def test_close_within2(self, setup):
g = setup.g.repeat(6, 0).repeat(6, 1)
for ia in g:
shapes = [Sphere(0.1, g[ia]), Sphere(1.5, g[ia])]
i = g.close(ia, R=(0.1, 1.5))
ii = g.within(shapes)
assert np.all(i[0] == ii[0])
assert np.all(i[1] == ii[1])
def test_close_within1(self, setup):
three = range(3)
for ia in setup.mol:
shapes = [Sphere(0.1, setup.mol[ia]), Sphere(1.1, setup.mol[ia])]
i = setup.mol.close(ia, R=(0.1, 1.1), idx=three)
ii = setup.mol.within(shapes, idx=three)
assert np.all(i[0] == ii[0])
assert np.all(i[1] == ii[1])
def test_close_within2(self):
g = self.g.repeat(6, 0).repeat(6, 1)
for ia in g:
shapes = [Sphere(0.1, g[ia, :]), Sphere(1.5, g[ia, :])]
i = g.close(ia, dR=(0.1, 1.5))
ii = g.within(shapes)
assert_true(np.all(i[0] == ii[0]))
assert_true(np.all(i[1] == ii[1]))
def test_close_within3(self, setup):
g = setup.g.repeat(6, 0).repeat(6, 1)
args = {'ret_xyz': True, 'ret_rij': True}
for ia in g:
shapes = [Sphere(0.1, g[ia]), Sphere(1.5, g[ia])]
i, xa, d = g.close(ia, R=(0.1, 1.5), **args)
ii, xai, di = g.within(shapes, **args)
for j in [0, 1]:
assert np.all(i[j] == ii[j])
assert np.allclose(xa[j], xai[j])
assert np.allclose(d[j], di[j])
def test_close_within3(self):
g = self.g.repeat(6, 0).repeat(6, 1)
args = {'ret_coord': True, 'ret_dist': True}
for ia in g:
shapes = [Sphere(0.1, g[ia, :]), Sphere(1.5, g[ia, :])]
i, xa, d = g.close(ia, dR=(0.1, 1.5), **args)
ii, xai, di = g.within(shapes, **args)
for j in [0, 1]:
assert_true(np.all(i[j] == ii[j]))
assert_true(np.allclose(xa[j], xai[j]))
assert_true(np.allclose(d[j], di[j]))
def test_iter_shape3(self, setup):
g = setup.g.tile(50, 0).tile(50, 1)
i = 0
for ias, _ in g.iter_block(method='sphere'):
i += len(ias)
assert i == len(g)
i = 0
for ias, _ in g.iter_block(method='cube'):
i += len(ias)
assert i == len(g)
i = 0
for ias, _ in g.iter_block_shape(Sphere(g.maxR() * 20)):
i += len(ias)
assert i == len(g)