def test_make_atomic_ring(self):
spacing = 1.
basis = 'sto-3g'
for n_atoms in range(2, 10):
molecule = make_atomic_ring(n_atoms, spacing, basis)
# Check that ring is centered.
vector_that_should_sum_to_zero = 0.
for atom in molecule.geometry:
for coordinate in atom[1]:
vector_that_should_sum_to_zero += coordinate
self.assertAlmostEqual(vector_that_should_sum_to_zero, 0.)
# Check that the spacing between the atoms is correct.
for atom_index in range(n_atoms):
if atom_index:
atom_b = molecule.geometry[atom_index]
coords_b = atom_b[1]
atom_a = molecule.geometry[atom_index - 1]
coords_a = atom_a[1]
observed_spacing = numpy.sqrt(
numpy.square(coords_b[0] - coords_a[0]) +
numpy.square(coords_b[1] - coords_a[1]) +
numpy.square(coords_b[2] - coords_a[2]))
self.assertAlmostEqual(observed_spacing, spacing)
y_log = 0
# Set chemical series parameters.
plot_elements = 0
max_electrons = 10
spacing = 0.7414
basis = 'sto-3g'
# Get chemical series.
molecular_series = []
for n_electrons in range(2, max_electrons + 1):
if plot_elements:
atomic_symbol = periodic_table[n_electrons]
molecule = make_atom(atomic_symbol, basis)
else:
molecule = make_atomic_ring(n_electrons, spacing, basis)
molecule.load()
molecular_series += [molecule]
# Get plot data.
x_values = []
y_values = []
for molecule in molecular_series:
# x-axis.
x_label = 'Number of Electrons'
x_values += [molecule.n_electrons]
# y-axis.
y_label = 'MP2 Energy'
y_values += [molecule.mp2_energy]