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 std::string	userOptions () const
	Return a JSON object string describing optional user-editable settings for this model. Empty string means no user options.
virtual bool	setUserOptions (const std::string &optionsJson)
	Set user-selected options serialized as a JSON object string.
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.
virtual Real	value (const Eigen::VectorXd &x)=0
virtual void	gradient (const Eigen::VectorXd &x, Eigen::VectorXd &grad)
void	finiteGradient (const Eigen::VectorXd &x, Eigen::VectorXd &grad, int accuracy=0)
virtual Real	evaluate (const Eigen::VectorXd &x, Eigen::VectorXd *grad=nullptr)
virtual void	hessian (const Eigen::VectorXd &x, Eigen::MatrixXd &hess)
void	finiteHessian (const Eigen::VectorXd &x, Eigen::MatrixXd &hess, int accuracy=0)
void	cleanGradients (Eigen::VectorXd &grad)
Real	constraintEnergies (const Eigen::VectorXd &x)
void	constraintGradients (const Eigen::VectorXd &x, Eigen::VectorXd &grad)
std::vector< Core::Constraint >	constraints () const
void	setConstraints (const std::vector< Core::Constraint > &constraints)
void	setMask (Eigen::VectorXd mask)
Eigen::VectorXd	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
Eigen::VectorXd	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.

setUserOptions()

virtual bool setUserOptions ( const std::string & optionsJson )

virtual

Returns

True on success.

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, and UFF.

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.

value()

virtual Real value ( const Eigen::VectorXd & x )

pure virtual

Calculate the energy for this method.

Implemented in LennardJones, and UFF.

gradient()

virtual void gradient ( const Eigen::VectorXd & x, Eigen::VectorXd & grad )

virtual

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

Reimplemented in LennardJones, and UFF.

finiteGradient()

void finiteGradient	(	const Eigen::VectorXd &	x,
		Eigen::VectorXd &	grad,
		int	accuracy = 0 )

Calculate numerical gradients for this method.

evaluate()

virtual Real evaluate ( const Eigen::VectorXd & x, Eigen::VectorXd * grad = nullptr )

virtual

Evaluate the energy and optionally gradients in one call.

Derived classes with efficient fused implementations should override this.

Reimplemented in LennardJones, and UFF.

hessian()

virtual void hessian ( const Eigen::VectorXd & x, Eigen::MatrixXd & hess )

virtual

Calculate the Hessian matrix for this method, defaulting to numerical finite-difference methods.

finiteHessian()

void finiteHessian	(	const Eigen::VectorXd &	x,
		Eigen::MatrixXd &	hess,
		int	accuracy = 0 )

Calculate numerical Hessian for this method.

cleanGradients()

void cleanGradients

(

Eigen::VectorXd &

grad

)

Called to 'clean' gradients

Parameters

grad	(e.g., for constraints)

constraintEnergies()

Real constraintEnergies

(

const Eigen::VectorXd &

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 Eigen::VectorXd &	x,
		Eigen::VectorXd &	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

(

Eigen::VectorXd

mask

)

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

mask()

Eigen::VectorXd 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