The Effective Medium Theory (EMT) potential. More...

#include <EMT.h>

Inheritance diagram for EMT:

Public Member Functions
	EMT (EMTParameterProvider *prov=0)
	Create an EMT potential optionally using a parameter provider.
virtual	~EMT ()
	Delete the EMT potential.
void	SetSubtractE0 (bool subtractE0)
virtual void	SetAtoms (Atoms *atoms)
	Set the atoms belonging to this potential.
virtual const Vec *	GetCartesianForces ()
	Calculate the forces on all atoms and return the result.
virtual const double *	GetPotentialEnergies ()
	Calculate the energy of all atoms.
virtual double	GetPotentialEnergy ()
	Calculate the total energy of the system.
virtual const symTensor *	GetStresses (const Vec *momenta=0)
	Calculate the stress on all atoms.
virtual void	GetStress (double stress[6], const Vec *momenta=0)
	Calculate the total stress of the system.
virtual void	CheckNeighborLists ()
	Check that neighbor lists are up to date, update them if not.
virtual double	GetCutoffRadius () const
	Return the cutoff radius used in the potential.
virtual double	GetLatticeConstant () const
	Return the lattice constant of the material, if well-defined.
virtual int	GetNumberOfAtoms () const
	Get the number of atoms.
virtual void	SetContinuumElement (int z)
	Specify the element in the continuum region of a QuasiContinuum simulation.
virtual void	UpdateSuperCell (const SuperCell *newSuperCell)
	Tell the Potential that a new SuperCell has been assigned to the atoms.
virtual double	CalculateLatticeEnergy (const Vec a[3])
	Calculate the energy of an atom in a regular fcc(?) lattice.
virtual void	CalculateDerivatives (const Vec a[3], double dEdaDota[6])
	Calculate derivative of the energy of an atom in a regular lattice.
virtual double	GetData () const
	Get data used by the QuasiContinuum method.
const double *	GetSigma1 (int n)
	Return a pointer to the EMT "density" sigma1.
const double *	GetSigma2 (int n)
	Return a pointer to the EMT "density" sigma2.
void	PrintParameters ()
	Print the EMT parameters.
NeighborList *	GetNeighborList () const
	Return a pointer to the neighbor list.
Public Member Functions inherited from AsapPotential
virtual	~AsapPotential ()

Protected Member Functions
virtual void	InitParameters ()
	Initialization of the EMT parameters.
virtual void	Allocate ()
	(Re)allocate storage for forces, energies and intermediate results.
virtual void	AllocateStress ()
	(Re)allocate storage for stresses
virtual void	CalculateIDs ()
	Calculate type numbers from the atomic numbers.
virtual void	CalculateSigmas (int calculatesigma2=1)
	Calculate sigma1 and perhaps sigma2.
virtual void	CalculateEnergiesAfterSigmas (double *Epot=0)
	Calculate energies once sigma1 is known.
virtual void	CalculateForcesAfterEnergies (Vec *forces, double stress[][6]=0)
	Calculate forces in a multicomponent system.
virtual void	CalculateForcesAfterEnergiesSingle (Vec *forces, double stress[][6]=0)
	Calculate forces in a system with only one element.
virtual void	CalculateStuff (const Vec a[3], double &sigma1, double &sigma2, double diffs2, double wght, double dsigma1, double dsigma2)
	Internal function used for the QuasiContinuum stuff.

Protected Attributes
Atoms *	atoms
	The atoms we are working on.
GhostAtoms *	ghostatoms
	Non-NULL if atoms are GhostAtoms.
int	nAtoms
	The number of (real) atoms.
int	nSize
	Number of atoms including ghost atoms.
NeighborList *	nblist
	The neighborlist object.
EMTParameterProvider *	provider
	The source of the EMT parameters.
bool	ownProvider
	May we delete the provider?
bool	subtractE0
	Whether we subtract E0 from atomic energies (defines the zero of potential energy; if we don't subtract, zero corresponds to infinite seperation.
std::vector< const emt_parameters * >	parameters
	The EMT parameters.
const emt_parameters *	continuumelement
	The element in the continuum region.
const TinyDoubleMatrix *	chi
	The Chi matrix of EMT.
int	nelements
	The number of different elements in the simulation.
double	rFermi
	Cutoff parameters (from EMTParameterProvider).
double	rNbCut
double	cutoffslope
	Cutoff slope.
int	sigma2isvalid
	For consistency checks.
vector< vector< double > >	sigma1
	Temporary data for the atoms.
vector< vector< double > >	sigma2
vector< double >	Ec
	Each atom has a single Ec, Eas, radius etc.
vector< double >	Eas
vector< double >	potentialenergy
vector< double >	radius
vector< double >	dEds
vector< Vec >	force
vector< double >	stress
	The stresses. Always remember to use six per atoms!
int	nAtomsRes
int	nSizeRes
	If there are ghostatoms, some extra space is reserved for the arrays.
vector< int >	id
	The atomic numbers are translated into IDs, integers in [0, nelements-1].
double	unnormalizedstress [6]
	The total stress before division by volume.
double	totalvolume
	Total volume during stresscalculation.
int	nHalfNeighbors
	For the quasicontinuum stuff.
int(*	coef )[6]
	For the quasicontinuum stuff.
double	dataSigma1
	For the quasicontinuum stuff.
struct {
int ids
int nblist
int sigma1
int sigma2
int beforeforces
int energies
int forces
int stresses
int fullstresses
}	counters
	A structure of counters to check if recalculations are necessary.

Private Member Functions
void	sigma_batch (int self, int other, Vec rnb[], double *sq_dist, int zs, int zo, int n, int calculatesigma2)
	sigma_batch does the hard work in CalculateSigmas().
void	force_batch (int self, int other, Vec rnb[], double sq_dist, double dEdss[], double dEdso[], int zs, int zo, int n, Vec force, double(*stress)[6])
	force_batch does the hard work in CalculateForcesAfterEnergy().

Detailed Description

The Effective Medium Theory (EMT) potential.

The Effective Medium Theory (EMT) as originally implemented in Per Stoltze's ARTwork program, and documented in

K. W. Jacobsen, P. Stoltze and J. K. Nørskov, Surf. Sci. vol. 366, p. 394-402 (1996).

Definition at line 24 of file EMT.h.

Constructor & Destructor Documentation

◆ EMT()

EMT::EMT ( EMTParameterProvider * prov = 0 )

Create an EMT potential optionally using a parameter provider.

◆ ~EMT()

virtual EMT::~EMT ( )

virtual

Delete the EMT potential.

Member Function Documentation

◆ Allocate()

virtual void EMT::Allocate ( )

protectedvirtual

(Re)allocate storage for forces, energies and intermediate results.

◆ AllocateStress()

virtual void EMT::AllocateStress ( )

protectedvirtual

(Re)allocate storage for stresses

◆ CalculateDerivatives()

virtual void EMT::CalculateDerivatives	(	const Vec	a[3],
		double	dEdaDota[6] )

virtual

Calculate derivative of the energy of an atom in a regular lattice.

Used by the QuasiContinuum method.

Reimplemented from AsapPotential.

◆ CalculateEnergiesAfterSigmas()

virtual void EMT::CalculateEnergiesAfterSigmas ( double * Epot = 0 )

protectedvirtual

Calculate energies once sigma1 is known.

If Epot is NULL, energies are not calculated, only derivatives needed for the force.

◆ CalculateForcesAfterEnergies()

virtual void EMT::CalculateForcesAfterEnergies	(	Vec *	forces,
		double	stress[][6] = 0 )

protectedvirtual

Calculate forces in a multicomponent system.

◆ CalculateForcesAfterEnergiesSingle()

virtual void EMT::CalculateForcesAfterEnergiesSingle	(	Vec *	forces,
		double	stress[][6] = 0 )

protectedvirtual

Calculate forces in a system with only one element.

◆ CalculateIDs()

virtual void EMT::CalculateIDs ( )

protectedvirtual

Calculate type numbers from the atomic numbers.

◆ CalculateLatticeEnergy()

virtual double EMT::CalculateLatticeEnergy ( const Vec a[3] )

virtual

Calculate the energy of an atom in a regular fcc(?) lattice.

Given the lattice vectors, this function calculates the energy of a single atom in the lattice. Used for the QuasiContinuum method.

Reimplemented from AsapPotential.

◆ CalculateSigmas()

virtual void EMT::CalculateSigmas ( int calculatesigma2 = 1 )

protectedvirtual

Calculate sigma1 and perhaps sigma2.

◆ CalculateStuff()

virtual void EMT::CalculateStuff	(	const Vec	a[3],
		double &	sigma1,
		double &	sigma2,
		double *	diffs2,
		double *	wght,
		double *	dsigma1,
		double *	dsigma2 )

protectedvirtual

Internal function used for the QuasiContinuum stuff.

◆ CheckNeighborLists()

virtual void EMT::CheckNeighborLists ( )

virtual

Check that neighbor lists are up to date, update them if not.

Implements AsapPotential.

◆ force_batch()

void EMT::force_batch	(	int *	self,
		int *	other,
		Vec	rnb[],
		double *	sq_dist,
		double	dEdss[],
		double	dEdso[],
		int	zs,
		int	zo,
		int	n,
		Vec *	force,
		double(*)	stress[6] )

private

force_batch does the hard work in CalculateForcesAfterEnergy().

Not virtual, do not reimplement without reimplementing CalculateForcesAfterEnergy().

◆ GetCartesianForces()

virtual const Vec * EMT::GetCartesianForces ( )

virtual

Calculate the forces on all atoms and return the result.

Implements AsapPotential.

◆ GetCutoffRadius()

virtual double EMT::GetCutoffRadius ( ) const

inlinevirtual

Return the cutoff radius used in the potential.

Implements AsapPotential.

Definition at line 42 of file EMT.h.

42{ return rNbCut; }

EMT::rNbCut

double rNbCut

Definition EMT.h:135

◆ GetData()

virtual double EMT::GetData ( ) const

inlinevirtual

Get data used by the QuasiContinuum method.

Reimplemented from AsapPotential.

Definition at line 54 of file EMT.h.

54{ return dataSigma1; }

EMT::dataSigma1

double dataSigma1

For the quasicontinuum stuff.

Definition EMT.h:178

◆ GetLatticeConstant()

virtual double EMT::GetLatticeConstant ( ) const

virtual

Return the lattice constant of the material, if well-defined.

If a lattice constant of the material can be defined, return it in Angstrom, otherwise throw an exception.

Implements AsapPotential.

◆ GetNeighborList()

NeighborList * EMT::GetNeighborList ( ) const

inline

Return a pointer to the neighbor list.

Definition at line 65 of file EMT.h.

65{ return nblist; }

EMT::nblist

NeighborList * nblist

The neighborlist object.

Definition EMT.h:120

◆ GetNumberOfAtoms()

virtual int EMT::GetNumberOfAtoms ( ) const

inlinevirtual

Get the number of atoms.

Implements AsapPotential.

Definition at line 44 of file EMT.h.

44{ return nAtoms; }

EMT::nAtoms

int nAtoms

The number of (real) atoms.

Definition EMT.h:118

◆ GetPotentialEnergies()

virtual const double * EMT::GetPotentialEnergies ( )

virtual

Calculate the energy of all atoms.

Implements AsapPotential.

◆ GetPotentialEnergy()

virtual double EMT::GetPotentialEnergy ( )

virtual

Calculate the total energy of the system.

Implements AsapPotential.

◆ GetSigma1()

const double * EMT::GetSigma1 ( int n )

inline

Return a pointer to the EMT "density" sigma1.

Definition at line 57 of file EMT.h.

57{ return &sigma1[n][0]; }

EMT::sigma1

vector< vector< double > > sigma1

Temporary data for the atoms.

Definition EMT.h:145

◆ GetSigma2()

const double * EMT::GetSigma2 ( int n )

inline

Return a pointer to the EMT "density" sigma2.

Definition at line 59 of file EMT.h.

59{ return &sigma2[n][0]; }

EMT::sigma2

vector< vector< double > > sigma2

Definition EMT.h:146

◆ GetStress()

virtual void EMT::GetStress	(	double	stress[6],
		const Vec *	momenta = 0 )

virtual

Calculate the total stress of the system.

Note that the output variable stress is not zeroed first. In quasicontinuum simulations and other situations where there is a contribution to the stress which is not from the atoms, the stress parameter can initially be set to the appropriate derivatives of the energy of that part of the calculation (without the volume normalization, which will be performed by the potential).

Implements AsapPotential.

◆ GetStresses()

virtual const symTensor * EMT::GetStresses ( const Vec * momenta = 0 )

virtual

Calculate the stress on all atoms.

Implements AsapPotential.

◆ InitParameters()

virtual void EMT::InitParameters ( )

protectedvirtual

Initialization of the EMT parameters.

◆ PrintParameters()

void EMT::PrintParameters ( )

Print the EMT parameters.

◆ SetAtoms()

virtual void EMT::SetAtoms ( Atoms * a )

virtual

Set the atoms belonging to this potential.

This is called automatically by Atoms.SetCalculator() and should not be called elsewhere.

Implements AsapPotential.

◆ SetContinuumElement()

virtual void EMT::SetContinuumElement ( int z )

virtual

Specify the element in the continuum region of a QuasiContinuum simulation.

◆ SetSubtractE0()

void EMT::SetSubtractE0 ( bool subtractE0 )

inline

Definition at line 31 of file EMT.h.

31{ this->subtractE0 = subtractE0; }

EMT::subtractE0

bool subtractE0

Whether we subtract E0 from atomic energies (defines the zero of potential energy; if we don't subtra...

Definition EMT.h:124

◆ sigma_batch()

void EMT::sigma_batch	(	int *	self,
		int *	other,
		Vec	rnb[],
		double *	sq_dist,
		int	zs,
		int	zo,
		int	n,
		int	calculatesigma2 )

private

sigma_batch does the hard work in CalculateSigmas().

Not virtual, do not reimplement without reimplementing CalculateSigmas().

◆ UpdateSuperCell()

virtual void EMT::UpdateSuperCell ( const SuperCell * newSuperCell )

virtual

Tell the Potential that a new SuperCell has been assigned to the atoms.

Implements AsapPotential.

Member Data Documentation

◆ atoms

Atoms* EMT::atoms

protected

The atoms we are working on.

Definition at line 116 of file EMT.h.

◆ beforeforces

int EMT::beforeforces

Definition at line 186 of file EMT.h.

◆ chi

const TinyDoubleMatrix* EMT::chi

protected

The Chi matrix of EMT.

Definition at line 132 of file EMT.h.

◆ coef

int(* EMT::coef)[6]

protected

For the quasicontinuum stuff.

Definition at line 177 of file EMT.h.

◆ continuumelement

const emt_parameters* EMT::continuumelement

protected

The element in the continuum region.

Definition at line 130 of file EMT.h.

◆ [struct]

struct { ... } EMT::counters

A structure of counters to check if recalculations are necessary.

◆ cutoffslope

double EMT::cutoffslope

protected

Cutoff slope.

Definition at line 137 of file EMT.h.

◆ dataSigma1

double EMT::dataSigma1

protected

For the quasicontinuum stuff.

Definition at line 178 of file EMT.h.

◆ dEds

vector<double> EMT::dEds

protected

Definition at line 154 of file EMT.h.

◆ Eas

vector<double> EMT::Eas

protected

Definition at line 151 of file EMT.h.

◆ Ec

vector<double> EMT::Ec

protected

Each atom has a single Ec, Eas, radius etc.

Definition at line 150 of file EMT.h.

◆ energies

int EMT::energies

Definition at line 187 of file EMT.h.

◆ force

vector<Vec> EMT::force

protected

Definition at line 155 of file EMT.h.

◆ forces

int EMT::forces

Definition at line 188 of file EMT.h.

◆ fullstresses

int EMT::fullstresses

Definition at line 190 of file EMT.h.

◆ ghostatoms

GhostAtoms* EMT::ghostatoms

protected

Non-NULL if atoms are GhostAtoms.

Definition at line 117 of file EMT.h.

◆ id

vector<int> EMT::id

protected

The atomic numbers are translated into IDs, integers in [0, nelements-1].

Definition at line 167 of file EMT.h.

◆ ids

int EMT::ids

Definition at line 182 of file EMT.h.

◆ nAtoms

int EMT::nAtoms

protected

The number of (real) atoms.

Definition at line 118 of file EMT.h.

◆ nAtomsRes

int EMT::nAtomsRes

protected

Definition at line 163 of file EMT.h.

◆ nblist [1/2]

int EMT::nblist

Definition at line 183 of file EMT.h.

◆ nblist [2/2]

NeighborList* EMT::nblist

protected

The neighborlist object.

Definition at line 120 of file EMT.h.

◆ nelements

int EMT::nelements

protected

The number of different elements in the simulation.

Definition at line 133 of file EMT.h.

◆ nHalfNeighbors

int EMT::nHalfNeighbors

protected

For the quasicontinuum stuff.

Definition at line 176 of file EMT.h.

◆ nSize

int EMT::nSize

protected

Number of atoms including ghost atoms.

Definition at line 119 of file EMT.h.

◆ nSizeRes

int EMT::nSizeRes

protected

If there are ghostatoms, some extra space is reserved for the arrays.

Definition at line 163 of file EMT.h.

◆ ownProvider

bool EMT::ownProvider

protected

May we delete the provider?

Definition at line 122 of file EMT.h.

◆ parameters

std::vector<const emt_parameters *> EMT::parameters

protected

The EMT parameters.

Definition at line 129 of file EMT.h.

◆ potentialenergy

vector<double> EMT::potentialenergy

protected

Definition at line 152 of file EMT.h.

◆ provider

EMTParameterProvider* EMT::provider

protected

The source of the EMT parameters.

Definition at line 121 of file EMT.h.

◆ radius

vector<double> EMT::radius

protected

Definition at line 153 of file EMT.h.

◆ rFermi

double EMT::rFermi

protected

Cutoff parameters (from EMTParameterProvider).

Definition at line 135 of file EMT.h.

◆ rNbCut

double EMT::rNbCut

protected

Definition at line 135 of file EMT.h.

◆ sigma1 [1/2]

int EMT::sigma1

Definition at line 184 of file EMT.h.

◆ sigma1 [2/2]

vector<vector<double> > EMT::sigma1

protected

Temporary data for the atoms.

Each atom has two sigmas for each possible neighboring element. So these are arrays (nelements long).

Definition at line 145 of file EMT.h.

◆ sigma2 [1/2]

int EMT::sigma2

Definition at line 185 of file EMT.h.

◆ sigma2 [2/2]

vector<vector<double> > EMT::sigma2

protected

Definition at line 146 of file EMT.h.

◆ sigma2isvalid

int EMT::sigma2isvalid

protected

For consistency checks.

Definition at line 139 of file EMT.h.

◆ stress

vector<double> EMT::stress

protected

The stresses. Always remember to use six per atoms!

Should really be declared as vector<double[6]>, but that breaks the vector library when attempting to resize!

Definition at line 160 of file EMT.h.

◆ stresses

int EMT::stresses

Definition at line 189 of file EMT.h.

◆ subtractE0

bool EMT::subtractE0

protected

Whether we subtract E0 from atomic energies (defines the zero of potential energy; if we don't subtract, zero corresponds to infinite seperation.

If we do, it is the bulk fcc crystal at the equilibrium lattice constant.)

Definition at line 124 of file EMT.h.

◆ totalvolume

double EMT::totalvolume

protected

Total volume during stresscalculation.

Definition at line 174 of file EMT.h.

◆ unnormalizedstress

double EMT::unnormalizedstress[6]

protected

The total stress before division by volume.

Definition at line 173 of file EMT.h.

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

/home/runner/work/eOn/eOn/include/eon/potentials/EMT/Asap/EMT.h

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ EMT()

◆ ~EMT()

Member Function Documentation

◆ Allocate()

◆ AllocateStress()

◆ CalculateDerivatives()

◆ CalculateEnergiesAfterSigmas()

◆ CalculateForcesAfterEnergies()

◆ CalculateForcesAfterEnergiesSingle()

◆ CalculateIDs()

◆ CalculateLatticeEnergy()

◆ CalculateSigmas()

◆ CalculateStuff()

◆ CheckNeighborLists()

◆ force_batch()

◆ GetCartesianForces()

◆ GetCutoffRadius()

◆ GetData()

◆ GetLatticeConstant()

◆ GetNeighborList()

◆ GetNumberOfAtoms()

◆ GetPotentialEnergies()

◆ GetPotentialEnergy()

◆ GetSigma1()

◆ GetSigma2()

◆ GetStress()

◆ GetStresses()

◆ InitParameters()

◆ PrintParameters()

◆ SetAtoms()

◆ SetContinuumElement()

◆ SetSubtractE0()

◆ sigma_batch()

◆ UpdateSuperCell()

Member Data Documentation

◆ atoms

◆ beforeforces

◆ chi

◆ coef

◆ continuumelement

◆ [struct]

◆ cutoffslope

◆ dataSigma1

◆ dEds

◆ Eas

◆ Ec

◆ energies

◆ force

◆ forces

◆ fullstresses

◆ ghostatoms

◆ id

◆ ids

◆ nAtoms

◆ nAtomsRes

◆ nblist [1/2]

◆ nblist [2/2]

◆ nelements

◆ nHalfNeighbors

◆ nSize

◆ nSizeRes

◆ ownProvider

◆ parameters

◆ potentialenergy

◆ provider

◆ radius

◆ rFermi

◆ rNbCut

◆ sigma1 [1/2]

◆ sigma1 [2/2]

◆ sigma2 [1/2]

◆ sigma2 [2/2]

◆ sigma2isvalid

◆ stress