AtomicBasisSet Class Reference

Contracted Gaussian basis. More...

#include <molecularbasis.h>

Classes
class	AnalysisSorter

Public Member Functions
	AtomicBasisSet ()
	AtomicBasisSet (std::string filename)
void	read_file (std::string filename)
void	atoms_to_bfn (const Molecule &molecule, std::vector< int > &at_to_bf, std::vector< int > &at_nbf)
	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, int ibf) const
	Returns the number of the atom the ibf'th basis function is on. More...
AtomicBasisFunction	get_atomic_basis_function (const Molecule &molecule, int ibf) const
	Returns the ibf'th atomic basis function. More...
int	nbf (const Molecule &molecule) const
	Given a molecule count the number of basis functions. 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...
bool	is_supported (int atomic_number) const
void	print (const Molecule &molecule) const
	Print basis info for atoms in the molecule (once for each unique atom type) More...
template<typename T >
void	print_anal (const Molecule &molecule, const Tensor< T > &v)
	Given a vector of AO coefficients prints an analysis. More...
void	print_all () const
	Print basis info for all supported atoms. More...
template<typename Archive >
void	serialize (Archive &ar)
	AtomicBasisSet ()
	AtomicBasisSet (std::string filename)
void	read_file (std::string filename)
void	atoms_to_bfn (const MolecularEntity &mentity, std::vector< int > &at_to_bf, std::vector< int > &at_nbf)
	Makes map from atoms to first basis function on atom and number of basis functions on atom. More...
int	basisfn_to_atom (const MolecularEntity &mentity, int ibf) const
	Returns the number of the atom the ibf'th basis function is on. More...
AtomicBasisFunction	get_atomic_basis_function (const MolecularEntity &mentity, int ibf) const
	Returns the ibf'th atomic basis function. More...
int	nbf (const MolecularEntity &mentity) const
	Given a molecule count the number of basis functions. More...
void	eval (const MolecularEntity &mentity, double x, double y, double z, double *bf) const
	Evaluates the basis functions. More...
double	eval_guess_density (const MolecularEntity &mentity, double x, double y, double z) const
	Evaluates the guess density. More...
bool	is_supported (int atomic_number) const
void	print (const MolecularEntity &mentity) const
	Print basis info for atoms in the molecule (once for each unique atom type) More...
template<typename T >
void	print_anal (const MolecularEntity &mentity, const Tensor< T > &v)
	Given a vector of AO coefficients prints an analysis. More...
void	print_all () const
	Print basis info for all supported atoms. More...
template<typename Archive >
void	serialize (Archive &ar)
	AtomicBasisSet ()
	AtomicBasisSet (std::string filename)
void	read_file (std::string filename)
void	atoms_to_bfn (const Molecule &molecule, std::vector< int > &at_to_bf, std::vector< int > &at_nbf)
	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, int ibf) const
	Returns the number of the atom the ibf'th basis function is on. More...
AtomicBasisFunction	get_atomic_basis_function (const Molecule &molecule, int ibf) const
	Returns the ibf'th atomic basis function. More...
int	nbf (const Molecule &molecule) const
	Given a molecule count the number of basis functions. 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...
bool	is_supported (int atomic_number) const
void	print (const Molecule &molecule) const
	Print basis info for atoms in the molecule (once for each unique atom type) More...
template<typename T >
void	print_anal (const Molecule &molecule, const Tensor< T > &v)
	Given a vector of AO coefficients prints an analysis. More...
void	print_all () const
	Print basis info for all supported atoms. More...
template<typename Archive >
void	serialize (Archive &ar)

Detailed Description

Contracted Gaussian basis.

Constructor & Destructor Documentation

AtomicBasisSet::AtomicBasisSet ( )

inline

AtomicBasisSet::AtomicBasisSet ( std::string  filename )

inline

References madness::AtomicBasisSet::read_file().

AtomicBasisSet::AtomicBasisSet ( )

inline

AtomicBasisSet::AtomicBasisSet ( std::string  filename )

inline

References madness::AtomicBasisSet::read_file().

AtomicBasisSet::AtomicBasisSet ( )

inline

AtomicBasisSet::AtomicBasisSet ( std::string  filename )

inline

References madness::AtomicBasisSet::read_file().

Member Function Documentation

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

inline

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

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::AtomicBasisSet::is_supported(), and madness::Molecule::natom().

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

inline

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

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::AtomicBasisSet::is_supported(), and madness::Molecule::natom().

void AtomicBasisSet::atoms_to_bfn ( const MolecularEntity &  mentity, std::vector< int > &  at_to_bf, std::vector< int > &  at_nbf  )

inline

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

References madness::Atom::atomic_number, MolecularEntity::get_atom(), madness::AtomicBasisSet::is_supported(), and MolecularEntity::natom().

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

inline

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

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::AtomicBasisSet::is_supported(), MADNESS_EXCEPTION, and madness::Molecule::natom().

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

inline

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

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::AtomicBasisSet::is_supported(), MADNESS_EXCEPTION, and madness::Molecule::natom().

int AtomicBasisSet::basisfn_to_atom ( const MolecularEntity &  mentity, int  ibf  ) const

inline

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

References madness::Atom::atomic_number, MolecularEntity::get_atom(), madness::AtomicBasisSet::is_supported(), MADNESS_EXCEPTION, and MolecularEntity::natom().

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

inline

Evaluates the basis functions.

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::Molecule::natom(), madness::Atom::x, madness::Atom::y, and madness::Atom::z.

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

inline

Evaluates the basis functions.

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::Molecule::natom(), madness::Atom::x, madness::Atom::y, and madness::Atom::z.

void AtomicBasisSet::eval ( const MolecularEntity &  mentity, double  x, double  y, double  z, double *  bf  ) const

inline

Evaluates the basis functions.

References madness::Atom::atomic_number, MolecularEntity::get_atom(), MolecularEntity::natom(), madness::Atom::x, madness::Atom::y, and madness::Atom::z.

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

inline

Evaluates the guess density.

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::Molecule::natom(), mpfr::sum(), madness::Atom::x, madness::Atom::y, and madness::Atom::z.

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

inline

Evaluates the guess density.

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::Molecule::natom(), mpfr::sum(), madness::Atom::x, madness::Atom::y, and madness::Atom::z.

double AtomicBasisSet::eval_guess_density ( const MolecularEntity &  mentity, double  x, double  y, double  z  ) const

inline

Evaluates the guess density.

References madness::Atom::atomic_number, MolecularEntity::get_atom(), MolecularEntity::natom(), mpfr::sum(), madness::Atom::x, madness::Atom::y, and madness::Atom::z.

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

inline

Returns the ibf'th atomic basis function.

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::AtomicBasisSet::is_supported(), MADNESS_EXCEPTION, madness::Molecule::natom(), madness::Atom::x, madness::Atom::y, and madness::Atom::z.

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

inline

Returns the ibf'th atomic basis function.

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::AtomicBasisSet::is_supported(), MADNESS_EXCEPTION, madness::Molecule::natom(), madness::Atom::x, madness::Atom::y, and madness::Atom::z.

AtomicBasisFunction AtomicBasisSet::get_atomic_basis_function ( const MolecularEntity &  mentity, int  ibf  ) const

inline

Returns the ibf'th atomic basis function.

References madness::Atom::atomic_number, MolecularEntity::get_atom(), madness::AtomicBasisSet::is_supported(), MADNESS_EXCEPTION, MolecularEntity::natom(), madness::Atom::x, madness::Atom::y, and madness::Atom::z.

bool AtomicBasisSet::is_supported ( int  atomic_number ) const

inline

bool AtomicBasisSet::is_supported ( int  atomic_number ) const

inline

bool AtomicBasisSet::is_supported ( int  atomic_number ) const

inline

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

inline

Given a molecule count the number of basis functions.

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::AtomicBasisSet::is_supported(), and madness::Molecule::natom().

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

inline

Given a molecule count the number of basis functions.

References madness::Atom::atomic_number, madness::Molecule::get_atom(), madness::AtomicBasisSet::is_supported(), and madness::Molecule::natom().

Referenced by print_all(), and SCFParameters::set_molecular_info().

int AtomicBasisSet::nbf ( const MolecularEntity &  mentity ) const

inline

Given a molecule count the number of basis functions.

References madness::Atom::atomic_number, MolecularEntity::get_atom(), madness::AtomicBasisSet::is_supported(), and MolecularEntity::natom().

void AtomicBasisSet::print

(

const Molecule &

molecule

)

const

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

void AtomicBasisSet::print

(

const Molecule &

molecule

)

const

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

void AtomicBasisSet::print ( const MolecularEntity &  mentity ) const

inline

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

References madness::Atom::atomic_number, MolecularEntity::get_atom(), madness::get_atomic_data(), MolecularEntity::natom(), and madness::AtomicData::symbol.

void AtomicBasisSet::print_all

(

)

const

Print basis info for all supported atoms.

void AtomicBasisSet::print_all

(

)

const

Print basis info for all supported atoms.

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

void AtomicBasisSet::print_all ( ) const

inline

Print basis info for all supported atoms.

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

template<typename T >

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

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 madness::Atom::atomic_number, madness::AtomicBasisSet::basisfn_to_atom(), madness::Molecule::get_atom(), madness::AtomicBasisSet::get_atomic_basis_function(), madness::get_atomic_data(), madness::AtomicBasisFunction::get_desc(), madness::Molecule::natom(), madness::AtomicBasisSet::nbf(), madness::AtomicData::symbol, and thresh.

template<typename T >

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

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 madness::Atom::atomic_number, madness::AtomicBasisSet::basisfn_to_atom(), madness::Molecule::get_atom(), madness::AtomicBasisSet::get_atomic_basis_function(), madness::get_atomic_data(), madness::AtomicBasisFunction::get_desc(), madness::Molecule::natom(), madness::AtomicBasisSet::nbf(), madness::AtomicData::symbol, and thresh.

template<typename T >

void AtomicBasisSet::print_anal ( const MolecularEntity &  mentity, const Tensor< T > &  v  )

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 madness::Atom::atomic_number, madness::AtomicBasisSet::basisfn_to_atom(), MolecularEntity::get_atom(), madness::AtomicBasisSet::get_atomic_basis_function(), madness::get_atomic_data(), madness::AtomicBasisFunction::get_desc(), MolecularEntity::natom(), madness::AtomicBasisSet::nbf(), madness::AtomicData::symbol, and thresh.

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

inline

References TiXmlElement::Attribute(), debug, TiXmlDocument::ErrorCol(), TiXmlDocument::ErrorDesc(), TiXmlDocument::ErrorRow(), TiXmlNode::FirstChildElement(), madness::g, TiXmlElement::GetText(), madness::AtomicBasisSet::is_supported(), TiXmlDocument::LoadFile(), MADNESS_EXCEPTION, madness::AtomicBasisSet::nbf(), TiXmlNode::NextSiblingElement(), madness::symbol_to_atomic_number(), and TiXmlNode::Value().

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

inline

References TiXmlElement::Attribute(), debug, TiXmlDocument::ErrorCol(), TiXmlDocument::ErrorDesc(), TiXmlDocument::ErrorRow(), TiXmlNode::FirstChildElement(), madness::g, TiXmlElement::GetText(), madness::AtomicBasisSet::is_supported(), TiXmlDocument::LoadFile(), MADNESS_EXCEPTION, madness::AtomicBasisSet::nbf(), TiXmlNode::NextSiblingElement(), madness::symbol_to_atomic_number(), and TiXmlNode::Value().

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

inline

References TiXmlElement::Attribute(), debug, TiXmlDocument::ErrorCol(), TiXmlDocument::ErrorDesc(), TiXmlDocument::ErrorRow(), TiXmlNode::FirstChildElement(), madness::g, TiXmlElement::GetText(), madness::AtomicBasisSet::is_supported(), TiXmlDocument::LoadFile(), MADNESS_EXCEPTION, madness::AtomicBasisSet::nbf(), TiXmlNode::NextSiblingElement(), madness::symbol_to_atomic_number(), and TiXmlNode::Value().

template<typename Archive >

void AtomicBasisSet::serialize ( Archive &  ar )

inline

template<typename Archive >

void AtomicBasisSet::serialize ( Archive &  ar )

inline

template<typename Archive >

void AtomicBasisSet::serialize ( Archive &  ar )

inline

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

• DFcode/molecularbasis.h
• jacob/molecularbasis.cc