Bayesian force fields

class SparseGP

Public Functions

SparseGP()

SparseGP(std::vector<Kernel*> kernels, double energy_noise, double force_noise, double stress_noise)

void initialize_sparse_descriptors(const Structure &structure)

void add_all_environments(const Structure &structure)

void add_specific_environments(const Structure &structure, const std::vector<int> atoms)

void add_random_environments(const Structure &structure, const std::vector<int> &n_added)

void add_uncertain_environments(const Structure &structure, const std::vector<int> &n_added)

std::vector<Eigen::VectorXd> compute_cluster_uncertainties(const Structure &structure)

std::vector<std::vector<int>> sort_clusters_by_uncertainty(const Structure &structure)

void add_training_structure(const Structure &structure, const std::vector<int> atom_indices = {-1}, double rel_e_noise = 1, double rel_f_noise = 1, double rel_s_noise = 1)

void update_Kuu(const std::vector<ClusterDescriptor> &cluster_descriptors)

void update_Kuf(const std::vector<ClusterDescriptor> &cluster_descriptors)

void stack_Kuu()

void stack_Kuf()

void update_matrices_QR()

void predict_mean(Structure &structure)

void predict_SOR(Structure &structure)

void predict_DTC(Structure &structure)

void predict_local_uncertainties(Structure &structure)

void compute_likelihood_stable()

double compute_likelihood_gradient_stable(bool precomputed_KnK = false)

void precompute_KnK()

void compute_KnK(bool precomputed = false)

Eigen::MatrixXd compute_dKnK(int i)

void compute_likelihood()

double compute_likelihood_gradient(const Eigen::VectorXd &hyperparameters)

void set_hyperparameters(Eigen::VectorXd hyps)

void write_mapping_coefficients(std::string file_name, std::string contributor, int kernel_index)

void write_varmap_coefficients(std::string file_name, std::string contributor, int kernel_index)

void write_sparse_descriptors(std::string file_name, std::string contributor)

void write_L_inverse(std::string file_name, std::string contributor)

Public Members

Eigen::VectorXd hyperparameters

std::vector<Kernel*> kernels

std::vector<Eigen::MatrixXd> Kuu_kernels

std::vector<Eigen::MatrixXd> Kuf_kernels

Eigen::MatrixXd Kuu

Eigen::MatrixXd Kuf

std::vector<Eigen::MatrixXd> Kuf_e_noise_Kfu

std::vector<Eigen::MatrixXd> Kuf_f_noise_Kfu

std::vector<Eigen::MatrixXd> Kuf_s_noise_Kfu

Eigen::MatrixXd KnK_e

Eigen::MatrixXd KnK_f

Eigen::MatrixXd KnK_s

int n_kernels = 0

double Kuu_jitter

Eigen::MatrixXd Sigma

Eigen::MatrixXd Kuu_inverse

Eigen::MatrixXd R_inv

Eigen::MatrixXd L_inv

Eigen::VectorXd alpha

Eigen::VectorXd R_inv_diag

Eigen::VectorXd L_diag

std::vector<ClusterDescriptor> sparse_descriptors

std::vector<Structure> training_structures

std::vector<std::vector<std::vector<int>>> sparse_indices

std::vector<std::vector<int>> training_atom_indices

Eigen::VectorXd noise_vector

Eigen::VectorXd y

Eigen::VectorXd label_count

Eigen::VectorXd e_noise_one

Eigen::VectorXd f_noise_one

Eigen::VectorXd s_noise_one

Eigen::VectorXd inv_e_noise_one

Eigen::VectorXd inv_f_noise_one

Eigen::VectorXd inv_s_noise_one

int n_energy_labels = 0

int n_force_labels = 0

int n_stress_labels = 0

int n_sparse = 0

int n_labels = 0

int n_strucs = 0

double energy_noise

double force_noise

double stress_noise

double log_marginal_likelihood

double data_fit

double complexity_penalty

double trace_term

double constant_term

Eigen::VectorXd likelihood_gradient

Eigen::MatrixXd varmap_coeffs

Public Static Functions

static NLOHMANN_DEFINE_TYPE_INTRUSIVE(SparseGP, hyperparameters, kernels, Kuu_kernels, Kuf_kernels, Kuu, Kuf, n_kernels, Kuu_jitter, Sigma, Kuu_inverse, R_inv, L_inv, alpha, R_inv_diag, L_diag, sparse_descriptors, training_structures, sparse_indices, noise_vector, y, label_count, 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) void to_json(std SparseGP from_json (std::string file_name)