#include <nudgedElasticBandClass.h>

Inheritance diagram for dftfe::nudgedElasticBandClass:

Public Member Functions
	nudgedElasticBandClass (const std::string parameter_file, const std::string restartFilesPath, const MPI_Comm &mpi_comm_parent, const bool restart, const int verbosity, const bool useDevice, const int d_numberOfImages, const bool imageFreeze, double Kmax, double Kmin, const double pathThreshold, const int maximumNEBIteration, const unsigned int _maxLineSearchIterCGPRP, const unsigned int _lbfgsNumPastSteps, const std::string &_bfgsStepMethod, const double optimizermaxIonUpdateStep, const std::string &optimizationSolver, const std::string &coordinatesFileNEB, const std::string &domainVectorsFileNEB, const std::string &ionRelaxFlagsFile)
	First, sets the nebRestart path. Second, creates Step0 folder with coordinaes and domainVectors file. Third, creates the array of pointers of dftClass for each image. If in restart mode, calls function to read coordinates and initialise parameters Sets solvermode: CGPT, LBFGS, BFGS.

int	findMEP ()
	Calls optimizer(nonLinearClass) solve. Prints the Final NEB energies and forces. References: 1. https://pubs.aip.org/aip/jcp/article/113/22/9978/184858/Improved-tangent-estimate-in-the-nudged-elastic 2. https://pubs.aip.org/aip/jcp/article/128/13/134106/977389/Optimization-methods-for-finding-minimum-energy.

void	ReturnNormedVector (std::vector< double > &, int)
	Returns the Normed vetor satistfying \|\|v\|\|_2 = 1.

void	LNorm (double &, std::vector< double >, int, int)
	Calculates the L-norm of a vector.

void	gradient (std::vector< double > &gradient)
	Identifies the images to freeze, calculates gradient. First prints the Image No., free energy and force error of each image Prints activation energy of current step.

unsigned int	getNumberUnknowns () const
	Returns the total DoFs of the optimizer problem.

void	update (const std::vector< double > &solution, const bool computeForces=true, const bool useSingleAtomSolutionsInitialGuess=false)
	Updates the positions of atoms and the total step count. Calls dftPtr colve to compute eenergy and force for current step.

void	save ()
	Saves the output files for restart.

void	init ()
	initializes the data member d_relaxationFlags, nonlinearSolver,

void	value (std::vector< double > &functionValue)
	Not working. Finds the saddle point energy.

void	precondition (std::vector< double > &s, const std::vector< double > &gradient)
	not implemented

void	solution (std::vector< double > &solution)
	not implemented

std::vector< unsigned int >	getUnknownCountFlag () const
	not implemented

Public Member Functions inherited from dftfe::nonlinearSolverProblem
	nonlinearSolverProblem ()
	Constructor.

virtual	~nonlinearSolverProblem ()=0
	Destructor.

Public Attributes
double	d_kmax = 0.1

double	d_kmin = 0.1

int	d_NEBImageno

Private Member Functions
const MPI_Comm &	getMPICommunicator ()
	get MPI communicator.

void	CalculatePathTangent (int, std::vector< double > &)
	Calculate the tangent between each image.

void	CalculateForceparallel (int, std::vector< double > &, const std::vector< double > &)
	Calculates the force on atom along the tangent between images.

void	CalculateForceperpendicular (int, std::vector< double > &, const std::vector< double > &, const std::vector< double > &)
	Calculates force perpendicular to the tangent.

void	CalculateSpringForce (int, std::vector< double > &, std::vector< double >)
	Calculates the force due to the spring.

void	CalculateForceonImage (const std::vector< double > &, const std::vector< double > &, std::vector< double > &)
	Calculates F_NEB = G_per+ F_spring.

double	CalculatePathLength (bool flag) const
	Calculate path length: max diaplacement of atoms.

void	WriteRestartFiles (int step)
	Write Restart files.

void	CalculateSpringConstant (int, double &)
	Find spring constant based on k_max and k_min.

void	ImageError (int image, double &Force)
	Calculate F_per norm.

void	set ()
	set() initalises all the private datamembers of nudgedElasticBandClass object from the parameters declared by user.

bool	isConverged () const
	check for convergence.

int	checkRestart (bool &periodic)
	Check the restart files.

Private Attributes
std::vector< std::unique_ptr< dftfeWrapper > >	d_dftfeWrapper

dftBase *	d_dftPtr

std::unique_ptr< nonLinearSolver >	d_nonLinearSolverPtr

const MPI_Comm	d_mpiCommParent

const unsigned int	d_this_mpi_process

dealii::ConditionalOStream	pcout

int	d_verbosity

std::string	d_restartFilesPath

std::string	d_solverRestartPath

bool	d_imageFreeze

int	d_totalUpdateCalls
	total number of calls to update()

int	d_startStep

int	d_solver

bool	d_isRestart

bool	d_solverRestart

unsigned int	d_restartFlag

unsigned int	d_numberGlobalCharges

double	d_maximumAtomForceToBeRelaxed

unsigned int	d_numberOfImages

unsigned int	d_countrelaxationFlags

unsigned int	d_maximumNEBIteration

double	d_optimizertolerance

unsigned int	maxLineSearchIterCGPRP

std::string	bfgsStepMethod

double	d_optimizermaxIonUpdateStep

unsigned int	lbfgsNumPastSteps

std::string	d_optimizationSolver

std::string	d_ionRelaxFlagsFile

std::map< int, std::vector< std::vector< double > > >	d_atomLocationsInitial

std::vector< unsigned int >	d_relaxationFlags

std::vector< double >	d_externalForceOnAtom

std::vector< double >	d_ImageError

std::vector< double >	d_Length

std::string	d_coordinatesFileNEB

std::string	d_domainVectorsFileNEB

Constructor & Destructor Documentation

◆ nudgedElasticBandClass()

dftfe::nudgedElasticBandClass::nudgedElasticBandClass	(	const std::string	parameter_file,
		const std::string	restartFilesPath,
		const MPI_Comm &	mpi_comm_parent,
		const bool	restart,
		const int	verbosity,
		const bool	useDevice,
		const int	d_numberOfImages,
		const bool	imageFreeze,
		double	Kmax,
		double	Kmin,
		const double	pathThreshold,
		const int	maximumNEBIteration,
		const unsigned int	_maxLineSearchIterCGPRP,
		const unsigned int	_lbfgsNumPastSteps,
		const std::string &	_bfgsStepMethod,
		const double	optimizermaxIonUpdateStep,
		const std::string &	optimizationSolver,
		const std::string &	coordinatesFileNEB,
		const std::string &	domainVectorsFileNEB,
		const std::string &	ionRelaxFlagsFile )

First, sets the nebRestart path. Second, creates Step0 folder with coordinaes and domainVectors file. Third, creates the array of pointers of dftClass for each image. If in restart mode, calls function to read coordinates and initialise parameters Sets solvermode: CGPT, LBFGS, BFGS.

Member Function Documentation

◆ CalculateForceonImage()

void dftfe::nudgedElasticBandClass::CalculateForceonImage	(	const std::vector< double > &	,
		const std::vector< double > &	,
		std::vector< double > &	)

private

Calculates F_NEB = G_per+ F_spring.

◆ CalculateForceparallel()

void dftfe::nudgedElasticBandClass::CalculateForceparallel	(	int	,
		std::vector< double > &	,
		const std::vector< double > &	)

private

Calculates the force on atom along the tangent between images.

◆ CalculateForceperpendicular()

void dftfe::nudgedElasticBandClass::CalculateForceperpendicular	(	int	,
		std::vector< double > &	,
		const std::vector< double > &	,
		const std::vector< double > &	)

private

Calculates force perpendicular to the tangent.

◆ CalculatePathLength()

double dftfe::nudgedElasticBandClass::CalculatePathLength ( bool flag ) const

private

Calculate path length: max diaplacement of atoms.

◆ CalculatePathTangent()

void dftfe::nudgedElasticBandClass::CalculatePathTangent	(	int	,
		std::vector< double > &	)

private

Calculate the tangent between each image.

◆ CalculateSpringConstant()

void dftfe::nudgedElasticBandClass::CalculateSpringConstant	(	int	,
		double &	)

private

Find spring constant based on k_max and k_min.

◆ CalculateSpringForce()

void dftfe::nudgedElasticBandClass::CalculateSpringForce	(	int	,
		std::vector< double > &	,
		std::vector< double >	)

private

Calculates the force due to the spring.

◆ checkRestart()

int dftfe::nudgedElasticBandClass::checkRestart ( bool & periodic )

private

Check the restart files.

◆ findMEP()

int dftfe::nudgedElasticBandClass::findMEP ( )

Calls optimizer(nonLinearClass) solve. Prints the Final NEB energies and forces. References: 1. https://pubs.aip.org/aip/jcp/article/113/22/9978/184858/Improved-tangent-estimate-in-the-nudged-elastic 2. https://pubs.aip.org/aip/jcp/article/128/13/134106/977389/Optimization-methods-for-finding-minimum-energy.

◆ getMPICommunicator()

const MPI_Comm & dftfe::nudgedElasticBandClass::getMPICommunicator ( )

privatevirtual

get MPI communicator.

Implements dftfe::nonlinearSolverProblem.

◆ getNumberUnknowns()

unsigned int dftfe::nudgedElasticBandClass::getNumberUnknowns ( ) const

virtual

Returns the total DoFs of the optimizer problem.

Implements dftfe::nonlinearSolverProblem.

◆ getUnknownCountFlag()

std::vector< unsigned int > dftfe::nudgedElasticBandClass::getUnknownCountFlag ( ) const

virtual

not implemented

Implements dftfe::nonlinearSolverProblem.

◆ gradient()

void dftfe::nudgedElasticBandClass::gradient ( std::vector< double > & gradient )

virtual

Identifies the images to freeze, calculates gradient. First prints the Image No., free energy and force error of each image Prints activation energy of current step.

Implements dftfe::nonlinearSolverProblem.

◆ ImageError()

void dftfe::nudgedElasticBandClass::ImageError	(	int	image,
		double &	Force )

private

Calculate F_per norm.

◆ init()

void dftfe::nudgedElasticBandClass::init ( )

initializes the data member d_relaxationFlags, nonlinearSolver,

◆ isConverged()

bool dftfe::nudgedElasticBandClass::isConverged ( ) const

privatevirtual

check for convergence.

Implements dftfe::nonlinearSolverProblem.

◆ LNorm()

void dftfe::nudgedElasticBandClass::LNorm	(	double &	,
		std::vector< double >	,
		int	,
		int	)

Calculates the L-norm of a vector.

◆ precondition()

void dftfe::nudgedElasticBandClass::precondition	(	std::vector< double > &	s,
		const std::vector< double > &	gradient )

virtual

not implemented

Implements dftfe::nonlinearSolverProblem.

◆ ReturnNormedVector()

void dftfe::nudgedElasticBandClass::ReturnNormedVector	(	std::vector< double > &	,
		int	)

Returns the Normed vetor satistfying ||v||_2 = 1.

◆ save()

void dftfe::nudgedElasticBandClass::save ( )

virtual

Saves the output files for restart.

Implements dftfe::nonlinearSolverProblem.

◆ set()

void dftfe::nudgedElasticBandClass::set ( )

private

set() initalises all the private datamembers of nudgedElasticBandClass object from the parameters declared by user.

◆ solution()

void dftfe::nudgedElasticBandClass::solution ( std::vector< double > & solution )

virtual

not implemented

Implements dftfe::nonlinearSolverProblem.

◆ update()

void dftfe::nudgedElasticBandClass::update	(	const std::vector< double > &	solution,
		const bool	computeForces = true,
		const bool	useSingleAtomSolutionsInitialGuess = false )

virtual

Updates the positions of atoms and the total step count. Calls dftPtr colve to compute eenergy and force for current step.

Implements dftfe::nonlinearSolverProblem.

◆ value()

void dftfe::nudgedElasticBandClass::value ( std::vector< double > & functionValue )

virtual

Not working. Finds the saddle point energy.

Implements dftfe::nonlinearSolverProblem.

◆ WriteRestartFiles()

void dftfe::nudgedElasticBandClass::WriteRestartFiles ( int step )

private

Write Restart files.

Member Data Documentation

◆ bfgsStepMethod

std::string dftfe::nudgedElasticBandClass::bfgsStepMethod

private

◆ d_atomLocationsInitial

std::map<int, std::vector<std::vector<double> > > dftfe::nudgedElasticBandClass::d_atomLocationsInitial

private

◆ d_coordinatesFileNEB

std::string dftfe::nudgedElasticBandClass::d_coordinatesFileNEB

private

◆ d_countrelaxationFlags

unsigned int dftfe::nudgedElasticBandClass::d_countrelaxationFlags

private

◆ d_dftfeWrapper

std::vector<std::unique_ptr<dftfeWrapper> > dftfe::nudgedElasticBandClass::d_dftfeWrapper

private

◆ d_dftPtr

dftBase* dftfe::nudgedElasticBandClass::d_dftPtr

private

◆ d_domainVectorsFileNEB

std::string dftfe::nudgedElasticBandClass::d_domainVectorsFileNEB

private

◆ d_externalForceOnAtom

std::vector<double> dftfe::nudgedElasticBandClass::d_externalForceOnAtom

private

◆ d_ImageError

std::vector<double> dftfe::nudgedElasticBandClass::d_ImageError

private

◆ d_imageFreeze

bool dftfe::nudgedElasticBandClass::d_imageFreeze

private

◆ d_ionRelaxFlagsFile

std::string dftfe::nudgedElasticBandClass::d_ionRelaxFlagsFile

private

◆ d_isRestart

bool dftfe::nudgedElasticBandClass::d_isRestart

private

◆ d_kmax

double dftfe::nudgedElasticBandClass::d_kmax = 0.1

◆ d_kmin

double dftfe::nudgedElasticBandClass::d_kmin = 0.1

◆ d_Length

std::vector<double> dftfe::nudgedElasticBandClass::d_Length

private

◆ d_maximumAtomForceToBeRelaxed

double dftfe::nudgedElasticBandClass::d_maximumAtomForceToBeRelaxed

private

◆ d_maximumNEBIteration

unsigned int dftfe::nudgedElasticBandClass::d_maximumNEBIteration

private

◆ d_mpiCommParent

const MPI_Comm dftfe::nudgedElasticBandClass::d_mpiCommParent

private

◆ d_NEBImageno

int dftfe::nudgedElasticBandClass::d_NEBImageno

◆ d_nonLinearSolverPtr

std::unique_ptr<nonLinearSolver> dftfe::nudgedElasticBandClass::d_nonLinearSolverPtr

private

◆ d_numberGlobalCharges

unsigned int dftfe::nudgedElasticBandClass::d_numberGlobalCharges

private

◆ d_numberOfImages

unsigned int dftfe::nudgedElasticBandClass::d_numberOfImages

private

◆ d_optimizationSolver

std::string dftfe::nudgedElasticBandClass::d_optimizationSolver

private

◆ d_optimizermaxIonUpdateStep

double dftfe::nudgedElasticBandClass::d_optimizermaxIonUpdateStep

private

◆ d_optimizertolerance

double dftfe::nudgedElasticBandClass::d_optimizertolerance

private

◆ d_relaxationFlags

std::vector<unsigned int> dftfe::nudgedElasticBandClass::d_relaxationFlags

private

◆ d_restartFilesPath

std::string dftfe::nudgedElasticBandClass::d_restartFilesPath

private

◆ d_restartFlag

unsigned int dftfe::nudgedElasticBandClass::d_restartFlag

private

◆ d_solver

int dftfe::nudgedElasticBandClass::d_solver

private

◆ d_solverRestart

bool dftfe::nudgedElasticBandClass::d_solverRestart

private

◆ d_solverRestartPath

std::string dftfe::nudgedElasticBandClass::d_solverRestartPath

private

◆ d_startStep

int dftfe::nudgedElasticBandClass::d_startStep

private

◆ d_this_mpi_process

const unsigned int dftfe::nudgedElasticBandClass::d_this_mpi_process

private

◆ d_totalUpdateCalls

int dftfe::nudgedElasticBandClass::d_totalUpdateCalls

private

total number of calls to update()

◆ d_verbosity

int dftfe::nudgedElasticBandClass::d_verbosity

private

◆ lbfgsNumPastSteps

unsigned int dftfe::nudgedElasticBandClass::lbfgsNumPastSteps

private

◆ maxLineSearchIterCGPRP

unsigned int dftfe::nudgedElasticBandClass::maxLineSearchIterCGPRP

private

◆ pcout

dealii::ConditionalOStream dftfe::nudgedElasticBandClass::pcout

private

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

workspace/include/nudgedElasticBandClass.h

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ nudgedElasticBandClass()

Member Function Documentation

◆ CalculateForceonImage()

◆ CalculateForceparallel()

◆ CalculateForceperpendicular()

◆ CalculatePathLength()

◆ CalculatePathTangent()

◆ CalculateSpringConstant()

◆ CalculateSpringForce()

◆ checkRestart()

◆ findMEP()

◆ getMPICommunicator()

◆ getNumberUnknowns()

◆ getUnknownCountFlag()

◆ gradient()

◆ ImageError()

◆ init()

◆ isConverged()

◆ LNorm()

◆ precondition()

◆ ReturnNormedVector()

◆ save()

◆ set()

◆ solution()

◆ update()

◆ value()

◆ WriteRestartFiles()

Member Data Documentation

◆ bfgsStepMethod

◆ d_atomLocationsInitial

◆ d_coordinatesFileNEB

◆ d_countrelaxationFlags

◆ d_dftfeWrapper

◆ d_dftPtr

◆ d_domainVectorsFileNEB

◆ d_externalForceOnAtom

◆ d_ImageError

◆ d_imageFreeze

◆ d_ionRelaxFlagsFile

◆ d_isRestart

◆ d_kmax

◆ d_kmin

◆ d_Length

◆ d_maximumAtomForceToBeRelaxed

◆ d_maximumNEBIteration

◆ d_mpiCommParent

◆ d_NEBImageno

◆ d_nonLinearSolverPtr

◆ d_numberGlobalCharges

◆ d_numberOfImages

◆ d_optimizationSolver

◆ d_optimizermaxIonUpdateStep

◆ d_optimizertolerance

◆ d_relaxationFlags

◆ d_restartFilesPath

◆ d_restartFlag

◆ d_solver

◆ d_solverRestart

◆ d_solverRestartPath

◆ d_startStep

◆ d_this_mpi_process

◆ d_totalUpdateCalls

◆ d_verbosity

◆ lbfgsNumPastSteps

◆ maxLineSearchIterCGPRP

◆ pcout