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}}
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]])
def setUp(self):
class DummyDescriber(MSONable):
def describe(self, obj):
pass
def describe_all(self, n):
return pd.DataFrame(n)
self.lm = LinearModel(DummyDescriber())
self.test_dir = tempfile.mkdtemp()
def from_config(param_file, coeff_file, **kwargs):
"""
Initialize potentials with parameters file and coefficient file.
Args:
param_file (str): The file storing the configuration of potentials.
coeff_file (str): The file storing the coefficients of potentials.
Return:
SNAPotential.
"""
with open(coeff_file) as f:
coeff_lines = f.readlines()
coeff_lines = [
line for line in coeff_lines if not line.startswith('#')
]
specie, r, w = coeff_lines[1].split()
r, w = float(r), int(w)
element_profile = {specie: {'r': r, 'w': w}}
rcut_pattern = re.compile('rcutfac (.*?)\n', re.S)
twojmax_pattern = re.compile('twojmax (\d*)\n', re.S)
rfac_pattern = re.compile('rfac0 (.*?)\n', re.S)
rmin_pattern = re.compile('rmin0 (.*?)\n', re.S)
diagonalstyle_pattern = re.compile('diagonalstyle (.*?)\n', re.S)
quadratic_pattern = re.compile('quadraticflag (.*?)(?=\n|$)', re.S)
with zopen(param_file, 'rt') as f:
param_lines = f.read()
rcut = float(rcut_pattern.findall(param_lines)[-1])
twojmax = int(twojmax_pattern.findall(param_lines)[-1])
rfac = float(rfac_pattern.findall(param_lines)[-1])
rmin = int(rmin_pattern.findall(param_lines)[-1])
diagonal = int(diagonalstyle_pattern.findall(param_lines)[-1])
if quadratic_pattern.findall(param_lines):
quadratic = bool(int(quadratic_pattern.findall(param_lines)[-1]))
else:
quadratic = False
describer = BispectrumCoefficients(rcutfac=rcut,
twojmax=twojmax,
rfac0=rfac,
element_profile=element_profile,
rmin0=rmin,
diagonalstyle=diagonal,
quadratic=quadratic,
pot_fit=True)
model = LinearModel(describer=describer, **kwargs)
model.model.coef_ = np.array(coeff_lines[2:], dtype=np.float)
model.model.intercept_ = 0
snap = SNAPotential(model=model)
snap.specie = Element(specie)
return 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.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 test_serialize(self):
json_str = json.dumps(self.lm.as_dict())
recover = LinearModel.from_dict(json.loads(json_str))
self.assertIsNotNone(recover)
class LinearModelTest(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.x_train = np.random.rand(10, 2)
cls.coef = np.random.rand(2)
cls.intercept = np.random.rand()
cls.y_train = cls.x_train.dot(cls.coef) + cls.intercept
def setUp(self):
class DummyDescriber(MSONable):
def describe(self, obj):
pass
def describe_all(self, n):
return pd.DataFrame(n)
self.lm = LinearModel(DummyDescriber())
self.test_dir = tempfile.mkdtemp()
def tearDown(self):
# Remove the directory after the test
shutil.rmtree(self.test_dir)
def test_fit_predict(self):
self.lm.fit(inputs=self.x_train, outputs=self.y_train)
x_test = np.random.rand(10, 2)
y_test = x_test.dot(self.coef) + self.intercept
y_pred = self.lm.predict(x_test)
np.testing.assert_array_almost_equal(y_test, y_pred)
np.testing.assert_array_almost_equal(self.coef, self.lm.coef)
self.assertAlmostEqual(self.intercept, self.lm.intercept)
def test_evaluate_fit(self):
self.lm.fit(inputs=self.x_train, outputs=self.y_train)
y_pred = self.lm.evaluate_fit()
np.testing.assert_array_almost_equal(y_pred, self.y_train)
def test_serialize(self):
json_str = json.dumps(self.lm.as_dict())
recover = LinearModel.from_dict(json.loads(json_str))
self.assertIsNotNone(recover)
def model_save_load(self):
self.lm.save(os.path.join(self.test_dir, 'test_lm.save'))
ori = self.lm.model.coef_
self.lm.load(os.path.join(self.test_dir, 'test_lm.save'))
loaded = self.lm.model.coef_
self.assertAlmostEqual(ori, loaded)