Public Member Functions
double	get_w ()

int	get_n_hist_max ()

double	get_initial_step_size ()

	periodic_optimizer (int &nat)
	Construct a new periodic optimizer::periodic optimizer object for free or fixed cell optimization with default parameters. More...

	periodic_optimizer (int &nat, double initial_step_size, int nhist_max, double alpha0, double eps_subsp)
	Construct a new periodic optimizer::periodic optimizer object for free or fixed cell optimization with custom parameters. More...

	periodic_optimizer (int &nat, Eigen::Vector3d &lat_a, Eigen::Vector3d &lat_b, Eigen::Vector3d &lat_c)
	Construct a new periodic optimizer::periodic optimizer object for variable cell shape optimization with default parameters. More...

	periodic_optimizer (int &nat, Eigen::Vector3d &lat_a, Eigen::Vector3d &lat_b, Eigen::Vector3d &lat_c, double initial_step_size, int nhist_max, double lattice_weight, double alpha0, double eps_subsp)
	Construct a new periodic optimizer::periodic optimizer object for variable cell shape optimization with custom parameters. More...

void	step (Eigen::MatrixXd &r, double &energy, Eigen::MatrixXd &f)
	Calculates new atomic coordinates that are closer to the local minimum. Fixed cell optimization. This function should be used the following way: More...

void	step (Eigen::MatrixXd &r, double &energy, Eigen::MatrixXd &f, Eigen::Vector3d &lat_a, Eigen::Vector3d &lat_b, Eigen::Vector3d &lat_c, Eigen::Matrix3d &stress)
	Calculates new atomic coordinates that are closer to the local minimum. Variable cell shape optimization. This function should be used the following way: More...

void	check_forces (Eigen::MatrixXd forces)

double	lower_bound ()
	Estimates a lower bound of the energy of the local minimum. More...

Private Member Functions
Eigen::VectorXd	combine_matrices (Eigen::MatrixXd a, Eigen::MatrixXd b)

void	split_matrices (Eigen::MatrixXd &a, Eigen::MatrixXd &b, Eigen::VectorXd &c)

Eigen::Matrix3d	calc_lattice_derivatices (Eigen::Matrix3d &stress, Eigen::Matrix3d &alat)

void	setupInitialLattice (int &nat, Eigen::Vector3d &lat_a, Eigen::Vector3d &lat_b, Eigen::Vector3d &lat_c)

Private Attributes
Eigen::Matrix3d	initial_latttice

Eigen::Matrix3d	initial_latttice_inv

Eigen::Matrix3d	lattice_transformer

Eigen::Matrix3d	lattice_transformer_inv

std::unique_ptr< sqnm_space::SQNM >	opt

int	nat

int	ndim

bool	opt_lattice

double	initial_step_size = 1

int	n_hist_max = 10

double	w = 2.0

double	f_std_deviation = 0.0

Detailed Description

Definition at line 20 of file periodic_optimizer.hpp.

Constructor & Destructor Documentation

◆ periodic_optimizer() [1/4]

vcsqnm::PES_optimizer::periodic_optimizer::periodic_optimizer ( int & nat )

inline

Construct a new periodic optimizer::periodic optimizer object for free or fixed cell optimization with default parameters.

Parameters

nat	number of atoms

Definition at line 55 of file periodic_optimizer.hpp.

◆ periodic_optimizer() [2/4]

vcsqnm::PES_optimizer::periodic_optimizer::periodic_optimizer	(	int &	nat,
		double	initial_step_size,
		int	nhist_max,
		double	alpha0,
		double	eps_subsp
	)

inline

Construct a new periodic optimizer::periodic optimizer object for free or fixed cell optimization with custom parameters.

Parameters

nat	number of atoms
initial_step_size	initial step size. default is 1.0. For systems with hard bonds (e.g. C-C) use a value between and 1.0 and 2.5. If a system only contains weaker bonds a value up to 5.0 may speed up the convergence.
nhist_max	Maximal number of steps that will be stored in the history list. Use a value between 3 and 20. Must be <= than 3*nat.
alpha0	Lower limit on the step size. 1.e-2 is the default.
eps_subsp	Lower limit on linear dependencies of basis vectors in history list. Default 1.e-4.

Definition at line 73 of file periodic_optimizer.hpp.

◆ periodic_optimizer() [3/4]

vcsqnm::PES_optimizer::periodic_optimizer::periodic_optimizer	(	int &	nat,
		Eigen::Vector3d &	lat_a,
		Eigen::Vector3d &	lat_b,
		Eigen::Vector3d &	lat_c
	)

inline

Construct a new periodic optimizer::periodic optimizer object for variable cell shape optimization with default parameters.

Parameters

nat	number of atoms
lat_a	first lattice vector
lat_b	second lattice vector
lat_c	third lattice vector

Definition at line 91 of file periodic_optimizer.hpp.

◆ periodic_optimizer() [4/4]

vcsqnm::PES_optimizer::periodic_optimizer::periodic_optimizer	(	int &	nat,
		Eigen::Vector3d &	lat_a,
		Eigen::Vector3d &	lat_b,
		Eigen::Vector3d &	lat_c,
		double	initial_step_size,
		int	nhist_max,
		double	lattice_weight,
		double	alpha0,
		double	eps_subsp
	)

inline

Construct a new periodic optimizer::periodic optimizer object for variable cell shape optimization with custom parameters.

Parameters

nat	number of atoms
lat_a	first lattice vector
lat_b	second lattice vector
lat_c	third lattice vector
initial_step_size	initial step size. default is 1.0. For systems with hard bonds (e.g. C-C) use a value between and 1.0 and 2.5. If a system only contains weaker bonds a value up to 5.0 may speed up the convergence.
nhist_max	Maximal number of steps that will be stored in the history list. Use a value between 3 and 20. Must be <= than 3*nat + 9.
lattice_weight	weight / size of the supercell that is used to transform lattice derivatives. Use a value between 1 and 2. Default is 2.
alpha0	Lower limit on the step size. 1.e-2 is the default.
eps_subsp	Lower limit on linear dependencies of basis vectors in history list. Default 1.e-4.

Definition at line 111 of file periodic_optimizer.hpp.

Member Function Documentation

◆ get_w()

double vcsqnm::PES_optimizer::periodic_optimizer::get_w ( )

inline

Definition at line 38 of file periodic_optimizer.hpp.

◆ get_n_hist_max()

int vcsqnm::PES_optimizer::periodic_optimizer::get_n_hist_max ( )

inline

Definition at line 42 of file periodic_optimizer.hpp.

◆ get_initial_step_size()

double vcsqnm::PES_optimizer::periodic_optimizer::get_initial_step_size ( )

inline

Definition at line 46 of file periodic_optimizer.hpp.

◆ step() [1/2]

void vcsqnm::PES_optimizer::periodic_optimizer::step	(	Eigen::MatrixXd &	r,
		double &	energy,
		Eigen::MatrixXd &	f
	)

inline

Calculates new atomic coordinates that are closer to the local minimum. Fixed cell optimization. This function should be used the following way:

calculate energies and forces at positions r.
call the step function to update positions r.
repeat.

Parameters

r	Input: atomic coordinates, dimension(3, nat). Output: improved coordinates that are calculated based on forces from this and previous iterations.
energy	Potential energy of the system in it's current state
f	Forces of the system in it's current state. dimension(3, nat)

Definition at line 130 of file periodic_optimizer.hpp.

◆ step() [2/2]

void vcsqnm::PES_optimizer::periodic_optimizer::step	(	Eigen::MatrixXd &	r,
		double &	energy,
		Eigen::MatrixXd &	f,
		Eigen::Vector3d &	lat_a,
		Eigen::Vector3d &	lat_b,
		Eigen::Vector3d &	lat_c,
		Eigen::Matrix3d &	stress
	)

inline

Calculates new atomic coordinates that are closer to the local minimum. Variable cell shape optimization. This function should be used the following way:

calculate energies, forces and stress tensor at positions r and lattice vectors a, b, c.
call the step function to update positions r and lattice vectors.
repeat.

Parameters

r	Input: atomic coordinates, dimension(3, nat). Output: improved coordinates that are calculated based on forces from this and previous iterations.
energy	Potential energy of the system in it's current state
f	Forces of the system in it's current state. dimension(3, nat)
lat_a	first lattice vector
lat_b	second lattice vector
lat_c	third lattice vector
stress	stress tensor of the system in it' current state.

Definition at line 157 of file periodic_optimizer.hpp.

◆ check_forces()

void vcsqnm::PES_optimizer::periodic_optimizer::check_forces ( Eigen::MatrixXd forces )

inline

Definition at line 194 of file periodic_optimizer.hpp.

◆ lower_bound()

double vcsqnm::PES_optimizer::periodic_optimizer::lower_bound ( )

inline

Estimates a lower bound of the energy of the local minimum.

Returns: double Lower bound estimate

Definition at line 213 of file periodic_optimizer.hpp.

◆ combine_matrices()

Eigen::VectorXd vcsqnm::PES_optimizer::periodic_optimizer::combine_matrices	(	Eigen::MatrixXd	a,
		Eigen::MatrixXd	b
	)

inlineprivate

Definition at line 219 of file periodic_optimizer.hpp.

◆ split_matrices()

void vcsqnm::PES_optimizer::periodic_optimizer::split_matrices	(	Eigen::MatrixXd &	a,
		Eigen::MatrixXd &	b,
		Eigen::VectorXd &	c
	)

inlineprivate

Definition at line 234 of file periodic_optimizer.hpp.

◆ calc_lattice_derivatices()

Eigen::Matrix3d vcsqnm::PES_optimizer::periodic_optimizer::calc_lattice_derivatices	(	Eigen::Matrix3d &	stress,
		Eigen::Matrix3d &	alat
	)

inlineprivate

Definition at line 247 of file periodic_optimizer.hpp.

◆ setupInitialLattice()

void vcsqnm::PES_optimizer::periodic_optimizer::setupInitialLattice	(	int &	nat,
		Eigen::Vector3d &	lat_a,
		Eigen::Vector3d &	lat_b,
		Eigen::Vector3d &	lat_c
	)

inlineprivate

Definition at line 252 of file periodic_optimizer.hpp.

Member Data Documentation

◆ initial_latttice

Eigen::Matrix3d vcsqnm::PES_optimizer::periodic_optimizer::initial_latttice

private

Definition at line 23 of file periodic_optimizer.hpp.

◆ initial_latttice_inv

Eigen::Matrix3d vcsqnm::PES_optimizer::periodic_optimizer::initial_latttice_inv

private

Definition at line 24 of file periodic_optimizer.hpp.

◆ lattice_transformer

Eigen::Matrix3d vcsqnm::PES_optimizer::periodic_optimizer::lattice_transformer

private

Definition at line 25 of file periodic_optimizer.hpp.

◆ lattice_transformer_inv

Eigen::Matrix3d vcsqnm::PES_optimizer::periodic_optimizer::lattice_transformer_inv

private

Definition at line 26 of file periodic_optimizer.hpp.

◆ opt

std::unique_ptr<sqnm_space::SQNM> vcsqnm::PES_optimizer::periodic_optimizer::opt

private

Definition at line 27 of file periodic_optimizer.hpp.

◆ nat

int vcsqnm::PES_optimizer::periodic_optimizer::nat

private

Definition at line 28 of file periodic_optimizer.hpp.

◆ ndim

int vcsqnm::PES_optimizer::periodic_optimizer::ndim

private

Definition at line 29 of file periodic_optimizer.hpp.

◆ opt_lattice

bool vcsqnm::PES_optimizer::periodic_optimizer::opt_lattice

private

Definition at line 30 of file periodic_optimizer.hpp.

◆ initial_step_size

double vcsqnm::PES_optimizer::periodic_optimizer::initial_step_size = 1

private

Definition at line 31 of file periodic_optimizer.hpp.

◆ n_hist_max

int vcsqnm::PES_optimizer::periodic_optimizer::n_hist_max = 10

private

Definition at line 32 of file periodic_optimizer.hpp.

◆ w

double vcsqnm::PES_optimizer::periodic_optimizer::w = 2.0

private

Definition at line 33 of file periodic_optimizer.hpp.

◆ f_std_deviation

double vcsqnm::PES_optimizer::periodic_optimizer::f_std_deviation = 0.0

private

Definition at line 34 of file periodic_optimizer.hpp.

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

periodic_optimizer.hpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ periodic_optimizer() [1/4]

◆ periodic_optimizer() [2/4]

◆ periodic_optimizer() [3/4]

◆ periodic_optimizer() [4/4]

Member Function Documentation

◆ get_w()

◆ get_n_hist_max()

◆ get_initial_step_size()

◆ step() [1/2]

◆ step() [2/2]

◆ check_forces()

◆ lower_bound()

◆ combine_matrices()

◆ split_matrices()

◆ calc_lattice_derivatices()

◆ setupInitialLattice()

Member Data Documentation

◆ initial_latttice

◆ initial_latttice_inv

◆ lattice_transformer

◆ lattice_transformer_inv

◆ opt

◆ nat

◆ ndim

◆ opt_lattice

◆ initial_step_size

◆ n_hist_max

◆ w

◆ f_std_deviation