def setUp(self):
profile = {'Mo': {'r': 0.6, 'w': 1.}}
self.describer1 = BispectrumCoefficients(cutoff=4.6,
twojmax=6,
element_profile=profile,
quadratic=False,
pot_fit=True)
model1 = SKLModel(describer=self.describer1, model=LinearRegression())
self.potential1 = SNAPotential(model=model1, name='test')
self.describer2 = BispectrumCoefficients(cutoff=4.6,
twojmax=6,
element_profile=profile,
quadratic=True,
pot_fit=True)
model2 = SKLModel(describer=self.describer2, model=LinearRegression())
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']
class GaussianProcessTest(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.this_dir = os.path.dirname(os.path.abspath(__file__))
cls.test_dir = tempfile.mkdtemp()
def setUp(self):
self.x_train = np.atleast_2d([1., 3., 5., 6., 7., 8.]).T
self.y_train = (self.x_train * np.sin(self.x_train)).ravel()
self.gpr = SKLModel(model=GaussianProcessRegressor())
@classmethod
def tearDownClass(cls):
os.chdir(cls.this_dir)
shutil.rmtree(cls.test_dir)
def test_fit_predict(self):
self.gpr.fit(features=self.x_train, targets=self.y_train)
x_test = np.atleast_2d(np.linspace(0, 9, 1000)).T
y_test = x_test * np.sin(x_test)
y_pred, sigma = self.gpr._predict(x_test, return_std=True)
upper_bound = y_pred + 1.96 * sigma
lower_bound = y_pred - 1.96 * sigma
self.assertTrue(
np.all([
l < y and y < u
for u, y, l in zip(upper_bound, y_test, lower_bound)
]))
def setUp(self):
element_profile = {'Ni': {'r': 0.5, 'w': 1}}
describer1 = BispectrumCoefficients(cutoff=4.1,
twojmax=8,
element_profile=element_profile,
quadratic=False,
pot_fit=True)
model1 = SKLModel(describer=describer1, model=LinearRegression())
model1.model.coef_ = coeff
model1.model.intercept_ = intercept
snap1 = SNAPotential(model=model1)
self.ff_settings1 = snap1
describer2 = BispectrumCoefficients(cutoff=4.1,
twojmax=8,
element_profile=element_profile,
quadratic=True,
pot_fit=True)
model2 = SKLModel(describer=describer2, model=LinearRegression())
model2.model.coef_ = coeff
model2.model.intercept_ = intercept
snap2 = SNAPotential(model=model2)
self.ff_settings2 = snap2
self.struct = Structure.from_spacegroup('Fm-3m', Lattice.cubic(3.506),
['Ni'], [[0, 0, 0]])
def test_model_none(self):
m = SKLModel(model=LinearRegression())
x = np.array([[1, 2], [2, 1], [1, 1]])
y = np.array([[3], [3], [2]])
m.train(x, y)
np.testing.assert_almost_equal(m.model.coef_.ravel(),
np.array([1.0, 1.0]))
def setUp(self):
profile = {"Mo": {"r": 0.6, "w": 1.0}}
self.describer1 = BispectrumCoefficients(rcutfac=4.6,
twojmax=6,
element_profile=profile,
quadratic=False,
pot_fit=True)
model1 = SKLModel(describer=self.describer1, model=LinearRegression())
self.potential1 = SNAPotential(model=model1, name="test")
self.describer2 = BispectrumCoefficients(rcutfac=4.6,
twojmax=6,
element_profile=profile,
quadratic=True,
pot_fit=True)
model2 = SKLModel(describer=self.describer2, model=LinearRegression())
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 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("#")
]
element_profile = {}
ne, nbc = coeff_lines[0].split()
ne, nbc = int(ne), int(nbc)
for n in range(ne):
specie, r, w = coeff_lines[1 + n * (nbc + 1)].split()
r, w = float(r), float(w)
element_profile[specie] = {"r": r, "w": w}
rcut_pattern = re.compile(r"rcutfac (.*?)\n", re.S)
twojmax_pattern = re.compile(r"twojmax (\d*)\n", re.S)
quadratic_pattern = re.compile(r"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])
if quadratic_pattern.findall(param_lines):
quadratic = bool(int(quadratic_pattern.findall(param_lines)[-1]))
else:
quadratic = False
describer = BispectrumCoefficients(rcutfac=rcut,
twojmax=twojmax,
element_profile=element_profile,
quadratic=quadratic,
pot_fit=True)
model = SKLModel(model=LinearRegression(),
describer=describer,
**kwargs)
coef = np.array(
np.concatenate([
coeff_lines[(2 + nbc * n + n):(2 + nbc * (n + 1) + n)]
for n in range(ne)
]),
dtype=np.float64,
)
model.model.coef_ = coef
model.model.intercept_ = 0
snap = SNAPotential(model=model)
return snap
def setUp(self):
element_profile = {'Ni': {'r': 0.5, 'w': 1}}
describer = BispectrumCoefficients(cutoff=4.1, twojmax=8,
element_profile=element_profile,
pot_fit=True)
model = SKLModel(describer=describer, model=LinearRegression())
model.model.coef_ = coeff
model.model.intercept_ = intercept
snap = SNAPotential(model=model)
self.ff_settings = snap
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):
self.lm = SKLModel(model=LinearRegression())
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(features=self.x_train, targets=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.model.coef_)
self.assertAlmostEqual(self.intercept, self.lm.model.intercept_)
def test_model_save_load(self):
self.lm.fit(features=self.x_train, targets=self.y_train)
with ScratchDir('.'):
self.lm.save('test_lm.save')
ori = self.lm.model.coef_
self.lm.load('test_lm.save')
loaded = self.lm.model.coef_
np.testing.assert_almost_equal(ori, loaded)
lm2 = SKLModel.from_file('test_lm.save')
np.testing.assert_almost_equal(lm2.model.coef_, ori)
def test_model_none(self):
m = SKLModel(model=LinearRegression())
x = np.array([[1, 2], [2, 1], [1, 1]])
y = np.array([[3], [3], [2]])
m.train(x, y)
np.testing.assert_almost_equal(m.model.coef_.ravel(),
np.array([1.0, 1.0]))
def test_model_save_load(self):
self.lm.fit(features=self.x_train, targets=self.y_train)
with ScratchDir('.'):
self.lm.save('test_lm.save')
ori = self.lm.model.coef_
self.lm.load('test_lm.save')
loaded = self.lm.model.coef_
np.testing.assert_almost_equal(ori, loaded)
lm2 = SKLModel.from_file('test_lm.save')
np.testing.assert_almost_equal(lm2.model.coef_, ori)
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 = SKLModel(describer=describer, model=LinearRegression())
model.model.coef_ = coeff
model.model.intercept_ = intercept
snap = SNAPotential(model=model)
self.struct = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.506),
["Ni"], [[0, 0, 0]])
self.ff_settings = snap
def setUp(self):
self.lm = SKLModel(model=LinearRegression())
self.test_dir = tempfile.mkdtemp()
def setUp(self):
self.x_train = np.atleast_2d([1., 3., 5., 6., 7., 8.]).T
self.y_train = (self.x_train * np.sin(self.x_train)).ravel()
self.gpr = SKLModel(model=GaussianProcessRegressor())