def test_becke_parameter_calc(self):
"""Test parameter function."""
R = BeckeTF.find_parameter(self.array, 0.1, 1.2)
# R = 1.1
assert np.isclose(R, 1.1)
btf = BeckeTF(0.1, R)
tf_array = btf.transform(self.array)
assert tf_array[9] == 1.2
# for even number of grid
R = BeckeTF.find_parameter(self.array_2, 0.2, 1.3)
btf_2 = BeckeTF(0.2, R)
tf_elemt = btf_2.transform(
np.array([(self.array_2[4] + self.array_2[5]) / 2]))
assert_allclose(tf_elemt, 1.3)
def test_errors_assert(self):
"""Test errors raise."""
# parameter error
with self.assertRaises(ValueError):
BeckeTF.find_parameter(np.arange(5), 0.5, 0.1)
# transform non array type
with self.assertRaises(TypeError):
btf = BeckeTF(0.1, 1.1)
btf.transform(0.5)
# inverse init error
with self.assertRaises(TypeError):
InverseTF(0.5)
# type error for transform_grid
with self.assertRaises(TypeError):
btf = BeckeTF(0.1, 1.1)
btf.transform_grid(np.arange(3))
def test_becke_infinite(self):
"""Test becke transformation when inf generated."""
inf_array = np.linspace(-1, 1, 21)
R = BeckeTF.find_parameter(inf_array, 0.1, 1.2)
btf = BeckeTF(0.1, R)
tf_array = btf.transform(inf_array, trim_inf=True)
inv_array = btf.inverse(tf_array)
assert_allclose(inv_array, inf_array)
def test_errors_assert(self):
"""Test errors raise."""
# parameter error
with self.assertRaises(ValueError):
BeckeTF.find_parameter(np.arange(5), 0.5, 0.1)
# transform non array type
with self.assertRaises(TypeError):
btf = BeckeTF(0.1, 1.1)
btf.transform("dafasdf")
# inverse init error
with self.assertRaises(TypeError):
InverseTF(0.5)
# type error for transform_1d_grid
with self.assertRaises(TypeError):
btf = BeckeTF(0.1, 1.1)
btf.transform_1d_grid(np.arange(3))
with self.assertRaises(ZeroDivisionError):
btf = BeckeTF(0.1, 0)
itf = InverseTF(btf)
itf._d1(0.5)
with self.assertRaises(ZeroDivisionError):
btf = BeckeTF(0.1, 0)
itf = InverseTF(btf)
itf._d1(np.array([0.1, 0.2, 0.3]))
def test_becke_infinite(self):
"""Test becke transformation when inf generated."""
inf_array = np.linspace(-1, 1, 21)
R = BeckeTF.find_parameter(inf_array, 0.1, 1.2)
btf = BeckeTF(0.1, R, trim_inf=True)
tf_array = btf.transform(inf_array)
inv_array = btf.inverse(tf_array)
assert_allclose(inv_array, inf_array)
# extra test for neg inf
# test for number
result = btf._convert_inf(-np.inf)
assert_almost_equal(result, -1e16)
result = btf._convert_inf(np.inf)
assert_almost_equal(result, 1e16)
# test for array
test_array = np.random.rand(5)
test_array[3] = -np.inf
result = btf._convert_inf(test_array)
assert_almost_equal(result[3], -1e16)
test_array[3] = np.inf
result = btf._convert_inf(test_array)
assert_almost_equal(result[3], 1e16)
alc_hf = Alchemical_tools(
basis,
molecule,
point_charge_positions=R,
point_charges_values=q,
coord_type="cartesian",
k="HF",
)
r0 = 1e-10
radii = get_cov_radii(molecule.atnums)
n_rad_points = 100
deg = 5
onedgrid = GaussChebyshev(n_rad_points)
molecule_at_grid = []
for i in range(len(molecule.atnums)):
Rad = BeckeTF.find_parameter(onedgrid.points, r0, radii[i])
rad_grid = BeckeTF(r0, Rad).transform_grid(onedgrid)
molecule_at_grid = molecule_at_grid + [
AtomicGrid.special_init(rad_grid, radii[i], degs=[deg], scales=[])
]
molgrid = MolGrid(molecule_at_grid, molecule.atnums)
alc_lda = Alchemical_tools(
basis,
molecule,
point_charge_positions=R,
point_charges_values=q,
coord_type="cartesian",
k="lda_x",
molgrid=molgrid,
)
two_electron_int = electron_repulsion_integral(basis,