GQCP::Molecule Class Reference

#include <Molecule.hpp>

Collaboration diagram for GQCP::Molecule:

Public Member Functions
	Molecule (const NuclearFramework &nuclear_framework, const int charge=0)
	Molecule (const std::vector< Nucleus > &nuclei, const int charge=0)
double	calculateInternuclearDistanceBetween (const size_t index1, const size_t index2) const
int	charge () const
std::string	description () const
const NuclearFramework &	nuclearFramework () const
size_t	numberOfAtoms () const
size_t	numberOfElectronPairs () const
size_t	numberOfElectrons () const
size_t	totalNucleicCharge () const

Static Public Member Functions
static Molecule	HChain (const size_t n, const double spacing, const int charge=0, const CartesianDirection axis=CartesianDirection::z)
static Molecule	H2Chain (const size_t n, const double a, const double b, const int charge=0, const CartesianDirection axis=CartesianDirection::z)
static Molecule	HRingFromDistance (const size_t n, const double distance, const int charge=0)
static Molecule	HRingFromRadius (const size_t n, const double radius, const int charge=0)
static Molecule	ReadXYZ (const std::string &xyz_filename, const int charge=0)

Friends
std::ostream &	operator<< (std::ostream &os, const Molecule &molecule)

Detailed Description

A molecule: a number of electrons and a collection of nuclei arranged in a nuclear framework.

Constructor & Destructor Documentation

Molecule() [1/2]

GQCP::Molecule::Molecule	(	const NuclearFramework &	nuclear_framework,
		const int	charge = 0
	)

Parameters

nuclear_framework	the nuclear framework that makes up the molecule, with coordinates in bohr
charge	the charge of the molecule: +1 -> cation (one electron less than the neutral molecule) 0 -> neutral molecule -1 -> anion (one electron more than the neutral molecule)

Molecule() [2/2]

GQCP::Molecule::Molecule	(	const std::vector< Nucleus > &	nuclei,
		const int	charge = 0
	)

Parameters

nuclei	the nuclei that make up the molecule, with coordinates in bohr
charge	the charge of the molecule: +1 -> cation (one electron less than the neutral molecule) 0 -> neutral molecule -1 -> anion (one electron more than the neutral molecule)

Member Function Documentation

calculateInternuclearDistanceBetween()

double GQCP::Molecule::calculateInternuclearDistanceBetween ( const size_t  index1, const size_t  index2  ) const

inline

Parameters

index1	the index of the first nucleus
index2	the index of the second nucleus

Returns

the distance between the two nuclei at index1 and index2 in bohr

charge()

int GQCP::Molecule::charge

(

)

const

Returns

the charge of this molecule (in a.u.)

description()

std::string GQCP::Molecule::description ( ) const

inline

Returns

a textual description of this molecule.

H2Chain()

Molecule GQCP::Molecule::H2Chain ( const size_t  n, const double  a, const double  b, const int  charge = 0, const CartesianDirection  axis = CartesianDirection::z  )

static

Parameters

n	the number of H2-molecules
a	the internuclear distance in bohr
b	the intermolecular distance in bohr
charge	the total charge

Returns

a charged H2-chain

HChain()

Molecule GQCP::Molecule::HChain ( const size_t  n, const double  spacing, const int  charge = 0, const CartesianDirection  axis = CartesianDirection::z  )

static

Parameters

n	the number of H nuclei
spacing	the internuclear spacing in bohr
charge	the total charge

Returns

a H-chain with equal internuclear spacing

Parameters

n	the number of H nuclei
spacing	the internuclear spacing in bohr
charge	the total charge

Returns

a charged H-chain with equal internuclear spacing

HRingFromDistance()

Molecule GQCP::Molecule::HRingFromDistance ( const size_t  n, const double  distance, const int  charge = 0  )

static

Parameters

n	the number of hydrogens
distance	the distance (in bohr) between neighbouring hydrogen atoms

Returns

a regular H-ring where neighbouring hydrogens are separated by the given distance

HRingFromRadius()

Molecule GQCP::Molecule::HRingFromRadius ( const size_t  n, const double  radius, const int  charge = 0  )

static

Parameters

n	the number of hydrogens
radius	the radius (in bohr) of the circumscribed circle

Returns

a regular H-ring whose hydrogens are on the circle with the given radius

nuclearFramework()

const NuclearFramework & GQCP::Molecule::nuclearFramework ( ) const

inline

Returns

The underlying nuclear framework.

numberOfAtoms()

size_t GQCP::Molecule::numberOfAtoms ( ) const

inline

Returns

the number of atoms in this molecule

numberOfElectronPairs()

size_t GQCP::Molecule::numberOfElectronPairs ( ) const

inline

Returns

the number of electron pairs in this molecule. For odd numbers of electrons, the number of electron pairs is equal to that of the (N-1)-even-electron system.

numberOfElectrons()

size_t GQCP::Molecule::numberOfElectrons ( ) const

inline

Returns

the number of electrons in the molecule

ReadXYZ()

Molecule GQCP::Molecule::ReadXYZ ( const std::string &  xyz_filename, const int  charge = 0  )

static

Construct a molecule based on the content of a given .xyz-file. In an .xyz-file, the molecular coordinates are in Angstrom

Parameters

xyz_filename	the .xyz-file that contains the molecular coordinates in Angstrom
charge	the charge of the molecule: +1 -> cation (one electron less than the neutral molecule) 0 -> neutral molecule -1 -> anion (one electron more than the neutral molecule)

totalNucleicCharge()

size_t GQCP::Molecule::totalNucleicCharge ( ) const

inline

Returns

the sum of all the charges of the nuclei that are in this molecule

Friends And Related Function Documentation

operator<<

std::ostream & operator<< ( std::ostream &  os, const Molecule &  molecule  )

friend

Parameters

os	the output stream which the molecule should be concatenated to
molecule	the molecule that should be concatenated to the output stream

Returns

the updated output stream

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

• /__w/GQCP/GQCP/gqcp/include/Molecule/Molecule.hpp
• /__w/GQCP/GQCP/gqcp/src/Molecule/Molecule.cpp