Provides the keyword DUMPDERIVATIVES . More...

Inheritance diagram for PLMD::generic::DumpDerivatives:

Public Types
typedef std::vector< Action * >	Dependencies

Public Member Functions
	DumpDerivatives (const ActionOptions &)
	~DumpDerivatives ()
virtual void	activate ()
	Set action to active.
void	addDependency (Action *)
	Specify that this Action depends on another one.
void	addForcesOnArguments (const std::vector< double > &forces)
	Add forces to arguments (used in apply).
void	apply () override
	Apply an Action.
virtual void	beforeUpdate ()
	Before Update.
double	bringBackInPbc (int i, double d1) const
	Takes one value and brings it back into the pbc of argument i.
void	calculate () override
	Calculate an Action.
void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input.
void	calculateNumericalDerivatives (ActionWithValue *a=NULL) override
	Calculate the numerical derivatives N.B.
virtual bool	checkNeedsGradients () const
	Check if the action needs gradient.
virtual bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be performed.
void	checkRead ()
	Check if Action was properly read.
bool	checkUpdate () const
	Check if action should be updated.
std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite.
void	clearDependencies ()
	Clear the dependence list for this Action.
virtual void	clearOptions ()
virtual void	deactivate ()
	Set action to inactive.
double	difference (int, double, double) const
	Takes the difference taking into account pbc for arg i.
void	error (const std::string &msg) const
	Crash calculation and print documentation.
void	exit (int c=0)
	Exit with error code c.
int	fclose (FILE *fp)
	Closes a file opened with Action::fclose().
void	fflush ()
	Tell to the Action to flush open files.
FILE *	fopen (const char path, const char mode)
	Opens a file.
double	getArgument (const unsigned n) const
	Returns the value of an argument.
virtual const std::vector< Value * > &	getArguments () const
	Returns an array of pointers to the arguments.
bool	getCPT () const
	Return true if we are doing at a checkpoint step.
std::string	getDefaultString () const
	Get the defaults.
const Dependencies &	getDependencies () const
	Return dependencies.
bool	getExchangeStep () const
	Check if we are on an exchange step.
std::string	getKeyword (const std::string &key)
	Just read one of the keywords and return the whole thing as a string.
const std::string &	getLabel () const
	Returns the label.
const std::string &	getName () const
	Returns the name.
virtual unsigned	getNumberOfArguments () const
	Returns the number of arguments.
Value *	getPntrToArgument (const unsigned n)
	Return a pointer to specific argument.
double	getProjection (unsigned i, unsigned j) const
	Get the scalar product between the gradients of two variables.
bool	getRestart () const
	Return true if we are doing a restart.
long long int	getStep () const
	Return the present timestep.
int	getStride () const
	Get the stride.
double	getTime () const
	Return the present time.
double	getTimeStep () const
	Return the timestep.
void	interpretArgumentList (const std::vector< std::string > &c, std::vector< Value * > &arg)
	Convert a list of argument names into a list of pointers to the values.
bool	isActive () const
	Check if action is active.
bool	isOptionOn (const std::string &s) const
	Check if an option is on.
void	lockRequests () override
virtual bool	onStep () const
	Check if the action is active on this step.
template<class T>
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type.
bool	parseArgumentList (const std::string &key, int i, std::vector< Value * > &args)
	Parse a numbered list of arguments.
void	parseArgumentList (const std::string &key, std::vector< Value * > &args)
	Parse a list of arguments.
void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag.
template<class T>
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type.
template<class T>
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number.
template<class T>
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector.
virtual void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.
virtual void	readAtomsFromPDB (const PDB &)
	This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.
void	requestArguments (const std::vector< Value * > &arg)
	Setup the dependencies.
void	requestExtraDependencies (const std::vector< Value * > &extra)
virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation.
virtual void	setOption (const std::string &s)
void	setStride (const int &n)
	Set the value of the stride.
void	unlockRequests () override
void	update () override
	Update.
void	warning (const std::string &msg)
	Issue a warning.

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

Public Attributes
Communicator &	comm
std::set< FILE * >	files
const Keywords &	keywords
Log &	log
	Reference to the log stream.
Communicator &	multi_sim_comm
PlumedMain &	plumed
	Reference to main plumed object.

Protected Member Functions
void	expandArgKeywordInPDB (const PDB &pdb)
	This changes the arg keyword in the pdb file.

Private Attributes
std::vector< Value * >	arguments
std::string	file
std::string	fmt
bool	lockRequestArguments
OFile	of
int	stride

Detailed Description

Provides the keyword DUMPDERIVATIVES .

Member Typedef Documentation

◆ Dependencies

typedef std::vector<Action*> PLMD::Action::Dependencies

inherited

Constructor & Destructor Documentation

◆ DumpDerivatives()

PLMD::generic::DumpDerivatives::DumpDerivatives ( const ActionOptions & ao )

explicit

◆ ~DumpDerivatives()

PLMD::generic::DumpDerivatives::~DumpDerivatives ( )

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addDependency()

void PLMD::Action::addDependency ( Action * action )

inherited

Specify that this Action depends on another one.

◆ addForcesOnArguments()

void PLMD::ActionWithArguments::addForcesOnArguments ( const std::vector< double > & forces )

inherited

Add forces to arguments (used in apply).

◆ apply()

void PLMD::generic::DumpDerivatives::apply ( )

inlineoverridevirtual

Apply an Action.

This method is called one time per step. The set of all Actions is applied in backward order.

Implements PLMD::Action.

◆ beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

inlinevirtualinherited

Before Update.

This is a special method that is called just before the update() method. It can be used by actions that want to do something irrespectively of the fact that update() is active or not. In other words, this is always called, even when action is not active.

Reimplemented in PLMD::generic::UpdateIf.

◆ bringBackInPbc()

double PLMD::ActionWithArguments::bringBackInPbc	(	int	i,
		double	d1 ) const

inlineinherited

Takes one value and brings it back into the pbc of argument i.

◆ calculate()

void PLMD::generic::DumpDerivatives::calculate ( )

inlineoverridevirtual

Calculate an Action.

This method is called one or more times per step. The set of all Actions is calculated in forward order.

Implements PLMD::Action.

◆ calculateFromPDB()

void PLMD::Action::calculateFromPDB ( const PDB & pdb )

inherited

Calculate the action given a pdb file as input.

This is used to initialize things like distance from a point in CV map space given a pdb as an input file

◆ calculateNumericalDerivatives()

void PLMD::ActionWithArguments::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

overridevirtualinherited

Calculate the numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::Action.

Reimplemented in PLMD::analysis::AnalysisBase, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::mapping::Mapping, PLMD::mapping::PCAVars, and PLMD::vesselbase::ActionWithAveraging.

◆ checkNeedsGradients()

virtual bool PLMD::Action::checkNeedsGradients ( ) const

inlinevirtualinherited

Check if the action needs gradient.

Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.

◆ checkNumericalDerivatives()

virtual bool PLMD::Action::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

This checks if Action::line is empty. It must be called after a final Action has been initialized

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

std::string PLMD::Action::cite ( const std::string & s )

inherited

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ difference()

double PLMD::ActionWithArguments::difference	(	int	i,
		double	d1,
		double	d2 ) const

inlineinherited

Takes the difference taking into account pbc for arg i.

◆ error()

void PLMD::Action::error ( const std::string & msg ) const

inherited

Crash calculation and print documentation.

◆ exit()

void PLMD::Action::exit ( int c = 0 )

inherited

Exit with error code c.

◆ expandArgKeywordInPDB()

void PLMD::ActionWithArguments::expandArgKeywordInPDB ( const PDB & pdb )

protectedinherited

This changes the arg keyword in the pdb file.

◆ fclose()

int PLMD::Action::fclose ( FILE * fp )

inherited

Closes a file opened with Action::fclose().

◆ fflush()

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

◆ fopen()

FILE * PLMD::Action::fopen	(	const char *	path,
		const char *	mode )

inherited

Opens a file.

This is similar to plain fopen, but with some extra functionality.

When opened for writing, processors other than the one with rank 0 just open /dev/null
PlumedMain::fopen is used, so that other tricks may appear (see PlumedMain::fopen)

◆ getArgument()

double PLMD::ActionWithArguments::getArgument ( const unsigned n ) const

inlineinherited

Returns the value of an argument.

◆ getArguments()

const std::vector< Value * > & PLMD::ActionWithArguments::getArguments ( ) const

inlinevirtualinherited

Returns an array of pointers to the arguments.

Reimplemented in PLMD::vesselbase::ActionWithAveraging.

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getDefaultString()

std::string PLMD::Action::getDefaultString ( ) const

inlineinherited

Get the defaults.

◆ getDependencies()

const Dependencies & PLMD::Action::getDependencies ( ) const

inlineinherited

Return dependencies.

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getKeyword()

std::string PLMD::Action::getKeyword ( const std::string & key )

inherited

Just read one of the keywords and return the whole thing as a string.

◆ getLabel()

const std::string & PLMD::Action::getLabel ( ) const

inlineinherited

Returns the label.

◆ getName()

const std::string & PLMD::Action::getName ( ) const

inlineinherited

Returns the name.

◆ getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const

inlinevirtualinherited

Returns the number of arguments.

Reimplemented in PLMD::vesselbase::ActionWithAveraging.

◆ getPntrToArgument()

Value * PLMD::ActionWithArguments::getPntrToArgument ( const unsigned n )

inlineinherited

Return a pointer to specific argument.

◆ getProjection()

double PLMD::ActionWithArguments::getProjection	(	unsigned	i,
		unsigned	j ) const

inherited

Get the scalar product between the gradients of two variables.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getStep()

long long int PLMD::Action::getStep ( ) const

inherited

Return the present timestep.

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ interpretArgumentList()

void PLMD::ActionWithArguments::interpretArgumentList	(	const std::vector< std::string > &	c,
		std::vector< Value * > &	arg )

inherited

Convert a list of argument names into a list of pointers to the values.

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isOptionOn()

bool PLMD::Action::isOptionOn ( const std::string & s ) const

inlineinherited

Check if an option is on.

◆ lockRequests()

void PLMD::ActionWithArguments::lockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::analysis::AnalysisBase, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::mapping::Mapping, PLMD::mapping::PCAVars, and PLMD::vesselbase::ActionWithAveraging.

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ parse()

template<class T>

void PLMD::Action::parse	(	const std::string &	key,
		T &	t )

inherited

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

bool PLMD::ActionWithArguments::parseArgumentList	(	const std::string &	key,
		int	i,
		std::vector< Value * > &	args )

inherited

Parse a numbered list of arguments.

◆ parseArgumentList() [2/2]

void PLMD::ActionWithArguments::parseArgumentList	(	const std::string &	key,
		std::vector< Value * > &	args )

inherited

Parse a list of arguments.

◆ parseFlag()

void PLMD::Action::parseFlag	(	const std::string &	key,
		bool &	t )

inherited

Parse one keyword as boolean flag.

◆ parseNumbered()

template<class T>

bool PLMD::Action::parseNumbered	(	const std::string &	key,
		const int	no,
		T &	t )

inherited

Parse one numbered keyword as generic type.

◆ parseNumberedVector()

template<class T>

bool PLMD::Action::parseNumberedVector	(	const std::string &	key,
		const int	no,
		std::vector< T > &	t )

inherited

Parse a vector with a number.

◆ parseVector()

template<class T>

void PLMD::Action::parseVector	(	const std::string &	key,
		std::vector< T > &	t )

inherited

Parse one keyword as std::vector.

◆ prepare()

void PLMD::Action::prepare ( )

virtualinherited

Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.

Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.

Reimplemented in PLMD::colvar::CoordinationBase, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, PLMD::function::FuncPathGeneral, PLMD::function::FuncPathMSD, PLMD::generic::DumpMassCharge, PLMD::generic::Plumed, PLMD::generic::Print, PLMD::generic::Read, PLMD::generic::UpdateIf, PLMD::GenericMolInfo, PLMD::gridtools::ConvertToFES, PLMD::isdb::EMMI, PLMD::maze::Optimizer, PLMD::multicolvar::MultiColvarBase, and PLMD::s2cm::S2ContactModel.

◆ readAtomsFromPDB()

virtual void PLMD::Action::readAtomsFromPDB ( const PDB & )

inlinevirtualinherited

This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.

Reimplemented in PLMD::ActionAtomistic.

◆ registerKeywords()

void PLMD::generic::DumpDerivatives::registerKeywords ( Keywords & keys )

static

◆ requestArguments()

void PLMD::ActionWithArguments::requestArguments ( const std::vector< Value * > & arg )

inherited

Setup the dependencies.

◆ requestExtraDependencies()

void PLMD::ActionWithArguments::requestExtraDependencies ( const std::vector< Value * > & extra )

inherited

◆ runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtualinherited

RunFinalJobs This method is called once at the very end of the calculation.

The set of all Actions in run for the final time in forward order.

Reimplemented in PLMD::analysis::AnalysisBase, PLMD::analysis::ReadDissimilarityMatrix, PLMD::gridtools::ConvertToFES, PLMD::gridtools::GridPrintingBase, and PLMD::vesselbase::ActionWithAveraging.

◆ setOption()

void PLMD::Action::setOption ( const std::string & s )

virtualinherited

◆ setStride()

void PLMD::ActionPilot::setStride ( const int & n )

inherited

Set the value of the stride.

◆ unlockRequests()

void PLMD::ActionWithArguments::unlockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::analysis::AnalysisBase, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::mapping::Mapping, PLMD::mapping::PCAVars, and PLMD::vesselbase::ActionWithAveraging.

◆ update()

void PLMD::generic::DumpDerivatives::update ( )

overridevirtual

Update.

This method is called one time per step. The set of all Actions is updated in forward order.

Reimplemented from PLMD::Action.

◆ warning()

void PLMD::Action::warning ( const std::string & msg )

inherited

Issue a warning.

Member Data Documentation

◆ arguments

std::vector<Value*> PLMD::ActionWithArguments::arguments

privateinherited

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ file

std::string PLMD::generic::DumpDerivatives::file

private

◆ files

std::set<FILE*> PLMD::Action::files

inherited

◆ fmt

std::string PLMD::generic::DumpDerivatives::fmt

private

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ lockRequestArguments

bool PLMD::ActionWithArguments::lockRequestArguments

privateinherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ of

OFile PLMD::generic::DumpDerivatives::of

private

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ stride

int PLMD::ActionPilot::stride

privateinherited

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

generic/DumpDerivatives.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ DumpDerivatives()

◆ ~DumpDerivatives()

Member Function Documentation

◆ activate()

◆ addDependency()

◆ addForcesOnArguments()

◆ apply()

◆ beforeUpdate()

◆ bringBackInPbc()

◆ calculate()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives()

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearOptions()

◆ deactivate()

◆ difference()

◆ error()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ fopen()

◆ getArgument()

◆ getArguments()

◆ getCPT()

◆ getDefaultString()

◆ getDependencies()

◆ getExchangeStep()

◆ getKeyword()

◆ getLabel()

◆ getName()

◆ getNumberOfArguments()

◆ getPntrToArgument()

◆ getProjection()

◆ getRestart()

◆ getStep()

◆ getStride()

◆ getTime()

◆ getTimeStep()

◆ interpretArgumentList()

◆ isActive()

◆ isOptionOn()

◆ lockRequests()

◆ onStep()

◆ parse()

◆ parseArgumentList() [1/2]

◆ parseArgumentList() [2/2]

◆ parseFlag()

◆ parseNumbered()

◆ parseNumberedVector()

◆ parseVector()

◆ prepare()

◆ readAtomsFromPDB()

◆ registerKeywords()

◆ requestArguments()

◆ requestExtraDependencies()

◆ runFinalJobs()

◆ setOption()

◆ setStride()

◆ unlockRequests()

◆ update()

◆ warning()

Member Data Documentation

◆ arguments

◆ comm