C++ Code Documentation

• Structures
  • Structure
    • neighbor_count
    • cumulative_neighbor_count
    • neighbor_species
    • structure_indices
    • cell
    • cell_transpose
    • cell_transpose_inverse
    • cell_dot
    • cell_dot_inverse
    • positions
    • wrapped_positions
    • relative_positions
    • descriptor_calculators
    • descriptors
    • energy
    • forces
    • stresses
    • mean_efs
    • variance_efs
    • mean_contributions
    • local_uncertainties
    • Structure()
    • Structure()
    • Structure()
    • wrap_positions()
    • get_single_sweep_cutoff()
    • compute_neighbors()
    • compute_descriptors()
    • cutoff
    • single_sweep_cutoff
    • volume
    • sweep
    • n_neighbors
    • species
    • noa
• Bayesian force fields
  • SparseGP
    • SparseGP()
    • SparseGP()
    • initialize_sparse_descriptors()
    • add_all_environments()
    • add_specific_environments()
    • add_random_environments()
    • add_uncertain_environments()
    • compute_cluster_uncertainties()
    • sort_clusters_by_uncertainty()
    • add_training_structure()
    • update_Kuu()
    • update_Kuf()
    • stack_Kuu()
    • stack_Kuf()
    • update_matrices_QR()
    • predict_mean()
    • predict_SOR()
    • predict_DTC()
    • predict_local_uncertainties()
    • compute_likelihood_stable()
    • compute_likelihood_gradient_stable()
    • precompute_KnK()
    • compute_KnK()
    • compute_dKnK()
    • compute_likelihood()
    • compute_likelihood_gradient()
    • set_hyperparameters()
    • write_mapping_coefficients()
    • write_varmap_coefficients()
    • write_sparse_descriptors()
    • write_L_inverse()
    • hyperparameters
    • kernels
    • Kuu_kernels
    • Kuf_kernels
    • Kuu
    • Kuf
    • Kuf_e_noise_Kfu
    • Kuf_f_noise_Kfu
    • Kuf_s_noise_Kfu
    • KnK_e
    • KnK_f
    • KnK_s
    • n_kernels
    • Kuu_jitter
    • Sigma
    • Kuu_inverse
    • R_inv
    • L_inv
    • alpha
    • R_inv_diag
    • L_diag
    • sparse_descriptors
    • training_structures
    • sparse_indices
    • training_atom_indices
    • noise_vector
    • y
    • label_count
    • e_noise_one
    • f_noise_one
    • s_noise_one
    • inv_e_noise_one
    • inv_f_noise_one
    • inv_s_noise_one
    • n_energy_labels
    • n_force_labels
    • n_stress_labels
    • n_sparse
    • n_labels
    • n_strucs
    • energy_noise
    • force_noise
    • stress_noise
    • log_marginal_likelihood
    • data_fit
    • complexity_penalty
    • trace_term
    • constant_term
    • likelihood_gradient
    • varmap_coeffs
• Descriptors
  • Descriptor
    • Descriptor()
    • compute_struc()
    • ~Descriptor()
    • write_to_file()
    • return_json()
    • descriptor_name
  • DescriptorValues
    • DescriptorValues()
    • n_descriptors
    • n_types
    • n_atoms
    • volume
    • descriptors
    • descriptor_force_dervs
    • neighbor_coordinates
    • descriptor_norms
    • descriptor_force_dots
    • cutoff_values
    • cutoff_dervs
    • neighbor_counts
    • cumulative_neighbor_counts
    • atom_indices
    • neighbor_indices
    • n_clusters
    • n_clusters_by_type
    • cumulative_type_count
    • n_neighbors_by_type
  • ClusterDescriptor
    • ClusterDescriptor()
    • ClusterDescriptor()
    • ClusterDescriptor()
    • ClusterDescriptor()
    • initialize_cluster()
    • add_clusters_by_type()
    • add_clusters()
    • add_all_clusters()
    • descriptors
    • descriptor_norms
    • cutoff_values
    • n_clusters_by_type
    • cumulative_type_count
    • n_descriptors
    • n_types
    • n_clusters
  • B2
    • B2()
    • B2()
    • B2()
    • compute_struc()
    • write_to_file()
    • return_json()
    • radial_pointer
    • cutoff_pointer
    • radial_basis
    • cutoff_function
    • radial_hyps
    • cutoff_hyps
    • descriptor_settings
    • descriptor_name
    • cutoffs
• Kernels
  • Kernel
    • Kernel()
    • Kernel()
    • envs_envs()
    • envs_envs_grad()
    • envs_struc()
    • envs_struc_grad()
    • self_kernel_struc()
    • struc_struc()
    • compute_mapping_coefficients()
    • compute_varmap_coefficients()
    • write_info()
    • Kuu_grad()
    • Kuf_grad()
    • set_hyperparameters()
    • ~Kernel()
    • return_json()
    • kernel_hyperparameters
    • kernel_name
  • NormalizedDotProduct
    • NormalizedDotProduct()
    • NormalizedDotProduct()
    • envs_envs()
    • envs_envs_grad()
    • envs_struc()
    • envs_struc_grad()
    • self_kernel_struc()
    • struc_struc()
    • Kuu_grad()
    • Kuf_grad()
    • set_hyperparameters()
    • compute_map_coeff_pow1()
    • compute_map_coeff_pow2()
    • compute_mapping_coefficients()
    • compute_varmap_coefficients()
    • write_info()
    • sigma
    • sig2
    • power