def test_atoms():
assert atoms.get_maximal_valance(atom_label='C') == 4
assert atoms.get_maximal_valance(atom_label='Aa') == 6
assert atoms.get_atomic_weight(atom_label='C') == 12.01
assert atoms.get_atomic_weight(atom_label='Aa') == 70
assert 0.9 < atoms.get_vdw_radius(atom_label='H') < 1.2
assert 2 < atoms.get_vdw_radius(atom_label='Aa') < 3
assert atoms.is_pi_atom(atom_label='C', valency=3) is True
assert atoms.is_pi_atom(atom_label='C', valency=4) is False
assert atoms.is_pi_atom(atom_label='Aa', valency=9) is False
def calc_atom_entropy(atom_label, temp):
"""
Calculate the entropy of a single atom, not available in ORCA as only the
translational contribution: S_trans = R (ln(q_trans) + 5R/2)
Arguments:
atom_label (str):
temp (float): Temperature in K
Returns:
(float):
"""
k_b = 1.38064852E-23 # J K-1
h = 6.62607004E-34 # J s
n_a = 6.022140857E23 # molecules mol-1
atm_to_pa = 101325 # Pa
amu_to_kg = 1.660539040E-27 # Kg
mass = amu_to_kg * get_atomic_weight(atom_label=atom_label)
v_eff = k_b * temp / atm_to_pa
q_trans = ((2.0 * np.pi * mass * k_b * temp / h**2)**1.5 * v_eff)
s = k_b * n_a * (np.log(q_trans) + 2.5)
# Convert from J K-1 mol-1 to K-1 Ha
return s / (Constants.ha2kJmol * 1000)
def get_atom_ids_sorted_type(species):
"""
Get a list of atom ids sorted by increasing atomic weight, useful for when
a molecular graph depends on the order
of atoms in what will be considered bonded
Arguments:
species (autode.species.Species):
Returns:
(list(int)):
"""
return sorted(
list(range(species.n_atoms)),
key=lambda i: get_atomic_weight(atom_label=species.atoms[i].label))
def density(self):
"""Calculate the density of the system in g cm-3"""
total_mw = sum([
get_atomic_weight(atom.label) for m in self.molecules
for atom in m.atoms
]) # g mol-1
# ρ = m / V -> ρ = (mw / Na) / (V) * 1E-3
n_a = 6.02214086E23 # thing mol^-1
a_m, b_m, c_m = self.box.size * 1E-10 # m
per_m3_to_per_cm3 = 1E-6
rho = (total_mw / n_a) / (a_m * b_m * c_m) # g m^-3
rho_g_per_cm3 = per_m3_to_per_cm3 * rho # g cm^-3
return rho_g_per_cm3
def weight(idx):
"""Given an atom index return the molecular weight in amu"""
return get_atomic_weight(atom_label=species.atoms[idx].label)