geom.classes.input_class

Classes

input_class

Manages user-defined parameters for geometric transformations and structure generation.

Module Contents

class geom.classes.input_class.input_class

Manages user-defined parameters for geometric transformations and structure generation.

This class stores user inputs related to translation, rotation, structure creation, and other transformations for metal nanoparticles and graphene structures.

- Transformation Flags

Enable operations such as translation, rotation, mirroring, and structure generation.

- Geometry Files

Stores input filenames for molecular structures.

- Translation & Rotation

Contains direction, distances, angles, and axis information.

- Structure Generation

Flags and parameters for generating different nanostructures.

- Miscellaneous

Handles alloy composition, verbosity settings, and file extensions.

Notes

• The full list of attributes is initialized in __init__().

• Methods validate inputs, read data, and apply transformations.

rdkit = False

rdkit_visualize = False

rdkit_visualize_2d = False

rdkit_visualize_3d = False

rdkit_bw = False

rdkit_match = False

rdkit_abbreviations = False

rdkit_file_conversion = False

rdkit_opt = False

rdkit_conformers = False

stereo_annotations = False

atom_index = False

remove_H = False

check_aromaticity = False

match_smiles = ''

rdkit_mol_file = ''

rdkit_mol_file_extension = ''

rdkit_force_field = ''

rdkit_output_file = ''

rdkit_confs_ext = '.pdb'

rdkit_max_iters = 200

rdkit_confs = 50

rdkit_confs_prune_rms = 0.3

small_tasks = False

translate = False

translate_controlled_distance = False

translate_1 = False

translate_center = False

move_geom_to_000 = False

move_geom_1_to_000 = False

move_geom_2_to_000 = False

distances = []

dir_factor = []

file_geom2_translated = ''

distances_input = ''

geom_file = ''

geom1_file = ''

geom2_file = ''

dir_axis_input = ''

origin_CM = ''

origin_CM_1 = ''

origin_CM_2 = ''

direction = 1.0

dimer_distance = 0.0

min_dist = False

rotate = False

rotate_angles = False

rotate_1 = False

angles = []

angles_input = ''

file_geom_rotated = ''

angle = 0.0

geom_center = False

geom_specular = False

create_dimer = False

create_bowtie = False

create_geom = False

create_ase_bulk = False

gen_3d_mesh = False

gen_3d_mesh_sphere = False

gen_3d_mesh_rod = False

gen_graphene = False

gen_core_shell = False

gen_sphere = False

gen_sphere_core_shell = False

gen_rod = False

gen_rod_core_shell = False

gen_tip = False

gen_cone = False

gen_icosahedra = False

gen_cto = False

gen_idh = False

gen_pyramid = False

gen_pentpyramid = False

gen_microscope = False

gen_bipyramid = False

gen_pencil = False

gen_pentbipyramid = False

pentbipyramid_type = ''

alloy = False

mesh_size = 1.0

alloy_perc = 0.0

elliptic_parabola_a = 1.0

elliptic_parabola_b = 1.0

elliptic_parabola_c = 0.0

z_min = 0.0

z_max = 0.0

z_max_paraboloid = 0.0

z_max_pyramid = 0.0

rod_length = 0.0

rod_length_in = 0.0

rod_length_out = 0.0

rod_width = 0.0

rod_width_in = 0.0

rod_width_out = 0.0

bipyramid_width = 0.0

bipyramid_length = 0.0

side_length = 0.0

base_width = 0.0

radius = 0.0

radius_in = 0.0

radius_out = 0.0

X_length = 0.0

Y_length = 0.0

sphere_center = [0.0, 0.0, 0.0]

xyz_output = ''

mesh_output = ''

tmp_folder = ''

alloy_string = ''

atomtype = ''

atomtype_in = ''

atomtype_out = ''

atomtypes_alloys = ['ag', 'au']

atomtypes_core_shell = ['ag', 'au']

axes = ['x', 'y', 'z']

graphene_structures = ['rib', 'disk', 'ring', 'triangle']

graphene_structure = ''

graphene_edge_types = ['armchair', 'zigzag']

graphene_edge_type = ''

merge = False

merge_cutoff = 0.0

verbose = False

verbose_inp = ''

check_input_case()

Validates and checks input requirements for selected operations.

Returns:

Performs necessary checks and raises errors if conditions are not met.

Return type:

None

Notes

• Ensures input files exist before processing.

• Checks file extensions for validity.

• Validates direction axis input.

• Ensures selected operations are correctly configured.

read_input(what)

Reads an input file containing distances or angles.

Parameters:

what (str) – Specifies whether to read ‘distances’ or ‘angles’.

Returns:

Populates the respective list attribute (self.distances or self.angles).

Return type:

None

Raises:

RuntimeError – If a blank line or multiple values are found in a single line.

Notes

• Reads a file line by line and converts values to floats.

• Ensures valid input formatting before processing.

change_trans_sense()

Reverses the direction factor for translations.

Returns:

The modified input_class instance with updated dir_factor.

Return type:

input_class

Notes

• Multiplies all direction factors by -1.

• Used to invert translation direction dynamically.