This is used to create PLMD::Action objects that are computed by calculating the same function multiple times. More...

#include <ActionWithVessel.h>

Inheritance diagram for PLMD::vesselbase::ActionWithVessel:

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

typedef std::set< FILE * > ::iterator	files_iterator

Public Member Functions
	ActionWithVessel (const ActionOptions &ao)

	~ActionWithVessel ()

virtual void	unlockContributors ()
	Used to make sure we are calculating everything during neighbor list update step. More...

virtual void	lockContributors ()

virtual void	deactivate_task ()
	Activate the jth colvar Deactivate the current task in future loops. More...

void	chainRuleForElementDerivatives (const unsigned &, const unsigned &, const double &, Vessel *)
	Merge the derivatives. More...

void	chainRuleForElementDerivatives (const unsigned &, const unsigned &, const unsigned &, const unsigned &, const double &, Vessel *)

virtual void	mergeDerivatives (const unsigned &ider, const double &df)

virtual void	clearDerivativesAfterTask (const unsigned &)

virtual bool	isPeriodic ()=0
	Are the base quantities periodic. More...

virtual void	retrieveDomain (std::string &min, std::string &max)
	What are the domains of the base quantities. More...

virtual unsigned	getNumberOfDerivatives ()=0
	Get the number of derivatives for final calculated quantity. More...

virtual void	doJobsRequiredBeforeTaskList ()
	Do any jobs that are required before the task list is undertaken. More...

virtual void	performTask (const unsigned &j)=0
	Calculate one of the functions in the distribution. More...

Vessel *	getVessel (const std::string &name)
	Return a pointer to the field. More...

void	addElementDerivative (const unsigned &, const double &)
	Add some derivative of the quantity in the sum wrt to a numbered element. More...

void	setElementValue (const unsigned &, const double &)
	Set the value of the element. More...

double	getElementValue (const unsigned &ival) const
	Get the value of this element. More...

double	getElementDerivative (const unsigned &) const
	Retrieve the derivative of the quantity in the sum wrt to a numbered element. More...

virtual void	applyBridgeForces (const std::vector< double > &bb)
	Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More...

void	addDependency (Action *)
	Specify that this Action depends on another one. More...

void	clearDependencies ()
	Clear the dependence list for this Action. More...

long int	getStep () const
	Return the present timestep. More...

double	getTime () const
	Return the present time. More...

double	getTimeStep () const
	Return the timestep. More...

template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. More...

template<class T >
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type. More...

template<class T >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...

template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...

void	error (const std::string &msg) const
	Crash calculation and print documentation. More...

void	warning (const std::string &msg)
	Issue a warning. More...

void	exit (int c=0)
	Exit with error code c. More...

void	checkRead ()
	Check if Action was properly read. More...

virtual void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...

virtual void	lockRequests ()

virtual void	unlockRequests ()

virtual void	calculate ()=0
	Calculate an Action. More...

virtual void	apply ()=0
	Apply an Action. More...

virtual void	update ()
	Update. More...

virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...

void	fflush ()
	Tell to the Action to flush open files. More...

virtual std::string	getDocumentation () const

const std::string &	getLabel () const
	Returns the label. More...

const std::string &	getName () const
	Returns the name. More...

virtual void	activate ()
	Set action to active. More...

virtual void	setOption (const std::string &s)

virtual void	clearOptions ()

virtual void	deactivate ()
	Set action to inactive. More...

bool	isActive () const
	Check if action is active. More...

bool	isOptionOn (const std::string &s) const
	Check if an option is on. More...

const Dependencies &	getDependencies () const
	Return dependencies. More...

virtual bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be performed. More...

virtual bool	checkNeedsGradients () const
	Check if the action needs gradient. More...

virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Perform calculation using numerical derivatives N.B. More...

FILE *	fopen (const char path, const char mode)
	Opens a file. More...

int	fclose (FILE *fp)
	Closes a file opened with Action::fclose(). More...

void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input. More...

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. More...

bool	getExchangeStep () const
	Check if we are on an exchange step. More...

std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite. More...

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

Public Attributes
PlumedMain &	plumed
	Reference to main plumed object. More...

Log &	log
	Reference to the log stream. More...

std::set< FILE * >	files

Communicator &	comm

Communicator &	multi_sim_comm

const Keywords &	keywords

Protected Member Functions
void	addVessel (const std::string &name, const std::string &input, const int numlab=0, const std::string thislab="")
	Add a vessel to the list of vessels. More...

void	addVessel (Vessel *vv)

BridgeVessel *	addBridgingVessel (ActionWithVessel *tome)
	Add a bridging vessel to the list of vessels. More...

void	readVesselKeywords ()
	Complete the setup of this object (this routine must be called after construction of ActionWithValue) More...

double	getTolerance () const
	Return the value of the tolerance. More...

double	getNLTolerance () const
	Return the value for the neighbor list tolerance. More...

unsigned	getNumberOfVessels () const
	Get the number of vessels. More...

Vessel *	getPntrToVessel (const unsigned &i)
	Get a pointer to the ith vessel. More...

void	runAllTasks ()
	Calculate the values of all the vessels. More...

void	finishComputations ()
	Finish running all the calculations. More...

void	resizeFunctions ()
	Resize all the functions when the number of derivatives change. More...

void	setElementDerivative (const unsigned &, const double &)
	Set the derivative of the jth element wrt to a numbered element. More...

bool	calculateAllVessels ()
	This loops over all the vessels calculating them and also sets all the element derivatives equal to zero. More...

bool	getForcesFromVessels (std::vector< double > &forcesToApply)
	Retrieve the forces from all the vessels (used in apply) More...

void	accumulateDerivative (const unsigned &ider, const double &df)
	This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives. More...

void	clearAfterTask ()
	Clear tempory data that is calculated for each task. More...

Protected Attributes
bool	contributorsAreUnlocked
	The terms in the series are locked. More...

bool	weightHasDerivatives
	Does the weight have derivatives. More...

unsigned	current
	The numerical index of the task we are curently performing. More...

unsigned	bridgeVariable
	This is used for numerical derivatives of bridge variables. More...

DynamicList< unsigned >	taskList
	The list of tasks we have to perform. More...

Private Attributes
bool	read
	This is used to ensure that we have properly read the action. More...

bool	serial
	Do all calculations in serial. More...

double	tolerance
	The tolerance on the accumulators. More...

double	nl_tolerance
	Tolerance for quantities being put in neighbor lists. More...

std::vector< double >	thisval
	The value of the current element in the sum. More...

std::vector< bool >	thisval_wasset
	A boolean that makes sure we don't accumulate very wrong derivatives. More...

std::vector< double >	derivatives
	Vector of derivatives for the object. More...

unsigned	current_buffer_start
	The buffers we use for mpi summing DistributionFunction objects. More...

unsigned	current_buffer_stride

std::vector< double >	buffer

std::vector< Vessel * >	functions
	Pointers to the functions we are using on each value. More...

std::vector< double >	tmpforces
	Tempory storage for forces. More...

Friends
class	Vessel

class	ShortcutVessel

class	FunctionVessel

class	BridgeVessel

Detailed Description

This is used to create PLMD::Action objects that are computed by calculating the same function multiple times.

This is used in PLMD::MultiColvar.

Definition at line 45 of file ActionWithVessel.h.

Member Typedef Documentation

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

inherited

Definition at line 75 of file Action.h.

typedef std::set<FILE*>::iterator PLMD::Action::files_iterator

inherited

Definition at line 140 of file Action.h.

Constructor & Destructor Documentation

PLMD::vesselbase::ActionWithVessel::ActionWithVessel ( const ActionOptions & ao )

Definition at line 46 of file ActionWithVessel.cpp.

PLMD::vesselbase::ActionWithVessel::~ActionWithVessel ( )

Definition at line 69 of file ActionWithVessel.cpp.

Member Function Documentation

void PLMD::vesselbase::ActionWithVessel::accumulateDerivative	(	const unsigned &	ider,
		const double &	df
	)

inlineprotected

This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives.

Definition at line 213 of file ActionWithVessel.h.

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

Definition at line 127 of file Action.cpp.

BridgeVessel * PLMD::vesselbase::ActionWithVessel::addBridgingVessel ( ActionWithVessel * tome )

protected

Add a bridging vessel to the list of vessels.

Definition at line 85 of file ActionWithVessel.cpp.

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

inherited

Specify that this Action depends on another one.

Definition at line 123 of file Action.cpp.

void PLMD::vesselbase::ActionWithVessel::addElementDerivative	(	const unsigned &	ider,
		const double &	der
	)

inline

Add some derivative of the quantity in the sum wrt to a numbered element.

Definition at line 197 of file ActionWithVessel.h.

void PLMD::vesselbase::ActionWithVessel::addVessel	(	const std::string &	name,
		const std::string &	input,
		const int	numlab = `0`,
		const std::string	thislab = `""`
	)

protected

Add a vessel to the list of vessels.

Definition at line 73 of file ActionWithVessel.cpp.

void PLMD::vesselbase::ActionWithVessel::addVessel ( Vessel * vv )

protected

Definition at line 79 of file ActionWithVessel.cpp.

virtual void PLMD::Action::apply ( )

pure virtualinherited

Apply an Action.

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

Implemented in PLMD::analysis::Analysis, PLMD::multicolvar::ActionVolume, PLMD::multicolvar::MultiColvarBase, PLMD::generic::WholeMolecules, PLMD::generic::DumpAtoms, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Group, PLMD::IMD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::generic::Print, PLMD::generic::Include, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::Debug, PLMD::Colvar, PLMD::generic::Time, PLMD::manyrestraints::ManyRestraintsBase, PLMD::bias::Bias, PLMD::generic::DumpProjections, PLMD::function::Function, PLMD::ActionWithVirtualAtom, and PLMD::ActionSetup.

virtual void PLMD::vesselbase::ActionWithVessel::applyBridgeForces ( const std::vector< double > & bb )

inlinevirtual

Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume.

Reimplemented in PLMD::multicolvar::ActionVolume.

Definition at line 152 of file ActionWithVessel.h.

virtual void PLMD::Action::calculate ( )

pure virtualinherited

Calculate an Action.

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

Implemented in PLMD::bias::MetaD, PLMD::function::FuncSumHills, PLMD::analysis::Analysis, PLMD::colvar::Distance, PLMD::bias::MovingRestraint, PLMD::function::FuncPathMSD, PLMD::multicolvar::ActionVolume, PLMD::bias::External, PLMD::generic::WholeMolecules, PLMD::generic::DumpAtoms, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Group, PLMD::bias::BiasValue, PLMD::colvar::DRMSD, PLMD::colvar::Gyration, PLMD::IMD, PLMD::colvar::ContactMap, PLMD::function::Matheval, PLMD::generic::RandomExchanges, PLMD::colvar::PathMSDBase, PLMD::generic::Read, PLMD::function::Piecewise, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::multicolvar::MultiColvar, PLMD::generic::Include, PLMD::generic::Print, PLMD::vatom::Center, PLMD::function::Combine, PLMD::bias::Restraint, PLMD::generic::Flush, PLMD::colvar::Energy, PLMD::function::Sort, PLMD::multicolvar::MultiColvarFunction, PLMD::vatom::Ghost, PLMD::colvar::Constant, PLMD::colvar::Torsion, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::vatom::COM, PLMD::generic::Debug, PLMD::colvar::Dipole, PLMD::colvar::Cell, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::colvar::Template, PLMD::generic::Time, PLMD::function::Target, PLMD::generic::DumpProjections, PLMD::colvar::RMSD, PLMD::colvar::CoordinationBase, PLMD::manyrestraints::Sphere, and PLMD::ActionSetup.

bool PLMD::vesselbase::ActionWithVessel::calculateAllVessels ( )

protected

This loops over all the vessels calculating them and also sets all the element derivatives equal to zero.

Definition at line 221 of file ActionWithVessel.cpp.

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

Definition at line 205 of file Action.cpp.

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

virtualinherited

Perform calculation using numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing.

Reimplemented in PLMD::ActionAtomistic, PLMD::multicolvar::ActionVolume, PLMD::ActionWithArguments, and PLMD::multicolvar::MultiColvarFunction.

Definition at line 187 of file Action.cpp.

void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives	(	const unsigned &	iout,
		const unsigned &	ider,
		const double &	df,
		Vessel *	valout
	)

Merge the derivatives.

Definition at line 240 of file ActionWithVessel.cpp.

void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives	(	const unsigned &	iout,
		const unsigned &	ider,
		const unsigned &	stride,
		const unsigned &	off,
		const double &	df,
		Vessel *	valout
	)

Definition at line 246 of file ActionWithVessel.cpp.

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

inlinevirtualinherited

Check if the action needs gradient.

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

Definition at line 230 of file Action.h.

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

Definition at line 227 of file Action.h.

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

Definition at line 161 of file Action.cpp.

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

inherited

Cite a paper see PlumedMain::cite.

Definition at line 221 of file Action.cpp.

void PLMD::vesselbase::ActionWithVessel::clearAfterTask ( )

protected

Clear tempory data that is calculated for each task.

Definition at line 208 of file ActionWithVessel.cpp.

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

Definition at line 153 of file Action.cpp.

void PLMD::vesselbase::ActionWithVessel::clearDerivativesAfterTask ( const unsigned & ider )

virtual

Reimplemented in PLMD::multicolvar::ActionVolume, PLMD::multicolvar::MultiColvarBase, and PLMD::secondarystructure::SecondaryStructureRMSD.

Definition at line 216 of file ActionWithVessel.cpp.

void PLMD::Action::clearOptions ( )

virtualinherited

Definition at line 147 of file Action.cpp.

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

Definition at line 369 of file Action.h.

void PLMD::vesselbase::ActionWithVessel::deactivate_task ( )

virtual

Activate the jth colvar Deactivate the current task in future loops.

Reimplemented in PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, and PLMD::manyrestraints::ManyRestraintsBase.

Definition at line 147 of file ActionWithVessel.cpp.

void PLMD::vesselbase::ActionWithVessel::doJobsRequiredBeforeTaskList ( )

virtual

Do any jobs that are required before the task list is undertaken.

Reimplemented in PLMD::multicolvar::ActionVolume.

Definition at line 165 of file ActionWithVessel.cpp.

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

inherited

Crash calculation and print documentation.

Definition at line 195 of file Action.cpp.

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

inherited

Exit with error code c.

Definition at line 183 of file Action.cpp.

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

inherited

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

Definition at line 93 of file Action.cpp.

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

Definition at line 98 of file Action.cpp.

void PLMD::vesselbase::ActionWithVessel::finishComputations ( )

protected

Finish running all the calculations.

Definition at line 232 of file ActionWithVessel.cpp.

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)

Definition at line 83 of file Action.cpp.

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

inlineinherited

Return dependencies.

Definition at line 224 of file Action.h.

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

virtualinherited

Definition at line 157 of file Action.cpp.

double PLMD::vesselbase::ActionWithVessel::getElementDerivative ( const unsigned & ider ) const

inline

Retrieve the derivative of the quantity in the sum wrt to a numbered element.

Definition at line 191 of file ActionWithVessel.h.

double PLMD::vesselbase::ActionWithVessel::getElementValue ( const unsigned & ival ) const

inline

Get the value of this element.

Definition at line 177 of file ActionWithVessel.h.

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

Definition at line 217 of file Action.cpp.

bool PLMD::vesselbase::ActionWithVessel::getForcesFromVessels ( std::vector< double > & forcesToApply )

protected

Retrieve the forces from all the vessels (used in apply)

Definition at line 261 of file ActionWithVessel.cpp.

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

inlineinherited

Returns the label.

Definition at line 263 of file Action.h.

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

inlineinherited

Returns the name.

Definition at line 268 of file Action.h.

double PLMD::vesselbase::ActionWithVessel::getNLTolerance ( ) const

inlineprotected

Return the value for the neighbor list tolerance.

Definition at line 161 of file ActionWithVessel.h.

virtual unsigned PLMD::vesselbase::ActionWithVessel::getNumberOfDerivatives ( )

pure virtual

Get the number of derivatives for final calculated quantity.

Implemented in PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::secondarystructure::SecondaryStructureRMSD, and PLMD::manyrestraints::ManyRestraintsBase.

unsigned PLMD::vesselbase::ActionWithVessel::getNumberOfVessels ( ) const

inlineprotected

Get the number of vessels.

Definition at line 166 of file ActionWithVessel.h.

Vessel * PLMD::vesselbase::ActionWithVessel::getPntrToVessel ( const unsigned & i )

inlineprotected

Get a pointer to the ith vessel.

Definition at line 171 of file ActionWithVessel.h.

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

inherited

Return the present timestep.

Definition at line 169 of file Action.cpp.

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

Definition at line 173 of file Action.cpp.

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

Definition at line 177 of file Action.cpp.

double PLMD::vesselbase::ActionWithVessel::getTolerance ( ) const

inlineprotected

Return the value of the tolerance.

Definition at line 156 of file ActionWithVessel.h.

Vessel* PLMD::vesselbase::ActionWithVessel::getVessel ( const std::string & name )

Return a pointer to the field.

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

Definition at line 375 of file Action.h.

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

inlineinherited

Check if an option is on.

Definition at line 380 of file Action.h.

virtual bool PLMD::vesselbase::ActionWithVessel::isPeriodic ( )

pure virtual

Are the base quantities periodic.

Implemented in PLMD::multicolvar::Angles, PLMD::multicolvar::ActionVolume, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::Distances, PLMD::multicolvar::AlphaBeta, PLMD::multicolvar::CoordinationNumbers, PLMD::multicolvar::Bridge, PLMD::multicolvar::Density, and PLMD::manyrestraints::Sphere.

void PLMD::vesselbase::ActionWithVessel::lockContributors ( )

inlinevirtual

Reimplemented in PLMD::multicolvar::MultiColvarFunction.

Definition at line 225 of file ActionWithVessel.h.

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::ActionAtomistic, and PLMD::ActionWithArguments.

Definition at line 172 of file Action.h.

void PLMD::vesselbase::ActionWithVessel::mergeDerivatives	(	const unsigned &	ider,
		const double &	df
	)

virtual

Reimplemented in PLMD::multicolvar::ActionVolume, PLMD::multicolvar::MultiColvarBase, and PLMD::secondarystructure::SecondaryStructureRMSD.

Definition at line 254 of file ActionWithVessel.cpp.

template<class T >

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

inherited

Parse one keyword as generic type.

Definition at line 273 of file Action.h.

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

inherited

Parse one keyword as boolean flag.

Definition at line 104 of file Action.cpp.

template<class T >

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

inherited

Parse one numbered keyword as generic type.

Definition at line 300 of file Action.h.

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.

Definition at line 352 of file Action.h.

template<class T >

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

inherited

Parse one keyword as std::vector.

Definition at line 311 of file Action.h.

virtual void PLMD::vesselbase::ActionWithVessel::performTask ( const unsigned & j )

pure virtual

Calculate one of the functions in the distribution.

Implemented in PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::secondarystructure::SecondaryStructureRMSD, and PLMD::manyrestraints::Sphere.

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::analysis::Analysis, PLMD::function::FuncPathMSD, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::Print, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

Definition at line 191 of file Action.cpp.

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.

Definition at line 251 of file Action.h.

void PLMD::vesselbase::ActionWithVessel::readVesselKeywords ( )

protected

Complete the setup of this object (this routine must be called after construction of ActionWithValue)

Definition at line 94 of file ActionWithVessel.cpp.

void PLMD::vesselbase::ActionWithVessel::registerKeywords ( Keywords & keys )

static

Definition at line 33 of file ActionWithVessel.cpp.

void PLMD::vesselbase::ActionWithVessel::resizeFunctions ( )

protected

Resize all the functions when the number of derivatives change.

Definition at line 130 of file ActionWithVessel.cpp.

void PLMD::vesselbase::ActionWithVessel::retrieveDomain	(	std::string &	min,
		std::string &	max
	)

virtual

What are the domains of the base quantities.

Definition at line 274 of file ActionWithVessel.cpp.

void PLMD::vesselbase::ActionWithVessel::runAllTasks ( )

protected

Calculate the values of all the vessels.

Definition at line 172 of file ActionWithVessel.cpp.

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::Analysis.

Definition at line 193 of file Action.h.

void PLMD::vesselbase::ActionWithVessel::setElementDerivative	(	const unsigned &	ider,
		const double &	der
	)

inlineprotected

Set the derivative of the jth element wrt to a numbered element.

Definition at line 207 of file ActionWithVessel.h.

void PLMD::vesselbase::ActionWithVessel::setElementValue	(	const unsigned &	ival,
		const double &	val
	)

inline

Set the value of the element.

Definition at line 182 of file ActionWithVessel.h.

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

virtualinherited

Definition at line 141 of file Action.cpp.

void PLMD::vesselbase::ActionWithVessel::unlockContributors ( )

inlinevirtual

Used to make sure we are calculating everything during neighbor list update step.

Reimplemented in PLMD::multicolvar::MultiColvarFunction.

Definition at line 219 of file ActionWithVessel.h.

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::ActionAtomistic, and PLMD::ActionWithArguments.

Definition at line 173 of file Action.h.

virtual void PLMD::Action::update ( )

inlinevirtualinherited

Update.

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

Reimplemented in PLMD::bias::MetaD, PLMD::analysis::Analysis, PLMD::generic::DumpAtoms, PLMD::generic::Read, PLMD::generic::Print, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, and PLMD::generic::DumpProjections.

Definition at line 188 of file Action.h.

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

inherited

Issue a warning.

Definition at line 201 of file Action.cpp.

Friends And Related Function Documentation

friend class BridgeVessel

friend

Definition at line 49 of file ActionWithVessel.h.

friend class FunctionVessel

friend

Definition at line 48 of file ActionWithVessel.h.

friend class ShortcutVessel

friend

Definition at line 47 of file ActionWithVessel.h.

friend class Vessel

friend

Definition at line 46 of file ActionWithVessel.h.

Member Data Documentation

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable

protected

This is used for numerical derivatives of bridge variables.

Definition at line 81 of file ActionWithVessel.h.

std::vector<double> PLMD::vesselbase::ActionWithVessel::buffer

private

Definition at line 68 of file ActionWithVessel.h.

Communicator& PLMD::Action::comm

inherited

Definition at line 158 of file Action.h.

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked

protected

The terms in the series are locked.

Definition at line 75 of file ActionWithVessel.h.

unsigned PLMD::vesselbase::ActionWithVessel::current

protected

The numerical index of the task we are curently performing.

Definition at line 79 of file ActionWithVessel.h.

unsigned PLMD::vesselbase::ActionWithVessel::current_buffer_start

private

The buffers we use for mpi summing DistributionFunction objects.

Definition at line 66 of file ActionWithVessel.h.

unsigned PLMD::vesselbase::ActionWithVessel::current_buffer_stride

private

Definition at line 67 of file ActionWithVessel.h.

std::vector<double> PLMD::vesselbase::ActionWithVessel::derivatives

private

Vector of derivatives for the object.

Definition at line 64 of file ActionWithVessel.h.

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

inherited

Definition at line 139 of file Action.h.

std::vector<Vessel*> PLMD::vesselbase::ActionWithVessel::functions

private

Pointers to the functions we are using on each value.

Definition at line 70 of file ActionWithVessel.h.

const Keywords& PLMD::Action::keywords

inherited

Definition at line 161 of file Action.h.

Log& PLMD::Action::log

inherited

Reference to the log stream.

Definition at line 93 of file Action.h.

Communicator& PLMD::Action::multi_sim_comm

inherited

Definition at line 159 of file Action.h.

double PLMD::vesselbase::ActionWithVessel::nl_tolerance

private

Tolerance for quantities being put in neighbor lists.

Definition at line 58 of file ActionWithVessel.h.

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

Definition at line 90 of file Action.h.

bool PLMD::vesselbase::ActionWithVessel::read

private

This is used to ensure that we have properly read the action.

Definition at line 52 of file ActionWithVessel.h.

bool PLMD::vesselbase::ActionWithVessel::serial

private

Do all calculations in serial.

Definition at line 54 of file ActionWithVessel.h.

DynamicList<unsigned> PLMD::vesselbase::ActionWithVessel::taskList

protected

The list of tasks we have to perform.

Definition at line 83 of file ActionWithVessel.h.

std::vector<double> PLMD::vesselbase::ActionWithVessel::thisval

private

The value of the current element in the sum.

Definition at line 60 of file ActionWithVessel.h.

std::vector<bool> PLMD::vesselbase::ActionWithVessel::thisval_wasset

private

A boolean that makes sure we don't accumulate very wrong derivatives.

Definition at line 62 of file ActionWithVessel.h.

std::vector<double> PLMD::vesselbase::ActionWithVessel::tmpforces

private

Tempory storage for forces.

Definition at line 72 of file ActionWithVessel.h.

double PLMD::vesselbase::ActionWithVessel::tolerance

private

The tolerance on the accumulators.

Definition at line 56 of file ActionWithVessel.h.

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protected

Does the weight have derivatives.

Definition at line 77 of file ActionWithVessel.h.

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

vesselbase/ActionWithVessel.h
vesselbase/ActionWithVessel.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation