lj_params.py

"""Universal Force Field Lennard-Jones parameters, keyed the way ReBind keys them.

ReBind's ``get_sigma_and_epsilon`` looks parameters up by ``node_type``, which is
the atomic number minus one, and its own table stops at index 35 (Kr). Everything
heavier — the 4d/5d metals, the lanthanides, iodine — fell through to a flat
default, which is most of what makes an organometallic complex an organometallic
complex. This table carries the full UFF set through index 102 (Lr).

Values as compiled by Luis Pinto (``rebind_utils.py``); indices 0-35 are
bit-identical to ReBind's own table, so QM9 behaviour is unchanged.
Sigma in angstrom, epsilon in kcal/mol.
"""

from __future__ import annotations

# node_type (Z - 1) -> (sigma, epsilon)
UFF_LJ_PARAMETERS: dict[int, tuple[float, float]] = {
    0: (2.886, 0.0440),  # H
    1: (2.362, 0.0560),  # He
    2: (2.451, 0.0250),  # Li
    3: (2.745, 0.0850),  # Be
    4: (3.637, 0.1800),  # B
    5: (3.431, 0.1050),  # C
    6: (3.260, 0.0690),  # N
    7: (3.118, 0.0600),  # O
    8: (2.996, 0.0500),  # F
    9: (2.889, 0.0420),  # Ne
    10: (2.983, 0.0300),  # Na
    11: (2.905, 0.1110),  # Mg
    12: (4.008, 0.5050),  # Al
    13: (3.826, 0.4020),  # Si
    14: (3.694, 0.3050),  # P
    15: (3.594, 0.2740),  # S
    16: (3.516, 0.2270),  # Cl
    17: (3.404, 0.1850),  # Ar
    18: (3.812, 0.0350),  # K
    19: (3.487, 0.2380),  # Ca
    20: (3.316, 0.0190),  # Sc
    21: (3.294, 0.0170),  # Ti
    22: (3.273, 0.0160),  # V
    23: (3.249, 0.0150),  # Cr
    24: (3.210, 0.0130),  # Mn
    25: (3.174, 0.0130),  # Fe
    26: (3.144, 0.0130),  # Co
    27: (3.116, 0.0130),  # Ni
    28: (3.083, 0.0050),  # Cu
    29: (3.002, 0.1240),  # Zn
    30: (4.383, 0.4150),  # Ga
    31: (4.310, 0.3790),  # Ge
    32: (4.280, 0.3090),  # As
    33: (4.336, 0.2910),  # Se
    34: (4.403, 0.2510),  # Br
    35: (4.463, 0.2200),  # Kr
    36: (4.114, 0.0400),  # Rb
    37: (3.641, 0.2350),  # Sr
    38: (3.345, 0.0720),  # Y
    39: (3.124, 0.0690),  # Zr
    40: (3.167, 0.0590),  # Nb
    41: (3.167, 0.0560),  # Mo
    42: (3.140, 0.0480),  # Tc
    43: (3.076, 0.0560),  # Ru
    44: (3.053, 0.0530),  # Rh
    45: (3.003, 0.0410),  # Pd
    46: (3.148, 0.0360),  # Ag
    47: (2.848, 0.2280),  # Cd
    48: (4.432, 0.4080),  # In
    49: (4.295, 0.3810),  # Sn
    50: (4.314, 0.3110),  # Sb
    51: (4.382, 0.2920),  # Te
    52: (4.436, 0.2520),  # I
    53: (4.465, 0.2210),  # Xe
    54: (4.302, 0.0320),  # Cs
    55: (3.666, 0.2200),  # Ba
    56: (3.522, 0.0130),  # La
    57: (3.493, 0.0130),  # Ce
    58: (3.468, 0.0130),  # Pr
    59: (3.441, 0.0130),  # Nd
    60: (3.415, 0.0130),  # Pm
    61: (3.391, 0.0130),  # Sm
    62: (3.364, 0.0130),  # Eu
    63: (3.340, 0.0130),  # Gd
    64: (3.315, 0.0130),  # Tb
    65: (3.289, 0.0130),  # Dy
    66: (3.265, 0.0130),  # Ho
    67: (3.241, 0.0130),  # Er
    68: (3.216, 0.0130),  # Tm
    69: (3.191, 0.0130),  # Yb
    70: (3.167, 0.0130),  # Lu
    71: (3.141, 0.0670),  # Hf
    72: (3.170, 0.0600),  # Ta
    73: (3.168, 0.0540),  # W
    74: (3.111, 0.0460),  # Re
    75: (3.120, 0.0310),  # Os
    76: (3.020, 0.0320),  # Ir
    77: (2.754, 0.0800),  # Pt
    78: (3.293, 0.0390),  # Au
    79: (2.730, 0.4090),  # Hg
    80: (4.347, 0.3790),  # Tl
    81: (4.355, 0.3450),  # Pb
    82: (4.370, 0.2840),  # Bi
    83: (4.450, 0.2220),  # Po
    84: (4.750, 0.2840),  # At
    85: (4.765, 0.2210),  # Rn
    86: (3.846, 0.0300),  # Fr
    87: (3.659, 0.2110),  # Ra
    88: (3.478, 0.0330),  # Ac
    89: (3.395, 0.0310),  # Th
    90: (3.424, 0.0100),  # Pa
    91: (3.397, 0.0110),  # U
    92: (3.424, 0.0050),  # Np
    93: (3.424, 0.0050),  # Pu
    94: (3.381, 0.0140),  # Am
    95: (3.326, 0.0140),  # Cm
    96: (3.339, 0.0140),  # Bk
    97: (3.313, 0.0140),  # Cf
    98: (3.286, 0.0140),  # Es
    99: (3.281, 0.0140),  # Fm
    100: (3.268, 0.0140),  # Md
    101: (3.254, 0.0140),  # No
    102: (3.240, 0.0070),  # Lr
}

MAX_NODE_TYPE = max(UFF_LJ_PARAMETERS)