class SimplexTest(PymatgenTest):
def setUp(self):
coords = []
coords.append([0, 0, 0])
coords.append([0, 1, 0])
coords.append([0, 0, 1])
coords.append([1, 0, 0])
self.simplex = Simplex(coords)
def test_in_simplex(self):
self.assertTrue(self.simplex.in_simplex([0.1, 0.1, 0.1]))
self.assertFalse(self.simplex.in_simplex([0.6, 0.6, 0.6]))
for i in range(10):
coord = np.random.random_sample(size=3) / 3
self.assertTrue(self.simplex.in_simplex(coord))
def test_2dtriangle(self):
s = Simplex([[0, 1], [1, 1], [1, 0]])
self.assertArrayAlmostEqual(s.bary_coords([0.5, 0.5]),
[0.5, 0, 0.5])
self.assertArrayAlmostEqual(s.bary_coords([0.5, 1]), [0.5, 0.5, 0])
self.assertArrayAlmostEqual(s.bary_coords([0.5, 0.75]), [0.5, 0.25, 0.25])
self.assertArrayAlmostEqual(s.bary_coords([0.75, 0.75]), [0.25, 0.5, 0.25])
s = Simplex([[1, 1], [1, 0]])
self.assertRaises(ValueError, s.bary_coords, [0.5, 0.5])
def test_volume(self):
# Should be value of a right tetrahedron.
self.assertAlmostEqual(self.simplex.volume, 1/6)
def _in_facet(self, facet, entry):
"""
Checks if a Pourbaix Entry is in a facet.
Args:
facet: facet to test.
entry: Pourbaix Entry to test.
"""
dim = len(self._keys)
if dim > 1:
coords = [np.array(self._pd.qhull_data[facet[i]][0:dim - 1])
for i in range(len(facet))]
simplex = Simplex(coords)
comp_point = [entry.npH, entry.nPhi]
return simplex.in_simplex(comp_point,
PourbaixAnalyzer.numerical_tol)
else:
return True
def _in_facet(self, facet, entry):
"""
Checks if a Pourbaix Entry is in a facet.
Args:
facet: facet to test.
entry: Pourbaix Entry to test.
"""
dim = len(self._keys)
if dim > 1:
coords = [
np.array(self._pd.qhull_data[facet[i]][0:dim - 1])
for i in range(len(facet))
]
simplex = Simplex(coords)
comp_point = [entry.npH, entry.nPhi]
return simplex.in_simplex(comp_point,
PourbaixAnalyzer.numerical_tol)
else:
return True
