Structures

class Structure

Neighbor attributes

Eigen::VectorXi neighbor_count: Neighbor count for each atom.

Eigen::VectorXi cumulative_neighbor_count: Cumulative neighbor count. The vector has length N+1, where N is the number of atoms in the structure, with first entry 0.

Eigen::VectorXi neighbor_species: Species of each neighbor. The vector has length equal to the total number of neighbors in the structure.

Eigen::VectorXi structure_indices: ID of each neighbor, where the ID is determined by the initial order of atoms used when the structure was constructed.

The periodic box

Eigen::MatrixXd cell

Eigen::MatrixXd cell_transpose

Eigen::MatrixXd cell_transpose_inverse

Eigen::MatrixXd cell_dot

Eigen::MatrixXd cell_dot_inverse

Atom coordinates

Eigen::MatrixXd positions

Eigen::MatrixXd wrapped_positions

Eigen::MatrixXd relative_positions

Descriptors

std::vector<Descriptor*> descriptor_calculators

std::vector<DescriptorValues> descriptors

Structure labels

Eigen::VectorXd energy

Eigen::VectorXd forces

Eigen::VectorXd stresses

Mean and variance predictions

Eigen::VectorXd mean_efs

Eigen::VectorXd variance_efs

std::vector<Eigen::VectorXd> mean_contributions

std::vector<Eigen::VectorXd> local_uncertainties

Public Functions

Structure(): Default structure constructor.

Structure(const Eigen::MatrixXd &cell, const std::vector<int> &species, const Eigen::MatrixXd &positions)

Basic structure constructor. Holds the cell, species, and positions of a periodic structure of atoms.

Parameters:

cell – 3x3 array whose rows are the Bravais lattice vectors of the periodic cell.
species – List of integers denoting the chemical species of each atom. Must lie between 0 and s-1 (inclusive), where s is the number of species in the system.
positions – Nx3 array of atomic coordinates.

Structure(const Eigen::MatrixXd &cell, const std::vector<int> &species, const Eigen::MatrixXd &positions, double cutoff, std::vector<Descriptor*> descriptor_calculators)

Eigen::MatrixXd wrap_positions()

double get_single_sweep_cutoff()

void compute_neighbors()

void compute_descriptors()

Public Members

double cutoff

double single_sweep_cutoff

double volume

int sweep

int n_neighbors

std::vector<int> species: Species of each atom.

int noa: Number of atoms in the structure.

Public Static Functions

static NLOHMANN_DEFINE_TYPE_INTRUSIVE(Structure, neighbor_count, cutoff, cumulative_neighbor_count, structure_indices, neighbor_species, cell, cell_transpose, cell_transpose_inverse, cell_dot, cell_dot_inverse, positions, wrapped_positions, relative_positions, cutoff, single_sweep_cutoff, volume, sweep, n_neighbors, species, noa, energy, forces, stresses, mean_efs, variance_efs, mean_contributions, local_uncertainties, descriptor_calculators, descriptors) void to_json(std Structure from_json (std::string file_name)