APEPM-Code-Implementation/APEPM visualizer code orbital overlap.py at main · halodma/APEPM-Code-Implementation · GitHub

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import matplotlib.pyplot as plt
import re

# Please note: This code is purely for visualization of values calculated by (APEPM code implementation.py) specifically
# the overlap radius value.
# Licensed under: CC BY-NC 4.0

# This model was created by: Dylan M. Armstrong
# creator contact: halodma07@gmail.com

electron_cloud_radii = {'H': 1.3, 'He': 1.60, 'Li': 2.05, 'Be': 1.75, 'B': 2.15, 'C': 1.90, 'N': 1.75, 'O': 1.72, 'F': 1.20,
                        'Ne': 1.75, 'Na': 1.76, 'Mg': 1.85, 'Al': 2.10, 'Si': 2.35, 'P': 2.05, 'S': 2.05, 'Cl': 1.95, 'Ar': 2.10,
                        'K': 2.55, 'Ca': 2.38, 'Sc': 2.25, 'Ti': 2.35, 'V': 2.35, 'Cr': 2.35, 'Mn': 2.40, 'Fe': 2.40, 'Ni': 1.85,
                        'Co': 2.82, 'Cu': 4.23, 'Zn': 2.38, 'Ga': 2.10, 'Ge': 2.35, 'As': 2.10, 'Se': 2.20, 'Br': 2.05, 'Kr': 2.25,
                        'Rb': 2.82, 'Sr': 2.82, 'Y': 2.82, 'Zr': 2.55, 'Nb': 2.55, 'Mo': 2.55, 'Tc': 2.60, 'Ru': 2.60, 'Rh': 2.55,
                        'Pd': 1.95, 'Ag': 5.32, 'Cd': 5.32, 'In': 2.20, 'Sn': 2.35, 'Sb': 2.20, 'I': 2.20, 'Xe': 2.35, 'Cs': 5.32,
                        'Te': 2.25,  'Ba': 5.32, 'La': 2.40, 'Ce': 2.55, 'Pr': 2.55, 'Nd': 2.55, 'Pm': 2.60, 'Sm': 2.70, 'Eu': 2.75,
                        'Gd': 2.80, 'Tb': 2.85, 'Dy': 2.90, 'Ho': 2.90, 'Er': 2.95, 'Tm': 3.00, 'Yb': 3.05, 'Lu': 3.10, 'Hf': 2.60,
                        'Ta': 2.60, 'W': 2.60, 'Re': 2.70, 'Os': 2.70, 'Ir': 2.70, 'Pt': 1.95, 'Au': 5.32, 'Hg': 5.32, 'Tl': 2.20,
                        'Pb': 2.20, 'Bi': 2.30, 'Po': 2.30, 'At': 2.30, 'Rn': 2.40, 'Fr': 5.32, 'Ra': 5.32, 'Ac': 5.32, 'Th': 2.85,
                        'Pa': 2.85, 'U': 2.85, 'Np': 2.95, 'Pu': 2.95, 'Am': 3.05, 'Cm': 3.05, 'Bk': 3.15, 'Cf': 3.15, 'Es': 3.25,
                        'Fm': 3.25, 'Md': 3.25, 'No': 3.35, 'Lr': 3.35, 'Rf': 3.00, 'Db': 3.00, 'Sg': 3.00, 'Bh': 3.00, 'Hs': 3.00,
                        'Mt': 3.00, 'Ds': 3.00, 'Rg': 3.00, 'Cn': 3.00, 'Nh': 3.00, 'Fl': 3.00, 'Mc': 3.00, 'Lv': 3.00, 'Ts': 3.00,
                        'Og': 3.00}

orbital_distances = {'1s': (0.0, 0.53), '2s': (0.53, 1.06), '2p': (0.53, 1.20), '3s': (1.06, 1.76), '3p': (1.20, 2.38), '3d': (1.76, 2.82),
                     '4s': (2.38, 4.23), '4p': (2.82, 4.76), '4d': (3.16, 5.32), '4f': (3.16, 4.23), '5s': (4.23, 6.61), '5p': (4.76, 8.46),
                     '5d': (5.32, 9.49), '5f': (5.32, 6.61), '5g': (5.32, 6.61), '6s': (6.61, 9.49), '6p': (8.46, 12.98), '6d': (9.49, 13.23),
                     '6f': (9.49, 12.00), '6g': (9.49, 11.00), '6h': (9.49, 10.00), '7s': (12.98, 18.97), '7p': (15.00, 25.96), '7d': (15.00, 20.00),
                     '7f': (15.00, 18.00), '7g': (15.00, 17.00), '7h': (15.00, 16.00), '7i': (15.00, 16.00)}

areecm_digital_dictionary = {
    "H": [1, {"1s": [0.0, 1.0]}],
    "He": [2, {"1s": [0.0, 1.0]}],
    "Li": [3, {"1s": [0.0, 0.67], "2s": [0.0, 0.33]}],
    "Be": [4, {"1s": [0.0, 0.53], "2s": [0.0, 0.47]}],
    "B": [5, {"1s": [0.0, 0.40], "2s": [0.0, 0.40], "2p": [0.0, 0.20]}],
    "C": [6, {"1s": [0.0, 0.33], "2s": [0.0, 0.33], "2p": [0.0, 0.33]}],
    "N": [7, {"1s": [0.0, 0.29], "2s": [0.0, 0.29], "2p": [0.0, 0.43]}],
    "O": [8, {"1s": [0.0, 0.25], "2s": [0.0, 0.25], "2p": [0.0, 0.50]}],
    "F": [9, {"1s": [0.0, 0.22], "2s": [0.0, 0.22], "2p": [0.0, 0.55]}],
    "Ne": [10, {"1s": [0.0, 0.20], "2s": [0.0, 0.20], "2p": [0.0, 0.60]}],
    "Na": [11, {"1s": [0.0, 0.18], "2s": [0.0, 0.18], "2p": [0.0, 0.55], "3s": [0.0, 0.09]}],
    "Mg": [12, {"1s": [0.0, 0.17], "2s": [0.0, 0.17], "2p": [0.0, 0.50], "3s": [0.0, 0.17]}],
    "Al": [13, {"1s": [0.0, 0.15], "2s": [0.0, 0.15], "2p": [0.0, 0.46], "3s": [0.0, 0.15], "3p": [0.0, 0.08]}],
    "Si": [14, {"1s": [0.0, 0.14], "2s": [0.0, 0.14], "2p": [0.0, 0.43], "3s": [0.0, 0.14], "3p": [0.0, 0.14]}],
    "P": [15, {"1s": [0.0, 0.13], "2s": [0.0, 0.13], "2p": [0.0, 0.40], "3s": [0.0, 0.13], "3p": [0.0, 0.20]}],
    "S": [16, {"1s": [0.0, 0.13], "2s": [0.0, 0.13], "2p": [0.0, 0.38], "3s": [0.0, 0.13], "3p": [0.0, 0.25]}],
    "Cl": [17, {"1s": [0.0, 0.12], "2s": [0.0, 0.12], "2p": [0.0, 0.35], "3s": [0.0, 0.12], "3p": [0.0, 0.29]}],
    "Ar": [18, {"1s": [0.0, 0.11], "2s": [0.0, 0.11], "2p": [0.0, 0.33], "3s": [0.0, 0.11], "3p": [0.0, 0.33]}],
    "K": [19, {"1s": [0.0, 0.11], "2s": [0.0, 0.11], "2p": [0.0, 0.32], "3s": [0.0, 0.11], "3p": [0.0, 0.32], "4s": [0.0, 0.053]}],
    "Ca": [20, {"1s": [0.0, 0.10], "2s": [0.0, 0.10], "2p": [0.0, 0.30], "3s": [0.0, 0.10], "3p": [0.0, 0.30], "4s": [0.0, 0.10]}], "Sc": [21, {"1s": [0.0, 0.10], "2s": [0.0, 0.10], "2p": [0.0, 0.29], "3s": [0.0, 0.10], "3p": [0.0, 0.29], "4s": [0.0, 0.10], "3d": [0.0, 0.05]}],
    "Ti": [22, {"1s": [0.0, 0.09], "2s": [0.0, 0.09], "2p": [0.0, 0.27], "3s": [0.0, 0.09], "3p": [0.0, 0.27], "4s": [0.0, 0.09], "3d": [0.0, 0.09]}],
    "V": [23, {"1s": [0.0, 0.09], "2s": [0.0, 0.09], "2p": [0.0, 0.26], "3s": [0.0, 0.09], "3p": [0.0, 0.26], "4s": [0.0, 0.09], "3d": [0.0, 0.13]}],
    "Cr": [24, {"1s": [0, 0.08], "2s": [0, 0.08], "2p": [0, 0.25], "3s": [0, 0.08], "3p": [0, 0.25], "4s": [0, 0.042], "3d": [0, 0.21]}],
    "Mn": [25, {"1s": [0, 0.08], "2s": [0, 0.08], "2p": [0, 0.24], "3s": [0, 0.08], "3p": [0, 0.24], "4s": [0, 0.08], "3d": [0, 0.20]}],
    "Fe": [26, {"1s": [0, 0.08], "2s": [0, 0.08], "2p": [0, 0.23], "3s": [0, 0.08], "3p": [0, 0.23], "4s": [0, 0.08], "3d": [0, 0.23]}],
    "Co": [27, {"1s": [0, 0.074], "2s": [0, 0.074], "2p": [0, 0.22], "3s": [0, 0.074], "3p": [0, 0.22], "4s": [0, 0.074], "3d": [0, 0.26]}],
    "Ni": [28, {"1s": [0, 0.07], "2s": [0, 0.07], "2p": [0, 0.21], "3s": [0, 0.07], "3p": [0, 0.21], "4s": [0, 0.07], "3d": [0, 0.29]}],
    "Cu": [29, {"1s": [0, 0.07], "2s": [0, 0.07], "2p": [0, 0.21], "3s": [0, 0.07], "3p": [0, 0.21], "4s": [0, 0.034], "3d": [0, 0.34]}],
    "Zn": [30, {"1s": [0, 0.07], "2s": [0, 0.07], "2p": [0, 0.20], "3s": [0, 0.07], "3p": [0, 0.20], "4s": [0, 0.07], "3d": [0, 0.33]}],
    "Ga": [31, {"1s": [0, 0.065], "2s": [0, 0.065], "2p": [0, 0.19], "3s": [0, 0.065], "3p": [0, 0.19], "4s": [0, 0.065], "3d": [0, 0.32], "4p": [0, 0.032]}],
    "Ge": [32, {"1s": [0, 0.063], "2s": [0, 0.063], "2p": [0, 0.19], "3s": [0, 0.063], "3p": [0, 0.19], "4s": [0, 0.063], "3d": [0, 0.31], "4p": [0, 0.063]}],
    "As": [33, {"1s": [0, 0.061], "2s": [0, 0.061], "2p": [0, 0.18], "3s": [0, 0.061], "3p": [0, 0.18], "4s": [0, 0.061], "3d": [0, 0.30], "4p": [0, 0.091]}],
    "Se": [34, {"1s": [0, 0.059], "2s": [0, 0.059], "2p": [0, 0.18], "3s": [0, 0.059], "3p": [0, 0.18], "4s": [0, 0.059], "3d": [0, 0.29], "4p": [0, 0.12]}],
    "Br": [35, {"1s": [0, 0.06], "2s": [0, 0.06], "2p": [0, 0.17], "3s": [0, 0.06], "3p": [0, 0.17], "4s": [0, 0.06], "3d": [0, 0.29], "4p": [0, 0.14]}],
    "Kr": [36, {"1s": [0, 0.06], "2s": [0, 0.06], "2p": [0, 0.17], "3s": [0, 0.06], "3p": [0, 0.17], "4s": [0, 0.06], "3d": [0, 0.28], "4p": [0, 0.17]}],
    "Rb": [37, {"1s": [0, 0.054], "2s": [0, 0.054], "2p": [0, 0.16], "3s": [0, 0.054], "3p": [0, 0.16], "4s": [0, 0.054], "3d": [0, 0.27], "4p": [0, 0.16], "5s": [0, 0.03]}],
    "Sr": [38, {"1s": [0, 0.053], "2s": [0, 0.053], "2p": [0, 0.16], "3s": [0, 0.053], "3p": [0, 0.16], "4s": [0, 0.053], "3d": [0, 0.26], "4p": [0, 0.16], "5s": [0, 0.053]}],
    "Y": [39, {"1s": [0, 0.051], "2s": [0, 0.051], "2p": [0, 0.15], "3s": [0, 0.051], "3p": [0, 0.15], "4s": [0, 0.051], "3d": [0, 0.26], "4p": [0, 0.15], "5s": [0, 0.051], "4d": [0, 0.03]}],
    "Zr": [40, {"1s": [0, 0.05], "2s": [0, 0.05], "2p": [0, 0.15], "3s": [0, 0.05], "3p": [0, 0.15], "4s": [0, 0.05], "3d": [0, 0.25], "4p": [0, 0.15], "5s": [0, 0.05], "4d": [0, 0.05]}],
    "Nb": [41, {"1s": [0, 0.05], "2s": [0, 0.05], "2p": [0, 0.15], "3s": [0, 0.05], "3p": [0, 0.15], "4s": [0, 0.05], "3d": [0, 0.24], "4p": [0, 0.15], "5s": [0, 0.024], "4d": [0, 0.10]}],
    "Mo": [42, {"1s": [0, 0.05], "2s": [0, 0.05], "2p": [0, 0.14], "3s": [0, 0.05], "3p": [0, 0.14], "4s": [0, 0.05], "3d": [0, 0.24], "4p": [0, 0.14], "5s": [0, 0.024], "4d": [0, 0.12]}],
    "Tc": [43, {"1s": [0, 0.05], "2s": [0, 0.05], "2p": [0, 0.14], "3s": [0, 0.05], "3p": [0, 0.14], "4s": [0, 0.05], "3d": [0, 0.23], "4p": [0, 0.14], "5s": [0, 0.05], "4d": [0, 0.12]}],
    "Ru": [44, {"1s": [0, 0.05], "2s": [0, 0.05], "2p": [0, 0.14], "3s": [0, 0.05], "3p": [0, 0.14], "4s": [0, 0.05], "3d": [0, 0.23], "4p": [0, 0.14], "5s": [0, 0.023], "4d": [0, 0.16]}],
    "Rh": [45, {"1s": [0, 0.044], "2s": [0, 0.044], "2p": [0, 0.133], "3s": [0, 0.044], "3p": [0, 0.133], "4s": [0, 0.044], "3d": [0, 0.222], "4p": [0, 0.133], "5s": [0, 0.022], "4d": [0, 0.133]}],
    "Pd": [46, {"1s": [0, 0.043], "2s": [0, 0.043], "2p": [0, 0.13], "3s": [0, 0.043], "3p": [0, 0.13], "4s": [0, 0.043], "3d": [0, 0.22], "4p": [0, 0.13], "5s": [0, 0], "4d": [0, 0.22]}],
    "Ag": [47, {"1s": [0, 0.043], "2s": [0, 0.043], "2p": [0, 0.13], "3s": [0, 0.043], "3p": [0, 0.13], "4s": [0, 0.043], "3d": [0, 0.21], "4p": [0, 0.13], "5s": [0, 0.021], "4d": [0, 0.21]}],
    "Cd": [48, {"1s": [0, 0.042], "2s": [0, 0.042], "2p": [0, 0.13], "3s": [0, 0.042], "3p": [0, 0.13], "4s": [0, 0.042], "3d": [0, 0.21], "4p": [0, 0.13], "5s": [0, 0.042], "4d": [0, 0.21]}],
    "In": [49, {"1s": [0, 0.041], "2s": [0, 0.041], "2p": [0, 0.122], "3s": [0, 0.041], "3p": [0, 0.122], "4s": [0, 0.041], "3d": [0, 0.204], "4p": [0, 0.122], "5s": [0, 0.041], "4d": [0, 0.204], "5p": [0, 0.02]}],
    "Sn": [50, {"1s": [0, 0.04], "2s": [0, 0.04], "2p": [0, 0.12], "3s": [0, 0.04], "3p": [0, 0.12], "4s": [0, 0.04], "3d": [0, 0.20], "4p": [0, 0.12], "5s": [0, 0.04], "4d": [0, 0.20], "5p": [0, 0.04]}],
    "Sb": [51, {"1s": [0, 0.04], "2s": [0, 0.04], "2p": [0, 0.12], "3s": [0, 0.04], "3p": [0, 0.12], "4s": [0, 0.04], "3d": [0, 0.20], "4p": [0, 0.12], "5s": [0, 0.04], "4d": [0, 0.20], "5p": [0, 0.06]}],
    "Te": [52, {"1s": [0, 0.04], "2s": [0, 0.04], "2p": [0, 0.12], "3s": [0, 0.04], "3p": [0, 0.12], "4s": [0, 0.04], "3d": [0, 0.20], "4p": [0, 0.12], "5s": [0, 0.04], "4d": [0, 0.20], "5p": [0, 0.077]}],
    "I": [53, {"1s": [0, 0.038], "2s": [0, 0.038], "2p": [0, 0.113], "3s": [0, 0.038], "3p": [0, 0.113], "4s": [0, 0.038], "3d": [0, 0.189], "4p": [0, 0.113], "5s": [0, 0.038], "4d": [0, 0.189], "5p": [0, 0.189]}],
    "Xe": [54, {"1s": [0, 0.037], "2s": [0, 0.037], "2p": [0, 0.111], "3s": [0, 0.037], "3p": [0, 0.111], "4s": [0, 0.037], "3d": [0, 0.185], "4p": [0, 0.111], "5s": [0, 0.037], "4d": [0, 0.185], "5p": [0, 0.111]}],
    "Cs": [55, {"1s": [0, 0.036], "2s": [0, 0.036], "2p": [0, 0.109], "3s": [0, 0.036], "3p": [0, 0.109], "4s": [0, 0.036], "3d": [0, 0.182], "4p": [0, 0.109], "5s": [0, 0.036], "4d": [0, 0.182], "5p": [0, 0.109], "6s": [0, 0.018]}],
    "Ba": [56, {"1s": [0, 0.036], "2s": [0, 0.036], "2p": [0, 0.107], "3s": [0, 0.036], "3p": [0, 0.107], "4s": [0, 0.036], "3d": [0, 0.179], "4p": [0, 0.107], "5s": [0, 0.036], "4d": [0, 0.179], "5p": [0, 0.107], "6s": [0, 0.036]}],
    "La": [57, {"1s": [0, 0.035], "2s": [0, 0.035], "2p": [0, 0.105], "3s": [0, 0.035], "3p": [0, 0.105], "4s": [0, 0.035], "3d": [0, 0.175], "4p": [0, 0.105], "5s": [0, 0.035], "4d": [0, 0.175], "5p": [0, 0.105], "6s": [0, 0.035], "5d": [0, 0.018]}],
    "Ce": [58, {"1s": [0, 0.034], "2s": [0, 0.034], "2p": [0, 0.103], "3s": [0, 0.034], "3p": [0, 0.103], "4s": [0, 0.034], "3d": [0, 0.172], "4p": [0, 0.103], "5s": [0, 0.034], "4d": [0, 0.172], "5p": [0, 0.103], "6s": [0, 0.034], "4f": [0, 0.017], "5d": [0, 0.017]}],
    "Pr": [59, {"1s": [0, 0.034], "2s": [0, 0.034], "2p": [0, 0.102], "3s": [0, 0.034], "3p": [0, 0.102], "4s": [0, 0.034], "3d": [0, 0.169], "4p": [0, 0.102], "5s": [0, 0.034], "4d": [0, 0.169], "5p": [0, 0.102], "6s": [0, 0.034], "4f": [0, 0.051], "5d": [0, 0.017]}],
    "Nd": [60, {"1s": [0, 0.033], "2s": [0, 0.033], "2p": [0, 0.10], "3s": [0, 0.033], "3p": [0, 0.10], "4s": [0, 0.033], "3d": [0, 0.167], "4p": [0, 0.10], "5s": [0, 0.033], "4d": [0, 0.167], "5p": [0, 0.10], "6s": [0, 0.033], "4f": [0, 0.067]}],
    "Pm": [61, {"1s": [0, 0.033], "2s": [0, 0.033], "2p": [0, 0.098], "3s": [0, 0.033], "3p": [0, 0.098], "4s": [0, 0.033], "3d": [0, 0.164], "4p": [0, 0.098], "5s": [0, 0.033], "4d": [0, 0.164], "5p": [0, 0.098], "6s": [0, 0.033], "4f": [0, 0.082]}],
    "Sm": [62, {"1s": [0, 0.032], "2s": [0, 0.032], "2p": [0, 0.097], "3s": [0, 0.032], "3p": [0, 0.097], "4s": [0, 0.032], "3d": [0, 0.161], "4p": [0, 0.097], "5s": [0, 0.032], "4d": [0, 0.161], "5p": [0, 0.097], "6s": [0, 0.032], "4f": [0, 0.097]}],
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    "Rf": [104, {"1s": [0, 0.019], "2s": [0, 0.019], "2p": [0, 0.058], "3s": [0, 0.019], "3p": [0, 0.058], "4s": [0, 0.019], "3d": [0, 0.096], "4p": [0, 0.058], "5s": [0, 0.019], "4d": [0, 0.096], "5p": [0, 0.058], "6s": [0, 0.019], "4f": [0, 0.13], "5d": [0, 0.096], "6p": [0, 0.058], "7s": [0, 0.019], "6d": [0, 0.019]}],
    "Db": [105, {"1s": [0, 0.019], "2s": [0, 0.019], "2p": [0, 0.057], "3s": [0, 0.019], "3p": [0, 0.057], "4s": [0, 0.019], "3d": [0, 0.095], "4p": [0, 0.057], "5s": [0, 0.019], "4d": [0, 0.095], "5p": [0, 0.057], "6s": [0, 0.019], "4f": [0, 0.133], "5d": [0, 0.095], "6p": [0, 0.057], "7s": [0, 0.019], "6d": [0, 0.029]}],
    "Sg": [106, {"1s": [0, 0.019], "2s": [0, 0.019], "2p": [0, 0.057], "3s": [0, 0.019], "3p": [0, 0.057], "4s": [0, 0.019], "3d": [0, 0.094], "4p": [0, 0.057], "5s": [0, 0.019], "4d": [0, 0.094], "5p": [0, 0.057], "6s": [0, 0.019], "4f": [0, 0.132], "5d": [0, 0.094], "6p": [0, 0.057], "7s": [0, 0.019], "6d": [0, 0.038]}],
    "Bh": [107, {"1s": [0, 0.019], "2s": [0, 0.019], "2p": [0, 0.056], "3s": [0, 0.019], "3p": [0, 0.056], "4s": [0, 0.019], "3d": [0, 0.093], "4p": [0, 0.056], "5s": [0, 0.019], "4d": [0, 0.093], "5p": [0, 0.056], "6s": [0, 0.019], "4f": [0, 0.131], "5d": [0, 0.093], "6p": [0, 0.056], "7s": [0, 0.019], "6d": [0, 0.047]}],
    "Hs": [108, {"1s": [0, 0.019], "2s": [0, 0.019], "2p": [0, 0.056], "3s": [0, 0.019], "3p": [0, 0.056], "4s": [0, 0.019], "3d": [0, 0.093], "4p": [0, 0.056], "5s": [0, 0.019], "4d": [0, 0.093], "5p": [0, 0.056], "6s": [0, 0.019], "4f": [0, 0.13], "5d": [0, 0.093], "6p": [0, 0.056], "7s": [0, 0.019], "6d": [0, 0.056]}],
    "Mt": [109, {"1s": [0, 0.018], "2s": [0, 0.018], "2p": [0, 0.055], "3s": [0, 0.018], "3p": [0, 0.055], "4s": [0, 0.018], "3d": [0, 0.092], "4p": [0, 0.055], "5s": [0, 0.018], "4d": [0, 0.092], "5p": [0, 0.055], "6s": [0, 0.018], "4f": [0, 0.13], "5d": [0, 0.092], "6p": [0, 0.055], "7s": [0, 0.018], "6d": [0, 0.064]}],
    "Ds": [110, {"1s": [0, 0.018], "2s": [0, 0.018], "2p": [0, 0.055], "3s": [0, 0.018], "3p": [0, 0.055], "4s": [0, 0.018], "3d": [0, 0.091], "4p": [0, 0.055], "5s": [0, 0.018], "4d": [0, 0.091], "5p": [0, 0.055], "6s": [0, 0.018], "4f": [0, 0.13], "5d": [0, 0.091], "6p": [0, 0.055], "7s": [0, 0.018], "6d": [0, 0.073]}],
    "Rg": [111, {"1s": [0, 0.018], "2s": [0, 0.018], "2p": [0, 0.054], "3s": [0, 0.018], "3p": [0, 0.054], "4s": [0, 0.018], "3d": [0, 0.090], "4p": [0, 0.054], "5s": [0, 0.018], "4d": [0, 0.090], "5p": [0, 0.054], "6s": [0, 0.018], "4f": [0, 0.13], "5d": [0, 0.090], "6p": [0, 0.054], "7s": [0, 0.018], "6d": [0, 0.081]}],
    "Cn": [112, {"1s": [0, 0.018], "2s": [0, 0.018], "2p": [0, 0.054], "3s": [0, 0.018], "3p": [0, 0.054], "4s": [0, 0.018], "3d": [0, 0.089], "4p": [0, 0.054], "5s": [0, 0.018], "4d": [0, 0.089], "5p": [0, 0.054], "6s": [0, 0.018], "4f": [0, 0.13], "5d": [0, 0.089], "6p": [0, 0.054], "7s": [0, 0.018], "6d": [0, 0.089]}],
    "Nh": [113, {"1s": [0, 0.018], "2s": [0, 0.018], "2p": [0, 0.053], "3s": [0, 0.018], "3p": [0, 0.053], "4s": [0, 0.018], "3d": [0, 0.088], "4p": [0, 0.053], "5s": [0, 0.018], "4d": [0, 0.088], "5p": [0, 0.053], "6s": [0, 0.018], "4f": [0, 0.12], "5d": [0, 0.088], "6p": [0, 0.053], "7s": [0, 0.018], "6d": [0, 0.088], "7p": [0, 0.009]}],
    "Fl": [114, {"1s": [0, 0.018], "2s": [0, 0.018], "2p": [0, 0.053], "3s": [0, 0.018], "3p": [0, 0.053], "4s": [0, 0.018], "3d": [0, 0.088], "4p": [0, 0.053], "5s": [0, 0.018], "4d": [0, 0.088], "5p": [0, 0.053], "6s": [0, 0.018], "4f": [0, 0.053], "5d": [0, 0.088], "6p": [0, 0.053], "7s": [0, 0.018], "6d": [0, 0.088], "7p": [0, 0.018]}],
    "Mc": [115, {"1s": [0, 0.017], "2s": [0, 0.017], "2p": [0, 0.052], "3s": [0, 0.017], "3p": [0, 0.052], "4s": [0, 0.017], "3d": [0, 0.087], "4p": [0, 0.052], "5s": [0, 0.017], "4d": [0, 0.087], "5p": [0, 0.052], "6s": [0, 0.017], "4f": [0, 0.12], "5d": [0, 0.087], "6p": [0, 0.052], "7s": [0, 0.017], "6d": [0, 0.087], "7p": [0, 0.026]}],
    "Lv": [116, {"1s": [0, 0.017], "2s": [0, 0.017], "2p": [0, 0.052], "3s": [0, 0.017], "3p": [0, 0.052], "4s": [0, 0.017], "3d": [0, 0.086], "4p": [0, 0.052], "5s": [0, 0.017], "4d": [0, 0.086], "5p": [0, 0.052], "6s": [0, 0.017], "4f": [0, 0.12], "5d": [0, 0.086], "6p": [0, 0.052], "7s": [0, 0.017], "6d": [0, 0.086], "7p": [0, 0.034]}],
    "Ts": [117, {"1s": [0, 0.017], "2s": [0, 0.017], "2p": [0, 0.051], "3s": [0, 0.017], "3p": [0, 0.051], "4s": [0, 0.017], "3d": [0, 0.085], "4p": [0, 0.051], "5s": [0, 0.017], "4d": [0, 0.085], "5p": [0, 0.051], "6s": [0, 0.017], "4f": [0, 0.12], "5d": [0, 0.085], "6p": [0, 0.051], "7s": [0, 0.017], "6d": [0, 0.085], "7p": [0, 0.043]}],
    "Og": [118, {"1s": [0, 0.017], "2s": [0, 0.017], "2p": [0, 0.051], "3s": [0, 0.017], "3p": [0, 0.051], "4s": [0, 0.017], "3d": [0, 0.085], "4p": [0, 0.051], "5s": [0, 0.017], "4d": [0, 0.085], "5p": [0, 0.051], "6s": [0, 0.017], "4f": [0, 0.12], "5d": [0, 0.085], "6p": [0, 0.051], "7s": [0, 0.017], "6d": [0, 0.085], "7p": [0, 0.051]}]}


input_bond = input("Please Enter Bond Here (e.g., O-H, C-O etc.): ")  # Only do 1 bond type at a time. Do not enter any numbers here
input_overlap_radius = float(input("Please Enter the Overlap Radius (Å): "))
# Parse bond elements
if "-" in input_bond:
    element1, element2 = input_bond.split("-")
else:
    elements = re.findall(r"[A-Z][a-z]*", input_bond)
    if len(elements) != 2:
        raise ValueError(f"Invalid bond format: {input_bond}")
    element1, element2 = elements

radius1 = electron_cloud_radii[element1]
radius2 = electron_cloud_radii[element2]

# Determine positions
x1 = 0
x2 = radius1 + radius2 - input_overlap_radius
y = 0

# Create plot
fig, ax = plt.subplots()
ax.set_aspect('equal')

# Draw electron clouds (transparent)
cloud1 = plt.Circle((x1, y), radius1, color='blue', alpha=0.3, label=f'{element1} electron cloud')
cloud2 = plt.Circle((x2, y), radius2, color='red', alpha=0.3, label=f'{element2} electron cloud')
ax.add_artist(cloud1)
ax.add_artist(cloud2)

# Draw nuclei
ax.plot(x1, y, 'bo', markersize=6, label=f'{element1} nucleus')
ax.plot(x2, y, 'ro', markersize=6, label=f'{element2} nucleus')

# Draw orbitals
def draw_orbitals(ax, x_center, y_center, element, color):
    orbitals = areecm_digital_dictionary[element][1]
    for orbital, fraction_range in orbitals.items():
        if orbital in orbital_distances:
            inner, outer = orbital_distances[orbital]
            circle = plt.Circle((x_center, y_center), outer, color=color, fill=False, linestyle='-', alpha=0.5)
            ax.add_artist(circle)


draw_orbitals(ax, x1, y, element1, 'blue')
draw_orbitals(ax, x2, y, element2, 'red')

# Labels and aesthetics
ax.set_xlim(-radius1*2, x2 + radius2*2)
ax.set_ylim(-max(radius1, radius2)*2, max(radius1, radius2)*2)
ax.set_xlabel("X-axis (Å)")
ax.set_ylabel("Y-axis (Å)")
ax.set_title(f"Visualization of {input_bond} bond with orbitals")
ax.legend(loc='upper right')
plt.grid(False)
plt.show()