EnergyMinimizer Class Reference
[Energy Minimizer]

#include <energyMinimizer.h>

Inheritance diagram for EnergyMinimizer:


Public Member Functions
bool	operator== (const EnergyMinimizer &energy_minimizer) throw ()
	Equality operator.
Constructors and Destructors
	EnergyMinimizer ()
	Default constructor.
	EnergyMinimizer (ForceField &force_field)
	Constructor.
	EnergyMinimizer (ForceField &force_field, const Options &options)
	Constructor.
	EnergyMinimizer (const EnergyMinimizer &energy_minimizer)
	Copy constructor.
virtual	~EnergyMinimizer ()
	Destructor.
Assignments
const EnergyMinimizer &	operator= (const EnergyMinimizer &energy_minimizer)
	Assignment operator.
Debugging and Diagnostics
bool	isValid () const
	Is the energy minimizer valid : did the setup work?
Setup methods
bool	setup (ForceField &force_field)
	Sets up the energy minimizer.
bool	setup (ForceField &force_field, SnapShotManager *ssm)
	Sets up the energy minimizer.
bool	setup (ForceField &force_field, SnapShotManager *ssm, const Options &options)
	Sets up the energy minimizer.
bool	setup (ForceField &force_field, const Options &options)
	Sets up the energy minimizer.
virtual bool	specificSetup ()
	Specific setup.
Accessors
virtual bool	isConverged () const
	Implements the convergence criterion.
virtual double	findStep ()
	Calculate the next step.
virtual void	updateDirection ()
	Update the search direction.
virtual double	updateEnergy ()
	Update energy.
virtual void	updateForces ()
	Update forces and store them in current_grad_.
void	storeGradientEnergy ()
	Store the current energy and gradient.
virtual void	printEnergy () const
	Print the energy.
virtual void	takeSnapShot () const
	Take a snapshot of the system.
virtual void	finishIteration ()
	Finishing step for this iteration.
Size	getNumberOfIterations () const
	Return the number of iterations performed.
Gradient &	getDirection ()
	Return a reference to the current search direction.
Gradient &	getGradient ()
	Return a reference to the current gradient.
Gradient &	getInitialGradient ()
	Return a reference to the initial gradient.
double	getEnergy () const
	Return the current energy.
double &	getEnergy ()
	Return a reference to the current energy.
double	getInitialEnergy () const
	Return the initial energy.
double &	getInitialEnergy ()
	Return a mutable reference to the initial energy.
void	setNumberOfIterations (Size number_of_iterations)
	Set the number of iterations performed so far.
Size	getMaxNumberOfIterations () const
	Get the maximum number of iterations.
void	setMaxNumberOfIterations (Size number_of_iterations)
	Set the maximum number of iterations.
void	setMaxSameEnergy (Size number)
	Set the maximum number of iterations allowed with equal energy (second convergence criterion).
Size	getMaxSameEnergy () const
	Get the maximum number of iterations allowed with equal energy (second convergence criterion).
void	setEnergyOutputFrequency (Size energy_output_frequency)
	Set the energy output frequency.
Size	getEnergyOutputFrequency () const
	Get the energy ouput frequency.
void	setEnergyDifferenceBound (float energy_difference_bound)
	Set the energy difference bound for convergence.
float	getEnergyDifferenceBound () const
	Get the energy difference bound.
void	setMaxGradient (float max_gradient)
	Set the maximum RMS gradient (first convergence criterion).
float	getMaxGradient () const
	Get the maximum RMS gradient (first convergence criterion).
void	setMaximumDisplacement (float maximum_displacement)
	Set the maximum displacement value.
float	getMaximumDisplacement () const
	Get the maximum displacement value.
void	setSnapShotFrequency (Size snapshot_frequency)
	Set the snapshot frequency.
Size	getSnapShotFrequency () const
	Get the snapshot output frequency.
ForceField *	getForceField ()
	Return the force field of the energy minimizer.
Size	getForceUpdateCounter () const throw ()
	Return the number of force updates since the start of the minimization.
Size	getEnergyUpdateCounter () const throw ()
	Return the number of energy updates since the start of the minimization.
virtual bool	minimize (Size steps=0, bool resume=false)
	Minimize the energy of the system bound to the force field.
void	enableEnergyAbortCondition (bool state)
	Specify if the MDSimulation aborts if the Energy is greater than abort_energy_.
bool	energyAbortConditionEnabled () const
	Query if the MDSimulation aborts if the Energy is greater than abort_energy_.
void	setEnergyToAbort (float value)
	Set the value for the energy, that will result in aborting the minization, if it will be surpassed.
float	getEnergyToAbort () const
bool	wasAborted () const throw ()
	Return true, if the minimization was aborted, e.g.
Public Attributes
Public Attributes
Options	options
	Options.
Protected Attributes
Protected Attributes
Gradient	initial_grad_
	The gradient at the beginning of the current minimization step.
Gradient	current_grad_
	The current gradient.
double	initial_energy_
	The energy at the beginning of the current minimization step.
double	current_energy_
	The current energy.
Gradient	old_grad_
	The gradient from the last step.
double	old_energy_
	The energy from the last step.
Gradient	direction_
	The current search direction.
bool	valid_
	The boolean variable indicates if the setup of the energy minimizer was successful.
SnapShotManager *	snapshot_
	Pointer to a SnapShotManager for storing snapshots of the system.
ForceField *	force_field_
	The force field bound to the energy minimizer.
Size	number_of_iterations_
	The current iteration number.
Size	maximal_number_of_iterations_
	Maximum number of iterations.
Size	energy_output_frequency_
	Frequency of energy output.
Size	snapshot_frequency_
	Frequency of atom coordinate ouput.
double	energy_difference_bound_
	If the energy difference (before and after an iteration) is smaller than this bound, the minimization procedure stops.
double	max_gradient_
	The maximum RMS gradient tolerated (first convergence criterion).
Size	max_same_energy_
	The maximum number of iterations with same energy.
Size	same_energy_counter_
	A counter for the number of steps with a similar energy.
float	maximum_displacement_
	The maximal shift of an atom per iteration step (in Angstrom).
Size	force_update_counter_
	Internal counter: how often is a force update done.
Size	energy_update_counter_
	Internal counter: how often is an energy update done.
float	cutlo_
	Numerical lower bound: we don't want to compute the reciprocal of a number which is lower than 'cutlo_'.
double	step_
	The last step size (in respect of the length of the computed direction vector), so the length of the last step was $step\cdot\|direction\|$ .
bool	abort_by_energy_enabled_
float	abort_energy_
bool	aborted_

Detailed Description

EnergyMinimizer.

Base class for all minimizer for geometry optimization.

Constructor & Destructor Documentation

EnergyMinimizer::EnergyMinimizer ( )

Default constructor.

EnergyMinimizer::EnergyMinimizer ( ForceField & force_field )

Constructor.

EnergyMinimizer::EnergyMinimizer ( ForceField & force_field,

const Options & options

)

Constructor.

virtual EnergyMinimizer::~EnergyMinimizer ( ) [virtual]

Destructor.

Member Function Documentation

virtual double EnergyMinimizer::findStep ( ) [virtual]

Calculate the next step.
This method is implemented in each minimizer class and tries to determine the next step to be taken. It typically performs a line search. The value returned is usually the step length with respect to the current direction.
Returns:
-1 to indicate failure

Reimplemented in ConjugateGradientMinimizer, ShiftedLVMMMinimizer, SteepestDescentMinimizer, and StrangLBFGSMinimizer.

virtual void EnergyMinimizer::finishIteration ( ) [virtual]

Finishing step for this iteration.
This method should be called at the end of the main iteration loop implemented in minimize . It takes over some administrative stuff:

increment the iteration counter number_of_iterations_
call takeSnapShot if necessary
call printEnergy if necessary
call ForceField::update if necessary (to rebuild the pair lists!)
update the same_energy_counter_ tested in isConverged

This method should be overwritten only in rare cases. Even then, the programmer should make sure to call EnergyMinimizer::finishIteration or has to take care of the above items himself.
All derived classes should call this method at the end of the minimize main loop. Otherwise strange things might happen.
See also:
minimize

Size EnergyMinimizer::getEnergyUpdateCounter ( ) const throw ()

Return the number of energy updates since the start of the minimization.

Size EnergyMinimizer::getForceUpdateCounter ( ) const throw ()

Return the number of force updates since the start of the minimization.

float EnergyMinimizer::getMaxGradient ( ) const

Get the maximum RMS gradient (first convergence criterion).
The gradient unit of the gradient is kJ/(mol ).

Size EnergyMinimizer::getNumberOfIterations ( ) const

Return the number of iterations performed.

virtual bool EnergyMinimizer::isConverged ( ) const [virtual]

Implements the convergence criterion.
If the convergence criterion is fulfilled, this method returns true. The convergence criterion is implemented as one of two conditions:
(1) {RMS gradient} is below max_rms_gradient_ (2) same_energy_counter_ is above max_same_energy_
If any of these conditions hold isConverged returns true. This method should be reimplemented in derived classes for a different convergence criterion.

virtual bool EnergyMinimizer::minimize ( Size steps = 0,

bool resume = false

) [virtual]

Minimize the energy of the system bound to the force field.
If a number of steps is given, the minimization is aborted after that number of steps, regardless of the number of steps given in the options (MAX_STEPS). Together with the resume option this feature is used to extract properties or visualize the results in the course of the minimization. If resume is set to true, the minimization continues with the former step width and settings.
Parameters:

steps maximum number of steps to be taken

resume true if the minimization is to be resumed with the previous settings

Returns:
bool - true if the minimization has converged

Reimplemented in ConjugateGradientMinimizer, ShiftedLVMMMinimizer, SteepestDescentMinimizer, and StrangLBFGSMinimizer.

virtual void EnergyMinimizer::printEnergy ( ) const [virtual]

Print the energy.
This method is called by finishIteration after every energy_output_frequency_ steps. It prints the current RMS gradient and the current energy to Log .info().
See also:
setEnergyOutputFrequency
getEnergyOutputFrequency

void EnergyMinimizer::setEnergyToAbort ( float value )

Set the value for the energy, that will result in aborting the minization, if it will be surpassed.
Default value: 10^9.

void EnergyMinimizer::setMaxGradient ( float max_gradient )

Set the maximum RMS gradient (first convergence criterion).
The gradient unit of the gradient is kJ/(mol ).

void EnergyMinimizer::setMaximumDisplacement ( float maximum_displacement )

Set the maximum displacement value.
This is the maximum distance an atom may be moved by the minimizer in one iteration.

void EnergyMinimizer::setNumberOfIterations ( Size number_of_iterations )

Set the number of iterations performed so far.

bool EnergyMinimizer::setup ( ForceField & force_field,

const Options & options

)

Sets up the energy minimizer.

bool EnergyMinimizer::setup ( ForceField & force_field,

SnapShotManager * ssm,

const Options & options

)

Sets up the energy minimizer.

bool EnergyMinimizer::setup ( ForceField & force_field,

SnapShotManager * ssm

)

Sets up the energy minimizer.

bool EnergyMinimizer::setup ( ForceField & force_field )

Sets up the energy minimizer.

void EnergyMinimizer::storeGradientEnergy ( )

Store the current energy and gradient.
The current gradient and current energy is copied into initial energy and initial gradient. This is usually done at the start of an iteration.

virtual void EnergyMinimizer::takeSnapShot ( ) const [virtual]

Take a snapshot of the system.
This method is called by finishIteration after every snapshot_frequency_ steps. It saves a SnapShot of the current atom coordinates to a SnapShotManager (if enabled).
See also:
setSnapShotFrequency
getSnapShotFrequency

virtual void EnergyMinimizer::updateDirection ( ) [virtual]

Update the search direction.
This method is implemented by the derived classes to implement a method to determine a new search direction.
Reimplemented in ConjugateGradientMinimizer, ShiftedLVMMMinimizer, SteepestDescentMinimizer, and StrangLBFGSMinimizer.

virtual double EnergyMinimizer::updateEnergy ( ) [virtual]

Update energy.
This method calls force_field_->updateEnergy() and stores the result in current_energy_.

virtual void EnergyMinimizer::updateForces ( ) [virtual]

Update forces and store them in current_grad_.
This method calls force_field_->updateForces() and stores them in current_grad_ .

bool EnergyMinimizer::wasAborted ( ) const throw ()

Return true, if the minimization was aborted, e.g.
because of strange energies or gradient.

Member Data Documentation

double EnergyMinimizer::current_energy_ [protected]

The current energy.

Gradient EnergyMinimizer::current_grad_ [protected]

The current gradient.

float EnergyMinimizer::cutlo_ [protected]

Numerical lower bound: we don't want to compute the reciprocal of a number which is lower than 'cutlo_'.

double EnergyMinimizer::energy_difference_bound_ [protected]

If the energy difference (before and after an iteration) is smaller than this bound, the minimization procedure stops.

Size EnergyMinimizer::energy_update_counter_ [protected]

Internal counter: how often is an energy update done.
Measure for the speed of minimization.

ForceField* EnergyMinimizer::force_field_ [protected]

The force field bound to the energy minimizer.
Among other data the force field contains the molecular system whose energy will be minimized by the energy minimizer.

Size EnergyMinimizer::force_update_counter_ [protected]

Internal counter: how often is a force update done.
Measure for the speed of minimization.

double EnergyMinimizer::initial_energy_ [protected]

The energy at the beginning of the current minimization step.

Gradient EnergyMinimizer::initial_grad_ [protected]

The gradient at the beginning of the current minimization step.

Size EnergyMinimizer::max_same_energy_ [protected]

The maximum number of iterations with same energy.
When this number is reached, we assume the system to have converged (second convergence criterion)

float EnergyMinimizer::maximum_displacement_ [protected]

The maximal shift of an atom per iteration step (in Angstrom).

Size EnergyMinimizer::same_energy_counter_ [protected]

A counter for the number of steps with a similar energy.

double EnergyMinimizer::step_ [protected]

The last step size (in respect of the length of the computed direction vector), so the length of the last step was $step\cdot|direction|$ .

EnergyMinimizer Class Reference [Energy Minimizer]

Public Member Functions

Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

EnergyMinimizer Class Reference
[Energy Minimizer]