#include <molecule.h>

Collaboration diagram for madness::Molecule:

[legend]

Classes
struct	apply_c2
struct	apply_inverse
struct	apply_sigma
struct	GeometryParameters

Public Member Functions
	Molecule ()
	Makes a molecule with zero atoms.
	Molecule (std::vector< Atom > atoms, double eprec, CorePotentialManager core_pot={}, madness::Tensor< double > field=madness::Tensor< double >(3L))
	makes a molecule from a list of atoms
	Molecule (World &world, const commandlineparser &parser)
	makes a molecule using contents of `parser`
void	add_atom (double x, double y, double z, double q, int atn)
void	add_atom (double x, double y, double z, double q, int atn, bool psat)
double	atomic_attraction_potential (int iatom, double x, double y, double z) const
	nuclear attraction potential for a specific atom in the molecule
double	bounding_cube () const
	Returns the half width of the bounding cube.
void	center ()
	Moves the center of nuclear charge to the origin.
Tensor< double >	center_of_mass () const
	compute the center of mass
double	core_derivative (int atom, int axis, unsigned int core, int m, double x, double y, double z) const
double	core_eval (int atom, unsigned int core, int m, double x, double y, double z) const
double	core_potential_derivative (int atom, int axis, double x, double y, double z) const
std::vector< std::string >	cubefile_header (const Vector< double, 3 > offset=Vector< double, 3 >(0.0)) const
	print out a Gaussian cubefile header
void	fix_phase ()
	rotates the molecule and the external field
void	from_json (const json &mol_json)
madness::Tensor< double >	get_all_coords () const
std::vector< madness::Vector< double, 3 > >	get_all_coords_vec () const
const Atom &	get_atom (unsigned int i) const
unsigned int	get_atom_charge (unsigned int i) const
unsigned int	get_atomic_number (unsigned int i) const
const std::vector< Atom > &	get_atoms () const
double	get_core_bc (unsigned int atn, unsigned int c) const
unsigned int	get_core_l (unsigned int atn, unsigned int c) const
double	get_eprec () const
std::string	get_pointgroup () const
bool	get_pseudo_atom (unsigned int i) const
std::vector< double >	get_rcut () const
void	get_structure ()
std::string	guess_file () const
hashT	hash () const
void	insert_symbols_and_geometry (json &mol_json) const
double	inter_atomic_distance (unsigned int i, unsigned int j) const
bool	is_potential_defined (unsigned int atn) const
bool	is_potential_defined_atom (int i) const
Tensor< double >	massweights () const
	compute the mass-weighting matrix for the hessian
double	molecular_core_potential (double x, double y, double z) const
Tensor< double >	moment_of_inertia () const
unsigned int	n_core_orb (unsigned int atn) const
unsigned int	n_core_orb_all () const
size_t	natom () const
double	nuclear_attraction_potential (double x, double y, double z) const
	nuclear attraction potential for the whole molecule
double	nuclear_attraction_potential_derivative (int atom, int axis, double x, double y, double z) const
double	nuclear_attraction_potential_second_derivative (int atom, int iaxis, int jaxis, double x, double y, double z) const
	the second derivative of the (smoothed) nuclear potential Z/r
double	nuclear_charge_density (double x, double y, double z, double rscale=1.) const
double	nuclear_dipole (int axis) const
	compute the dipole moment of the nuclei
Tensor< double >	nuclear_dipole_derivative (const int atom, const int axis) const
	compute the derivative of the nuclear dipole wrt a nuclear displacement
double	nuclear_repulsion_derivative (size_t iatom, int axis) const
double	nuclear_repulsion_energy () const
Tensor< double >	nuclear_repulsion_hessian () const
	return the hessian matrix of the second derivatives d^2/dxdy V
double	nuclear_repulsion_second_derivative (int iatom, int jatom, int iaxis, int jaxis) const
	compute the nuclear-nuclear contribution to the second derivatives
bool	operator== (const Molecule &other) const
void	orient (bool verbose=false)
	Centers and orients the molecule in a standard manner.
void	print (std::ostream &os=std::cout, const bool defined_only=false) const
	print all parameters and the molecular geometry
void	print_defined_only (std::ostream &os=std::cout) const
	print user-defined parameters and the molecular geometry
void	read (std::istream &f)
void	read_core_file (const std::string &filename)
void	read_file (const std::string &filename)
void	read_structure_from_library (const std::string &name)
void	read_xyz (const std::string filename)
void	rotate (const Tensor< double > &D)
template<typename Archive>
void	serialize (Archive &ar)
void	set_all_coords (const madness::Tensor< double > &newcoords)
void	set_atom_charge (unsigned int i, double zeff)
void	set_atom_coords (unsigned int i, double x, double y, double z)
void	set_core_eprec (double value)
void	set_core_rcut (double value)
void	set_pseudo_atom (unsigned int i, bool psat)
void	set_rcut (double value)
double	smallest_length_scale () const
std::string	symmetrize_and_identify_point_group (const double symtol)
json	to_json () const
json	to_json_if_precedence (std::string const &precedence) const
double	total_nuclear_charge () const
void	translate (const Tensor< double > &translation)
	translate the molecule
void	update_rcut_with_eprec (double value)
	updates rcuts with given eprec

Static Public Member Functions
static std::string	get_structure_library_path ()
static std::istream &	position_stream_in_library (std::ifstream &f, const std::string &name)
static void	print_parameters ()

Public Attributes
std::vector< double >	atomic_radii
GeometryParameters	parameters

Static Public Attributes
static constexpr char const *	tag = "molecule"

Private Member Functions
template<typename opT>
int	find_symmetry_equivalent_atom (int iatom, opT op, const double symtol) const
void	swapaxes (int ix, int iy)
template<typename opT>
void	symmetrize_for_op (opT op, const double symtol)
bool	test_for_c2 (double xaxis, double yaxis, double zaxis, const double symtol) const
bool	test_for_inverse (const double symtol) const
template<typename opT>
bool	test_for_op (opT op, const double symtol) const
bool	test_for_sigma (double xaxis, double yaxis, double zaxis, const double symtol) const

Private Attributes
std::vector< Atom >	atoms
CorePotentialManager	core_pot
madness::Tensor< double >	field
std::string	pointgroup_ = "c1"
std::vector< double >	rcut

Constructor & Destructor Documentation

◆ Molecule() [1/3]

madness::Molecule::Molecule ( )

inline

Makes a molecule with zero atoms.

References atoms, core_pot, field, and rcut.

Referenced by operator==().

◆ Molecule() [2/3]

madness::Molecule::Molecule	(	std::vector< Atom >	atoms,
		double	eprec,
		CorePotentialManager	core_pot = {},
		madness::Tensor< double >	field = madness::Tensor<double>(3L) )

makes a molecule from a list of atoms

References atomic_radii, atoms, core_pot, eprec, and field.

◆ Molecule() [3/3]

madness::Molecule::Molecule	(	World &	world,
		const commandlineparser &	parser )

makes a molecule using contents of parser

References atoms, madness::WorldGopInterface::broadcast_serializable(), core_pot, field, get_structure(), madness::World::gop, MADNESS_CHECK, parameters, madness::World::rank(), rcut, and read_core_file().

Member Function Documentation

◆ add_atom() [1/2]

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

References atomic_radii, madness::constants::atomic_unit_of_length, atoms, c, madness::AtomicData::covalent_radius, e(), madness::get_atomic_data(), get_eprec(), q(), rcut, and madness::smoothing_parameter().

Referenced by from_json(), main(), read(), and read_xyz().

◆ add_atom() [2/2]

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

References atomic_radii, madness::constants::atomic_unit_of_length, atoms, c, madness::AtomicData::covalent_radius, e(), madness::get_atomic_data(), get_eprec(), q(), rcut, and madness::smoothing_parameter().

◆ atomic_attraction_potential()

double madness::Molecule::atomic_attraction_potential	(	int	iatom,
		double	x,
		double	y,
		double	z ) const

nuclear attraction potential for a specific atom in the molecule

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

◆ bounding_cube()

double madness::Molecule::bounding_cube ( ) const

Returns the half width of the bounding cube.

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

References atoms, and L.

◆ center()

void madness::Molecule::center ( )

Moves the center of nuclear charge to the origin.

References atoms, and translate().

Referenced by orient().

◆ center_of_mass()

Tensor< double > madness::Molecule::center_of_mass ( ) const

compute the center of mass

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

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

◆ core_derivative()

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

References atoms, axis, core_pot, m, and xi.

◆ core_eval()

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

References atoms, core_pot, and m.

◆ core_potential_derivative()

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

References atoms, axis, core_pot, madness::distance(), natom(), and xi.

◆ cubefile_header()

std::vector< std::string > madness::Molecule::cubefile_header ( const Vector< double, 3 > offset = Vector<double, 3>(0.0) ) const

print out a Gaussian cubefile header

Parameters

[in] offset the offset to be subtracted from the coordinates

References get_atom(), madness::Atom::get_atomic_number(), madness::Atom::get_coords(), natom(), and offset.

◆ find_symmetry_equivalent_atom()

template<typename opT>

int madness::Molecule::find_symmetry_equivalent_atom	(	int	iatom,
		opT	op,
		const double	symtol ) const

private

References atoms, madness::distance(), and op().

Referenced by symmetrize_for_op(), and test_for_op().

◆ fix_phase()

void madness::Molecule::fix_phase ( )

rotates the molecule and the external field

References atoms, and e().

Referenced by orient().

◆ from_json()

void madness::Molecule::from_json ( const json & mol_json )

References add_atom(), madness::constants::atomic_unit_of_length, atoms, e(), orient(), parameters, q(), rcut, madness::scale(), and madness::symbol_to_atomic_number().

◆ get_all_coords()

madness::Tensor< double > madness::Molecule::get_all_coords ( ) const

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

Referenced by madness::DispersionCorrection::compute(), madness::DispersionCorrection::hessian(), main(), run_all_calculations(), test_gradient(), test_hessian(), test_read_restartaodata(), and test_read_restartdata().

◆ get_all_coords_vec()

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

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

◆ get_atom()

const Atom & madness::Molecule::get_atom ( unsigned int i ) const

References atoms.

Referenced by center_of_mass(), madness::compare_geometry(), cubefile_header(), get_all_coords(), get_all_coords_vec(), massweights(), madness::plan_restart(), madness::MolecularOptimizer::projector_external_dof(), projector_external_dof(), test_ethylene(), and test_XCOperator_matrix().

◆ get_atom_charge()

unsigned int madness::Molecule::get_atom_charge ( unsigned int i ) const

References atoms.

◆ get_atomic_number()

unsigned int madness::Molecule::get_atomic_number ( unsigned int i ) const

References atoms.

Referenced by madness::DispersionCorrection::atomic_numbers(), madness::compare_geometry(), and get_structure().

◆ get_atoms()

const std::vector< Atom > & madness::Molecule::get_atoms ( ) const

inline

References atoms.

Referenced by madness::Znemo::custom_guess().

◆ get_core_bc()

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

inline

References c, and core_pot.

◆ get_core_l()

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

inline

References c, and core_pot.

◆ get_eprec()

double madness::Molecule::get_eprec ( ) const

inline

References parameters.

Referenced by madness::poly4erfc::poly4erfc(), madness::Slater::Slater(), add_atom(), add_atom(), read_core_file(), and update_rcut_with_eprec().

◆ get_pointgroup()

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

inline

References pointgroup_.

◆ get_pseudo_atom()

bool madness::Molecule::get_pseudo_atom ( unsigned int i ) const

References atoms.

Referenced by get_structure().

◆ get_rcut()

std::vector< double > madness::Molecule::get_rcut ( ) const

inline

References rcut.

◆ get_structure()

void madness::Molecule::get_structure ( )

References get_atomic_number(), madness::get_charge_from_file(), get_pseudo_atom(), MADNESS_EXCEPTION, natom(), orient(), parameters, read(), read_core_file(), read_structure_from_library(), read_xyz(), set_atom_charge(), and set_pseudo_atom().

Referenced by Molecule().

◆ get_structure_library_path()

std::string madness::Molecule::get_structure_library_path ( )

static

Referenced by position_stream_in_library(), and madness::Molecule::GeometryParameters::set_derived_values().

◆ guess_file()

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

inline

References core_pot.

◆ hash()

hashT madness::Molecule::hash ( ) const

inline

References atoms, h(), madness::hash_combine(), madness::hash_range(), pointgroup_, and rcut.

◆ insert_symbols_and_geometry()

void madness::Molecule::insert_symbols_and_geometry ( json & mol_json ) const

References madness::constants::atomic_unit_of_length, atoms, e(), madness::get_atomic_data(), natom(), parameters, and madness::scale().

Referenced by to_json(), and to_json_if_precedence().

◆ inter_atomic_distance()

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

References atoms, and madness::distance().

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

◆ is_potential_defined()

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

inline

References core_pot.

◆ is_potential_defined_atom()

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

inline

References atoms, and core_pot.

◆ massweights()

Tensor< double > madness::Molecule::massweights ( ) const

inline

compute the mass-weighting matrix for the hessian

use as mass_weighted_hessian=inner(massweights,inner(hessian,massweights));

References get_atom(), and natom().

Referenced by madness::Nemo::compute_IR_intensities().

◆ molecular_core_potential()

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

References atoms, core_pot, madness::distance(), natom(), and madness::sum().

◆ moment_of_inertia()

Tensor< double > madness::Molecule::moment_of_inertia ( ) const

References atoms, madness::FunctionDefaults< NDIM >::k, I, and q().

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

◆ n_core_orb()

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

inline

References core_pot.

◆ n_core_orb_all()

unsigned int madness::Molecule::n_core_orb_all ( ) const

References atoms, core_pot, natom(), and madness::sum().

◆ natom()

size_t madness::Molecule::natom ( ) const

inline

References atoms.

Referenced by madness::DispersionCorrection::atomic_numbers(), center_of_mass(), madness::compare_geometry(), madness::DispersionCorrection::compute(), madness::Nemo::compute_IR_intensities(), core_potential_derivative(), cubefile_header(), get_all_coords(), get_all_coords_vec(), get_structure(), madness::DispersionCorrection::gradient(), madness::DispersionCorrection::hessian(), madness::Nemo::hessian(), insert_symbols_and_geometry(), madness::Nemo::make_incomplete_hessian(), madness::Nemo::make_incomplete_hessian_response_part(), massweights(), molecular_core_potential(), n_core_orb_all(), nuclear_repulsion_hessian(), madness::plan_restart(), print(), madness::MolecularOptimizer::projector_external_dof(), projector_external_dof(), read_core_file(), read_xyz(), set_all_coords(), madness::Nemo::solve_cphf(), test_gradient(), and test_XCOperator_matrix().

◆ nuclear_attraction_potential()

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

nuclear attraction potential for the whole molecule

References atoms, madness::distance(), field, rcut, madness::smoothed_potential(), and madness::sum().

◆ nuclear_attraction_potential_derivative()

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

References atoms, axis, madness::distance(), madness::dsmoothed_potential(), field, and rcut.

◆ nuclear_attraction_potential_second_derivative()

double madness::Molecule::nuclear_attraction_potential_second_derivative	(	int	atom,
		int	iaxis,
		int	jaxis,
		double	x,
		double	y,
		double	z ) const

the second derivative of the (smoothed) nuclear potential Z/r

$\‍[V(R,r_{el}) -V(r) =\frac{Z}{|R-r_{el}|} \approx Z u(r) \‍]$

with

$\‍[\frac{\partial^2 V}{\partial X_i\partial X_j} = Z \left(\frac{\partial^2 u(r)}{\partial r^2} \frac{\partial r}{\partial X_i} \frac{\partial r}{\partial X_j} + \frac{\partial u}{\partial r} \frac{\partial^2 r}{\partial X_i \partial X_j}\right) \‍]$

References atoms, madness::d2smoothed_potential(), madness::Vector< T, N >::normf(), rcut, madness::smoothed_potential(), and u().

◆ nuclear_charge_density()

double madness::Molecule::nuclear_charge_density	(	double	x,
		double	y,
		double	z,
		double	rscale = 1. ) const

evaluate the nuclear charge density at point {x,y,z} using the default MADNESS nuclear model. See smoothed_density() for the description of the default nuclear model.

Parameters

x,y,z	the point at which the nuclear charge density is evaluated
rscale	setting rscale>1 will make a nucleus larger by a factor of `rscale` (in other words, rcut is multiplied by the inverse of by this)

Returns: the nuclear charge density at point {x,y,z}

See also: smoothed_density()

References atoms, madness::distance_sq(), MADNESS_ASSERT, rcut, and madness::smoothed_density().

◆ nuclear_dipole()

double madness::Molecule::nuclear_dipole ( int axis ) const

compute the dipole moment of the nuclei

Parameters

[in] axis the axis (x, y, z)

References atoms, axis, core_pot, MADNESS_EXCEPTION, and madness::sum().

◆ nuclear_dipole_derivative()

Tensor< double > madness::Molecule::nuclear_dipole_derivative	(	const int	atom,
		const int	axis ) const

compute the derivative of the nuclear dipole wrt a nuclear displacement

Parameters

[in]	atom	the atom which will be displaced
[in]	axis	the axis where the atom will be displaced

Returns: a vector which all 3 components of the dipole derivative

References atoms, and axis.

Referenced by madness::Nemo::compute_IR_intensities().

◆ nuclear_repulsion_derivative()

double madness::Molecule::nuclear_repulsion_derivative	(	size_t	iatom,
		int	axis ) const

References atoms, axis, core_pot, inter_atomic_distance(), and madness::sum().

◆ nuclear_repulsion_energy()

double madness::Molecule::nuclear_repulsion_energy ( ) const

References atoms, core_pot, inter_atomic_distance(), and madness::sum().

◆ nuclear_repulsion_hessian()

Tensor< double > madness::Molecule::nuclear_repulsion_hessian ( ) const

return the hessian matrix of the second derivatives d^2/dxdy V

compute the nuclear-nuclear contribution to the molecular hessian

no factor 0.5 included

References natom(), and nuclear_repulsion_second_derivative().

Referenced by madness::Nemo::hessian(), and madness::Nemo::make_incomplete_hessian().

◆ nuclear_repulsion_second_derivative()

double madness::Molecule::nuclear_repulsion_second_derivative	(	int	iatom,
		int	jatom,
		int	iaxis,
		int	jaxis ) const

compute the nuclear-nuclear contribution to the second derivatives

Parameters

[in]	iatom	the i-th atom (row of the hessian)
[in]	jatom	the j-th atom (column of the hessian)
[in]	iaxis	the xyz axis of the i-th atom
[in]	jaxis	the xyz axis of the j-th atom return the (3iatom + iaxis, 3jatom + jaxis) matix element of the hessian
[in]	iatom	the i-th atom (row of the hessian)
[in]	jatom	the j-th atom (column of the hessian)
[in]	iaxis	the xyz axis of the i-th atom
[in]	jaxis	the xyz axis of the j-th atom return the (3iatom + iaxis, 3jatom + jaxis) matix element

References atoms, core_pot, inter_atomic_distance(), MADNESS_EXCEPTION, and madness::sum().

Referenced by nuclear_repulsion_hessian().

◆ operator==()

bool madness::Molecule::operator== ( const Molecule & other ) const

inline

References Molecule(), atoms, field, parameters, pointgroup_, and rcut.

◆ orient()

void madness::Molecule::orient ( bool verbose = false )

Centers and orients the molecule in a standard manner.

References atoms, center(), e(), fix_phase(), madness::FunctionDefaults< NDIM >::k, I, MADNESS_CHECK, parameters, pointgroup_, madness::print(), q(), rotate(), madness::syev(), and symmetrize_and_identify_point_group().

Referenced by from_json(), and get_structure().

◆ position_stream_in_library()

std::istream & madness::Molecule::position_stream_in_library	(	std::ifstream &	f,
		const std::string &	name )

static

References errmsg(), madness::f, get_structure_library_path(), MADNESS_CHECK_THROW, madness::name(), and madness::position_stream_to_word().

Referenced by read_structure_from_library(), and madness::Molecule::GeometryParameters::set_derived_values().

◆ print()

void madness::Molecule::print	(	std::ostream &	os = std::cout,
		const bool	defined_only = false ) const

print all parameters and the molecular geometry

References atoms, madness::get_atomic_data(), natom(), p(), parameters, and madness::AtomicData::symbol.

Referenced by madness::SCF::load_mos(), main(), print_defined_only(), and test_ethylene().

◆ print_defined_only()

void madness::Molecule::print_defined_only ( std::ostream & os = std::cout ) const

inline

print user-defined parameters and the molecular geometry

References print().

◆ print_parameters()

void madness::Molecule::print_parameters ( )

static

References param, and madness::print().

Referenced by madness::CC2::print_parameters(), madness::MP2::print_parameters(), madness::Nemo::print_parameters(), madness::OEP::print_parameters(), madness::PNO::print_parameters(), madness::SCF::print_parameters(), madness::TDHF::print_parameters(), madness::Zcis::print_parameters(), and madness::Znemo::print_parameters().

◆ read()

void madness::Molecule::read ( std::istream & f )

References add_atom(), madness::constants::atomic_unit_of_length, atoms, madness::check_if_pseudo_atom(), e(), madness::f, p(), parameters, madness::position_stream_at_coordinates(), rcut, madness::scale(), madness::symbol_to_atomic_number(), tag, and update_rcut_with_eprec().

Referenced by get_structure(), read_file(), and read_structure_from_library().

◆ read_core_file()

void madness::Molecule::read_core_file ( const std::string & filename )

References atoms, core_pot, madness::filename, get_eprec(), natom(), madness::print(), q(), rcut, and madness::smoothing_parameter().

Referenced by Molecule(), and get_structure().

◆ read_file()

void madness::Molecule::read_file ( const std::string & filename )

References errmsg(), madness::f, madness::filename, MADNESS_EXCEPTION, and read().

◆ read_structure_from_library()

void madness::Molecule::read_structure_from_library ( const std::string & name )

References errmsg(), madness::f, MADNESS_EXCEPTION, madness::name(), position_stream_in_library(), and read().

Referenced by get_structure().

◆ read_xyz()

void madness::Molecule::read_xyz ( const std::string filename )

References add_atom(), madness::constants::atomic_unit_of_length, atoms, madness::check_if_pseudo_atom(), e(), errmsg(), madness::f, madness::filename, MADNESS_CHECK, MADNESS_EXCEPTION, natom(), parameters, rcut, madness::scale(), madness::symbol_to_atomic_number(), tag, and update_rcut_with_eprec().

Referenced by get_structure().

◆ rotate()

void madness::Molecule::rotate ( const Tensor< double > & D )

Parameters

[in] D the rotation matrix

References atoms, field, and madness::inner().

Referenced by orient().

◆ serialize()

template<typename Archive>

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

inline

References atoms, core_pot, field, parameters, pointgroup_, and rcut.

◆ set_all_coords()

void madness::Molecule::set_all_coords ( const madness::Tensor< double > & newcoords )

References atoms, c, MADNESS_ASSERT, and natom().

Referenced by test_gradient().

◆ set_atom_charge()

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

References atoms.

Referenced by get_structure().

◆ set_atom_coords()

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

References atoms.

◆ set_core_eprec()

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

inline

References core_pot, and madness::Future< void >::value.

◆ set_core_rcut()

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

inline

References core_pot, and madness::Future< void >::value.

◆ set_pseudo_atom()

void madness::Molecule::set_pseudo_atom	(	unsigned int	i,
		bool	psat )

References atoms.

Referenced by get_structure().

◆ set_rcut()

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

References atoms, madness::Future< void >::value, and rcut.

◆ smallest_length_scale()

double madness::Molecule::smallest_length_scale ( ) const

References atoms, and rcut.

◆ swapaxes()

void madness::Molecule::swapaxes	(	int	ix,
		int	iy )

private

References atoms, and field.

Referenced by symmetrize_and_identify_point_group().

◆ symmetrize_and_identify_point_group()

std::string madness::Molecule::symmetrize_and_identify_point_group ( const double symtol )

References madness::inverse(), madness::print(), swapaxes(), symmetrize_for_op(), test_for_c2(), test_for_inverse(), and test_for_sigma().

Referenced by orient().

◆ symmetrize_for_op()

template<typename opT>

void madness::Molecule::symmetrize_for_op	(	opT	op,
		const double	symtol )

private

References atoms, madness::distance(), find_symmetry_equivalent_atom(), MADNESS_CHECK, op(), and test_for_op().

Referenced by symmetrize_and_identify_point_group().

◆ test_for_c2()

bool madness::Molecule::test_for_c2	(	double	xaxis,
		double	yaxis,
		double	zaxis,
		const double	symtol ) const

private

References test_for_op().

Referenced by symmetrize_and_identify_point_group().

◆ test_for_inverse()

bool madness::Molecule::test_for_inverse ( const double symtol ) const

private

References test_for_op().

Referenced by symmetrize_and_identify_point_group().

◆ test_for_op()

template<typename opT>

bool madness::Molecule::test_for_op	(	opT	op,
		const double	symtol ) const

private

References atoms, find_symmetry_equivalent_atom(), and op().

Referenced by symmetrize_for_op(), test_for_c2(), test_for_inverse(), and test_for_sigma().

◆ test_for_sigma()

bool madness::Molecule::test_for_sigma	(	double	xaxis,
		double	yaxis,
		double	zaxis,
		const double	symtol ) const

private

References test_for_op().

Referenced by symmetrize_and_identify_point_group().

◆ to_json()

nlohmann::json madness::Molecule::to_json ( ) const

nodiscard

References insert_symbols_and_geometry(), and parameters.

Referenced by madness::MolecularEnergy::output_calc_info_schema(), and to_json_if_precedence().

◆ to_json_if_precedence()

json madness::Molecule::to_json_if_precedence ( std::string const & precedence ) const

inlinenodiscard

References insert_symbols_and_geometry(), parameters, and to_json().

◆ total_nuclear_charge()

double madness::Molecule::total_nuclear_charge ( ) const

References atoms, and madness::sum().

◆ translate()

void madness::Molecule::translate ( const Tensor< double > & translation )

translate the molecule

References atoms.

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

◆ update_rcut_with_eprec()

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

updates rcuts with given eprec

References atoms, core_pot, madness::Future< void >::value, get_eprec(), parameters, rcut, and madness::smoothing_parameter().

Referenced by dnuclear_anchor_test(), read(), and read_xyz().

Member Data Documentation

◆ atomic_radii

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

Referenced by Molecule(), add_atom(), and add_atom().

◆ atoms

std::vector<Atom> madness::Molecule::atoms

private

Referenced by Molecule(), Molecule(), Molecule(), add_atom(), add_atom(), atomic_attraction_potential(), bounding_cube(), center(), core_derivative(), core_eval(), core_potential_derivative(), find_symmetry_equivalent_atom(), fix_phase(), from_json(), get_atom(), get_atom_charge(), get_atomic_number(), get_atoms(), get_pseudo_atom(), hash(), insert_symbols_and_geometry(), inter_atomic_distance(), is_potential_defined_atom(), molecular_core_potential(), moment_of_inertia(), n_core_orb_all(), natom(), nuclear_attraction_potential(), nuclear_attraction_potential_derivative(), nuclear_attraction_potential_second_derivative(), nuclear_charge_density(), nuclear_dipole(), nuclear_dipole_derivative(), nuclear_repulsion_derivative(), nuclear_repulsion_energy(), nuclear_repulsion_second_derivative(), operator==(), orient(), print(), read(), read_core_file(), read_xyz(), rotate(), serialize(), set_all_coords(), set_atom_charge(), set_atom_coords(), set_pseudo_atom(), set_rcut(), smallest_length_scale(), swapaxes(), symmetrize_for_op(), test_for_op(), total_nuclear_charge(), translate(), and update_rcut_with_eprec().

◆ core_pot

CorePotentialManager madness::Molecule::core_pot

private

◆ field

madness::Tensor<double> madness::Molecule::field

private

Referenced by Molecule(), Molecule(), Molecule(), nuclear_attraction_potential(), nuclear_attraction_potential_derivative(), operator==(), rotate(), serialize(), and swapaxes().

◆ parameters

GeometryParameters madness::Molecule::parameters

Referenced by Molecule(), from_json(), get_eprec(), get_structure(), insert_symbols_and_geometry(), madness::make_restart_plan(), operator==(), orient(), print(), read(), read_xyz(), serialize(), to_json(), to_json_if_precedence(), and update_rcut_with_eprec().

◆ pointgroup_

std::string madness::Molecule::pointgroup_ = "c1"

private

The molecular point group is automatically assigned in the identify_pointgroup function

Referenced by get_pointgroup(), hash(), operator==(), orient(), and serialize().

◆ rcut

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

private

◆ tag

char const* madness::Molecule::tag = "molecule"

staticconstexpr

Referenced by madness::Molecule::GeometryParameters::GeometryParameters(), madness::Molecule::GeometryParameters::input_tag(), read(), and read_xyz().

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

Classes

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ Molecule() [1/3]

◆ Molecule() [2/3]

◆ Molecule() [3/3]

Member Function Documentation

◆ add_atom() [1/2]

◆ add_atom() [2/2]

◆ atomic_attraction_potential()

◆ bounding_cube()

◆ center()

◆ center_of_mass()

◆ core_derivative()

◆ core_eval()

◆ core_potential_derivative()

◆ cubefile_header()

◆ find_symmetry_equivalent_atom()

◆ fix_phase()

◆ from_json()

◆ get_all_coords()

◆ get_all_coords_vec()

◆ get_atom()

◆ get_atom_charge()

◆ get_atomic_number()

◆ get_atoms()

◆ get_core_bc()

◆ get_core_l()

◆ get_eprec()

◆ get_pointgroup()

◆ get_pseudo_atom()

◆ get_rcut()

◆ get_structure()

◆ get_structure_library_path()

◆ guess_file()

◆ hash()

◆ insert_symbols_and_geometry()

◆ inter_atomic_distance()

◆ is_potential_defined()

◆ is_potential_defined_atom()

◆ massweights()

◆ molecular_core_potential()

◆ moment_of_inertia()

◆ n_core_orb()

◆ n_core_orb_all()

◆ natom()

◆ nuclear_attraction_potential()

◆ nuclear_attraction_potential_derivative()

◆ nuclear_attraction_potential_second_derivative()

◆ nuclear_charge_density()

◆ nuclear_dipole()

◆ nuclear_dipole_derivative()

◆ nuclear_repulsion_derivative()

◆ nuclear_repulsion_energy()

◆ nuclear_repulsion_hessian()

◆ nuclear_repulsion_second_derivative()

◆ operator==()

◆ orient()

◆ position_stream_in_library()

◆ print()

◆ print_defined_only()

◆ print_parameters()

◆ read()

◆ read_core_file()

◆ read_file()

◆ read_structure_from_library()

◆ read_xyz()

◆ rotate()

◆ serialize()

◆ set_all_coords()

◆ set_atom_charge()

◆ set_atom_coords()

◆ set_core_eprec()

◆ set_core_rcut()

◆ set_pseudo_atom()