Public Types
enum	TolerancePreset { Uniform, Balanced, AccurateEnergies }
	Specifies presets for tolerance parameters. More...

Public Member Functions
	FitJob ()
	Constructor.

	~FitJob ()
	Destructor.

const FPString &	name () const
	Returns the user-defined name of this job.

double	getDefaultPropertyTolerance (FitProperty *property)
	Returns the default tolerance for the given property based on the selected tolerance preset.

int	numAtomTypes () const
	Returns the number of atom types used in this job.

bool	addAtomType (const FPString &name, double mass=0.0, int atomicNumber=0)
	Adds a new atom type to the job.

const FPString &	atomTypeName (int i) const
	Returns the name of the i-th atom type.

double	atomTypeMass (int i) const

int	atomTypeAtomicNumber (int i) const

int	atomTypeIndex (const FPString &s) const
	Returns the index of the atom type.

double	maximumCutoff () const
	Returns the maximum cutoff radius of all potentials used by this job.

const std::vector< Potential * > &	potentials () const
	Returns the list of all potentials used in this job.

const std::vector< AtomicStructure * > &	structures () const
	Returns the list of all atomic structures used for fitting.

const std::vector< AtomicStructure * > &	referencedStructures () const

void	addReferencedStructure (AtomicStructure *structure)
	Add a structure to the list of referenced structures.

const std::vector< AtomicStructure * > &	unreferencedStructures () const

void	addUnreferencedStructure (AtomicStructure *structure)
	Add a structure to the list of unreferenced structures.

const std::vector< DerivedProperty * > &	derivedProperties ()
	Returns the list of all derived properties.

const std::vector< FitProperty * > &	fitProperties ()
	Returns the global list of active properties which are included in the fit and which need to be computed.

FitGroup &	rootGroup ()
	Returns the root node of the property group tree.

ScalarFitProperty *	getScalarFitProperty (const FPString &id)

AtomicStructure *	getAtomicStructure (const FPString &id)

DerivedProperty *	getDerivedProperty (const FPString &id)

const Matrix3 *	lookupDeformation (const FPString &deformationId) const
	Returns the deformation with the given id. Returns NULL if no such deformation has been defined.

bool	fittingEnabled () const
	Returns whether fitting will be performed.

std::shared_ptr< Minimizer >	fitMinimizer ()
	Returns the minimizer.

void	performFitting ()
	Performs the actual fitting by minimizing the residual.

void	printPotentialDOFList (bool printFullDOFList)
	Outputs the current values of all DOFs of the potentials. More...

void	printFittingProperties ()
	Outputs the list of properties being fitted.

bool	potentialValidationEnabled () const
	Returns whether validation of the force/energy calculation routines has been requested by the user.

void	validatePotentials ()
	Performs a check of the energy/force calculation routines using numerical differentiation.

int	numActiveDOF () const
	Returns the total number of active degrees of freedom.

void	packDOF (double *destination)
	Packs the values of all degrees of freedom into a linear vector, which can be passed to the minimizer routine. More...

void	packDOF (std::vector< double > &destination)
	Packs the values of all degrees of freedom into a linear vector, which can be passed to the minimizer routine. More...

void	unpackDOF (const double *source)
	Unpacks the values of all degrees of freedom from a linear vector. More...

void	unpackDOF (const std::vector< double > &source)
	Unpacks the values of all degrees of freedom from a linear vector. More...

void	parse (const FPString &file)
	Parses the job description from the XML file. More...

int	parseAtomTypeAttribute (XML::Element element, const char *attributeName)
	Returns the atom type index of the species specified in the given element attribute. More...

int	parseAtomTypeElement (XML::Element element, const char *elementName)
	Returns the atom type index of the species specified in the given element. More...

std::vector< int >	parseAtomTypesAttribute (XML::Element element, const char *attributeName)
	Returns the list of atom types corresponding to the species specified in the given element attribute. More...

ScalarFitProperty *	parseScalarFitPropertyAttribute (XML::Element element, const char *attributeName)
	Returns the ScalarFitProperty specified in the given element attribute. More...

double	calculateResidual (FitProperty::ResidualNorm norm=FitProperty::UserDefined)
	Calculates the total residual, i.e. the objective function to be minimized during fitting. More...

void	prepareFitting ()
	Prepares a list of all degrees of freedom and properties that are to be fitted.

Friends
class	FitGroup

class	AtomicStructure

class	DerivedProperty

Member Enumeration Documentation

◆ TolerancePreset

enum atomicrex::FitJob::TolerancePreset

Specifies presets for tolerance parameters.

Enumerator
Uniform	All tolerances are 1.0.
Balanced	Specifies a balanced unit based assignment of tolerance parameters.
AccurateEnergies	Specifies a unit based assignment that emphasizes energies.

Member Function Documentation

◆ atomTypeAtomicNumber()

int atomicrex::FitJob::atomTypeAtomicNumber ( int i ) const

inline

Returns the atomic of the i-th atom type. May be zero if not set.

◆ atomTypeMass()

double atomicrex::FitJob::atomTypeMass ( int i ) const

inline

Returns the mass of the i-th atom type. May be zero if not set.

◆ calculateResidual()

double atomicrex::FitJob::calculateResidual ( FitProperty::ResidualNorm norm = FitProperty::UserDefined )

Calculates the total residual, i.e. the objective function to be minimized during fitting.

Parameters

norm	The style to be used for computing the residual, see #FitProperty::ResidualNorm.

◆ getAtomicStructure()

AtomicStructure * atomicrex::FitJob::getAtomicStructure ( const FPString & id )

Returns the atomic structure with the given ID. Return NULL if no such structure exists.

◆ getDerivedProperty()

DerivedProperty * atomicrex::FitJob::getDerivedProperty ( const FPString & id )

Returns the derived property with the given ID. Return NULL if no such property exists.

◆ getScalarFitProperty()

ScalarFitProperty * atomicrex::FitJob::getScalarFitProperty ( const FPString & id )

Returns the atomic structure with the given ID. Return NULL if no such structure exists.

◆ packDOF() [1/2]

void atomicrex::FitJob::packDOF ( double * destination )

Packs the values of all degrees of freedom into a linear vector, which can be passed to the minimizer routine.

Parameters

destination A pointer to a contiguous array of doubles that will receive the values of all the degrees of freedom.

◆ packDOF() [2/2]

void atomicrex::FitJob::packDOF ( std::vector< double > & destination )

inline

Packs the values of all degrees of freedom into a linear vector, which can be passed to the minimizer routine.

Parameters

destination A vector of doubles that will receive the values of all the degrees of freedom.

◆ parse()

void atomicrex::FitJob::parse ( const FPString & file )

Parses the job description from the XML file.

Parameters

file	Name of input file.

◆ parseAtomTypeAttribute()

int atomicrex::FitJob::parseAtomTypeAttribute	(	XML::Element	element,
		const char *	attributeName
	)

Returns the atom type index of the species specified in the given element attribute.

Throws exception if species has not been defined.

Parameters

element	XML::Element object to be parsed
attributeName	The name of the attribute

Returns: atom type index as integer

◆ parseAtomTypeElement()

int atomicrex::FitJob::parseAtomTypeElement	(	XML::Element	element,
		const char *	elementName
	)

Returns the atom type index of the species specified in the given element.

Throws exception if species has not been defined.

Parameters

element	XML::Element object to be parsed
elementName	The name of the element

Returns: atom type index as integer

◆ parseAtomTypesAttribute()

vector< int > atomicrex::FitJob::parseAtomTypesAttribute	(	XML::Element	element,
		const char *	attributeName
	)

Returns the list of atom types corresponding to the species specified in the given element attribute.

Throws exception if some species has not been defined.

Parameters

element	XML::Element object to be parsed
attributeName	The name of the attribute

Returns: list of integers representing atom types

◆ parseScalarFitPropertyAttribute()

ScalarFitProperty * atomicrex::FitJob::parseScalarFitPropertyAttribute	(	XML::Element	element,
		const char *	attributeName
	)

Returns the ScalarFitProperty specified in the given element attribute.

Throws exception if property has not been defined.

Parameters

element	XML::Element object to be parsed
attributeName	The name of the attribute

Returns: ScalarFitProperty specified in the element attribute

◆ printPotentialDOFList()

void atomicrex::FitJob::printPotentialDOFList ( bool printFullDOFList )

Outputs the current values of all DOFs of the potentials.

Parameters

printFullDOFList Controls whether inactive DOFs are also printed. This option is used once before fitting to report the full list of DOFs.

◆ referencedStructures()

const std::vector<AtomicStructure*>& atomicrex::FitJob::referencedStructures ( ) const

inline

Returns the list of all referenced atomic structures used for fitting. i.e. these structured need to be computed first as other structures depend on them.

◆ unpackDOF() [1/2]

void atomicrex::FitJob::unpackDOF ( const double * source )

Unpacks the values of all degrees of freedom from a linear vector.

Parameters

source A pointer to a contiguous array of doubles that contains the values of all the degrees of freedom.

◆ unpackDOF() [2/2]

void atomicrex::FitJob::unpackDOF ( const std::vector< double > & source )

inline

Unpacks the values of all degrees of freedom from a linear vector.

Parameters

source A vector of doubles that contains the values of all the degrees of freedom.

◆ unreferencedStructures()

const std::vector<AtomicStructure*>& atomicrex::FitJob::unreferencedStructures ( ) const

inline

Returns the list of all unreferenced atomic structures used for fitting. These structures can be computed without any particular order.

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

FitJob.h
FitJob.cpp
Fitting.cpp
Validation.cpp

Public Types

Public Member Functions

Friends

Member Enumeration Documentation

◆ TolerancePreset

Member Function Documentation

◆ atomTypeAtomicNumber()

◆ atomTypeMass()

◆ calculateResidual()

◆ getAtomicStructure()

◆ getDerivedProperty()

◆ getScalarFitProperty()

◆ packDOF() [1/2]

◆ packDOF() [2/2]

◆ parse()

◆ parseAtomTypeAttribute()

◆ parseAtomTypeElement()

◆ parseAtomTypesAttribute()

◆ parseScalarFitPropertyAttribute()

◆ printPotentialDOFList()

◆ referencedStructures()

◆ unpackDOF() [1/2]

◆ unpackDOF() [2/2]

◆ unreferencedStructures()