Memory layout

Configuration storage

struct Atom

Storage for a single atom.

Public Members

std::size_t index

Index number of this atom.

std::size_t element

Element index of this atom.

double energy

Atomic energy determined by neural network.

double charge

Atomic charge determined by neural network.

Vec3D r

Cartesian coordinates.

Vec3D f

Force vector calculated by neural network.

Vec3D fRef

Reference force vector from data set.

std::vector<double> G

Symmetry function values.

std::vector<double> dEdG

Derivative of atomic energy with respect to symmetry functions.

Also contains dEdQ in the last element if HDNNP-4G is used.

std::vector<Vec3D> dGdr

Derivative of symmetry functions with respect to this atom’s coordinates.

std::vector<Neighbor> neighbors

Neighbor array (maximum number defined in macros.h.

struct Neighbor

Struct to store information on neighbor atoms.

Public Members

std::size_t index

Index of neighbor atom.

std::size_t element

Element index of neighbor atom.

double d

Distance to neighbor atom.

Vec3D dr

Distance vector to neighbor atom.

std::vector<Vec3D> dGdr

Derivatives of symmetry functions with respect to neighbor coordinates.

May be empty, only filled when needed. Contains \( \frac{\partial G_i}{\partial \alpha_j} \), where \(G_i\) is a symmetry function of atom \(i\) and \(\alpha_j\) is a coordinate \( \alpha = x,y,z \) of neighbor atom \( j \), necessary for force calculation.

struct Structure

Storage for one atomic configuration.

Public Members

std::size_t index

Index number of this structure.

double energy

Potential energy determined by neural network.

double energyRef

Reference potential energy.

double chargeRef

Reference charge.

Vec3D box[3]

Simulation box vectors.

std::vector<Atom> atoms

Vector of all atoms in this structure.

class Dataset : public nnp::Mode

Collect and process large data sets.

Subclassed by nnp::Training

Public Members

std::vector<Structure> structures

All structures in this dataset.

Helper classes and functions

class ElementMap

Contains element map.

Public Functions

inline std::string operator[](std::size_t const index) const

Overload [] operator for index search.

Parameters:

index – [in] Element index.

Returns:

Symbol of element in map.

inline std::size_t operator[](std::string const symbol) const

Overload [] operator for symbol search.

Parameters:

symbol – [in] Element symbol.

Returns:

Index of element in map.

struct Vec3D

Vector in 3 dimensional real space.

Public Functions

inline double norm() const

Calculate norm of vector.

Returns:

Norm of vector.

inline double norm2() const

Calculate square of norm of vector.

Returns:

Square of norm of vector.

inline Vec3D &normalize()

Normalize vector, norm equals 1.0 afterwards.

inline Vec3D cross(Vec3D const &v) const

Cross product, argument vector is second in product.

Returns:

Cross product of two vectors.

Public Members

double r[3]

cartesian coordinates.

vector<string> nnp::split(std::string const &input, char delimiter = ' ')

Split string at each delimiter.

Parameters:

• input – [in] Input string.

• delimiter – [in] Delimiter character (default ‘ ‘).

Returns:

Vector containing the string parts.

string nnp::strpr(const char *format, ...)

String version of printf function.