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:

[legend]

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

Public Member Functions
	ActionWithVessel (const ActionOptions &ao)

	~ActionWithVessel ()

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

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

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

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

virtual void	beforeUpdate ()
	Before Update. More...

StoreDataVessel *	buildDataStashes (ActionWithVessel *actionThatUses)
	Ensure that data required in other vessels is stored. More...

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

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

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

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

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

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

bool	checkUpdate () const
	Check if action should be updated. More...

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

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

virtual void	clearOptions ()

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

bool	derivativesAreRequired () const
	Are derivatives required for this quantity. More...

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

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

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

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

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

virtual void	finishComputations (const std::vector< double > &buffer)
	Finish running all the calculations. More...

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

unsigned	getActiveTask (const unsigned &ii) const
	Get the ith of the currently active tasks. More...

bool	getCPT () const
	Return true if we are doing at a checkpoint step. More...

unsigned	getCurrentNumberOfActiveTasks () const
	Get the number of tasks that are currently active. More...

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

virtual std::string	getDocumentation () const

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

unsigned	getFullNumberOfTasks () const
	Get the full size of the taskList dynamic list. More...

std::string	getKeyword (const std::string &key)
	Just read one of the keywords and return the whole thing as a string. More...

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

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

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

virtual unsigned	getNumberOfQuantities () const
	Get the number of quantities that are calculated during each task. More...

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

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

unsigned	getPositionInCurrentTaskList (const unsigned &myind) const
	Return the position in the current task list. More...

unsigned	getPositionInFullTaskList (const unsigned &ii) const
	Get the position of the ith active task in the full list. More...

bool	getRestart () const
	Return true if we are doing a restart. More...

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

unsigned	getTaskCode (const unsigned &ii) const
	Get the code for the ii th task in the list. More...

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

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

Vessel *	getVesselWithName (const std::string &mynam)
	These are overwritten in MultiColvarFunction. More...

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

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

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

void	lockContributors ()

virtual void	lockRequests ()

virtual void	normalizeVector (std::vector< double > &vals) const
	These normalizes vectors and is used in StoreDataVessel. More...

virtual void	normalizeVectorDerivatives (MultiValue &myvals) const

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

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. 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 >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...

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

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

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

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

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

bool	taskIsCurrentlyActive (const unsigned &index) const
	Check whether or not a particular task is currently active. More...

virtual bool	threadSafe () const
	Is this action thread safe. More...

virtual void	transformBridgedDerivatives (const unsigned &current, MultiValue &invals, MultiValue &outvals) const
	Do the task if we have a bridge. More...

virtual void	unlockRequests ()

virtual void	update ()
	Update. More...

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

bool	weightWithDerivatives () const
	Does the weight have derivatives. More...

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. More...

Communicator &	multi_sim_comm

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

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

void	addTaskToList (const unsigned &taskCode)
	Add a task to the full list. More...

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

void	addVessel (std::unique_ptr< Vessel > vv)

void	calculateAllVessels (const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list)
	This loops over all the vessels calculating them and also sets all the element derivatives equal to zero. More...

void	deactivateAllTasks ()
	Deactivate all the tasks in the task list. More...

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

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

unsigned	getSizeOfBuffer (unsigned &bufsize)
	Get the size of the buffer. More...

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

void	needsDerivatives ()
	Turn on the derivatives in the vessel. More...

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

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

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

bool	serialCalculation () const
	Is the calculation being done in serial. More...

void	setLowMemOption (const bool &)
	Set that we are using low memory. More...

bool	usingLowMem () const
	Are we using low memory. More...

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

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

bool	dertime
	This is also used to minimise computational expense in complex functions. More...

StoreDataVessel *	mydata
	A pointer to the object that stores data. More...

std::vector< unsigned >	taskFlags
	This list is used to update the neighbor list. More...

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

Private Attributes
bool	actionIsBridged
	This tells plumed that this is used in a bridge. More...

std::vector< double >	buffer
	The buffer that we use (we keep a copy here to avoid resizing) More...

std::vector< unsigned >	der_list
	The list of atoms involved in derivatives (we keep a copy here to avoid resizing) More...

bool	dertime_can_be_off
	These are used to minmise computational expense in complex functions. More...

std::vector< unsigned >	fullTaskList
	Ths full list of tasks we have to perform. More...

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

std::vector< unsigned >	indexOfTaskInFullList
	The indices of the tasks in the full list of tasks. More...

bool	lowmem
	Lower memory requirements. More...

unsigned	maxderivatives
	The maximum number of derivatives we can use before we need to invoke lowmem. More...

unsigned	nactive_tasks
	The current number of active tasks. More...

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

bool	noderiv
	Are we skipping the calculation of the derivatives. More...

std::vector< unsigned >	partialTaskList
	The list of currently active tasks. More...

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

Stopwatch &	stopwatch =*stopwatch_fwd
	The stopwatch that times the different parts of the calculation. More...

ForwardDecl< Stopwatch >	stopwatch_fwd

bool	timers
	Do we want to output information on the timings of different parts of the calculation. More...

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

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

Friends
class	ActionWithInputVessel

class	BridgeVessel

class	FunctionVessel

class	OrderingVessel

class	ShortcutVessel

class	StoreDataVessel

class	Vessel

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.

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ ActionWithVessel()

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

explicit

◆ ~ActionWithVessel()

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

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addBridgingVessel()

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

protected

Add a bridging vessel to the list of vessels.

◆ addDependency()

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

inherited

Specify that this Action depends on another one.

◆ addTaskToList()

void PLMD::vesselbase::ActionWithVessel::addTaskToList ( const unsigned & taskCode )

protected

Add a task to the full list.

◆ addVessel() [1/2]

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

protected

Add a vessel to the list of vessels.

◆ addVessel() [2/2]

void PLMD::vesselbase::ActionWithVessel::addVessel ( std::unique_ptr< Vessel > vv )

protected

◆ apply()

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::Histogram, PLMD::isdb::MetainferenceBase, PLMD::generic::FitToTemplate, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::multicolvar::MultiColvarBase, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::generic::DumpAtoms, PLMD::generic::Group, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::WholeMolecules, PLMD::generic::ResetCell, PLMD::generic::DumpMassCharge, PLMD::multicolvar::MultiColvarDensity, PLMD::ves::OutputFesBias, PLMD::adjmat::Sprint, PLMD::analysis::Average, PLMD::generic::Read, PLMD::mapping::Mapping, PLMD::analysis::AnalysisBase, PLMD::multicolvar::DistanceFromContour, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::ves::OutputBasisFunctions, PLMD::ves::OutputTargetDistribution, PLMD::adjmat::OutputCluster, PLMD::generic::RandomExchanges, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::manyrestraints::ManyRestraintsBase, PLMD::generic::DumpProjections, PLMD::generic::Debug, PLMD::Colvar, PLMD::adjmat::DumpGraph, PLMD::adjmat::ClusteringBase, PLMD::bias::Bias, PLMD::generic::Time, PLMD::function::Function, PLMD::bias::ReweightBase, PLMD::ActionShortcut, PLMD::ActionWithVirtualAtom, PLMD::gridtools::ActionWithInputGrid, PLMD::gridtools::ActionWithIntegral, PLMD::ActionAnyorder, PLMD::ActionSetup, and PLMD::gridtools::GridPrintingBase.

◆ applyBridgeForces()

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::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.

◆ 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.

◆ buildDataStashes()

StoreDataVessel * PLMD::vesselbase::ActionWithVessel::buildDataStashes ( ActionWithVessel * actionThatUses )

Ensure that data required in other vessels is stored.

◆ calculate()

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::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::logmfd::LogMFD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::isdb::EMMI, PLMD::eds::EDS, PLMD::function::FuncPathMSD, PLMD::isdb::RDC, PLMD::piv::PIV, PLMD::function::FuncSumHills, PLMD::generic::FitToTemplate, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::function::Custom, PLMD::ves::VesDeltaF, PLMD::multicolvar::MultiColvarBase, PLMD::bias::MaxEnt, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::isdb::Rescale, PLMD::generic::Include, PLMD::generic::DumpAtoms, PLMD::generic::Group, PLMD::isdb::SAXS, PLMD::colvar::Dimer, PLMD::maze::OptimizerBias, PLMD::vatom::Center, PLMD::bias::ExtendedLagrangian, PLMD::bias::External, PLMD::colvar::DRMSD, PLMD::colvar::ContactMap, PLMD::colvar::Distance, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::MovingRestraint, PLMD::colvar::ERMSD, PLMD::generic::WholeMolecules, PLMD::function::Target, PLMD::generic::ResetCell, PLMD::generic::DumpMassCharge, PLMD::mapping::AdaptivePath, PLMD::function::annfunc::ANN, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::adjmat::Sprint, PLMD::colvar::Torsion, PLMD::colvar::EEFSolv, PLMD::generic::Read, PLMD::analysis::Average, PLMD::analysis::AnalysisBase, PLMD::isdb::Caliber, PLMD::multicolvar::CenterOfMultiColvar, PLMD::vatom::FixedAtom, PLMD::colvar::Gyration, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::colvar::PathMSDBase, PLMD::isdb::FretEfficiency, PLMD::generic::UpdateIf, PLMD::maze::Optimizer, PLMD::multicolvar::DistanceFromContour, PLMD::isdb::PRE, PLMD::ves::OutputBasisFunctions, PLMD::function::Combine, PLMD::generic::Print, PLMD::colvar::Position, PLMD::ves::OutputTargetDistribution, PLMD::function::LocalEnsemble, PLMD::adjmat::OutputCluster, PLMD::bias::BiasValue, PLMD::isdb::NOE, PLMD::colvar::Puckering, PLMD::generic::RandomExchanges, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::DumpMultiColvar, PLMD::adjmat::ClusterDistribution, PLMD::function::Piecewise, PLMD::bias::LWalls, PLMD::isdb::Select, PLMD::maze::Loss, PLMD::bias::UWalls, PLMD::adjmat::ClusterDiameter, PLMD::analysis::Committor, PLMD::adjmat::ClusterSize, PLMD::colvar::Dipole, PLMD::colvar::Energy, PLMD::bias::Restraint, PLMD::colvar::Constant, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::adjmat::ClusterProperties, PLMD::function::Ensemble, PLMD::function::Stats, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::function::Sort, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::colvar::ExtraCV, PLMD::generic::Debug, PLMD::colvar::Template, PLMD::generic::DumpProjections, PLMD::manyrestraints::ManyRestraintsBase, PLMD::vatom::Ghost, PLMD::colvar::Cell, PLMD::adjmat::DumpGraph, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::generic::Time, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, PLMD::colvar::MultiRMSD, PLMD::colvar::PCARMSD, PLMD::colvar::RMSD, PLMD::ActionShortcut, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::gridtools::GridPrintingBase, and PLMD::mapping::PathBase.

◆ calculateAllVessels()

void PLMD::vesselbase::ActionWithVessel::calculateAllVessels	(	const unsigned &	taskCode,
		MultiValue &	myvals,
		MultiValue &	bvals,
		std::vector< double > &	buffer,
		std::vector< unsigned > &	der_list
	)

protected

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

◆ 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::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::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::multicolvar::MultiColvarBase, PLMD::analysis::AnalysisBase, PLMD::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionWithArguments, PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::vesselbase::ActionWithInputVessel.

◆ 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.

◆ deactivateAllTasks()

void PLMD::vesselbase::ActionWithVessel::deactivateAllTasks ( )

protected

Deactivate all the tasks in the task list.

◆ derivativesAreRequired()

bool PLMD::vesselbase::ActionWithVessel::derivativesAreRequired ( ) const

inline

Are derivatives required for this quantity.

◆ doJobsRequiredBeforeTaskList()

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

virtual

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

Reimplemented in PLMD::manyrestraints::ManyRestraintsBase, PLMD::multicolvar::VolumeGradientBase, and PLMD::multicolvar::MultiColvarFilter.

◆ 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.

◆ 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.

◆ finishComputations()

void PLMD::vesselbase::ActionWithVessel::finishComputations ( const std::vector< double > & buffer )

virtual

Finish running all the calculations.

◆ 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)

◆ getActiveTask()

unsigned PLMD::vesselbase::ActionWithVessel::getActiveTask ( const unsigned & ii ) const

inline

Get the ith of the currently active tasks.

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getCurrentNumberOfActiveTasks()

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

inline

Get the number of tasks that are currently active.

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ getDocumentation()

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

virtualinherited

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getForcesFromVessels()

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

protected

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

◆ getFullNumberOfTasks()

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

inline

Get the full size of the taskList dynamic list.

◆ 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.

◆ getNLTolerance()

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

inlineprotected

Return the value for the neighbor list tolerance.

◆ getNumberOfDerivatives()

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

pure virtual

Get the number of derivatives for final calculated quantity.

Implemented in PLMD::analysis::Histogram, PLMD::multicolvar::MultiColvarBase, PLMD::analysis::AnalysisBase, PLMD::mapping::Mapping, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::ClusterWithSurface, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ActionWithInputMatrix, PLMD::manyrestraints::ManyRestraintsBase, PLMD::gridtools::ContourFindingBase, and PLMD::gridtools::ActionWithIntegral.

◆ getNumberOfQuantities()

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

inlinevirtual

◆ getNumberOfVessels()

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

inline

Get the number of vessels.

◆ getPntrToVessel()

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

inline

Get a pointer to the ith vessel.

◆ getPositionInCurrentTaskList()

unsigned PLMD::vesselbase::ActionWithVessel::getPositionInCurrentTaskList ( const unsigned & myind ) const

inline

Return the position in the current task list.

◆ getPositionInFullTaskList()

unsigned PLMD::vesselbase::ActionWithVessel::getPositionInFullTaskList ( const unsigned & ii ) const

inline

Get the position of the ith active task in the full list.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getSizeOfBuffer()

unsigned PLMD::vesselbase::ActionWithVessel::getSizeOfBuffer ( unsigned & bufsize )

protected

Get the size of the buffer.

◆ getStep()

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

inherited

Return the present timestep.

◆ getTaskCode()

unsigned PLMD::vesselbase::ActionWithVessel::getTaskCode ( const unsigned & ii ) const

inline

Get the code for the ii th task in the list.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getTolerance()

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

inlineprotected

Return the value of the tolerance.

◆ getVesselWithName()

Vessel * PLMD::vesselbase::ActionWithVessel::getVesselWithName ( const std::string & mynam )

These are overwritten in MultiColvarFunction.

Return a particular named vessel

◆ 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.

◆ isPeriodic()

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

pure virtual

Are the base quantities periodic.

◆ lockContributors()

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

◆ lockRequests()

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

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

◆ needsDerivatives()

void PLMD::vesselbase::ActionWithVessel::needsDerivatives ( )

protected

Turn on the derivatives in the vessel.

◆ normalizeVector()

virtual void PLMD::vesselbase::ActionWithVessel::normalizeVector ( std::vector< double > & vals ) const

inlinevirtual

These normalizes vectors and is used in StoreDataVessel.

Reimplemented in PLMD::multicolvar::LocalAverage, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::crystallization::VectorMultiColvar, and PLMD::crystallization::MoleculeOrientation.

◆ normalizeVectorDerivatives()

virtual void PLMD::vesselbase::ActionWithVessel::normalizeVectorDerivatives ( MultiValue & myvals ) const

inlinevirtual

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::crystallization::VectorMultiColvar, and PLMD::crystallization::MoleculeOrientation.

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ 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.

◆ performTask()

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

pure virtual

Calculate one of the functions in the distribution.

Implemented in PLMD::multicolvar::MultiColvarBase, PLMD::mapping::AdaptivePath, PLMD::analysis::Average, PLMD::vesselbase::ActionWithAveraging, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterDistribution, PLMD::adjmat::ClusterDiameter, PLMD::adjmat::ClusterSize, PLMD::analysis::ReadDissimilarityMatrix, PLMD::adjmat::ClusterProperties, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::dimred::ProjectNonLandmarkPoints, PLMD::dimred::DimensionalityReductionBase, PLMD::analysis::LandmarkSelectionBase, PLMD::manyrestraints::ManyRestraintsBase, PLMD::analysis::ReadAnalysisFrames, PLMD::analysis::EuclideanDissimilarityMatrix, PLMD::analysis::OutputColvarFile, PLMD::dimred::OutputPCAProjection, PLMD::analysis::OutputPDBFile, PLMD::analysis::PrintDissimilarityMatrix, and PLMD::mapping::PathBase.

◆ 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::isdb::EMMI, PLMD::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::multicolvar::MultiColvarBase, PLMD::generic::DumpMassCharge, PLMD::generic::Read, PLMD::maze::Optimizer, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::colvar::Energy, PLMD::SetupMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::ExtraCV, and PLMD::colvar::CoordinationBase.

◆ 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.

◆ readVesselKeywords()

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

protected

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

◆ registerKeywords()

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

static

◆ resizeFunctions()

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

protected

Resize all the functions when the number of derivatives change.

◆ retrieveDomain()

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

virtual

What are the domains of the base quantities.

Reimplemented in PLMD::multicolvar::XYTorsion, PLMD::crystallization::InterMolecularTorsions, and PLMD::multicolvar::Torsions.

◆ runAllTasks()

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

protected

Calculate the values of all the vessels.

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

◆ serialCalculation()

bool PLMD::vesselbase::ActionWithVessel::serialCalculation ( ) const

inlineprotected

Is the calculation being done in serial.

◆ setLowMemOption()

void PLMD::vesselbase::ActionWithVessel::setLowMemOption ( const bool & l )

inlineprotected

Set that we are using low memory.

◆ setOption()

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

virtualinherited

◆ taskIsCurrentlyActive()

bool PLMD::vesselbase::ActionWithVessel::taskIsCurrentlyActive ( const unsigned & index ) const

Check whether or not a particular task is currently active.

◆ threadSafe()

virtual bool PLMD::vesselbase::ActionWithVessel::threadSafe ( ) const

inlinevirtual

Is this action thread safe.

Reimplemented in PLMD::analysis::Histogram, and PLMD::multicolvar::MultiColvarBase.

◆ transformBridgedDerivatives()

void PLMD::vesselbase::ActionWithVessel::transformBridgedDerivatives	(	const unsigned &	current,
		MultiValue &	invals,
		MultiValue &	outvals
	)		const

virtual

Do the task if we have a bridge.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.

◆ unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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

◆ update()

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::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::logmfd::LogMFD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::eds::EDS, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::ves::TargetDistribution, PLMD::ves::VesDeltaF, PLMD::bias::MaxEnt, PLMD::generic::Plumed, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeTetrapore, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::generic::DumpMassCharge, PLMD::isdb::JCoupling, PLMD::ves::OutputFesBias, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::Print, PLMD::isdb::PRE, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::OutputCluster, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::analysis::ReadDissimilarityMatrix, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, PLMD::analysis::ReadAnalysisFrames, and PLMD::gridtools::GridPrintingBase.

◆ usingLowMem()

bool PLMD::vesselbase::ActionWithVessel::usingLowMem ( ) const

inlineprotected

Are we using low memory.

◆ warning()

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

inherited

Issue a warning.

◆ weightWithDerivatives()

bool PLMD::vesselbase::ActionWithVessel::weightWithDerivatives ( ) const

inline

Does the weight have derivatives.

Friends And Related Function Documentation

◆ ActionWithInputVessel

friend class ActionWithInputVessel

friend

◆ BridgeVessel

friend class BridgeVessel

friend

◆ FunctionVessel

friend class FunctionVessel

friend

◆ OrderingVessel

friend class OrderingVessel

friend

◆ ShortcutVessel

friend class ShortcutVessel

friend

◆ StoreDataVessel

friend class StoreDataVessel

friend

◆ Vessel

friend class Vessel

friend

Member Data Documentation

◆ actionIsBridged

bool PLMD::vesselbase::ActionWithVessel::actionIsBridged

private

This tells plumed that this is used in a bridge.

◆ bridgeVariable

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable

protected

This is used for numerical derivatives of bridge variables.

◆ buffer

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

private

The buffer that we use (we keep a copy here to avoid resizing)

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ contributorsAreUnlocked

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked

protected

The terms in the series are locked.

◆ der_list

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::der_list

private

The list of atoms involved in derivatives (we keep a copy here to avoid resizing)

◆ dertime

bool PLMD::vesselbase::ActionWithVessel::dertime

protected

This is also used to minimise computational expense in complex functions.

◆ dertime_can_be_off

bool PLMD::vesselbase::ActionWithVessel::dertime_can_be_off

private

These are used to minmise computational expense in complex functions.

◆ files

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

inherited

◆ fullTaskList

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::fullTaskList

private

Ths full list of tasks we have to perform.

◆ functions

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

private

Pointers to the functions we are using on each value.

◆ indexOfTaskInFullList

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::indexOfTaskInFullList

private

The indices of the tasks in the full list of tasks.

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ lowmem

bool PLMD::vesselbase::ActionWithVessel::lowmem

private

Lower memory requirements.

◆ maxderivatives

unsigned PLMD::vesselbase::ActionWithVessel::maxderivatives

private

The maximum number of derivatives we can use before we need to invoke lowmem.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ mydata

StoreDataVessel* PLMD::vesselbase::ActionWithVessel::mydata

protected

A pointer to the object that stores data.

◆ nactive_tasks

unsigned PLMD::vesselbase::ActionWithVessel::nactive_tasks

private

The current number of active tasks.

◆ nl_tolerance

double PLMD::vesselbase::ActionWithVessel::nl_tolerance

private

Tolerance for quantities being put in neighbor lists.

◆ noderiv

bool PLMD::vesselbase::ActionWithVessel::noderiv

private

Are we skipping the calculation of the derivatives.

◆ partialTaskList

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::partialTaskList

private

The list of currently active tasks.

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ serial

bool PLMD::vesselbase::ActionWithVessel::serial

private

Do all calculations in serial.

◆ stopwatch

Stopwatch& PLMD::vesselbase::ActionWithVessel::stopwatch =*stopwatch_fwd

private

The stopwatch that times the different parts of the calculation.

◆ stopwatch_fwd

ForwardDecl<Stopwatch> PLMD::vesselbase::ActionWithVessel::stopwatch_fwd

private

◆ taskFlags

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::taskFlags

protected

This list is used to update the neighbor list.

◆ timers

bool PLMD::vesselbase::ActionWithVessel::timers

private

Do we want to output information on the timings of different parts of the calculation.

◆ tmpforces

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

private

Tempory storage for forces.

◆ tolerance

double PLMD::vesselbase::ActionWithVessel::tolerance

private

The tolerance on the accumulators.

◆ weightHasDerivatives

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protected

Does the weight have derivatives.

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

◆ Dependencies

Constructor & Destructor Documentation

◆ ActionWithVessel()

◆ ~ActionWithVessel()

Member Function Documentation

◆ activate()

◆ addBridgingVessel()

◆ addDependency()

◆ addTaskToList()

◆ addVessel() [1/2]

◆ addVessel() [2/2]

◆ apply()

◆ applyBridgeForces()

◆ beforeUpdate()

◆ buildDataStashes()

◆ calculate()

◆ calculateAllVessels()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives()

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearOptions()

◆ deactivate()

◆ deactivateAllTasks()

◆ derivativesAreRequired()

◆ doJobsRequiredBeforeTaskList()

◆ error()

◆ exit()

◆ fclose()

◆ fflush()

◆ finishComputations()

◆ fopen()

◆ getActiveTask()

◆ getCPT()

◆ getCurrentNumberOfActiveTasks()

◆ getDependencies()

◆ getDocumentation()

◆ getExchangeStep()

◆ getForcesFromVessels()

◆ getFullNumberOfTasks()

◆ getKeyword()

◆ getLabel()

◆ getName()

◆ getNLTolerance()

◆ getNumberOfDerivatives()

◆ getNumberOfQuantities()

◆ getNumberOfVessels()

◆ getPntrToVessel()

◆ getPositionInCurrentTaskList()

◆ getPositionInFullTaskList()

◆ getRestart()

◆ getSizeOfBuffer()

◆ getStep()

◆ getTaskCode()

◆ getTime()

◆ getTimeStep()

◆ getTolerance()

◆ getVesselWithName()

◆ isActive()

◆ isOptionOn()

◆ isPeriodic()

◆ lockContributors()

◆ lockRequests()

◆ needsDerivatives()

◆ normalizeVector()

◆ normalizeVectorDerivatives()