gaussian_to_xyz.py

import argparse
from tqdm import tqdm

def main(dye_atoms, lines_to_skip, snapshots, qm_atoms, input_file_template, output_file_template):
    """
    Convert Gaussian input files to XYZ format for QM:Dye + Solvent Files.

    Args:
        dye_atoms (int): Number of dye atoms.
        lines_to_skip (int): Number of Gaussian head lines to skip.
        snapshots (list): List of snapshot indices.
        qm_atoms (list): List of qm_atoms values corresponding to snapshots.
        input_file_template (str): Template for input filenames.
        output_file_template (str): Template for output filenames.
    """
    for index, snapshot in enumerate(tqdm(snapshots, desc="Converting Gaussian to XYZ")):
        with open(input_file_template.format(snapshot), 'r') as f:
            data = f.read().split('\n')
            data_dye = data[lines_to_skip:lines_to_skip + dye_atoms]
            data_solvent = data[lines_to_skip + dye_atoms:int(qm_atoms[index]) + lines_to_skip]

        with open(output_file_template.format(snapshot), 'w') as file:
            file.write(f'{qm_atoms[index]}\n\n')
            file.writelines(f'{line}\n' for line in data_dye)

        with open(output_file_template.format(snapshot), 'a') as file:
            for line in data_solvent:
                if len(line) > 4:
                    file.writelines(f'{line[0]}{line[4:]}\n')
                else:
                    file.write(line + '\n')

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Convert Gaussian input files to XYZ format for QM:Dye + Solvent Files.')
    parser.add_argument('dye_atoms', type=int, help='Number of dye atoms.')
    parser.add_argument('lines_to_skip', type=int, help='Number of Gaussian head lines to skip.')
    parser.add_argument('snapshots', type=lambda s: s.split(','), help='List of snapshot indices (comma-separated).')
    parser.add_argument('qm_atoms', type=lambda s: s.split(','), help='List of qm_atoms values corresponding to snapshots (comma-separated).')
    parser.add_argument('--input-file-template', default='nbdnh2_dmso_frame{}_ex.com', help='Template for input filenames. Use "{}" as a placeholder for the snapshot index.')
    parser.add_argument('--output-file-template', default='optex_geom{}.xyz', help='Template for output filenames. Use "{}" as a placeholder for the snapshot index.')

    args = parser.parse_args()

    if len(args.snapshots) != len(args.qm_atoms):
        print("Error: The number of snapshots and qm_atoms must be equal.")
        exit(1)

    main(args.dye_atoms, args.lines_to_skip, args.snapshots, args.qm_atoms, args.input_file_template, args.output_file_template)