag', 'au', 'al', 'ni', 'cu', 'pd', 'pt', 'pb', 'th', 'ce', 'yb', 'na', 'fe', 'mo', 'w', 'v',...[source]

rdkit_file_extensions = ['.smi', '.sdf', '.mol', '.pdb', '.xyz'][source]

rdkit_file_extensions_opt = ['.pdb', '.xyz', '.sdf'][source]

rdkit_file_extensions_confs = ['.pdb', '.xyz', '.sdf'][source]

rdkit_force_fields = ['mmff94', 'mmff94s', 'uff'][source]