#include <segmentmapper.h>

Collaboration diagram for votca::xtp::SegmentMapper< AtomContainer >:

[legend]

Classes
struct	FragInfo
struct	Seginfo

Public Member Functions
	SegmentMapper (Logger &log)
void	LoadMappingFile (const std::string &mapfile)
AtomContainer	map (const Segment &seg, const SegId &segid) const
AtomContainer	map (const Segment &seg, QMState state) const
AtomContainer	map (const Segment &seg, const std::string &coordfilename) const

Private Types
using	mapAtom = typename AtomContainer::Atom_Type
using	atom_id = std::pair<Index, std::string>

Private Member Functions
void	AttachChargeResponse (AtomContainer &, const Seginfo &, const QMState &) const
Index	FindVectorIndexFromAtomId (Index atomid, const std::vector< mapAtom * > &fragment_mapatoms) const
void	ParseFragment (Seginfo &seginfo, const tools::Property &frag)
template<typename T>
Eigen::Vector3d	CalcWeightedPos (const std::vector< double > &weights, const T &atoms) const
void	PlaceMapAtomonMD (const std::vector< mapAtom * > &fragment_mapatoms, const std::vector< const Atom * > &fragment_mdatoms) const
void	MapMapAtomonMD (const FragInfo &frag, const std::vector< mapAtom * > &fragment_mapatoms, const std::vector< const Atom * > &fragment_mdatoms) const
void	TransferExternalBondDirection (mapAtom , const Atom , const Eigen::Matrix3d &) const
void	TransferBondedPartners (mapAtom , const Atom , const std::map< Index, mapAtom * > &) const
void	RemapBondedPartners (mapAtom &, const std::map< Index, Index > &) const
std::pair< Index, Index >	CalcAtomIdRange (const Segment &seg) const
std::pair< Index, Index >	CalcAtomIdRange (const std::vector< Index > &seg) const
atom_id	StringToMapIndex (const std::string &map_string) const
atom_id	StringToMDIndex (const std::string &md_string) const
Index	getRank (const mapAtom &atom) const
std::vector< double >	getWeights (const tools::Property &frag) const
std::string	getFrame (const tools::Property &frag) const
void	FillMap ()
void	FillMap ()
Index	getRank (const QMAtom &) const
void	TransferExternalBondDirection (QMAtom map_atom, const Atom md_atom, const Eigen::Matrix3d &rot) const
void	TransferBondedPartners (QMAtom map_atom, const Atom md_atom, const std::map< Index, QMAtom * > &md_id_to_map_atom) const
void	RemapBondedPartners (QMAtom &atom, const std::map< Index, Index > &old_to_new) const
void	AttachChargeResponse (PolarSegment &result, const Seginfo &seginfo, const QMState &state) const
void	AttachChargeResponse (PolarSegment &result, const Seginfo &seginfo, const QMState &state) const

Private Attributes
std::map< std::string, std::string >	mapatom_xml_
std::map< std::string, Seginfo >	segment_info_
Logger &	log_

Detailed Description

template<class AtomContainer>
class votca::xtp::SegmentMapper< AtomContainer >

Definition at line 39 of file segmentmapper.h.

Member Typedef Documentation

◆ atom_id

template<class AtomContainer>

using votca::xtp::SegmentMapper< AtomContainer >::atom_id = std::pair<Index, std::string>

private

Definition at line 54 of file segmentmapper.h.

◆ mapAtom

template<class AtomContainer>

using votca::xtp::SegmentMapper< AtomContainer >::mapAtom = typename AtomContainer::Atom_Type

private

Definition at line 52 of file segmentmapper.h.

Constructor & Destructor Documentation

◆ SegmentMapper()

template<class AtomContainer>

votca::xtp::SegmentMapper< AtomContainer >::SegmentMapper ( Logger & log )

Definition at line 30 of file segmentmapper.cc.

Member Function Documentation

◆ AttachChargeResponse() [1/3]

template<class AtomContainer>

void votca::xtp::SegmentMapper< AtomContainer >::AttachChargeResponse	(	AtomContainer &	,
		const Seginfo &	,
		const QMState &	) const

inlineprivate

Definition at line 80 of file segmentmapper.h.

◆ AttachChargeResponse() [2/3]

void votca::xtp::SegmentMapper< PolarSegment >::AttachChargeResponse	(	PolarSegment &	result,
		const Seginfo &	seginfo,
		const QMState &	state ) const

private

◆ AttachChargeResponse() [3/3]

void votca::xtp::SegmentMapper< PolarSegment >::AttachChargeResponse	(	PolarSegment &	result,
		const Seginfo &	seginfo,
		const QMState &	state ) const

private

Definition at line 419 of file segmentmapper.cc.

◆ CalcAtomIdRange() [1/2]

template<class AtomContainer>

std::pair< Index, Index > votca::xtp::SegmentMapper< AtomContainer >::CalcAtomIdRange ( const Segment & seg ) const

private

Definition at line 270 of file segmentmapper.cc.

◆ CalcAtomIdRange() [2/2]

template<class AtomContainer>

std::pair< Index, Index > votca::xtp::SegmentMapper< AtomContainer >::CalcAtomIdRange ( const std::vector< Index > & seg ) const

private

Definition at line 263 of file segmentmapper.cc.

◆ CalcWeightedPos()

template<class AtomContainer>

template<typename T>

Eigen::Vector3d votca::xtp::SegmentMapper< AtomContainer >::CalcWeightedPos	(	const std::vector< double > &	weights,
		const T &	atoms ) const

private

Definition at line 52 of file segmentmapper.cc.

◆ FillMap() [1/2]

void votca::xtp::SegmentMapper< QMMolecule >::FillMap ( )

inlineprivate

Definition at line 150 of file segmentmapper.h.

◆ FillMap() [2/2]

template<class AtomContainer>

void votca::xtp::SegmentMapper< AtomContainer >::FillMap ( )

inlineprivate

Definition at line 139 of file segmentmapper.h.

◆ FindVectorIndexFromAtomId()

template<class AtomContainer>

Index votca::xtp::SegmentMapper< AtomContainer >::FindVectorIndexFromAtomId	(	Index	atomid,
		const std::vector< mapAtom * > &	fragment_mapatoms ) const

private

Definition at line 301 of file segmentmapper.cc.

◆ getFrame()

template<class AtomContainer>

std::string votca::xtp::SegmentMapper< AtomContainer >::getFrame ( const tools::Property & frag ) const

inlineprivate

Definition at line 132 of file segmentmapper.h.

◆ getRank() [1/2]

template<class AtomContainer>

Index votca::xtp::SegmentMapper< AtomContainer >::getRank ( const mapAtom & atom ) const

inlineprivate

Definition at line 128 of file segmentmapper.h.

◆ getRank() [2/2]

Index votca::xtp::SegmentMapper< QMMolecule >::getRank ( const QMAtom & ) const

inlineprivate

Definition at line 160 of file segmentmapper.h.

◆ getWeights()

template<class AtomContainer>

std::vector< double > votca::xtp::SegmentMapper< AtomContainer >::getWeights ( const tools::Property & frag ) const

private

Definition at line 64 of file segmentmapper.cc.

◆ LoadMappingFile()

template<class AtomContainer>

void votca::xtp::SegmentMapper< AtomContainer >::LoadMappingFile ( const std::string & mapfile )

Definition at line 181 of file segmentmapper.cc.

◆ map() [1/3]

template<class AtomContainer>

AtomContainer votca::xtp::SegmentMapper< AtomContainer >::map	(	const Segment &	seg,
		const SegId &	segid ) const

Definition at line 35 of file segmentmapper.cc.

◆ map() [2/3]

template<class AtomContainer>

AtomContainer votca::xtp::SegmentMapper< AtomContainer >::map	(	const Segment &	seg,
		const std::string &	coordfilename ) const

Definition at line 457 of file segmentmapper.cc.

◆ map() [3/3]

template<class AtomContainer>

AtomContainer votca::xtp::SegmentMapper< AtomContainer >::map	(	const Segment &	seg,
		QMState	state ) const

Definition at line 397 of file segmentmapper.cc.

◆ MapMapAtomonMD()

template<class AtomContainer>

void votca::xtp::SegmentMapper< AtomContainer >::MapMapAtomonMD	(	const FragInfo &	frag,
		const std::vector< mapAtom * > &	fragment_mapatoms,
		const std::vector< const Atom * > &	fragment_mdatoms ) const

private

Definition at line 312 of file segmentmapper.cc.

◆ ParseFragment()

template<class AtomContainer>

void votca::xtp::SegmentMapper< AtomContainer >::ParseFragment	(	Seginfo &	seginfo,
		const tools::Property &	frag )

private

Definition at line 101 of file segmentmapper.cc.

◆ PlaceMapAtomonMD()

template<class AtomContainer>

void votca::xtp::SegmentMapper< AtomContainer >::PlaceMapAtomonMD	(	const std::vector< mapAtom * > &	fragment_mapatoms,
		const std::vector< const Atom * > &	fragment_mdatoms ) const

private

Definition at line 287 of file segmentmapper.cc.

◆ RemapBondedPartners() [1/2]

template<class AtomContainer>

void votca::xtp::SegmentMapper< AtomContainer >::RemapBondedPartners	(	mapAtom &	,
		const std::map< Index, Index > &	) const

inlineprivate

Definition at line 118 of file segmentmapper.h.

◆ RemapBondedPartners() [2/2]

void votca::xtp::SegmentMapper< QMMolecule >::RemapBondedPartners	(	QMAtom &	atom,
		const std::map< Index, Index > &	old_to_new ) const

inlineprivate

Definition at line 192 of file segmentmapper.h.

◆ StringToMapIndex()

template<class AtomContainer>

std::pair< Index, std::string > votca::xtp::SegmentMapper< AtomContainer >::StringToMapIndex ( const std::string & map_string ) const

private

Definition at line 233 of file segmentmapper.cc.

◆ StringToMDIndex()

template<class AtomContainer>

std::pair< Index, std::string > votca::xtp::SegmentMapper< AtomContainer >::StringToMDIndex ( const std::string & md_string ) const

private

Definition at line 244 of file segmentmapper.cc.

◆ TransferBondedPartners() [1/2]

template<class AtomContainer>

void votca::xtp::SegmentMapper< AtomContainer >::TransferBondedPartners	(	mapAtom *	,
		const Atom *	,
		const std::map< Index, mapAtom * > &	) const

inlineprivate

Definition at line 112 of file segmentmapper.h.

◆ TransferBondedPartners() [2/2]

void votca::xtp::SegmentMapper< QMMolecule >::TransferBondedPartners	(	QMAtom *	map_atom,
		const Atom *	md_atom,
		const std::map< Index, QMAtom * > &	md_id_to_map_atom ) const

inlineprivate

Definition at line 176 of file segmentmapper.h.

◆ TransferExternalBondDirection() [1/2]

template<class AtomContainer>

void votca::xtp::SegmentMapper< AtomContainer >::TransferExternalBondDirection	(	mapAtom *	,
		const Atom *	,
		const Eigen::Matrix3d &	) const

inlineprivate

Definition at line 105 of file segmentmapper.h.

◆ TransferExternalBondDirection() [2/2]

void votca::xtp::SegmentMapper< QMMolecule >::TransferExternalBondDirection	(	QMAtom *	map_atom,
		const Atom *	md_atom,
		const Eigen::Matrix3d &	rot ) const

inlineprivate

Definition at line 165 of file segmentmapper.h.

Member Data Documentation

◆ log_

template<class AtomContainer>

Logger& votca::xtp::SegmentMapper< AtomContainer >::log_

private

Definition at line 120 of file segmentmapper.h.

◆ mapatom_xml_

template<class AtomContainer>

std::map<std::string, std::string> votca::xtp::SegmentMapper< AtomContainer >::mapatom_xml_

private

Definition at line 82 of file segmentmapper.h.

◆ segment_info_

template<class AtomContainer>

std::map<std::string, Seginfo> votca::xtp::SegmentMapper< AtomContainer >::segment_info_

private

Definition at line 83 of file segmentmapper.h.

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

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

Classes

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ atom_id

◆ mapAtom

Constructor & Destructor Documentation

◆ SegmentMapper()

Member Function Documentation

◆ AttachChargeResponse() [1/3]

◆ AttachChargeResponse() [2/3]

◆ AttachChargeResponse() [3/3]

◆ CalcAtomIdRange() [1/2]

◆ CalcAtomIdRange() [2/2]

◆ CalcWeightedPos()

◆ FillMap() [1/2]

◆ FillMap() [2/2]

◆ FindVectorIndexFromAtomId()

◆ getFrame()

◆ getRank() [1/2]

◆ getRank() [2/2]

◆ getWeights()

◆ LoadMappingFile()

◆ map() [1/3]

◆ map() [2/3]

◆ map() [3/3]

◆ MapMapAtomonMD()

◆ ParseFragment()

◆ PlaceMapAtomonMD()

◆ RemapBondedPartners() [1/2]

◆ RemapBondedPartners() [2/2]

◆ StringToMapIndex()

◆ StringToMDIndex()

◆ TransferBondedPartners() [1/2]

◆ TransferBondedPartners() [2/2]

◆ TransferExternalBondDirection() [1/2]

◆ TransferExternalBondDirection() [2/2]

Member Data Documentation

◆ log_

◆ mapatom_xml_

◆ segment_info_