def test_errors_raise(self):
"""Test errors raise."""
# grid init
with self.assertRaises(ValueError):
Grid(self._ref_points, np.ones(len(self._ref_weights) + 1))
with self.assertRaises(ValueError):
Grid(self._ref_points.reshape(self.grid.size, 1, 1),
self._ref_weights)
with self.assertRaises(ValueError):
Grid(self._ref_points, self._ref_weights.reshape(-1, 1))
# integral
with self.assertRaises(ValueError):
self.grid.integrate()
with self.assertRaises(TypeError):
self.grid.integrate(5)
if self._ref_points.ndim == 2:
with self.assertRaises(ValueError):
self.grid.integrate(self._ref_points)
# get_localgrid
with self.assertRaises(ValueError):
self.grid.get_localgrid(self._ref_points[0], -1)
with self.assertRaises(ValueError):
self.grid.get_localgrid(self._ref_points[0], -np.inf)
with self.assertRaises(ValueError):
self.grid.get_localgrid(self._ref_points[0], np.nan)
if self._ref_points.ndim == 2:
with self.assertRaises(ValueError):
self.grid.get_localgrid(
np.zeros(self._ref_points.shape[1] + 1), 5.0)
else:
with self.assertRaises(ValueError):
self.grid.get_localgrid(np.zeros(2), 5.0)
def test_get_localgrid_small_radius(self):
"""Basic checks for the get_localgrid method.
In this unit test, the cutoff sphere fits inside a primitive cell, such
that each grid point from the parent periodic grid will at most appear
once in the local grid.
"""
center = self.grid.points[3]
radius = 0.19475
# Check that the sphere fits inside the primitive cell:
assert (2 * radius < self.grid.spacings).all()
# Build local grids.
localgrids = [
self.grid.get_localgrid(center, radius),
self.wrapped_grid.get_localgrid(center, radius),
]
# When there are no lattice vectors, the local grid from the base class
# should also be the same.
if self._ref_realvecs is None:
aperiodic_grid = Grid(self._ref_points, self._ref_weights)
localgrids.append(aperiodic_grid.get_localgrid(center, radius))
# One should get the same local grid with or without wrapping, possibly
# with a different ordering of the points. We can perform a relatively
# simple check here because each point appears at most once.
order0 = localgrids[0].indices.argsort()
for localgrid in localgrids[1:]:
assert_allclose(localgrids[0].center, localgrid.center)
order = localgrid.indices.argsort()
assert_allclose(localgrids[0].points[order0],
localgrid.points[order])
assert_allclose(localgrids[0].weights[order0],
localgrid.weights[order])
# Other sanity checks on the grids.
for localgrid in localgrids:
# Just make sure we are testing with an actual local grid with at least
# some points.
assert localgrid.size > 0
assert localgrid.size <= self.grid.size
assert len(localgrid.indices) == len(set(localgrid.indices))
# Test that the localgrid contains sensible results.
assert_allclose(localgrid.center, center)
assert localgrid.points.ndim == self.grid.points.ndim
assert localgrid.weights.ndim == self.grid.weights.ndim
if self._ref_points.ndim == 2:
assert (np.linalg.norm(localgrid.points - center, axis=1) <=
radius).all()
else:
assert (abs(localgrid.points - center) <= radius).all()
def test_getitem(self):
"""Test Grid index and slicing."""
# test index
grid_index = self.grid[10]
ref_grid = Grid(np.array([0]), np.array([0.1]))
assert_allclose(grid_index.points, ref_grid.points)
assert_allclose(grid_index.weights, ref_grid.weights)
assert isinstance(grid_index, Grid)
# test slice
ref_grid_slice = Grid(np.linspace(-1, 0, 11), np.ones(11) * 0.1)
grid_slice = self.grid[:11]
assert_allclose(grid_slice.points, ref_grid_slice.points)
assert_allclose(grid_slice.weights, ref_grid_slice.weights)
assert isinstance(grid_slice, Grid)
a = np.array([1, 3, 5])
ref_smt_index = self.grid[a]
assert_allclose(ref_smt_index.points, np.array([-0.9, -0.7, -0.5]))
assert_allclose(ref_smt_index.weights, np.array([0.1, 0.1, 0.1]))
def test_error_raises(self):
"""Tests for error raises."""
with self.assertRaises(TypeError):
AtomGrid.from_pruned(np.arange(3),
1.0,
r_sectors=np.arange(2),
degs=np.arange(3))
with self.assertRaises(ValueError):
AtomGrid.from_pruned(
OneDGrid(np.arange(3), np.arange(3)),
radius=1.0,
r_sectors=np.arange(2),
degs=np.arange(0),
)
with self.assertRaises(ValueError):
AtomGrid.from_pruned(
OneDGrid(np.arange(3), np.arange(3)),
radius=1.0,
r_sectors=np.arange(2),
degs=np.arange(4),
)
with self.assertRaises(ValueError):
AtomGrid._generate_atomic_grid(
OneDGrid(np.arange(3), np.arange(3)), np.arange(2))
with self.assertRaises(ValueError):
AtomGrid.from_pruned(
OneDGrid(np.arange(3), np.arange(3)),
radius=1.0,
r_sectors=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):
AtomGrid(OneDGrid(np.arange(3), np.arange(3)), size=110)
with self.assertRaises(TypeError):
AtomGrid(OneDGrid(np.arange(3), np.arange(3)), degs=17)
with self.assertRaises(ValueError):
AtomGrid(OneDGrid(np.arange(3), np.arange(3)),
degs=[17],
rotate=-1)
with self.assertRaises(TypeError):
AtomGrid(OneDGrid(np.arange(3), np.arange(3)),
degs=[17],
rotate="asdfaf")
# error of radial grid
with self.assertRaises(TypeError):
AtomGrid(Grid(np.arange(1, 5, 1), np.ones(4)), degs=[2, 3, 4, 5])
with self.assertRaises(TypeError):
AtomGrid(OneDGrid(np.arange(-2, 2, 1), np.ones(4)),
degs=[2, 3, 4, 5])
with self.assertRaises(TypeError):
rgrid = OneDGrid(np.arange(1, 3, 1), np.ones(2), domain=(-1, 5))
AtomGrid(rgrid, degs=[2])
with self.assertRaises(TypeError):
rgrid = OneDGrid(np.arange(-1, 1, 1), np.ones(2))
AtomGrid(rgrid, degs=[2])
def test_getitem(self):
"""Test Grid index and slicing."""
# test index
grid_index = self.grid[10]
ref_grid = Grid(self._ref_points[10:11], self._ref_weights[10:11])
assert_allclose(grid_index.points, ref_grid.points)
assert_allclose(grid_index.weights, ref_grid.weights)
assert isinstance(grid_index, Grid)
# test slice
ref_grid_slice = Grid(self._ref_points[:11], self._ref_weights[:11])
grid_slice = self.grid[:11]
assert_allclose(grid_slice.points, ref_grid_slice.points)
assert_allclose(grid_slice.weights, ref_grid_slice.weights)
assert isinstance(grid_slice, Grid)
a = np.array([1, 3, 5])
ref_smt_index = self.grid[a]
assert_allclose(ref_smt_index.points, self._ref_points[a])
assert_allclose(ref_smt_index.weights, self._ref_weights[a])
def test_get_localgrid_large_radius(self):
"""Basic checks for the get_localgrid method.
In this unit test, the cutoff sphere fits inside a primitive cell, such
that each grid point from the parent periodic grid will at most appear
once in the local grid.
"""
center = self.grid.points[3]
radius = 2.51235
# Check that the sphere flows over the primitive cell, when there are
# some lattice vectors.
if self._ref_realvecs is not None:
assert (2 * radius > self.grid.spacings).any()
# Build local grids.
localgrids = [
self.grid.get_localgrid(center, radius),
self.wrapped_grid.get_localgrid(center, radius),
]
# When there are no lattice vectors, the local grid from the base class
# should also be the same.
if self._ref_realvecs is None:
aperiodic_grid = Grid(self._ref_points, self._ref_weights)
localgrids.append(aperiodic_grid.get_localgrid(center, radius))
# One should get the same local grid with or without wrapping, possibly
# with a different ordering of the points.
for localgrid in localgrids[1:]:
assert_equal_localgrids(localgrids[0], localgrid)
# Other sanity checks.
for localgrid in localgrids:
# With a large radius there will never be less points in the local grid.
if self._ref_realvecs is None:
assert localgrid.size == self.grid.size
else:
assert localgrid.size > self.grid.size
# Test that the local grid contains sensible results.
assert_allclose(localgrid.center, center)
assert localgrid.points.ndim == self.grid.points.ndim
assert localgrid.weights.ndim == self.grid.weights.ndim
if self._ref_points.ndim == 2:
assert (
np.linalg.norm(localgrid.points - center, axis=1) <= radius
).all()
else:
assert (abs(localgrid.points - center) <= radius).all()
def test_find_l_for_rad_list(self):
"""Test private method find_l_for_rad_list."""
radial_pts = np.arange(0.1, 1.1, 0.1)
radial_wts = np.ones(10) * 0.1
radial_grid = Grid(radial_pts, radial_wts)
atomic_rad = 1
scales = np.array([0.2, 0.4, 0.8])
degs = np.array([3, 5, 7, 3])
atomic_grid_degree = AtomicGrid._find_l_for_rad_list(
radial_grid.points, atomic_rad, scales, degs)
assert_equal(atomic_grid_degree, [3, 3, 5, 5, 7, 7, 7, 7, 3, 3])
def test_error_raises(self):
"""Tests for error raises."""
with self.assertRaises(TypeError):
AtomicGrid(np.arange(3),
1.0,
scales=np.arange(2),
degs=np.arange(3))
with self.assertRaises(ValueError):
AtomicGrid(
Grid(np.arange(3), np.arange(3)),
1.0,
scales=np.arange(2),
degs=np.arange(0),
)
with self.assertRaises(ValueError):
AtomicGrid(
Grid(np.arange(3), np.arange(3)),
1.0,
scales=np.arange(2),
degs=np.arange(4),
)
with self.assertRaises(ValueError):
AtomicGrid._generate_atomic_grid(Grid(np.arange(3), np.arange(3)),
np.arange(2), np.array([0, 0, 0]))
with self.assertRaises(TypeError):
AtomicGrid(
Grid(np.arange(3), np.arange(3)),
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(
Grid(np.arange(3), np.arange(3)),
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]),
)
def test_errors_raise(self):
"""Test errors raise."""
# grid init
weights = np.ones(4)
points = np.arange(5)
with self.assertRaises(ValueError):
Grid(points, weights)
# integral
with self.assertRaises(ValueError):
self.grid.integrate()
with self.assertRaises(TypeError):
self.grid.integrate(5)
with self.assertRaises(ValueError):
self.grid.integrate(points)
def test_atomic_grid(center):
"""Test atomic grid center transilation."""
rad_pts = np.array([0.1, 0.5, 1])
rad_wts = np.array([0.3, 0.4, 0.3])
rad_grid = Grid(rad_pts, rad_wts)
degs = np.array([3, 5, 7])
# origin center
center = np.array([0, 0, 0])
# randome center
ref_center = np.random.rand(3)
pts, wts, ind = AtomicGrid._generate_atomic_grid(
rad_grid, degs, center)
ref_pts, ref_wts, ref_ind = AtomicGrid._generate_atomic_grid(
rad_grid, degs, ref_center)
# diff grid points diff by center and same weights
assert_allclose(pts, ref_pts)
assert_allclose(wts, ref_wts)
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 = Grid(radial_pts, radial_wts)
atomic_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(radial_grid, atomic_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(radial_grid,
atomic_rad,
scales=np.array([]),
degs=np.array([6]))
assert isinstance(ag_ob, AtomicGrid)
assert len(ag_ob.indices) == 11
def test_generate_atomic_grid(self):
"""Test for generating atomic grid."""
# setup testing class
rad_pts = np.array([0.1, 0.5, 1])
rad_wts = np.array([0.3, 0.4, 0.3])
rad_grid = Grid(rad_pts, rad_wts)
degs = np.array([3, 5, 7])
center = np.array([0, 0, 0])
pts, wts, ind = AtomicGrid._generate_atomic_grid(
rad_grid, degs, center)
assert len(pts) == 46
assert_equal(ind, [0, 6, 20, 46])
# set tests for slicing grid from atomic grid
for i in range(3):
# set each layer of points
ref_grid = generate_lebedev_grid(degree=degs[i])
# check for each point
assert_allclose(pts[ind[i]:ind[i + 1]],
ref_grid.points * rad_pts[i])
# check for each weight
assert_allclose(
wts[ind[i]:ind[i + 1]],
ref_grid.weights * rad_wts[i] * rad_pts[i]**2,
)
def setUp(self):
"""Test setup function."""
points = np.linspace(-1, 1, 21)
weights = np.ones(21) * 0.1
self.grid = Grid(points, weights)
class TestGrid(TestCase):
"""Grid testcase class."""
def setUp(self):
"""Test setup function."""
points = np.linspace(-1, 1, 21)
weights = np.ones(21) * 0.1
self.grid = Grid(points, weights)
def test_init_grid(self):
"""Test Grid init."""
# tests property
assert isinstance(self.grid, Grid)
ref_pts = np.arange(-1, 1.1, 0.1)
ref_wts = np.ones(21) * 0.1
assert_allclose(self.grid.points, ref_pts, atol=1e-7)
assert_allclose(self.grid.weights, ref_wts)
assert self.grid.size == 21
def test_integrate(self):
"""Test Grid integral."""
# integral test1
result2 = self.grid.integrate(np.ones(21))
assert_allclose(result2, 2.1)
# integral test2
value1 = np.linspace(-1, 1, 21)
value2 = value1**2
result3 = self.grid.integrate(value1, value2)
assert_allclose(result3, 0, atol=1e-7)
def test_getitem(self):
"""Test Grid index and slicing."""
# test index
grid_index = self.grid[10]
ref_grid = Grid(np.array([0]), np.array([0.1]))
assert_allclose(grid_index.points, ref_grid.points)
assert_allclose(grid_index.weights, ref_grid.weights)
assert isinstance(grid_index, Grid)
# test slice
ref_grid_slice = Grid(np.linspace(-1, 0, 11), np.ones(11) * 0.1)
grid_slice = self.grid[:11]
assert_allclose(grid_slice.points, ref_grid_slice.points)
assert_allclose(grid_slice.weights, ref_grid_slice.weights)
assert isinstance(grid_slice, Grid)
a = np.array([1, 3, 5])
ref_smt_index = self.grid[a]
assert_allclose(ref_smt_index.points, np.array([-0.9, -0.7, -0.5]))
assert_allclose(ref_smt_index.weights, np.array([0.1, 0.1, 0.1]))
def test_errors_raise(self):
"""Test errors raise."""
# grid init
weights = np.ones(4)
points = np.arange(5)
with self.assertRaises(ValueError):
Grid(points, weights)
# integral
with self.assertRaises(ValueError):
self.grid.integrate()
with self.assertRaises(TypeError):
self.grid.integrate(5)
with self.assertRaises(ValueError):
self.grid.integrate(points)
class TestGrid(TestCase):
"""Grid testcase class."""
def setUp(self):
"""Test setup function."""
self._ref_points = np.linspace(-1, 1, 21)
self._ref_weights = np.ones(21) * 0.1
self.grid = Grid(self._ref_points, self._ref_weights)
def test_init_grid(self):
"""Test Grid init."""
# tests property
assert isinstance(self.grid, Grid)
assert_allclose(self.grid.points, self._ref_points, atol=1e-7)
assert_allclose(self.grid.weights, self._ref_weights)
assert self.grid.size == self._ref_weights.size
def test_integrate(self):
"""Test Grid integral."""
# integral test1
result2 = self.grid.integrate(np.ones(21))
assert_allclose(result2, 2.1)
# integral test2
value1 = np.linspace(-1, 1, 21)
value2 = value1**2
result3 = self.grid.integrate(value1, value2)
assert_allclose(result3, 0, atol=1e-7)
def test_getitem(self):
"""Test Grid index and slicing."""
# test index
grid_index = self.grid[10]
ref_grid = Grid(self._ref_points[10:11], self._ref_weights[10:11])
assert_allclose(grid_index.points, ref_grid.points)
assert_allclose(grid_index.weights, ref_grid.weights)
assert isinstance(grid_index, Grid)
# test slice
ref_grid_slice = Grid(self._ref_points[:11], self._ref_weights[:11])
grid_slice = self.grid[:11]
assert_allclose(grid_slice.points, ref_grid_slice.points)
assert_allclose(grid_slice.weights, ref_grid_slice.weights)
assert isinstance(grid_slice, Grid)
a = np.array([1, 3, 5])
ref_smt_index = self.grid[a]
assert_allclose(ref_smt_index.points, self._ref_points[a])
assert_allclose(ref_smt_index.weights, self._ref_weights[a])
def test_get_localgrid(self):
"""Test the creation of the local grid with a normal radius."""
center = self.grid.points[3]
radius = 0.2
localgrid = self.grid.get_localgrid(center, radius)
# Just make sure we are testing with an actual local grid with less (but
# not zero) points.
assert localgrid.size > 0
assert localgrid.size < self.grid.size
# Test that the local grid contains the correct results.
assert localgrid.points.ndim == self.grid.points.ndim
assert localgrid.weights.ndim == self.grid.weights.ndim
assert_allclose(localgrid.points, self.grid.points[localgrid.indices])
assert_allclose(localgrid.weights,
self.grid.weights[localgrid.indices])
if self._ref_points.ndim == 2:
assert (np.linalg.norm(localgrid.points - center, axis=1) <=
radius).all()
else:
assert (abs(localgrid.points - center) <= radius).all()
def test_get_localgrid_radius_inf(self):
"""Test the creation of the local grid with an infinite radius."""
localgrid = self.grid.get_localgrid(self.grid.points[3], np.inf)
# Just make sure we are testing with a real local grid
assert localgrid.size == self.grid.size
assert_allclose(localgrid.points, self.grid.points)
assert_allclose(localgrid.weights, self.grid.weights)
assert_allclose(localgrid.indices, np.arange(self.grid.size))
def test_errors_raise(self):
"""Test errors raise."""
# grid init
with self.assertRaises(ValueError):
Grid(self._ref_points, np.ones(len(self._ref_weights) + 1))
with self.assertRaises(ValueError):
Grid(self._ref_points.reshape(self.grid.size, 1, 1),
self._ref_weights)
with self.assertRaises(ValueError):
Grid(self._ref_points, self._ref_weights.reshape(-1, 1))
# integral
with self.assertRaises(ValueError):
self.grid.integrate()
with self.assertRaises(TypeError):
self.grid.integrate(5)
if self._ref_points.ndim == 2:
with self.assertRaises(ValueError):
self.grid.integrate(self._ref_points)
# get_localgrid
with self.assertRaises(ValueError):
self.grid.get_localgrid(self._ref_points[0], -1)
with self.assertRaises(ValueError):
self.grid.get_localgrid(self._ref_points[0], -np.inf)
with self.assertRaises(ValueError):
self.grid.get_localgrid(self._ref_points[0], np.nan)
if self._ref_points.ndim == 2:
with self.assertRaises(ValueError):
self.grid.get_localgrid(
np.zeros(self._ref_points.shape[1] + 1), 5.0)
else:
with self.assertRaises(ValueError):
self.grid.get_localgrid(np.zeros(2), 5.0)
def test_error_raises(self):
"""Tests for error raises."""
with self.assertRaises(TypeError):
AtomGrid.from_pruned(np.arange(3),
1.0,
sectors_r=np.arange(2),
sectors_degree=np.arange(3))
with self.assertRaises(ValueError):
AtomGrid.from_pruned(
OneDGrid(np.arange(3), np.arange(3)),
radius=1.0,
sectors_r=np.arange(2),
sectors_degree=np.arange(0),
)
with self.assertRaises(ValueError):
AtomGrid.from_pruned(
OneDGrid(np.arange(3), np.arange(3)),
radius=1.0,
sectors_r=np.arange(2),
sectors_degree=np.arange(4),
)
with self.assertRaises(ValueError):
AtomGrid._generate_atomic_grid(
OneDGrid(np.arange(3), np.arange(3)), np.arange(2))
with self.assertRaises(ValueError):
AtomGrid.from_pruned(
OneDGrid(np.arange(3), np.arange(3)),
radius=1.0,
sectors_r=np.array([0.3, 0.5, 0.7]),
sectors_degree=np.array([3, 5, 7, 5]),
center=np.array([0, 0, 0, 0]),
)
# test preset
with self.assertRaises(ValueError):
AtomGrid.from_preset(atnum=1, preset="fine")
with self.assertRaises(TypeError):
AtomGrid(OneDGrid(np.arange(3), np.arange(3)), sizes=110)
with self.assertRaises(TypeError):
AtomGrid(OneDGrid(np.arange(3), np.arange(3)), degrees=17)
with self.assertRaises(ValueError):
AtomGrid(OneDGrid(np.arange(3), np.arange(3)),
degrees=[17],
rotate=-1)
with self.assertRaises(TypeError):
AtomGrid(OneDGrid(np.arange(3), np.arange(3)),
degrees=[17],
rotate="asdfaf")
# error of radial grid
with self.assertRaises(TypeError):
AtomGrid(Grid(np.arange(1, 5, 1), np.ones(4)),
degrees=[2, 3, 4, 5])
with self.assertRaises(TypeError):
AtomGrid(OneDGrid(np.arange(-2, 2, 1), np.ones(4)),
degrees=[2, 3, 4, 5])
with self.assertRaises(TypeError):
rgrid = OneDGrid(np.arange(1, 3, 1), np.ones(2), domain=(-1, 5))
AtomGrid(rgrid, degrees=[2])
with self.assertRaises(TypeError):
rgrid = OneDGrid(np.arange(-1, 1, 1), np.ones(2))
AtomGrid(rgrid, degrees=[2])
with self.assertRaises(ValueError):
AtomGrid._generate_real_sph_harm(-1, np.random.rand(10),
np.random.rand(10))
with self.assertRaises(ValueError):
oned = GaussLegendre(30)
btf = BeckeTF(0.0001, 1.5)
rad = btf.transform_1d_grid(oned)
atgrid = AtomGrid.from_preset(rad, atnum=1, preset="fine")
atgrid.fit_values(np.random.rand(100))
def setUp(self):
"""Test setup function."""
self._ref_points = np.linspace(-1, 1, 21)
self._ref_weights = np.ones(21) * 0.1
self.grid = Grid(self._ref_points, self._ref_weights)