MolecularEntity Class Reference

#include <mentity.h>

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

Private Attributes
std::vector< Atom >	atoms
std::vector< double >	rcut
std::vector< double >	rsqasymptotic

Constructor & Destructor Documentation

MolecularEntity() [1/2]

MolecularEntity::MolecularEntity ( )

inline

Makes a MolecularEntity with zero atoms.

MolecularEntity() [2/2]

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!

References madness::filename, and read_file().

Member Function Documentation

add_atom()

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

References atoms, c, e(), q(), rcut, rsqasymptotic, and smoothing_parameter().

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

bounding_cube()

double MolecularEntity::bounding_cube

(

)

const

Returns the half width of the bounding cube.

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

References atoms, and L.

center()

void MolecularEntity::center

(

)

Moves the center of nuclear charge to the origin.

References atoms.

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().

get_atom()

const Atom & MolecularEntity::get_atom

(

unsigned int

i

)

const

References atoms.

Referenced by EwaldNuclearPotentialFunctor::EwaldNuclearPotentialFunctor(), AtomicBasisSet::atoms_to_bfn(), AtomicBasisSet::basisfn_to_atom(), compute_madelung_energy(), compute_madelung_energy_PWSCF(), EwaldNuclearPotentialFunctor::do_G_sum_v2(), EwaldNuclearPotentialFunctor::do_R_sum_v1(), 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(), MolecularNuclearPotentialFunctor2::operator()(), AtomicBasisSet::print(), AtomicBasisSet::print_anal(), and test_nuclear_potential_big_unit_cell().

inter_atomic_distance()

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

References atoms, and distance().

Referenced by nuclear_repulsion_energy().

natom()

int MolecularEntity::natom ( ) const

inline

References atoms.

Referenced by EwaldNuclearPotentialFunctor::EwaldNuclearPotentialFunctor(), AtomicBasisSet::atoms_to_bfn(), AtomicBasisSet::basisfn_to_atom(), compute_madelung_energy(), compute_madelung_energy_PWSCF(), EwaldNuclearPotentialFunctor::do_G_sum_v1(), EwaldNuclearPotentialFunctor::do_G_sum_v2(), EwaldNuclearPotentialFunctor::do_R_sum_v1(), 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(), MolecularNuclearPotentialFunctor2::operator()(), print(), AtomicBasisSet::print(), AtomicBasisSet::print_anal(), and read_file().

nuclear_attraction_potential()

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

References atoms, distance(), rcut, smoothed_potential(), and sum.

Referenced by MolecularPotentialFunctor::operator()().

nuclear_charge_density()

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

References atoms, rcut, rsqasymptotic, and smoothed_density().

Referenced by MolecularNuclearChargeDensityFunctor::operator()().

nuclear_repulsion_energy()

double MolecularEntity::nuclear_repulsion_energy

(

)

const

References atoms, inter_atomic_distance(), and sum.

print()

void MolecularEntity::print

(

)

const

References atomic_data, atoms, natom(), and q().

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

read_file()

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

References add_atom(), madness::constants::atomic_unit_of_length, atoms, e(), f, madness::filename, madness::FunctionDefaults< NDIM >::get_cell_width(), MADNESS_ASSERT, natom(), madness::position_stream(), rcut, rsqasymptotic, madness::scale(), and symbol_to_atomic_number().

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

serialize()

template<typename Archive >

void MolecularEntity::serialize ( Archive &  ar )

inline

References atoms, rcut, and rsqasymptotic.

set_atom_coords()

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

References atoms.

smallest_length_scale()

double MolecularEntity::smallest_length_scale

(

)

const

References atoms, and rcut.

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

total_nuclear_charge()

double MolecularEntity::total_nuclear_charge

(

)

const

References atoms, and sum.

Referenced by MolecularNuclearChargeDensityFunctor::MolecularNuclearChargeDensityFunctor(), compute_madelung_energy(), compute_madelung_energy_PWSCF(), EwaldNuclearPotentialFunctor::do_G_sum_v1(), EwaldNuclearPotentialFunctor::do_G_sum_v2(), madness::Solver< T, NDIM >::init(), and test_nuclear_potential().

Member Data Documentation

atoms

std::vector<Atom> MolecularEntity::atoms

private

Referenced by add_atom(), bounding_cube(), center(), get_atom(), inter_atomic_distance(), natom(), nuclear_attraction_potential(), nuclear_charge_density(), nuclear_repulsion_energy(), print(), read_file(), serialize(), set_atom_coords(), smallest_length_scale(), and total_nuclear_charge().

rcut

std::vector<double> MolecularEntity::rcut

private

Referenced by add_atom(), nuclear_attraction_potential(), nuclear_charge_density(), read_file(), serialize(), and smallest_length_scale().

rsqasymptotic

std::vector<double> MolecularEntity::rsqasymptotic

private

Referenced by add_atom(), nuclear_charge_density(), read_file(), and serialize().

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

• mentity.h
• mentity.cc