madness::Molecule Class Reference

#include <molecule.h>

Collaboration diagram for madness::Molecule:

Public Member Functions
	Molecule ()
	Makes a molecule with zero atoms. More...
	Molecule (const std::string &filename)
	Read coordinates from a file. More...
void	read_file (const std::string &filename)
void	read_core_file (const std::string &filename)
std::string	guess_file () const
unsigned int	n_core_orb_all () const
unsigned int	n_core_orb (unsigned int atn) const
unsigned int	get_core_l (unsigned int atn, unsigned int c) const
double	get_core_bc (unsigned int atn, unsigned int c) const
double	core_eval (int atom, unsigned int core, int m, double x, double y, double z) const
double	core_derivative (int atom, int axis, unsigned int core, int m, double x, double y, double z) const
bool	is_potential_defined (unsigned int atn) const
bool	is_potential_defined_atom (int i) const
void	add_atom (double x, double y, double z, double q, int atn)
int	natom () const
void	set_atom_charge (unsigned int i, double zeff)
unsigned int	get_atom_number (unsigned int i)
void	set_atom_coords (unsigned int i, double x, double y, double z)
madness::Tensor< double >	get_all_coords () const
std::vector< madness::Vector < double, 3 > >	get_all_coords_vec () const
void	set_all_coords (const madness::Tensor< double > &newcoords)
void	set_eprec (double value)
	updates rcuts with given eprec More...
void	set_rcut (double value)
void	set_core_eprec (double value)
void	set_core_rcut (double value)
double	get_eprec () const
double	bounding_cube () const
	Returns the half width of the bounding cube. More...
const Atom &	get_atom (unsigned int i) const
void	print () const
double	inter_atomic_distance (unsigned int i, unsigned int j) const
double	nuclear_repulsion_energy () const
double	nuclear_repulsion_energy_pseudo () const
double	nuclear_repulsion_derivative (int i, int j) const
double	nuclear_dipole (int axis) const
double	nuclear_charge_density (double x, double y, double z) const
double	mol_nuclear_charge_density (double x, double y, double z) const
double	smallest_length_scale () const
void	identify_point_group ()
void	center ()
	Moves the center of nuclear charge to the origin. More...
void	orient ()
	Centers and orients the molecule in a standard manner. More...
double	total_nuclear_charge () const
double	nuclear_attraction_potential (double x, double y, double z) const
double	molecular_core_potential (double x, double y, double z) const
double	core_potential_derivative (int atom, int axis, double x, double y, double z) const
double	nuclear_attraction_potential_derivative (int atom, int axis, double x, double y, double z) const
template<typename Archive >
void	serialize (Archive &ar)

Public Attributes
std::string	pointgroup_
std::vector< double >	atomic_radii

Constructor & Destructor Documentation

madness::Molecule::Molecule ( )

inline

Makes a molecule with zero atoms.

References L.

Molecule::Molecule

(

const std::string &

filename

)

Read coordinates from a file.

Scans the file for the first geometry block in the format

geometry
   tag x y z
   ...
end

The charge q is inferred from the tag which is assumed to be the standard symbol for an element. Same as the simplest NWChem format. For ghost atoms (bq ) the charge is read as a fifth field on the line.

This code is just for the examples ... don't trust it!

References read_file().

Member Function Documentation

void Molecule::add_atom	(	double	x,
		double	y,
		double	z,
		double	q,
		int	atn
	)

References atomic_radii, madness::constants::atomic_unit_of_length, c, madness::AtomicData::covalent_radius, madness::get_atomic_data(), and madness::smoothing_parameter().

Referenced by main(), and read_file().

double Molecule::bounding_cube

(

)

const

Returns the half width of the bounding cube.

The molecule will be contained in the cube [-L,+L].

References mpfr::fabs(), L, and max.

Referenced by madness::CalculationParameters::set_molecular_info().

void Molecule::center

(

)

Moves the center of nuclear charge to the origin.

Referenced by orient().

double Molecule::core_derivative	(	int	atom,
		int	axis,
		unsigned int	core,
		int	m,
		double	x,
		double	y,
		double	z
	)		const

References madness::CorePotentialManager::core_derivative().

Referenced by madness::CoreOrbitalDerivativeFunctor::operator()().

double Molecule::core_eval	(	int	atom,
		unsigned int	core,
		int	m,
		double	x,
		double	y,
		double	z
	)		const

References madness::CorePotentialManager::core_eval().

Referenced by madness::CoreOrbitalFunctor::operator()().

double Molecule::core_potential_derivative	(	int	atom,
		int	axis,
		double	x,
		double	y,
		double	z
	)		const

References natom(), and madness::CorePotentialManager::potential_derivative().

Referenced by madness::CorePotentialDerivativeFunctor::operator()().

madness::Tensor< double > Molecule::get_all_coords

(

)

const

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

Referenced by main(), and madness::HartreeFock< T, NDIM >::value().

std::vector< madness::Vector< double, 3 > > Molecule::get_all_coords_vec

(

)

const

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

Referenced by madness::MolecularPotentialFunctor::special_points(), madness::MolecularCorePotentialFunctor::special_points(), and madness::MolecularGuessDensityFunctor::special_points().

const Atom & Molecule::get_atom

(

unsigned int

i

)

const

Referenced by madness::GTHPseudopotential< double >::apply_potential(), madness::GTHPseudopotential< double >::apply_potential_simple(), madness::AtomicBasisSet::atoms_to_bfn(), AtomicBasisSet::atoms_to_bfn(), madness::AtomicBasisSet::basisfn_to_atom(), AtomicBasisSet::basisfn_to_atom(), madness::PotentialManager::core_projection(), madness::SCF::core_projection(), madness::PotentialManager::core_projector_derivative(), madness::SCF::core_projector_derivative(), madness::SCF::derivatives(), madness::AtomicBasisSet::eval(), AtomicBasisSet::eval(), madness::AtomicBasisSet::eval_guess_density(), AtomicBasisSet::eval_guess_density(), get_all_coords(), get_all_coords_vec(), madness::AtomicBasisSet::get_atomic_basis_function(), AtomicBasisSet::get_atomic_basis_function(), madness::GTHPseudopotential< double >::load_pseudo_from_file(), madness::GTHPseudopotential< double >::make_pseudo_potential(), madness::AtomicBasisSet::nbf(), AtomicBasisSet::nbf(), madness::AtomicBasisSet::print(), madness::AtomicBasisSet::print_anal(), AtomicBasisSet::print_anal(), and madness::MolecularDerivativeFunctor::special_points().

unsigned int Molecule::get_atom_number

(

unsigned int

i

)

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

double madness::Molecule::get_core_bc ( unsigned int  atn, unsigned int  c  ) const

inline

References madness::CorePotentialManager::get_core_bc().

Referenced by madness::PotentialManager::core_projection(), madness::SCF::core_projection(), madness::PotentialManager::core_projector_derivative(), and madness::SCF::core_projector_derivative().

unsigned int madness::Molecule::get_core_l ( unsigned int  atn, unsigned int  c  ) const

inline

References madness::CorePotentialManager::get_core_l().

Referenced by madness::PotentialManager::core_projection(), madness::SCF::core_projection(), madness::PotentialManager::core_projector_derivative(), and madness::SCF::core_projector_derivative().

double madness::Molecule::get_eprec ( ) const

inline

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

std::string madness::Molecule::guess_file ( ) const

inline

References madness::CorePotentialManager::guess_file().

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

void Molecule::identify_point_group

(

)

References pointgroup_, and madness::print().

Referenced by orient().

double Molecule::inter_atomic_distance	(	unsigned int	i,
		unsigned int	j
	)		const

Referenced by nuclear_repulsion_derivative(), nuclear_repulsion_energy(), and nuclear_repulsion_energy_pseudo().

bool madness::Molecule::is_potential_defined ( unsigned int  atn ) const

inline

References madness::CorePotentialManager::is_defined().

bool madness::Molecule::is_potential_defined_atom ( int  i ) const

inline

References madness::CorePotentialManager::is_defined().

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

double Molecule::mol_nuclear_charge_density	(	double	x,
		double	y,
		double	z
	)		const

References madness::smoothed_density().

double Molecule::molecular_core_potential	(	double	x,
		double	y,
		double	z
	)		const

References madness::CorePotentialManager::is_defined(), natom(), madness::CorePotentialManager::potential(), mpfr::sum(), TAU_START, and TAU_STOP.

Referenced by madness::MolecularCorePotentialFunctor::operator()().

unsigned int madness::Molecule::n_core_orb ( unsigned int  atn ) const

inline

References madness::CorePotentialManager::is_defined(), and madness::CorePotentialManager::n_core_orb_base().

Referenced by madness::PotentialManager::core_projection(), madness::SCF::core_projection(), madness::PotentialManager::core_projector_derivative(), and madness::SCF::core_projector_derivative().

unsigned int Molecule::n_core_orb_all

(

)

const

References madness::CorePotentialManager::is_defined(), madness::CorePotentialManager::n_core_orb(), natom(), and mpfr::sum().

Referenced by madness::SCF::initial_guess(), madness::SCF::load_mos(), and madness::SCF::SCF().

int madness::Molecule::natom ( ) const

inline

Referenced by madness::AtomicBasisSet::atoms_to_bfn(), AtomicBasisSet::atoms_to_bfn(), madness::AtomicBasisSet::basisfn_to_atom(), AtomicBasisSet::basisfn_to_atom(), core_potential_derivative(), madness::PotentialManager::core_projection(), madness::SCF::core_projection(), madness::SCF::derivatives(), madness::AtomicBasisSet::eval(), AtomicBasisSet::eval(), madness::AtomicBasisSet::eval_guess_density(), AtomicBasisSet::eval_guess_density(), get_all_coords(), get_all_coords_vec(), madness::AtomicBasisSet::get_atomic_basis_function(), AtomicBasisSet::get_atomic_basis_function(), madness::GTHPseudopotential< double >::load_pseudo_from_file(), SCF::localize_PM_task_kernel(), main(), madness::GTHPseudopotential< double >::make_pseudo_potential(), molecular_core_potential(), n_core_orb_all(), madness::AtomicBasisSet::nbf(), AtomicBasisSet::nbf(), print(), madness::AtomicBasisSet::print(), madness::AtomicBasisSet::print_anal(), AtomicBasisSet::print_anal(), read_core_file(), read_file(), madness::SCF::SCF(), set_all_coords(), madness::SCF::solve(), madness::HartreeFock< T, NDIM >::value(), and madness::MolecularEnergy::value().

double Molecule::nuclear_attraction_potential	(	double	x,
		double	y,
		double	z
	)		const

References madness::smoothed_potential(), mpfr::sum(), TAU_START, and TAU_STOP.

Referenced by madness::MolecularPotentialFunctor::operator()().

double Molecule::nuclear_attraction_potential_derivative	(	int	atom,
		int	axis,
		double	x,
		double	y,
		double	z
	)		const

References madness::dsmoothed_potential().

Referenced by madness::MolecularDerivativeFunctor::operator()().

double Molecule::nuclear_charge_density	(	double	x,
		double	y,
		double	z
	)		const

References madness::smoothed_density(), and sqrt().

double Molecule::nuclear_dipole

(

int

axis

)

const

References madness::CorePotentialManager::is_defined(), MADNESS_EXCEPTION, madness::CorePotentialManager::n_core_orb(), and mpfr::sum().

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

double Molecule::nuclear_repulsion_derivative	(	int	i,
		int	j
	)		const

References inter_atomic_distance(), madness::CorePotentialManager::is_defined(), madness::CorePotentialManager::n_core_orb(), and mpfr::sum().

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

double Molecule::nuclear_repulsion_energy

(

)

const

References inter_atomic_distance(), madness::CorePotentialManager::is_defined(), madness::CorePotentialManager::n_core_orb(), and mpfr::sum().

Referenced by main(), and madness::SCF::solve().

double Molecule::nuclear_repulsion_energy_pseudo

(

)

const

References inter_atomic_distance(), madness::CorePotentialManager::is_defined(), madness::CorePotentialManager::n_core_orb(), and mpfr::sum().

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

void Molecule::orient

(

)

Centers and orients the molecule in a standard manner.

References center(), mpfr::fabs(), I(), identify_point_group(), madness::inner(), k, L, madness::print(), and madness::syev().

Referenced by main(), and madness::SCF::SCF().

void Molecule::print

(

)

const

References madness::get_atomic_data(), and natom().

Referenced by main(), madness::MP2::MP2(), and madness::AtomicBasisSet::print().

void Molecule::read_core_file

(

const std::string &

filename

)

References madness::CorePotentialManager::is_defined(), madness::CorePotentialManager::n_core_orb(), natom(), madness::print(), madness::CorePotentialManager::read_file(), and madness::smoothing_parameter().

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

void Molecule::read_file

(

const std::string &

filename

)

References add_atom(), madness::constants::atomic_unit_of_length, madness::f, MADNESS_EXCEPTION, natom(), madness::position_stream(), madness::scale(), set_eprec(), and madness::symbol_to_atomic_number().

Referenced by Molecule(), and madness::SCF::SCF().

template<typename Archive >

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

inline

void Molecule::set_all_coords

(

const madness::Tensor< double > &

newcoords

)

References c, and natom().

Referenced by madness::HartreeFock< T, NDIM >::value(), and madness::MolecularEnergy::value().

void Molecule::set_atom_charge	(	unsigned int	i,
		double	zeff
	)

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

void Molecule::set_atom_coords	(	unsigned int	i,
		double	x,
		double	y,
		double	z
	)

void madness::Molecule::set_core_eprec ( double  value )

inline

References madness::CorePotentialManager::set_eprec().

void madness::Molecule::set_core_rcut ( double  value )

inline

References madness::CorePotentialManager::set_rcut().

void Molecule::set_eprec

(

double

value

)

updates rcuts with given eprec

References madness::CorePotentialManager::set_eprec(), and madness::smoothing_parameter().

Referenced by main(), madness::MP2::MP2(), read_file(), and madness::SCF::set_protocol().

void Molecule::set_rcut

(

double

value

)

double Molecule::smallest_length_scale

(

)

const

References max.

Referenced by madness::CalculationParameters::set_molecular_info().

double Molecule::total_nuclear_charge

(

)

const

References mpfr::sum().

Referenced by madness::SCF::initial_guess(), and madness::CalculationParameters::set_molecular_info().

Member Data Documentation

std::vector<double> madness::Molecule::atomic_radii

Referenced by add_atom().

std::string madness::Molecule::pointgroup_

The molecular point group is automatically assigned in the identify_pointgroup function

Referenced by identify_point_group().

---

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

• chem/molecule.h
• chem/molecule.cc