def test_total_atomic_grid(self):
"""Normal initialization test."""
radial_pts = np.arange(0.1, 1.1, 0.1)
radial_wts = np.ones(10) * 0.1
radial_grid = RadialGrid(radial_pts, radial_wts)
rad = 0.5
scales = np.array([0.5, 1, 1.5])
degs = np.array([6, 14, 14, 6])
# generate a proper instance without failing.
ag_ob = AtomicGrid.special_init(radial_grid,
radius=rad,
scales=scales,
degs=degs)
assert isinstance(ag_ob, AtomicGrid)
assert len(ag_ob.indices) == 11
assert ag_ob.l_max == 15
ag_ob = AtomicGrid.special_init(radial_grid,
radius=rad,
scales=np.array([]),
degs=np.array([6]))
assert isinstance(ag_ob, AtomicGrid)
assert len(ag_ob.indices) == 11
ag_ob = AtomicGrid(radial_grid, nums=[110])
assert ag_ob.l_max == 17
assert_array_equal(ag_ob._rad_degs, np.ones(10) * 17)
assert ag_ob.size == 110 * 10
# new init AtomicGrid
ag_ob2 = AtomicGrid(radial_grid, degs=[17])
assert ag_ob2.l_max == 17
assert_array_equal(ag_ob2._rad_degs, np.ones(10) * 17)
assert ag_ob2.size == 110 * 10
def test_error_raises(self):
"""Tests for error raises."""
with self.assertRaises(TypeError):
AtomicGrid.special_init(np.arange(3),
1.0,
scales=np.arange(2),
degs=np.arange(3))
with self.assertRaises(ValueError):
AtomicGrid.special_init(
RadialGrid(np.arange(3), np.arange(3)),
radius=1.0,
scales=np.arange(2),
degs=np.arange(0),
)
with self.assertRaises(ValueError):
AtomicGrid.special_init(
RadialGrid(np.arange(3), np.arange(3)),
radius=1.0,
scales=np.arange(2),
degs=np.arange(4),
)
with self.assertRaises(ValueError):
AtomicGrid._generate_atomic_grid(
RadialGrid(np.arange(3), np.arange(3)), np.arange(2))
with self.assertRaises(TypeError):
AtomicGrid.special_init(
RadialGrid(np.arange(3), np.arange(3)),
radius=1.0,
scales=np.array([0.3, 0.5, 0.7]),
degs=np.array([3, 5, 7, 5]),
center=(0, 0, 0),
)
with self.assertRaises(ValueError):
AtomicGrid.special_init(
RadialGrid(np.arange(3), np.arange(3)),
radius=1.0,
scales=np.array([0.3, 0.5, 0.7]),
degs=np.array([3, 5, 7, 5]),
center=np.array([0, 0, 0, 0]),
)
with self.assertRaises(TypeError):
AtomicGrid(RadialGrid(np.arange(3), np.arange(3)), nums=110)
with self.assertRaises(TypeError):
AtomicGrid(RadialGrid(np.arange(3), np.arange(3)), degs=17)
with self.assertRaises(ValueError):
AtomicGrid(RadialGrid(np.arange(3), np.arange(3)),
degs=[17],
rotate=-1)
with self.assertRaises(ValueError):
AtomicGrid(RadialGrid(np.arange(3), np.arange(3)),
degs=[17],
rotate="asdfaf")
def test_horton_molgrid(self):
"""Test horton style grid."""
coors = np.array([[0, 0, -0.5], [0, 0, 0.5]])
nums = [1, 1]
mol_grid = MolGrid.horton_molgrid(coors, nums, self.rgrid, 110)
atg1 = AtomicGrid.special_init(
self.rgrid, 0.5, scales=np.array([]), degs=np.array([17]), center=coors[0]
)
atg2 = AtomicGrid.special_init(
self.rgrid, 0.5, scales=np.array([]), degs=np.array([17]), center=coors[1]
)
ref_grid = MolGrid([atg1, atg2], nums, store=True)
assert_allclose(ref_grid.points, mol_grid.points)
assert_allclose(ref_grid.weights, mol_grid.weights)
def test_spline_with_sph_harms(self):
"""Test spline projection the same as spherical harmonics."""
rad = IdentityRTransform().transform_grid(HortonLinear(10))
rad._points += 1
atgrid = AtomicGrid.special_init(rad, 1, scales=[], degs=[7])
sph_coor = atgrid.convert_cart_to_sph()
values = self.helper_func_power(atgrid.points)
l_max = atgrid.l_max // 2
r_sph = generate_real_sph_harms(l_max, sph_coor[:, 0], sph_coor[:, 1])
result = spline_with_sph_harms(
r_sph, values, atgrid.weights, atgrid.indices, rad.points
)
# generate ref
# for shell in range(1, 11):
for shell in range(1, 11):
sh_grid = atgrid.get_shell_grid(shell - 1, r_sq=False)
r = np.linalg.norm(sh_grid._points, axis=1)
theta = np.arctan2(sh_grid._points[:, 1], sh_grid._points[:, 0])
phi = np.arccos(sh_grid._points[:, 2] / r)
r_sph = generate_real_sph_harms(l_max, theta, phi)
r_sph_proj = np.sum(
r_sph * self.helper_func_power(sh_grid.points) * sh_grid.weights,
axis=-1,
)
assert_allclose(r_sph_proj, result(shell), atol=1e-10)
def test_raise_errors(self):
"""Test molgrid errors raise."""
atg = AtomicGrid.special_init(
self.rgrid,
0.5,
scales=np.array([]),
degs=np.array([17]),
center=np.array([0.0, 0.0, 0.0]),
)
# initilize errors
with self.assertRaises(NotImplementedError):
MolGrid([atg], np.array([1]), aim_weights="test")
with self.assertRaises(ValueError):
MolGrid([atg], np.array([1]), aim_weights=np.array(3))
with self.assertRaises(TypeError):
MolGrid([atg], np.array([1]), aim_weights=[3, 5])
# integrate errors
molg = MolGrid([atg], np.array([1]))
with self.assertRaises(ValueError):
molg.integrate()
with self.assertRaises(TypeError):
molg.integrate(1)
with self.assertRaises(ValueError):
molg.integrate(np.array([3, 5]))
with self.assertRaises(NotImplementedError):
molg.get_atomic_grid(0)
with self.assertRaises(ValueError):
molg.get_aim_weights(-3)
molg = MolGrid([atg], np.array([1]), store=True)
with self.assertRaises(ValueError):
molg.get_atomic_grid(-5)
def test_molgrid_attrs_subgrid(self):
"""Test sub atomic grid attributes."""
# numbers = np.array([6, 8], int)
coordinates = np.array([[0.0, 0.2, -0.5], [0.1, 0.0, 0.5]], float)
atg1 = AtomicGrid.special_init(
self.rgrid,
1.228,
scales=np.array([]),
degs=np.array([17]),
center=coordinates[0],
)
atg2 = AtomicGrid.special_init(
self.rgrid,
0.945,
scales=np.array([]),
degs=np.array([17]),
center=coordinates[1],
)
mg = MolGrid([atg1, atg2], np.array([6, 8]), store=True)
# mg = BeckeMolGrid(coordinates, numbers, None, (rgrid, 110), mode='keep')
assert mg.size == 2 * 110 * 100
assert mg.points.shape == (mg.size, 3)
assert mg.weights.shape == (mg.size,)
assert mg.aim_weights.shape == (mg.size,)
assert len(mg._indices) == 2 + 1
# assert mg.k == 3
# assert mg.random_rotate
for i in range(2):
atgrid = mg[i]
assert isinstance(atgrid, AtomicGrid)
assert atgrid.size == 100 * 110
assert atgrid.points.shape == (100 * 110, 3)
assert atgrid.weights.shape == (100 * 110,)
assert (atgrid.center == coordinates[i]).all()
mg = MolGrid([atg1, atg2], np.array([6, 8]))
for i in range(2):
atgrid = mg[i]
assert isinstance(atgrid, SimpleAtomicGrid)
assert_allclose(atgrid.center, mg._coors[i])
def test_integrate_hydrogen_trimer_1s(self):
"""Test molecular integral in H3."""
coordinates = np.array(
[[0.0, 0.0, -0.5], [0.0, 0.0, 0.5], [0.0, 0.5, 0.0]], float
)
atg1 = AtomicGrid.special_init(
self.rgrid,
0.5,
scales=np.array([]),
degs=np.array([17]),
center=coordinates[0],
)
atg2 = AtomicGrid.special_init(
self.rgrid,
0.5,
scales=np.array([]),
degs=np.array([17]),
center=coordinates[1],
)
atg3 = AtomicGrid.special_init(
self.rgrid,
0.5,
scales=np.array([]),
degs=np.array([17]),
center=coordinates[2],
)
mg = MolGrid([atg1, atg2, atg3], np.array([1, 1, 1]))
dist0 = np.sqrt(((coordinates[0] - mg.points) ** 2).sum(axis=1))
dist1 = np.sqrt(((coordinates[1] - mg.points) ** 2).sum(axis=1))
dist2 = np.sqrt(((coordinates[2] - mg.points) ** 2).sum(axis=1))
fn = (
np.exp(-2 * dist0) / np.pi
+ np.exp(-2 * dist1) / np.pi
+ np.exp(-2 * dist2) / np.pi
)
occupation = mg.integrate(fn)
assert_almost_equal(occupation, 3.0, decimal=4)
def test_different_aim_weights_h2(self):
"""Test different aim_weights for molgrid."""
coordinates = np.array([[0.0, 0.0, -0.5], [0.0, 0.0, 0.5]], float)
atg1 = AtomicGrid.special_init(
self.rgrid,
0.5,
scales=np.array([]),
degs=np.array([17]),
center=coordinates[0],
)
atg2 = AtomicGrid.special_init(
self.rgrid,
0.5,
scales=np.array([]),
degs=np.array([17]),
center=coordinates[1],
)
aim_weights = np.ones(22000)
mg = MolGrid([atg1, atg2], np.array([1, 1]), aim_weights=aim_weights)
dist0 = np.sqrt(((coordinates[0] - mg.points) ** 2).sum(axis=1))
dist1 = np.sqrt(((coordinates[1] - mg.points) ** 2).sum(axis=1))
fn = np.exp(-2 * dist0) / np.pi + np.exp(-2 * dist1) / np.pi
occupation = mg.integrate(fn)
assert_almost_equal(occupation, 4.0, decimal=4)
def test_molgrid_attrs(self):
"""Test MolGrid attributes."""
# numbers = np.array([6, 8], int)
coordinates = np.array([[0.0, 0.2, -0.5], [0.1, 0.0, 0.5]], float)
atg1 = AtomicGrid.special_init(
self.rgrid,
1.228,
scales=np.array([]),
degs=np.array([17]),
center=coordinates[0],
)
atg2 = AtomicGrid.special_init(
self.rgrid,
0.945,
scales=np.array([]),
degs=np.array([17]),
center=coordinates[1],
)
mg = MolGrid([atg1, atg2], np.array([6, 8]), store=True)
assert mg.size == 2 * 110 * 100
assert mg.points.shape == (mg.size, 3)
assert mg.weights.shape == (mg.size,)
assert mg.aim_weights.shape == (mg.size,)
assert mg.get_atomic_grid(0) is atg1
assert mg.get_atomic_grid(1) is atg2
simple_ag1 = mg.get_simple_atomic_grid(0)
simple_ag2 = mg.get_simple_atomic_grid(1)
assert_allclose(simple_ag1.points, atg1.points)
assert_allclose(simple_ag2.points, atg2.points)
aim_at1 = mg.get_aim_weights(0)
aim_at2 = mg.get_aim_weights(1)
assert_allclose(simple_ag1.weights, atg1.weights * aim_at1)
assert_allclose(simple_ag2.weights, atg2.weights * aim_at2)
def test_integrate_hydrogen_8_1s(self):
"""Test molecular integral in H2."""
x, y, z = np.meshgrid(*(3 * [[-0.5, 0.5]]))
centers = np.stack([x.ravel(), y.ravel(), z.ravel()], axis=1)
atgs = [
AtomicGrid.special_init(
self.rgrid, 0.5, scales=np.array([]), degs=np.array([17]), center=center
)
for center in centers
]
mg = MolGrid(atgs, np.array([1] * len(centers)))
fn = 0
for center in centers:
dist = np.linalg.norm(center - mg.points, axis=1)
fn += np.exp(-2 * dist) / np.pi
occupation = mg.integrate(fn)
assert_almost_equal(occupation, len(centers), decimal=2)
def test_integrate_hydrogen_single_1s(self):
"""Test molecular integral in H atom."""
# numbers = np.array([1], int)
coordinates = np.array([0.0, 0.0, -0.5], float)
# rgrid = BeckeTF.transform_grid(oned, 0.001, 0.5)[0]
# rtf = ExpRTransform(1e-3, 1e1, 100)
# rgrid = RadialGrid(rtf)
atg1 = AtomicGrid.special_init(
self.rgrid,
0.5,
scales=np.array([]),
degs=np.array([17]),
center=coordinates,
)
mg = MolGrid([atg1], np.array([1]))
# mg = BeckeMolGrid(coordinates, numbers, None, (rgrid, 110), random_rotate=False)
dist0 = np.sqrt(((coordinates - mg.points) ** 2).sum(axis=1))
fn = np.exp(-2 * dist0) / np.pi
occupation = mg.integrate(fn)
assert_almost_equal(occupation, 1.0, decimal=6)
def test_cubicspline_and_deriv(self):
"""Test spline for derivation."""
rad = IdentityRTransform().transform_grid(HortonLinear(10))
rad._points += 1
atgrid = AtomicGrid.special_init(rad, 1, scales=[], degs=[7])
sph_coor = atgrid.convert_cart_to_sph()
values = self.helper_func_power(atgrid.points)
l_max = atgrid.l_max // 2
r_sph = generate_real_sph_harms(l_max, sph_coor[:, 0], sph_coor[:, 1])
result = spline_with_sph_harms(
r_sph, values, atgrid.weights, atgrid.indices, rad.points
)
semi_sph_c = sph_coor[atgrid.indices[5] : atgrid.indices[6]]
interp = interpolate(result, 6, semi_sph_c[:, 0], semi_sph_c[:, 1], deriv=1)
# same result from points and interpolation
ref_deriv = self.helper_func_power_deriv(
atgrid.points[atgrid.indices[5] : atgrid.indices[6]]
)
assert_allclose(interp, ref_deriv)
# test random x, y, z with fd
xyz = np.random.rand(1, 3)
xyz /= np.linalg.norm(xyz, axis=-1)[:, None]
rad = np.random.normal() * np.random.randint(1, 11)
xyz *= rad
ref_value = self.helper_func_power_deriv(xyz)
r = np.linalg.norm(xyz, axis=-1)
theta = np.arctan2(xyz[:, 1], xyz[:, 0])
phi = np.arccos(xyz[:, 2] / r)
interp = interpolate(result, np.abs(rad), theta, phi, deriv=1)
assert_allclose(interp, ref_value)
with self.assertRaises(ValueError):
interp = interpolate(result, 6, semi_sph_c[:, 0], semi_sph_c[:, 1], deriv=4)
with self.assertRaises(ValueError):
interp = interpolate(
result, 6, semi_sph_c[:, 0], semi_sph_c[:, 1], deriv=-1
)
def test_cubicspline_and_interp(self):
"""Test cubicspline interpolation values."""
rad = IdentityRTransform().transform_grid(HortonLinear(10))
rad._points += 1
atgrid = AtomicGrid.special_init(rad, 1, scales=[], degs=[7])
sph_coor = atgrid.convert_cart_to_sph()
values = self.helper_func_power(atgrid.points)
l_max = atgrid.l_max // 2
r_sph = generate_real_sph_harms(l_max, sph_coor[:, 0], sph_coor[:, 1])
result = spline_with_sph_harms(
r_sph, values, atgrid.weights, atgrid.indices, rad.points
)
semi_sph_c = sph_coor[atgrid.indices[5] : atgrid.indices[6]]
interp = interpolate(result, 6, semi_sph_c[:, 0], semi_sph_c[:, 1])
# same result from points and interpolation
assert_allclose(interp, values[atgrid.indices[5] : atgrid.indices[6]])
# random multiple interpolation test
for _ in range(100):
indices = np.random.randint(1, 11, np.random.randint(1, 10))
interp = interpolate(result, indices, semi_sph_c[:, 0], semi_sph_c[:, 1])
for i, j in enumerate(indices):
assert_allclose(
interp[i], values[atgrid.indices[j - 1] : atgrid.indices[j]]
)
# test random x, y, z
xyz = np.random.rand(10, 3)
xyz /= np.linalg.norm(xyz, axis=-1)[:, None]
rad = np.random.normal() * np.random.randint(1, 11)
xyz *= rad
ref_value = self.helper_func_power(xyz)
r = np.linalg.norm(xyz, axis=-1)
theta = np.arctan2(xyz[:, 1], xyz[:, 0])
phi = np.arccos(xyz[:, 2] / r)
interp = interpolate(result, np.abs(rad), theta, phi)
assert_allclose(interp, ref_value)
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,
transform=molecule.mo.coeffs.T,
coord_type="cartesian",
notation="chemist")