geom.functions.tools

Functions

calc_min_distance(geom1, geom2)	Calculates the minimum distance between two molecular geometries.
rotate(mol, angle, dir_axis_input, mol_rot)	Rotates a molecular geometry by a given angle around a specified axis.
merge_geoms(inp, geom1, geom2)	Merges two molecular geometries while avoiding overlap based on a cutoff distance.
subtract_geoms(inp, geom1, geom2)	Subtracts one geometry from another based on a cutoff distance.
determine_sphere_center(inp, sense)	Determines the center of a sphere within a rod-like structure.
copy_geometry_file(source_file, destination_file)	Copies the geometry file from 'results_geom/' to the current working directory.
delete_geometry_file(file_path)	Deletes the temporary geometry file from the execution directory.
delete_all_files(pattern)	Deletes all files matching a given pattern in the execution directory.
create_dimer(inp)	Creates a molecular dimer by translating a geometry to a controlled distance.
create_bowtie(inp)	Generates a molecular bowtie structure by rotating and translating a geometry.
calculate_normal_and_rhs(center_a, center_b, apex)	Calculate the plane normal and RHS for the plane through three points.

Module Contents

geom.functions.tools.calc_min_distance(geom1, geom2)

Calculates the minimum distance between two molecular geometries.

Parameters:

• geom1 (molecule) – The first molecule object.

• geom2 (molecule) – The second molecule object.

Returns:

The minimum distance between the two geometries.

Return type:

float

Notes

• Uses NumPy broadcasting for efficient pairwise distance computation.

geom.functions.tools.rotate(mol, angle, dir_axis_input, mol_rot)

Rotates a molecular geometry by a given angle around a specified axis.

Parameters:

• mol (molecule) – The original molecule object.

• angle (float) – The rotation angle in degrees.

• dir_axis_input (str) – The rotation axis and sense (e.g., +x, -y).

• mol_rot (molecule) – A new molecule object to store the rotated geometry.

Returns:

The rotated molecule object.

Return type:

molecule

Notes

• Rotation is performed using standard rotation matrices.

• Supports rotation around x, y, and z axes.

geom.functions.tools.merge_geoms(inp, geom1, geom2)

Merges two molecular geometries while avoiding overlap based on a cutoff distance.

Parameters:

• inp (input_class) – Input object containing cutoff distance.

• geom1 (molecule) – The first molecule object.

• geom2 (molecule) – The second molecule object.

Returns:

The merged molecular geometry.

Return type:

molecule

Notes

• Uses pairwise distance calculations to avoid overlapping atoms.

• Atoms from geom2 that are too close to geom1 are removed.

• The merged geometry retains properties such as center and bounding box.

geom.functions.tools.subtract_geoms(inp, geom1, geom2)

Subtracts one geometry from another based on a cutoff distance.

Parameters:

• inp (input_class) – Input object containing cutoff distance.

• geom1 (molecule) – The first molecule object (to be subtracted).

• geom2 (molecule) – The second molecule object.

Returns:

A new molecule object representing geom2 - geom1.

Return type:

molecule

Notes

• Atoms from geom2 that are within the cutoff distance of geom1 are removed.

• The resulting geometry retains calculated properties such as center and bounding box.

geom.functions.tools.determine_sphere_center(inp, sense)

Determines the center of a sphere within a rod-like structure.

Parameters:

• inp (input_class) – Input object containing rod and sphere dimensions.

• sense (str) – Direction (‘+’ or ‘-’) to position the sphere.

Returns:

The updated sphere center coordinates.

Return type:

list[float]

Notes

• The sphere’s radius is computed as half the rod width.

• The center is positioned based on the rod’s main axis.

geom.functions.tools.copy_geometry_file(source_file, destination_file)

Copies the geometry file from ‘results_geom/’ to the current working directory.

Parameters:

• source_file (str) – Path to the source geometry file.

• destination_file (str) – Path where the file should be copied.

• output (module) – The output module for error handling.

Returns:

None

geom.functions.tools.delete_geometry_file(file_path)

Deletes the temporary geometry file from the execution directory.

Parameters:

• file_path (str) – Path to the temporary geometry file to be deleted.

• output (module) – The output module for error handling.

Returns:

None

geom.functions.tools.delete_all_files(pattern)

Deletes all files matching a given pattern in the execution directory.

Parameters:

pattern (str) – File path pattern to match (e.g., “results_geom/*.xyz”).

Returns:

None

geom.functions.tools.create_dimer(inp)

Creates a molecular dimer by translating a geometry to a controlled distance.

Parameters:

inp (input_class) – Input object containing: - xyz_output (str): Name of the geometry file. - geom1_file, geom2_file (str): Paths to the geometry files. - move_geom_1_to_000, move_geom_2_to_000 (bool): Flags to center geometries at the origin. - dir_axis_input (str): Translation direction (+x, -y, etc.). - distances (list[float]): List containing the interatomic distance for the dimer. - file_geom2_translated (str): Name of the translated geometry file.

Returns:

The function updates input parameters and generates output files.

Return type:

None

Notes

• Copies the initial geometry file from results_geom/ to the execution directory.

• Prepares input parameters for translation.

• Translates the second molecule to maintain the specified interatomic distance.

• Reads and merges the initial and translated geometries.

• Saves the final dimer structure as an output file.

• Deletes temporary geometry files after processing.

geom.functions.tools.create_bowtie(inp)

Generates a molecular bowtie structure by rotating and translating a geometry.

Parameters:

inp (input_class) – Input object containing: - xyz_output (str): Name of the geometry file. - geom1_file, geom2_file (str): Paths to the geometry files. - move_geom_1_to_000, move_geom_2_to_000 (bool): Flags to center geometries at the origin. - dir_axis_input (str): Translation direction (+x, -y, etc.). - distances (list[float]): List containing the interatomic distance for the bowtie. - file_geom2_translated (str): Name of the translated geometry file. - angle (float): Rotation angle in degrees.

Returns:

The function updates input parameters and generates output files.

Return type:

None

Notes

• Copies the initial geometry file from results_geom/ to the execution directory.

• Rotates the geometry by 180 degrees around the +x axis.

• Copies the rotated geometries for translation.

• Translates one geometry along the +z or -z axis depending on the structure type.

• Merges the rotated and translated geometries into a final bowtie structure.

• Saves the final structure and deletes temporary files.

geom.functions.tools.calculate_normal_and_rhs(center_a, center_b, apex)

Calculate the plane normal and RHS for the plane through three points.

The plane is defined by the apex and the two points on an edge (center_a, center_b). The equation returned is:

n · x + rhs = 0

where the normal vector is computed as:

n = (center_a - apex) × (center_b - apex)

Notes

• The orientation of the normal follows the right-hand rule and depends on the order of center_a and center_b.

• The normal is not normalized.

• This helper is useful for constructing side planes of a pyramid.

Parameters:

• center_a (array_like) – 3-element sequence (x, y, z) for the first point on the edge.

• center_b (array_like) – 3-element sequence (x, y, z) for the second point on the edge.

• apex (array_like) – 3-element sequence (x, y, z) for the apex of the pyramid/face.

Returns:

A pair (normal, rhs) where: * normal (numpy.ndarray): The 3D normal vector of the plane (shape (3,)). * rhs (float): The right-hand-side constant so that normal · x + rhs = 0.

Return type:

tuple