yu-mcal 0.1.4__py3-none-any.whl

mcal/mcal.py

@@ -0,0 +1,844 @@
+"""mcal"""
+import argparse
+import functools
+import pickle
+from pathlib import Path
+from time import time
+from typing import Dict, List, Literal, Optional, Tuple, Union
+
+import numpy as np
+from numpy.typing import NDArray
+from tcal import Tcal
+
+from mcal.utils.cif_reader import CifReader
+from mcal.utils.gaus_log_reader import check_normal_termination
+from mcal.utils.gjf_maker import GjfMaker
+from mcal.calculations.hopping_mobility_model import (
+    diffusion_coefficient_tensor,
+    diffusion_coefficient_tensor_MC,
+    diffusion_coefficient_tensor_ODE,
+    marcus_rate,
+    mobility_tensor
+)
+from mcal.calculations.rcal import Rcal
+
+
+print = functools.partial(print, flush=True)
+
+
+def main():
+    """Calculate mobility tensor considering anisotropy and path continuity.
+
+    Examples
+    --------
+    Basic usage:
+        - Calculate p-type mobility for xxx crystal\n
+        $ python hop_mcal.py xxx.cif p
+
+        - Calculate n-type mobility for xxx crystal\n
+        $ python hop_mcal.py xxx.cif n
+
+    With resource options:
+        - Use 8 CPUs and 16GB memory\n
+        $ python hop_mcal.py xxx.cif p -c 8 -m 16
+
+        - Use different calculation method (default is B3LYP/6-31G(d,p))\n
+        $ python hop_mcal.py 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\n
+        $ python hop_mcal.py xxx.cif p --fullcal
+
+        - Expand calculation range to 3x3x3 supercell\n
+        $ python hop_mcal.py xxx.cif p --cellsize 1
+
+        - Expand calculation range to 5x5x5 supercell to widen transfer integral calculation range\n
+        $ python hop_mcal.py xxx.cif p --cellsize 2
+
+    Resume and save results:
+        - Resume from existing calculations\n
+        $ python hop_mcal.py xxx.cif p --resume
+
+        - Save results to pickle file\n
+        $ python hop_mcal.py xxx.cif p --pickle
+
+        - Read results from existing pickle file\n
+        $ python hop_mcal.py xxx_result.pkl p -rp
+
+        - Read results from existing log files without running Gaussian\n
+        $ python hop_mcal.py xxx.cif p -r
+
+    Compare calculation methods:
+        - Compare results using kinetic Monte Carlo and ODE methods\n
+        $ python hop_mcal.py xxx.cif p --mc --ode
+    """
+    # Error range for skipping calculation of transfer integrals using moment of inertia and distance between centers of weight.
+    CENTER_OF_WEIGHT_ERROR = 1.0e-7
+    MOMENT_OF_INERTIA_ERROR = np.array([[1.0e-3, 1.0e-3, 1.0e-3]])
+
+    """This code is to execute hop_mcal for command line."""
+    parser = argparse.ArgumentParser()
+    parser.add_argument('file', help='cif file name or pickle file name if you want to use -rp option', type=str)
+    parser.add_argument('osc_type', help='organic semiconductor type', type=str)
+    parser.add_argument(
+        '-M', '--method',
+        help='calculation method used in Gaussian calculations (default is B3LYP/6-31G(d,p))',
+        type=str,
+        default='B3LYP/6-31G(d,p)',
+    )
+    parser.add_argument('-c', '--cpu', help='setting the number of cpu (default is 4)', type=int, default=4)
+    parser.add_argument(
+        '-m', '--mem',
+        help='setting the number of memory [GB] (default is 10 GB)',
+        type=int,
+        default=10,
+    )
+    parser.add_argument('-g', '--g09', help='use Gaussian 09 (default is Gaussian 16)', action='store_true')
+    parser.add_argument('-r', '--read', help='read log files without executing Gaussian', action='store_true')
+    parser.add_argument(
+        '-rp', '--read_pickle',
+        help='read results from existing pickle file',
+        action='store_true'
+    )
+    parser.add_argument('-p', '--pickle', help='save to pickle the result of calculation', action='store_true')
+    parser.add_argument(
+        '--cellsize',
+        help='number of unit cells to expand in each direction around the central unit cell '
+            '(Examples: 1 creates 3x3x3, 2 creates 5x5x5 supercell (default is 2))',
+        type=int,
+        default=2,
+    )
+    parser.add_argument(
+        '--fullcal',
+        help='do not process for speeding up using moment of inertia and distance between centers of weight',
+        action='store_true',
+    )
+    parser.add_argument('--mc', help='use Monte Carlo method to calculate diffusion coefficient', action='store_true')
+    parser.add_argument(
+        '--ode',
+        help='use Ordinary Differential Equation method to calculate diffusion coefficient',
+        action='store_true',
+    )
+    parser.add_argument(
+        '--resume',
+        help='resume calculation',
+        action='store_true',
+    )
+    args = parser.parse_args()
+
+    args.osc_type = args.osc_type.lower()
+
+    if args.g09:
+        gau_com = 'g09'
+    else:
+        gau_com = 'g16'
+
+    # file info
+    cif_file = Path(args.file)
+    directory = cif_file.parent
+    filename = cif_file.stem
+    cif_path_without_ext = f'{directory}/{filename}'
+
+    print('----------------------------------------')
+    print(' mcal 0.1.4 (2026/01/20) by Matsui Lab. ')
+    print('----------------------------------------')
+
+    if args.read_pickle:
+        read_pickle(args.file)
+        exit()
+
+    print(f'\nCalculate as {args.osc_type}-type organic semiconductor.')
+    print(f'\nInput File Name: {args.file}')
+    Tcal.print_timestamp()
+    print()
+    start_time = time()
+
+    ##### Calculate reorganization energy #####
+    cif_reader = CifReader(cif_path=cif_file)
+    print(f'Export {cif_path_without_ext}_unit_cell.mol')
+    cif_reader.export_unit_cell_file(f'{cif_path_without_ext}_unit_cell.mol', format='mol')
+    print('Please verify that the created unit cell is correct.\n')
+    symbols = cif_reader.unique_symbols[0]
+    coordinates = cif_reader.unique_coords[0]
+    coordinates = cif_reader.convert_frac_to_cart(coordinates)
+
+    if not args.read:
+        print('Create gjf for reorganization energy.')
+        create_reorg_gjf(
+            symbols,
+            coordinates,
+            filename,
+            directory,
+            args.cpu,
+            args.mem,
+            args.method,
+        )
+
+    if args.osc_type == 'p':
+        rcal = Rcal(gjf_file=f'{cif_path_without_ext}_opt_n.gjf')
+    elif args.osc_type == 'n':
+        rcal = Rcal(gjf_file=f'{cif_path_without_ext}_opt_n.gjf', osc_type='n')
+    else:
+        raise OSCTypeError
+
+    skip_specified_cal = []
+    if args.read:
+        print('Skip calculation of reorganization energy.')
+    elif args.resume:
+        rcal.check_extension_log(f'{cif_path_without_ext}_opt_n.gjf')
+        skip_specified_cal = check_reorganization_energy_completion(cif_path_without_ext, args.osc_type, extension_log=rcal._extension_log)
+    else:
+        print('Calculate reorganization energy.')
+
+    reorg_energy = rcal.calc_reorganization(gau_com=gau_com, only_read=args.read, is_output_detail=True, skip_specified_cal=skip_specified_cal)
+
+    print_reorg_energy(args.osc_type, reorg_energy)
+
+    ##### Calculate transfer integrals #####
+    transfer_integrals = []
+    mom_dis_ti = [] # Store moment of inertia, distance between centers of weight and transfer integral
+
+    expand_mols = cif_reader.expand_mols(args.cellsize)
+    for s in range(len(cif_reader.unique_symbols.keys())):
+        unique_symbols = cif_reader.unique_symbols[s]
+        unique_coords = cif_reader.unique_coords[s]
+        unique_coords = cif_reader.convert_frac_to_cart(unique_coords)
+        for (i, j, k), expand_mol in expand_mols.items():
+            for t, (symbols, coordinates) in expand_mol.items():
+                # Skip creating gjf for transfer integrals because they are molecules with translation symmetry
+                if s > t:
+                    continue
+                elif s == t:
+                    if (i, j, k) == (0, 0, 0):
+                        continue
+                    elif i < 0 or (i == 0 and (j < 0 or (j == 0 and k < 0))):
+                        continue
+
+                coordinates = cif_reader.convert_frac_to_cart(coordinates)
+
+                min_distance = cal_min_distance(
+                    unique_symbols, unique_coords,
+                    symbols, coordinates
+                )
+                if min_distance > 5:
+                    print()
+                    print(f'Skip calculation of transfer integral from {s}-th in (0,0,0) cell to {t}-th in ({i},{j},{k}) cell because the minimum distance is over 5 \u212B.\n')
+                    continue
+
+                moment, _ = cal_moment_of_inertia(
+                    unique_symbols, unique_coords,
+                    symbols, coordinates
+                )
+
+                distance = cal_distance_between_cen_of_weight(
+                    unique_symbols, unique_coords,
+                    symbols, coordinates
+                )
+
+                is_run_ti = True
+                same_ti = 0
+
+                # skip calculation of transfer integrals using moment of inertia and distance between centers of weight.
+                if not args.fullcal:
+                    for m, d, ti in mom_dis_ti:
+                        if (np.all(m - MOMENT_OF_INERTIA_ERROR < moment) and np.all(moment < m + MOMENT_OF_INERTIA_ERROR)) and (d - CENTER_OF_WEIGHT_ERROR < distance < d + CENTER_OF_WEIGHT_ERROR):
+                            is_run_ti = False
+                            same_ti = ti
+                            break
+
+                if is_run_ti:
+                    gjf_name = f'{filename}-({s}_{t}_{i}_{j}_{k})'
+                    gjf_file = f'{directory}/{gjf_name}'
+
+                    tcal = Tcal(gjf_file)
+
+                    is_normal_term = False
+                    if args.resume:
+                        tcal.check_extension_log()
+                        is_normal_term = check_transfer_integral_completion(gjf_file, extension_log=tcal._extension_log)
+
+                    if not args.read and not is_normal_term:
+                        print()
+                        print('Create gjf for transfer integral.')
+                        create_ti_gjf(
+                            {'symbols': unique_symbols, 'coordinates': unique_coords},
+                            {'symbols': symbols, 'coordinates': coordinates},
+                            gjf_basename=gjf_name,
+                            save_dir=directory,
+                            cpu=args.cpu,
+                            mem=args.mem,
+                            method=args.method,
+                        )
+                        tcal.create_monomer_file()
+
+                        if args.g09:
+                            gaussian_command = 'g09'
+                        else:
+                            gaussian_command = 'g16'
+                        print(f'Calculate transfer integral from {s}-th in (0,0,0) cell to {t}-th in ({i},{j},{k}) cell.')
+                        tcal.run_gaussian(gaussian_command)
+                    else:
+                        print()
+                        print(f'Skip calculation of transfer integral from {s}-th in (0,0,0) cell to {t}-th in ({i},{j},{k}) cell.')
+
+                    tcal.check_extension_log()
+                    tcal.read_monomer1()
+                    tcal.read_monomer2()
+                    tcal.read_dimer()
+
+                    if args.osc_type == 'p':
+                        transfer = Tcal.cal_transfer_integrals(
+                            tcal.mo1[tcal.n_elect1-1], tcal.overlap, tcal.fock, tcal.mo2[tcal.n_elect2-1]
+                        )
+                    elif args.osc_type == 'n':
+                        transfer = Tcal.cal_transfer_integrals(
+                            tcal.mo1[tcal.n_elect1], tcal.overlap, tcal.fock, tcal.mo2[tcal.n_elect2]
+                        )
+
+                    transfer = transfer * 1e-3 # meV to eV
+                    print_transfer_integral(args.osc_type, transfer)
+                    transfer_integrals.append((s, t, i, j, k, transfer))
+                    mom_dis_ti.append((moment, distance, transfer))
+                else:
+                    print()
+                    print(f'Skip calculation of transfer integral from {s}-th in (0,0,0) cell to {t}-th in ({i},{j},{k}) cell due to identical moment of inertia and distance between centers of weight.')
+                    print_transfer_integral(args.osc_type, same_ti)
+                    transfer_integrals.append((s, t, i, j, k, same_ti))
+
+    ##### Calculate mobility tensor considering anisotropy. #####
+    hop = []
+
+    for s, t, i, j, k, ti in transfer_integrals:
+        hop.append((s, t, i, j, k, marcus_rate(ti, reorg_energy)))
+
+    diffusion_coef_tensor = diffusion_coefficient_tensor(cif_reader.lattice * 1e-8, hop)
+    print_tensor(diffusion_coef_tensor, msg="Diffusion coefficient tensor (cm^2/s)")
+    mu = mobility_tensor(diffusion_coef_tensor)
+    print_tensor(mu, msg="Mobility tensor (cm^2/Vs)")
+    value, vector = cal_eigenvalue_decomposition(mu)
+    print_mobility(value, vector)
+
+    ##### Simulate mobility tensor calculation using Monte Carlo method #####
+    if args.mc:
+        D_MC = diffusion_coefficient_tensor_MC(cif_reader.lattice * 1e-8, hop)
+        print_tensor(D_MC, msg="Diffusion coefficient tensor (cm^2/s) (MC)")
+        mu_MC = mobility_tensor(D_MC)
+        print_tensor(mu_MC, msg="Mobility tensor (cm^2/Vs) (MC)")
+        value_MC, vector_MC = cal_eigenvalue_decomposition(mu_MC)
+        print_mobility(value_MC, vector_MC, sim_type='MC')
+
+    ##### Simulate mobility tensor calculation using Ordinary Differential Equation method #####
+    if args.ode:
+        D_ODE = diffusion_coefficient_tensor_ODE(cif_reader.lattice * 1e-8, hop)
+        print_tensor(D_ODE, msg="Diffusion coefficient tensor (cm^2/s) (ODE)")
+        mu_ODE = mobility_tensor(D_ODE)
+        print_tensor(mu_ODE, msg="Mobility tensor (cm^2/Vs) (ODE)")
+        value_ODE, vector_ODE = cal_eigenvalue_decomposition(mu_ODE)
+        print_mobility(value_ODE, vector_ODE, sim_type='ODE')
+
+    # Save reorganization, transfer integrals, hop, mobility tensor
+    if args.pickle:
+        with open(f'{cif_path_without_ext}_result.pkl', 'wb') as f:
+            pickle.dump({
+                'osc_type': args.osc_type,
+                'lattice': cif_reader.lattice,
+                'z_value': cif_reader.z_value,
+                'reorganization': reorg_energy,
+                'transfer_integrals': transfer_integrals,
+                'hop': hop,
+                'diffusion_coefficient_tensor': diffusion_coef_tensor,
+                'mobility_tensor': mu,
+                'mobility_value': value,
+                'mobility_vector': vector
+            }, f)
+
+    Tcal.print_timestamp()
+    end_time = time()
+    elapsed_time = end_time - start_time
+    elapsed_time_h = int(elapsed_time // 3600)
+    elapsed_time_min = int((elapsed_time - elapsed_time_h * 3600) // 60)
+    elapsed_time_sec = int(elapsed_time - elapsed_time_h * 3600 - elapsed_time_min * 60)
+    elapsed_time_ms = (elapsed_time - elapsed_time_h * 3600 - elapsed_time_min * 60 - elapsed_time_sec) * 1000
+    if elapsed_time < 1:
+        print(f'Elapsed Time: {elapsed_time_ms:.0f} ms')
+    elif elapsed_time < 60:
+        print(f'Elapsed Time: {elapsed_time_sec} sec')
+    elif elapsed_time < 3600:
+        print(f'Elapsed Time: {elapsed_time_min} min {elapsed_time_sec} sec')
+    else:
+        print(f'Elapsed Time: {elapsed_time_h} h {elapsed_time_min} min {elapsed_time_sec} sec')
+
+
+def atom_weight(symbol: str) -> float:
+    """Get atom weight
+
+    Parameters
+    ----------
+    symbol : str
+        Symbol of atom
+
+    Returns
+    -------
+    float
+        Atomic weight
+    """
+    ELEMENT_PROP = CifReader.ELEMENT_PROP
+    weight = ELEMENT_PROP[ELEMENT_PROP['symbol'] == symbol]['weight'].values[0]
+
+    return weight
+
+
+def cal_cen_of_weight(
+    symbols1: NDArray[str],
+    coordinates1: NDArray[np.float64],
+    symbols2: Optional[NDArray[str]] = None,
+    coordinates2: Optional[NDArray[np.float64]] = None,
+) -> NDArray[np.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
+    -------
+    NDArray[np.float64]
+        Center of weight
+    """
+    if symbols2 is not None and coordinates2 is not None:
+        symbols1 = np.concatenate((symbols1, symbols2), axis=0)
+        coordinates1 = np.concatenate((coordinates1, coordinates2), axis=0)
+
+    weights = np.array([atom_weight(sym) for sym in symbols1])
+    total_weight = np.sum(weights)
+
+    weighted_coords = weights[:, np.newaxis] * coordinates1
+    weighted_sum = np.sum(weighted_coords, axis=0)
+
+    cen_of_weight = weighted_sum / total_weight
+
+    return cen_of_weight
+
+
+def cal_distance_between_cen_of_weight(
+    symbols1: NDArray[str],
+    coordinates1: NDArray[np.float64],
+    symbols2: NDArray[str],
+    coordinates2: NDArray[np.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
+    -------
+    float
+        Distance between centers of weight
+    """
+    mol1_cen_coord = cal_cen_of_weight(symbols1, coordinates1)
+    mol2_cen_coord = cal_cen_of_weight(symbols2, coordinates2)
+    distance = np.sqrt(np.sum(np.square(mol1_cen_coord-mol2_cen_coord)))
+
+    return distance
+
+
+def cal_eigenvalue_decomposition(mobility_tensor: NDArray[np.float64]) -> Tuple[NDArray[np.float64], NDArray[np.float64]]:
+    """Calculate eigenvalue decomposition of mobility tensor
+
+    Parameters
+    ----------
+    mobility_tensor : NDArray[np.float64]
+        Mobility tensor
+
+    Returns
+    -------
+    Tuple[NDArray[np.float64], NDArray[np.float64]]
+        Eigenvalue(mobility value) and eigenvector(mobility vector)
+    """
+    value, vector = np.linalg.eig(mobility_tensor)
+    return value, vector
+
+
+def cal_min_distance(
+    symbols1: NDArray[str],
+    coords1: NDArray[np.float64],
+    symbols2: NDArray[str],
+    coords2: NDArray[np.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
+    -------
+    float
+        Minimum distance between two sets of atoms
+    """
+    ELEMENT_PROP = CifReader.ELEMENT_PROP
+    VDW_RADII = ELEMENT_PROP[['symbol', 'vdw_radius']].set_index('symbol').to_dict()['vdw_radius']
+
+    radii1 = np.array(
+        [VDW_RADII[symbol] for symbol in symbols1]
+    )
+    radii2 = np.array(
+        [VDW_RADII[symbol] for symbol in symbols2]
+    )
+
+    distances = np.sqrt(np.sum((coords1[:, np.newaxis] - coords2)**2, axis=2)) - radii1[:, np.newaxis] - radii2
+
+    min_distance = np.min(distances)
+
+    return min_distance
+
+
+def cal_moment_of_inertia(
+    symbols1: NDArray[str],
+    coordinates1: NDArray[np.float64],
+    symbols2: NDArray[str],
+    coordinates2: NDArray[np.float64],
+) -> Tuple[NDArray[np.float64], NDArray[np.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
+    -------
+    Tuple[NDArray[np.float64], NDArray[np.float64]]
+        Moment of inertia and eigenvectors of the inertia tensor
+    """
+    symbols1 = np.concatenate((symbols1, symbols2), axis=0)
+    coordinates1 = np.concatenate((coordinates1, coordinates2), axis=0)
+
+    cen_of_weight = cal_cen_of_weight(symbols1, coordinates1)
+
+    weights = np.array([atom_weight(sym) for sym in symbols1])
+
+    xi = coordinates1[:, 0] - cen_of_weight[0]
+    yi = coordinates1[:, 1] - cen_of_weight[1]
+    zi = coordinates1[:, 2] - cen_of_weight[2]
+
+    tmp_coords = np.column_stack((xi, yi, zi))
+
+    moment = np.zeros((3, 3))
+
+    for i in range(3):
+        moment[i, i] = np.sum(weights * (tmp_coords[:, (i+1)%3]**2 + tmp_coords[:, (i+2)%3]**2))
+
+    for i in range(3):
+        for j in range(i+1, 3):
+            moment[i, j] = moment[j, i] = -np.sum(weights * tmp_coords[:, i] * tmp_coords[:, j])
+
+    moment, p = np.linalg.eig(moment)
+
+    return moment, p
+
+
+def 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[Literal['opt_neutral', 'opt_ion', 'neutral', 'ion']]
+        List of calculations to skip
+    """
+    skip_specified_cal = []
+    if check_normal_termination(f'{cif_path_without_ext}_opt_n{extension_log}'):
+        skip_specified_cal.append('opt_neutral')
+    if check_normal_termination(f'{cif_path_without_ext}_n{extension_log}'):
+        skip_specified_cal.append('neutral')
+
+    if osc_type == 'p':
+        if check_normal_termination(f'{cif_path_without_ext}_opt_c{extension_log}'):
+            skip_specified_cal.append('opt_ion')
+        if check_normal_termination(f'{cif_path_without_ext}_c{extension_log}'):
+            skip_specified_cal.append('ion')
+    elif osc_type == 'n':
+        if check_normal_termination(f'{cif_path_without_ext}_opt_a{extension_log}'):
+            skip_specified_cal.append('opt_ion')
+        if check_normal_termination(f'{cif_path_without_ext}_a{extension_log}'):
+            skip_specified_cal.append('ion')
+
+    return skip_specified_cal
+
+
+def 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
+    -------
+    bool
+        True if all calculations (dimer, monomer1, monomer2) terminated normally
+    """
+    required_files = ['', '_m1', '_m2']
+    return all(
+        check_normal_termination(f'{gjf_file}{suffix}{extension_log}')
+        for suffix in required_files
+    )
+
+
+def create_reorg_gjf(
+    symbols: NDArray[str],
+    coordinates: NDArray[np.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
+    """
+    gjf_maker = GjfMaker()
+    gjf_maker.set_function(method)
+    gjf_maker.create_chk_file()
+    gjf_maker.output_detail()
+    gjf_maker.opt()
+
+    gjf_maker.set_symbols(symbols)
+    gjf_maker.set_coordinates(coordinates)
+    gjf_maker.set_resource(cpu_num=cpu, mem_num=mem)
+
+    gjf_maker.export_gjf(
+        file_name=f'{basename}_opt_n',
+        save_dir=save_dir,
+        chk_rwf_name=f'{save_dir}/{basename}_opt_n'
+    )
+
+
+def create_ti_gjf(
+    unique_mol: Dict[str, Union[NDArray[str], NDArray[np.float64]]],
+    neighbor_mol: Dict[str, Union[NDArray[str], NDArray[np.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)'
+    """
+    gjf_maker = GjfMaker()
+    gjf_maker.set_resource(cpu_num=cpu, mem_num=mem)
+    gjf_maker.set_function(method)
+    gjf_maker.create_chk_file()
+    gjf_maker.add_root('Symmetry=None')
+
+    gjf_maker.set_symbols(unique_mol['symbols'])
+    gjf_maker.set_coordinates(unique_mol['coordinates'])
+    gjf_maker.set_symbols(neighbor_mol['symbols'])
+    gjf_maker.set_coordinates(neighbor_mol['coordinates'])
+
+    gjf_maker.add_link()
+    gjf_maker.add_root('Symmetry=None')
+    gjf_maker.add_root('Pop=Full')
+    gjf_maker.add_root('IOp(3/33=4,5/33=3)')
+
+    gjf_maker.export_gjf(file_name=gjf_basename, save_dir=save_dir)
+
+
+def print_mobility(value: NDArray[np.float64], vector: NDArray[np.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)
+    """
+    msg_value = 'Mobility eigenvalues (cm^2/Vs)'
+    msg_vector = 'Mobility eigenvectors'
+    direction = ['x', 'y', 'z']
+
+    if sim_type:
+        msg_value += f' ({sim_type})'
+        msg_vector += f' ({sim_type})'
+
+    print()
+    print('-' * (len(msg_value)+2))
+    print(f' {msg_value} ')
+    print('-' * (len(msg_value)+2))
+    print(f"{value[0]:12.6g} {value[1]:12.6g} {value[2]:12.6g}")
+    print()
+
+    print()
+    print('-' * (len(msg_vector)+2))
+    print(f' {msg_vector} ')
+    print('-' * (len(msg_vector)+2))
+    print('       vector1      vector2      vector3')
+    for v, d in zip(vector, direction):
+        print(f'{d} {v[0]:12.6g} {v[1]:12.6g} {v[2]:12.6g}')
+    print()
+
+
+def 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]
+    """
+    print()
+    print('-----------------------')
+    print(' Reorganization energy ')
+    print('-----------------------')
+    print(f'{osc_type}-type: {reorg_energy:10.6g} eV\n')
+
+
+def print_tensor(mu: NDArray[np.float64], msg: str = 'Mobility tensor'):
+    """Print mobility tensor
+
+    Parameters
+    ----------
+    mu : NDArray[np.float64]
+        Mobility tensor
+    msg : str
+        Message, by default 'Mobility tensor'
+    """
+    print()
+    print('-' * (len(msg)+2))
+    print(f' {msg} ')
+    print('-' * (len(msg)+2))
+    for a in mu:
+        print(f"{a[0]:12.6g} {a[1]:12.6g} {a[2]:12.6g}")
+    print()
+
+
+def 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]
+    """
+    mol_orb = {'p': 'HOMO', 'n': 'LUMO'}
+    print()
+    print('-------------------')
+    print(' Transfer integral ')
+    print('-------------------')
+    print(f'{mol_orb[osc_type]}: {transfer:12.6g} eV\n')
+
+
+def read_pickle(file_name: str):
+    print(f'\nInput File Name: {file_name}')
+
+    with open(file_name, 'rb') as f:
+        results = pickle.load(f)
+
+    # print(results)
+
+    print(f'\nCalculate as {results["osc_type"]}-type organic semiconductor.')
+
+    print_reorg_energy(results['osc_type'], results['reorganization'])
+
+    for s, t, i, j, k, ti in results['transfer_integrals']:
+        print()
+        print(f'{s}-th in (0,0,0) cell to {t}-th in ({i},{j},{k}) cell')
+        print_transfer_integral(results['osc_type'], ti)
+
+    print_tensor(results['diffusion_coefficient_tensor'], msg="Diffusion coefficient tensor (cm^2/s)")
+
+    print_tensor(results['mobility_tensor'], msg="Mobility tensor (cm^2/Vs)")
+
+    print_mobility(results['mobility_value'], results['mobility_vector'])
+
+
+class OSCTypeError(Exception):
+    """Exception for semiconductor type"""
+    pass
+
+
+if __name__ == '__main__':
+    main()