A container for Gaussian type outputs from QM codes. More...

#include <avogadro/core/gaussianset.h>

Inheritance diagram for GaussianSet:

Public Types
enum	orbital { S , SP , P , D , D5 , F , F7 , G , G9 , H , H11 , I , I13 , UU }

Public Types inherited from BasisSet
enum	ElectronType { Paired , Alpha , Beta }
	The ElectronType enum describes the type of electrons being set or retrieved. If Paired, then Alpha and Beta cannot be set, if Alpha or Beta then both must be set.

Public Member Functions
	GaussianSet ()

	~GaussianSet () override=default

GaussianSet *	clone () const override

unsigned int	addBasis (unsigned int atom, orbital type)

unsigned int	addGto (unsigned int basis, double c, double a)

void	setMolecularOrbitals (const std::vector< double > &MOs, ElectronType type=Paired)

void	setMolecularOrbitals (const std::vector< double > &MOs, ElectronType type, Index index)

int	setCount ()

bool	setActiveSetStep (int index)

void	setMolecularOrbitalNumber (const std::vector< unsigned int > &nums, ElectronType type=Paired)
	This enables support of sparse orbital sets, and provides a mapping from the index in memory to the actual molecular orbital number.

bool	setDensityMatrix (const MatrixX &m)

bool	setSpinDensityMatrix (const MatrixX &m)

bool	generateDensityMatrix ()
	Generate the density matrix if we have the required information.

bool	generateSpinDensityMatrix ()
	Generate the spin density matrix if we have the required information.

unsigned int	molecularOrbitalCount (ElectronType type=Paired) const override

void	outputAll (ElectronType type=Paired)

bool	isValid () override

void	setScfType (ScfType type)

ScfType	scfType () const

void	setFunctionalName (const std::string &name)

std::string	functionalName () const

void	initCalculation ()

std::vector< int > &	symmetry ()

std::vector< int >	symmetry () const

std::vector< unsigned int > &	atomIndices ()

std::vector< unsigned int >	atomIndices () const

std::vector< unsigned int > &	moIndices ()

std::vector< unsigned int >	moIndices () const

std::vector< unsigned int > &	gtoIndices ()

std::vector< unsigned int >	gtoIndices () const

std::vector< unsigned int > &	cIndices ()

std::vector< unsigned int >	cIndices () const

std::vector< double > &	gtoA ()

std::vector< double >	gtoA () const

std::vector< double > &	gtoC ()

std::vector< double >	gtoC () const

std::vector< double > &	gtoCN ()

MatrixX &	moMatrix (ElectronType type=Paired)

MatrixX	moMatrix (ElectronType type=Paired) const

std::vector< unsigned int > &	moNumber (ElectronType type=Paired)

std::vector< unsigned int >	moNumber (ElectronType type=Paired) const

MatrixX &	densityMatrix ()

MatrixX &	spinDensityMatrix ()

Public Member Functions inherited from BasisSet
	BasisSet ()=default

virtual	~BasisSet ()=default

virtual void	setElectronCount (unsigned int n, ElectronType type=Paired)

unsigned int	electronCount (ElectronType type=Paired) const

void	setMolecule (Molecule *molecule_)

Molecule *	molecule ()

const Molecule *	molecule () const

void	setName (const std::string &name)

std::string	name () const

void	setTheoryName (const std::string &name)

std::string	theoryName () const

unsigned int	homo (ElectronType type=Paired) const

unsigned int	lumo (ElectronType type=Paired) const

std::vector< std::string >	symmetryLabels (ElectronType type=Paired) const

void	setSymmetryLabels (const std::vector< std::string > &labels, ElectronType type=Paired)

void	setMolecularOrbitalEnergy (const std::vector< double > &energies, ElectronType type=Paired)
	Set the molecular orbital energies, expected in Hartrees.

void	setMolecularOrbitalOccupancy (const std::vector< unsigned char > &occ, ElectronType type=Paired)
	Set the molecular orbital occupancies.

std::vector< double > &	moEnergy (ElectronType type=Paired)

std::vector< double >	moEnergy (ElectronType type=Paired) const

std::vector< unsigned char > &	moOccupancy (ElectronType type=Paired)

std::vector< unsigned char >	moOccupancy (ElectronType type=Paired) const

Additional Inherited Members
Protected Attributes inherited from BasisSet
std::array< unsigned int, 2 >	m_electrons = {}

Molecule *	m_molecule = nullptr

std::string	m_name

std::string	m_theoryName

std::vector< std::string >	m_symmetryLabels [2]

std::vector< double >	m_moEnergy [2]
	This block stores energies for the molecular orbitals (same convention as the molecular orbital coefficients).

std::vector< unsigned char >	m_moOccupancy [2]
	The occupancy of the molecular orbitals.

Detailed Description

Author: Marcus D. Hanwell

The GaussianSet class has a transparent data structure for storing the basis sets output by many quantum mechanical codes. It has a certain hierarchy where shells are built up from n primitives, in this case Gaussian Type Orbitals (GTOs). Each shell has a type (S, P, D, F, etc) and is composed of one or more GTOs. Each GTO has a contraction coefficient, c, and an exponent, a.

When calculating Molecular Orbitals (MOs) each orthogonal shell has an independent coefficient. That is the S type orbitals have one coefficient, the P type orbitals have three coefficients (Px, Py and Pz), the D type orbitals have five (or six if cartesian types) coefficients, and so on.

Member Enumeration Documentation

◆ orbital

enum orbital

Enumeration of the Gaussian type orbitals.

Constructor & Destructor Documentation

◆ GaussianSet()

GaussianSet ( )

Constructor.

◆ ~GaussianSet()

~GaussianSet ( )

overridedefault

Destructor.

Member Function Documentation

◆ clone()

GaussianSet * clone ( ) const

overridevirtual

Clone.

Implements BasisSet.

◆ addBasis()

unsigned int addBasis	(	unsigned int	atom,
		orbital	type
	)

Add a basis to the basis set.

Parameters

atom	Index of the atom to add the Basis to.
type	The type of the Basis being added.

Returns: The index of the added Basis.

◆ addGto()

unsigned int addGto	(	unsigned int	basis,
		double	c,
		double	a
	)

Add a GTO to the supplied basis.

Parameters

basis	The index of the Basis to add the GTO to.
c	The contraction coefficient of the GTO.
a	The exponent of the GTO.

Returns: The index of the added GTO.

◆ setMolecularOrbitals() [1/2]

void setMolecularOrbitals	(	const std::vector< double > &	MOs,
		ElectronType	type = `Paired`
	)

Set the molecular orbital (MO) coefficients to the GaussianSet.

Parameters

MOs	Vector containing the MO coefficients for the GaussianSet.
type	The type of the MOs (Paired, Alpha, Beta).

◆ setMolecularOrbitals() [2/2]

void setMolecularOrbitals	(	const std::vector< double > &	MOs,
		ElectronType	type,
		Index	index
	)

Set the molecular orbital (MO) coefficients for a given index. Note that this must be used with coordinate sets to work correctly.

Parameters

MOs	Vector containing the MO coefficients for the GaussianSet.
type	The type of the MOs (Paired, Alpha, Beta).
index	The index of the MO in the sequence.

◆ setCount()

int setCount ( )

Get the number of elements in the set.

◆ setActiveSetStep()

bool setActiveSetStep ( int index )

Set the active element in the set, this expects a corresponding coordinate set element, and will change the active MO matrix.

◆ setMolecularOrbitalNumber()

void setMolecularOrbitalNumber	(	const std::vector< unsigned int > &	nums,
		ElectronType	type = `Paired`
	)

Parameters

nums	The MO numbers (starting with an index of 1 for the first one).
type	The MO type (Paired, Alpha, Beta).

◆ setDensityMatrix()

bool setDensityMatrix ( const MatrixX & m )

Set the SCF density matrix for the GaussianSet.

◆ setSpinDensityMatrix()

bool setSpinDensityMatrix ( const MatrixX & m )

Set the spin density matrix for the GaussianSet.

◆ generateDensityMatrix()

bool generateDensityMatrix ( )

Returns: True on success, false on failure.

◆ generateSpinDensityMatrix()

bool generateSpinDensityMatrix ( )

Returns: True on success, false on failure.

◆ molecularOrbitalCount()

unsigned int molecularOrbitalCount ( ElectronType type = Paired ) const

overridevirtual

Returns: The number of molecular orbitals in the GaussianSet.

Implements BasisSet.

◆ outputAll()

void outputAll ( ElectronType type = Paired )

Debug routine, outputs all of the data in the GaussianSet.

Parameters

type	The electrons to output the information for.

◆ isValid()

bool isValid ( )

overridevirtual

Returns: True of the basis set is valid, false otherwise. Default is true, if false then the basis set is likely unusable.

Implements BasisSet.

◆ setScfType()

void setScfType ( ScfType type )

Set the SCF type for the object.

◆ scfType()

ScfType scfType ( ) const

Get the SCF type for the object.

◆ setFunctionalName()

void setFunctionalName ( const std::string & name )

Set the functional name (if applicable).

◆ functionalName()

std::string functionalName ( ) const

Get the functional name (empty if none used).

◆ initCalculation()

void initCalculation ( )

Initialize the calculation, this must normally be done before anything.

◆ symmetry()

std::vector< int > & symmetry ( )

Accessors for the various properties of the GaussianSet.

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

gaussianset.h

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ orbital

Constructor & Destructor Documentation

◆ GaussianSet()

◆ ~GaussianSet()

Member Function Documentation

◆ clone()

◆ addBasis()

◆ addGto()

◆ setMolecularOrbitals() [1/2]

◆ setMolecularOrbitals() [2/2]

◆ setCount()

◆ setActiveSetStep()

◆ setMolecularOrbitalNumber()

◆ setDensityMatrix()

◆ setSpinDensityMatrix()

◆ generateDensityMatrix()

◆ generateSpinDensityMatrix()

◆ molecularOrbitalCount()

◆ outputAll()

◆ isValid()

◆ setScfType()

◆ scfType()

◆ setFunctionalName()

◆ functionalName()

◆ initCalculation()

◆ symmetry()