Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Private Member Functions | Private Attributes | Friends | List of all members
PLMD::Action Class Referenceabstract

Base class for all the input Actions. More...

#include <Action.h>

Inheritance diagram for PLMD::Action:
Inheritance graph

Public Types

typedef std::vector< Action * > Dependencies

Public Member Functions

 Action (const ActionOptions &)
 Standard constructor from ActionOptions. More...
virtual ~Action ()
 Destructor. More...
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 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...
const DependenciesgetDependencies () const
 Return dependencies. More...
virtual std::string getDocumentation () const
bool getExchangeStep () const
 Check if we are on an exchange step. 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 int getStep () const
 Return the present timestep. 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 ()
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...
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
virtual void setOption (const std::string &s)
virtual void unlockRequests ()
virtual void update ()
 Update. More...
void warning (const std::string &msg)
 Issue a warning. More...

Static Public Member Functions

static void registerKeywords (Keywords &keys)
 Register all the relevant keywords for the action. More...

Public Attributes

std::set< FILE * > files
const Keywordskeywords
 Reference to the log stream. More...
 Reference to main plumed object. More...

Private Member Functions

 Action (const Action &a)=delete
 Copy constructor is deleted. More...
Actionoperator= (const Action &a)=delete
 Assignment operator is deleted. More...

Private Attributes

bool active
 Switch to activate Action on this step. More...
Dependencies after
 Actions on which this Action depends. 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...
std::set< std::string > options
 Option that you might have enabled. More...
int replica_index
bool restart
double update_from
 Update only after this time. More...
double update_until
 Update only until this time. More...


class ActionShortcut

Detailed Description

Base class for all the input Actions.

The input Actions are more or less corresponding to the directives in the plumed.dat file and are applied in order at each time-step.

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ Action() [1/2]

PLMD::Action::Action ( const ActionOptions ao)

Standard constructor from ActionOptions.

◆ ~Action()

PLMD::Action::~Action ( )


◆ Action() [2/2]

PLMD::Action::Action ( const Action a)

Copy constructor is deleted.

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

Set action to active.

◆ addDependency()

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

Specify that this Action depends on another one.

◆ apply()

virtual void PLMD::Action::apply ( )
pure virtual

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

◆ beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

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 virtual

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::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::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::function::Custom, PLMD::ves::VesDeltaF, PLMD::opes::OPESexpanded, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::bias::MaxEnt, PLMD::generic::Group, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::vatom::Center, PLMD::colvar::Dimer, PLMD::bias::ExtendedLagrangian, PLMD::colvar::DRMSD, PLMD::bias::External, PLMD::generic::EffectiveEnergyDrift, PLMD::colvar::Distance, PLMD::colvar::ContactMap, PLMD::generic::WholeMolecules, PLMD::bias::MovingRestraint, PLMD::colvar::ERMSD, PLMD::mapping::AdaptivePath, PLMD::ves::OutputFesBias, PLMD::function::Target, PLMD::adjmat::Sprint, PLMD::generic::ResetCell, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::colvar::EEFSolv, PLMD::analysis::Average, PLMD::analysis::AnalysisBase, PLMD::colvar::Torsion, PLMD::multicolvar::CenterOfMultiColvar, PLMD::vatom::FixedAtom, PLMD::colvar::PathMSDBase, PLMD::bias::ABMD, PLMD::generic::DumpMassCharge, PLMD::multicolvar::DistanceFromContour, PLMD::isdb::FretEfficiency, PLMD::ves::OutputBasisFunctions, PLMD::colvar::Gyration, PLMD::generic::UpdateIf, PLMD::colvar::Angle, PLMD::generic::Print, PLMD::ves::OutputTargetDistribution, PLMD::function::Combine, PLMD::isdb::PRE, PLMD::adjmat::OutputCluster, PLMD::function::LocalEnsemble, PLMD::colvar::Position, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::RandomExchanges, PLMD::adjmat::ClusterDistribution, PLMD::bias::BiasValue, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::maze::Loss, PLMD::colvar::Puckering, PLMD::function::Piecewise, PLMD::adjmat::ClusterDiameter, PLMD::analysis::Committor, PLMD::adjmat::ClusterSize, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::adjmat::ClusterProperties, PLMD::colvar::Energy, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::colvar::Dipole, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::bias::Restraint, PLMD::function::Ensemble, PLMD::colvar::Constant, PLMD::GenericMolInfo, PLMD::function::Stats, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::manyrestraints::ManyRestraintsBase, PLMD::colvar::ExtraCV, PLMD::function::Sort, PLMD::generic::Debug, PLMD::generic::DumpProjections, PLMD::vatom::Ghost, PLMD::adjmat::DumpGraph, PLMD::colvar::Template, PLMD::colvar::Cell, PLMD::opes::ExpansionCVs, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, PLMD::colvar::Volume, PLMD::generic::Time, PLMD::colvar::ColvarFake, PLMD::ActionShortcut, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::colvar::MultiRMSD, PLMD::colvar::PCARMSD, PLMD::colvar::RMSD, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::gridtools::GridPrintingBase, PLMD::mapping::PathBase, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::piv::PIV, PLMD::fisst::FISST, PLMD::sasa::SASA_HASEL, PLMD::sasa::SASA_LCPO, 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::colvar::ProjectionOnAxis, PLMD::s2cm::S2ContactModel, and PLMD::isdb::Select.

◆ calculateFromPDB()

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

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)

◆ checkNeedsGradients()

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

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

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )

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

Check if action should be updated.

◆ cite()

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

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

Clear the dependence list for this Action.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

◆ deactivate()

void PLMD::Action::deactivate ( )

Set action to inactive.

◆ error()

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

Crash calculation and print documentation.

◆ exit()

void PLMD::Action::exit ( int  c = 0)

Exit with error code c.

◆ fclose()

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

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

◆ fflush()

void PLMD::Action::fflush ( )

Tell to the Action to flush open files.

◆ fopen()

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

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)

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

Return true if we are doing at a checkpoint step.

◆ getDependencies()

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

Return dependencies.

◆ getDocumentation()

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

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

Check if we are on an exchange step.

◆ getKeyword()

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

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

◆ getLabel()

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

Returns the label.

◆ getName()

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

Returns the name.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

Return true if we are doing a restart.

◆ getStep()

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

Return the present timestep.

◆ getTime()

double PLMD::Action::getTime ( ) const

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

Return the timestep.

◆ isActive()

bool PLMD::Action::isActive ( ) const

Check if action is active.

◆ isOptionOn()

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

Check if an option is on.

◆ lockRequests()

virtual void PLMD::Action::lockRequests ( )

◆ operator=()

Action& PLMD::Action::operator= ( const Action a)

Assignment operator is deleted.

◆ parse()

template<class T >
void PLMD::Action::parse ( const std::string &  key,
T &  t 

Parse one keyword as generic type.

◆ parseFlag()

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

Parse one keyword as boolean flag.

◆ parseNumbered()

template<class T >
bool PLMD::Action::parseNumbered ( const std::string &  key,
const int  no,
T &  t 

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 

Parse a vector with a number.

◆ parseVector()

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

Parse one keyword as std::vector.

◆ prepare()

void PLMD::Action::prepare ( )

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::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, PLMD::colvar::CoordinationBase, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.

◆ readAtomsFromPDB()

virtual void PLMD::Action::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.

Reimplemented in PLMD::ActionAtomistic.

◆ registerKeywords()

void PLMD::Action::registerKeywords ( Keywords keys)

Register all the relevant keywords for the action.

◆ runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )

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.

◆ setOption()

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

◆ unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

◆ update()

virtual void PLMD::Action::update ( )

◆ warning()

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

Issue a warning.

Friends And Related Function Documentation

◆ ActionShortcut

friend class ActionShortcut

Member Data Documentation

◆ active

bool PLMD::Action::active

Switch to activate Action on this step.

◆ after

Dependencies PLMD::Action::after

Actions on which this Action depends.

◆ comm

Communicator& PLMD::Action::comm

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

◆ files

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

◆ keywords

const Keywords& PLMD::Action::keywords

◆ label

std::string PLMD::Action::label

Label of the Action, as set with LABEL= in the plumed.dat file.

◆ line

std::vector<std::string> PLMD::Action::line

Directive line.

This line is progressively erased during Action construction so as to check if all the present keywords are correct.

◆ log

Log& PLMD::Action::log

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

◆ name

const std::string PLMD::Action::name

Name of the directive in the plumed.dat file.

◆ options

std::set<std::string> PLMD::Action::options

Option that you might have enabled.

◆ plumed

PlumedMain& PLMD::Action::plumed

Reference to main plumed object.

◆ replica_index

int PLMD::Action::replica_index

◆ restart

bool PLMD::Action::restart

◆ update_from

double PLMD::Action::update_from

Update only after this time.

◆ update_until

double PLMD::Action::update_until

Update only until this time.

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