H-saturated, DFT + POD2-based electronic coupling calculator. More...

#include <ipodcoupling.h>

Inheritance diagram for votca::xtp::IPodCoupling:

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Collaboration diagram for votca::xtp::IPodCoupling:

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Public Member Functions
std::string	Identify () const
	Calculator name.
Job::JobResult	EvalJob (const Topology &top, Job &job, QMThread &opThread)
void	WriteJobFile (const Topology &top)
void	ReadJobFile (Topology &top)
Public Member Functions inherited from votca::xtp::ParallelXJobCalc< std::vector< Job > >
	ParallelXJobCalc ()=default
	~ParallelXJobCalc () override=default
void	ParseOptions (const tools::Property &opt) final
bool	Evaluate (const Topology &top) final
virtual void	CustomizeLogger (QMThread &thread)
virtual Result	EvalJob (const Topology &top, Job &job, QMThread &thread)=0
void	LockCout ()
void	UnlockCout ()
void	LockLog ()
void	UnlockLog ()
Public Member Functions inherited from votca::xtp::JobCalculator
	JobCalculator ()=default
	~JobCalculator () override=default
std::string	Package () const final
	Package name.
bool	EvaluateFrame (const Topology &top)
void	Initialize (const tools::Property &opt) final
	Initializes a calculator from an XML file with options.
void	setOpenMPThreads (Index ompthreads)
void	setProgObserver (ProgObserver< std::vector< Job > > *obs)
Public Member Functions inherited from votca::tools::Calculator
	Calculator ()=default
virtual	~Calculator ()=default
void	setnThreads (Index nThreads)
	Sets number of threads to use.

Protected Member Functions
void	ParseSpecificOptions (const tools::Property &user_options)
Protected Member Functions inherited from votca::xtp::ParallelXJobCalc< std::vector< Job > >
tools::Property	UpdateDFTOptions (const tools::Property &options)
tools::Property	UpdateGWBSEOptions (const tools::Property &options)

Private Member Functions
void	SetJobToFailed (Job::JobResult &jres, Logger &pLog, const std::string &errormessage)
void	WriteLoggerToFile (const std::string &logfile, Logger &logger)
double	GetPODCouplingFromProp (const tools::Property &podprop, Index levelA, Index levelB) const
const Atom &	FindBoundaryAtomTowardSegment (const Segment &seg, Index target_segment_id) const
std::vector< Segment >	PositionLinkersAlongChain (const Topology &top, const Segment &seg1_positioned, const std::vector< const Segment * > &linkers, const Segment &seg2_positioned) const

Private Attributes
tools::Property	dftpackage_options_
tools::Property	podcoupling_options_
Index	numberofstatesA_ = 1
Index	numberofstatesB_ = 1
bool	include_linkers_ = false
bool	do_dft_input_ = false
bool	do_dft_run_ = false
bool	do_dft_parse_ = false
bool	do_podcoupling_ = false
bool	store_dft_ = false

Additional Inherited Members
Public Types inherited from votca::xtp::ParallelXJobCalc< std::vector< Job > >
using	Job
using	Result
Protected Attributes inherited from votca::xtp::ParallelXJobCalc< std::vector< Job > >
std::vector< Job >	XJobs_
tools::Mutex	coutMutex_
tools::Mutex	logMutex_
std::string	mapfile_
std::string	jobfile_
Protected Attributes inherited from votca::xtp::JobCalculator
Index	openmp_threads_
ProgObserver< std::vector< Job > > *	progObs_
Protected Attributes inherited from votca::tools::Calculator
Index	nThreads_
bool	maverick_

Detailed Description

H-saturated, DFT + POD2-based electronic coupling calculator.

A new, separate jobcalculator (deliberately not a modification of IQM itself – IQM already has an established, widely-used role, and directly entangling this genuinely different workflow into it would risk breaking existing behavior for everyone who already relies on it, per the design worked through directly with the user before starting this implementation).

For each neighbor-list pair: maps both segments (plus, in future, any linking segments – see this class's own EvalJob header comment for the current, still-open status of that piece), combines them into one supermolecule, saturates any remaining covalently-cut fragment boundaries with new H atoms (FragmentSaturator:: SaturateExternalBonds, geometric placement, then RelaxNewAtoms, a constrained OpenBabel MMFF94/UFF relaxation – both already built and tested earlier this session), runs the actual DFT calculation on the resulting, H-saturated geometry, then runs PODCoupling on the resulting orbitals.

Callname: ipodcoupling

Definition at line 58 of file ipodcoupling.h.

Member Function Documentation

◆ EvalJob()

Job::JobResult votca::xtp::IPodCoupling::EvalJob	(	const Topology &	top,
		Job &	job,
		QMThread &	opThread )

Definition at line 232 of file ipodcoupling.cc.

◆ FindBoundaryAtomTowardSegment()

const Atom & votca::xtp::IPodCoupling::FindBoundaryAtomTowardSegment	(	const Segment &	seg,
		Index	target_segment_id ) const

private

Definition at line 139 of file ipodcoupling.cc.

◆ GetPODCouplingFromProp()

double votca::xtp::IPodCoupling::GetPODCouplingFromProp	(	const tools::Property &	podprop,
		Index	levelA,
		Index	levelB ) const

private

Definition at line 688 of file ipodcoupling.cc.

◆ Identify()

std::string votca::xtp::IPodCoupling::Identify ( ) const

inlinevirtual

Calculator name.

This name is used to register a calculator in a Factory It the name of the XML file with the default calculator options stored in VOTCASHARE

Returns: calculator name

Implements votca::xtp::ParallelXJobCalc< std::vector< Job > >.

Definition at line 60 of file ipodcoupling.h.

◆ ParseSpecificOptions()

void votca::xtp::IPodCoupling::ParseSpecificOptions ( const tools::Property & user_options )

protectedvirtual

Implements votca::xtp::ParallelXJobCalc< std::vector< Job > >.

Definition at line 47 of file ipodcoupling.cc.

◆ PositionLinkersAlongChain()

std::vector< Segment > votca::xtp::IPodCoupling::PositionLinkersAlongChain	(	const Topology &	top,
		const Segment &	seg1_positioned,
		const std::vector< const Segment * > &	linkers,
		const Segment &	seg2_positioned ) const

private

Definition at line 157 of file ipodcoupling.cc.

◆ ReadJobFile()

void votca::xtp::IPodCoupling::ReadJobFile ( Topology & top )

virtual

Implements votca::xtp::JobCalculator.

Definition at line 700 of file ipodcoupling.cc.

◆ SetJobToFailed()

void votca::xtp::IPodCoupling::SetJobToFailed	(	Job::JobResult &	jres,
		Logger &	pLog,
		const std::string &	errormessage )

private

Definition at line 793 of file ipodcoupling.cc.

◆ WriteJobFile()

void votca::xtp::IPodCoupling::WriteJobFile ( const Topology & top )

virtual

Implements votca::xtp::JobCalculator.

Definition at line 83 of file ipodcoupling.cc.

◆ WriteLoggerToFile()

void votca::xtp::IPodCoupling::WriteLoggerToFile	(	const std::string &	logfile,
		Logger &	logger )

private

Definition at line 801 of file ipodcoupling.cc.

Member Data Documentation

◆ dftpackage_options_

tools::Property votca::xtp::IPodCoupling::dftpackage_options_

private

Definition at line 131 of file ipodcoupling.h.

◆ do_dft_input_

bool votca::xtp::IPodCoupling::do_dft_input_ = false

private

Definition at line 160 of file ipodcoupling.h.

◆ do_dft_parse_

bool votca::xtp::IPodCoupling::do_dft_parse_ = false

private

Definition at line 162 of file ipodcoupling.h.

◆ do_dft_run_

bool votca::xtp::IPodCoupling::do_dft_run_ = false

private

Definition at line 161 of file ipodcoupling.h.

◆ do_podcoupling_

bool votca::xtp::IPodCoupling::do_podcoupling_ = false

private

Definition at line 163 of file ipodcoupling.h.

◆ include_linkers_

bool votca::xtp::IPodCoupling::include_linkers_ = false

private

Definition at line 154 of file ipodcoupling.h.

◆ numberofstatesA_

Index votca::xtp::IPodCoupling::numberofstatesA_ = 1

private

Definition at line 141 of file ipodcoupling.h.

◆ numberofstatesB_

Index votca::xtp::IPodCoupling::numberofstatesB_ = 1

private

Definition at line 142 of file ipodcoupling.h.

◆ podcoupling_options_

tools::Property votca::xtp::IPodCoupling::podcoupling_options_

private

Definition at line 132 of file ipodcoupling.h.

◆ store_dft_

bool votca::xtp::IPodCoupling::store_dft_ = false

private

Definition at line 165 of file ipodcoupling.h.

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

xtp/src/libxtp/jobcalculators/ipodcoupling.h
xtp/src/libxtp/jobcalculators/ipodcoupling.cc

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ EvalJob()

◆ FindBoundaryAtomTowardSegment()

◆ GetPODCouplingFromProp()

◆ Identify()

◆ ParseSpecificOptions()

◆ PositionLinkersAlongChain()

◆ ReadJobFile()

◆ SetJobToFailed()

◆ WriteJobFile()

◆ WriteLoggerToFile()

Member Data Documentation

◆ dftpackage_options_

◆ do_dft_input_

◆ do_dft_parse_

◆ do_dft_run_

◆ do_podcoupling_

◆ include_linkers_

◆ numberofstatesA_

◆ numberofstatesB_

◆ podcoupling_options_

◆ store_dft_