#include <csg_reupdate.h>

Inheritance diagram for CsgREupdate:

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Collaboration diagram for CsgREupdate:

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Public Member Functions
std::string	ProgramName () override
	program name

void	HelpText (std::ostream &out) override
	help text of application without version information

bool	DoTrajectory () override
	overload and return true to enable trajectory command line options

bool	DoMapping () override
	overload and return true to enable mapping command line options

bool	DoThreaded () override

bool	SynchronizeThreads () override

bool	NeedsTopology () override
	if topology is always needed

void	Initialize () override
	Initialize application data.

bool	EvaluateOptions () override
	Process command line options.

void	BeginEvaluate (Topology top, Topology top_atom=nullptr) override
	called before the first frame

void	LoadOptions (const std::string &file)

void	Run () override
	Main body of application.

void	EndEvaluate () override
	called after the last frame

std::unique_ptr< CsgApplication::Worker >	ForkWorker (void) override

void	MergeWorker (Worker *worker) override

Public Member Functions inherited from votca::csg::CsgApplication
	CsgApplication ()=default

	~CsgApplication () override=default

void	Initialize () override
	Initialize application data.

bool	EvaluateOptions () override
	Process command line options.

void	Run (void) override
	Main body of application.

void	ShowHelpText (std::ostream &out) override

virtual bool	DoMapping (void)
	overload and return true to enable mapping command line options

virtual bool	DoMappingDefault (void)
	if DoMapping is true, will by default require mapping or not

virtual bool	DoTrajectory (void)
	overload and return true to enable trajectory command line options

virtual bool	DoThreaded (void)

virtual bool	SynchronizeThreads (void)

virtual bool	NeedsTopology (void)
	if topology is always needed

virtual bool	EvaluateTopology (Topology , Topology =nullptr)
	called after topology was loaded

void	AddObserver (CGObserver *observer)

virtual void	BeginEvaluate (Topology top, Topology top_ref=nullptr)
	called before the first frame

virtual void	EndEvaluate ()
	called after the last frame

virtual void	EvalConfiguration (Topology top, Topology top_ref=nullptr)

bool	ProcessData (Worker *worker)
	Gets frames from TrajectoryReader in an ordered way and, if successful, calls Worker::EvalConfiguration for that frame.

virtual std::unique_ptr< Worker >	ForkWorker (void)

virtual void	MergeWorker (Worker *worker)

Public Member Functions inherited from votca::tools::Application
	Application ()

virtual	~Application ()

int	Exec (int argc, char **argv)
	executes the program

virtual std::string	ProgramName ()=0
	program name

virtual std::string	VersionString ()
	version string of application

virtual void	HelpText (std::ostream &out)=0
	help text of application without version information

virtual void	Initialize ()=0
	Initialize application data.

virtual bool	EvaluateOptions ()=0
	Process command line options.

void	CheckRequired (const std::string &option_name, const std::string &error_msg="")
	Check weather required option is set.

virtual void	Run ()=0
	Main body of application.

boost::program_options::options_description_easy_init	AddProgramOptions (const std::string &group="")
	add option for command line

boost::program_options::variables_map &	OptionsMap ()
	get available program options & descriptions

boost::program_options::options_description &	OptionsDesc ()

boost::program_options::options_description &	VisibleOptions ()
	filters out the Hidden group from the options descriptions

void	StopExecution ()
	call StopExecution after EvaluateOptions

Protected Types
using	PotentialContainer = std::vector< PotentialInfo * >

Protected Member Functions
void	WriteOutFiles ()

void	EvalBonded (Topology conf, PotentialInfo potinfo)

void	EvalNonbonded (Topology conf, PotentialInfo potinfo)

void	AAavgBonded (PotentialInfo *potinfo)

void	AAavgNonbonded (PotentialInfo *potinfo)

void	REFormulateLinEq ()

void	REUpdateLamda ()

virtual void	ShowHelpText (std::ostream &out)

Protected Attributes
Property	options_

std::vector< Property * >	nonbonded_

PotentialContainer	potentials_

votca::Index	nlamda_

Eigen::VectorXd	lamda_

Eigen::MatrixXd	HS_

Eigen::VectorXd	DS_

Eigen::VectorXd	dUFrame_

bool	hessian_check_

double	UavgAA_

double	UavgCG_

double	beta_

double	relax_

votca::Index	nframes_

bool	gentable_

std::vector< Table * >	aardfs_

std::vector< double * >	aardfnorms_

std::string	param_in_ext_

std::string	param_out_ext_

std::string	pot_out_ext_

std::string	rdf_ext_

Protected Attributes inherited from votca::csg::CsgApplication
std::list< CGObserver * >	observers_

bool	do_mapping_

std::vector< std::unique_ptr< Worker > >	myWorkers_

Index	nframes_

bool	is_first_frame_

Index	nthreads_

tools::Mutex	nframesMutex_

tools::Mutex	traj_readerMutex_

std::vector< std::unique_ptr< tools::Mutex > >	threadsMutexesIn_
	stores Mutexes used to impose order for input

std::vector< std::unique_ptr< tools::Mutex > >	threadsMutexesOut_
	stores Mutexes used to impose order for output

std::unique_ptr< TrajectoryReader >	traj_reader_

Protected Attributes inherited from votca::tools::Application
std::map< std::string, boost::program_options::options_description >	op_groups_

bool	continue_execution_ = true

Detailed Description

Definition at line 61 of file csg_reupdate.h.

Member Typedef Documentation

◆ PotentialContainer

using CsgREupdate::PotentialContainer = std::vector<PotentialInfo *>

protected

Definition at line 93 of file csg_reupdate.h.

Member Function Documentation

◆ AAavgBonded()

void CsgREupdate::AAavgBonded ( PotentialInfo * potinfo )

protected

Definition at line 456 of file csg_reupdate.cc.

◆ AAavgNonbonded()

void CsgREupdate::AAavgNonbonded ( PotentialInfo * potinfo )

protected

Definition at line 367 of file csg_reupdate.cc.

◆ BeginEvaluate()

void CsgREupdate::BeginEvaluate	(	Topology *	top,
		Topology *	top_ref = `nullptr`
	)

overridevirtual

called before the first frame

Reimplemented from votca::csg::CsgApplication.

Definition at line 97 of file csg_reupdate.cc.

◆ DoMapping()

bool CsgREupdate::DoMapping ( void )

inlineoverridevirtual

overload and return true to enable mapping command line options

Reimplemented from votca::csg::CsgApplication.

Definition at line 70 of file csg_reupdate.h.

◆ DoThreaded()

bool CsgREupdate::DoThreaded ( void )

inlineoverridevirtual

Reimplemented from votca::csg::CsgApplication.

Definition at line 72 of file csg_reupdate.h.

◆ DoTrajectory()

bool CsgREupdate::DoTrajectory ( void )

inlineoverridevirtual

overload and return true to enable trajectory command line options

Reimplemented from votca::csg::CsgApplication.

Definition at line 68 of file csg_reupdate.h.

◆ EndEvaluate()

void CsgREupdate::EndEvaluate ( )

overridevirtual

called after the last frame

Reimplemented from votca::csg::CsgApplication.

Definition at line 233 of file csg_reupdate.cc.

◆ EvalBonded()

void CsgREupdate::EvalBonded	(	Topology *	conf,
		PotentialInfo *	potinfo
	)

protected

◆ EvalNonbonded()

void CsgREupdate::EvalNonbonded	(	Topology *	conf,
		PotentialInfo *	potinfo
	)

protected

◆ EvaluateOptions()

bool CsgREupdate::EvaluateOptions ( )

overridevirtual

Process command line options.

Returns: true to continue, false to stop

EvaluateOptions is called by Run after parsing the command line. return true if everything is ok, false to stop and show help text.

Reimplemented from votca::csg::CsgApplication.

Definition at line 78 of file csg_reupdate.cc.

◆ ForkWorker()

std::unique_ptr< CsgApplication::Worker > CsgREupdate::ForkWorker ( void )

overridevirtual

User is required to overload ForkWorker and initialize workers.

Returns: worker

Reimplemented from votca::csg::CsgApplication.

Definition at line 458 of file csg_reupdate.cc.

◆ HelpText()

void CsgREupdate::HelpText ( std::ostream & out )

inlineoverridevirtual

help text of application without version information

Parameters

out	ostream for output

Implements votca::tools::Application.

Definition at line 64 of file csg_reupdate.h.

◆ Initialize()

void CsgREupdate::Initialize ( )

overridevirtual

Initialize application data.

Initialize is called by run before parsing the command line. All necessary command line arguments can be added here

Reimplemented from votca::csg::CsgApplication.

Definition at line 45 of file csg_reupdate.cc.

◆ LoadOptions()

void CsgREupdate::LoadOptions ( const std::string & file )

Definition at line 91 of file csg_reupdate.cc.

◆ MergeWorker()

void CsgREupdate::MergeWorker ( Worker * worker )

overridevirtual

User is required to overload MergeWorker and merge data from each worker.

Parameters

worker

Reimplemented from votca::csg::CsgApplication.

Definition at line 505 of file csg_reupdate.cc.

◆ NeedsTopology()

bool CsgREupdate::NeedsTopology ( void )

inlineoverridevirtual

if topology is always needed

Reimplemented from votca::csg::CsgApplication.

Definition at line 75 of file csg_reupdate.h.

◆ ProgramName()

std::string CsgREupdate::ProgramName ( )

inlineoverridevirtual

program name

Returns: string with program name

overload this function to set the program name

Implements votca::tools::Application.

Definition at line 63 of file csg_reupdate.h.

◆ REFormulateLinEq()

void CsgREupdate::REFormulateLinEq ( )

protected

Definition at line 277 of file csg_reupdate.cc.

◆ REUpdateLamda()

void CsgREupdate::REUpdateLamda ( )

protected

Definition at line 307 of file csg_reupdate.cc.

◆ Run()

void CsgREupdate::Run ( )

overridevirtual

Main body of application.

Run is called after command line was parsed + evaluated. All the work should be done in here.

Reimplemented from votca::csg::CsgApplication.

Definition at line 197 of file csg_reupdate.cc.

◆ SynchronizeThreads()

bool CsgREupdate::SynchronizeThreads ( void )

inlineoverridevirtual

Reimplemented from votca::csg::CsgApplication.

Definition at line 73 of file csg_reupdate.h.

◆ WriteOutFiles()

void CsgREupdate::WriteOutFiles ( )

protected

Definition at line 254 of file csg_reupdate.cc.

Member Data Documentation

◆ aardfnorms_

std::vector<double *> CsgREupdate::aardfnorms_

protected

Definition at line 113 of file csg_reupdate.h.

◆ aardfs_

std::vector<Table *> CsgREupdate::aardfs_

protected

Definition at line 112 of file csg_reupdate.h.

◆ beta_

double CsgREupdate::beta_

protected

Definition at line 106 of file csg_reupdate.h.

◆ DS_

Eigen::VectorXd CsgREupdate::DS_

protected

Definition at line 100 of file csg_reupdate.h.

◆ dUFrame_

Eigen::VectorXd CsgREupdate::dUFrame_

protected

Definition at line 101 of file csg_reupdate.h.

◆ gentable_

bool CsgREupdate::gentable_

protected

Definition at line 110 of file csg_reupdate.h.

◆ hessian_check_

bool CsgREupdate::hessian_check_

protected

Definition at line 102 of file csg_reupdate.h.

◆ HS_

Eigen::MatrixXd CsgREupdate::HS_

protected

Definition at line 99 of file csg_reupdate.h.

◆ lamda_

Eigen::VectorXd CsgREupdate::lamda_

protected

Definition at line 97 of file csg_reupdate.h.

◆ nframes_

votca::Index CsgREupdate::nframes_

protected

Definition at line 108 of file csg_reupdate.h.

◆ nlamda_

votca::Index CsgREupdate::nlamda_

protected

Definition at line 96 of file csg_reupdate.h.

◆ nonbonded_

std::vector<Property *> CsgREupdate::nonbonded_

protected

Definition at line 91 of file csg_reupdate.h.

◆ options_

Property CsgREupdate::options_

protected

Definition at line 90 of file csg_reupdate.h.

◆ param_in_ext_

std::string CsgREupdate::param_in_ext_

protected

Definition at line 116 of file csg_reupdate.h.

◆ param_out_ext_

std::string CsgREupdate::param_out_ext_

protected

Definition at line 116 of file csg_reupdate.h.

◆ pot_out_ext_

std::string CsgREupdate::pot_out_ext_

protected

Definition at line 117 of file csg_reupdate.h.

◆ potentials_

PotentialContainer CsgREupdate::potentials_

protected

Definition at line 94 of file csg_reupdate.h.

◆ rdf_ext_

std::string CsgREupdate::rdf_ext_

protected

Definition at line 118 of file csg_reupdate.h.

◆ relax_

double CsgREupdate::relax_

protected

Definition at line 107 of file csg_reupdate.h.

◆ UavgAA_

double CsgREupdate::UavgAA_

protected

Definition at line 104 of file csg_reupdate.h.

◆ UavgCG_

double CsgREupdate::UavgCG_

protected

Definition at line 105 of file csg_reupdate.h.

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

csg/src/tools/csg_reupdate.h
csg/src/tools/csg_reupdate.cc

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ PotentialContainer

Member Function Documentation

◆ AAavgBonded()

◆ AAavgNonbonded()

◆ BeginEvaluate()

◆ DoMapping()

◆ DoThreaded()

◆ DoTrajectory()

◆ EndEvaluate()

◆ EvalBonded()

◆ EvalNonbonded()

◆ EvaluateOptions()

◆ ForkWorker()

◆ HelpText()

◆ Initialize()

◆ LoadOptions()

◆ MergeWorker()

◆ NeedsTopology()

◆ ProgramName()

◆ REFormulateLinEq()

◆ REUpdateLamda()

◆ Run()

◆ SynchronizeThreads()

◆ WriteOutFiles()

Member Data Documentation

◆ aardfnorms_

◆ aardfs_

◆ beta_

◆ DS_

◆ dUFrame_

◆ gentable_

◆ hessian_check_

◆ HS_

◆ lamda_

◆ nframes_

◆ nlamda_

◆ nonbonded_

◆ options_

◆ param_in_ext_

◆ param_out_ext_

◆ pot_out_ext_

◆ potentials_

◆ rdf_ext_

◆ relax_

◆ UavgAA_

◆ UavgCG_