geom.functions.general

Functions

read_command_line(argv, inp)	Parses command-line arguments and determines the operation mode.
print_help()	Prints the help message with usage instructions and exits the program.
parse_translation(argv, inp)	Parses translation-related command-line arguments.
parse_rotation(argv, inp)	Parses rotation-related command-line arguments.
parse_mirror(argv, inp)	Parses command-line arguments for performing a mirror reflection.
parse_merge(argv, inp)	Parses command-line arguments for merging geometries.
parse_min(argv, inp)	Parses command-line arguments for calculating the minimum distance between two geometries.
parse_center(argv, inp)	Parses command-line arguments for computing the geometric center of a structure.
parse_create(argv, inp)	Parses command-line arguments for generating different types of geometries.
parse_dimer_argument(argv, inp, output)	Parses dimer-related command-line arguments and updates the inp object.
parse_bowtie_argument(argv, inp, output)	Parses bowtie-related command-line arguments and updates the inp object.
parse_alloy_arguments(argv, inp, output)	Parses alloy-related command-line arguments and updates the inp object.
check_file_exists(infile)	Checks if a given file exists.
check_FCC(atomtype, string)	Checks if the given metallic atom type follows an FCC arrangement.
check_FCC_or_BCC(atomtype)	Checks if the given metallic atom type follows either an FCC or BCC arrangement.
check_file_extension(infile, extension)	Checks if the input file has the correct extension.
check_dir_axis(inp)	Validates the direction axis input for translation or rotation.
create_results_geom()	Creates the results_geom directory if it does not already exist.

Module Contents

geom.functions.general.read_command_line(argv, inp)

Parses command-line arguments and determines the operation mode.

Parameters:

• argv (list[str]) – List of command-line arguments.

• inp (input_class) – An instance containing input parameters.

Returns:

Calls the appropriate parsing function or displays help.

Return type:

None

Notes

• If no arguments are provided, an error is raised.

• Recognizes different command-line options and triggers the corresponding function.

• Prints help if -h or -help is passed.

geom.functions.general.print_help()

Prints the help message with usage instructions and exits the program.

Returns:

Displays the help text and terminates execution.

Return type:

None

geom.functions.general.parse_translation(argv, inp)

Parses translation-related command-line arguments.

Parameters:

• argv (list[str]) – List of command-line arguments.

• inp (input_class) – An instance containing input parameters.

Returns:

Sets translation-related attributes in inp.

Return type:

None

Notes

• Handles both controlled distance translation (-t) and simple shift translation (-t1).

• Extracts input filenames, translation parameters, and verbosity settings.

geom.functions.general.parse_rotation(argv, inp)

Parses rotation-related command-line arguments.

Parameters:

• argv (list[str]) – List of command-line arguments.

• inp (input_class) – An instance containing input parameters.

Returns:

Sets rotation-related attributes in inp.

Return type:

None

Notes

• Handles both list-based rotation (-r) and single-angle rotation (-r1).

• Extracts input filenames and rotation parameters.

geom.functions.general.parse_mirror(argv, inp)

Parses command-line arguments for performing a mirror reflection.

Parameters:

• argv (list[str]) – List of command-line arguments.

• inp (input_class) – An instance containing input parameters.

Returns:

Sets mirroring attributes in inp.

Return type:

None

geom.functions.general.parse_merge(argv, inp)

Parses command-line arguments for merging geometries.

Parameters:

• argv (list[str]) – List of command-line arguments.

• inp (input_class) – An instance containing input parameters.

Returns:

Sets merging attributes in inp.

Return type:

None

Notes

• Requires two geometry files and a cutoff distance.

geom.functions.general.parse_min(argv, inp)

Parses command-line arguments for calculating the minimum distance between two geometries.

Parameters:

• argv (list[str]) – List of command-line arguments.

• inp (input_class) – An instance containing input parameters.

Returns:

Sets minimum distance calculation attributes in inp.

Return type:

None

geom.functions.general.parse_center(argv, inp)

Parses command-line arguments for computing the geometric center of a structure.

Parameters:

• argv (list[str]) – List of command-line arguments.

• inp (input_class) – An instance containing input parameters.

Returns:

Sets geometric centering attributes in inp.

Return type:

None

geom.functions.general.parse_create(argv, inp)

Parses command-line arguments for generating different types of geometries.

Parameters:

• argv (list[str]) – List of command-line arguments.

• inp (input_class) – An instance containing input parameters.

Returns:

Sets attributes in inp for geometry generation.

Return type:

None

Notes

• Handles the creation of graphene structures, nanoparticles, and bulk metal structures.

• Validates input parameters and extracts atomic and structural properties.

geom.functions.general.parse_dimer_argument(argv, inp, output)

Parses dimer-related command-line arguments and updates the inp object.

Parameters:

• argv (list[str]) – Command-line arguments list.

• inp (input_class) – The input class instance where dimer attributes are stored.

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

Returns:

Updates inp.create_dimer, inp.distances, and inp.dir_axis_input.

Return type:

None

Notes

• Searches for “-dimer” in argv.

• Reads the next argument as a float and stores it in inp.distances as a list.

• Reads the following argument as an axis specification (+x, -y, +z, etc.).

• Ensures the extracted values are valid.

geom.functions.general.parse_bowtie_argument(argv, inp, output)

Parses bowtie-related command-line arguments and updates the inp object.

Parameters:

• argv (list[str]) – List of command-line arguments.

• inp (input_class) – An instance of the input class where bowtie attributes are stored.

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

Returns:

This function does not return a value but updates inp.create_bowtie, inp.distances, and inp.dir_axis_input.

Return type:

None

Raises:

ValueError – If bowtie arguments are missing or contain invalid values.

Notes

• This function checks if “-bowtie” is present in argv.

• If found, it ensures that the bowtie structure is only available for tip, pyramid, cone, and microscope structures.

• The function then extracts the bowtie distance (must be a positive float).

• If any validation fails, it calls output.error() to handle errors.

geom.functions.general.parse_alloy_arguments(argv, inp, output)

Parses alloy-related command-line arguments and updates the inp object.

Parameters:

• argv (list[str]) – Command-line arguments list.

• inp (input_class) – The input class instance where alloy attributes are stored.

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

Returns:

Updates inp attributes based on the parsed alloy arguments.

Return type:

None

Notes

• Handles both cases:

  1. -alloy atom_type -percentual float

  2. -alloy -percentual float

• Ensures inp.alloy_perc is a valid float and between 0 and 100.

• If atom type is omitted, it defaults to inp.atomtype.

geom.functions.general.check_file_exists(infile)

Checks if a given file exists.

Parameters:

infile (str) – Path to the input file.

Returns:

Raises an error if the file is not found.

Return type:

None

geom.functions.general.check_FCC(atomtype, string)

Checks if the given metallic atom type follows an FCC arrangement.

Parameters:

• atomtype (str) – Type of metal atom.

• string (str) – Structure name being validated.

Returns:

Raises an error if the atom type is not FCC.

Return type:

None

geom.functions.general.check_FCC_or_BCC(atomtype)

Checks if the given metallic atom type follows either an FCC or BCC arrangement.

Parameters:

atomtype (str) – Type of metal atom.

Returns:

Raises an error if the atom type is not FCC or BCC.

Return type:

None

geom.functions.general.check_file_extension(infile, extension)

Checks if the input file has the correct extension.

Parameters:

• infile (str) – Path to the input file.

• extension (str) – Expected file extension.

Returns:

Raises an error if the file does not have the expected extension.

Return type:

None

geom.functions.general.check_dir_axis(inp)

Validates the direction axis input for translation or rotation.

Parameters:

inp (input_class) – An instance containing input parameters.

Returns:

Updated inp with validated direction axis settings.

Return type:

input_class

Notes

• Ensures that the axis is properly formatted (e.g., +x, -y).

• Assigns the corresponding numerical translation factor.

geom.functions.general.create_results_geom()

Creates the results_geom directory if it does not already exist.

Returns:

Ensures that output files can be stored in the correct location.

Return type:

None