EnergyCalculator Class Reference

Inheritance diagram for EnergyCalculator:

Public Member Functions
virtual EnergyCalculator *	newInstance () const =0
virtual std::string	identifier () const =0
virtual std::string	name () const =0
virtual std::string	description () const =0
virtual bool	setConfiguration (Core::VariantMap &config)
virtual Core::Molecule::ElementMask	elements () const =0
	Indicate if your method only treats a subset of elements.
virtual bool	acceptsUnitCell () const
	Indicate if your method can handle unit cells.
virtual bool	acceptsIons () const
	Indicate if your method can handle ions Many methods only treat neutral systems, either a neutral molecule or a neutral unit cell.
virtual bool	acceptsRadicals () const
	Indicate if your method can handle radicals Most methods only treat closed-shell molecules.
void	gradient (const TVector &x, TVector &grad) override
void	cleanGradients (TVector &grad)
Real	constraintEnergies (const TVector &x)
void	constraintGradients (const TVector &x, TVector &grad)
std::vector< Core::Constraint >	constraints () const
void	setConstraints (const std::vector< Core::Constraint > &constraints)
void	setMask (TVector mask)
TVector	mask () const
virtual void	setMolecule (Core::Molecule *mol)=0

Protected Member Functions
void	appendError (const std::string &errorString, bool newLine=true) const
	Append an error to the error string for the model.

Protected Attributes
TVector	m_mask
std::vector< Core::Constraint >	m_distanceConstraints
std::vector< Core::Constraint >	m_angleConstraints
std::vector< Core::Constraint >	m_torsionConstraints
std::vector< Core::Constraint >	m_outOfPlaneConstraints

Member Function Documentation

newInstance()

virtual EnergyCalculator * newInstance ( ) const

pure virtual

Create a new instance of the model. Ownership passes to the caller.

Implemented in LennardJones, and UFF.

identifier()

virtual std::string identifier ( ) const

pure virtual

Returns

a unique identifier for this calculator.

Implemented in LennardJones, and UFF.

name()

virtual std::string name ( ) const

pure virtual

Returns

A short translatable name for this method (e.g., MMFF94, UFF, etc.)

Implemented in LennardJones, and UFF.

description()

virtual std::string description ( ) const

pure virtual

Returns

a description of the method

Implemented in LennardJones, and UFF.

setConfiguration()

virtual bool setConfiguration ( Core::VariantMap & config )

virtual

Called to set the configuration (e.g., for a GUI options dialog)

elements()

virtual Core::Molecule::ElementMask elements ( ) const

pure virtual

Returns

an element mask corresponding to the defined subset

Implemented in LennardJones, and UFF.

acceptsUnitCell()

virtual bool acceptsUnitCell ( ) const

virtual

Returns

true if unit cells are supported

Reimplemented in LennardJones.

acceptsIons()

virtual bool acceptsIons ( ) const

virtual

Returns

true if ions are supported

Reimplemented in LennardJones, and UFF.

acceptsRadicals()

virtual bool acceptsRadicals ( ) const

virtual

Returns

true if radicals are supported

Reimplemented in LennardJones, and UFF.

gradient()

void gradient ( const TVector & x, TVector & grad )

override

Calculate the gradients for this method, defaulting to numerical finite-difference methods

cleanGradients()

void cleanGradients

(

TVector &

grad

)

Called to 'clean' gradients

Parameters

grad	(e.g., for constraints)

constraintEnergies()

Real constraintEnergies

(

const TVector &

x

)

Called to get the energies for the current set of constraints. which should be added to the value() method for real energies in derived classes

Returns

the sum of the constraint energies

constraintGradients()

void constraintGradients	(	const TVector &	x,
		TVector &	grad )

Called to get the gradients for the current set of constraints. which should be added to the gradient() method in derived classes.

Parameters

x	the current coordinates
grad	the gradient vector to be updated with constraint gradients

constraints()

std::vector< Core::Constraint > constraints

(

)

const

Called to get the constraints for this method.

Returns

the constraints for this method

setMask()

void setMask

(

TVector

mask

)

Called to update the "frozen" mask (e.g., during editing)

mask()

TVector mask

(

)

const

Returns

the frozen atoms mask

setMolecule()

virtual void setMolecule ( Core::Molecule * mol )

pure virtual

Called when the current molecule changes.

Implemented in LennardJones, and UFF.

appendError()

void appendError ( const std::string & errorString, bool newLine = true ) const

protected

Parameters

errorString	The error to be added.
newLine	Add a new line after the error string?

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

• energycalculator.h