yu-mcal 0.1.0__py3-none-any.whl

mcal/calculations/rcal.py

@@ -0,0 +1,408 @@
+"""Rcal"""
+import argparse
+import functools
+import os
+import subprocess
+from datetime import datetime
+from pathlib import Path
+from time import time
+from typing import List, Literal
+
+from mcal.utils.cif_reader import CifReader
+from mcal.utils.gjf_maker import GjfMaker
+
+
+print = functools.partial(print, flush=True)
+
+
+def main():
+    """This code is to execute rcal for command line."""
+    parser = argparse.ArgumentParser()
+    parser.add_argument('file', help='cif file name or gjf file name', 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)). ' \
+            + 'But if you use a gjf file instead of a cif file, the method in the gjf file will be used',
+        type=str,
+        default='B3LYP/6-31G(d,p)',
+    )
+    parser.add_argument(
+        '-c', '--cpu',
+        help='setting the number of cpu (default is 4). ' \
+            + 'But if you use a gjf file instead of a cif file, the number of cpu in the gjf file will be used',
+        type=int, default=4
+    )
+    parser.add_argument(
+        '-m', '--mem',
+        help='setting the number of memory [GB] (default is 10 GB). ' \
+            + 'But if you use a gjf file instead of a cif file, the number of memory in the gjf file will be used',
+        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')
+    args = parser.parse_args()
+
+    print('---------------------------------------')
+    print(' rcal beta (2025/06/21) by Matsui Lab. ')
+    print('---------------------------------------')
+    print(f'\nInput File Name: {args.file}')
+    Rcal.print_timestamp()
+    before = time()
+
+    if args.file.endswith('.cif'):
+        cif_file = Path(args.file)
+        directory = cif_file.parent
+        filename = cif_file.stem.replace('_opt_n', '')
+        file_path_without_ext = f'{directory}/{filename}_opt_n'
+
+        cif_reader = CifReader(cif_path=cif_file)
+        symbols = cif_reader.unique_symbols[0]
+        coordinates = cif_reader.unique_coords[0]
+        coordinates = cif_reader.convert_frac_to_cart(coordinates)
+
+        gjf_maker = GjfMaker()
+        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_function(args.method)
+        gjf_maker.set_charge_spin(charge=0, spin=1)
+        gjf_maker.set_resource(cpu_num=args.cpu, mem_num=args.mem)
+
+        gjf_maker.export_gjf(
+            file_name=f'{file_path_without_ext}',
+            chk_rwf_name=f'{file_path_without_ext}',
+        )
+    elif args.file.endswith('.gjf'):
+        gjf_file = Path(args.file)
+        directory = gjf_file.parent
+        filename = gjf_file.stem
+
+        file_path_without_ext = f'{directory}/{filename}'
+    else:
+        raise ValueError('Input file must be a cif file or a gjf file.')
+
+    if args.osc_type.lower() == 'p':
+        rcal = Rcal(gjf_file=f'{file_path_without_ext}.gjf')
+    elif args.osc_type.lower() == 'n':
+        rcal = Rcal(gjf_file=f'{file_path_without_ext}.gjf', osc_type='n')
+    else:
+        raise OSCTypeError
+
+    if args.g09:
+        gau_com = 'g09'
+    else:
+        gau_com = 'g16'
+
+    reorg_energy = rcal.calc_reorganization(gau_com=gau_com, only_read=args.read, is_output_detail=True)
+
+    print()
+    print('-----------------------')
+    print(' Reorganization energy ')
+    print('-----------------------')
+    print(f'{reorg_energy:12.6f} eV')
+    print()
+
+    Rcal.print_timestamp()
+    after = time()
+    print(f'Elapsed Time: {(after - before) * 1000:.0f} ms')
+
+
+class Rcal:
+    """Calculate organization energy."""
+    def __init__(self, gjf_file: str, osc_type: Literal['p', 'n'] = 'p'):
+        """
+        Initialize Rcal.
+
+        Parameters
+        ----------
+        gjf_file : str
+            gjf file name.
+        osc_type : Literal['p', 'n']
+            organic semiconductor type, 'p' is positive, 'n' is negative, by default 'p'.
+        """
+        self.gjf_file = gjf_file
+        self.ion = None
+        self._extension_log = '.log'
+        self._gjf_lines = {'%': [], '#': []}
+
+        self._input_gjf()
+
+        if osc_type.lower() == 'p':
+            self.ion = 'c'
+        elif osc_type.lower() == 'n':
+            self.ion = 'a'
+
+    @ staticmethod
+    def check_error_term(line: str) -> None:
+        """
+        Check the error term of Gaussian.
+
+        Parameters
+        ----------
+        line : str
+            last line of the log file.
+
+        Raises
+        ------
+        GausTermError
+            if the calculation of Gaussian was error termination.
+        """
+        line = line.strip()
+
+        if 'Normal termination' not in line:
+            raise GausTermError('The calculation of Gaussian was error termination.')
+
+    @staticmethod
+    def print_timestamp() -> None:
+        """Print timestamp."""
+        month = {
+            1: 'Jan', 2: 'Feb', 3: 'Mar', 4: 'Apr', 5: 'May', 6: 'Jun',
+            7: 'Jul', 8: 'Aug', 9: 'Sep', 10: 'Oct', 11: 'Nov', 12: 'Dec',
+        }
+        dt_now = datetime.now()
+        print(f"Timestamp: {dt_now.strftime('%a')} {month[dt_now.month]} {dt_now.strftime('%d %H:%M:%S %Y')}")
+
+    def calc_reorganization(
+        self,
+        gau_com: str = 'g16',
+        only_read: bool = False,
+        is_output_detail: bool = False,
+        skip_specified_cal: List[Literal['opt_neutral', 'opt_ion', 'neutral', 'ion']] = [],
+    ) -> float:
+        """
+        Calculate reorganization energy.
+
+        Parameters
+        ----------
+        gau_com : str
+            Gaussian command, by default 'g16'.
+        only_read : bool
+            if True, the calculation is only read, by default False.
+        is_output_detail : bool
+            if True, the calculation detail will be output, by default False.
+        skip_specified_cal : List[Literal['opt_neutral', 'opt_ion', 'neutral', 'ion']]
+            if specified, the calculation of the specified type will be skipped, by default [].
+
+        Returns
+        -------
+        float
+            reorganization energy [eV].
+        """
+        file_path = Path(self.gjf_file)
+        filename = file_path.stem.replace('_opt_n', '')
+        directory = file_path.parent
+        basename = f'{directory}/{filename}'
+
+        energy = []
+
+        # 中性分子の構造最適化とエネルギー計算
+        only_read_opt_n = only_read
+        if not only_read and 'opt_neutral' not in skip_specified_cal:
+            print('>', gau_com, self.gjf_file)
+            subprocess.run([gau_com, self.gjf_file])
+
+        skip_opt_neutral = True if 'opt_neutral' in skip_specified_cal else False
+
+        energy.append(self.extract_energy(self.gjf_file, only_read=only_read_opt_n, is_output_detail=is_output_detail, skip_cal=skip_opt_neutral))
+
+        # カチオンかアニオンのエネルギー計算
+        only_read_ion = only_read
+        previous_name, _ = os.path.splitext(self.gjf_file)
+        gjf = f'{basename}_{self.ion}.gjf'
+        if not only_read and 'ion' not in skip_specified_cal:
+            self._create_gjf(file_name=gjf, prevous_name=previous_name, ion=self.ion)
+            print('>', gau_com, gjf)
+            subprocess.run([gau_com, gjf])
+
+        skip_ion = True if 'ion' in skip_specified_cal else False
+
+        energy.append(self.extract_energy(gjf, only_read=only_read_ion, is_output_detail=is_output_detail, skip_cal=skip_ion))
+
+        # カチオンかアニオンの構造最適化とエネルギー計算
+        only_read_opt_ion = only_read
+        gjf = f'{basename}_opt_{self.ion}.gjf'
+        if not only_read and 'opt_ion' not in skip_specified_cal:
+            self._create_gjf(file_name=gjf, prevous_name=previous_name, ion=self.ion, is_opt=True)
+            print('>', gau_com, gjf)
+            subprocess.run([gau_com, gjf])
+
+        skip_opt_ion = True if 'opt_ion' in skip_specified_cal else False
+
+        energy.append(self.extract_energy(gjf, only_read=only_read_opt_ion, is_output_detail=is_output_detail, skip_cal=skip_opt_ion))
+
+
+        # 中性分子のエネルギー計算
+        only_read_neutral = only_read
+        previous_name, _ = os.path.splitext(gjf)
+        ion = 'n'
+        gjf = f'{basename}_{ion}.gjf'
+        if not only_read and 'neutral' not in skip_specified_cal:
+            self._create_gjf(file_name=gjf, prevous_name=previous_name, ion=ion)
+            print('>', gau_com, gjf)
+            subprocess.run([gau_com, gjf])
+
+        skip_neutral = True if 'neutral' in skip_specified_cal else False
+
+        energy.append(self.extract_energy(gjf, only_read=only_read_neutral, is_output_detail=is_output_detail, skip_cal=skip_neutral))
+
+        return ((energy[3] - energy[2]) + (energy[1] - energy[0]))
+
+    def check_extension_log(self, gjf: str) -> None:
+        """Check the extension of log file.
+
+        Parameters
+        ----------
+        gjf : str
+            gjf file name.
+        """
+        if os.path.exists(f'{os.path.splitext(gjf)[0]}.out'):
+            self._extension_log = '.out'
+        else :
+            self._extension_log = '.log'
+
+    def extract_energy(
+        self,
+        gjf: str,
+        only_read: bool = False,
+        is_output_detail: bool = False,
+        skip_cal: bool = False
+    ) -> float:
+        """Extract energy from log file.
+
+        Parameters
+        ----------
+        gjf : str
+            gjf file name.
+        only_read : bool
+            if True, the calculation is only read, by default False.
+        is_output_detail : bool
+            if True, the calculation detail will be output, by default False.
+
+        Returns
+        -------
+        float
+            total energy.
+        """
+        self.check_extension_log(gjf)
+        log_file = f'{os.path.splitext(gjf)[0]}{self._extension_log}'
+
+        with open(log_file) as f:
+            last_line = ''
+            while True:
+                line = f.readline()
+                if not line:
+                    break
+                line = line.strip()
+
+                if line:
+                    last_line = line
+
+                if line.startswith('SCF Done:'):
+                    energy = float(line.split()[4]) * 27.2114
+
+            self.check_error_term(last_line)
+
+            if is_output_detail:
+                gjf = Path(gjf)
+                if not only_read and not skip_cal:
+                    print(f'{gjf} calculation completed.')
+                elif skip_cal:
+                    print(f'{gjf} calculation skipped.')
+
+                print(f'reading {gjf.parent}/{gjf.stem}{self._extension_log}')
+                print()
+                print('--------------')
+                print(' Total energy ')
+                print('--------------')
+                print(f'{energy:12.6f} eV')
+                print()
+
+            return energy
+
+    def _create_gjf(
+        self,
+        file_name: str,
+        prevous_name: str,
+        ion: Literal['c', 'a', 'n'],
+        is_opt: bool = False,
+    ) -> None:
+        """
+        Create gjf file.
+
+        Parameters
+        ----------
+        file_name : str
+            file name.
+        prevous_name : str
+            previous file name.
+        ion : Literal['c', 'a', 'n']
+            ion type. 'c' is cation, 'a' is anion, 'n' is neutral molecule.
+        is_opt : bool
+            if True, the calculation is optimization, by default False.
+        """
+        file_name, _ = os.path.splitext(file_name)
+
+        with open(f'{file_name}.gjf', 'w') as f:
+            for line in self._gjf_lines['%']:
+                if r'%oldchk' in line.lower():
+                    continue
+                elif r'%chk' in line.lower():
+                    continue
+                else:
+                    f.write(line)
+
+            f.write(f'%oldchk={prevous_name}.chk\n')
+            if is_opt:
+                f.write(f'%chk={file_name}.chk\n')
+
+            for line in self._gjf_lines['#']:
+                if 'geom' in line.lower():
+                    continue
+                elif 'opt' in line.lower():
+                    continue
+                else:
+                    f.write(line)
+
+            f.write('#  Geom=Checkpoint\n')
+            if is_opt:
+                f.write('#  Opt=Tight\n')
+            f.write('\n')
+            f.write('Defalut Title\n')
+            f.write('\n')
+
+            if ion == 'c':
+                f.write('1 2\n\n')
+            elif ion == 'a':
+                f.write('-1, 2\n\n')
+            else:
+                f.write('0 1\n\n')
+
+    def _input_gjf(self) -> None:
+        """Input link 0 command and root options from gjf file."""
+        with open(self.gjf_file, 'r') as f:
+            for line in f:
+                if line.startswith('%'):
+                    self._gjf_lines['%'].append(line)
+                elif line.startswith('#'):
+                    self._gjf_lines['#'].append(line)
+                elif 'link' in line.lower():
+                    raise ValueError("Please do not use Link.")
+
+
+class GausTermError(Exception):
+    """Exception for Gaussian error termination."""
+    pass
+
+
+class OSCTypeError(Exception):
+    """Exception for organic semiconductor type."""
+    pass
+
+
+if __name__ == '__main__':
+    main()