Adds/subtracts forces from given atomistic trajectories. More...

#include <traj_force.h>

Inheritance diagram for TrajForce:

[legend]

Collaboration diagram for TrajForce:

[legend]

Public Member Functions
string	ProgramName () override
	program name

void	HelpText (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

void	Initialize (void) override
	Initialize application data.

bool	EvaluateOptions () override
	Process command line options.

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

void	EndEvaluate () override
	called after the last frame

void	EvalConfiguration (Topology conf, Topology conf_atom) override
	called for each frame which is mapped

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 Member Functions
void	WriteOutFiles ()
	Write results to output files.

void	OpenForcesTrajectory ()

virtual void	ShowHelpText (std::ostream &out)

Protected Attributes
double	scale_
	Scaling of forces, +1 for addition and -1 for subtraction.

Topology	top_force_

std::unique_ptr< TrajectoryReader >	trjreader_force_

std::unique_ptr< TrajectoryWriter >	trjwriter_

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

Adds/subtracts forces from given atomistic trajectories.

Definition at line 39 of file traj_force.h.

Member Function Documentation

◆ BeginEvaluate()

void TrajForce::BeginEvaluate	(	Topology *	top,
		Topology *	top_atom
	)

overridevirtual

called before the first frame

Reimplemented from votca::csg::CsgApplication.

Definition at line 66 of file traj_force.cc.

◆ DoMapping()

bool TrajForce::DoMapping ( void )

inlineoverridevirtual

overload and return true to enable mapping command line options

Reimplemented from votca::csg::CsgApplication.

Definition at line 47 of file traj_force.h.

◆ DoTrajectory()

bool TrajForce::DoTrajectory ( void )

inlineoverridevirtual

overload and return true to enable trajectory command line options

Reimplemented from votca::csg::CsgApplication.

Definition at line 46 of file traj_force.h.

◆ EndEvaluate()

void TrajForce::EndEvaluate ( )

overridevirtual

called after the last frame

Reimplemented from votca::csg::CsgApplication.

Definition at line 89 of file traj_force.cc.

◆ EvalConfiguration()

void TrajForce::EvalConfiguration	(	Topology *	conf,
		Topology *	conf_atom
	)

overridevirtual

called for each frame which is mapped

Reimplemented from votca::csg::CsgApplication.

Definition at line 97 of file traj_force.cc.

◆ EvaluateOptions()

bool TrajForce::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 57 of file traj_force.cc.

◆ HelpText()

void TrajForce::HelpText ( ostream & out )

inlineoverridevirtual

help text of application without version information

Parameters

out	ostream for output

Implements votca::tools::Application.

Definition at line 42 of file traj_force.h.

◆ Initialize()

void TrajForce::Initialize ( void )

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 40 of file traj_force.cc.

◆ OpenForcesTrajectory()

void TrajForce::OpenForcesTrajectory ( )

protected

◆ ProgramName()

string TrajForce::ProgramName ( )

inlineoverridevirtual

program name

Returns: string with program name

overload this function to set the program name

Implements votca::tools::Application.

Definition at line 41 of file traj_force.h.

◆ WriteOutFiles()

void TrajForce::WriteOutFiles ( )

protected

Write results to output files.

Definition at line 95 of file traj_force.cc.

Member Data Documentation

◆ scale_

double TrajForce::scale_

protected

Scaling of forces, +1 for addition and -1 for subtraction.

Definition at line 61 of file traj_force.h.

◆ top_force_

Topology TrajForce::top_force_

protected

Definition at line 66 of file traj_force.h.

◆ trjreader_force_

std::unique_ptr<TrajectoryReader> TrajForce::trjreader_force_

protected

Definition at line 67 of file traj_force.h.

◆ trjwriter_

std::unique_ptr<TrajectoryWriter> TrajForce::trjwriter_

protected

Definition at line 68 of file traj_force.h.

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

csg/src/csgapps/traj_force/traj_force.h
csg/src/csgapps/traj_force/traj_force.cc

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

◆ BeginEvaluate()

◆ DoMapping()

◆ DoTrajectory()

◆ EndEvaluate()

◆ EvalConfiguration()

◆ EvaluateOptions()

◆ HelpText()

◆ Initialize()

◆ OpenForcesTrajectory()

◆ ProgramName()

◆ WriteOutFiles()

Member Data Documentation

◆ scale_

◆ top_force_

◆ trjreader_force_

◆ trjwriter_