def calculate_gp(self, atoms):
# Compute energy, forces, and stresses and their uncertainties
if self.par:
res = predict_on_structure_efs_par(atoms,
self.gp_model,
write_to_structure=False)
else:
res = predict_on_structure_efs(atoms,
self.gp_model,
write_to_structure=False)
# Set the energy, force, and stress attributes of the calculator.
res_name = [
"local_energies",
"forces",
"partial_stresses",
"local_energy_stds",
"stds",
"partial_stress_stds",
]
res_dims = [1, 3, 6, 1, 3, 6]
for i in range(len(res_name)):
if len(res[i].shape) == 2:
assert (
res[i].shape[1] == res_dims[i],
f"{res_name[i]} shape doesn't match, "
f"{res[i].shape[1]} and {res_dims[i]}",
)
elif len(res[i].shape) == 1:
assert res_dims[i] == 1
self.results[res_name[i]] = res[i]
def test_predict_efs(two_plus_three_gp):
test_structure, _ = \
get_random_structure(np.eye(3), [1, 2], 3)
ens, forces, stresses, en_stds, force_stds, stress_stds = \
predict_on_structure_efs(test_structure, two_plus_three_gp)
forces_2, force_stds_2 = \
predict_on_structure(test_structure, two_plus_three_gp)
ens_p, forces_p, stresses_p, en_stds_p, force_stds_p, stress_stds_p = \
predict_on_structure_efs_par(test_structure, two_plus_three_gp)
# Check agreement between efs and standard prediction.
assert (np.isclose(forces, forces_2).all())
assert (np.isclose(force_stds, force_stds_2).all())
# Check agreement between serial and parallel efs methods.
assert (np.isclose(ens, ens_p).all())
assert (np.isclose(forces, forces_p).all())
assert (np.isclose(stresses, stresses_p).all())
assert (np.isclose(en_stds, en_stds_p).all())
assert (np.isclose(force_stds, force_stds_p).all())
assert (np.isclose(stress_stds, stress_stds_p).all())
# Check that the prediction has been recorded within the structure.
assert(np.equal(stress_stds, test_structure.partial_stress_stds).all())
def calculate_gp(self, atoms):
# Compute energy, forces, and stresses and their uncertainties
if self.par:
res = predict_on_structure_efs_par(atoms,
self.gp_model,
write_to_structure=False)
else:
res = predict_on_structure_efs(atoms,
self.gp_model,
write_to_structure=False)
# Set the energy, force, and stress attributes of the calculator.
self.results["local_energies"] = res[0]
self.results["forces"] = res[1]
self.results["partial_stresses"] = -res[2][:, [0, 3, 5, 4, 2, 1]]
self.results["local_energy_stds"] = res[3]
self.results["stds"] = res[4]
self.results["partial_stress_stds"] = res[5][:, [0, 3, 5, 4, 2, 1]]