def test_becke_sum3_one(self):
"""Test becke weights add up to one with three centers."""
npoint = 100
points = np.random.uniform(-5, 5, (npoint, 3))
weights0 = np.ones(npoint, float)
weights1 = np.ones(npoint, float)
weights2 = np.ones(npoint, float)
radii = np.array([0.5, 0.8, 5.0])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2],
[2.2, -1.5, 0.0]])
weights0 = BeckeWeights.generate_becke_weights(points,
radii,
centers,
select=[0],
order=3)
weights1 = BeckeWeights.generate_becke_weights(points,
radii,
centers,
select=[1],
order=3)
weights2 = BeckeWeights.generate_becke_weights(points,
radii,
centers,
select=[2],
order=3)
assert_allclose(weights0 + weights1 + weights2, np.ones(100))
def test_becke_sum2_one(self):
"""Test becke weights add up to one."""
npoint = 100
points = np.random.uniform(-5, 5, (npoint, 3))
nums = np.array([1, 2])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2]])
becke = BeckeWeights({1: 0.5, 2: 0.8}, order=3)
weights0 = becke.generate_weights(points, centers, nums, select=[0])
weights1 = becke.generate_weights(points, centers, nums, select=[1])
assert_allclose(weights0 + weights1, np.ones(100))
def test_noble_gas_radius(self):
"""Test np.nan value to be handled properly."""
noble_list = [2, 10, 18, 36, 54, 85, 86]
for i in noble_list:
nums = np.array([i, i - 1]) if i != 86 else np.array([i, i - 2])
centers = np.array([[0.5, 0.0, 0.0], [-0.5, 0.0, 0.0]])
pts = np.zeros((10, 3), dtype=float)
pts[:, 1:] += np.random.rand(10, 2)
becke = BeckeWeights(order=3)
wts = becke.generate_weights(pts, centers, nums, pt_ind=[0, 5, 10])
assert_allclose(wts, 0.5)
wts = becke.compute_weights(pts, centers, nums, pt_ind=[0, 5, 10])
assert_allclose(wts, 0.5)
def test_becke_special_points(self):
"""Test becke weights for special cases."""
nums = np.array([1, 2, 3])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2], [2.2, -1.5, 0.0]])
becke = BeckeWeights({1: 0.5, 2: 0.8, 3: 5.0}, order=3)
weights = becke.generate_weights(centers, centers, nums, select=0)
assert_allclose(weights, [1, 0, 0])
weights = becke.generate_weights(centers, centers, nums, select=1)
assert_allclose(weights, [0, 1, 0])
weights = becke.generate_weights(centers, centers, nums, select=2)
assert_allclose(weights, [0, 0, 1])
# each point in seperate sectors.
weights = becke.generate_weights(centers, centers, nums, pt_ind=[0, 1, 2, 3])
assert_allclose(weights, [1, 1, 1])
weights = becke.generate_weights(
centers, centers, nums, select=[0, 1], pt_ind=[0, 1, 3]
)
assert_allclose(weights, [1, 1, 0])
weights = becke.generate_weights(
centers, centers, nums, select=[2, 0], pt_ind=[0, 2, 3]
)
assert_allclose(weights, [0, 0, 0])
def test_from_size(self):
"""Test horton style grid."""
nums = np.array([1, 1])
coors = np.array([[0, 0, -0.5], [0, 0, 0.5]])
becke = BeckeWeights(order=3)
mol_grid = MolGrid.from_size(nums,
coors,
self.rgrid,
110,
becke,
rotate=False)
atg1 = AtomGrid.from_pruned(
self.rgrid,
0.5,
sectors_r=np.array([]),
sectors_degree=np.array([17]),
center=coors[0],
)
atg2 = AtomGrid.from_pruned(
self.rgrid,
0.5,
sectors_r=np.array([]),
sectors_degree=np.array([17]),
center=coors[1],
)
ref_grid = MolGrid(nums, [atg1, atg2], becke, store=True)
assert_allclose(ref_grid.points, mol_grid.points)
assert_allclose(ref_grid.weights, mol_grid.weights)
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_1s1s(self):
"""Test local grid for a molecule with one atom."""
nums = np.array([1, 3])
coords = np.array([[0.0, 0.0, -0.5], [0.0, 0.0, 0.5]])
grid = MolGrid.horton_molgrid(coords,
nums,
self.rgrid,
110,
BeckeWeights(),
store=True)
fn0 = np.exp(-4.0 * np.linalg.norm(grid.points - coords[0], axis=-1))
fn1 = np.exp(-8.0 * np.linalg.norm(grid.points - coords[1], axis=-1))
assert_allclose(grid.integrate(fn0), np.pi / 8, rtol=1e-5)
assert_allclose(grid.integrate(fn1), np.pi / 64)
# local grid centered on atom 0 to evaluate fn0
local0 = grid.get_localgrid(coords[0], 5.0)
assert local0.size < grid.size
localfn0 = np.exp(-4.0 *
np.linalg.norm(local0.points - coords[0], axis=-1))
assert_allclose(fn0[local0.indices], localfn0)
assert_allclose(local0.integrate(localfn0), np.pi / 8, rtol=1e-5)
# local grid centered on atom 1 to evaluate fn1
local1 = grid.get_localgrid(coords[1], 2.5)
assert local1.size < grid.size
localfn1 = np.exp(-8.0 *
np.linalg.norm(local1.points - coords[1], axis=-1))
assert_allclose(local1.integrate(localfn1), np.pi / 64, rtol=1e-6)
assert_allclose(fn1[local1.indices], localfn1)
# approximate the sum of fn0 and fn2 by combining results from local grids.
fnsum = np.zeros(grid.size)
fnsum[local0.indices] += localfn0
fnsum[local1.indices] += localfn1
assert_allclose(grid.integrate(fnsum),
np.pi * (1 / 8 + 1 / 64),
rtol=1e-5)
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_compute_weights(self):
"""Tes compute weights function."""
# generate random points
npoint = 50
points = np.random.uniform(-5, 5, (npoint, 3))
nums = np.array([1, 2, 3])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2],
[2.2, -1.5, 0.0]])
becke = BeckeWeights({1: 0.5, 2: 0.8, 3: 5.0}, order=3)
indices = [0, 13, 29, 50]
# compute with old generate_weights method
weights_ref = becke.generate_weights(points,
centers,
nums,
pt_ind=indices)
# compute with compute_weights
weights_compute = becke.compute_weights(points,
centers,
nums,
pt_ind=indices)
assert_allclose(weights_ref, weights_compute)
# compute with one selected atom weights
weights_ref2 = becke.generate_weights(points, centers, nums, select=1)
weights_compute2 = becke.compute_weights(points,
centers,
nums,
select=1)
assert_allclose(weights_ref2, weights_compute2)
def __init__(self, atomic_grids, radii, aim_weights="becke", store=False):
"""Initialize molgrid class.
Parameters
----------
atomic_grids : list[AtomicGrid]
list of atomic grid
radii : np.ndarray(N,)
Radii for each atom in the molecular grid
aim_weights : str or np.ndarray(K,), default to "becke"
Atoms in molecule weights. If str, certain function will be called
to compute aim_weights, if np.ndarray, it will be treated as the
aim_weights
"""
# initialize these attributes
self._coors = np.zeros((len(radii), 3))
self._indices = np.zeros(len(radii) + 1, dtype=int)
self._size = np.sum([atomgrid.size for atomgrid in atomic_grids])
self._points = np.zeros((self._size, 3))
self._weights = np.zeros(self._size)
self._atomic_grids = atomic_grids if store else None
for i, atom_grid in enumerate(atomic_grids):
self._coors[i] = atom_grid.center
self._indices[i + 1] += self._indices[i] + atom_grid.size
self._points[self._indices[i] : self._indices[i + 1]] = atom_grid.points
self._weights[self._indices[i] : self._indices[i + 1]] = atom_grid.weights
if isinstance(aim_weights, str):
if aim_weights == "becke":
self._aim_weights = BeckeWeights.generate_becke_weights(
self._points, radii, self._coors, pt_ind=self._indices
)
else:
raise NotImplementedError(
f"Given aim_weights is not supported, got {aim_weights}"
)
elif isinstance(aim_weights, np.ndarray):
if aim_weights.size != self.size:
raise ValueError(
"aim_weights is not the same size as grid.\n"
f"aim_weights.size: {aim_weights.size}, grid.size: {self.size}."
)
self._aim_weights = aim_weights
else:
raise TypeError(f"Not supported aim_weights type, got {type(aim_weights)}.")
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 = AtomGrid.from_pruned(
self.rgrid,
1.228,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates[0],
)
atg2 = AtomGrid.from_pruned(
self.rgrid,
0.945,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates[1],
)
becke = BeckeWeights(order=3)
mg = MolGrid([atg1, atg2], becke, 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_atomic_grid(0)
simple_ag2 = mg.get_atomic_grid(1)
assert_allclose(simple_ag1.points, atg1.points)
assert_allclose(simple_ag1.weights, atg1.weights)
assert_allclose(simple_ag2.weights, atg2.weights)
# test molgrid is not stored
mg2 = MolGrid([atg1, atg2], becke, np.array([6, 8]), store=False)
assert mg2._atomic_grids is None
simple2_ag1 = mg2.get_atomic_grid(0)
simple2_ag2 = mg2.get_atomic_grid(1)
assert isinstance(simple2_ag1, LocalGrid)
assert isinstance(simple2_ag2, LocalGrid)
assert_allclose(simple2_ag1.points, atg1.points)
assert_allclose(simple2_ag1.weights, atg1.weights)
assert_allclose(simple2_ag2.weights, atg2.weights)
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 = AtomGrid.from_pruned(
self.rgrid,
1.228,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates[0],
)
atg2 = AtomGrid.from_pruned(
self.rgrid,
0.945,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates[1],
)
becke = BeckeWeights(order=3)
mg = MolGrid([atg1, atg2], becke, 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, AtomGrid)
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], becke, np.array([6, 8]))
for i in range(2):
atgrid = mg[i]
assert isinstance(atgrid, LocalGrid)
assert_allclose(atgrid.center, mg._coors[i])
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 = AtomGrid.from_pruned(
self.rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=coordinates,
)
becke = BeckeWeights(order=3)
mg = MolGrid([atg1], becke, 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_becke_special_points(self):
"""Test becke weights for special cases."""
radii = np.array([0.5, 0.8, 5.0])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2],
[2.2, -1.5, 0.0]])
weights = BeckeWeights.generate_becke_weights(centers,
radii,
centers,
select=[0],
order=3)
assert_allclose(weights, [1, 0, 0])
weights = BeckeWeights.generate_becke_weights(centers,
radii,
centers,
select=[1],
order=3)
assert_allclose(weights, [0, 1, 0])
weights = BeckeWeights.generate_becke_weights(centers,
radii,
centers,
select=[2],
order=3)
assert_allclose(weights, [0, 0, 1])
# each point in seperate sectors.
weights = BeckeWeights.generate_becke_weights(centers,
radii,
centers,
pt_ind=[0, 1, 2, 3])
assert_allclose(weights, [1, 1, 1])
weights = BeckeWeights.generate_becke_weights(centers,
radii,
centers,
select=[0, 1],
pt_ind=[0, 1, 3])
assert_allclose(weights, [1, 1, 0])
weights = BeckeWeights.generate_becke_weights(centers,
radii,
centers,
select=[2, 0],
pt_ind=[0, 2, 3])
assert_allclose(weights, [0, 0, 0])
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_horton_molgrid(self):
"""Test horton style grid."""
nums = np.array([1, 1])
coors = np.array([[0, 0, -0.5], [0, 0, 0.5]])
becke = BeckeWeights(order=3)
mol_grid = MolGrid.horton_molgrid(coors, nums, self.rgrid, 110, becke)
atg1 = AtomGrid.from_pruned(
self.rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=coors[0],
)
atg2 = AtomGrid.from_pruned(
self.rgrid,
0.5,
r_sectors=np.array([]),
degs=np.array([17]),
center=coors[1],
)
ref_grid = MolGrid([atg1, atg2], becke, nums, store=True)
assert_allclose(ref_grid.points, mol_grid.points)
assert_allclose(ref_grid.weights, mol_grid.weights)
def test_make_grid_integral(self):
"""Test molecular make_grid works as designed."""
pts = HortonLinear(70)
tf = ExpRTransform(1e-5, 2e1)
rgrid = tf.transform_1d_grid(pts)
numbers = np.array([1, 1])
coordinates = np.array([[0.0, 0.0, -0.5], [0.0, 0.0, 0.5]], float)
becke = BeckeWeights(order=3)
# construct molgrid
for grid_type, deci in (
("coarse", 3),
("medium", 4),
("fine", 5),
("veryfine", 6),
("ultrafine", 6),
("insane", 6),
):
mg = MolGrid.from_preset(numbers, coordinates, rgrid, grid_type, 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=deci)
def test_becke_compute_atom_weight(self):
"""Test becke compute pa function."""
npoint = 10
points = np.random.uniform(-5, 5, (npoint, 3))
nums = np.array([1, 2, 3])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2], [2.2, -1.5, 0.0]])
becke = BeckeWeights({1: 0.5, 2: 0.8, 3: 5.0}, order=3)
weights0 = becke.generate_weights(points, centers, nums, select=[0])
weights1 = becke.generate_weights(points, centers, nums, select=[1])
weights2 = becke.generate_weights(points, centers, nums, select=[2])
aw_0 = becke.compute_atom_weight(points, centers, nums, 0)
aw_1 = becke.compute_atom_weight(points, centers, nums, 1)
aw_2 = becke.compute_atom_weight(points, centers, nums, 2)
assert_allclose(weights0, aw_0)
assert_allclose(weights1, aw_1)
assert_allclose(weights2, aw_2)
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)
def test_make_grid_different_grid_type(self):
"""Test different kind molgrid initizalize setting."""
# three different radial grid
rad2 = GaussLaguerre(50)
rad3 = GaussLaguerre(70)
# construct grid
numbers = np.array([1, 8, 1])
coordinates = np.array(
[[0.0, 0.0, -0.5], [0.0, 0.0, 0.5], [0.0, 0.5, 0.0]], float)
becke = BeckeWeights(order=3)
# grid_type test with list
mg = MolGrid.make_grid(
numbers,
coordinates,
rad2,
["fine", "veryfine", "medium"],
becke,
store=True,
)
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.exp(-2 * dist1) +
np.exp(-2 * dist2)) / np.pi
occupation = mg.integrate(fn)
assert_almost_equal(occupation, 3, decimal=3)
atgrid1 = AtomGrid.from_predefined(numbers[0],
rad2,
"fine",
center=coordinates[0])
atgrid2 = AtomGrid.from_predefined(numbers[1],
rad2,
"veryfine",
center=coordinates[1])
atgrid3 = AtomGrid.from_predefined(numbers[2],
rad2,
"medium",
center=coordinates[2])
assert_allclose(mg._atomic_grids[0].points, atgrid1.points)
assert_allclose(mg._atomic_grids[1].points, atgrid2.points)
assert_allclose(mg._atomic_grids[2].points, atgrid3.points)
# grid type test with dict
mg = MolGrid.make_grid(numbers,
coordinates,
rad3, {
1: "fine",
8: "veryfine"
},
becke,
store=True)
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.exp(-2 * dist1) +
np.exp(-2 * dist2)) / np.pi
occupation = mg.integrate(fn)
assert_almost_equal(occupation, 3, decimal=3)
atgrid1 = AtomGrid.from_predefined(numbers[0],
rad3,
"fine",
center=coordinates[0])
atgrid2 = AtomGrid.from_predefined(numbers[1],
rad3,
"veryfine",
center=coordinates[1])
atgrid3 = AtomGrid.from_predefined(numbers[2],
rad3,
"fine",
center=coordinates[2])
assert_allclose(mg._atomic_grids[0].points, atgrid1.points)
assert_allclose(mg._atomic_grids[1].points, atgrid2.points)
assert_allclose(mg._atomic_grids[2].points, atgrid3.points)
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,
)
def __init__(self,
atomic_grids,
numbers,
aim_weights="becke",
store=False):
"""Initialize molgrid class.
Parameters
----------
atomic_grids : list[AtomicGrid]
list of atomic grid
radii : np.ndarray(N,)
Radii for each atom in the molecular grid
aim_weights : str or np.ndarray(K,), default to "becke"
Atoms in molecule weights. If str, certain function will be called
to compute aim_weights, if np.ndarray, it will be treated as the
aim_weights
"""
# initialize these attributes
numbers = np.array(numbers)
radii = get_cov_radii(numbers)
self._coors = np.zeros((len(radii), 3))
self._indices = np.zeros(len(radii) + 1, dtype=int)
self._size = np.sum([atomgrid.size for atomgrid in atomic_grids])
self._points = np.zeros((self._size, 3))
self._weights = np.zeros(self._size)
self._atomic_grids = atomic_grids if store else None
for i, atom_grid in enumerate(atomic_grids):
self._coors[i] = atom_grid.center
self._indices[i + 1] += self._indices[i] + atom_grid.size
self._points[self._indices[i]:self._indices[i +
1]] = atom_grid.points
self._weights[self._indices[i]:self.
_indices[i + 1]] = atom_grid.weights
if isinstance(aim_weights, str):
if aim_weights == "becke":
# Becke weights are computed for "chunks" of grid points
# to counteract the scaling of the memory usage of the
# vectorized implementation of the Becke partitioning.
chunk_size = max(1,
(10 * self._size) // self._coors.shape[0]**2)
self._aim_weights = np.concatenate([
BeckeWeights.generate_becke_weights(
self._points[ibegin:ibegin + chunk_size],
radii,
self._coors,
pt_ind=(self._indices - ibegin).clip(min=0),
) for ibegin in range(0, self._size, chunk_size)
])
else:
raise NotImplementedError(
f"Given aim_weights is not supported, got {aim_weights}")
elif isinstance(aim_weights, np.ndarray):
if aim_weights.size != self.size:
raise ValueError(
"aim_weights is not the same size as grid.\n"
f"aim_weights.size: {aim_weights.size}, grid.size: {self.size}."
)
self._aim_weights = aim_weights
else:
raise TypeError(
f"Not supported aim_weights type, got {type(aim_weights)}.")
def test_make_grid_different_rad_type(self):
"""Test different radial grid input for make molgrid."""
# radial grid test with list
rad1 = GaussLaguerre(30)
rad2 = GaussLaguerre(50)
rad3 = GaussLaguerre(70)
# construct grid
numbers = np.array([1, 8, 1])
coordinates = np.array(
[[0.0, 0.0, -0.5], [0.0, 0.0, 0.5], [0.0, 0.5, 0.0]], float
)
becke = BeckeWeights(order=3)
# construct molgrid
mg = MolGrid.from_preset(
numbers,
coordinates,
[rad1, rad2, rad3],
{1: "fine", 8: "veryfine"},
becke,
store=True,
rotate=False,
)
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.exp(-2 * dist1) + np.exp(-2 * dist2)) / np.pi
occupation = mg.integrate(fn)
assert_almost_equal(occupation, 3, decimal=3)
atgrid1 = AtomGrid.from_preset(
rad1, atnum=numbers[0], preset="fine", center=coordinates[0]
)
atgrid2 = AtomGrid.from_preset(
rad2, atnum=numbers[1], preset="veryfine", center=coordinates[1]
)
atgrid3 = AtomGrid.from_preset(
rad3, atnum=numbers[2], preset="fine", center=coordinates[2]
)
assert_allclose(mg._atgrids[0].points, atgrid1.points)
assert_allclose(mg._atgrids[1].points, atgrid2.points)
assert_allclose(mg._atgrids[2].points, atgrid3.points)
# radial grid test with dict
mg = MolGrid.from_preset(
numbers,
coordinates,
{1: rad1, 8: rad3},
{1: "fine", 8: "veryfine"},
becke,
store=True,
rotate=False,
)
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.exp(-2 * dist1) + np.exp(-2 * dist2)) / np.pi
occupation = mg.integrate(fn)
assert_almost_equal(occupation, 3, decimal=3)
atgrid1 = AtomGrid.from_preset(
rad1, atnum=numbers[0], preset="fine", center=coordinates[0]
)
atgrid2 = AtomGrid.from_preset(
rad3, atnum=numbers[1], preset="veryfine", center=coordinates[1]
)
atgrid3 = AtomGrid.from_preset(
rad1, atnum=numbers[2], preset="fine", center=coordinates[2]
)
assert_allclose(mg._atgrids[0].points, atgrid1.points)
assert_allclose(mg._atgrids[1].points, atgrid2.points)
assert_allclose(mg._atgrids[2].points, atgrid3.points)
def test_raise_errors(self):
"""Test errors raise."""
npoint = 100
points = np.random.uniform(-5, 5, (npoint, 3))
nums = np.array([1, 2])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2]])
# error of select and pt_ind
becke = BeckeWeights({1: 0.5, 2: 0.8})
with self.assertRaises(ValueError):
becke.generate_weights(points, centers, nums, select=[])
with self.assertRaises(ValueError):
becke.generate_weights(points, centers, nums, pt_ind=[3])
with self.assertRaises(ValueError):
becke.generate_weights(points, centers, nums, pt_ind=[3, 6])
with self.assertRaises(ValueError):
becke.generate_weights(points, centers, nums, select=[], pt_ind=[])
with self.assertRaises(ValueError):
becke.generate_weights(points,
centers,
nums,
select=[0, 1],
pt_ind=[0, 10, 50, 99])
with self.assertRaises(ValueError):
becke.compute_weights(points, centers, nums, select=[])
with self.assertRaises(ValueError):
becke.compute_weights(points, centers, nums, pt_ind=[3])
with self.assertRaises(ValueError):
becke.compute_weights(points, centers, nums, pt_ind=[3, 6])
with self.assertRaises(ValueError):
becke.compute_weights(points, centers, nums, select=[], pt_ind=[])
with self.assertRaises(ValueError):
becke.compute_weights(points,
centers,
nums,
select=[0, 1],
pt_ind=[0, 10, 50, 99])
# error of order
with self.assertRaises(ValueError):
BeckeWeights({1: 0.5, 2: 0.8}, order=3.0)
# error of radii
with self.assertRaises(TypeError):
BeckeWeights({1.0: 0.5, 2: 0.8}, order=3)
with self.assertRaises(TypeError):
BeckeWeights(np.array([0.5, 0.8]), order=3)
def test_raise_errors(self):
"""Test errors raise."""
npoint = 100
points = np.random.uniform(-5, 5, (npoint, 3))
radii = np.array([0.5, 0.8])
centers = np.array([[1.2, 2.3, 0.1], [-0.4, 0.0, -2.2]])
with self.assertRaises(ValueError):
BeckeWeights.generate_becke_weights(points,
radii,
centers,
select=[])
with self.assertRaises(ValueError):
BeckeWeights.generate_becke_weights(points,
radii,
centers,
pt_ind=[3])
with self.assertRaises(ValueError):
BeckeWeights.generate_becke_weights(points,
radii,
centers,
pt_ind=[3, 6])
with self.assertRaises(ValueError):
BeckeWeights.generate_becke_weights(points,
radii,
centers,
select=[],
pt_ind=[])
with self.assertRaises(ValueError):
BeckeWeights.generate_becke_weights(points,
radii,
centers,
select=[0, 1],
pt_ind=[0, 10, 50, 99])
with self.assertRaises(ValueError):
BeckeWeights.generate_becke_weights(points,
radii,
centers[0],
select=[0, 1],
pt_ind=[0, 10, 50, 99])
