This class defines the ABOP potential format. More...

#include <ABOPotential.h>

Inheritance diagram for atomicrex::ABOPotential:

Classes
struct	ABOParamSet

Public Member Functions
	ABOPotential (const FPString &id, FitJob *job, const FPString &tag=FPString("Tersoff"))
	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	outputResults () override
	This function is called by the fit job on shutdown, i.e. after the fitting process has finished.

void	writePotential (const FPString &filename) const
	Generates a potential file to be used with simulation codes.

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

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 size_t	perAtomDataSize () const

virtual size_t	perBondDataSize () 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.

Protected Member Functions
const ABOParamSet &	getParamSet (int itype, int jtype, int ktype) const
	Returns the parameter set for the i-j-k triplet interaction.

void	parseTersoffFile (const FPString &filename)
	Parses Tersoff parameters from a LAMMPS potential file.

void	linkDOF ()
	Links the DOF together to get only doublett interaction as in the classical ABOP.

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
double	_cutoff

std::vector< ABOParamSet >	_params

int	_numAtomTypes
	The number of atom types.

FPString	_exportPotentialFile
	Potential file that is written after fitting.

int	_dofMode
	Constrain Mode (0 = All DOF independent, 1 = DOFs connected as in "classical" ABOP)

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 the ABOP potential format.

The ABOP potential is a reformulation of the Tersoff potential as implemented in atomicPoet and in LAMMPS. The difference lies in the two-body parameters $A$ , $B$ , $\lambda_1$ , and $\lambda_2$ , which have been rewritten in terms of the more physical choices, $r_0$ , $D_0$ , $\beta$ , and $S$ , which relate to dimer properties and the Pauling relation.

In this format, the potential can be written

$E = \frac{1}{2} \sum_i \sum_{j\neq i} V_{ij}$

with

$V_{ij} = f_C(r_{ij})[f_R(r_{ij}) + b_{ij} f_A(r_{ij})].$

Here, $V_R(r) = \frac{D_0}{S-1} \exp[-\beta\sqrt{2S} (r-r_0)]$ and $V_A(r) = -\frac{SD_0}{S-1}\exp[-\beta \sqrt{2/S}(r-r_0)]$ are repulsive and attractive pair potential branches, respectively, and $f_C(r_{ij})$ is a cut-off function that is unity and decays sinusodially in the interval $(R-D,R+D)$ , after which it vanishes. The three-body contributions arise due to the bond-order parameter

$b_{ij} = (1+\beta_2^n\zeta_{ij}^n)^{-\frac{1}{2n}}$

where

$\zeta_{ij} = \sum_{k\neq i,j} f_C(r_{ij})g(\theta_{ijk})\exp [\lambda_3^m(r_{ij}-r_{ik})^m].$

The angular dependence is due to the factor

$g(\theta) = \gamma_{ijk} \left( 1+\frac{c^2}{d^2} - \frac{c^2}{d^2 + (h + \cos \theta)^2}\right).$

Parameter files are in LAMMPS tersoff format. In the output files, commented blocks containing the $r_0$ , $D_0$ , $\beta$ , and $S$ parameters are also written.

Note that the $h$ parameter in the ABOP form has the opposite sign than in the Tersoff formulation.

The following code snippet, to be inserted in the potentials block, illustrates the definition of this potential type in the input file.

 <abop id="Si" species-a="*" species-b="*">
    <param-file>ABOP_potential.tersoff</param-file>
    <export-potential>ABOP_potential_fitted.tersoff</export-potential>
    <fit-dof>
       <r0 tag="SiSiSi" enabled="true" />
       <D0 tag="SiSiSi" enabled="true" />
       <beta tag="SiSiSi" enabled="true" />
       <S tag="SiSiSi" enabled="true" />
       <gamma tag="SiSiSi" enabled="true" />
       <c tag="SiSiSi" enabled="true" />
       <d tag="SiSiSi" enabled="true" />
       <h tag="SiSiSi" enabled="true" />
       <twomu tag="SiSiSi" enabled="false" />
       <beta2 tag="SiSiSi" enabled="false" />
       <powern tag="SiSiSi" enabled="false" />
  </fit-dof>
</abop>

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

ABOPotential.h
ABOPotential.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description