Class to represent Atom/Site in electrostatic+polarization. More...

#include <polarsite.h>

Inheritance diagram for votca::xtp::PolarSite:

Collaboration diagram for votca::xtp::PolarSite:

[legend]

Classes
struct	data

Public Member Functions
void	WriteData (StaticSite::data &d) const =delete

void	ReadData (StaticSite::data &d)=delete

	PolarSite (Index id, std::string element, Eigen::Vector3d pos)

	PolarSite (Index id, std::string element)

	~PolarSite () final=default

void	setpolarization (const Eigen::Matrix3d &pol) final

Eigen::Matrix3d	getpolarization () const

const Eigen::Matrix3d &	getPInv () const

Eigen::Vector3d	getDipole () const final

double	getSqrtInvEigenDamp () const

void	Rotate (const Eigen::Matrix3d &R, const Eigen::Vector3d &ref_pos) final

const Eigen::Vector3d &	V () const

Eigen::Vector3d &	V ()

const Eigen::Vector3d &	V_noE () const

Eigen::Vector3d &	V_noE ()

void	Reset ()

double	deltaQ_V_ext () const

double	InternalEnergy () const

const Eigen::Vector3d &	Induced_Dipole () const

void	setInduced_Dipole (const Eigen::Vector3d &induced_dipole)

	PolarSite (const data &d)

double	DipoleChange () const

void	WriteData (data &d) const

void	ReadData (const data &d)

std::string	identify () const final

Public Member Functions inherited from votca::xtp::StaticSite
	StaticSite (Index id, std::string element, Eigen::Vector3d pos)

	StaticSite (Index id, std::string element)

	StaticSite (const data &d)

	StaticSite (const QMAtom &atom, double charge)

virtual	~StaticSite ()=default

Index	getId () const

Index	getRank () const

const std::string &	getElement () const

const Eigen::Vector3d &	getPos () const

void	setMultipole (const Vector9d &multipole, Index rank)

void	setCharge (double q)

void	setPos (const Eigen::Vector3d &position)

void	Translate (const Eigen::VectorXd &shift)

virtual void	Rotate (const Eigen::Matrix3d &R, const Eigen::Vector3d &refPos)

double	getCharge () const

const Vector9d &	Q () const

virtual Eigen::Vector3d	getDipole () const

Eigen::Matrix3d	CalculateCartesianMultipole () const

std::string	WriteMpsLine (std::string unit="bohr") const

void	WriteData (data &d) const

void	ReadData (const data &d)

virtual void	setpolarization (const Eigen::Matrix3d &)

virtual std::string	identify () const

Static Public Member Functions
static void	SetupCptTable (CptTable &table)

Static Public Member Functions inherited from votca::xtp::StaticSite
static Eigen::VectorXd	CalculateSphericalMultipole (const Eigen::Matrix3d &quad_cart)

static void	SetupCptTable (CptTable &table)

Private Member Functions
std::string	writepolarization () const final

Private Attributes
Eigen::Vector3d	V_ = Eigen::Vector3d::Zero()

Eigen::Vector3d	V_noE_ = Eigen::Vector3d::Zero()

Eigen::Vector3d	induced_dipole_ = Eigen::Vector3d::Zero()

Eigen::Matrix3d	pinv_ = Eigen::Matrix3d::Zero()

double	eigendamp_invsqrt_ = 0.0

Friends
std::ostream &	operator<< (std::ostream &out, const PolarSite &site)

Additional Inherited Members
Protected Member Functions inherited from votca::xtp::StaticSite
	StaticSite ()=default

virtual std::string	writepolarization () const

Protected Attributes inherited from votca::xtp::StaticSite
Index	id_ = -1

std::string	element_ = ""

Eigen::Vector3d	pos_ = Eigen::Vector3d::Zero()

Index	rank_ = 0

Vector9d	Q_ = Vector9d::Zero()

Detailed Description

Class to represent Atom/Site in electrostatic+polarization.

The units are atomic units, e.g. Bohr, Hartree.

Definition at line 36 of file polarsite.h.

Constructor & Destructor Documentation

◆ PolarSite() [1/3]

votca::xtp::PolarSite::PolarSite	(	Index	id,
		std::string	element,
		Eigen::Vector3d	pos
	)

Definition at line 39 of file polarsite.cc.

◆ PolarSite() [2/3]

votca::xtp::PolarSite::PolarSite	(	Index	id,
		std::string	element
	)

inline

Definition at line 45 of file polarsite.h.

◆ ~PolarSite()

votca::xtp::PolarSite::~PolarSite ( )

finaldefault

◆ PolarSite() [3/3]

votca::xtp::PolarSite::PolarSite ( const data & d )

Definition at line 52 of file polarsite.cc.

Member Function Documentation

◆ deltaQ_V_ext()

double votca::xtp::PolarSite::deltaQ_V_ext ( ) const

inline

Definition at line 79 of file polarsite.h.

◆ DipoleChange()

double votca::xtp::PolarSite::DipoleChange ( ) const

◆ getDipole()

Eigen::Vector3d votca::xtp::PolarSite::getDipole ( ) const

finalvirtual

Reimplemented from votca::xtp::StaticSite.

Definition at line 54 of file polarsite.cc.

◆ getPInv()

const Eigen::Matrix3d & votca::xtp::PolarSite::getPInv ( ) const

inline

Definition at line 54 of file polarsite.h.

◆ getpolarization()

Eigen::Matrix3d votca::xtp::PolarSite::getpolarization ( ) const

inline

Definition at line 52 of file polarsite.h.

◆ getSqrtInvEigenDamp()

double votca::xtp::PolarSite::getSqrtInvEigenDamp ( ) const

inline

Definition at line 59 of file polarsite.h.

◆ identify()

std::string votca::xtp::PolarSite::identify ( ) const

inlinefinalvirtual

Reimplemented from votca::xtp::StaticSite.

Definition at line 137 of file polarsite.h.

◆ Induced_Dipole()

const Eigen::Vector3d & votca::xtp::PolarSite::Induced_Dipole ( ) const

inline

Definition at line 85 of file polarsite.h.

◆ InternalEnergy()

double votca::xtp::PolarSite::InternalEnergy ( ) const

inline

Definition at line 81 of file polarsite.h.

◆ ReadData() [1/2]

void votca::xtp::PolarSite::ReadData ( const data & d )

Definition at line 155 of file polarsite.cc.

◆ ReadData() [2/2]

void votca::xtp::PolarSite::ReadData ( StaticSite::data & d )

delete

◆ Reset()

void votca::xtp::PolarSite::Reset ( )

inline

Definition at line 74 of file polarsite.h.

◆ Rotate()

void votca::xtp::PolarSite::Rotate	(	const Eigen::Matrix3d &	R,
		const Eigen::Vector3d &	ref_pos
	)

inlinefinalvirtual

Reimplemented from votca::xtp::StaticSite.

Definition at line 61 of file polarsite.h.

◆ setInduced_Dipole()

void votca::xtp::PolarSite::setInduced_Dipole ( const Eigen::Vector3d & induced_dipole )

inline

Definition at line 86 of file polarsite.h.

◆ setpolarization()

void votca::xtp::PolarSite::setpolarization ( const Eigen::Matrix3d & pol )

finalvirtual

Reimplemented from votca::xtp::StaticSite.

Definition at line 58 of file polarsite.cc.

◆ SetupCptTable()

void votca::xtp::PolarSite::SetupCptTable ( CptTable & table )

static

Definition at line 75 of file polarsite.cc.

◆ V() [1/2]

Eigen::Vector3d & votca::xtp::PolarSite::V ( )

inline

Definition at line 68 of file polarsite.h.

◆ V() [2/2]

const Eigen::Vector3d & votca::xtp::PolarSite::V ( ) const

inline

Definition at line 66 of file polarsite.h.

◆ V_noE() [1/2]

Eigen::Vector3d & votca::xtp::PolarSite::V_noE ( )

inline

Definition at line 72 of file polarsite.h.

◆ V_noE() [2/2]

const Eigen::Vector3d & votca::xtp::PolarSite::V_noE ( ) const

inline

Definition at line 70 of file polarsite.h.

◆ WriteData() [1/2]

void votca::xtp::PolarSite::WriteData ( data & d ) const

Definition at line 115 of file polarsite.cc.

◆ WriteData() [2/2]

void votca::xtp::PolarSite::WriteData ( StaticSite::data & d ) const

delete

◆ writepolarization()

std::string votca::xtp::PolarSite::writepolarization ( ) const

finalprivatevirtual

Reimplemented from votca::xtp::StaticSite.

Definition at line 66 of file polarsite.cc.

Friends And Related Symbol Documentation

◆ operator<<

std::ostream & operator<<	(	std::ostream &	out,
		const PolarSite &	site
	)

friend

Definition at line 139 of file polarsite.h.

Member Data Documentation

◆ eigendamp_invsqrt_

double votca::xtp::PolarSite::eigendamp_invsqrt_ = 0.0

private

Definition at line 160 of file polarsite.h.

◆ induced_dipole_

Eigen::Vector3d votca::xtp::PolarSite::induced_dipole_ = Eigen::Vector3d::Zero()

private

Definition at line 158 of file polarsite.h.

◆ pinv_

Eigen::Matrix3d votca::xtp::PolarSite::pinv_ = Eigen::Matrix3d::Zero()

private

Definition at line 159 of file polarsite.h.

◆ V_

Eigen::Vector3d votca::xtp::PolarSite::V_ = Eigen::Vector3d::Zero()

private

Definition at line 152 of file polarsite.h.

◆ V_noE_

Eigen::Vector3d votca::xtp::PolarSite::V_noE_ = Eigen::Vector3d::Zero()

private

Definition at line 156 of file polarsite.h.

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

xtp/include/votca/xtp/polarsite.h
xtp/src/libxtp/polarsite.cc

Classes

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PolarSite() [1/3]

◆ PolarSite() [2/3]

◆ ~PolarSite()

◆ PolarSite() [3/3]

Member Function Documentation

◆ deltaQ_V_ext()

◆ DipoleChange()

◆ getDipole()

◆ getPInv()

◆ getpolarization()

◆ getSqrtInvEigenDamp()

◆ identify()

◆ Induced_Dipole()

◆ InternalEnergy()

◆ ReadData() [1/2]

◆ ReadData() [2/2]

◆ Reset()

◆ Rotate()

◆ setInduced_Dipole()

◆ setpolarization()

◆ SetupCptTable()

◆ V() [1/2]

◆ V() [2/2]

◆ V_noE() [1/2]

◆ V_noE() [2/2]

◆ WriteData() [1/2]

◆ WriteData() [2/2]

◆ writepolarization()

Friends And Related Symbol Documentation

◆ operator<<

Member Data Documentation

◆ eigendamp_invsqrt_

◆ induced_dipole_

◆ pinv_

◆ V_

◆ V_noE_