def test_find_triangle_critical_pt(self):
"""Test three atom ring critical pts."""
atoms = np.array([[-2, -2, 0], [2, -2, 0], [0, 1, 0]])
alf = 1
def fun_v(coors):
return (self.gauss_func(coors, atoms[0], alphas=alf) +
self.gauss_func(coors, atoms[1], alphas=alf) +
self.gauss_func(coors, atoms[2], alphas=alf))
def fun_d(coors):
return (self.gauss_deriv(coors, atoms[0], alphas=alf) +
self.gauss_deriv(coors, atoms[1], alphas=alf) +
self.gauss_deriv(coors, atoms[2], alphas=alf))
def fun_d2(coors):
return (self.gauss_deriv2(coors, atoms[0], alphas=alf) +
self.gauss_deriv2(coors, atoms[1], alphas=alf) +
self.gauss_deriv2(coors, atoms[2], alphas=alf))
tp_ins = Topo(atoms, fun_v, fun_d, fun_d2, extra=1)
tp_ins.find_critical_pts()
assert len(tp_ins._crit_bond) == 3
assert len(tp_ins._crit_ring) == 1
assert len(tp_ins._crit_max) == 0
assert len(tp_ins._crit_cage) == 0
def test_is_coors_pt(self):
"""Test same pts as nuclear position."""
coors = np.array([[1, 1, 1], [-1, -1, -1]])
pts = np.random.rand(4, 3)
topo = Topo(coors, self.gauss_func, self.gauss_deriv,
self.gauss_deriv2, pts)
for i in coors:
result = topo._is_coors_pt(i)
assert result
pt = (np.random.rand(4, 3) + 0.1) / 2
for i in pt:
result = topo._is_coors_pt(i)
assert not result
def test_get_gradietn(self):
"""Test get proper gradient."""
# initiate topo obj.
coors = np.array([[1, 1, 1], [-1, -1, -1]])
pts = np.random.rand(4, 3)
topo = Topo(coors, self.gauss_func, self.gauss_deriv,
self.gauss_deriv2, pts)
# get cage points
pts = Topo._construct_cage(np.array([0.5, 0.5, 0.5]), 0.1)
g_pts = topo.get_gradient(pts)
# assert len(g_pts) == 4
ref_g = self.gauss_deriv(pts)
assert_allclose(ref_g, g_pts)
def test_topo(self):
"""Test properly initiate topo instance."""
coors = np.array([[1, 1, 1], [-1, -1, -1]])
pts = np.random.rand(4, 3)
topo = Topo(coors, self.gauss_func, self.gauss_deriv,
self.gauss_deriv2, pts)
assert isinstance(topo, Topo)
def test_add_critical_points(self):
"""Test add critical points to class."""
coors = np.array([[1, 1, 1], [-1, -1, -1]])
pts = np.random.rand(4, 3)
topo = Topo(coors, self.gauss_func, self.gauss_deriv,
self.gauss_deriv2, pts)
pt = CriticalPoint(np.random.rand(3), None, None)
# bond
ct_type = -1
topo._add_critical_point(pt, ct_type)
assert_allclose(topo._crit_bond[0].point, pt.point, atol=1e-10)
# maxima
ct_type = -3
topo._add_critical_point(pt, ct_type)
assert_allclose(topo._crit_max[0].point, pt.point, atol=1e-10)
# ring
ct_type = 1
topo._add_critical_point(pt, ct_type)
assert_allclose(topo._crit_ring[0].point, pt.point, atol=1e-10)
# cage
ct_type = 3
topo._add_critical_point(pt, ct_type)
assert_allclose(topo._crit_cage[0].point, pt.point, atol=1e-10)
def test_find_one_critical_pt(self):
"""Test two atoms critical pts."""
atoms = np.array([[-2, -2, -2], [2, 2, 2]])
alf = 0.3
def fun_v(coors):
"""Generate value function."""
return self.gauss_func(coors, atoms[0],
alphas=alf) + self.gauss_func(
coors, atoms[1], alphas=alf)
def fun_d(coors):
"""Generate 1st order deriv function."""
return self.gauss_deriv(coors, atoms[0],
alphas=alf) + self.gauss_deriv(
coors, atoms[1], alphas=alf)
def fun_d2(coors):
"""Generate 2nd order deriv function."""
return self.gauss_deriv2(coors, atoms[0],
alphas=alf) + self.gauss_deriv2(
coors, atoms[1], alphas=alf)
pts = np.random.rand(20, 3) * 0.5
pts = np.vstack((pts, np.array([0.05, 0.05,
0.05]), np.array([-0.05, -0.05,
-0.05])))
tp_ins = Topo(atoms, fun_v, fun_d, fun_d2, pts)
tp_ins.find_critical_pts()
# one critical pt
assert len(tp_ins._found_ct) == 1
assert len(tp_ins._crit_bond) == 1
# one critical type bond
assert tp_ins._found_ct_type[0] == -1
# one critical point at origin
assert_allclose(tp_ins._found_ct[0], [0, 0, 0], atol=1e-10)
def test_construct_cage(self):
"""Test construct cage among target points."""
pts = Topo._construct_cage(np.array([0, 0, 0]), 1)
assert len(pts) == 4
dis = np.linalg.norm(pts[:] - np.array([0, 0, 0]), axis=-1)
assert_allclose(dis, np.ones(4) * 4.89898, rtol=1e-5)
def test_default_cube(self):
"""Test default cube for points."""
coors = np.array([[1, 1, 1], [-1, -1, -1]])
topo = Topo(coors, self.gauss_func, self.gauss_deriv,
self.gauss_deriv2)
assert topo._kdtree.data.shape == (60 * 60 * 60, 3)