def test_distance6(self, setup):
# Create a 1D chain
geom = Geometry([0]*3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 1, 1])
d = geom.distance(0)
assert len(d) == 1
assert np.allclose(d, [1.])
# Do twice
d = geom.distance(R=2)
assert len(d) == 2
assert np.allclose(d, [1., 2.])
# Do all
d = geom.distance(R=np.inf)
assert len(d) == 77 // 2
# Add one due arange not adding the last item
assert np.allclose(d, range(1, 78 // 2))
# Create a 2D grid
geom.set_nsc([3, 3, 1])
d = geom.distance(R=2, tol=[.4, .3, .2, .1])
assert len(d) == 2 # 1, sqrt(2)
# Add one due arange not adding the last item
assert np.allclose(d, [1, 2 ** .5])
# Create a 2D grid
geom.set_nsc([5, 5, 1])
d = geom.distance(R=2, tol=[.4, .3, .2, .1])
assert len(d) == 3 # 1, sqrt(2), 2
# Add one due arange not adding the last item
assert np.allclose(d, [1, 2 ** .5, 2])
def test_distance8(self, setup):
geom = Geometry([0]*3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 1, 1])
d = geom.distance(0, method='min')
assert len(d) == 1
d = geom.distance(0, method='median')
assert len(d) == 1
d = geom.distance(0, method='mode')
assert len(d) == 1
def test_distance7(self):
# Create a 1D chain
geom = Geometry([0] * 3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 1, 1])
# Try with a short R and a long tolerance list
d = geom.distance(R=1, tol=np.ones(10) * .5)
assert_equal(len(d), 1)
assert_true(np.allclose(d, [1.]))
def test_distance7(self, setup):
# Create a 1D chain
geom = Geometry([0]*3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 1, 1])
# Try with a short R and a long tolerance list
# We know that the tolerance list prevails, because
d = geom.distance(R=1, tol=np.ones(10) * .5)
assert len(d) == 1
assert np.allclose(d, [1.])
def test_distance2(self, setup):
geom = Geometry(setup.g.xyz, Atom[6])
d = geom.distance(R=1.42, method='unknown_numpy_function')
def test_distance1(self, setup):
geom = Geometry(setup.g.xyz, Atom[6])
# maxR is undefined
d = geom.distance()
def test_distance2(self, setup):
geom = Geometry(setup.g.xyz, Atom[6])
with pytest.raises(ValueError):
d = geom.distance(R=1.42, method='unknown_numpy_function')
def test_distance1(self, setup):
geom = Geometry(setup.g.xyz, Atom[6])
# maxR is undefined
with pytest.raises(ValueError):
d = geom.distance()