MolecularEntity Class Reference

#include <mentity.h>

Public Member Functions
	MolecularEntity ()
	Makes a MolecularEntity with zero atoms. More...
	MolecularEntity (const std::string &filename, bool fractional)
	Read coordinates from a file. More...
void	read_file (const std::string &filename, bool fractional)
void	add_atom (double x, double y, double z, int atn, double q)
int	natom () const
void	set_atom_coords (unsigned int i, double x, double y, double z)
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	smallest_length_scale () const
void	center ()
	Moves the center of nuclear charge to the origin. More...
double	total_nuclear_charge () const
double	nuclear_attraction_potential (double x, double y, double z) const
double	nuclear_charge_density (double x, double y, double z) const
template<typename Archive >
void	serialize (Archive &ar)

Constructor & Destructor Documentation

MolecularEntity::MolecularEntity ( )

inline

Makes a MolecularEntity with zero atoms.

MolecularEntity::MolecularEntity	(	const std::string &	filename,
		bool	fractional = false
	)

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!

Member Function Documentation

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

References madness::smoothing_parameter().

Referenced by test_nuclear_energy(), test_nuclear_potential(), test_nuclear_potential2(), test_nuclear_potential3(), and test_nuclear_potential_big_unit_cell().

double MolecularEntity::bounding_cube

(

)

const

Returns the half width of the bounding cube.

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

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

void MolecularEntity::center

(

)

Moves the center of nuclear charge to the origin.

Referenced by madness::Solver< T, NDIM >::init(), test_nuclear_energy(), test_nuclear_potential(), test_nuclear_potential2(), test_nuclear_potential3(), and test_nuclear_potential_big_unit_cell().

const Atom & MolecularEntity::get_atom

(

unsigned int

i

)

const

Referenced by AtomicBasisSet::atoms_to_bfn(), AtomicBasisSet::basisfn_to_atom(), compute_madelung_energy(), compute_madelung_energy_PWSCF(), AtomicBasisSet::eval(), AtomicBasisSet::eval_guess_density(), AtomicBasisSet::get_atomic_basis_function(), make_nuclear_charge_density(), madness::Solver< T, NDIM >::make_nuclear_charge_density_impl(), make_nuclear_charge_density_individual(), AtomicBasisSet::nbf(), AtomicBasisSet::print(), AtomicBasisSet::print_anal(), and test_nuclear_potential_big_unit_cell().

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

References distance().

int MolecularEntity::natom ( ) const

inline

Referenced by AtomicBasisSet::atoms_to_bfn(), AtomicBasisSet::basisfn_to_atom(), compute_madelung_energy(), compute_madelung_energy_PWSCF(), AtomicBasisSet::eval(), AtomicBasisSet::eval_guess_density(), AtomicBasisSet::get_atomic_basis_function(), make_nuclear_charge_density(), madness::Solver< T, NDIM >::make_nuclear_charge_density_impl(), make_nuclear_charge_density_individual(), AtomicBasisSet::nbf(), AtomicBasisSet::print(), and AtomicBasisSet::print_anal().

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

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

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

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

Referenced by MolecularNuclearChargeDensityFunctor::operator()().

double MolecularEntity::nuclear_repulsion_energy

(

)

const

References mpfr::sum().

void MolecularEntity::print

(

)

const

Referenced by compute_madelung_energy_PWSCF(), test_nuclear_energy(), test_nuclear_potential2(), and test_nuclear_potential_big_unit_cell().

void MolecularEntity::read_file	(	const std::string &	filename,
		bool	fractional = false
	)

References madness::constants::atomic_unit_of_length, madness::f, madness::FunctionDefaults< NDIM >::get_cell_width(), madness::position_stream(), madness::scale(), and madness::symbol_to_atomic_number().

Referenced by madness::Solver< T, NDIM >::init().

template<typename Archive >

void MolecularEntity::serialize ( Archive &  ar )

inline

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

double MolecularEntity::smallest_length_scale

(

)

const

References max.

Referenced by MolecularNuclearChargeDensityFunctor::operator()(), and madness::ElectronicStructureParams::set_molecular_info().

double MolecularEntity::total_nuclear_charge

(

)

const

References mpfr::sum().

Referenced by compute_madelung_energy(), compute_madelung_energy_PWSCF(), madness::Solver< T, NDIM >::init(), MolecularNuclearChargeDensityFunctor::MolecularNuclearChargeDensityFunctor(), and test_nuclear_potential().

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

• mentity.h
• mentity.cc