def test_example08(self):
nice_measures = [[1.976, 3.699], [6.955, 0.602]]
molecules, options = classic_inputs.read_old_input(
'data/shape/example08.dat')
central_atom = options['%central_atom']
reference_polyhedron = []
if options['%labels'] != 0:
for number in options['%labels']:
if int(number) == 0:
for ref in file_io.get_geometry_from_file_ref(
'data/shape/example08.ref', read_multiple=True):
reference_polyhedron.append(ref)
else:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number),
options['%n_atoms']))
results = [[
shape.Shape(molecule).measure(reference_polyhedron[0],
central_atom=central_atom)
for molecule in molecules
],
[
shape.Shape(molecule).measure(reference_polyhedron[1],
central_atom=central_atom)
for molecule in molecules
]]
calculated_results = np.column_stack((results[0], results[1]))
self.assertTrue(
np.allclose(nice_measures, calculated_results, atol=1e-2))
def test_example05(self):
nice_gen_coord = [84., 84., 25.4, 79.1, 23.7, 25., 54.6]
nice_measures = [[12.011, 0.954], [12.012, 0.957], [1.142, 11.245],
[10.707, 1.236], [0.993, 12.826], [1.105, 11.783],
[5.203, 5.085]]
nice_dev_path = [7.2, 7.2, 6.5, 5.5, 10.6, 8.1, 8.6]
nice_path_coordinates = np.array([[0., 16.737], [0.035, 15.355],
[0.144, 14.002], [0.329, 12.681],
[0.593, 11.398], [0.94, 10.158],
[1.371, 8.966], [1.89, 7.828],
[2.497, 6.748], [3.195, 5.732],
[3.984, 4.785], [4.865, 3.911],
[5.837, 3.116], [6.901, 2.403],
[8.055, 1.777], [9.298, 1.241],
[10.626, 0.798], [12.038, 0.45],
[13.53, 0.201], [15.097, 0.05],
[16.737, 0.]])
molecules, options = classic_inputs.read_old_input(
'data/shape/example05.dat')
reference_polyhedron = []
for number in options['%labels']:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number), options['%n_atoms']))
results = [[
shape.Shape(molecule).measure(
reference_polyhedron[0], central_atom=options['%central_atom'])
for molecule in molecules
],
[
shape.Shape(molecule).measure(
reference_polyhedron[1],
central_atom=options['%central_atom'])
for molecule in molecules
]]
dev_path = [
molecule.get_path_deviation(reference_polyhedron[0],
reference_polyhedron[1],
central_atom=options['%central_atom'])
for molecule in molecules
]
gen_coord = [
molecule.get_generalized_coordinate(
reference_polyhedron[0],
reference_polyhedron[1],
central_atom=options['%central_atom'])
for molecule in molecules
]
map = maps.get_shape_map(reference_polyhedron[0],
reference_polyhedron[1],
num_points=20)
self.assertTrue(np.allclose(nice_gen_coord, gen_coord, atol=1e-1))
calculated_results = np.column_stack((results[0], results[1]))
self.assertTrue(
np.allclose(nice_measures, calculated_results, atol=1e-1))
self.assertTrue(np.allclose(nice_dev_path, dev_path, atol=1e-1))
self.assertTrue(
np.allclose(nice_path_coordinates.T, map[:2], atol=1e-1))
def test_example03(self):
nice_measures = [[31.375, 0.97], [33.44, 0.16]]
molecules, options = classic_inputs.read_old_input(
'data/shape/example03.dat')
reference_polyhedron = []
for number in options['%labels']:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number), options['%n_atoms']))
results = []
for reference in reference_polyhedron:
results.append([
shape.Shape(molecule).measure(
reference, central_atom=options['%central_atom'])
for molecule in molecules
])
calculated_results = np.column_stack((results[0], results[1]))
self.assertTrue(
np.allclose(nice_measures, calculated_results, atol=1e-3))
def test_example07(self):
molecules, options = classic_inputs.read_old_input(
'data/shape/example06.dat')
reference_polyhedron = []
for number in options['%labels']:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number), options['%n_atoms']))
symobj = Cosymlib(molecules)
shape_measure, devpath, get_coord = symobj.get_path_parameters(
reference_polyhedron[0],
reference_polyhedron[1],
central_atom=options['%central_atom'])
filter_mask = [
dv < 5.0 and 40 < gc < 60 for dv, gc in zip(devpath, get_coord)
]
devpath = np.array(devpath)[filter_mask]
self.assertTrue(np.allclose(0.2, devpath, atol=1e-1))
def test_example02(self):
nice_measures = [[5.271, 36.847], [5.184, 36.789], [5.047, 36.698],
[5.234, 36.822], [5.1, 36.733]]
molecules, options = classic_inputs.read_old_input(
'data/shape/example02.dat')
reference_polyhedron = []
for number in options['%labels']:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number), options['%n_atoms']))
results = [[
shape.Shape(molecule).measure(reference_polyhedron[0],
options['%central_atom'])
for molecule in molecules
],
[
shape.Shape(molecule).measure(reference_polyhedron[1],
options['%central_atom'])
for molecule in molecules
]]
calculated_results = np.column_stack((results[0], results[1]))
self.assertTrue(
np.allclose(nice_measures, calculated_results, atol=1e-3))
def test_example06(self):
nice_dev_path = [
0.9, 3.7, 4.1, 3.7, 3.1, 0.1, 0.7, 3.9, 4., 1.7, 1.9, 2.6, 1.4,
2.1, 1.5, 1.4, 4.3, 3.4, 1.1, 0.9, 1.6, 1.6, 0.1, 1.5, 2.5, 0.2,
0.6, 3.1, 1.6, 1.1, 0.5, 1.1, 0.5, 1.6, 0.3, 4.8, 3.4, 3., 4.4,
0.6, 0.8, 1., 0.6, 2.8, 3.3, 0.5, 0.6, 2.1, 3.5, 2.6, 4.7, 0.6,
0.7, 0.8, 4., 4.8, 1.3, 1.5, 1.3, 0.9, 2.2, 2.5, 4.6, 4.7, 4.7,
2.4, 0.8, 0., 1.3, 1.4, 1.4, 0.5, 1.7, 3.4, 4., 2.2, 0.4, 0., 1.5,
1.8, 1., 4.5, 1.5, 1.5, 1.6, 0.7, 0.6, 2.3, 0.3, 0.2, 0.3, 4.2,
0.2, 0.4, 0.9, 0.3, 0.4, 0., 3.2, 1.4, 1.8, 1., 1.3, 0.6, 2., 0.3,
0., 0.1, 0.6, 2.1, 4.2, 1.6, 2.8, 1.5, 2.6, 2.8, 1.7, 0.3, 0.7,
0.5, 0.6, 0.6, 2.5, 1.5, 0.8, 0.3, 0.2, 0.8, 0.7, 3.6, 3.8, 4.5,
2.8, 1.5, 3.8, 1.8, 3.9, 1.5, 0.2, 0.4, 0.8, 2.5, 0.5, 2.6, 1.3,
0.8, 1.2, 1.9, 3.9, 2.4, 0.9, 0.4, 2.6, 0., 2.4, 1.7, 4.4, 1.6,
3.5, 3.8, 3.6, 4.7, 4.8, 3.7, 1.8, 1.6, 2.3, 3.7, 3., 1.3, 0.9,
2.8, 0.9, 4.1, 3.2, 4.6, 1.7, 0.8, 1., 0.7, 0.6, 0.2, 4.6, 1.5,
1.5, 1.7, 2.5, 2.9, 0.5, 0.8, 1.3
]
molecules, options = classic_inputs.read_old_input(
'data/shape/example06.dat')
reference_polyhedron = []
for number in options['%labels']:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number), options['%n_atoms']))
symobj = Cosymlib(molecules)
shape_measure, devpath, get_coord = symobj.get_path_parameters(
reference_polyhedron[0],
reference_polyhedron[1],
central_atom=options['%central_atom'])
filter_mask = [
dv < 5.0 and gc < 101 for dv, gc in zip(devpath, get_coord)
]
devpath = np.array(devpath)[filter_mask]
self.assertTrue(np.allclose(nice_dev_path, devpath, atol=1e-1))
def test_example04(self):
nice_measures = [[31.375, 0.97], [33.44, 0.16]]
nice_structures = [[2.63702000e+00, 9.00254000e+00, 1.50230800e+01],
[4.04611899e+00, 8.76816018e+00, 1.39529277e+01],
[2.90730181e+00, 8.13748396e+00, 1.65607229e+01],
[1.17328859e+00, 8.36062228e+00, 1.42286293e+01],
[2.42137060e+00, 1.07438936e+01, 1.53500401e+01],
[-3.47837193e-17, -9.20929468e-18, 2.51183874e-17],
[3.77908106e-01, 9.50150647e-01, -8.46343078e-01],
[-3.77908106e-01, -9.50150647e-01, 8.46343078e-01],
[-1.14966271e+00, 6.33326997e-01, 1.97661211e-01],
[1.14966271e+00, -6.33326997e-01, -1.97661211e-01],
[2.63702000e+00, 9.00254000e+00, 1.50230800e+01],
[3.76728743e+00, 7.46687014e+00, 1.40425715e+01],
[4.02414490e+00, 8.97967996e+00, 1.66578721e+01],
[1.24989510e+00, 9.02540004e+00, 1.33882879e+01],
[1.50675257e+00, 1.05382099e+01, 1.60035885e+01],
[9.74091060e-17, 1.01739088e-17, -5.98080786e-17],
[5.66862241e-01, 1.42522607e+00, -1.26951447e+00],
[-5.66862241e-01, -1.42522607e+00, 1.26951447e+00],
[-1.72449417e+00, 9.49990377e-01, 2.96491640e-01],
[1.72449417e+00, -9.49990377e-01, -2.96491640e-01]]
molecules, options = classic_inputs.read_old_input(
'data/shape/example04.dat')
reference_polyhedron = []
for number in options['%labels']:
reference_polyhedron.append(
shape.tools.get_shape_label(int(number), options['%n_atoms']))
results = [[
shape.Shape(molecule).structure(
reference_polyhedron[0], central_atom=options['%central_atom'])
for molecule in molecules
]]
calculated_results = np.concatenate((results[0][0], results[0][1]))
results.append([
shape.Shape(molecule).structure(
reference_polyhedron[1], central_atom=options['%central_atom'])
for molecule in molecules
])
calculated_results = np.concatenate(
(calculated_results, np.concatenate(
(results[1][0], results[1][1]))))
results = []
results.append([
shape.Shape(molecule).measure(
reference_polyhedron[0], central_atom=options['%central_atom'])
for molecule in molecules
])
results.append([
shape.Shape(molecule).measure(
reference_polyhedron[1], central_atom=options['%central_atom'])
for molecule in molecules
])
calculated_results = [
calculated_results,
np.column_stack((results[0], results[1]))
]
self.assertTrue(
np.allclose(nice_structures, calculated_results[0], atol=1e-3))
self.assertTrue(
np.allclose(nice_measures, calculated_results[1], atol=1e-3))