def setUp(self):
profile = {'Mo': {'r': 0.6, 'w': 1.}}
self.describer1 = BispectrumCoefficients(rcutfac=4.6,
twojmax=6,
element_profile=profile,
quadratic=False,
pot_fit=True)
model1 = LinearModel(describer=self.describer1)
self.potential1 = SNAPotential(model=model1, name='test')
self.describer2 = BispectrumCoefficients(rcutfac=4.6,
twojmax=6,
element_profile=profile,
quadratic=True,
pot_fit=True)
model2 = LinearModel(describer=self.describer2)
self.potential2 = SNAPotential(model=model2, name='test')
self.test_pool = test_datapool
self.test_structures = []
self.test_energies = []
self.test_forces = []
self.test_stresses = []
for d in self.test_pool:
self.test_structures.append(d['structure'])
self.test_energies.append(d['outputs']['energy'])
self.test_forces.append(d['outputs']['forces'])
self.test_stresses.append(d['outputs']['virial_stress'])
self.test_struct = self.test_pool[-1]['structure']
def setUp(self):
element_profile = {'Ni': {'r': 0.5, 'w': 1}}
describer = BispectrumCoefficients(rcutfac=4.1, twojmax=8,
element_profile=element_profile,
pot_fit=True)
model = LinearModel(describer=describer)
model.model.coef_ = coeff
model.model.intercept_ = intercept
snap = SNAPotential(model=model)
snap.specie = Element('Ni')
self.ff_settings = snap
def setUp(self):
element_profile = {'Ni': {'r': 0.5, 'w': 1}}
describer = BispectrumCoefficients(rcutfac=4.1, twojmax=8,
element_profile=element_profile,
pot_fit=True)
model = LinearModel(describer=describer)
model.model.coef_ = coeff
model.model.intercept_ = intercept
snap = SNAPotential(model=model)
snap.specie = Element('Ni')
self.struct = Structure.from_spacegroup('Fm-3m',
Lattice.cubic(3.506),
['Ni'], [[0, 0, 0]])
self.ff_settings = snap
def setUp(self):
element_profile = {'Ni': {'r': 0.5, 'w': 1}}
describer1 = BispectrumCoefficients(rcutfac=4.1,
twojmax=8,
element_profile=element_profile,
quadratic=False,
pot_fit=True)
model1 = LinearModel(describer=describer1)
model1.model.coef_ = coeff
model1.model.intercept_ = intercept
snap1 = SNAPotential(model=model1)
snap1.specie = Element('Ni')
self.ff_settings1 = snap1
describer2 = BispectrumCoefficients(rcutfac=4.1,
twojmax=8,
element_profile=element_profile,
quadratic=True,
pot_fit=True)
model2 = LinearModel(describer=describer2)
model2.model.coef_ = coeff
model2.model.intercept_ = intercept
snap2 = SNAPotential(model=model2)
snap2.specie = Element('Ni')
self.ff_settings2 = snap2
self.struct = Structure.from_spacegroup('Fm-3m', Lattice.cubic(3.506),
['Ni'], [[0, 0, 0]])
class SNAPotentialTest(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.this_dir = os.path.dirname(os.path.abspath(__file__))
cls.test_dir = tempfile.mkdtemp()
os.chdir(cls.test_dir)
@classmethod
def tearDownClass(cls):
os.chdir(CWD)
shutil.rmtree(cls.test_dir)
def setUp(self):
profile = {'Mo': {'r': 0.6, 'w': 1.}}
self.describer1 = BispectrumCoefficients(rcutfac=4.6,
twojmax=6,
element_profile=profile,
quadratic=False,
pot_fit=True)
model1 = LinearModel(describer=self.describer1)
self.potential1 = SNAPotential(model=model1, name='test')
self.describer2 = BispectrumCoefficients(rcutfac=4.6,
twojmax=6,
element_profile=profile,
quadratic=True,
pot_fit=True)
model2 = LinearModel(describer=self.describer2)
self.potential2 = SNAPotential(model=model2, name='test')
self.test_pool = test_datapool
self.test_structures = []
self.test_energies = []
self.test_forces = []
self.test_stresses = []
for d in self.test_pool:
self.test_structures.append(d['structure'])
self.test_energies.append(d['outputs']['energy'])
self.test_forces.append(d['outputs']['forces'])
self.test_stresses.append(d['outputs']['virial_stress'])
self.test_struct = self.test_pool[-1]['structure']
def test_train(self):
self.potential1.train(train_structures=self.test_structures,
energies=self.test_energies,
forces=self.test_forces,
stresses=self.test_stresses)
self.assertEqual(len(self.potential1.model.coef),
len(self.describer1.subscripts) + 1)
self.potential2.train(train_structures=self.test_structures,
energies=self.test_energies,
forces=self.test_forces,
stresses=self.test_stresses)
nss = len(self.describer2.subscripts)
self.assertEqual(len(self.potential2.model.coef), nss + int(
(1 + nss) * nss / 2) + 1)
def test_evaluate(self):
self.potential1.train(train_structures=self.test_structures,
energies=self.test_energies,
forces=self.test_forces,
stresses=self.test_stresses)
df_orig, df_tar = self.potential1.evaluate(
test_structures=self.test_structures,
ref_energies=self.test_energies,
ref_forces=self.test_forces,
ref_stresses=self.test_stresses)
self.assertEqual(df_orig.shape[0], df_tar.shape[0])
self.potential2.train(train_structures=self.test_structures,
energies=self.test_energies,
forces=self.test_forces,
stresses=self.test_stresses)
df_orig, df_tar = self.potential2.evaluate(
test_structures=self.test_structures,
ref_energies=self.test_energies,
ref_forces=self.test_forces,
ref_stresses=self.test_stresses)
self.assertEqual(df_orig.shape[0], df_tar.shape[0])
def test_predict(self):
self.potential1.train(train_structures=self.test_structures,
energies=self.test_energies,
forces=self.test_forces,
stresses=self.test_stresses)
energy, forces, stress = self.potential1.predict(self.test_struct)
self.assertEqual(len(forces), len(self.test_struct))
self.assertEqual(len(stress), 6)
self.potential2.train(train_structures=self.test_structures,
energies=self.test_energies,
forces=self.test_forces,
stresses=self.test_stresses)
energy, forces, stress = self.potential2.predict(self.test_struct)
self.assertEqual(len(forces), len(self.test_struct))
self.assertEqual(len(stress), 6)
def test_from_config(self):
snap = SNAPotential.from_config(param_file, coeff_file)
self.assertTrue(getattr(snap.model.model, 'coef_') is not None)
def test_from_config(self):
snap = SNAPotential.from_config(param_file, coeff_file)
self.assertTrue(getattr(snap.model.model, 'coef_') is not None)