Public Member Functions
	NEP (const std::string &model_filename, int N_atoms, std::vector< RealType > box, std::vector< std::string > atom_symbols, std::vector< RealType > positions, std::vector< RealType > masses)
std::vector< RealType >	getDescriptors ()
std::vector< RealType >	getDipole ()
std::vector< RealType >	getDipoleGradient (RealType displacement, int method, RealType charge)
std::vector< RealType >	getPolarizability ()
std::vector< RealType >	getPolarizabilityGradient (RealType displacement, std::vector< int > components)
std::vector< RealType >	getLatentSpace ()
std::tuple< std::vector< RealType >, std::vector< RealType >, std::vector< RealType > >	getPotentialForcesAndVirials ()
std::vector< std::string >	_getAtomSymbols (std::string model_filename)
void	_convertAtomTypeNEPIndex (int N, std::vector< std::string > atom_symbols, std::vector< std::string > model_atom_symbols, std::vector< int > &type)
void	_getCenterOfMass (std::vector< RealType > center_of_mass)
void	setPositions (std::vector< RealType > positions)
void	setCell (std::vector< RealType > cell)
void	setMasses (std::vector< RealType > masses)
void	setSymbols (std::vector< std::string > atom_symbols)

Detailed Description

Definition at line 17 of file nep.hpp.

Constructor & Destructor Documentation

◆ NEP()

OpenMD::NEP::NEP	(	const std::string &	model_filename,
		int	N_atoms,
		std::vector< RealType >	box,
		std::vector< std::string >	atom_symbols,
		std::vector< RealType >	positions,
		std::vector< RealType >	masses )

Wrapper class for NEP3 in nep.cpp.

This class wraps the setup functionality of the NEP3 class in nep.cpp.

Parameters

model_filename	Path to the NEP model (/path/nep.txt).
N_atoms	The number of atoms in the structure.
cell	The cell vectors for the structure.
atom_symbols	The atomic symbol for each atom in the structure.
positions	The position for each atom in the structure.
masses	The mass for each atom in the structure.

Definition at line 12 of file nep.cpp.

References _convertAtomTypeNEPIndex(), and _getAtomSymbols().

Member Function Documentation

◆ _convertAtomTypeNEPIndex()

void OpenMD::NEP::_convertAtomTypeNEPIndex	(	int	N,
		std::vector< std::string >	atom_symbols,
		std::vector< std::string >	model_atom_symbols,
		std::vector< int > &	type )

Converts atom species to NEP index.

Converts atomic species to indicies, which are used in NEP.

Parameters

atom_symbols	List of atom symbols.
model_atom_symbols	List of atom symbols used in the model.
type	List of indices corresponding to atom type.

Definition at line 448 of file nep.cpp.

Referenced by NEP(), and setSymbols().

◆ _getAtomSymbols()

std::vector< std::string > OpenMD::NEP::_getAtomSymbols ( std::string model_filename )

Fetches atomic symbols

This function fetches the atomic symbols from the header of a NEP model. These are later used to ensure consistent indices for the atom types.

Parameters

model_filename Path to the NEP model (/path/nep.txt).

Definition at line 421 of file nep.cpp.

Referenced by NEP(), and setSymbols().

◆ _getCenterOfMass()

void OpenMD::NEP::_getCenterOfMass ( std::vector< RealType > center_of_mass )

Computes the center of mass for current atoms object.

Computes the center of mass (COM) for the structure with positions defined by atoms.position. The COM will be written as a three vector, with in the order [x_component, y_component, z_component].

Parameters

center_of_mass Vector to hold the center of mass.

Definition at line 69 of file nep.cpp.

Referenced by getDipoleGradient().

◆ getDescriptors()

std::vector< RealType > OpenMD::NEP::getDescriptors ( )

Get NEP descriptors.

Calculates NEP descriptors for a given structure and NEP model.

Definition at line 38 of file nep.cpp.

◆ getDipole()

std::vector< RealType > OpenMD::NEP::getDipole ( )

Get dipole.

Calculates the dipole (a vector of length 3) for the whole box.

Definition at line 59 of file nep.cpp.

◆ getDipoleGradient()

std::vector< RealType > OpenMD::NEP::getDipoleGradient	(	RealType	displacement,
		int	method,
		RealType	charge )

Get dipole gradient through finite differences.

Calculates the dipole gradient, a (N_atoms, 3, 3) tensor for the gradients dµ_k/dr_ij, for atom i, Cartesian direction j (x, y, z) and dipole moment component k. Mode is either forward difference (method=0) or first or second order central difference (method=1 and method=2 respectively). Before computing the gradient the dipoles are corrected using the center of mass and the total system charge, supplied via the parameter charge.

Parameters

displacement	Displacement in Å.
method	0 or 1, corresponding to forward or central differences.
charge	Total system charge, used to correct dipoles.

Definition at line 92 of file nep.cpp.

References _getCenterOfMass().

◆ getLatentSpace()

std::vector< RealType > OpenMD::NEP::getLatentSpace ( )

Get the NEP latent space.

Calculates the latent space of a NEP model, i.e., the activations after the first layer.

Definition at line 48 of file nep.cpp.

◆ getPolarizability()

std::vector< RealType > OpenMD::NEP::getPolarizability ( )

Get polarizability.

Calculates the polarizability (a 2-tensor, represented as vector of length 9) for the whole box. Output order is pxx pxy pxz pyx pyy pyz pzx pzy pzz.

Definition at line 308 of file nep.cpp.

◆ getPolarizabilityGradient()

std::vector< RealType > OpenMD::NEP::getPolarizabilityGradient	(	RealType	displacement,
		std::vector< int >	components )

Get polarizability gradient through finite differences.

Calculates the polarizability gradient, a (N_atoms, 3, 6) tensor for the gradients dp_k/dr_ij, for atom i, Cartesian direction j (x, y, z) and polarizability component k, using second order finite differences.

Parameters

displacement Displacement in Å.

Definition at line 321 of file nep.cpp.

◆ getPotentialForcesAndVirials()

std::tuple< std::vector< RealType >, std::vector< RealType >, std::vector< RealType > > OpenMD::NEP::getPotentialForcesAndVirials ( )

Calculate potential, forces and virials.

Calculates potential energy, forces and virials for a given structure and NEP model.

Definition at line 408 of file nep.cpp.

◆ setCell()

void OpenMD::NEP::setCell ( std::vector< RealType > cell )

Sets cell.

Sets the cell of the atoms object.

Parameters

Cell	Cell vectors.

Definition at line 492 of file nep.cpp.

◆ setMasses()

void OpenMD::NEP::setMasses ( std::vector< RealType > masses )

Sets masses.

Sets the masses of the atoms object.

Parameters

Cell	Atom masses.

Definition at line 503 of file nep.cpp.

◆ setPositions()

void OpenMD::NEP::setPositions ( std::vector< RealType > positions )

Sets positions.

Sets the positions of the atoms object. Also updates the center of mass.

Parameters

positions List of positions.

Definition at line 480 of file nep.cpp.

◆ setSymbols()

void OpenMD::NEP::setSymbols ( std::vector< std::string > atom_symbols )

Sets symbols.

Sets the symbols of the atoms object from the ones used in the model.

Parameters

atom_symbols List of symbols.

Definition at line 514 of file nep.cpp.

References _convertAtomTypeNEPIndex(), and _getAtomSymbols().

The documentation for this class was generated from the following files:

nonbonded/nep.hpp
nonbonded/nep.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ NEP()

Member Function Documentation

◆ _convertAtomTypeNEPIndex()

◆ _getAtomSymbols()

◆ _getCenterOfMass()

◆ getDescriptors()

◆ getDipole()

◆ getDipoleGradient()

◆ getLatentSpace()

◆ getPolarizability()

◆ getPolarizabilityGradient()

◆ getPotentialForcesAndVirials()

◆ setCell()

◆ setMasses()

◆ setPositions()

◆ setSymbols()