def _get_neighbor_coeffs(self, mol: Molecule) -> Counter:
"""
Get a counter containing the coefficients for the gamma
(bond_corr_neighbor) variables.
Args:
mol: RMG-Py molecule.
Returns:
Counter containing gamma coefficients.
"""
if hasattr(mol, 'id') and mol.id is not None:
if mol.id in self._gamma_coeffs:
return self._gamma_coeffs[mol.id]
coeffs = Counter()
for bond in mol.get_all_edges():
atom1 = bond.atom1
atom2 = bond.atom2
# Atoms adjacent to atom1
counts1 = Counter(a.element.symbol for a, b in atom1.bonds.items() if b is not bond)
counts1[atom1.element.symbol] += max(0, len(atom1.bonds) - 1)
# Atoms adjacent to atom2
counts2 = Counter(a.element.symbol for a, b in atom2.bonds.items() if b is not bond)
counts2[atom2.element.symbol] += max(0, len(atom2.bonds) - 1)
coeffs += counts1 + counts2
if hasattr(mol, 'id'):
self._gamma_coeffs[mol.id] = coeffs
return coeffs
def _get_length_coeffs(self, mol: Molecule) -> defaultdict:
"""
Get a dictionary containing the coefficients for the beta
(bond_corr_length) variables. There is one coefficient per atom
type and an additional coefficient for each combination of atom
types.
Example: If the atoms are H, C, and O, there are (at most)
coefficients for H, C, O, (C, H), (H, O), and (C, O).
Args:
mol: RMG-Py molecule.
Returns:
Defaultdict containing beta coefficients.
"""
if hasattr(mol, 'id') and mol.id is not None:
if mol.id in self._beta_coeffs:
return self._beta_coeffs[mol.id]
coeffs = defaultdict(float)
for bond in mol.get_all_edges():
atom1 = bond.atom1
atom2 = bond.atom2
symbol1 = atom1.element.symbol
symbol2 = atom2.element.symbol
c = np.exp(-self.exp_coeff * np.linalg.norm(atom1.coords - atom2.coords))
k = symbol1 if symbol1 == symbol2 else tuple(sorted([symbol1, symbol2]))
coeffs[k] += c
if hasattr(mol, 'id'):
self._beta_coeffs[mol.id] = coeffs
return coeffs