Molecule Class Reference

#include <molecule.h>

Public Member Functions
	Molecule ()
	Makes a molecule with zero atoms. More...
	Molecule (const std::string &filename, const std::string &geomname="")
	Read coordinates from a file. More...
void	read_file (const std::string &filename)
void	read_file (const std::string &filename, const std::string &geomname)
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_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_derivative (int i, int j) const
double	nuclear_dipole (int axis) const
double	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)
	Molecule ()
	Makes a molecule with zero atoms. 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_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
std::vector< double >	charge_center ()
	get the coordinates of the nuclear charge center More...
void	set_all_coords (const madness::Tensor< double > &newcoords)
void	set_eprec (double value)
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
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_derivative (int i, int j) const
double	nuclear_dipole (int axis) const
double	nuclear_charge_density (double x, double y, double z) const
double	smallest_length_scale () const
void	identify_point_group ()
void	center ()
void	orient ()
double	Qnxx () const
double	Qnyy () const
double	Qnzz () const
double	Qnxz () const
double	Qnxy () const
double	Qnyz () const
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::vector< double >	atomic_radii

Constructor & Destructor Documentation

Molecule::Molecule ( )

inline

Makes a molecule with zero atoms.

References L.

Molecule::Molecule	(	const std::string &	filename,
		const std::string &	geomname = ""
	)

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().

Molecule::Molecule ( )

inline

Makes a molecule with zero atoms.

References L.

Member Function Documentation

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

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

References c, and madness::smoothing_parameter().

Referenced by read_file().

double Molecule::bounding_cube

(

)

const

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 SCFParameters::set_molecular_info().

void Molecule::center

(

)

void Molecule::center

(

)

Moves the center of nuclear charge to the origin.

Referenced by orient().

std::vector< double > Molecule::charge_center

(

)

get the coordinates of the nuclear charge center

References c.

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

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

References CorePotentialManager::core_derivative().

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

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

References CorePotentialManager::core_eval().

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

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

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

madness::Tensor<double> Molecule::get_all_coords

(

)

const

madness::Tensor< double > Molecule::get_all_coords

(

)

const

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

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

(

)

const

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

(

)

const

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

const Atom& Molecule::get_atom

(

unsigned int

i

)

const

const Atom & Molecule::get_atom

(

unsigned int

i

)

const

Referenced by get_all_coords(), and get_all_coords_vec().

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

inline

References CorePotentialManager::get_core_bc().

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

inline

References CorePotentialManager::get_core_bc().

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

inline

References CorePotentialManager::get_core_l().

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

inline

References CorePotentialManager::get_core_l().

double Molecule::get_eprec ( ) const

inline

double Molecule::get_eprec ( ) const

inline

std::string Molecule::guess_file ( ) const

inline

References CorePotentialManager::guess_file().

std::string Molecule::guess_file ( ) const

inline

References CorePotentialManager::guess_file().

void Molecule::identify_point_group

(

)

void Molecule::identify_point_group

(

)

References madness::print().

Referenced by orient().

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

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

References distance().

Referenced by nuclear_repulsion_derivative(), and nuclear_repulsion_energy().

bool Molecule::is_potential_defined ( unsigned int  atn ) const

inline

References CorePotentialManager::is_defined().

bool Molecule::is_potential_defined ( unsigned int  atn ) const

inline

References CorePotentialManager::is_defined().

bool Molecule::is_potential_defined_atom ( int  i ) const

inline

References CorePotentialManager::is_defined().

bool Molecule::is_potential_defined_atom ( int  i ) const

inline

References CorePotentialManager::is_defined().

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

References distance(), CorePotentialManager::is_defined(), natom(), CorePotentialManager::potential(), and mpfr::sum().

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

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

inline

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

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

inline

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

unsigned int Molecule::n_core_orb_all

(

)

const

unsigned int Molecule::n_core_orb_all

(

)

const

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

int Molecule::natom ( ) const

inline

int Molecule::natom ( ) const

inline

Referenced by core_potential_derivative(), get_all_coords(), get_all_coords_vec(), molecular_core_potential(), n_core_orb_all(), print(), read_core_file(), read_file(), and set_all_coords().

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

References distance(), madness::smoothed_potential(), and mpfr::sum().

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

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

References distance(), and madness::dsmoothed_potential().

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

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

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

double Molecule::nuclear_dipole

(

int

axis

)

const

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

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

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

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

double Molecule::nuclear_repulsion_energy

(

)

const

double Molecule::nuclear_repulsion_energy

(

)

const

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

void Molecule::orient

(

)

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().

void Molecule::print

(

)

const

void Molecule::print

(

)

const

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

double Molecule::Qnxx

(

)

const

References mpfr::sum().

double Molecule::Qnxy

(

)

const

References mpfr::sum().

double Molecule::Qnxz

(

)

const

References mpfr::sum().

double Molecule::Qnyy

(

)

const

References mpfr::sum().

double Molecule::Qnyz

(

)

const

References mpfr::sum().

double Molecule::Qnzz

(

)

const

References mpfr::sum().

void Molecule::read_core_file

(

const std::string &

filename

)

void Molecule::read_core_file

(

const std::string &

filename

)

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

void Molecule::read_file

(

const std::string &

filename

)

void Molecule::read_file

(

const std::string &

filename

)

Referenced by Molecule().

void Molecule::read_file	(	const std::string &	filename,
		const std::string &	geomname
	)

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

template<typename Archive >

void Molecule::serialize ( Archive &  ar )

inline

template<typename Archive >

void Molecule::serialize ( Archive &  ar )

inline

References atomic_radii.

void Molecule::set_all_coords

(

const madness::Tensor< double > &

newcoords

)

void Molecule::set_all_coords

(

const madness::Tensor< double > &

newcoords

)

References c, and natom().

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

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

void Molecule::set_core_eprec ( double  value )

inline

References CorePotentialManager::set_eprec().

void Molecule::set_core_eprec ( double  value )

inline

References CorePotentialManager::set_eprec().

void Molecule::set_core_rcut ( double  value )

inline

References CorePotentialManager::set_rcut().

void Molecule::set_core_rcut ( double  value )

inline

References CorePotentialManager::set_rcut().

void Molecule::set_eprec

(

double

value

)

void Molecule::set_eprec

(

double

value

)

updates rcuts with given eprec

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

void Molecule::set_rcut

(

double

value

)

void Molecule::set_rcut

(

double

value

)

double Molecule::smallest_length_scale

(

)

const

double Molecule::smallest_length_scale

(

)

const

References max.

Referenced by SCFParameters::set_molecular_info().

double Molecule::total_nuclear_charge

(

)

const

References mpfr::sum().

Referenced by SCFParameters::set_molecular_info().

double Molecule::total_nuclear_charge

(

)

const

Member Data Documentation

std::vector<double> Molecule::atomic_radii

Referenced by serialize().

---

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

• DFcode/molecule.h
• DFcode/molecule.cc