def test_fill_in_crystal_units_list(self):
a = LazyValues(elements=ELEMENTS, coords=COORDS, numbers=NUMBERS,
connections=CONNECTIONS, unit_cell=UNIT_CELL)
a.fill_in_crystal(units=[1, 2, 3])
length = 3 * 5 * 7
self.assertEqual(a.elements.tolist(), ELEMENTS * length)
self.assertEqual(a.numbers.tolist(), NUMBERS * length)
def test_fill_in_crystal(self):
a = LazyValues(elements=ELEMENTS, coords=COORDS, numbers=NUMBERS,
connections=CONNECTIONS, unit_cell=UNIT_CELL)
a.fill_in_crystal(radius=1.)
length = 3
self.assertEqual(a.elements.tolist(), ELEMENTS * length)
expected_results = numpy.array([
[0.99826008, -0.00246000, -1.00436000],
[2.09021016, -0.00243000, -0.99586000],
[0.63379005, 1.02686007, -0.99586000],
[0.62704006, -0.52773003, -0.12188990],
[0.64136006, -0.50747003, -1.90540005],
[0.99826008, -0.00246000, -0.00436000],
[2.09021016, -0.00243000, 0.00414000],
[0.63379005, 1.02686007, 0.00414000],
[0.62704006, -0.52773003, 0.87811010],
[0.64136006, -0.50747003, -0.90540005],
[0.99826008, -0.00246000, 0.99564000],
[2.09021016, -0.00243000, 1.00414000],
[0.63379005, 1.02686007, 1.00414000],
[0.62704006, -0.52773003, 1.87811010],
[0.64136006, -0.50747003, 0.09459995],
])
try:
numpy.testing.assert_array_almost_equal(
a.coords,
expected_results)
except AssertionError as e:
self.fail(e)
self.assertEqual(a.numbers.tolist(), NUMBERS * length)
def test_fill_in_crystal(self):
a = LazyValues(elements=ELEMENTS, coords=COORDS, numbers=NUMBERS,
connections=CONNECTIONS, unit_cell=UNIT_CELL)
a.fill_in_crystal(radius=1.)
length = 3
self.assertEqual(a.elements.tolist(), ELEMENTS * length)
expected_results = numpy.array([
[0.99826008, -0.00246000, -1.00436000],
[2.09021016, -0.00243000, -0.99586000],
[0.63379005, 1.02686007, -0.99586000],
[0.62704006, -0.52773003, -0.12188990],
[0.64136006, -0.50747003, -1.90540005],
[0.99826008, -0.00246000, -0.00436000],
[2.09021016, -0.00243000, 0.00414000],
[0.63379005, 1.02686007, 0.00414000],
[0.62704006, -0.52773003, 0.87811010],
[0.64136006, -0.50747003, -0.90540005],
[0.99826008, -0.00246000, 0.99564000],
[2.09021016, -0.00243000, 1.00414000],
[0.63379005, 1.02686007, 1.00414000],
[0.62704006, -0.52773003, 1.87811010],
[0.64136006, -0.50747003, 0.09459995],
])
try:
numpy.testing.assert_array_almost_equal(
a.coords,
expected_results)
except AssertionError as e:
self.fail(e)
self.assertEqual(a.numbers.tolist(), NUMBERS * length)
def test_fill_in_crystal_units_list(self):
a = LazyValues(elements=ELEMENTS, coords=COORDS, numbers=NUMBERS,
connections=CONNECTIONS, unit_cell=UNIT_CELL)
a.fill_in_crystal(units=[1, 2, 3])
length = 3 * 5 * 7
self.assertEqual(a.elements.tolist(), ELEMENTS * length)
self.assertEqual(a.numbers.tolist(), NUMBERS * length)
def test_all(self):
a = LazyValues(elements=ELEMENTS, coords=COORDS, numbers=NUMBERS,
connections=CONNECTIONS, unit_cell=UNIT_CELL)
self.assertEqual(a.elements.tolist(), ELEMENTS)
self.assertEqual(a.coords.tolist(), COORDS)
self.assertEqual(a.numbers.tolist(), NUMBERS)
self.assertEqual(a.connections, CONNECTIONS)
self.assertEqual(a.unit_cell.tolist(), UNIT_CELL)
def test_fill_in_crystal_units_list_invalid(self):
a = LazyValues(elements=ELEMENTS, coords=COORDS, numbers=NUMBERS,
connections=CONNECTIONS, unit_cell=UNIT_CELL)
with self.assertRaises(ValueError):
a.fill_in_crystal(units=[1, 2, 3, 4])
with self.assertRaises(ValueError):
a.fill_in_crystal(units=[1, 2])
with self.assertRaises(ValueError):
a.fill_in_crystal(units=[1, 2], radius=2)
def test_fill_in_crystal_conn(self):
eles = ['H']
coords = numpy.array([[0.0, 0.0, 0.0]])
nums = [1]
connections = {0: {}}
unit_cell = numpy.array([[1., 0, 0], [0, 1., 0], [0, 0, 1.]])
a = LazyValues(elements=eles,
coords=coords,
numbers=nums,
connections=connections,
unit_cell=unit_cell)
a.fill_in_crystal(radius=1.)
self.assertEqual(a.elements.tolist(), eles * 7)
expected = {
0: {
3: '1'
},
1: {
3: '1'
},
2: {
3: '1'
},
3: {
0: '1',
1: '1',
2: '1',
4: '1',
5: '1',
6: '1'
},
4: {
3: '1'
},
5: {
3: '1'
},
6: {
3: '1'
},
}
self.assertEqual(a.connections, expected)
def test_fill_in_crystal_conn(self):
eles = ['H']
coords = numpy.array([[0.0, 0.0, 0.0]])
nums = [1]
connections = {0: {}}
unit_cell = numpy.array([[1., 0, 0],
[0, 1., 0],
[0, 0, 1.]])
a = LazyValues(elements=eles, coords=coords, numbers=nums,
connections=connections, unit_cell=unit_cell)
a.fill_in_crystal(radius=1.)
self.assertEqual(a.elements.tolist(), eles * 7)
expected = {
0: {3: '1'},
1: {3: '1'},
2: {3: '1'},
3: {0: '1', 1: '1', 2: '1', 4: '1', 5: '1', 6: '1'},
4: {3: '1'},
5: {3: '1'},
6: {3: '1'},
}
self.assertEqual(a.connections, expected)
def test_fill_in_crystal_units_list_invalid(self):
a = LazyValues(elements=ELEMENTS, coords=COORDS, numbers=NUMBERS,
connections=CONNECTIONS, unit_cell=UNIT_CELL)
with self.assertRaises(ValueError):
a.fill_in_crystal(units=[1, 2, 3, 4])
with self.assertRaises(ValueError):
a.fill_in_crystal(units=[1, 2])
with self.assertRaises(ValueError):
a.fill_in_crystal(units=[1, 2], radius=2)
def test_fill_in_crystal_null(self):
a = LazyValues()
with self.assertRaises(ValueError):
a.fill_in_crystal(radius=1.)
a = LazyValues(unit_cell=UNIT_CELL)
with self.assertRaises(ValueError):
a.fill_in_crystal(radius=1.)
length = 3
a = LazyValues(numbers=NUMBERS, coords=COORDS, unit_cell=UNIT_CELL)
a.fill_in_crystal(radius=1.)
self.assertEqual(a.numbers.tolist(), NUMBERS * length)
a = LazyValues(elements=ELEMENTS, coords=COORDS, unit_cell=UNIT_CELL)
a.fill_in_crystal(radius=1.)
self.assertEqual(a.elements.tolist(), ELEMENTS * length)
feat = CoulombMatrix()
H2_conn = (H2_ELES, H2_COORDS, H2_CONNS)
HCN_conn = (HCN_ELES, HCN_COORDS, HCN_CONNS)
print(feat.fit_transform([H2_conn, HCN_conn]))
print()
# Example of generating the Coulomb matrix using a specified input_type
print("User specified input_type")
feat = CoulombMatrix(input_type=("coords", "numbers"))
H2_spec = (H2_COORDS, H2_NUMS)
HCN_spec = (HCN_COORDS, HCN_NUMS)
print(feat.fit_transform([H2_spec, HCN_spec]))
print()
# Example of generating the Local Coulomb matrix (atom-wise
# representation)
print("Atom feature")
feat = LocalCoulombMatrix()
print(feat.fit_transform([H2, HCN]))
# Example of generating AtomKernel
print("Atom Kernel")
feat = AtomKernel(transformer=LocalCoulombMatrix())
print(feat.fit_transform([H2, HCN]))
# Example of using arbitrary function to load data
# This example is useless, but it shows the possibility
feat = CoulombMatrix(
input_type=lambda x: LazyValues(elements=HCN_ELES, coords=HCN_COORDS))
feat.fit_transform(list(range(10)))
def test_connections(self):
a = LazyValues(elements=ELEMENTS, coords=COORDS, numbers=NUMBERS)
self.assertEqual(a.connections, CONNECTIONS)
def test_no_ele_or_num(self):
a = LazyValues(coords=COORDS)
with self.assertRaises(ValueError):
a.elements
with self.assertRaises(ValueError):
a.numbers
def test_no_unit_cell(self):
a = LazyValues(elements=ELEMENTS, numbers=NUMBERS)
with self.assertRaises(ValueError):
a.unit_cell
def test_no_coords(self):
a = LazyValues(elements=ELEMENTS, numbers=NUMBERS)
with self.assertRaises(ValueError):
a.coords
def test_ele_from_num(self):
a = LazyValues(numbers=NUMBERS)
self.assertEqual(a.elements.tolist(), ELEMENTS)
def test_num_from_ele(self):
a = LazyValues(elements=ELEMENTS)
self.assertEqual(a.numbers.tolist(), NUMBERS)
# Define some base data
H_ELES = ['H']
H_NUMS = [1]
H_COORDS = numpy.array([
[0.0, 0.0, 0.0],
])
H_CONNS = {
0: {},
}
H_UNIT = numpy.array([
[1., 0., 0.],
[0., 1., 0.],
[0., 0., 1.],
])
radius = 3
if __name__ == "__main__":
vals = LazyValues(coords=H_COORDS, unit_cell=H_UNIT,
elements=H_ELES, numbers=H_NUMS)
vals.fill_in_crystal(radius=radius)
plot_cell(vals.coords, radius, vals.unit_cell,
connections=vals.connections)
vals = read_cry_data("../tests/data/methane.cry")
vals.fill_in_crystal(radius=radius)
plot_cell(vals.coords, radius, vals.unit_cell,
connections=vals.connections)
feat = CoulombMatrix()
H2_conn = (H2_ELES, H2_COORDS, H2_CONNS)
HCN_conn = (HCN_ELES, HCN_COORDS, HCN_CONNS)
print(feat.fit_transform([H2_conn, HCN_conn]))
print()
# Example of generating the Coulomb matrix using a specified input_type
print("User specified input_type")
feat = CoulombMatrix(input_type=("coords", "numbers"))
H2_spec = (H2_COORDS, H2_NUMS)
HCN_spec = (HCN_COORDS, HCN_NUMS)
print(feat.fit_transform([H2_spec, HCN_spec]))
print()
# Example of generating the Local Coulomb matrix (atom-wise
# representation)
print("Atom feature")
feat = LocalCoulombMatrix()
print(feat.fit_transform([H2, HCN]))
# Example of generating AtomKernel
print("Atom Kernel")
feat = AtomKernel(transformer=LocalCoulombMatrix())
print(feat.fit_transform([H2, HCN]))
# Example of using arbitrary function to load data
# This example is useless, but it shows the possibility
feat = CoulombMatrix(input_type=lambda x: LazyValues(elements=HCN_ELES,
coords=HCN_COORDS))
feat.fit_transform(list(range(10)))
def test_fill_in_crystal_null(self):
a = LazyValues()
with self.assertRaises(ValueError):
a.fill_in_crystal(radius=1.)
a = LazyValues(unit_cell=UNIT_CELL)
with self.assertRaises(ValueError):
a.fill_in_crystal(radius=1.)
length = 3
a = LazyValues(numbers=NUMBERS, coords=COORDS, unit_cell=UNIT_CELL)
a.fill_in_crystal(radius=1.)
self.assertEqual(a.numbers.tolist(), NUMBERS * length)
a = LazyValues(elements=ELEMENTS, coords=COORDS, unit_cell=UNIT_CELL)
a.fill_in_crystal(radius=1.)
self.assertEqual(a.elements.tolist(), ELEMENTS * length)
H_COORDS = numpy.array([
[0.0, 0.0, 0.0],
])
H_CONNS = {
0: {},
}
H_UNIT = numpy.array([
[1., 0., 0.],
[0., 1., 0.],
[0., 0., 1.],
])
radius = 3
if __name__ == "__main__":
vals = LazyValues(coords=H_COORDS,
unit_cell=H_UNIT,
elements=H_ELES,
numbers=H_NUMS)
vals.fill_in_crystal(radius=radius)
plot_cell(vals.coords,
radius,
vals.unit_cell,
connections=vals.connections)
vals = read_cry_data("../tests/data/methane.cry")
vals.fill_in_crystal(radius=radius)
plot_cell(vals.coords,
radius,
vals.unit_cell,
connections=vals.connections)