Descriptors

class Descriptor

Subclassed by B1, B2, B2_Simple, B3, FourBody, ThreeBody, ThreeBodyWide, TwoBody

Public Functions

Descriptor()

virtual DescriptorValues compute_struc(Structure &structure) = 0

virtual ~Descriptor() = default

virtual 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.

virtual DescriptorValues compute_struc(Structure &structure)

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

virtual 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.