votca::xtp::Topology Class Reference

Container for segments and box and atoms. More...

#include <topology.h>

Collaboration diagram for votca::xtp::Topology:

Public Member Functions
	Topology ()=default
	Topology (const Topology &top)
Topology &	operator= (const Topology &top)
Segment &	AddSegment (std::string segment_name)
Segment &	getSegment (Index id)
const Segment &	getSegment (Index id) const
std::vector< Segment > &	Segments ()
const std::vector< Segment > &	Segments () const
Eigen::Vector3d	PbShortestConnect (const Eigen::Vector3d &r1, const Eigen::Vector3d &r2) const
const Eigen::Matrix3d &	getBox () const
double	BoxVolume () const
void	setBox (const Eigen::Matrix3d &box, csg::BoundaryCondition::eBoxtype boxtype=csg::BoundaryCondition::typeAuto)
QMNBList &	NBList ()
const QMNBList &	NBList () const
Index	getStep () const
void	setStep (Index step)
double	getTime () const
void	setTime (double time)
void	WriteToCpt (CheckpointWriter &w) const
void	WriteToPdb (std::string filename) const
void	ReadFromCpt (CheckpointReader &r)
double	GetShortestDist (const Segment &seg1, const Segment &seg2) const
std::vector< const Segment * >	FindAllSegmentsOnMolecule (const Segment &seg1, const Segment &seg2) const

Private Member Functions
csg::BoundaryCondition::eBoxtype	AutoDetectBoxType (const Eigen::Matrix3d &box)

Static Private Member Functions
static constexpr int	topology_version ()

Private Attributes
std::vector< Segment >	segments_
std::unique_ptr< csg::BoundaryCondition >	bc_ = nullptr
QMNBList	nblist_
double	time_
Index	step_

Detailed Description

Container for segments and box and atoms.

Definition at line 41 of file topology.h.

Constructor & Destructor Documentation

Topology() [1/2]

votca::xtp::Topology::Topology ( )

default

Topology() [2/2]

votca::xtp::Topology::Topology

(

const Topology &

top

)

Definition at line 37 of file topology.cc.

Member Function Documentation

AddSegment()

Segment & votca::xtp::Topology::AddSegment

(

std::string

segment_name

)

Definition at line 65 of file topology.cc.

AutoDetectBoxType()

csg::BoundaryCondition::eBoxtype votca::xtp::Topology::AutoDetectBoxType ( const Eigen::Matrix3d & box )

private

Definition at line 103 of file topology.cc.

BoxVolume()

double votca::xtp::Topology::BoxVolume ( ) const

inline

Definition at line 65 of file topology.h.

FindAllSegmentsOnMolecule()

std::vector< const Segment * > votca::xtp::Topology::FindAllSegmentsOnMolecule	(	const Segment &	seg1,
		const Segment &	seg2 ) const

Definition at line 149 of file topology.cc.

getBox()

const Eigen::Matrix3d & votca::xtp::Topology::getBox ( ) const

inline

Definition at line 64 of file topology.h.

getSegment() [1/2]

Segment & votca::xtp::Topology::getSegment ( Index id )

inline

Definition at line 55 of file topology.h.

getSegment() [2/2]

const Segment & votca::xtp::Topology::getSegment ( Index id ) const

inline

Definition at line 56 of file topology.h.

GetShortestDist()

double votca::xtp::Topology::GetShortestDist	(	const Segment &	seg1,
		const Segment &	seg2 ) const

Definition at line 134 of file topology.cc.

getStep()

Index votca::xtp::Topology::getStep ( ) const

inline

Definition at line 75 of file topology.h.

getTime()

double votca::xtp::Topology::getTime ( ) const

inline

Definition at line 77 of file topology.h.

NBList() [1/2]

QMNBList & votca::xtp::Topology::NBList ( )

inline

Definition at line 70 of file topology.h.

NBList() [2/2]

const QMNBList & votca::xtp::Topology::NBList ( ) const

inline

Definition at line 71 of file topology.h.

operator=()

Topology & votca::xtp::Topology::operator=

(

const Topology &

top

)

Definition at line 49 of file topology.cc.

PbShortestConnect()

Eigen::Vector3d votca::xtp::Topology::PbShortestConnect	(	const Eigen::Vector3d &	r1,
		const Eigen::Vector3d &	r2 ) const

Definition at line 129 of file topology.cc.

ReadFromCpt()

void votca::xtp::Topology::ReadFromCpt

(

CheckpointReader &

r

)

Definition at line 198 of file topology.cc.

Segments() [1/2]

std::vector< Segment > & votca::xtp::Topology::Segments ( )

inline

Definition at line 58 of file topology.h.

Segments() [2/2]

const std::vector< Segment > & votca::xtp::Topology::Segments ( ) const

inline

Definition at line 59 of file topology.h.

setBox()

void votca::xtp::Topology::setBox	(	const Eigen::Matrix3d &	box,
		csg::BoundaryCondition::eBoxtype	boxtype = csg::BoundaryCondition::typeAuto )

Definition at line 74 of file topology.cc.

setStep()

void votca::xtp::Topology::setStep ( Index step )

inline

Definition at line 76 of file topology.h.

setTime()

void votca::xtp::Topology::setTime ( double time )

inline

Definition at line 78 of file topology.h.

topology_version()

static constexpr int votca::xtp::Topology::topology_version ( )

inlinestaticconstexprprivate

Definition at line 103 of file topology.h.

WriteToCpt()

void votca::xtp::Topology::WriteToCpt

(

CheckpointWriter &

w

)

const

Definition at line 183 of file topology.cc.

WriteToPdb()

void votca::xtp::Topology::WriteToPdb

(

std::string

filename

)

const

Definition at line 171 of file topology.cc.

Member Data Documentation

bc_

std::unique_ptr<csg::BoundaryCondition> votca::xtp::Topology::bc_ = nullptr

private

Definition at line 94 of file topology.h.

nblist_

QMNBList votca::xtp::Topology::nblist_

private

Definition at line 95 of file topology.h.

segments_

std::vector<Segment> votca::xtp::Topology::segments_

private

Definition at line 92 of file topology.h.

step_

Index votca::xtp::Topology::step_

private

Definition at line 98 of file topology.h.

time_

double votca::xtp::Topology::time_

private

Definition at line 97 of file topology.h.

---

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

• xtp/include/votca/xtp/topology.h
• xtp/src/libxtp/topology.cc