#include <BALL/MOLMEC/MINIMIZATION/shiftedLVMM.h>

Inheritance diagram for BALL::ShiftedLVMMMinimizer:

Classes
struct	Default

struct	Option

Public Types
Enums
enum	UpdateMethod { RANK_1 = 1, RANK_2 = 2 }

enum	CorrectionParameter { UNIT_VALUE = 1, BALANCING_VALUE = 2, SQUARE_ROOT = 3, GEOMETRIC_MEAN = 4, RATIO_OF_SHIFT_PARAMS = 5 }

Public Member Functions
Constructors and Destructors
	ShiftedLVMMMinimizer ()

	ShiftedLVMMMinimizer (ForceField &force_field)

	ShiftedLVMMMinimizer (ForceField &force_field, SnapShotManager *ssm)

	ShiftedLVMMMinimizer (ForceField &force_field, SnapShotManager *ssm, const Options &options)

	ShiftedLVMMMinimizer (ForceField &force_field, const Options &options)

	ShiftedLVMMMinimizer (const ShiftedLVMMMinimizer &rhs)

virtual	~ShiftedLVMMMinimizer ()

Assignments
const ShiftedLVMMMinimizer &	operator= (const ShiftedLVMMMinimizer &rhs)

Setup methods. They do all necessary preparations.
virtual bool	specificSetup ()

Accessors
void	setUpdateMethod (UpdateMethod updt)

UpdateMethod	getUpdateMethod () const

void	setCorrectionParameter (CorrectionParameter corr)

CorrectionParameter	getCorrectionParameter () const

void	setMaxNumOfColumns (Size num)

Size	getMaxNumOfColumns () const

virtual double	findStep ()

virtual void	updateDirection ()

virtual bool	minimize (Size iterations=0, bool resume=false)

Public Member Functions inherited from BALL::EnergyMinimizer
bool	operator== (const EnergyMinimizer &energy_minimizer)

	EnergyMinimizer ()

	EnergyMinimizer (ForceField &force_field)

	EnergyMinimizer (ForceField &force_field, const Options &options)

	EnergyMinimizer (const EnergyMinimizer &energy_minimizer)

virtual	~EnergyMinimizer ()

const EnergyMinimizer &	operator= (const EnergyMinimizer &energy_minimizer)

bool	isValid () const

bool	setup (ForceField &force_field)

bool	setup (ForceField &force_field, SnapShotManager *ssm)

bool	setup (ForceField &force_field, SnapShotManager *ssm, const Options &options)

bool	setup (ForceField &force_field, const Options &options)

virtual bool	isConverged () const

virtual double	updateEnergy ()

virtual void	updateForces ()

void	storeGradientEnergy ()

virtual void	printEnergy () const

virtual void	takeSnapShot () const

virtual void	finishIteration ()

Size	getNumberOfIterations () const

Gradient &	getDirection ()

Gradient &	getGradient ()

Gradient &	getInitialGradient ()

double	getEnergy () const

double &	getEnergy ()

double	getInitialEnergy () const

double &	getInitialEnergy ()

void	setNumberOfIterations (Size number_of_iterations)

Size	getMaxNumberOfIterations () const

void	setMaxNumberOfIterations (Size number_of_iterations)

void	setMaxSameEnergy (Size number)

Size	getMaxSameEnergy () const

void	setEnergyOutputFrequency (Size energy_output_frequency)

Size	getEnergyOutputFrequency () const

void	setEnergyDifferenceBound (float energy_difference_bound)

float	getEnergyDifferenceBound () const

void	setMaxGradient (float max_gradient)

float	getMaxGradient () const

void	setMaximumDisplacement (float maximum_displacement)

float	getMaximumDisplacement () const

void	setSnapShotFrequency (Size snapshot_frequency)

Size	getSnapShotFrequency () const

ForceField *	getForceField ()

Size	getForceUpdateCounter () const

Size	getEnergyUpdateCounter () const

void	enableEnergyAbortCondition (bool state)

bool	energyAbortConditionEnabled () const
	Query if the MDSimulation aborts if the Energy is greater than abort_energy_. More...

void	setEnergyToAbort (float value)

float	getEnergyToAbort () const

bool	wasAborted () const

Protected Attributes
Protected Attributes
LineSearch	line_search_

bool	first_iter_

Size	number_of_atoms_

Size	max_number_of_cols_

Size	curr_number_of_cols_

Size	updt_method_

Size	corr_par_

double	prev_shift_val_

vector< Vector3 >	shift_s_

vector< Vector3 >	grad_diff_

vector< float >	updt_u_

vector< float >	updt_v_

vector< Vector3 >	shifted_direction_

vector< Vector3 >	hess_factor_

vector< Vector3 >	initial_atoms_

Protected Attributes inherited from BALL::EnergyMinimizer
Gradient	initial_grad_

Gradient	current_grad_

double	initial_energy_

double	current_energy_

Gradient	old_grad_

double	old_energy_

Gradient	direction_

bool	valid_

SnapShotManager *	snapshot_

ForceField *	force_field_

Size	number_of_iterations_

Size	maximal_number_of_iterations_

Size	energy_output_frequency_

Size	snapshot_frequency_

double	energy_difference_bound_

double	max_gradient_

Size	max_same_energy_

Size	same_energy_counter_

float	maximum_displacement_

Size	force_update_counter_

Size	energy_update_counter_

float	cutlo_

double	step_

bool	abort_by_energy_enabled_

float	abort_energy_

bool	aborted_

Additional Inherited Members
Public Attributes inherited from BALL::EnergyMinimizer
Options	options

Detailed Description

Shifted limited-memory variable metric methods minimizer. A minimizer for geometry optimization based upon the shifted limited-memory variable metric methods proposed in

[1] Vlcek J., Luksan L.. New variable metric methods for unconstrained minimization covering the large-scale case. Report V-876, Prague, ICS AS CR, 2002.

[2] Vlcek J., Luksan L.. Additional properties of shifted variable metric methods. Report V-899, Prague, ICS AS CR, 2004.

[3] Vlcek J., Luksan L.. Shifted limited-memory variable metric methods for large-scale unconstrained optimization. Journal of Computational and Applied Mathematics 186 (2), pp. 365-390.

Definition at line 36 of file shiftedLVMM.h.

Member Enumeration Documentation

enum BALL::ShiftedLVMMMinimizer::CorrectionParameter

The different correction parameters implemented.

Enumerator
UNIT_VALUE	Unit value, i.e. rho = 1.0.
BALANCING_VALUE	Balancing value.
SQUARE_ROOT	Square root.
GEOMETRIC_MEAN	Geometric mean.
RATIO_OF_SHIFT_PARAMS	Ratio of shift parameters.

Definition at line 106 of file shiftedLVMM.h.

enum BALL::ShiftedLVMMMinimizer::UpdateMethod

The different variationally derived methods implemented.

Enumerator
RANK_1	Rank 1 variationally derived method.
RANK_2	Rank 2 variationally derived method.

Definition at line 93 of file shiftedLVMM.h.

Constructor & Destructor Documentation

BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer ( )

Default constructor.

BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer ( ForceField & force_field )

Constructor expecting a valid force field

BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer	(	ForceField &	force_field,
		SnapShotManager *	ssm
	)

Constructor expecting a valid force field and a snapshot manager

BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer	(	ForceField &	force_field,
		SnapShotManager *	ssm,
		const Options &	options
	)

Constructor expecting a valid force field, a snapshot manager and options

BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer	(	ForceField &	force_field,
		const Options &	options
	)

Constructor expecting a valid force field and options

BALL::ShiftedLVMMMinimizer::ShiftedLVMMMinimizer ( const ShiftedLVMMMinimizer & rhs )

Copy constructor

virtual BALL::ShiftedLVMMMinimizer::~ShiftedLVMMMinimizer ( )

virtual

Destructor.

Member Function Documentation

virtual double BALL::ShiftedLVMMMinimizer::findStep ( )

virtual

Calculate the next step. First, this method updates the model. Second, it performs a line search along the calculated direction afterwards.

Returns: double $\geq 0$ if the line search found an acceptable solution, otherwise -1.

See Also: EnergyMinimizer::findStep

Reimplemented from BALL::EnergyMinimizer.

CorrectionParameter BALL::ShiftedLVMMMinimizer::getCorrectionParameter ( ) const

Return the correction parameter

Size BALL::ShiftedLVMMMinimizer::getMaxNumOfColumns ( ) const

Return the maximum number of columns of the factor of the shifted inverse hessian approximation.

UpdateMethod BALL::ShiftedLVMMMinimizer::getUpdateMethod ( ) const

Return the update method

virtual bool BALL::ShiftedLVMMMinimizer::minimize	(	Size	iterations = `0`,
		bool	resume = `false`
	)

virtual

Minimize the energy of the system. This method executes at most iterations minimization steps. If the number of iterations is not given, the number specified in the options is taken.

Parameters

iterations	the maximum number of iterations
resume	true to resume a previous run

See Also: EnergyMinimizer::minimize

Reimplemented from BALL::EnergyMinimizer.

const ShiftedLVMMMinimizer& BALL::ShiftedLVMMMinimizer::operator= ( const ShiftedLVMMMinimizer & rhs )

Assignment operator

void BALL::ShiftedLVMMMinimizer::setCorrectionParameter ( CorrectionParameter corr )

Set explicitly the correction parameter

void BALL::ShiftedLVMMMinimizer::setMaxNumOfColumns ( Size num )

Set explicitly the maximum number of columns of the factor of the shifted inverse hessian approximation.

void BALL::ShiftedLVMMMinimizer::setUpdateMethod ( UpdateMethod updt )

Set explicitly the update method

virtual bool BALL::ShiftedLVMMMinimizer::specificSetup ( )

virtual

Specific setup

Reimplemented from BALL::EnergyMinimizer.

virtual void BALL::ShiftedLVMMMinimizer::updateDirection ( )

virtual

Update the shifted inverse hessian approximation. Afterwards, compute the search direction.

Reimplemented from BALL::EnergyMinimizer.

Member Data Documentation

Size BALL::ShiftedLVMMMinimizer::corr_par_

protected

Correction parameter

Definition at line 269 of file shiftedLVMM.h.

Size BALL::ShiftedLVMMMinimizer::curr_number_of_cols_

protected

Current number of columns of the factor of the shifted inverse hessian approximation.

Definition at line 261 of file shiftedLVMM.h.

bool BALL::ShiftedLVMMMinimizer::first_iter_

protected

Is this an initial first iteration?

Definition at line 247 of file shiftedLVMM.h.

vector<Vector3> BALL::ShiftedLVMMMinimizer::grad_diff_

protected

Current gradient difference.

Definition at line 281 of file shiftedLVMM.h.

vector<Vector3> BALL::ShiftedLVMMMinimizer::hess_factor_

protected

Factor of the shifted inverse hessian approximation in column order, $U_k$ in [3].

Definition at line 298 of file shiftedLVMM.h.

vector<Vector3> BALL::ShiftedLVMMMinimizer::initial_atoms_

protected

Positions of the movable atoms when we start an iteration. This is used to reduce slightly rounding errors

Definition at line 303 of file shiftedLVMM.h.

LineSearch BALL::ShiftedLVMMMinimizer::line_search_

protected

The line search

Definition at line 243 of file shiftedLVMM.h.

Size BALL::ShiftedLVMMMinimizer::max_number_of_cols_

protected

Maximum number of columns of the factor of the shifted inverse hessian approximation.

Definition at line 256 of file shiftedLVMM.h.

Size BALL::ShiftedLVMMMinimizer::number_of_atoms_

protected

Number of movable atoms.

Definition at line 251 of file shiftedLVMM.h.

double BALL::ShiftedLVMMMinimizer::prev_shift_val_

protected

Shift value of the previous iteration.

Definition at line 273 of file shiftedLVMM.h.

vector<Vector3> BALL::ShiftedLVMMMinimizer::shift_s_

protected

Shifted previous step.

Definition at line 277 of file shiftedLVMM.h.

vector<Vector3> BALL::ShiftedLVMMMinimizer::shifted_direction_

protected

Direction of the shifted step, i. e. $-U_k \cdot U_k^T \cdot g_k$ .

Definition at line 293 of file shiftedLVMM.h.

Size BALL::ShiftedLVMMMinimizer::updt_method_

protected

Update method

Definition at line 265 of file shiftedLVMM.h.

vector<float> BALL::ShiftedLVMMMinimizer::updt_u_

protected

Needed vector for the update.

Definition at line 285 of file shiftedLVMM.h.

vector<float> BALL::ShiftedLVMMMinimizer::updt_v_

protected

Needed vector for the update.

Definition at line 289 of file shiftedLVMM.h.

Classes

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation