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.from_size(
nums, coords, self.rgrid, 110, BeckeWeights(), store=True, rotate=False
)
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_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_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)