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

Inheritance diagram for BALL::ConjugateGradientMinimizer:

Classes
struct	Default

struct	Option

Public Types
Enums
enum	UpdateMethod { POLAK_RIBIERE = 1, FLETCHER_REEVES = 2, SHANNO = 3 }

Public Member Functions
Constructors and Destructors
	ConjugateGradientMinimizer ()

	ConjugateGradientMinimizer (ForceField &force_field)

	ConjugateGradientMinimizer (ForceField &force_field, SnapShotManager *ssm)

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

	ConjugateGradientMinimizer (ForceField &force_field, const Options &options)

	ConjugateGradientMinimizer (const ConjugateGradientMinimizer &rhs)

virtual	~ConjugateGradientMinimizer ()

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

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

Accessors
void	setUpdateMethod (UpdateMethod method)

UpdateMethod	getUpdateMethod () 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_

Gradient	unscaled_direction_

Size	number_of_atoms_

Size	updt_method_

bool	first_iter_

double	old_gtg_

vector< Vector3 >	a_i_

vector< Vector3 >	b_i_

vector< Vector3 >	p_t_

vector< Vector3 >	y_t_

vector< Vector3 >	p_i_

vector< Vector3 >	y_i_

double	D_1_

double	D_4_

Size	restart_frequency_

Size	last_restart_iter_

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

A minimizer for geometry optimization based on different conjugate gradient (CG) algorithms. See

[1] Fletcher, R. and Reeves, C.M. "Function Minimization by Conjugate Gradients" Comp. J., 7, 149-154, 1964

[2] David Shanno "Conjugate Gradient Methods With Inexact Searches" Mathematics of Operations Research, Vol. 3, No. 3, August 1978, pp. 244-256

[3] S. Watowich et. al "A Stable Rapidly Converging Conjugate Gradient Method for Energy Minimization" Journal of Computational Chemistry, Vol. 9, No. 6, pp. 650-661 (1988)

[4] M.J.D. Powell "Convergence properties of algorithms for nonlinear optimization" Report No. DAMPT 1985/NA1, University of Cambridge, 1985

[5] D.F. Shanno "Globally convergent conjugate gradient algorithms" Mathematical Programming 33 (1985), pp. 61-67

Definition at line 40 of file conjugateGradient.h.

Member Enumeration Documentation

enum BALL::ConjugateGradientMinimizer::UpdateMethod

The different conjugate gradient methods implemented.

See also: updateDirection for details on the implementation and references

Enumerator
POLAK_RIBIERE	Polak-Ribiere method
FLETCHER_REEVES	Fletcher-Reeves method
SHANNO	Shanno

Definition at line 52 of file conjugateGradient.h.

Constructor & Destructor Documentation

BALL::ConjugateGradientMinimizer::ConjugateGradientMinimizer ( )

Default constructor.

BALL::ConjugateGradientMinimizer::ConjugateGradientMinimizer ( ForceField & force_field )

Constructor expecting a valid force field

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

Constructor expecting a valid force field and a snapshot manager

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

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

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

Constructor expecting a valid force field and options

BALL::ConjugateGradientMinimizer::ConjugateGradientMinimizer ( const ConjugateGradientMinimizer & rhs )

Copy constructor

virtual BALL::ConjugateGradientMinimizer::~ConjugateGradientMinimizer ( )

virtual

Destructor.

Member Function Documentation

virtual double BALL::ConjugateGradientMinimizer::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.

UpdateMethod BALL::ConjugateGradientMinimizer::getUpdateMethod ( ) const

Returns the current method for updateDirection.

virtual bool BALL::ConjugateGradientMinimizer::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 ConjugateGradientMinimizer& BALL::ConjugateGradientMinimizer::operator= ( const ConjugateGradientMinimizer & rhs )

Assignment operator

void BALL::ConjugateGradientMinimizer::setUpdateMethod ( UpdateMethod method )

Set explicitly the criterion used for updateDirection. If the method is not recognized, this function fails.

virtual bool BALL::ConjugateGradientMinimizer::specificSetup ( )

virtual

Specific setup

Reimplemented from BALL::EnergyMinimizer.

virtual void BALL::ConjugateGradientMinimizer::updateDirection ( )

virtual

Update the search direction. This method updates the search direction. It uses the different conjugate gradient caculations dependend on the options.

Reimplemented from BALL::EnergyMinimizer.

Member Data Documentation

vector<Vector3> BALL::ConjugateGradientMinimizer::a_i_

protected

Variable needed for the Shanno direction calculation

Definition at line 216 of file conjugateGradient.h.

vector<Vector3> BALL::ConjugateGradientMinimizer::b_i_

protected

Variable needed for the Shanno direction calculation

Definition at line 220 of file conjugateGradient.h.

double BALL::ConjugateGradientMinimizer::D_1_

protected

Variable needed for the Shanno direction calculation

Definition at line 240 of file conjugateGradient.h.

double BALL::ConjugateGradientMinimizer::D_4_

protected

Variable needed for the Shanno direction calculation

Definition at line 244 of file conjugateGradient.h.

bool BALL::ConjugateGradientMinimizer::first_iter_

protected

Is this the (initial) first iteration?

Definition at line 208 of file conjugateGradient.h.

Size BALL::ConjugateGradientMinimizer::last_restart_iter_

protected

We count the iterations since the last restart. There are other necessities for a restart so the iteration counter may not coincide (by modulo) with the restart frequency.

Definition at line 255 of file conjugateGradient.h.

LineSearch BALL::ConjugateGradientMinimizer::line_search_

protected

The line search

Definition at line 192 of file conjugateGradient.h.

Size BALL::ConjugateGradientMinimizer::number_of_atoms_

protected

Number of movable atoms.

Definition at line 200 of file conjugateGradient.h.

double BALL::ConjugateGradientMinimizer::old_gtg_

protected

$g^T \cdot g$ where $g$ is the gradient of the last iteration

Definition at line 212 of file conjugateGradient.h.

vector<Vector3> BALL::ConjugateGradientMinimizer::p_i_

protected

Variable needed for the Shanno direction calculation

Definition at line 232 of file conjugateGradient.h.

vector<Vector3> BALL::ConjugateGradientMinimizer::p_t_

protected

Variable needed for the Shanno direction calculation

Definition at line 224 of file conjugateGradient.h.

Size BALL::ConjugateGradientMinimizer::restart_frequency_

protected

Frequency for restarts.

Definition at line 248 of file conjugateGradient.h.

Gradient BALL::ConjugateGradientMinimizer::unscaled_direction_

protected

Unscaled last search direction

Definition at line 196 of file conjugateGradient.h.

Size BALL::ConjugateGradientMinimizer::updt_method_

protected

Update method used for the CG

Definition at line 204 of file conjugateGradient.h.

vector<Vector3> BALL::ConjugateGradientMinimizer::y_i_

protected

Variable needed for the Shanno direction calculation

Definition at line 236 of file conjugateGradient.h.

vector<Vector3> BALL::ConjugateGradientMinimizer::y_t_

protected

Variable needed for the Shanno direction calculation

Definition at line 228 of file conjugateGradient.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