mcal package

Subpackages

• mcal.calculations package
  • Submodules
  • mcal.calculations.hopping_mobility_model module
    • cal_pinv()
    • demo()
    • diffusion_coefficient_tensor()
    • diffusion_coefficient_tensor_MC()
    • diffusion_coefficient_tensor_ODE()
    • marcus_rate()
    • mobility_tensor()
    • print_tensor()
  • mcal.calculations.rcal module
    • GausTermError
    • OSCTypeError
    • Rcal
      • Rcal.calc_reorganization()
      • Rcal.check_error_term()
      • Rcal.check_extension_log()
      • Rcal.extract_energy()
      • Rcal.print_timestamp()
    • main()
  • Module contents
• mcal.utils package
  • Submodules
  • mcal.utils.cif_reader module
    • CifReader
      • CifReader.ATOMIC_WEIGHTS
      • CifReader.COVALENT_RADII
      • CifReader.ELEMENT_PROP
      • CifReader.calc_cen_of_weight()
      • CifReader.convert_cart_to_frac()
      • CifReader.convert_frac_to_cart()
      • CifReader.expand_mols()
      • CifReader.export_unit_cell_file()
      • CifReader.parent_dir
      • CifReader.remove_duplicates()
    • ElementPropertiesIsNotDefinedError
    • FileIO
      • FileIO.add_adjacency_mat()
      • FileIO.add_coordinates()
      • FileIO.add_symbols()
      • FileIO.export_mol_file()
      • FileIO.export_xyz_file()
    • SymmetryIsNotDefinedError
    • ZValueIsNotMatchError
  • mcal.utils.gaus_log_reader module
    • FileReader
      • FileReader.close()
      • FileReader.reversed_readline()
    • check_normal_termination()
  • mcal.utils.gjf_maker module
    • GjfMaker
      • GjfMaker.ELEMENTS_NUM
      • GjfMaker.ELEMENT_PROP
      • GjfMaker.add_link()
      • GjfMaker.add_root()
      • GjfMaker.create_chk_file()
      • GjfMaker.create_rwf_file()
      • GjfMaker.export_gjf()
      • GjfMaker.opt()
      • GjfMaker.output_detail()
      • GjfMaker.parent_dir
      • GjfMaker.reset_variable()
      • GjfMaker.set_charge_spin()
      • GjfMaker.set_coordinates()
      • GjfMaker.set_function()
      • GjfMaker.set_resource()
      • GjfMaker.set_symbols()
      • GjfMaker.set_title()
  • Module contents

Submodules

mcal.mcal module

mcal

exception mcal.mcal.OSCTypeError

Bases: Exception

Exception for semiconductor type

mcal.mcal.atom_weight(symbol: str) → float

Get atom weight

Parameters:

symbol (str) – Symbol of atom

Returns:

Atomic weight

Return type:

float

mcal.mcal.cal_cen_of_weight(symbols1: ndarray[Any, dtype[str]], coordinates1: ndarray[Any, dtype[float64]], symbols2: ndarray[Any, dtype[str]] | None = None, coordinates2: ndarray[Any, dtype[float64]] | None = None) → ndarray[Any, dtype[float64]]

Calculate center of weight

Parameters:

• symbols1 (NDArray[str]) – Symbols of atoms in one monomer

• coordinates1 (NDArray[np.float64]) – Coordinates of atoms in one monomer

• symbols2 (Optional[NDArray[str]], optional) – Symbols of atoms in another monomer, by default None

• coordinates2 (Optional[NDArray[np.float64]], optional) – Coordinates of atoms in another monomer, by default None

Returns:

Center of weight

Return type:

NDArray[np.float64]

mcal.mcal.cal_distance_between_cen_of_weight(symbols1: ndarray[Any, dtype[str]], coordinates1: ndarray[Any, dtype[float64]], symbols2: ndarray[Any, dtype[str]], coordinates2: ndarray[Any, dtype[float64]]) → float

Calculate distance between centers of weight

Parameters:

• symbols1 (NDArray[str]) – Symbols of atoms in one monomer

• coordinates1 (NDArray[np.float64]) – Coordinates of atoms in one monomer

• symbols2 (NDArray[str]) – Symbols of atoms in another monomer

• coordinates2 (NDArray[np.float64]) – Coordinates of atoms in another monomer

Returns:

Distance between centers of weight

Return type:

float

mcal.mcal.cal_eigenvalue_decomposition(mobility_tensor: ndarray[Any, dtype[float64]]) → Tuple[ndarray[Any, dtype[float64]], ndarray[Any, dtype[float64]]]

Calculate eigenvalue decomposition of mobility tensor

Parameters:

mobility_tensor (NDArray[np.float64]) – Mobility tensor

Returns:

Eigenvalue(mobility value) and eigenvector(mobility vector)

Return type:

Tuple[NDArray[np.float64], NDArray[np.float64]]

mcal.mcal.cal_min_distance(symbols1: ndarray[Any, dtype[str]], coords1: ndarray[Any, dtype[float64]], symbols2: ndarray[Any, dtype[str]], coords2: ndarray[Any, dtype[float64]]) → float

Calculate minimum distance between two sets of atoms.

Parameters:

• symbols1 (NDArray[str]) – Symbols of atoms in one monomer

• coords1 (NDArray[np.float64]) – Coordinates of atoms in one monomer

• symbols2 (NDArray[str]) – Symbols of atoms in another monomer

• coords2 (NDArray[np.float64]) – Coordinates of atoms in another monomer

Returns:

Minimum distance between two sets of atoms

Return type:

float

mcal.mcal.cal_moment_of_inertia(symbols1: ndarray[Any, dtype[str]], coordinates1: ndarray[Any, dtype[float64]], symbols2: ndarray[Any, dtype[str]], coordinates2: ndarray[Any, dtype[float64]]) → Tuple[ndarray[Any, dtype[float64]], ndarray[Any, dtype[float64]]]

Calculate moment of inertia and eigenvectors of the inertia tensor.

Parameters:

• symbols1 (NDArray[str]) – Symbols of atoms in one monomer

• coordinates1 (NDArray[np.float64]) – Coordinates of atoms in one monomer

• symbols2 (NDArray[str]) – Symbols of atoms in another monomer

• coordinates2 (NDArray[np.float64]) – Coordinates of atoms in another monomer

Returns:

Moment of inertia and eigenvectors of the inertia tensor

Return type:

Tuple[NDArray[np.float64], NDArray[np.float64]]

mcal.mcal.check_reorganization_energy_completion(cif_path_without_ext: str, osc_type: Literal['p', 'n'], extension_log: str = '.log') → List[Literal['opt_neutral', 'opt_ion', 'neutral', 'ion']]

Check if all reorganization energy calculations are completed normally.

Parameters:

• cif_path_without_ext (str) – Base path of cif file (without extension)

• osc_type (Literal['p', 'n']) – Semiconductor type (p-type or n-type)

• extension_log (str) – Extension of log file

Returns:

List of calculations to skip

Return type:

List[Literal[‘opt_neutral’, ‘opt_ion’, ‘neutral’, ‘ion’]]

mcal.mcal.check_transfer_integral_completion(gjf_file: str, extension_log: str = '.log') → bool

Check if all transfer integral calculations are completed normally.

Parameters:

gjf_file (str) – Base path of gjf file (without extension)

Returns:

True if all calculations (dimer, monomer1, monomer2) terminated normally

Return type:

bool

mcal.mcal.create_reorg_gjf(symbols: ndarray[Any, dtype[str]], coordinates: ndarray[Any, dtype[float64]], basename: str, save_dir: str, cpu: int, mem: int, method: str) → None

Create gjf file for reorganization energy calculation.

Parameters:

• symbols (NDArray[str]) – Symbols of atoms

• coordinates (NDArray[np.float64]) – Coordinates of atoms

• basename (str) – Base name of gjf file

• save_dir (str) – Directory to save gjf file

• cpu (int) – Number of cpu

• mem (int) – Number of memory [GB]

• method (str) – Calculation method used in Gaussian calculations

mcal.mcal.create_ti_gjf(unique_mol: Dict[str, ndarray[Any, dtype[str]] | ndarray[Any, dtype[float64]]], neighbor_mol: Dict[str, ndarray[Any, dtype[str]] | ndarray[Any, dtype[float64]]], gjf_basename: str, save_dir: str = '.', cpu: int = 4, mem: int = 16, method: str = 'B3LYP/6-31G*') → None

Create gjf file for transfer integral calculation.

Parameters:

• unique_mol (Dict[str, Union[NDArray[str], NDArray[np.float64]]]) – Dictionary containing symbols and coordinates of unique monomer

• neighbor_mol (Dict[str, Union[NDArray[str], NDArray[np.float64]]]) – Dictionary containing symbols and coordinates of neighbor monomer

• gjf_basename (str) – Base name of gjf file

• save_dir (str) – Directory to save gjf file, by default ‘.’

• cpu (int) – Number of cpu, by default 4

• mem (int) – Number of memory [GB], by default 16

• method (str) – Calculation method used in Gaussian calculations, by default ‘B3LYP/6-31G(d,p)’

mcal.mcal.main()

Calculate mobility tensor considering anisotropy and path continuity.

Examples

Basic usage:

• Calculate p-type mobility for xxx crystal

$ mcal xxx.cif p

• Calculate n-type mobility for xxx crystal

$ mcal xxx.cif n

With resource options:

• Use 8 CPUs and 16GB memory

$ mcal xxx.cif p -c 8 -m 16

• Use different calculation method (default is B3LYP/6-31G(d,p))

$ mcal xxx.cif p -M “B3LYP/6-311G(d,p)”

High-precision calculation:

• Calculate all transfer integrals without speedup using moment of inertia and distance between centers of weight

$ mcal xxx.cif p –fullcal

• Expand calculation range to 5x5x5 supercell to widen transfer integral calculation range

$ mcal xxx.cif p –cellsize 2

Resume and save results:

• Resume from existing calculations

$ mcal xxx.cif p –resume

• Save results to pickle file

$ mcal xxx.cif p –pickle

• Read results from existing pickle file

$ mcal xxx_result.pkl p -rp

• Read results from existing log files without running Gaussian

$ mcal xxx.cif p -r

Plot mobility tensor in 2D plane:

• Plot mobility tensor in 2D plane (Examples: ab, ac, ba, bc, ca, cb (default is ab))

$ python hop_mcal.py xxx.cif p –plot-plane ab

Compare calculation methods:

• Compare results using kinetic Monte Carlo and ODE methods

$ python hop_mcal.py xxx.cif p –mc –ode

mcal.mcal.plot_mobility_2d(save_path: Path, mobility_tensor: ndarray[Any, dtype[float64]], lattice: ndarray[Any, dtype[float64]], plane: Literal['ab', 'ac', 'ba', 'bc', 'ca', 'cb'] = 'ab') → None

Plot mobility tensor in 2D plane.

Parameters:

• save_path (Path) – Path to save the plot

• mobility_tensor (NDArray[np.float64]) – Mobility tensor

• lattice (NDArray[np.float64]) – Lattice vectors [Å]

• plane (Literal['ab', 'ac', 'ba', 'bc', 'ca', 'cb']) – Plane to plot, by default ‘ab’

mcal.mcal.print_mobility(value: ndarray[Any, dtype[float64]], vector: ndarray[Any, dtype[float64]], sim_type: Literal['MC', 'ODE'] = '')

Print mobility and mobility vector

Parameters:

• value (NDArray[np.float64]) – Mobility value

• vector (NDArray[np.float64]) – Mobility vector

• sim_type (str) – Simulation type (MC or ODE)

mcal.mcal.print_reorg_energy(osc_type: Literal['p', 'n'], reorg_energy: float)

Print reorganization energy

Parameters:

• osc_type (Literal['p', 'n']) – Semiconductor type (p-type or n-type)

• reorg_energy (float) – Reorganization energy [eV]

mcal.mcal.print_tensor(mu: ndarray[Any, dtype[float64]], msg: str = 'Mobility tensor')

Print mobility tensor

Parameters:

• mu (NDArray[np.float64]) – Mobility tensor

• msg (str) – Message, by default ‘Mobility tensor’

mcal.mcal.print_transfer_integral(osc_type: Literal['p', 'n'], transfer: float)

Print transfer integral

Parameters:

• osc_type (Literal['p', 'n']) – Semiconductor type (p-type or n-type)

• transfer (float) – Transfer integral [eV]

mcal.mcal.read_pickle(file_name: str, plot_plane: Literal['ab', 'ac', 'ba', 'bc', 'ca', 'cb'] | None = None) → None

Read pickle file and plot mobility tensor in 2D plane.

Parameters:

• file_name (str) – Path to the pickle file

• plot_plane (Optional[Literal['ab', 'ac', 'ba', 'bc', 'ca', 'cb']]) – Plane to plot, by default None

Module contents