def GenGrid_serial(self, GP):
'''
generate grid data of mean prediction and L^{-1}k* for each triplet
implemented in a parallelized style
'''
# ------ get 3body kernel info ------
kernel, efk, cutoffs, hyps, hyps_mask = get_3bkernel(GP)
# ------ construct grids ------
nop = self.grid_num[0]
noa = self.grid_num[2]
bond_lengths = np.linspace(self.l_bounds[0], self.u_bounds[0], nop)
cos_angles = np.linspace(self.l_bounds[2], self.u_bounds[2], noa)
bond_means = np.zeros([nop, nop, noa])
bond_vars = np.zeros([nop, nop, noa, len(GP.alpha)])
env12 = AtomicEnvironment(self.bond_struc, 0, self.cutoffs)
if self.update:
if 'kv3' in os.listdir():
os.rmdir('kv3')
os.mkdir('kv3')
size = len(GP.training_data)
ds = [1, 2, 3]
k_v = np.zeros(3)
k12_v_all = np.zeros([len(bond_lengths), len(bond_lengths),
len(cos_angles), size*3])
for b1, r1 in enumerate(bond_lengths):
for b2, r2 in enumerate(bond_lengths):
for a12, cos_angle12 in enumerate(cos_angles):
x2 = r2 * cos_angle12
y2 = r2 * np.sqrt(1-cos_angle12**2)
r12 = np.linalg.norm(np.array([x2-r1, y2, 0]))
env12.bond_array_3 = np.array([[r1, 1, 0, 0],
[r2, 0, 0, 0]])
env12.cross_bond_dists = np.array([[0, r12], [r12, 0]])
for isample, sample in enumerate(GP.training_data):
for d in ds:
k_v[d-1] = kernel(env12, sample, 1, d,
hyps, cutoffs)
k12_v_all[b1, b2, a12, isample*3:isample*3+3] = k_v
for b1, r1 in enumerate(bond_lengths):
for b2, r2 in enumerate(bond_lengths):
for a12, cos_angle in enumerate(cos_angles):
k12_v = k12_v_all[b1, b2, a12, :]
bond_means[b1, b2, a12] = np.matmul(k12_v, GP.alpha)
if not self.mean_only:
bond_vars[b1, b2, a12, :] = solve_triangular(GP.l_mat, k12_v, lower=True)
# # ------ save mean and var to file -------
np.save('grid3_mean', bond_means)
np.save('grid3_var', bond_vars)
return bond_means, bond_vars
def get_grid_env(species, parameter, kernel_name, same_hyps):
'''generate a single triplet environment'''
env1, env2, hm1, hm2 = parameter[kernel_name]
hm = hm1 if same_hyps else hm2
big_cell = np.eye(3) * 100
r1 = 0.5
r2 = 0.5
if kernel_name == 'twobody':
positions = [[0, 0, 0], [r1, 0, 0]]
grid_struc = Structure(big_cell, species, positions)
env = AtomicEnvironment(grid_struc, 0, hm['cutoffs'], hm)
grid = np.array([[r1]])
elif kernel_name == 'threebody':
positions = [[0, 0, 0], [r1, 0, 0], [0, r2, 0]]
grid_struc = Structure(big_cell, species, positions)
env = AtomicEnvironment(grid_struc, 0, hm['cutoffs'], hm)
env.bond_array_3 = np.array([[r1, 1, 0, 0], [r2, 0, 0, 0]])
grid = np.array([[r1, r2, np.sqrt(r1**2 + r2**2)]])
return env, grid
