APEPM_full_code_implementation.py

import re
import math
import matplotlib.pyplot as plt

# This code provides a reference implementation of the APEPM framework.
# Its purpose is to support transparency, reproducibility, and experimentation
# with the geometric and probabilistic quantities discussed in the accompanying paper.
#
# The implementation is intentionally simplified and optimized for clarity rather
# than throughput or large-scale screening. Production-oriented, high-throughput
# implementations used by the author for batch and pipeline integration are
# maintained separately.

# Armstrong’s Probabilistic Electron Phase-Space Overlap Model (APEPM)
# Licensed under: CC BY-NC 4.0

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

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)}

electron_cloud_radii = {'H': 1.30, 'He': 1.60, 'Li': 2.05, 'Be': 1.75, 'B': 2.15, 'C': 1.90, 'N': 1.75, 'O': 1.72, 'F': 0.85,
                        'Ne': 1.75, 'Na': 2.15, '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': 2.20, 'Sc': 2.25, 'Ti': 2.35, 'V': 2.35, 'Cr': 2.35, 'Mn': 2.40, 'Fe': 2.40, 'Ni': 1.85,
                        'Co': 1.75, 'Cu': 1.60, 'Zn': 1.60, 'Ga': 2.10, 'Ge': 2.35, 'As': 2.10, 'Se': 2.20, 'Br': 2.05, 'Kr': 2.25,
                        'Rb': 2.65, 'Sr': 2.35, 'Y': 2.40, 'Zr': 2.55, 'Nb': 2.55, 'Mo': 2.55, 'Tc': 2.60, 'Ru': 2.60, 'Rh': 2.55,
                        'Pd': 1.95, 'Ag': 1.80, 'Cd': 1.80, 'In': 2.20, 'Sn': 2.35, 'Sb': 2.20, 'I': 2.20, 'Xe': 2.35, 'Cs': 2.80,
                        'Te': 2.25,  'Ba': 2.55, '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': 1.65, 'Hg': 1.75, 'Tl': 2.20,
                        'Pb': 2.20, 'Bi': 2.30, 'Po': 2.30, 'At': 2.30, 'Rn': 2.40, 'Fr': 2.85, 'Ra': 2.60, 'Ac': 2.60, '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}

covalent_radii = {'H': 32, 'He': 31, 'Li': 128, 'Be': 96, 'B': 84, 'C': 77, 'N': 75, 'O': 73, 'F': 63, 'Ne': 38,
                  'Na': 166, 'Mg': 141, 'Al': 121, 'Si': 111, 'P': 110, 'S': 104, 'Cl': 99, 'Ar': 71, 'K': 203, 'Ca': 176,
                  'Sc': 162, 'Ti': 146, 'V': 134, 'Cr': 139, 'Mn': 139, 'Fe': 140, 'Co': 135, 'Ni': 124, 'Cu': 128, 'Zn': 139,
                  'Ga': 122, 'Ge': 122, 'As': 119, 'Se': 116, 'Br': 114, 'Kr': 88, 'Rb': 303, 'Sr': 249, 'Y': 211, 'Zr': 160,
                  'Nb': 146, 'Mo': 139, 'Tc': 138, 'Ru': 139, 'Rh': 137, 'Pd': 139, 'Ag': 145, 'Cd': 144, 'In': 144, 'Sn': 141,
                  'Sb': 139, 'I': 133, 'Te': 138, 'Xe': 108, 'Cs': 303, 'Ba': 253, 'La': 195, 'Ce': 198, 'Pr': 200, 'Nd': 200,
                  'Pm': 202, 'Sm': 203, 'Eu': 206, 'Gd': 207, 'Tb': 208, 'Dy': 209, 'Ho': 210, 'Er': 211, 'Tm': 212, 'Yb': 214,
                  'Lu': 215, 'Hf': 159, 'Ta': 146, 'W': 139, 'Re': 137, 'Os': 136, 'Ir': 135, 'Pt': 139, 'Au': 144, 'Hg': 150,
                  'Tl': 146, 'Pb': 154, 'Bi': 157, 'Po': 150, 'At': 150, 'Rn': 140, 'Fr': 330, 'Ra': 283, 'Ac': 221, 'Th': 206,
                  'Pa': 200, 'U': 196, 'Np': 190, 'Pu': 186, 'Am': 184, 'Cm': 183, 'Bk': 182, 'Cf': 181, 'Es': 180, 'Fm': 179,
                  'Md': 178, 'No': 177, 'Lr': 176, 'Rf': 175, 'Db': 174, 'Sg': 173, 'Bh': 172, 'Hs': 171, 'Mt': 170, 'Ds': 169,
                  'Rg': 168, 'Cn': 167, 'Nh': 166, 'Fl': 165, 'Mc': 164, 'Lv': 163, 'Ts': 162, 'Og': 161}

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]}],
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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]}]}

print()
user_input = input("Please enter your molecule or bond here here: ")
print()
print("If you entered a molecule press enter to skip the following input request ")
enter_bond_length_confirmation = input("Would you like to enable Custom Bond Length Entry (Yes, No): ").upper()
print()
visualizer_mode_confirmation = input("Would you like to enable APEPM Visualization Mode (Yes, No): ").upper()
print()

elements = []

# Regular expression to find element symbols and optional numbers
# ([A-Z][a-z]?) matches element symbols (e.g., H, He, O, Cl, etc.)
# (\d*) matches the number after the element symbol (subscript); optional
pattern = r'([A-Z][a-z]?)(\d*)'

# Find all matches in the formula, e.g., C6H12O6 -> [('C', '6'), ('H', '12'), ('O', '6')]
matches = re.findall(pattern, user_input)

# Loop through each match and build the elements list
for symbol, count in matches:
    # If there's no number after the element (e.g., H in H2O), count defaults to 1
    count = int(count) if count else 1

    # Append a dictionary with the element and its subscript
    elements.append({symbol: count})

bond_length_list = []
element_counts = {}
for ele_dict in elements:
    for ele, count in ele_dict.items():
        element_counts[ele] = element_counts.get(ele, 0) + count
unique_elements = list(element_counts.keys())
for i in range(len(unique_elements)):
    for j in range(i, len(unique_elements)):
        e1 = unique_elements[i]
        e2 = unique_elements[j]
        if e1 == e2 and element_counts[e1] < 2:
            continue
        if e1 in covalent_radii and e2 in covalent_radii:
            bond_length = covalent_radii[e1] + covalent_radii[e2]
            bond_name = f"{e1}-{e2}"
            if enter_bond_length_confirmation == 'YES' or enter_bond_length_confirmation == 'Y':
                enter_bond_length = input(f"Please enter your bond length in pm for {bond_name}: ")
                if not enter_bond_length:
                    bond_length_list.append({bond_name: bond_length})
                else:
                    bond_length_list.append({bond_name: float(enter_bond_length)})
            else:
                bond_length_list.append({bond_name: bond_length})
# All bond values are in "pm" and will be converted later to be in angstroms

# Please note that this bond length predictor is not made to be precise since this is just a simple model for APEPM
# and artifacts like H-H in H2O are to be expected because it's not predicting the types of bonds that will form between elements
# just the bond lengths between elements.
overlap_radius_list = []
overlap_area_list = []
overlap_volume_list = []
for bond in bond_length_list:
    for key_bond, value_bond in bond.items():
        key_bond_split = key_bond.split("-")
        ele_1 = key_bond_split[0]
        ele_2 = key_bond_split[1]
        era = electron_cloud_radii[ele_1]
        ern = electron_cloud_radii[ele_2]
        reff = (era + ern) / 2  # Averaged ERa and ERn Electron cloud Radii
        converted_bond_length = value_bond / 100  # Converted to angstroms
        if converted_bond_length < 2 * reff:
            R_overlap_radius = math.sqrt((2 * reff) ** 2 - converted_bond_length ** 2) / 2  # Calculates the Radius of the overlap
            Roa = math.pi * R_overlap_radius ** 2  # Calculates the Area of the overlap
            Rov = (math.pi * (4*reff + converted_bond_length) * (2*reff - converted_bond_length)**2) / 12  # Calculates the volume of the overlap
        else:  # Only happens if the bond length is too large and there is no overlap (This prevents ValueError: math domain error)
            R_overlap_radius = 0.0
            Roa = 0.0
            Rov = 0.0
        overlap_radius_list.append({key_bond: R_overlap_radius})
        overlap_area_list.append({key_bond: Roa})
        overlap_volume_list.append({key_bond: Rov})

# AREECM Related Calculations
orbital_participation = []

for item_orl in overlap_radius_list:
    for key_orl, R in item_orl.items():
        # Split the bond string into elements
        ele_1_orl, ele_2_orl = key_orl.split("-")

        # Extract orbitals for each element
        orbital_ele1 = list(areecm_digital_dictionary[ele_1_orl][1].keys())
        orbital_ele2 = list(areecm_digital_dictionary[ele_2_orl][1].keys())

        # Electron cloud radii
        Rcloud_1 = electron_cloud_radii[ele_1_orl]
        Rcloud_2 = electron_cloud_radii[ele_2_orl]

        # Portion of electron cloud within overlap
        D1 = Rcloud_1 - R
        D2 = Rcloud_2 - R

        # Determine participating orbitals
        orbitals_participating_1 = [orb for orb in orbital_ele1 if (orbital_distances[orb][1] >= D1 and orbital_distances[orb][1] <= Rcloud_1)]
        orbitals_participating_2 = [orb for orb in orbital_ele2 if (orbital_distances[orb][1] >= D2 and orbital_distances[orb][1] <= Rcloud_2)]
        orbital_participation.append({key_orl: [{ele_1_orl: orbitals_participating_1}, {ele_2_orl: orbitals_participating_2}]})

print()
print("----------------------------------------------------------------")
print("Overlap Radius, Area, and Volume Calculations: ")
print(bond_length_list, 'Estimated_bond_lengths (pm)')
print(overlap_radius_list, 'overlap_radius_list (angstroms)')
print(overlap_area_list, 'overlap_area_list (angstroms squared)')
print(overlap_volume_list, 'overlap_volume_list (angstroms cubed)')
print()
print("----------------------------------------------------------------")
print("Orbital, and AREECM Calculations: ")
print("These reflect only geometric overlap, not energetic contribution")
print()
print(orbital_participation, "orbital_participation")

# Visualizer Code:
if visualizer_mode_confirmation == 'YES' or visualizer_mode_confirmation == 'Y':
    figures = []  # store figures

    for item_orl in overlap_radius_list:
        for key_orl, R in item_orl.items():
            if "-" in key_orl:
                element1, element2 = key_orl.split("-")
            else:
                elements = re.findall(r"[A-Z][a-z]*", key_orl)
                if len(elements) != 2:
                    raise ValueError(f"Invalid bond format: {key_orl}")
                element1, element2 = elements
            radius1 = electron_cloud_radii[element1]
            radius2 = electron_cloud_radii[element2]

            # Determine positions
            x1 = 0
            x2 = radius1 + radius2 - R
            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 {key_orl} bond with orbitals")
            ax.legend(loc='upper right')
            plt.grid(False)
    plt.show()
else:
    pass