def test_log_marginal_likelihood_derivative(self):
kernel = RBFKernel(length_scale=2.1) + RBFKernel(length_scale=.345)
theta0 = np.exp(kernel.theta)
calc = GPRCalculator(kernel=kernel, C1=1e8, C2=1e8, opt_restarts=0)
atoms = molecule('C2H6')
atoms.set_calculator(EMT())
calc.add_data(atoms)
calc.fit()
dt = 1e-5
L, dL = calc.log_marginal_likelihood()
dL_num = np.zeros_like(dL)
for i in range(len(theta0)):
dti = np.zeros(len(theta0))
dti[i] = dt
calc.kernel.theta = np.log(theta0 + dti)
L_plus = calc.log_marginal_likelihood()[0]
calc.kernel.theta = np.log(theta0 - dti)
L_minus = calc.log_marginal_likelihood()[0]
calc.kernel.theta = np.log(theta0)
dL_num[i] = (L_plus - L_minus)/(2*dt)
np.testing.assert_allclose(dL, dL_num)
def test_RBF_times_ConstantKernel(self):
n = 3
m = 4
n_dim = 12
X = np.random.randn(n, n_dim)
Y = np.random.randn(m, n_dim)
factor = 10.0
prod_kernel = Product(RBFKernel(), ConstantKernel(constant=factor))
ref_kernel = RBFKernel()
K_prod, dK_prod = prod_kernel(
X, Y, dx=True, dy=True, eval_gradient=True)
K_ref, dK_ref1 = ref_kernel(X, Y, dx=True, dy=True, eval_gradient=True)
# Derivative with respect to the second hyperparameter:
dK_ref2 = np.zeros((n*(1+n_dim), m*(1+n_dim), 1))
dK_ref2[:, :, 0] = K_ref
K_ref *= factor
dK_ref1 *= factor
np.testing.assert_allclose(K_prod, K_ref)
np.testing.assert_allclose(dK_prod[:, :, :-1], dK_ref1)
np.testing.assert_allclose(dK_prod[:, :, -1:], dK_ref2)
def test_rbf_squared(self):
X = np.random.randn(3, 4)
Y = np.random.randn(3, 4)
kernel1 = Exponentiation(RBFKernel(length_scale=2.0), exponent=4)
kernel2 = RBFKernel(length_scale=1.0)
K1, dK1 = kernel1(X, Y, dx=True, dy=True, eval_gradient=True)
K2, dK2 = kernel2(X, Y, dx=True, dy=True, eval_gradient=True)
np.testing.assert_allclose(K1, K2)
np.testing.assert_allclose(2*dK1, dK2)
def test_comparison2product(self):
X = np.random.randn(3, 4)
Y = np.random.randn(3, 4)
kernel1 = Exponentiation(RBFKernel(length_scale=1.23), exponent=2)
kernel2 = Product(RBFKernel(length_scale=1.23),
RBFKernel(length_scale=1.23))
K1 = kernel1(X, Y, dx=True, dy=True)
K2 = kernel2(X, Y, dx=True, dy=True)
np.testing.assert_allclose(K1, K2)
def test_versus_anisotropic_rbf(self):
X = np.random.randn(8, 2)
Y = np.random.randn(8, 2)
kernel = Product(Masking(RBFKernel(length_scale=1.5), slice(0, 1)),
Masking(RBFKernel(length_scale=0.5), slice(1, 2)))
ref_kernel = RBFKernel(length_scale=np.array([1.5, 0.5]))
K, dK = kernel(X, Y, dx=True, dy=True, eval_gradient=True)
K_ref, dK_ref = ref_kernel(X, Y, dx=True, dy=True, eval_gradient=True)
np.testing.assert_allclose(K, K_ref)
np.testing.assert_allclose(dK, dK_ref)
def test__mul__(self):
X = np.random.randn(3, 4)
Y = np.random.randn(3, 4)
factor = 10.0
kernel1 = RBFKernel() * factor
kernel2 = RBFKernel() * ConstantKernel(constant=factor)
np.testing.assert_equal(kernel1.theta, kernel2.theta)
K1, dK1 = kernel1(X, Y, dx=True, dy=True, eval_gradient=True)
K2, dK2 = kernel2(X, Y, dx=True, dy=True, eval_gradient=True)
np.testing.assert_allclose(K1, K2)
np.testing.assert_allclose(dK1, dK2)
def test_prediction_variance(self):
direction = np.array([1., 2., 3.])
direction /= np.linalg.norm(direction)
r_train = [0.7, 1.7]
images_train = []
for ri in r_train:
image = Atoms(
['C', 'O'],
positions=np.array([-0.5*ri*direction, 0.5*ri*direction]))
image.set_calculator(EMT())
images_train.append(image)
r_test = np.linspace(0.5, 1.9, 101)
images_test = []
for ri in r_test:
image = Atoms(
['C', 'O'],
positions=np.array([-0.5*ri*direction, 0.5*ri*direction]))
image.set_calculator(EMT())
images_test.append(image)
kernel = RBFKernel(constant=100., length_scale=.1)
calc = GPRCalculator(kernel=kernel, C1=1E8, C2=1E8, opt_restarts=0)
[calc.add_data(im) for im in images_train]
calc.fit()
prediction_var = [calc.predict_var(im)[0] for im in images_test]
max_var = np.argmax(prediction_var)
np.testing.assert_equal(r_test[max_var], 1.2)
def test_h2(self):
mol = molecule('H2')
mol.set_calculator(EMT())
kernel = Rescaling(RBFKernel())
ml_calc = GPRCalculator(kernel=kernel,
opt_restarts=1,
normalize_y='max+10')
r_test = np.linspace(0.6, 2.0)
atoms_test = [
Atoms(['H', 'H'],
positions=np.array([[0, 0, 0.5 * ri], [0, 0, -0.5 * ri]]))
for ri in r_test
]
E_test = [EMT().get_potential_energy(atoms) for atoms in atoms_test]
# import matplotlib.pyplot as plt
def callback_after(ml_calc):
plt.plot(r_test, E_test)
plt.plot(r_test,
[ml_calc.predict(atoms)[0] for atoms in atoms_test])
for atoms in ml_calc.atoms_train:
xyzs = atoms.get_positions()
r = xyzs[0, 2] - xyzs[1, 2]
print(r)
plt.plot(r, ml_calc.predict(atoms)[0], 'o')
plt.show()
opt = MLOptimizer(mol,
ml_calc) #, callback_after_ml_opt=callback_after)
opt.run()
def test_build_diag(self):
direction = np.array([1., 2., 3.])
direction /= np.linalg.norm(direction)
r_train = np.linspace(0.5, 7, 11)
energies_train = []
images_train = []
for ri in r_train:
image = Atoms(['C', 'O'],
positions=np.array(
[-0.5 * ri * direction, 0.5 * ri * direction]))
image.set_calculator(EMT())
energies_train.append(image.get_potential_energy())
images_train.append(image)
cut = 6.5
with SymmetryFunctionSet(["C", "O"], cutoff=cut) as sfs:
sfs.add_Artrith_Kolpak_set()
kernel = RBFKernel(constant=100.0, length_scale=1e-2)
calc = GAPCalculator(descriptor_set=sfs,
kernel=kernel,
C1=1e8,
C2=1e8,
opt_restarts=0)
[calc.add_data(im) for im in images_train]
calc.fit()
np.testing.assert_allclose(
calc.build_kernel_diagonal((calc.Gs_norm, calc.dGs_norm)),
np.diag(calc.build_kernel_matrix()))
def test_comparison2product(self):
n = 3
m = 4
n_dim = 12
X = np.random.randn(n, n_dim)
Y = np.random.randn(m, n_dim)
factor = 10.0
kernel1 = Rescaling(RBFKernel(), factor)
kernel2 = Product(ConstantKernel(constant=factor), RBFKernel())
K1, dK1 = kernel1(X, Y, dx=True, dy=True, eval_gradient=True)
K2, dK2 = kernel2(X, Y, dx=True, dy=True, eval_gradient=True)
np.testing.assert_allclose(K1, K2)
np.testing.assert_allclose(dK1, dK2)
def test_butadiene(self):
mol = molecule('butadiene')
mol.set_calculator(EMT())
kernel = Rescaling(RBFKernel())
ml_calc = GPRCalculator(kernel=kernel,
opt_restarts=1,
normalize_y='max+10')
opt = MLOptimizer(mol, ml_calc)
opt.run()
def test_co_kernel_derivative(self):
direction = np.array([1., 2., 3.])
direction /= np.linalg.norm(direction)
atoms = Atoms(['C', 'O'],
positions=np.array([-0.5 * direction, 0.5 * direction]))
atoms.set_calculator(EMT())
def to_radius(x):
xyzs = x.get_positions()
r = np.sqrt(np.sum((xyzs[1, :] - xyzs[0, :])**2))
dr = np.zeros((1, 6))
dr[0, 0] = (xyzs[0, 0] - xyzs[1, 0]) / r
dr[0, 1] = (xyzs[0, 1] - xyzs[1, 1]) / r
dr[0, 2] = (xyzs[0, 2] - xyzs[1, 2]) / r
dr[0, 3] = (xyzs[1, 0] - xyzs[0, 0]) / r
dr[0, 4] = (xyzs[1, 1] - xyzs[0, 1]) / r
dr[0, 5] = (xyzs[1, 2] - xyzs[0, 2]) / r
return [r], dr
kernel = RBFKernel(constant=100.0, length_scale=0.23)
calc = NCGPRCalculator(input_transform=to_radius,
kernel=kernel,
C1=1e8,
C2=1e8,
opt_restarts=0)
calc.add_data(atoms)
K = calc.build_kernel_matrix()
K_num = np.zeros_like(K)
# kernel value is not tested:
K_num[0, 0] = K[0, 0]
x0 = atoms.get_positions()
dx = 1e-4
def K_fun(x, y):
a = np.array([to_radius(Atoms(['C', 'O'], positions=x))[0]])
b = np.array([to_radius(Atoms(['C', 'O'], positions=y))[0]])
return calc.kernel(a, b, dx=True, dy=True)[0, 0]
for i in range(6):
dxi = np.zeros(6)
dxi[i] = dx
dxi = dxi.reshape((2, 3))
# Test first derivative
K_num[1 + i, 0] = self.num_dx_forth_order(K_fun, x0, x0, dxi)
for j in range(6):
dxj = np.zeros(6)
dxj[j] = dx
dxj = dxj.reshape((2, 3))
K_num[1 + i, 1 + j] = self.num_dxdy_forth_order(
K_fun, x0, x0, dxi, dxj)
# Test symmetry of derivatives
K_num[0, 1 + i] = self.num_dy_forth_order(K_fun, x0, x0, dxi)
np.testing.assert_allclose(K, K_num, atol=1E-5)
class RescalingTest(KernelTest.KernelTest):
kernel = Rescaling(RBFKernel(), 10.0)
def test_comparison2product(self):
n = 3
m = 4
n_dim = 12
X = np.random.randn(n, n_dim)
Y = np.random.randn(m, n_dim)
factor = 10.0
kernel1 = Rescaling(RBFKernel(), factor)
kernel2 = Product(ConstantKernel(constant=factor), RBFKernel())
K1, dK1 = kernel1(X, Y, dx=True, dy=True, eval_gradient=True)
K2, dK2 = kernel2(X, Y, dx=True, dy=True, eval_gradient=True)
np.testing.assert_allclose(K1, K2)
np.testing.assert_allclose(dK1, dK2)
def test__rmul__(self):
X = np.random.randn(3, 4)
Y = np.random.randn(3, 4)
factor = 10.0
kernel1 = factor * RBFKernel()
kernel2 = ConstantKernel(constant=factor) * RBFKernel()
np.testing.assert_equal(kernel1.theta, kernel2.theta)
K1, dK1 = kernel1(X, Y, dx=True, dy=True, eval_gradient=True)
K2, dK2 = kernel2(X, Y, dx=True, dy=True, eval_gradient=True)
np.testing.assert_allclose(K1, K2)
np.testing.assert_allclose(dK1, dK2)
def test__mul__(self):
X = np.random.randn(3, 4)
Y = np.random.randn(3, 4)
factor = 10.0
kernel1 = RBFKernel() * factor
kernel2 = RBFKernel() * ConstantKernel(constant=factor)
np.testing.assert_equal(kernel1.theta, kernel2.theta)
K1, dK1 = kernel1(X, Y, dx=True, dy=True, eval_gradient=True)
K2, dK2 = kernel2(X, Y, dx=True, dy=True, eval_gradient=True)
np.testing.assert_allclose(K1, K2)
np.testing.assert_allclose(dK1, dK2)
def test_RBF_plus_ConstantKernel(self):
n = 3
m = 4
n_dim = 12
X = np.random.randn(n, n_dim)
Y = np.random.randn(m, n_dim)
constant = 10.0
sum_kernel = Sum(RBFKernel(), ConstantKernel(constant=constant))
ref_kernel = RBFKernel()
K_sum, dK_sum = sum_kernel(X, Y, dx=True, dy=True, eval_gradient=True)
K_ref, dK_ref1 = ref_kernel(X, Y, dx=True, dy=True, eval_gradient=True)
K_ref[:n, :m] += constant
# Derivative with respect to the second hyperparameter:
dK_ref2 = np.zeros((n*(1+n_dim), m*(1+n_dim), 1))
dK_ref2[:n, :m, 0] = 1.0
np.testing.assert_allclose(K_sum, K_ref)
np.testing.assert_allclose(dK_sum[:, :, :-1], dK_ref1)
np.testing.assert_allclose(dK_sum[:, :, -1:], dK_ref2)
def test_equivalence_to_GPR(self):
def to_cartesian(atoms):
xyzs = atoms.get_positions().flatten()
return xyzs, np.eye(len(xyzs))
gpr_calc = GPRCalculator(kernel=RBFKernel(constant=100.0,
length_scale=0.456),
C1=1e8,
C2=1e8,
opt_restarts=1)
ncgpr_calc = NCGPRCalculator(kernel=RBFKernel(constant=100.0,
length_scale=0.456),
input_transform=to_cartesian,
C1=1e8,
C2=1e8,
opt_restarts=1)
atoms = molecule('cyclobutane')
atoms.set_calculator(EMT())
xyzs = atoms.get_positions()
gpr_calc.add_data(atoms)
ncgpr_calc.add_data(atoms)
for i in range(8):
a = atoms.copy()
a.set_calculator(EMT())
a.set_positions(xyzs + 0.5 * np.random.randn(*xyzs.shape))
gpr_calc.add_data(a)
ncgpr_calc.add_data(a)
np.testing.assert_allclose(ncgpr_calc.build_kernel_matrix(),
gpr_calc.build_kernel_matrix())
gpr_calc.fit()
ncgpr_calc.fit()
np.testing.assert_allclose(ncgpr_calc.kernel.theta,
gpr_calc.kernel.theta)
np.testing.assert_allclose(ncgpr_calc.alpha, gpr_calc.alpha)
class RBFKernelTest(KernelTest.KernelTest):
kernel = RBFKernel(constant=23.4, factor=1.234, length_scale=1.321)
def test_symmetry(self):
atomsX = np.random.randn(1, 12)
atomsY = np.random.randn(1, 12)
constant = 23.4
factor = 1.234
length_scale = 1.321
kernel = RBFKernel(constant=constant,
factor=factor,
length_scale=length_scale)
K1 = kernel(atomsX, atomsY, dx=True, dy=True)
K2 = kernel(atomsY, atomsX, dx=True, dy=True)
N = len(atomsX)
# K and H blocks are symmmetric
np.testing.assert_allclose(K1[:N, :N], K2[:N, :N])
np.testing.assert_allclose(K1[N:, N:], K2[N:, N:])
# J and J^T are antisymmetric
np.testing.assert_allclose(K1[:N, N:], -K2[:N, N:])
np.testing.assert_allclose(K1[N:, :N], -K2[N:, :N])
def test_equivalence_to_RBFKernel_with_factor(self):
atoms = np.random.randn(10, 9)
constant = 23.4
factor = 1.234
length_scale = 0.4321
kernel_with = RBFKernel_with_factor(constant=constant,
factor=factor,
length_scale=length_scale)
kernel_without = RBFKernel(constant=constant,
factor=factor,
length_scale=length_scale)
K_with, dK_with = kernel_with(atoms,
atoms,
dx=True,
dy=True,
eval_gradient=True)
K_without, dK_without = kernel_without(atoms,
atoms,
dx=True,
dy=True,
eval_gradient=True)
np.testing.assert_allclose(K_with, K_without)
np.testing.assert_allclose(dK_with[:, :, 1:], dK_without)
def test_symmetry(self):
atomsX = np.random.randn(1, 12)
atomsY = np.random.randn(1, 12)
constant = 23.4
factor = 1.234
length_scale = 1.321
kernel = RBFKernel(constant=constant,
factor=factor,
length_scale=length_scale)
K1 = kernel(atomsX, atomsY, dx=True, dy=True)
K2 = kernel(atomsY, atomsX, dx=True, dy=True)
N = len(atomsX)
# K and H blocks are symmmetric
np.testing.assert_allclose(K1[:N, :N], K2[:N, :N])
np.testing.assert_allclose(K1[N:, N:], K2[N:, N:])
# J and J^T are antisymmetric
np.testing.assert_allclose(K1[:N, N:], -K2[:N, N:])
np.testing.assert_allclose(K1[N:, :N], -K2[N:, :N])
class ExponentiationTest(KernelTest.KernelTest):
kernel = Exponentiation(RBFKernel(), 2.0)
def test_rbf_squared(self):
X = np.random.randn(3, 4)
Y = np.random.randn(3, 4)
kernel1 = Exponentiation(RBFKernel(length_scale=2.0), exponent=4)
kernel2 = RBFKernel(length_scale=1.0)
K1, dK1 = kernel1(X, Y, dx=True, dy=True, eval_gradient=True)
K2, dK2 = kernel2(X, Y, dx=True, dy=True, eval_gradient=True)
np.testing.assert_allclose(K1, K2)
np.testing.assert_allclose(2*dK1, dK2)
def test_dot_product(self):
X = np.random.randn(3, 4)
Y = np.random.randn(3, 4)
kernel1 = Exponentiation(DotProductKernel(exponent=2), exponent=2)
kernel2 = DotProductKernel(exponent=4)
K1 = kernel1(X, Y, dx=True, dy=True)
K2 = kernel2(X, Y, dx=True, dy=True)
np.testing.assert_allclose(K1, K2)
def test_comparison2product(self):
X = np.random.randn(3, 4)
Y = np.random.randn(3, 4)
kernel1 = Exponentiation(RBFKernel(length_scale=1.23), exponent=2)
kernel2 = Product(RBFKernel(length_scale=1.23),
RBFKernel(length_scale=1.23))
K1 = kernel1(X, Y, dx=True, dy=True)
K2 = kernel2(X, Y, dx=True, dy=True)
np.testing.assert_allclose(K1, K2)
def test_co_potential_curve(self):
direction = np.array([1., 2., 3.])
direction /= np.linalg.norm(direction)
r_train = np.linspace(0.5, 7, 11)
energies_train = []
images_train = []
for ri in r_train:
image = Atoms(
['C', 'O'],
positions=np.array([-0.5*ri*direction, 0.5*ri*direction]))
image.set_calculator(EMT())
energies_train.append(image.get_potential_energy())
images_train.append(image)
kernel = RBFKernel(constant=100.0, length_scale=1e-1)
calc = GPRCalculator(kernel=kernel, C1=1e8, C2=1e8, opt_restarts=0)
[calc.add_data(im) for im in images_train]
calc.fit()
np.testing.assert_allclose(
energies_train,
[calc.predict(im)[0] for im in images_train])
def test_build_diag(self):
direction = np.array([1., 2., 3.])
direction /= np.linalg.norm(direction)
r_train = np.linspace(0.5, 7, 11)
energies_train = []
images_train = []
for ri in r_train:
image = Atoms(['C', 'O'],
positions=np.array(
[-0.5 * ri * direction, 0.5 * ri * direction]))
image.set_calculator(EMT())
energies_train.append(image.get_potential_energy())
images_train.append(image)
def to_radius(x):
xyzs = x.get_positions()
r = np.sqrt(np.sum((xyzs[1, :] - xyzs[0, :])**2))
dr = np.zeros((1, 6))
dr[0, 0] = (xyzs[0, 0] - xyzs[1, 0]) / r
dr[0, 1] = (xyzs[0, 1] - xyzs[1, 1]) / r
dr[0, 2] = (xyzs[0, 2] - xyzs[1, 2]) / r
dr[0, 3] = (xyzs[1, 0] - xyzs[0, 0]) / r
dr[0, 4] = (xyzs[1, 1] - xyzs[0, 1]) / r
dr[0, 5] = (xyzs[1, 2] - xyzs[0, 2]) / r
return [r], dr
kernel = RBFKernel(constant=100.0, length_scale=1e-1)
calc = NCGPRCalculator(input_transform=to_radius,
kernel=kernel,
C1=1e8,
C2=1e8,
opt_restarts=0)
[calc.add_data(im) for im in images_train]
calc.fit()
np.testing.assert_allclose(
calc.build_kernel_diagonal((calc.q_train, calc.dq_train)),
np.diag(calc.build_kernel_matrix()))
def test_equivalence_to_RBFKernel_with_factor(self):
atoms = np.random.randn(10, 9)
constant = 23.4
factor = 1.234
length_scale = 0.4321
kernel_with = RBFKernel_with_factor(constant=constant,
factor=factor,
length_scale=length_scale)
kernel_without = RBFKernel(constant=constant,
factor=factor,
length_scale=length_scale)
K_with, dK_with = kernel_with(atoms,
atoms,
dx=True,
dy=True,
eval_gradient=True)
K_without, dK_without = kernel_without(atoms,
atoms,
dx=True,
dy=True,
eval_gradient=True)
np.testing.assert_allclose(K_with, K_without)
np.testing.assert_allclose(dK_with[:, :, 1:], dK_without)
class RBFtimesRBFTest(KernelTest.KernelTest):
kernel = Product(RBFKernel(length_scale=0.8),
RBFKernel(length_scale=1.2))
def test_ethane_primitives_kernel_derivative(self):
atoms = molecule('C2H6')
atoms.set_calculator(EMT())
symbols = atoms.get_chemical_symbols()
# Add gaussian noise because of numerical problem for
# the 180 degree angle
images = []
np.random.seed(123)
for _ in range(4):
image = atoms.copy()
image.set_positions(image.get_positions() +
0.05 * np.random.randn(len(atoms), 3))
image.set_calculator(EMT())
images.append(image)
np.random.seed()
atomsX = images[:-1]
atomsY = images[-1:]
n = len(atomsX)
m = len(atomsY)
# Ethane bonds:
bonds = [(0, 1), (0, 2), (0, 3), (0, 4), (1, 5), (1, 6), (1, 7)]
transform, _, _ = to_primitives_factory(bonds)
kernel = RBFKernel(constant=0.0, length_scale=3.21)
calc = NCGPRCalculator(input_transform=transform,
kernel=kernel,
C1=1e8,
C2=1e8,
opt_restarts=0)
[calc.add_data(a) for a in atomsX]
qY, dqY = transform(atomsY[0])
K = calc.build_kernel_matrix(X_star=(qY, dqY))
K_num = np.zeros_like(K)
# kernel value is not tested:
K_num[:n, :m] = K[:n, :m]
dx = 1e-4
calc.atoms_train = [atoms]
def K_fun(x, y):
qx, dqx = transform(Atoms(symbols, positions=x))
calc.q_train, calc.dq_train = [qx], [dqx]
return calc.build_kernel_matrix(
X_star=transform(Atoms(symbols, positions=y)))[0, 0]
def K_dY(x, y):
qx, dqx = transform(Atoms(symbols, positions=x))
calc.q_train, calc.dq_train = [qx], [dqx]
return calc.build_kernel_matrix(
X_star=transform(Atoms(symbols, positions=y)))[0, 1:]
for i in range(n):
x0 = atomsX[i].get_positions()
for j in range(m):
y0 = atomsY[j].get_positions()
for k in range(len(atoms) * 3):
dxk = np.zeros((len(atoms), 3))
dxk.flat[k] = dx
# Test first derivative
K_num[n + i * calc.n_dim + k,
j] = self.num_dx_forth_order(K_fun, x0, y0, dxk)
# Approximate second derivative as numerical derivative of
# analytical first derivative
K_num[n + i * calc.n_dim + k,
m:] = self.num_dx_forth_order(K_dY, x0, y0, dxk)
# Test symmetry of derivatives
K_num[i, m + j * calc.n_dim + k] = self.num_dy_forth_order(
K_fun, x0, y0, dxk)
np.testing.assert_allclose(K, K_num, atol=1E-5)
class RBFKernelAnisoTest(KernelTest.KernelTest):
kernel = RBFKernel(constant=23.4,
factor=1.234,
length_scale=np.array([1.321] * 12))
class RBFplusRBFTest(KernelTest.KernelTest):
kernel = Sum(RBFKernel(length_scale=0.8),
RBFKernel(length_scale=1.2))
from ase.io import read, write
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.neb import NEB
from mlpot.mlneb import run_mla_neb
from mlpot.calculators.gprcalculator import GPRCalculator
from mlpot.kernels import RBFKernel
initial = read('initial.traj')
final = read('final.traj')
constraint = FixAtoms(mask=[atom.tag > 0 for atom in initial])
images = [initial]
for i in range(5):
image = initial.copy()
image.set_calculator(EMT())
image.set_constraint(constraint)
images.append(image)
images.append(final)
neb = NEB(images)
neb.interpolate()
kernel = RBFKernel(constant=100.0, length_scale=1.0)
ml_calc = GPRCalculator(kernel=kernel, C1=1E8, C2=1E8, opt_restarts=1)
run_mla_neb(neb, ml_calc)
write('minimum_energy_path.traj', images)