#include <ActionPilot.h>

Inheritance diagram for PLMD::ActionPilot:

[legend]

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

Public Member Functions
	ActionPilot (const ActionOptions &)

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	beforeUpdate ()
	Before Update. 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 ActionAtomistic *	castToActionAtomistic () noexcept

virtual ActionForInterface *	castToActionForInterface () noexcept

virtual ActionShortcut *	castToActionShortcut () noexcept

virtual ActionToGetData *	castToActionToGetData () noexcept

virtual ActionToPutData *	castToActionToPutData () noexcept

virtual ActionWithArguments *	castToActionWithArguments () noexcept

virtual ActionWithValue *	castToActionWithValue () noexcept
	Specialized casts, to make PlumedMain run faster. More...

virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept

virtual DomainDecomposition *	castToDomainDecomposition () noexcept

virtual PbcAction *	castToPbcAction () noexcept

bool	checkForDependency (Action *)
	Check that this action does not depend on the action in the argument. 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...

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...

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

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

std::string	getDefaultString () const
	Get the defaults. More...

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

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

double	getkBT ()
	Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code. 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...

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

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

int	getStride () const
	Get the stride. More...

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

double	getTimeStep () const
	Return the timestep. 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 void	lockRequests ()

virtual bool	onStep () const
	Check if the action is active on this step. More...

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	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...

void	resetStoredTimestep ()
	Set the timestep that is stored in the action to the correct value. 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)

void	setStride (const int &n)
	Set the value of the stride. More...

void	setupConstantValues (const bool &have_atoms)
	This calculates any values that are constant and ensures that we don't calculate these actions on every timestep. More...

virtual void	unlockRequests ()

virtual void	update ()
	Update. More...

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

virtual std::string	writeInGraph () const
	Get the info on what to calculate. More...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)
	Create the keywords for actionPilot. More...

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
double	getKBoltzmann () const
	Get the value of Boltzmann's constant. More...

const Units &	getUnits () const
	Get the units that we are operating in. More...

bool	usingNaturalUnits () const
	Are we using natural units. More...

Private Attributes
bool	active
	Switch to activate Action on this step. More...

Dependencies	after
	Actions on which this Action depends. More...

std::string	defaults
	The set of default arguments that we are using. More...

bool	doCheckPoint

std::string	label
	Label of the Action, as set with LABEL= in the plumed.dat file. More...

std::vector< std::string >	line
	Directive line. More...

const std::string	name
	Name of the directive in the plumed.dat file. More...

bool	never_activate

std::set< std::string >	options
	Option that you might have enabled. More...

int	replica_index

bool	restart

int	stride

double	timestep
	Save the timestep here. More...

double	update_from
	Update only after this time. More...

double	update_until
	Update only until this time. More...

Detailed Description

This is used to create PLMD::Action objects that are run with some set frequency. Any PLMD::Action that does not inherit from PLMD::Action is only run when some other Action requires the output from it in order to run. This class is used in PLMD::Bias Action which drives the execution of other Action's. Action's of this kind are executed with a fixed stride which is specified on the directive line with a STRIDE= keyword

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ ActionPilot()

PLMD::ActionPilot::ActionPilot ( const ActionOptions & ao )

explicit

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.

◆ 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::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::FitToTemplate, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::generic::DumpAtoms, PLMD::metatensor::MetatensorPlumedAction, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::WholeMolecules, PLMD::generic::ResetCell, PLMD::ves::OutputFesBias, PLMD::generic::Read, PLMD::DomainDecomposition, PLMD::clusters::ClusterDistribution, PLMD::generic::UpdateIf, PLMD::generic::DumpMassCharge, PLMD::wham::Wham, PLMD::generic::Print, PLMD::ves::OutputBasisFunctions, PLMD::ves::OutputTargetDistribution, PLMD::ActionToPutData, PLMD::generic::RandomExchanges, PLMD::colvar::Energy, PLMD::generic::Committor, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::GenericMolInfo, PLMD::generic::Constant, PLMD::dimred::ArrangePoints, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::generic::DumpPDB, PLMD::generic::DumpProjections, PLMD::clusters::ClusterWeights, PLMD::generic::Debug, PLMD::bias::Bias, PLMD::valtools::SelectWithMask, PLMD::ActionShortcut, PLMD::Colvar, PLMD::dimred::ProjectPoints, PLMD::generic::PrintNDX, PLMD::vatom::ArgsToVatom, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::gridtools::FunctionOfGrid< T >, PLMD::clusters::ClusteringBase, PLMD::generic::DumpVector, PLMD::colvar::RMSDVector, PLMD::generic::CreateMask, PLMD::matrixtools::InvertMatrix, PLMD::opes::ExpansionCVs, PLMD::contour::DumpContour, PLMD::valtools::Flatten, PLMD::function::Function, PLMD::generic::Time, PLMD::matrixtools::TransposeMatrix, PLMD::bias::ReweightBase, PLMD::landmarks::FarthestPointSampling, PLMD::matrixtools::MatrixOperationBase, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::Group, PLMD::ActionWithVector, PLMD::ActionWithVirtualAtom, PLMD::mapping::PathReparameterization, PLMD::contour::DistanceFromContourBase, PLMD::mapping::PathDisplacements, PLMD::valtools::Concatenate, PLMD::ActionToGetData, and PLMD::generic::GatherReplicas.

◆ 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.

◆ 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::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::isdb::SAXS, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::EMMI, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::function::FuncPathMSD, PLMD::generic::FitToTemplate, PLMD::function::FuncSumHills, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::opes::OPESexpanded, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::vatom::Center, PLMD::colvar::Distance, PLMD::metatensor::MetatensorPlumedAction, PLMD::colvar::Dimer, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::ExtendedLagrangian, PLMD::colvar::Torsion, PLMD::bias::MovingRestraint, PLMD::bias::External, PLMD::colvar::ContactMap, PLMD::generic::WholeMolecules, PLMD::colvar::ERMSD, PLMD::colvar::Angle, PLMD::crystdistrib::Quaternion, PLMD::isdb::Shadow, PLMD::colvar::Position, PLMD::generic::ResetCell, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::colvar::EEFSolv, PLMD::generic::Read, PLMD::sizeshape::position_linear_proj, PLMD::colvar::Dipole, PLMD::vatom::FixedAtom, PLMD::colvar::PathMSDBase, PLMD::colvar::SelectMassCharge, PLMD::ActionWithMatrix, PLMD::bias::ABMD, PLMD::clusters::ClusterDistribution, PLMD::generic::DumpMassCharge, PLMD::wham::Wham, PLMD::colvar::Gyration, PLMD::isdb::FretEfficiency, PLMD::ves::OutputBasisFunctions, PLMD::generic::UpdateIf, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::generic::Print, PLMD::ves::OutputTargetDistribution, PLMD::isdb::PRE, PLMD::membranefusion::memFusionP, PLMD::sizeshape::position_maha_dist, PLMD::fourier::FourierTransform, PLMD::membranefusion::fusionPoreNucleationP, PLMD::function::LocalEnsemble, PLMD::membranefusion::fusionPoreExpansionP, PLMD::generic::RandomExchanges, PLMD::bias::BiasValue, PLMD::contour::DistanceFromContour, PLMD::isdb::NOE, PLMD::maze::Loss, PLMD::bias::Restraint, PLMD::colvar::DihedralCorrelation, PLMD::colvar::Puckering, PLMD::colvar::Plane, PLMD::ActionForInterface, PLMD::generic::Committor, PLMD::vatom::Ghost, PLMD::function::FunctionOfVector< T >, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::function::Ensemble, PLMD::GenericMolInfo, PLMD::generic::Constant, PLMD::function::Stats, PLMD::dimred::ArrangePoints, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::generic::DumpPDB, PLMD::generic::Debug, PLMD::gridtools::FindGridOptimum, PLMD::clusters::ClusterWeights, PLMD::generic::DumpProjections, PLMD::dimred::ProjectPoints, PLMD::valtools::SelectWithMask, PLMD::colvar::Template, PLMD::ActionShortcut, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::vatom::ArgsToVatom, PLMD::generic::DumpVector, PLMD::colvar::Cell, PLMD::opes::ExpansionCVs, PLMD::matrixtools::DiagonalizeMatrix, PLMD::valtools::Concatenate, PLMD::clusters::ClusteringBase, PLMD::generic::CreateMask, PLMD::colvar::RMSDVector, PLMD::contour::DumpContour, PLMD::function::FunctionOfScalar< T >, PLMD::matrixtools::InvertMatrix, PLMD::colvar::MultiColvarTemplate< T >, PLMD::colvar::Volume, PLMD::generic::PrintNDX, PLMD::generic::Time, PLMD::valtools::Flatten, PLMD::colvar::ColvarFake, PLMD::landmarks::FarthestPointSampling, PLMD::matrixtools::TransposeMatrix, PLMD::mapping::GeometricPath, PLMD::symfunc::ThreeBodyGFunctions, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::refdist::MatrixProductDiagonal, PLMD::colvar::PCARMSD, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::colvar::RMSD, PLMD::gridtools::ActionWithGrid, PLMD::Group, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::piv::PIV, PLMD::sasa::SASA_HASEL, PLMD::sasa::SASA_LCPO, PLMD::fisst::FISST, PLMD::isdb::Rescale, PLMD::maze::OptimizerBias, PLMD::funnel::Funnel, PLMD::function::FuncPathGeneral, PLMD::funnel::FUNNEL_PS, PLMD::function::annfunc::ANN, PLMD::isdb::Caliber, PLMD::maze::Optimizer, PLMD::s2cm::S2ContactModel, PLMD::colvar::ProjectionOnAxis, PLMD::isdb::Select, PLMD::mapping::PathReparameterization, PLMD::volumes::ActionVolume, PLMD::mapping::PathDisplacements, PLMD::ActionToGetData, PLMD::generic::GatherReplicas, and PLMD::contour::DistanceFromSphericalContour.

◆ 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::ActionWithVector, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::contour::DistanceFromContourBase.