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(
self.rgrid,
0.5,
scales=np.array([]),
degs=np.array([17]),
center=coordinates[0],
)
atg2 = AtomicGrid(
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([0.5, 0.5]),
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_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 = AtomGrid.from_pruned(
self.rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates[0],
)
atg2 = AtomGrid.from_pruned(
self.rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates[1],
)
atg3 = AtomGrid.from_pruned(
self.rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates[2],
)
becke = BeckeWeights(order=3)
mg = MolGrid([atg1, atg2, atg3], becke, 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_get_localgrid_1s(self):
"""Test local grid for a molecule with one atom."""
nums = np.array([1])
coords = np.array([0.0, 0.0, 0.0])
# initialize MolGrid with atomic grid
atg1 = AtomGrid.from_pruned(
self.rgrid,
0.5,
sectors_r=np.array([]),
sectors_degree=np.array([17]),
center=coords,
)
grid = MolGrid(np.array([1]), [atg1], BeckeWeights(), store=False)
fn = np.exp(-2 * np.linalg.norm(grid.points, axis=-1))
assert_allclose(grid.integrate(fn), np.pi)
# conventional local grid
localgrid = grid.get_localgrid(coords, 12.0)
localfn = np.exp(-2 * np.linalg.norm(localgrid.points, axis=-1))
assert localgrid.size < grid.size
assert localgrid.size == 10560
assert_allclose(localgrid.integrate(localfn), np.pi)
assert_allclose(fn[localgrid.indices], localfn)
# "whole" loal grid, useful for debugging code using local grids
wholegrid = grid.get_localgrid(coords, np.inf)
assert wholegrid.size == grid.size
assert_allclose(wholegrid.points, grid.points)
assert_allclose(wholegrid.weights, grid.weights)
assert_allclose(wholegrid.indices, np.arange(grid.size))
# initialize MolGrid like horton
grid = MolGrid.from_size(nums,
coords[np.newaxis, :],
self.rgrid,
110,
BeckeWeights(),
store=True)
fn = np.exp(-4.0 * np.linalg.norm(grid.points, axis=-1))
assert_allclose(grid.integrate(fn), np.pi / 8)
localgrid = grid.get_localgrid(coords, 5.0)
localfn = np.exp(-4.0 * np.linalg.norm(localgrid.points, axis=-1))
assert localgrid.size < grid.size
assert localgrid.size == 9900
assert_allclose(localgrid.integrate(localfn), np.pi / 8, rtol=1e-5)
assert_allclose(fn[localgrid.indices], localfn)
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_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_hirshfeld_weights_single_1s(self):
"""Test molecular integral in H atom with Hirshfeld weights."""
pts = HortonLinear(100)
tf = ExpRTransform(1e-5, 2e1)
rgrid = tf.transform_1d_grid(pts)
coordinates = np.array([0.0, 0.0, -0.5])
atg1 = AtomGrid.from_pruned(
rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates,
)
mg = MolGrid([atg1], HirshfeldWeights(), np.array([7]))
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_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_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 = [
AtomGrid.from_pruned(
self.rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=center,
) for center in centers
]
becke = BeckeWeights(order=3)
mg = MolGrid(atgs, becke, 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_hirshfeld_weights_pair_1s(self):
"""Test molecular integral in H2."""
coordinates = np.array([[0.0, 0.0, -0.5], [0.0, 0.0, 0.5]])
atg1 = AtomGrid.from_pruned(
self.rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates[0],
)
atg2 = AtomGrid.from_pruned(
self.rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates[1],
)
mg = MolGrid([atg1, atg2], HirshfeldWeights(), np.array([1, 1]))
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 + 1.5 * np.exp(-2 * dist1) / np.pi
occupation = mg.integrate(fn)
assert_almost_equal(occupation, 2.5, decimal=5)
def test_integrate_hydrogen_pair_1s(self):
"""Test molecular integral in H2."""
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],
)
mg = MolGrid([atg1, atg2], np.array([1, 1]))
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, 2.0, decimal=6)
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 = AtomGrid.from_pruned(
self.rgrid,
0.5,
sectors_r=np.array([]),
sectors_degree=np.array([17]),
center=coordinates[0],
)
atg2 = AtomGrid.from_pruned(
self.rgrid,
0.5,
sectors_r=np.array([]),
sectors_degree=np.array([17]),
center=coordinates[1],
)
# use an array as aim_weights
mg = MolGrid(np.array([1, 1]), [atg1, atg2], np.ones(22000))
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_integrate_hydrogen_pair_1s(self):
"""Test molecular integral in H2."""
coordinates = np.array([[0.0, 0.0, -0.5], [0.0, 0.0, 0.5]], float)
atg1 = AtomGrid.from_pruned(
self.rgrid,
0.5,
sectors_r=np.array([]),
sectors_degree=np.array([17]),
center=coordinates[0],
)
atg2 = AtomGrid.from_pruned(
self.rgrid,
0.5,
sectors_r=np.array([]),
sectors_degree=np.array([17]),
center=coordinates[1],
)
becke = BeckeWeights(order=3)
mg = MolGrid(np.array([1, 1]), [atg1, atg2], becke)
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, 2.0, decimal=6)
ias = (s * len(indices[0][0]) * len(indices[1][0]) +
i_c * len(indices[1][s]) + a_c)
for t in range(2):
for j_c, j in enumerate(indices[0][t]):
for b_c, b in enumerate(indices[1][t]):
jbt = (t * len(indices[0][0]) * len(indices[1][0]) +
j_c * len(indices[1][t]) + b_c)
M_HF[ias][jbt] = (M_HF[ias][jbt] +
2 * two_electron_int[i, a, j, b])
M_LDA[ias][jbt] = (M_LDA[ias][jbt] +
2 * two_electron_int[i, a, j, b])
values = (f_xc_values[s + t] *
MO_values_conjugated[i] * MO_values[a] *
MO_values_conjugated[j] * MO_values[b])
M_LDA[ias][jbt] = M_LDA[ias][
jbt] + 2 * molgrid.integrate(values)
if s == t:
M_HF[ias][jbt] = (M_HF[ias][jbt] -
2 * two_electron_int[i, a, j, b])
if s == t and i == j and a == b:
M_HF[ias][jbt] = (M_HF[ias][jbt] +
molecule.mo.energies[a] -
molecule.mo.energies[i])
M_LDA[ias][jbt] = (M_LDA[ias][jbt] +
molecule.mo.energies[a] -
molecule.mo.energies[i])
M_HF_inv = np.linalg.inv(M_HF)
M_LDA_inv = np.linalg.inv(M_LDA)
def test_Alchemical_tools_density_matrix_variation():
def test_raise_errors(self):
"""Test molgrid errors raise."""
atg = AtomGrid.from_pruned(
self.rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=np.array([0.0, 0.0, 0.0]),
)
# errors of aim_weight
with self.assertRaises(TypeError):
MolGrid([atg], aim_weights="test", atom_nums=np.array([1]))
with self.assertRaises(ValueError):
MolGrid([atg], aim_weights=np.array(3), atom_nums=np.array([1]))
with self.assertRaises(TypeError):
MolGrid([atg], aim_weights=[3, 5], atom_nums=np.array([1]))
# integrate errors
becke = BeckeWeights({1: 0.472_431_53}, order=3)
molg = MolGrid([atg], becke, 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(ValueError):
molg.get_atomic_grid(-3)
molg = MolGrid([atg], becke, np.array([1]), store=True)
with self.assertRaises(ValueError):
molg.get_atomic_grid(-5)
# test make_grid error
pts = HortonLinear(70)
tf = ExpRTransform(1e-5, 2e1)
rgrid = tf.transform_1d_grid(pts)
numbers = np.array([1, 1])
becke = BeckeWeights(order=3)
# construct molgrid
with self.assertRaises(ValueError):
MolGrid.make_grid(numbers, np.array([0.0, 0.0, 0.0]), rgrid,
"fine", becke)
with self.assertRaises(ValueError):
MolGrid.make_grid(np.array([1, 1]), np.array([[0.0, 0.0, 0.0]]),
rgrid, "fine", becke)
with self.assertRaises(ValueError):
MolGrid.make_grid(np.array([1, 1]), np.array([[0.0, 0.0, 0.0]]),
rgrid, "fine", becke)
with self.assertRaises(TypeError):
MolGrid.make_grid(
np.array([1, 1]),
np.array([[0.0, 0.0, -0.5], [0.0, 0.0, 0.5]]),
{3, 5},
"fine",
becke,
)
with self.assertRaises(TypeError):
MolGrid.make_grid(
np.array([1, 1]),
np.array([[0.0, 0.0, -0.5], [0.0, 0.0, 0.5]]),
rgrid,
np.array([3, 5]),
becke,
)