THeSeuSS package

Submodules

THeSeuSS.CheckPeriodicvsNonPeriodic module

Verifies whether the simulation of spectra is intended for a periodic or non-periodic system.

class THeSeuSS.CheckPeriodicvsNonPeriodic.PeriodicvsNonPeriodic(code: str, cell_dims: str, output_file: str, dispersion: bool, restart: bool, commands: str, functional: str = None)

Bases: object

check_periodic_vs_non_periodic() → bool

Checks if the system is periodic or non-periodic.

code_initialization()

Starts the code based on the periodicity of the system. If the system is periodic, and a .cif file is provided, the geometry is converted and the international space group number of the experimental structure is determined. If the system is non-periodic, no action is taken.

decision_submission_cell()

Determines the appropriate approach for generating the displaced structures. If the system is periodic, submits calculations using the PhonopyCalculator class. If the system is non-periodic, generates displaced structures using the GenerateDisplacements class.

dyn_mat_for_eigvec_eig_val_freq()

Returns eigenvalues, eigenvectors and in turn frequencies.

eigenvec_eigenval_freq() → [<class 'numpy.ndarray'>, <class 'numpy.ndarray'>, <class 'numpy.ndarray'>]

If successful, it returns the eigenvectors, eigenvalues and frequencies. If an error occurs, it prints an error message.

periodic_space_group_calc()

Calculate the space group of the periodic structure after cell and geometry optimization.

print_periodic_vs_non_periodic()

Prints if the system is periodic or non-periodic.

THeSeuSS.CheckSuccessOutput module

It checks if the single point calculations have been succesfully finished.

class THeSeuSS.CheckSuccessOutput.CheckOutputSuccess(code: str, output: str, dispersion: bool, restart: bool, functional: str = None)

Bases: object

check_for_success_calc_before_spectra()

Checks for successful completion of calculations before proceeding to spectra generation. FileNotFoundError: If the file does not exist. ValueError: If the file does not contain the expected patterns.

single_successful_output() → bool

Checks if the cell and geometry optimization calculation has been successful.

THeSeuSS.Constants module

Constants

class THeSeuSS.Constants.ConstantsSpectra(code: str)

Bases: object

constants_definition() → [<class 'float'>, <class 'float'>, <class 'float'>, <class 'float'>]

Constants

hubbard_derivates_dict()

Dictionary containing all atomic Hubbard derivates (atomic units). Retrieved by https://dftb.org/parameters/download/3ob/3ob-3-1-cc.

max_angular_mom_dict()

Dictionary containing maximum angular momenta.

THeSeuSS.Coordinates module

It converts the coordinates from cartesian to fractional.

class THeSeuSS.Coordinates.ConversionUnitsCoordinates(code: str)

Bases: object

PATH = '/mnt/aiongpfs/users/aboziki/THeSeuSS'

cartesian_to_fractional_DFTBplus(path_of_current_directory, supercell: bool = False)

Converts cartesian coordinates to fractional - DFTB+.

cartesian_to_fractional_FHIaims(path_of_current_directory, supercell: bool = False)

It converts cartesian coordinates to fractional - FHI-aims.’’’

THeSeuSS.EigenvectorsFrequenciesPHONOPY module

Eigenvectors and eigenvalues from PHONOPY code

class THeSeuSS.EigenvectorsFrequenciesPHONOPY.VibrationalFrequencies(code: str, output_file_of_SCFSs: str, dispersion: bool)

Bases: object

GEOMETRY_IN = 'geometry.in'

GEO_GEN = 'geo.gen'

read_eig_vec_phonopy(hessian: ndarray) → [<class 'numpy.ndarray'>, <class 'numpy.ndarray'>, <class 'numpy.ndarray'>]

Returns eigenvalues, eigenvectors and in turn frequencies.

THeSeuSS.FiniteDisplacements_phonopy module

Creation of the subdirectories of the finite displaced geometries.

class THeSeuSS.FiniteDisplacements_phonopy.FDSubdirectoriesGeneration(code: str, kpoints: str, functional: str, eev: str, rho: str, etot: str, forces: str, sc_iter_limit: str, species: str, pol_grid: str, SCC_tolerance: str, max_SCC_iterations: str, output_file: str, dispersion: bool, dispersion_type: str, restart: bool)

Bases: object

iterate_over_files()

Processes displaced structures and generates required input files accordingly. Copies necessary files into directories containing displaced structures. Note: Exception handling is implemented to catch any errors during the iteration.

THeSeuSS.GenerateDisplacementsMolecules module

Prepares perturbed structures to facilitate the application of the finite displacements method, enabling the subsequent calculation of molecular vibrational frequencies.

class THeSeuSS.GenerateDisplacementsMolecules.GenerateDisplacements(code: str)

Bases: object

GEOMETRY_IN = 'vibrations/geometry.in'

GEO_GEN = 'vibrations/geo.gen'

create_the_displaced_structures()

Generate displaced input structures by adding and subtracting the displacement value.

THeSeuSS.GeometryInputConversion module

Conversion of .cif file to either FHIaims or DFTB+ geometry input files.

class THeSeuSS.GeometryInputConversion.GeometryConversion(code: str)

Bases: object

check_cif_file()

Verifies the presence of a file with the .cif extension within the directory.

THeSeuSS.IRRamanSpectra module

IR and Raman intensities. For periodic systems.

class THeSeuSS.IRRamanSpectra.IntensityCalculator(code: str, eig_vec: ndarray, cartesian_pol: ndarray, pol: ndarray, output_file: str, no_negfreqs: int, restart: bool, functional: str = None)

Bases: object

IRintensity()

Calculates the IR intensity.

Ramanactivity()

Calculates the Raman Activity.

spectra_calculation() → [<class 'numpy.ndarray'>, <class 'numpy.ndarray'>]

Saves the IR intensity and Raman activity.

THeSeuSS.InputOutputFiles module

Preparation of inputs for cell and geometry optimization / single point calculations

class THeSeuSS.InputOutputFiles.InputsGenerator(code: str, kpoints: str = None, functional: str = None, eev: str = None, rho: str = None, etot: str = None, forces: str = None, sc_iter_limit: str = None, species: str = None, frequencies: str = None, geometry: str = None, energy: str = None, steps: str = None, pol_grid: str = None, max_force_component: str = None, max_steps: str = None, SCC_tolerance: str = None, max_SCC_iterations: str = None, output_file: str = None, dispersion: bool = False, dispersion_type: str = None, restart: bool = False)

Bases: object

DFTB_parameters_input_file(dftb_in_file)

Generates the dftb_in.hsd input file of DFTB+

species_path_updated: str

Directory path where the .skf files are located

data: dict

It stores the parameters found in the dftb_in.hsd file

FHIaims_control_file(control_file)

Generates the control input file of FHIaims.

number_atype: int, list

The number of each atom within the crystal structure

atype: str, list

The atom type of each atom within the crystal structure

unique_atype: str, list

The atom types present in the crystal structure (appearing only once)

input_parameters: dict

It stores the parameters found in the control file and is utilized to display the input information in the output

species_path_updated: str

Directory path where the species defaults settings are located

path_of_file_atype: str

Path of the species defaults of an atom type

source_data: str

Data of the species defaults of an atom type

GEOMETRY_IN = 'geometry.in'

GEO_GEN = 'geo.gen'

Generation of FHIaims and DFTB+ inputs.

code

Code

Type:

str

kpoints

K-points (Three values: they are converted to integer)

Type:

str

functional

Functional (FHIaims)

Type:

str

eev

Convergence criterion for the self-consistency cycle, based on the sum of eigenvalues (FHIaims)

Type:

str

rho

Convergence criterion for the self-consistency cycle, based on the charge density (FHIaims)

Type:

str

etot

Convergence criterion for the self-consistency cycle, based on the total energy (FHIaims)

Type:

str

forces

Convergence criterion for the self-consistency cycle, based on energy derivatives/forces (FHIaims)

Type:

str

sc_iter_limit

Maximum number of s.c.f. cycles before a calculation is considered and abandoned (FHIaims)

Type:

str

species

Species defaults settings; basis set, integration grids, accuracy of the Hartree potential (FHIaims)

Type:

str

frequencies

Type:

bool

geometry

Maximum residual force component per atom, below which the geometry relaxation is considered converged (geometry relaxation) (FHIaims)

Type:

str

energy

Energy amount by which a relaxation step can move upwards and is still accepted (FHIaims)

Type:

str

steps

Maximum number of steps after which a structure optimization will be aborted (FHIaims)

Type:

str

pol_grid

Polarization grid

Type:

str

max_force_component

Optimization is stopped, if the force component with the maximal absolute value goes below this value (DFTB+)

Type:

str / converted to float

max_steps

Maximum number of steps after which the optimization should stop (DFTB+)

Type:

str

SCC_tolerance

Stopping criteria for the scc. Tolerance for the maximum difference in any charge between two scc cycles (DFTB+)

Type:

str

max_SCC_iterations

Maximal number of scc cycles to reach convergence (DFTB+)

Type:

str

output_file

Output file

Type:

str

dispersion

Type:

bool

path

Path of the directory from which the code has been executed

Type:

str

package_path

Path of the directory where the code is located

Type:

str

dispersion_type

Dispersion type (MBD_NL or TS)

Type:

str

file_exists()

Checks the existence of input files required for cell and geometry optimization in FHI-aims or DFTB+ calculations. If the file does not exist, it generates the required input file.

THeSeuSS.InputsPreparation module

Preparation and modification of input files

class THeSeuSS.InputsPreparation.GeometryProcessor(geom_input: str, code: str)

Bases: object

Class for exctracting information out of a geometry input file.

geom_input

Namefile of the geometry input file.

Type:

str

code

Code

Type:

str

number_of_atoms() → int

It returns the number of atoms in the structure.

index: int

Number of atoms in a given geometry input file.

read_coordinates() → list

It returns the coordinates from the geometry input file.

coordlist

List containing coordinate tuples as floats.

read_lattice() → list

It returns the lattice cell (9 elements) from the geometry input file.

cell: list

List containing the lattice cell elements as floats.

read_the_atom_type() → [<class 'list'>, <class 'list'>]

It returns the atom type of the atoms of the structure from the geometry input file.

atom_type_no: tuple

Tuple containing lists of atom type numbers.

atom_type: tuple

Tuple containing lists of atom types.

THeSeuSS.MapAtoms module

It takes care of equivalent atoms. It maps the polarizability and cartesian polarization of irreducible atoms back to reducible atoms.

class THeSeuSS.MapAtoms.spglibProcessor(code: str)

Bases: object

GEOMETRY_IN = 'geometry.in'

GEO_GEN = 'geo.gen'

get_international_space_group_number(source_path) → int

Returns the international space group number.

prop_equivalent_atoms(pol: ndarray, cartesian_pol: ndarray, element_axis_coord: ndarray) → [<class 'numpy.ndarray'>, <class 'numpy.ndarray'>]

Returns the polarizability and Cartesian polarization arrays after removing the last two columns, which represent the atom number and coordinate (axis) of each atom.

THeSeuSS.PlotSpectra module

It applies the spectrum broadening and prepares the IR and Raman plots.

class THeSeuSS.PlotSpectra.SpectraPlotter(freq: ndarray, IRintensity: ndarray, Ramanactivity: ndarray, broadening: str, fwhm: float)

Bases: object

plot_spectra()

Plots the IR and Raman spectra.

plot_spectrum_IR()

Prepares the plot for the IR spectrum.

plot_spectrum_Raman()

Prepares the plot for the Raman spectrum.

THeSeuSS.Restart module

Restart module of the package

class THeSeuSS.Restart.RestartCalculation(code: str, output: str, dispersion: bool, restart: bool, functional: str = None, commands: str = None)

Bases: object

directory_non_completed_calculations() → list

Returns the directories of single-point calculations that failed to complete successfully.

restart_calculations()

Restart the submission of single-point calculations that failed to complete successfully.

THeSeuSS.SubmitCalculations module

Submission of FHI-aims and PHONOPY calculations

class THeSeuSS.SubmitCalculations.Calculator(code: str, output_file: str, dispersion: bool, restart: bool, functional: str = None, commands: str = None)

Bases: object

frozen_phonon_approximation_drct()

Creates a directory to store files associated with the frozen phonon approximation.

run_command(command: str) → str

Executes the given command in the shell environment and returns the output.

submit_job()

Submission of electronic structure calculations, (FHIaims and DFTB+).

submit_jobs_in_parallel()

Submits multiple jobs in parallel using a ThreadPoolExecutor. Note: Adjust the number of threads based on the available computational resources and the number of folders.

class THeSeuSS.SubmitCalculations.PhonopyCalculator(code: str, cell_dims: str, output_file_of_SCFSs: str)

Bases: object

animate_eigenvectors()

Creates the xyz_jmol file to animate the vibrations using jmol package.

disp_forces_dataset_dyn_matrix()

Generates a dataset for producing the force constants and calculating the dynamical matrix based on displacements and forces obtained from FHIaims or DFTB+ output files.

force_identifier(drct: str) → str

Constructs the path to the output file containing forces for a specific calculation.

plot_band_structure()

Plots the band structure using predefined paths in reciprocal space. Uses Phonopy to calculate and visualize the band structure.

read_forces_from_output(output_path: str)

Extracts the forces from the FHIaims output and results.tag DFTB+ file.

sort_directories() → list

Sorts directories in the current directory that contain the substring ‘Coord’, based on the numeric value in their names.

submit_phonopy_displacements()

Generate structures with displacements using PHONOPY. If successful, it prints a confirmation message. If an error occurs it prints an error message.

supercell_disp_PHONOPY()

Retrieves the supercells with atomic displacements generated by Phonopy and the supercell. Writes the supercells with displacements to output files based on the code.

THeSeuSS.TwoPointCentralDifference module

Two-point central difference to calculate the polarizability and cartesian polarization. For periodic systems.

class THeSeuSS.TwoPointCentralDifference.TwoPointCentralDiff(code: str, output_file: str, dispersion: bool, supercell: bool, restart: bool, functional: str = None)

Bases: object

calculate_pol_cart_pol()

Calculates the polarizability and cartesian polarization, utilizing spglibProcessor to map equivalent atoms and coordinates. If a supercell is specified, adjusts the number of atoms and lines accordingly.

coord_conversion_cartesian_to_fractional()

Converts Cartesian coordinates to fractional coordinates. Utilizes the ConversionUnitsCoordinates class to perform the conversion.

get_volume() → float64

Retrieves the volume.

pol_cart_pol_processor() → [<class 'numpy.ndarray'>, <class 'numpy.ndarray'>]

Processes the polarizability and cartesian polarization.

Module contents