MADNESS: madness::Atom Class Reference

MADNESS 0.10.1

#include <molecule.h>

Public Member Functions
	Atom ()
	Default construct makes a zero charge ghost atom at origin. More...

	Atom (const Atom &a)

	Atom (double x, double y, double z, double q, unsigned int atomic_number)

	Atom (double x, double y, double z, double q, unsigned int atomic_number, bool pseudo_atom)

int	get_atomic_number () const

madness::Vector< double, 3 >	get_coords () const

double	get_mass_in_au () const
	return the mass in atomic units (electron mass = 1 a.u.) More...

hashT	hash () const

template<typename Archive >
void	serialize (Archive &ar)

Public Attributes
unsigned int	atomic_number
	Atomic number. More...

double	mass
	Mass. More...

bool	pseudo_atom
	Indicates if this atom uses a pseudopotential. More...

double	q
	Coordinates and charge in atomic units. More...

double	x

double	y

double	z

Constructor & Destructor Documentation

◆ Atom() [1/4]

madness::Atom::Atom	(	double	x,
		double	y,
		double	z,
		double	q,
		unsigned int	atomic_number,
		bool	pseudo_atom
	)

inlineexplicit

References atomic_number, madness::get_atomic_data(), MADNESS_EXCEPTION, madness::AtomicData::mass, and mass.

◆ Atom() [2/4]

madness::Atom::Atom	(	double	x,
		double	y,
		double	z,
		double	q,
		unsigned int	atomic_number
	)

inlineexplicit

References atomic_number, madness::get_atomic_data(), MADNESS_EXCEPTION, madness::AtomicData::mass, mass, and pseudo_atom.

◆ Atom() [3/4]

madness::Atom::Atom ( const Atom & a )

inline

◆ Atom() [4/4]

madness::Atom::Atom ( )

inline

Default construct makes a zero charge ghost atom at origin.

Member Function Documentation

◆ get_atomic_number()

int madness::Atom::get_atomic_number ( ) const

inline

References atomic_number.

Referenced by madness::Molecule::cubefile_header().

◆ get_coords()

madness::Vector<double,3> madness::Atom::get_coords ( ) const

inline

References x, y, and z.

Referenced by madness::GTHPseudopotential< Q >::apply_potential(), madness::GTHPseudopotential< Q >::apply_potential_simple(), madness::Molecule::cubefile_header(), madness::GTHPseudopotential< Q >::make_pseudo_potential(), madness::NuclearCorrelationFactor::R_functor::operator()(), madness::NuclearCorrelationFactor::U1_functor::operator()(), madness::NuclearCorrelationFactor::U1_atomic_functor::operator()(), madness::NuclearCorrelationFactor::U1_dot_U1_functor::operator()(), madness::NuclearCorrelationFactor::U2_functor::operator()(), madness::NuclearCorrelationFactor::U3_functor::operator()(), madness::NuclearCorrelationFactor::U2_atomic_functor::operator()(), madness::NuclearCorrelationFactor::U3_atomic_functor::operator()(), madness::NuclearCorrelationFactor::square_times_V_functor::operator()(), madness::NuclearCorrelationFactor::square_times_V_derivative_functor::operator()(), madness::NuclearCorrelationFactor::RX_functor::operator()(), madness::NuclearCorrelationFactor::U1X_functor::operator()(), madness::NuclearCorrelationFactor::U2X_functor::operator()(), madness::NuclearCorrelationFactor::U3X_functor::operator()(), madchem::AtomicAttractionFunctor::special_points(), madchem::MolecularDerivativeFunctor::special_points(), madchem::MolecularSecondDerivativeFunctor::special_points(), and test_ethylene().

◆ get_mass_in_au()

double madness::Atom::get_mass_in_au ( ) const

inline

return the mass in atomic units (electron mass = 1 a.u.)

References madness::constants::atomic_mass_in_au, and mass.

Referenced by projector_external_dof(), and madness::MolecularOptimizer::projector_external_dof().

◆ hash()

hashT madness::Atom::hash ( ) const

inline

References atomic_number, h(), madness::hash_combine(), madness::hash_value(), mass, pseudo_atom, q, x, y, and z.

◆ serialize()

template<typename Archive >

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

inline

References atomic_number, mass, pseudo_atom, q, x, y, and z.

Member Data Documentation

◆ atomic_number

unsigned int madness::Atom::atomic_number

Atomic number.

Referenced by Atom(), madness::GTHPseudopotential< Q >::apply_potential(), madness::GTHPseudopotential< Q >::apply_potential_simple(), madness::AtomicBasisSet::atoms_to_bfn(), madness::AtomicBasisSet::basisfn_to_atom(), madness::PotentialManager::core_projection(), madness::PotentialManager::core_projector_derivative(), madness::AtomicBasisSet::eval(), madness::AtomicBasisSet::eval_guess_density(), madness::AtomicBasisSet::get_aeps(), madness::AtomicBasisSet::get_atomic_basis_function(), get_atomic_number(), madness::AtomicBasisSet::get_avec(), madness::Nemo::gradient(), madness::BasisFunctions::guess_virtuals_internal(), hash(), madness::SCF::initial_guess(), madness::GTHPseudopotential< Q >::load_pseudo_from_file(), madness::GTHPseudopotential< Q >::make_pseudo_potential(), madness::AtomicBasisSet::nbf(), operator<<(), madness::operator<<(), madness::AtomicBasisSet::print(), madness::AtomicBasisSet::print_anal(), serialize(), and madness::AtomicBasisSet::shells_to_bfn().

◆ mass

double madness::Atom::mass

Mass.

Referenced by Atom(), madness::Molecule::center_of_mass(), get_mass_in_au(), hash(), and serialize().

◆ pseudo_atom

bool madness::Atom::pseudo_atom

Indicates if this atom uses a pseudopotential.

Referenced by Atom(), madness::AtomicBasisSet::eval_guess_density(), hash(), madness::GTHPseudopotential< Q >::make_pseudo_potential(), and serialize().

◆ q

double madness::Atom::q

Coordinates and charge in atomic units.

Referenced by EwaldNuclearPotentialFunctor::EwaldNuclearPotentialFunctor(), madness::NuclearCorrelationFactor::U1X_functor::U1X_functor(), madness::NuclearCorrelationFactor::U2X_functor::U2X_functor(), compute_madelung_energy(), compute_madelung_energy_PWSCF(), EwaldNuclearPotentialFunctor::do_G_sum_v2(), EwaldNuclearPotentialFunctor::do_R_sum_v1(), hash(), madness::NuclearCorrelationFactor::R_functor::operator()(), madness::NuclearCorrelationFactor::U1_functor::operator()(), madness::NuclearCorrelationFactor::U1_atomic_functor::operator()(), madness::NuclearCorrelationFactor::U1_dot_U1_functor::operator()(), madness::NuclearCorrelationFactor::U2_functor::operator()(), madness::NuclearCorrelationFactor::U3_functor::operator()(), madness::NuclearCorrelationFactor::U2_atomic_functor::operator()(), madness::NuclearCorrelationFactor::U3_atomic_functor::operator()(), madness::NuclearCorrelationFactor::square_times_V_functor::operator()(), madness::NuclearCorrelationFactor::square_times_V_derivative_functor::operator()(), madness::NuclearCorrelationFactor::RX_functor::operator()(), madness::NuclearCorrelationFactor::U1X_functor::operator()(), madness::NuclearCorrelationFactor::U2X_functor::operator()(), madness::NuclearCorrelationFactor::U3X_functor::operator()(), MolecularNuclearPotentialFunctor2::operator()(), madchem::AtomicAttractionFunctor::operator()(), operator<<(), madness::operator<<(), serialize(), and test_nuclear_potential_big_unit_cell().

◆ x

double madness::Atom::x

Referenced by EwaldNuclearPotentialFunctor::EwaldNuclearPotentialFunctor(), madness::Molecule::center_of_mass(), compute_madelung_energy(), compute_madelung_energy_PWSCF(), madness::SCF::derivatives(), EwaldNuclearPotentialFunctor::do_G_sum_v2(), EwaldNuclearPotentialFunctor::do_R_sum_v1(), madness::AtomicBasisSet::eval(), madness::AtomicBasisSet::eval_guess_density(), madness::Molecule::get_all_coords(), madness::Molecule::get_all_coords_vec(), madness::AtomicBasisSet::get_atomic_basis_function(), get_coords(), madness::Nemo::gradient(), madness::Znemo::gradient(), hash(), madness::SCF::initial_guess(), make_nuclear_charge_density(), madness::Solver< T, NDIM >::make_nuclear_charge_density_impl(), make_nuclear_charge_density_individual(), MolecularNuclearPotentialFunctor2::operator()(), madchem::AtomicAttractionFunctor::operator()(), operator<<(), madness::operator<<(), projector_external_dof(), madness::MolecularOptimizer::projector_external_dof(), serialize(), madness::NuclearCorrelationFactor::U1_atomic_functor::special_points(), madness::NuclearCorrelationFactor::U2_atomic_functor::special_points(), madness::NuclearCorrelationFactor::U3_atomic_functor::special_points(), madness::NuclearCorrelationFactor::U1X_functor::special_points(), madness::NuclearCorrelationFactor::U2X_functor::special_points(), and test_nuclear_potential_big_unit_cell().

◆ y

double madness::Atom::y

Referenced by EwaldNuclearPotentialFunctor::EwaldNuclearPotentialFunctor(), madness::Molecule::center_of_mass(), compute_madelung_energy(), compute_madelung_energy_PWSCF(), madness::SCF::derivatives(), EwaldNuclearPotentialFunctor::do_G_sum_v2(), EwaldNuclearPotentialFunctor::do_R_sum_v1(), madness::AtomicBasisSet::eval(), madness::AtomicBasisSet::eval_guess_density(), madness::Molecule::get_all_coords(), madness::Molecule::get_all_coords_vec(), madness::AtomicBasisSet::get_atomic_basis_function(), get_coords(), madness::Nemo::gradient(), madness::Znemo::gradient(), hash(), madness::SCF::initial_guess(), make_nuclear_charge_density(), madness::Solver< T, NDIM >::make_nuclear_charge_density_impl(), make_nuclear_charge_density_individual(), MolecularNuclearPotentialFunctor2::operator()(), madchem::AtomicAttractionFunctor::operator()(), operator<<(), madness::operator<<(), projector_external_dof(), madness::MolecularOptimizer::projector_external_dof(), serialize(), madness::NuclearCorrelationFactor::U1_atomic_functor::special_points(), madness::NuclearCorrelationFactor::U2_atomic_functor::special_points(), madness::NuclearCorrelationFactor::U3_atomic_functor::special_points(), madness::NuclearCorrelationFactor::U1X_functor::special_points(), madness::NuclearCorrelationFactor::U2X_functor::special_points(), and test_nuclear_potential_big_unit_cell().

◆ z

double madness::Atom::z

Referenced by EwaldNuclearPotentialFunctor::EwaldNuclearPotentialFunctor(), madness::Molecule::center_of_mass(), compute_madelung_energy(), compute_madelung_energy_PWSCF(), madness::SCF::derivatives(), EwaldNuclearPotentialFunctor::do_G_sum_v2(), EwaldNuclearPotentialFunctor::do_R_sum_v1(), madness::AtomicBasisSet::eval(), madness::AtomicBasisSet::eval_guess_density(), madness::Molecule::get_all_coords(), madness::Molecule::get_all_coords_vec(), madness::AtomicBasisSet::get_atomic_basis_function(), get_coords(), madness::Nemo::gradient(), madness::Znemo::gradient(), hash(), madness::SCF::initial_guess(), make_nuclear_charge_density(), madness::Solver< T, NDIM >::make_nuclear_charge_density_impl(), make_nuclear_charge_density_individual(), MolecularNuclearPotentialFunctor2::operator()(), madchem::AtomicAttractionFunctor::operator()(), operator<<(), madness::operator<<(), projector_external_dof(), madness::MolecularOptimizer::projector_external_dof(), serialize(), madness::NuclearCorrelationFactor::U1_atomic_functor::special_points(), madness::NuclearCorrelationFactor::U2_atomic_functor::special_points(), madness::NuclearCorrelationFactor::U3_atomic_functor::special_points(), madness::NuclearCorrelationFactor::U1X_functor::special_points(), madness::NuclearCorrelationFactor::U2X_functor::special_points(), and test_nuclear_potential_big_unit_cell().

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

molecule.h