Pseudopotential for a species of ions, and atom positions and other properties for that species. More...

#include <SpeciesInfo.h>

Classes
struct	Constraint
	Contains the information on the constraints of motion for each ion. More...

Public Types
enum	PseudopotentialFormat { Fhi , Uspp , UPF }

Public Member Functions
void	sync_atpos ()
	update changes in atpos; call whenever atpos is changed (this will update atposManaged and invalidate cached projectors, if any)

void	setup (const Everything &)

void	print (FILE *fp) const
	print ionic positions from current species

void	populationAnalysis (const std::vector< matrix > &RhoAll) const
	print population analysis given the density matrix in the Lowdin basis

bool	isRelativistic () const
	whether pseudopotential is relativistic

bool	isUltrasoft () const
	whether pseudopotential is ultrasoft

PseudopotentialFormat	getPSPFormat ()
	Returns the pseudopotential format.

std::shared_ptr< ColumnBundle >	getV (const ColumnBundle &Cq, const vector3<> *derivDir=0, const int stressDir=-1) const

ColumnBundle	getVatom (const ColumnBundle &Cq, int atom) const
	Single atom version.

int	nProjectors () const
	total number of projectors for all atoms in this species (number of columns in result of getV)

double	EnlAndGrad (const QuantumNumber &qnum, const diagMatrix &Fq, const matrix &VdagCq, matrix &HVdagCq, int atom=-1) const

void	augmentOverlap (const ColumnBundle &Cq, ColumnBundle &OCq, matrix *VdagCq=0) const
	Accumulate pseudopotential contribution to the overlap in OCq.

void	augmentOverlapDeriv (const ColumnBundle &Cq, ColumnBundle &OCq, ColumnBundle &V, ColumnBundle &dV) const
	Derivative of augmented overlap operator w.r.t. atomic position.

void	augmentOverlapSecondDeriv (const ColumnBundle &Cq, ColumnBundle &OCq, ColumnBundle &V, ColumnBundle &dV_A, ColumnBundle &dV_B, ColumnBundle &dsqV) const
	Second derivative of augmented overlap operator w.r.t. atomic position.

void	augmentSpinOverlap (const ColumnBundle &Cq, vector3< matrix > &Sq) const
	Accumulate pseudopotential contribution to spin overlap of a columnbundle.

void	augmentDensityInit (int atom=-1)
	Clear internal data and prepare for density augmentation (call before a loop over augmentDensitySpherical per k-point)

void	augmentDensitySpherical (const QuantumNumber &qnum, const diagMatrix &Fq, const matrix &VdagCq, const matrix VdagdCqL=0, const matrix VdagdCqR=0, int atom=-1)
	Accumulate the pseudopotential dependent contribution to the density in the spherical functions nAug (call once per k-point)

void	augmentDensityGrid (ScalarFieldArray &n, int atom=-1, const vector3<> *atposDeriv=0) const
	Accumulate the spherical augmentation functions nAug to the grid electron density (call only once, after augmentDensitySpherical on all k-points)

void	augmentDensityGridGrad (const ScalarFieldArray &E_n, std::vector< vector3<> > forces=0, matrix3<> Eaug_RRT=0)
	Gradient propagation corresponding to augmentDensityGrid (stores intermediate spherical function results to E_nAug; call only once). Optionally collect forces and stress contributions.

void	augmentDensityGridGradDeriv (const ScalarFieldArray &E_n, int atom, const vector3<> *atposDeriv)

void	augmentDensitySphericalGrad (const QuantumNumber &qnum, const matrix &VdagCq, matrix &HVdagCq, int atom=-1) const
	Gradient propagation corresponding to augmentDensitySpherical (uses intermediate spherical function results from E_nAug; call once per k-point after augmentDensityGridGrad)

size_t	rhoAtom_nMatrices () const

void	rhoAtom_initZero (matrix *rhoAtomPtr) const

void	rhoAtom_calc (const std::vector< diagMatrix > &F, const std::vector< ColumnBundle > &C, matrix *rhoAtomPtr) const

double	rhoAtom_computeU (const matrix rhoAtomPtr, matrix U_rhoAtomPtr) const

void	rhoAtom_grad (const ColumnBundle &Cq, const matrix *U_rhoAtomPtr, ColumnBundle &HCq) const

void	rhoAtom_forces (const std::vector< diagMatrix > &F, const std::vector< ColumnBundle > &C, const matrix U_rhoAtomPtr, std::vector< vector3<> > &forces, matrix3<> EU_RRT) const

void	rhoAtom_getV (const ColumnBundle &Cq, const matrix U_rhoAtomPtr, ColumnBundle &Opsi, matrix &M, const vector3<> derivDir=0, const int stressDir=-1) const

void	accumulateAtomicDensity (ScalarFieldTildeArray &nTilde) const
	Accumulate atomic density from this species.

void	accumulateAtomicPotential (ScalarFieldTilde &dTilde) const
	Accumulate electrostatic potential of neutral atoms from this species.

void	setAtomicOrbitals (ColumnBundle &Y, bool applyO, int colOffset=0, const vector3<> *derivDir=0, const int stressDir=-1) const
	Calculate atomic orbitals with/without O preapplied (store in Y with an optional column offset, or calculate derivatives instead)

void	setAtomicOrbitals (ColumnBundle &Y, bool applyO, unsigned n, int l, int colOffset=0, int atomColStride=0, const vector3<> *derivDir=0, const int stressDir=-1) const
	If non-zero, atomColStride overrides the number of columns between the same orbital of multiple atoms (default = number of orbitals at current n and l) More...

int	nAtomicOrbitals () const
	return number of atomic orbitals in this species (all atoms)

int	lMaxAtomicOrbitals () const
	return maximum angular momentum in available atomic orbitals

int	nAtomicOrbitals (int l) const
	return number of (pseudo-)principal quantum numbers for atomic orbitals of given l

int	atomicOrbitalOffset (unsigned iAtom, unsigned n, int l, int m, int s) const
	s is 0/1 for up/dn spinors in non-relativistic case, s=0/1 is for j=l+/-0.5 and mj=m+/-0.5 in relativistic case More...

void	updateLocal (ScalarFieldTilde &Vlocps, ScalarFieldTilde &rhoIon, ScalarFieldTilde &nChargeball, ScalarFieldTilde &nCore, ScalarFieldTilde &tauCore, int atom=-1) const
	Add contributions from this species to Vlocps, rhoIon, nChargeball and nCore/tauCore (if any)

std::vector< vector3<> >	getLocalForces (const ScalarFieldTilde &ccgrad_Vlocps, const ScalarFieldTilde &ccgrad_rhoIon, const ScalarFieldTilde &ccgrad_nChargeball, const ScalarFieldTilde &ccgrad_nCore, const ScalarFieldTilde &ccgrad_tauCore) const
	Return the local forces (due to Vlocps, rhoIon, nChargeball and nCore/tauCore)

matrix3	getLocalStress (const ScalarFieldTilde &ccgrad_Vlocps, const ScalarFieldTilde &ccgrad_rhoIon, const ScalarFieldTilde &ccgrad_nChargeball, const ScalarFieldTilde &ccgrad_nCore, const ScalarFieldTilde &ccgrad_tauCore) const
	Return the local forces (due to Vlocps, rhoIon, nChargeball and nCore/tauCore)

void	accumNonlocalForces (const ColumnBundle &Cq, const matrix &VdagC, const matrix &E_VdagC, const matrix &grad_CdagOCq, std::vector< vector3<> > &forces, matrix3<> *Enl_RRT) const

Static Public Member Functions
static matrix	getYlmToSpinAngleMatrix (int l, int j2)
	Spin-angle helper functions: More...

static matrix	getYlmOverlapMatrix (int l, int j2)
	Get the ((2l+1)2)x((2l+1)2) overlap matrix of the spin-spherical harmonics for total angular momentum j (note j2=2*j)

Public Attributes
double	Z
	Valence charge of the species (prefactor to 1/r in long-range part of pseudopotential)

int	atomicNumber
	Atomic number of the species (0 if unavailable)

string	name
	Identifier.

string	potfilename
	pseudopotential filename

string	pulayfilename
	pulay correction filename

bool	fromWildcard
	whether this pseudopotential was automatically added using a wildcard (for command printing purposes only)

std::vector< vector3<> >	atpos
	array of atomic positions of this species

std::vector< vector3<> >	velocities
	array of atomic velocities (NAN unless running MD) in lattice coordinates

ManagedArray< vector3<> >	atposManaged
	managed copy of atpos accessed from operator code (for auto cpu/gpu transfers)

double	dE_dnG
	Derivative of [total energy per atom] w.r.t [nPlanewaves per unit volume] (for Pulay corrections)

double	mass
	ionic mass (currently unused)

double	coreRadius
	maximum pseudopotential core radius (used for core overlap checks during ionic/lattice relaxation)

double	ZfullCore
	number of electrons in full-core correction (atomicNumber - Z - integral(nCore))

std::vector< Constraint >	constraints
	List of all constraints on ions of this species.

std::vector< vector3<> >	initialMagneticMoments
	Initial magnetic moments of each atom (used only for LCAO and symmetries) (x and y magnetizations only used in noncollinear calculations)

double	initialOxidationState
	Initial oxidation state of this species (only affects LCAO)

matrix	MnlAll
	block matrix containing Mnl for all l,m

matrix	E_nAug
	Gradient w.r.t nAug (in the same layout)

Friends
struct	CommandAddU

struct	CommandChargeball

struct	CommandIonSpecies

struct	CommandSetVDW

struct	CommandSetAtomicRadius

struct	CommandTauCore

struct	CommandWavefunction

struct	ElectronScattering

struct	FluidSolverParams

class	ColumnBundleTransform

class	Dump

class	BGW

class	IonicMinimizer

class	IonInfo

class	ElecInfo

class	PCM

class	Phonon

class	VanDerWaalsD2

class	DefectSupercell

class	WannierMinimizer

Detailed Description

Pseudopotential for a species of ions, and atom positions and other properties for that species.

Member Enumeration Documentation

◆ PseudopotentialFormat

enum SpeciesInfo::PseudopotentialFormat

Enumerator
Fhi	FHI format with ABINIT header (.fhi files)
Uspp	USPP format ultrasoft pseudopotential.
UPF	Quantum Espresso's Universal Pseudopotential Format (the XML version 2 only)

Member Function Documentation

◆ accumNonlocalForces()

void SpeciesInfo::accumNonlocalForces	(	const ColumnBundle &	Cq,
		const matrix &	VdagC,
		const matrix &	E_VdagC,
		const matrix &	grad_CdagOCq,
		std::vector< vector3<> > &	forces,
		matrix3<> *	Enl_RRT
	)		const

Propagate gradient with respect to atomic projections (in E_VdagC, along with additional overlap contributions from grad_CdagOC) to forces Additionally accumulate nonlocal stresses if Enl_RRT is non-null

◆ atomicOrbitalOffset()

int SpeciesInfo::atomicOrbitalOffset	(	unsigned	iAtom,
		unsigned	n,
		int	l,
		int	m,
		int	s
	)		const

s is 0/1 for up/dn spinors in non-relativistic case, s=0/1 is for j=l+/-0.5 and mj=m+/-0.5 in relativistic case

offset of specified atomic orbital in output of current species (when not using the fixed n and l version)

◆ EnlAndGrad()

double SpeciesInfo::EnlAndGrad	(	const QuantumNumber &	qnum,
		const diagMatrix &	Fq,
		const matrix &	VdagCq,
		matrix &	HVdagCq,
		int	atom = `-1`
	)		const

Return non-local energy for this species and quantum number q and optionally accumulate projected electronic gradient in HVdagCq (if non-null)

◆ getV()

std::shared_ptr<ColumnBundle> SpeciesInfo::getV	(	const ColumnBundle &	Cq,
		const vector3<> *	derivDir = `0`,
		const int	stressDir = `-1`
	)		const

Get projectors with qnum and basis matching Cq (optionally cached). If derivDir is non-null, return the derivative with respct to Cartesian k direction *derivDir instead (never cached). If stressDir is >=0, then calculate (i,j) component of dVnl/dR . RT where stressDir = 3*i+j

◆ getYlmToSpinAngleMatrix()

static matrix SpeciesInfo::getYlmToSpinAngleMatrix	(	int	l,
		int	j2
	)

static

Spin-angle helper functions:

Get the ((2l+1)*2)x(j2+1) matrix that transforms the Ylm+spin to the spin-angle functions, where j2=2*j with j = l+/-0.5

◆ setAtomicOrbitals()

void SpeciesInfo::setAtomicOrbitals	(	ColumnBundle &	Y,
		bool	applyO,
		unsigned	n,
		int	l,
		int	colOffset = `0`,
		int	atomColStride = `0`,
		const vector3<> *	derivDir = `0`,
		const int	stressDir = `-1`
	)		const

If non-zero, atomColStride overrides the number of columns between the same orbital of multiple atoms (default = number of orbitals at current n and l)

Same as above, but for specific n and l.

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

electronic/SpeciesInfo.h

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Friends