This class defines general modified embedded atom method (MEAM) potentials. More...

#include <MEAMPotential.h>

Inheritance diagram for atomicrex::MEAMPotential:

Public Member Functions
	MEAMPotential (const FPString &id, FitJob *job)
	Constructor.

virtual double	cutoff () const override
	Returns the maximum cutoff of the potential.

virtual double	computeEnergyAndForces (AtomicStructure &structure, NeighborList &neighborList) override
	Computes the total energy and forces of the structure.

virtual double	computeEnergy (AtomicStructure &structure, NeighborList &neighborList) override
	Computes the total energy of the structure.

virtual void	parse (XML::Element potentialElement) override
	Parses any potential-specific parameters in the XML element in the job file.

virtual size_t	perAtomDataSize () const override

virtual size_t	perBondDataSize () const override

FunctionBase *	pairPotential (int speciesA, int speciesB) const
	Returns the pair potential function for the interaction between the given atom types.

FunctionBase *	electronDensity (int speciesA, int speciesB) const
	Returns the electron density function for the given pair of atom types.

FunctionBase *	embeddingEnergy (int species) const
	Returns the embedding energy function for the given atom type.

FunctionBase *	ffunction (int speciesA, int speciesB) const
	Returns the f-function for the given pair of atom types.

FunctionBase *	gfunction (int speciesA, int speciesB, int speciesC) const
	Returns the f-function for the given triplet of atom types.

FunctionBase *	findFunctionById (const FPString &id) const
	Returns the function with the given ID, or nullptr if no such function is defined.

virtual void	outputResults () override
	This function is called by the fit job on shutdown, i.e. after the fitting process has finished.

void	writeTables (const FPString &basename) const
	Writes the tabulated functionals to a set of text files for visualization with Gnuplot.

Public Member Functions inherited from atomicrex::Potential
	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 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

This class defines general modified embedded atom method (MEAM) potentials.

The total energy for MEAM potentials can be written in the general form

$E = \sum_{ij} V(r_{ij}) + \sum_i F(\rho_i)$

where

$\rho_i= \sum_j \rho(r_{ij}) + \sum_{jk} f(r_{ij}) f(r_{ik}) g\left(\cos(\theta_{ijk})\right).$

In the present implementation it is possible to compose practically arbitrary functional forms using a math parser.

The following code block illustrates the main blocks in the potential definition. More complex cases can be found in the examples directory.

<potentials>
  <meam id='my-meam-potential' species-a='*' species-b='*'>
    <export-functions>meam_out</export-functions>
    <functions>
      <user-function id="V">
    ...
  </user-function>
  ...
    </functions>
    <mapping>
      <pair-interaction species-a='*' species-b='*' function='V' />
 <electron-density species-a='*' species-b='*' function='rho' />
 <f-function species-a='*' species-b='*' function='f' />
 <g-function species-a='*' species-b='*' species-c='*' function='g' />
 <embedding-energy species='*' function='U' />
    </mapping>
  </meam>
</potentials>