atomicrex::Potential Class Reference

Base class for potential. More...

#include <Potential.h>

Inheritance diagram for atomicrex::Potential:

Public Member Functions
	Potential (const FPString &id, FitJob *job, const FPString &tag=FPString())
	Constructor.
void	enableInteraction (int speciesA, int speciesB)
	Enables the interaction between two atom types.
bool	interacting (int speciesA, int speciesB) const
	Returns whether the interaction between two atom types is enabled for this potential.
bool	isAtomTypeEnabled (int species) const
virtual double	cutoff () const =0
	Returns the maximum cutoff of the potential.
virtual double	computeEnergyAndForces (AtomicStructure &structure, NeighborList &neighborList)=0
	Computes the total energy and forces of the structure.
virtual double	computeEnergy (AtomicStructure &structure, NeighborList &neighborList)=0
	Computes the total energy of the structure.
virtual void	outputResults ()
virtual size_t	perAtomDataSize () const
virtual size_t	perBondDataSize () const
virtual void	parse (XML::Element potentialElement) override
	Parses any potential-specific parameters in the XML element in the job file.
virtual void	preparePotential ()
virtual XML::OElement	generateXMLDefinition ()
Public Member Functions inherited from atomicrex::FitObject
virtual	~FitObject ()=default
	Virtual destructor.
double	relativeWeight () const
	Returns the relative fit weight assigned to this object.
void	setRelativeWeight (double weight)
	Assigns a relative fit weight to this object.
virtual void	assignAbsoluteWeights (double absoluteWeight)
	Recursively assigns absolute weights to the properties of this object and its sub-objects.
virtual bool	computeProperties (bool isFitting)
	Computes all enabled properties of the object.
const std::vector< FitProperty * > &	properties () const
	Returns a list of fitting properties of this object.
void	listAllProperties (std::vector< FitProperty *> &list) const
	Builds a list of properties of this object and all its sub-objects.
FitProperty *	propertyById (const FPString &id) const
	Returns the property with the given ID.
const std::vector< DegreeOfFreedom * > &	DOF () const
	Returns a list of degrees of freedom of this object.
void	listAllDOF (std::vector< DegreeOfFreedom *> &list) const
	Builds a list of degrees of freedom of this object and all its sub-objects.
DegreeOfFreedom *	DOFById (const FPString &id, const FPString &tag=FPString()) const
	Returns the degree of freedom with the given ID (and tag).
virtual void	dofValueChanged (DegreeOfFreedom &dof)
	This callback function is called by the DOFs of this fit object each time when their values changes.
const std::vector< FitObject * > &	fitObjects () const
	Returns the list of FitObjects which are part of this group.
void	registerSubObject (FitObject *subobject, bool deleteOnShutdown=false)
	Registers a sub-object.
virtual void	print (MsgLogger &stream)
	Outputs the name of the object.
bool	fitEnabled () const
	Returns whether this object and it's children are included in the fit.
void	setFitEnabled (bool enable)
	Sets whether this object and it's children are included in the fit.
bool	outputEnabled () const
void	setOutputEnabled (bool enable)
const FPString &	id () const
	Returns the identifier of this object instance.
void	setId (const FPString &id)
	Sets the main identification tag.
const FPString &	tag () const
	Returns the assigned tag string.
void	setTag (const FPString &tag)
	Sets the complementary identification tag.
FitJob *	job () const
	Returns a pointer to the job to which this object belongs.
FitObject *	parent () const
	Returns the parent of this object in the hierarchy.

Additional Inherited Members
Protected Member Functions inherited from atomicrex::FitObject
	FitObject ()
	Default Constructor.
	FitObject (const FPString &id, FitJob *job, const FPString &tag=FPString())
	Constructor.
void	registerProperty (FitProperty *prop, bool deleteOnShutdown=false)
	Registers a property of this object.
void	registerDOF (DegreeOfFreedom *dof)
	Registers a DOF of this object.
Protected Attributes inherited from atomicrex::FitObject
bool	_fitEnabled = true
	Controls whether this object and it's children are included in the fit.
bool	_outputEnabled = true
FitJob *	_job = nullptr
	Pointer to the job this object belongs to.
FPString	_id
	The identifier string of this object instance.
double	_relativeWeight = 1.0
	The relative fit weight assigned to this object.

Detailed Description

Base class for potential.

This class is used to store structure specific information including atomic coordinates, neighbor lists, total energy, volume, pressure etc.

Member Function Documentation

generateXMLDefinition()

virtual XML::OElement atomicrex::Potential::generateXMLDefinition ( )

inlinevirtual

Produces an XML representation of the potential's current parameter values and DOFs that can be used as input in a subsequent fit job.

Reimplemented in atomicrex::CDIPotential, atomicrex::PairPotential, and atomicrex::LennardJonesPotential.

isAtomTypeEnabled()

bool atomicrex::Potential::isAtomTypeEnabled ( int  species ) const

inline

Returns whether the given atom type is handled by this potential. If not, atoms of this species are completely ignored in the potential routine.

outputResults()

void atomicrex::Potential::outputResults ( )

virtual

This function is called by the fit job on shutdown, i.e. after the fitting process has finished. Subclasses can override this function to output the fitted potential to a file.

Reimplemented in atomicrex::MEAMPotential, atomicrex::EAMPotential, atomicrex::ABOPotential, atomicrex::CDIPotential, atomicrex::PairPotential, and atomicrex::TersoffPotential.

perAtomDataSize()

virtual size_t atomicrex::Potential::perAtomDataSize ( ) const

inlinevirtual

Returns the number of bytes of working memory per atom required by the potential routine. The system will provide a memory buffer of the given size for each atomic structure that can be used by the potential routine.

Reimplemented in atomicrex::MEAMPotential, atomicrex::EAMPotential, atomicrex::TabulatedMEAMPotential, and atomicrex::TabulatedEAMPotential.

perBondDataSize()

virtual size_t atomicrex::Potential::perBondDataSize ( ) const

inlinevirtual

Returns the number of bytes of working memory per atom neighbor required by the potential routine. The system will provide a memory buffer of the given size for each atomic structure that can be used by the potential routine.

Reimplemented in atomicrex::MEAMPotential, and atomicrex::TabulatedMEAMPotential.

preparePotential()

virtual void atomicrex::Potential::preparePotential ( )

inlinevirtual

This virtual method is called by the system before the potential is being used to compute energy and forces. Note that the method may be called several times. The default implementation does nothing.

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

• Potential.h
• Potential.cpp