def test_from_predefined(self):
"""Test grid construction with predefined grid."""
# test coarse grid
pts = HortonLinear(20)
tf = PowerRTransform(7.0879993828935345e-06, 16.05937640019924)
rad_grid = tf.transform_1d_grid(pts)
atgrid = AtomGrid.from_preset(rad_grid, atnum=1, preset="coarse")
# 604 points for coarse H atom
assert_equal(atgrid.size, 604)
assert_almost_equal(
np.sum(np.exp(-np.sum(atgrid.points**2, axis=1)) * atgrid.weights),
5.56840953,
)
# test medium grid
pts = HortonLinear(24)
tf = PowerRTransform(3.69705074304963e-06, 19.279558946793685)
rad_grid = tf.transform_1d_grid(pts)
atgrid = AtomGrid.from_preset(rad_grid, atnum=1, preset="medium")
# 928 points for coarse H atom
assert_equal(atgrid.size, 928)
assert_almost_equal(
np.sum(np.exp(-np.sum(atgrid.points**2, axis=1)) * atgrid.weights),
5.56834559,
)
# test fine grid
pts = HortonLinear(34)
tf = PowerRTransform(2.577533167224667e-07, 16.276983371222354)
rad_grid = tf.transform_1d_grid(pts)
atgrid = AtomGrid.from_preset(rad_grid, atnum=1, preset="fine")
# 1984 points for coarse H atom
assert_equal(atgrid.size, 1984)
assert_almost_equal(
np.sum(np.exp(-np.sum(atgrid.points**2, axis=1)) * atgrid.weights),
5.56832800,
)
# test veryfine grid
pts = HortonLinear(41)
tf = PowerRTransform(1.1774580743206259e-07, 20.140888089596444)
rad_grid = tf.transform_1d_grid(pts)
atgrid = AtomGrid.from_preset(rad_grid, atnum=1, preset="veryfine")
# 3154 points for coarse H atom
assert_equal(atgrid.size, 3154)
assert_almost_equal(
np.sum(np.exp(-np.sum(atgrid.points**2, axis=1)) * atgrid.weights),
5.56832800,
)
# test ultrafine grid
pts = HortonLinear(49)
tf = PowerRTransform(4.883104847991021e-08, 21.05456999309752)
rad_grid = tf.transform_1d_grid(pts)
atgrid = AtomGrid.from_preset(rad_grid, atnum=1, preset="ultrafine")
# 4546 points for coarse H atom
assert_equal(atgrid.size, 4546)
assert_almost_equal(
np.sum(np.exp(-np.sum(atgrid.points**2, axis=1)) * atgrid.weights),
5.56832800,
)
# test insane grid
pts = HortonLinear(59)
tf = PowerRTransform(1.9221827244049134e-08, 21.413278983919113)
rad_grid = tf.transform_1d_grid(pts)
atgrid = AtomGrid.from_preset(rad_grid, atnum=1, preset="insane")
# 6622 points for coarse H atom
assert_equal(atgrid.size, 6622)
assert_almost_equal(
np.sum(np.exp(-np.sum(atgrid.points**2, axis=1)) * atgrid.weights),
5.56832800,
)
def from_preset(
cls,
atnums,
atcoords,
rgrid,
preset,
aim_weights,
*_,
rotate=37,
store=False,
):
"""Construct molecular grid wih preset parameters.
Parameters
----------
atnums : np.ndarray(N,)
array of atomic number
atcoords : np.ndarray(N, 3)
atomic coordinates of atoms
rgrid : OneDGrid
one dimension grid to construct spherical grid
preset : str
preset grid accuracy scheme, support "coarse", "medium", "fine",
"veryfine", "ultrafine", "insane"
aim_weights : Callable or np.ndarray(K,)
Atoms in molecule weights.
rotate : bool, optional
Random rotate for each shell of atomic grid
store : bool, optional
Store atomic grid separately
"""
# construct for a atom molecule
if atcoords.ndim != 2:
raise ValueError("The dimension of coordinates need to be 2\n"
f"got shape: {atcoords.ndim}")
if len(atnums) != atcoords.shape[0]:
raise ValueError(
"shape of atomic nums does not match with coordinates\n"
f"atomic numbers: {atnums.shape}, coordinates: {atcoords.shape}"
)
total_atm = len(atnums)
atomic_grids = []
for i in range(total_atm):
# get proper radial grid
if isinstance(rgrid, OneDGrid):
rad = rgrid
elif isinstance(rgrid, list):
rad = rgrid[i]
elif isinstance(rgrid, dict):
rad = rgrid[atnums[i]]
else:
raise TypeError(
f"not supported radial grid input; got input type: {type(rgrid)}"
)
# get proper grid type
if isinstance(preset, str):
gd_type = preset
elif isinstance(preset, list):
gd_type = preset[i]
elif isinstance(preset, dict):
gd_type = preset[atnums[i]]
else:
raise TypeError(
f"Not supported preset type; got preset {preset} with type {type(preset)}"
)
at_grid = AtomGrid.from_preset(rad,
atnum=atnums[i],
preset=gd_type,
center=atcoords[i],
rotate=rotate)
atomic_grids.append(at_grid)
return cls(atnums, atomic_grids, aim_weights, store=store)
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 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.from_preset(
numbers,
coordinates,
rad2,
["fine", "veryfine", "medium"],
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(
rad2, 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(
rad2, atnum=numbers[2], preset="medium", 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)
# grid type test with dict
mg = MolGrid.from_preset(
numbers,
coordinates,
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(
rad3, 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(
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)
