Descriptors¶

class Descriptor¶

Subclassed by B2, B2_Simple, B3, FourBody, ThreeBody, ThreeBodyWide, TwoBody

Public Functions

Descriptor()¶

virtual DescriptorValues compute_struc(Structure &structure) = 0¶

virtual ~Descriptor()¶

void write_to_file(std::ofstream &coeff_file, int coeff_size)¶

virtual nlohmann::json return_json() = 0¶

Public Members

std::string descriptor_name¶

class DescriptorValues¶

Public Functions

DescriptorValues()¶

Public Members

int n_descriptors¶

int n_types¶

int n_atoms¶

double volume¶

std::vector<Eigen::MatrixXd> descriptors¶

std::vector<Eigen::MatrixXd> descriptor_force_dervs¶

std::vector<Eigen::MatrixXd> neighbor_coordinates¶

std::vector<Eigen::VectorXd> descriptor_norms¶

std::vector<Eigen::VectorXd> descriptor_force_dots¶

std::vector<Eigen::VectorXd> cutoff_values¶

std::vector<Eigen::VectorXd> cutoff_dervs¶

std::vector<Eigen::VectorXi> neighbor_counts¶

std::vector<Eigen::VectorXi> cumulative_neighbor_counts¶

std::vector<Eigen::VectorXi> atom_indices¶

std::vector<Eigen::VectorXi> neighbor_indices¶

int n_clusters = 0¶

std::vector<int> n_clusters_by_type¶

std::vector<int> cumulative_type_count¶

std::vector<int> n_neighbors_by_type¶

class ClusterDescriptor¶

Public Functions

ClusterDescriptor()¶

ClusterDescriptor(const DescriptorValues &structure)¶

ClusterDescriptor(const DescriptorValues &structure, const std::vector<std::vector<int>> &clusters)¶

ClusterDescriptor(const DescriptorValues &structure, const std::vector<int> &clusters)¶

void initialize_cluster(int n_types, int n_descriptors)¶

void add_clusters_by_type(const DescriptorValues &structure, const std::vector<std::vector<int>> &clusters)¶

void add_clusters(const DescriptorValues &structure, const std::vector<int> &clusters)¶

void add_all_clusters(const DescriptorValues &structure)¶

Public Members

std::vector<Eigen::MatrixXd> descriptors¶

std::vector<Eigen::VectorXd> descriptor_norms¶

std::vector<Eigen::VectorXd> cutoff_values¶

std::vector<int> n_clusters_by_type¶

std::vector<int> cumulative_type_count¶

int n_descriptors¶

int n_types¶

int n_clusters = 0¶

class B2 : public Descriptor ¶

Subclassed by B2_Norm

Public Functions

B2()¶

B2(const std::string &radial_basis, const std::string &cutoff_function, const std::vector<double> &radial_hyps, const std::vector<double> &cutoff_hyps, const std::vector<int> &descriptor_settings)¶

B2(const std::string &radial_basis, const std::string &cutoff_function, const std::vector<double> &radial_hyps, const std::vector<double> &cutoff_hyps, const std::vector<int> &descriptor_settings, const Eigen::MatrixXd &cutoffs)¶: Construct the B2 descriptor with distinct cutoffs for each pair of species.

DescriptorValues compute_struc(Structure &structure)¶

void write_to_file(std::ofstream &coeff_file, int coeff_size)¶

nlohmann::json return_json()¶

Public Members

std::function<void(std::vector<double>&, std::vector<double>&, double, int, std::vector<double>)> radial_pointer¶

std::function<void(std::vector<double>&, double, double, std::vector<double>)> cutoff_pointer¶

std::string radial_basis¶

std::string cutoff_function¶

std::vector<double> radial_hyps¶

std::vector<double> cutoff_hyps¶

std::vector<int> descriptor_settings¶

std::string descriptor_name = "B2"¶

Eigen::MatrixXd cutoffs¶: Matrix of cutoff values, with element (i, j) corresponding to the cutoff assigned to the species pair (i, j), where i is the central species and j is the environment species.