#include <molecularbasis.h>

Collaboration diagram for madness::AtomicBasisSet:

Classes
class	AnalysisSorter

Public Member Functions
	AtomicBasisSet ()

	AtomicBasisSet (std::string filename)

void	atoms_to_bfn (const Molecule &molecule, std::vector< int > &at_to_bf, std::vector< int > &at_nbf) const
	Makes map from atoms to first basis function on atom and number of basis functions on atom. More...

int	basisfn_to_atom (const Molecule &molecule, size_t ibf) const
	Returns the number of the atom the ibf'th basis function is on. More...

void	eval (const Molecule &molecule, double x, double y, double z, double *bf) const
	Evaluates the basis functions. More...

double	eval_guess_density (const Molecule &molecule, double x, double y, double z) const
	Evaluates the guess density. More...

const Tensor< double > &	get_aeps (const Molecule &molecule, size_t iat) const
	Returns the atomic alpha eigenvalues for atom iat. More...

AtomicBasisFunction	get_atomic_basis_function (const Molecule &molecule, size_t ibf) const
	Returns the ibf'th atomic basis function. More...

const Tensor< double > &	get_avec (const Molecule &molecule, size_t iat) const
	Returns the atomic alpha eigenvectors for atom iat. More...

std::string	get_name () const

bool	is_supported (int atomic_number) const

void	modify_dmat_psp (int atn, double zeff)
	Eliminates core orbitals from the density matrix for pseudopotential calculations. More...

int	nbf (const Molecule &molecule) const
	Given a molecule count the number of basis functions. More...

void	print (const Molecule &molecule) const
	Print basis info for atoms in the molecule (once for each unique atom type) More...

void	print_all () const
	Print basis info for all supported atoms. More...

template<typename T >
void	print_anal (const Molecule &molecule, const Tensor< T > &v) const
	Given a vector of AO coefficients prints an analysis. More...

void	read_file (std::string filename)
	read the atomic basis set from file More...

void	read_nw_file (std::string filename)
	read the atomic basis set from file More...

template<typename Archive >
void	serialize (Archive &ar)

void	shells_to_bfn (const Molecule &molecule, std::vector< int > &sh_to_bf, std::vector< int > &sh_nbf) const
	Makes map from shells to first basis function on she and number of basis functions on sh. More...

Private Member Functions
template<typename T >
Tensor< T >	load_tixml_matrix (TiXmlElement node, int n, int m, const char name)

template<typename T >
std::vector< T >	load_tixml_vector (TiXmlElement node, int n, const char name)

Private Attributes
std::vector< AtomicBasis >	ag
	Basis associated by atomic number = 1, 2, ...; 0=Bq. More...

std::string	name

Detailed Description

Contracted Gaussian basis.

Constructor & Destructor Documentation

◆ AtomicBasisSet() [1/2]

madness::AtomicBasisSet::AtomicBasisSet ( )

inline

◆ AtomicBasisSet() [2/2]

madness::AtomicBasisSet::AtomicBasisSet ( std::string filename )

inline

References madness::filename, and read_file().

Member Function Documentation

◆ atoms_to_bfn()

void madness::AtomicBasisSet::atoms_to_bfn	(	const Molecule &	molecule,
		std::vector< int > &	at_to_bf,
		std::vector< int > &	at_nbf
	)		const

inline

Makes map from atoms to first basis function on atom and number of basis functions on atom.

References ag, at_nbf, at_to_bf, madness::Atom::atomic_number, is_supported(), MADNESS_ASSERT, and molecule.

Referenced by madness::Localizer::Localizer(), MiniDFT::makeao(), and madness::SCF::project_ao_basis().

◆ basisfn_to_atom()

int madness::AtomicBasisSet::basisfn_to_atom	(	const Molecule &	molecule,
		size_t	ibf
	)		const

inline

Returns the number of the atom the ibf'th basis function is on.

References ag, madness::Atom::atomic_number, is_supported(), MADNESS_ASSERT, MADNESS_EXCEPTION, and molecule.

Referenced by print_anal().

◆ eval()

void madness::AtomicBasisSet::eval	(	const Molecule &	molecule,
		double	x,
		double	y,
		double	z,
		double *	bf
	)		const

inline

Evaluates the basis functions.

References ag, madness::Atom::atomic_number, molecule, madness::Atom::x, madness::Atom::y, and madness::Atom::z.

◆ eval_guess_density()

double madness::AtomicBasisSet::eval_guess_density	(	const Molecule &	molecule,
		double	x,
		double	y,
		double	z
	)		const

inline

Evaluates the guess density.

References ag, madness::Atom::atomic_number, molecule, madness::Atom::pseudo_atom, madness::sum(), madness::Atom::x, madness::Atom::y, and madness::Atom::z.

Referenced by MolecularGuessDensityFunctor::operator()(), madness::Solver< T, NDIM >::GuessDensity::operator()(), and madchem::MolecularGuessDensityFunctor::operator()().

◆ get_aeps()

const Tensor<double>& madness::AtomicBasisSet::get_aeps	(	const Molecule &	molecule,
		size_t	iat
	)		const

inline

Returns the atomic alpha eigenvalues for atom iat.

References ag, madness::Atom::atomic_number, is_supported(), MADNESS_ASSERT, and molecule.

◆ get_atomic_basis_function()

AtomicBasisFunction madness::AtomicBasisSet::get_atomic_basis_function	(	const Molecule &	molecule,
		size_t	ibf
	)		const

inline

Returns the ibf'th atomic basis function.

References ag, madness::Atom::atomic_number, is_supported(), MADNESS_ASSERT, MADNESS_EXCEPTION, molecule, madness::Atom::x, madness::Atom::y, and madness::Atom::z.

Referenced by MiniDFT::makeao(), makeao(), makeao_slow(), print_anal(), madness::Solver< T, NDIM >::project_ao_basis(), and madness::SCF::project_ao_basis_only().

◆ get_avec()

const Tensor<double>& madness::AtomicBasisSet::get_avec	(	const Molecule &	molecule,
		size_t	iat
	)		const

inline

Returns the atomic alpha eigenvectors for atom iat.

References ag, madness::Atom::atomic_number, is_supported(), MADNESS_ASSERT, and molecule.

Referenced by madness::Localizer::localize_new().

◆ get_name()

std::string madness::AtomicBasisSet::get_name ( ) const

inline

References name.

Referenced by madness::Localizer::print_info(), and madness::MolecularOrbitals< T, NDIM >::read_restartaodata().

◆ is_supported()

bool madness::AtomicBasisSet::is_supported ( int atomic_number ) const

inline

References ag.

Referenced by atoms_to_bfn(), basisfn_to_atom(), get_aeps(), get_atomic_basis_function(), get_avec(), nbf(), read_file(), and shells_to_bfn().

◆ load_tixml_matrix()

template<typename T >

Tensor<T> madness::AtomicBasisSet::load_tixml_matrix	(	TiXmlElement *	node,
		int	n,
		int	m,
		const char *	name
	)

inlineprivate

References m, MADNESS_ASSERT, and name.

◆ load_tixml_vector()

template<typename T >

std::vector<T> madness::AtomicBasisSet::load_tixml_vector	(	TiXmlElement *	node,
		int	n,
		const char *	name
	)

inlineprivate

References MADNESS_ASSERT, and name.

◆ modify_dmat_psp()

void AtomicBasisSet::modify_dmat_psp	(	int	atn,
		double	zeff
	)

Eliminates core orbitals from the density matrix for pseudopotential calculations.

References ag, debug, e(), madness::inner(), MADNESS_EXCEPTION, madness::BaseTensor::size(), madness::Tensor< T >::sum(), and madness::transpose().

Referenced by madness::SCF::initial_guess().

◆ nbf()

int madness::AtomicBasisSet::nbf ( const Molecule & molecule ) const

inline

Given a molecule count the number of basis functions.

References ag, madness::Atom::atomic_number, is_supported(), MADNESS_ASSERT, and molecule.

Referenced by madness::Solver< T, NDIM >::initial_guess(), MiniDFT::makeao(), makeao(), makeao_slow(), print_all(), print_anal(), madness::Solver< T, NDIM >::project_ao_basis(), madness::SCF::project_ao_basis_only(), read_file(), read_nw_file(), and shells_to_bfn().

◆ print()

void AtomicBasisSet::print ( const Molecule & molecule ) const

Print basis info for atoms in the molecule (once for each unique atom type)

References ag, madness::Atom::atomic_number, madness::get_atomic_data(), molecule, name, and madness::AtomicData::symbol.

◆ print_all()

void AtomicBasisSet::print_all ( ) const

Print basis info for all supported atoms.

References ag, madness::get_atomic_data(), name, nbf(), and madness::AtomicData::symbol.

◆ print_anal()

template<typename T >

void madness::AtomicBasisSet::print_anal	(	const Molecule &	molecule,
		const Tensor< T > &	v
	)		const

inline

Given a vector of AO coefficients prints an analysis.

For each significant coeff it prints

atomic symbol
atom number
basis function type (e.g., dxy)
basis function number
MO coeff

References std::abs(), madness::Atom::atomic_number, basisfn_to_atom(), get_atomic_basis_function(), madness::get_atomic_data(), madness::AtomicBasisFunction::get_desc(), molecule, nbf(), madness::AtomicData::symbol, thresh, and v.

Referenced by madness::SCF::analyze_vectors().

◆ read_file()

void AtomicBasisSet::read_file ( std::string filename )

read the atomic basis set from file

use the default location MRA_CHEMDATA_DIR as defined in the Makefile.am unless it is overridden by the environment variable MRA_CHEMDATA_DIR

Parameters

[in] filename the name of the basis set (sto-3g, 6-31g, etc)

References ag, debug, madness::filename, madness::g, is_supported(), MADNESS_ASSERT, MADNESS_EXCEPTION, name, nbf(), madness::symbol_to_atomic_number(), and madness::type().

Referenced by AtomicBasisSet(), madness::Znemo::Znemo(), MiniDFT::doit(), madness::Solver< T, NDIM >::init(), main(), and madness::SCF::reset_aobasis().

◆ read_nw_file()

void AtomicBasisSet::read_nw_file ( std::string filename )

read the atomic basis set from file

Parameters

[in] filename the base name of nwchem files (.out and .movecs)

References ag, slymer::Properties::Atoms, slymer::ES_Interface::atoms, madness::filename, madness::g, nbf(), slymer::NWChem_Interface::read(), slymer::Atom::symbol, and madness::symbol_to_atomic_number().

Referenced by madness::SCF::SCF().

◆ serialize()

template<typename Archive >

void madness::AtomicBasisSet::serialize ( Archive & ar )

inline

References ag, and name.

◆ shells_to_bfn()

void madness::AtomicBasisSet::shells_to_bfn	(	const Molecule &	molecule,
		std::vector< int > &	sh_to_bf,
		std::vector< int > &	sh_nbf
	)		const

inline

Makes map from shells to first basis function on she and number of basis functions on sh.

References ag, madness::Atom::atomic_number, is_supported(), MADNESS_ASSERT, molecule, and nbf().

Referenced by madness::Localizer::localize_new().

Member Data Documentation

◆ ag

std::vector<AtomicBasis> madness::AtomicBasisSet::ag

private

Basis associated by atomic number = 1, 2, ...; 0=Bq.

Referenced by atoms_to_bfn(), basisfn_to_atom(), eval(), eval_guess_density(), get_aeps(), get_atomic_basis_function(), get_avec(), is_supported(), modify_dmat_psp(), nbf(), print(), print_all(), read_file(), read_nw_file(), serialize(), and shells_to_bfn().

◆ name

std::string madness::AtomicBasisSet::name

private

Referenced by get_name(), load_tixml_matrix(), load_tixml_vector(), print(), print_all(), read_file(), and serialize().

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

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AtomicBasisSet() [1/2]

◆ AtomicBasisSet() [2/2]

Member Function Documentation

◆ atoms_to_bfn()

◆ basisfn_to_atom()

◆ eval()

◆ eval_guess_density()

◆ get_aeps()

◆ get_atomic_basis_function()

◆ get_avec()

◆ get_name()

◆ is_supported()

◆ load_tixml_matrix()

◆ load_tixml_vector()

◆ modify_dmat_psp()

◆ nbf()

◆ print()

◆ print_all()

◆ print_anal()

◆ read_file()

◆ read_nw_file()

◆ serialize()

◆ shells_to_bfn()

Member Data Documentation

◆ ag

◆ name